Next: Acknowledgements [Contents][Index]

This is a guide to extending R, describing the process of creating R add-on

packages, writing R documentation, R’s system and foreign language interfaces,
and the R API.
This manual is for R, version 4.3.1 (2023-06-16).
Copyright © 1999–2023 R Core Team
Permission is granted to make and distribute verbatim copies of this manual
provided the copyright notice and this permission notice are preserved on all
copies.
Permission is granted to copy and distribute modified versions of this manual
under the conditions for verbatim copying, provided that the entire resulting
derived work is distributed under the terms of a permission notice identical to this
one.
Permission is granted to copy and distribute translations of this manual into
another language, under the above conditions for modified versions, except that
this permission notice may be stated in a translation approved by the R Core Team.

Table of Contents
 Acknowledgements
 1 Creating R packages
o 1.1 Package structure
 1.1.1 The DESCRIPTION file
 1.1.2 Licensing
 1.1.3 Package Dependencies
 [Link] Suggested packages
 1.1.4 The INDEX file
 1.1.5 Package subdirectories
 1.1.6 Data in packages
 1.1.7 Non-R scripts in packages
 1.1.8 Specifying URLs
o 1.2 Configure and cleanup
 1.2.1 Using Makevars
 [Link] OpenMP support
 [Link] Using pthreads
 [Link] Compiling in sub-directories
 1.2.2 Configure example
 1.2.3 Using F9x code
 1.2.4 Using C++ code
  1.2.5 C standards
 1.2.6 Using cmake
o 1.3 Checking and building packages
 1.3.1 Checking packages
 1.3.2 Building package tarballs
 1.3.3 Building binary packages
o 1.4 Writing package vignettes
 1.4.1 Encodings and vignettes
 1.4.2 Non-Sweave vignettes
o 1.5 Package namespaces
 1.5.1 Specifying imports and exports
 1.5.2 Registering S3 methods
 1.5.3 Load hooks
 1.5.4 useDynLib
 1.5.5 An example
 1.5.6 Namespaces with S4 classes and methods
o 1.6 Writing portable packages
 1.6.1 PDF size
 1.6.2 Check timing
 1.6.3 Encoding issues
 1.6.4 Portable C and C++ code
 [Link] Common symbols
 [Link] C++17 issues
 1.6.5 Binary distribution
o 1.7 Diagnostic messages
o 1.8 Internationalization
 1.8.1 C-level messages
 1.8.2 R messages
 1.8.3 Preparing translations
o 1.9 CITATION files
o 1.10 Package types
 1.10.1 Frontend
o 1.11 Services
 2 Writing R documentation files
o 2.1 Rd format
 2.1.1 Documenting functions
 2.1.2 Documenting data sets
 2.1.3 Documenting S4 classes and methods
 2.1.4 Documenting packages
o 2.2 Sectioning
 o 2.3 Marking text
o 2.4 Lists and tables
o 2.5 Cross-references
o 2.6 Mathematics
o 2.7 Figures
o 2.8 Insertions
o 2.9 Indices
o 2.10 Platform-specific documentation
o 2.11 Conditional text
o 2.12 Dynamic pages
o 2.13 User-defined macros
o 2.14 Encoding
o 2.15 Processing documentation files
o 2.16 Editing Rd files
 3 Tidying and profiling R code
o 3.1 Tidying R code
o 3.2 Profiling R code for speed
o 3.3 Profiling R code for memory use
 3.3.1 Memory statistics from Rprof
 3.3.2 Tracking memory allocations
 3.3.3 Tracing copies of an object
o 3.4 Profiling compiled code
 3.4.1 Linux
 [Link] oprofile and operf
 [Link] sprof
 3.4.2 macOS
 4 Debugging
o 4.1 Browsing
o 4.2 Debugging R code
o 4.3 Checking memory access
 4.3.1 Using gctorture
 4.3.2 Using valgrind
 4.3.3 Using the Address Sanitizer
 [Link] Using the Leak Sanitizer
 4.3.4 Using the Undefined Behaviour Sanitizer
 4.3.5 Other analyses with ‘clang’
 4.3.6 Other analyses with ‘gcc’
 4.3.7 Using ‘Dr. Memory’
 4.3.8 Fortran array bounds checking
o 4.4 Debugging compiled code
  4.4.1 Finding entry points in dynamically loaded code
 4.4.2 Inspecting R objects when debugging
 4.4.3 Debugging on macOS
o 4.5 Using Link-time Optimization
 5 System and foreign language interfaces
o 5.1 Operating system access
o 5.2 Interface functions .C and .Fortran
o 5.3 [Link] and [Link]
o 5.4 Registering native routines
 5.4.1 Speed considerations
 5.4.2 Example: converting a package to use registration
 5.4.3 Linking to native routines in other packages
o 5.5 Creating shared objects
o 5.6 Interfacing C++ code
 5.6.1 External C++ code
o 5.7 Fortran I/O
o 5.8 Linking to other packages
 5.8.1 Unix-alikes
 5.8.2 Windows
o 5.9 Handling R objects in C
 5.9.1 Handling the effects of garbage collection
 5.9.2 Allocating storage
 5.9.3 Details of R types
 5.9.4 Attributes
 5.9.5 Classes
 5.9.6 Handling lists
 5.9.7 Handling character data
 5.9.8 Finding and setting variables
 5.9.9 Some convenience functions
 [Link] Semi-internal convenience functions
 5.9.10 Named objects and copying
o 5.10 Interface functions .Call and .External
 5.10.1 Calling .Call
 5.10.2 Calling .External
 5.10.3 Missing and special values
o 5.11 Evaluating R expressions from C
 5.11.1 Zero-finding
 5.11.2 Calculating numerical derivatives
o 5.12 Parsing R code from C
 5.12.1 Accessing source references
 o 5.13 External pointers and weak references
 5.13.1 An example
o 5.14 Vector accessor functions
o 5.15 Character encoding issues
 6 The R API: entry points for C code
o 6.1 Memory allocation
 6.1.1 Transient storage allocation
 6.1.2 User-controlled memory
o 6.2 Error signaling
 6.2.1 Error signaling from Fortran
o 6.3 Random number generation
o 6.4 Missing and IEEE special values
o 6.5 Printing
 6.5.1 Printing from Fortran
o 6.6 Calling C from Fortran and vice versa
 6.6.1 Fortran character strings
 6.6.2 Fortran LOGICAL
 6.6.3 Passing functions
o 6.7 Numerical analysis subroutines
 6.7.1 Distribution functions
 6.7.2 Mathematical functions
 6.7.3 Numerical Utilities
 6.7.4 Mathematical constants
o 6.8 Optimization
o 6.9 Integration
o 6.10 Utility functions
o 6.11 Re-encoding
o 6.12 Condition handling and cleanup code
o 6.13 Allowing interrupts
o 6.14 Platform and version information
o 6.15 Inlining C functions
o 6.16 Controlling visibility
o 6.17 Using these functions in your own C code
o 6.18 Organization of header files
 7 Generic functions and methods
o 7.1 Adding new generics
 8 Linking GUIs and other front-ends to R
o 8.1 Embedding R under Unix-alikes
 8.1.1 Compiling against the R library
 8.1.2 Setting R callbacks
  8.1.3 Registering symbols
 8.1.4 Meshing event loops
 8.1.5 Threading issues
o 8.2 Embedding R under Windows
 8.2.1 Using (D)COM
 8.2.2 Calling [Link] directly
 8.2.3 Finding R_HOME
 Function and variable index
 Concept index

Next: Creating R packages, Previous: Writing R Extensions, Up: Writing R

Extensions [Contents][Index]

Acknowledgements
The contributions to early versions of this manual by Saikat DebRoy (who wrote
the first draft of a guide to using .Call and .External) and Adrian Trapletti (who
provided information on the C++ interface) are gratefully acknowledged.

Next: Writing R documentation files, Previous: Acknowledgements, Up: Writing R

Extensions [Contents][Index]

1 Creating R packages
Packages provide a mechanism for loading optional code, data and documentation
as needed. The R distribution itself includes about 30 packages.
In the following, we assume that you know the library() command, including
its [Link] argument, and we also assume basic knowledge of the R CMD
INSTALL utility. Otherwise, please look at R’s help pages on
?library
?INSTALL
before reading on.
For packages which contain code to be compiled, a computing environment
including a number of tools is assumed; the “R Installation and Administration”
manual describes what is needed for each OS.
Once a source package is created, it must be installed by the command R CMD
INSTALL. See Add-on-packages in R Installation and Administration.

Other types of extensions are supported (but rare): See Package types.
Some notes on terminology complete this introduction. These will help with the
reading of this manual, and also in describing concepts accurately when asking for
help.
A package is a directory of files which extend R, a source package (the master
files of a package), or a tarball containing the files of a source package, or
an installed package, the result of running R CMD INSTALL on a source package. On
some platforms (notably macOS and Windows) there are also binary packages, a
zip file or tarball containing the files of an installed package which can be
unpacked rather than installing from sources.
A package is not1 a library. The latter is used in two senses in R documentation.
 A directory into which packages are installed,
e.g. /usr/lib/R/library: in that sense it is sometimes referred to as
a library directory or library tree (since the library is a directory which
contains packages as directories, which themselves contain directories).
 That used by the operating system, as a shared, dynamic or static library or
(especially on Windows) a DLL, where the second L stands for ‘library’.
Installed packages may contain compiled code in what is known on Unix-
alikes as a shared object and on Windows as a DLL. The concept of
a shared library (dynamic library on macOS) as a collection of compiled
code to which a package might link is also used, especially for R itself on
some platforms. On most platforms these concepts are interchangeable
(shared objects and DLLs can both be loaded into the R process and be
linked against), but macOS distinguishes between shared objects
(extension .so) and dynamic libraries (extension .dylib).
There are a number of well-defined operations on source packages.
 The most common is installation which takes a source package and installs
it in a library using R CMD INSTALL or [Link].
 Source packages can be built. This involves taking a source directory and
creating a tarball ready for distribution, including cleaning it up and creating
PDF/HTML documentation from any vignettes it may contain. Source
packages (and most often tarballs) can be checked, when a test installation is
done and tested (including running its examples); also, the contents of the
package are tested in various ways for consistency and portability.
 Compilation is not a correct term for a package. Installing a source package
which contains C, C++ or Fortran code will involve compiling that code.
There is also the possibility of ‘byte’ compiling the R code in a package
(using the facilities of package compiler): nowadays this is enabled by
default for all packages. So compiling a package may come to mean byte-
compiling its R code.
 It used to be unambiguous to talk about loading an installed package
using library(), but since the advent of package namespaces this has been
less clear: people now often talk about loading the package’s namespace and
 then attaching the package so it becomes visible on the search path.
Function library performs both steps, but a package’s namespace can be
loaded without the package being attached (for example by calls
like splines::ns).
The concept of lazy loading of code or data is mentioned at several points. This is
part of the installation, always selected for R code but optional for data. When used
the R objects of the package are created at installation time and stored in a database
in the R directory of the installed package, being loaded into the session at first use.
This makes the R session start up faster and use less (virtual) memory. (For
technical details, see Lazy loading in R Internals.)
CRAN is a network of WWW sites holding the R distributions and contributed
code, especially R packages. Users of R are encouraged to join in the collaborative
project and to submit their own packages to CRAN: current instructions are linked
from [Link]
 Package structure
 Configure and cleanup
 Checking and building packages
 Writing package vignettes
 Package namespaces
 Writing portable packages
 Diagnostic messages
 Internationalization
 CITATION files
 Package types
 Services

Next: Configure and cleanup, Previous: Creating R packages, Up: Creating R

packages [Contents][Index]

1.1 Package structure

The sources of an R package consist of a subdirectory containing the
files DESCRIPTION and NAMESPACE, and the
subdirectories R, data, demo, exec, inst, man, po, src, tests, tools and
vignettes (some of which can be missing, but which should not be empty). The
package subdirectory may also contain
files INDEX, configure, cleanup, LICENSE, LICENCE and NEWS. Other
files such as INSTALL (for non-standard installation
instructions), README/README.md2, or ChangeLog will be ignored by R, but
may be useful to end users. The utility R CMD build may add files in
a build directory (but this should not be used for other purposes).
Except where specifically mentioned,3 packages should not contain Unix-style
‘hidden’ files/directories (that is, those whose name starts with a dot).
The DESCRIPTION and INDEX files are described in the subsections below.
The NAMESPACE file is described in the section on Package namespaces.
The optional files configure and cleanup are (Bourne) shell scripts which
are, respectively, executed before and (if option --clean was given) after
installation on Unix-alikes, see Configure and cleanup. The analogues on Windows
are [Link] and [Link]. Since R 4.2.0 on
Windows, [Link] and [Link] are supported and take
precedence over [Link] and [Link]. They can hence be used
to provide content specific to UCRT or Rtools42 and newer, if needed, but the
support for .ucrt files may be removed in future when building packages from
source on the older versions of R will no longer be needed, and hence the files may
be renamed back to .win.
For the conventions for files NEWS and ChangeLog in the GNU project
see [Link]
The package subdirectory should be given the same name as the package. Because
some file systems (e.g., those on Windows and by default on macOS) are not case-
sensitive, to maintain portability it is strongly recommended that case distinctions
not be used to distinguish different packages. For example, if you have a package
named foo, do not also create a package named Foo.
To ensure that file names are valid across file systems and supported operating
systems, the ASCII control characters as well as the characters ‘"’, ‘*’, ‘:’, ‘/’,
‘<’, ‘>’, ‘?’, ‘\’, and ‘|’ are not allowed in file names. In addition, files with
names ‘con’, ‘prn’, ‘aux’, ‘clock$’, ‘nul’, ‘com1’ to ‘com9’, and ‘lpt1’ to
‘lpt9’ after conversion to lower case and stripping possible “extensions” (e.g.,
‘[Link]’), are disallowed. Also, file names in the same directory must
not differ only by case (see the previous paragraph). In addition, the basenames of
‘.Rd’ files may be used in URLs and so must be ASCII and not contain %. For
maximal portability filenames should only contain only ASCII characters not
excluded already (that is A-Za-z0-9._!#$%&+,;=@^(){}'[] — we exclude space as
many utilities do not accept spaces in file paths): non-English alphabetic characters
cannot be guaranteed to be supported in all locales. It would be good practice to
avoid the shell metacharacters (){}'[]$~: ~ is also used as part of ‘8.3’ filenames
on Windows. In addition, packages are normally distributed as tarballs, and these
have a limit on path lengths: for maximal portability 100 bytes.
A source package if possible should not contain binary executable files: they are
not portable, and a security risk if they are of the appropriate architecture. R CMD
4
check will warn about them unless they are listed (one filepath per line) in a
file BinaryFiles at the top level of the package. Note that CRAN will not
accept submissions containing binary files even if they are listed.
The R function [Link] can help to create the structure for a new
package: see its help page for details.
 The DESCRIPTION file
 Licensing
 Package Dependencies
 The INDEX file
 Package subdirectories
 Data in packages
 Non-R scripts in packages
 Specifying URLs

Next: Licensing, Previous: Package structure, Up: Package structure [Contents]

[Index]
1.1.1 The DESCRIPTION file

The DESCRIPTION file contains basic information about the package in the
following format:
Package: pkgname
Version: 0.5-1
Date: 2015-01-01
Title: My First Collection of Functions
Authors@R: c(person("Joe", "Developer", role = c("aut", "cre"),
email = "[Link]@[Link]"),
person("Pat", "Developer", role = "aut"),
person("A.", "User", role = "ctb",
email = "[Link]@[Link]"))
Author: Joe Developer [aut, cre],
Pat Developer [aut],
A. User [ctb]
Maintainer: Joe Developer <[Link]@[Link]>
Depends: R (>= 3.1.0), nlme
Suggests: MASS
Description: A (one paragraph) description of what
the package does and why it may be useful.
License: GPL (>= 2)
URL: [Link] [Link]
BugReports: [Link]

The format is that of a version of a ‘Debian Control File’ (see the help for
‘[Link]’ and [Link]
R does not require encoding in UTF-8 and does not support comments starting
with ‘#’). Fields start with an ASCII name immediately followed by a colon: the
value starts after the colon and a space. Continuation lines (for example, for
descriptions longer than one line) start with a space or tab. Field names are case-
sensitive: all those used by R are capitalized.
For maximal portability, the DESCRIPTION file should be written entirely
in ASCII — if this is not possible it must contain an ‘Encoding’ field (see
below).
Several optional fields take logical values: these can be specified as ‘yes’,
‘true’, ‘no’ or ‘false’: capitalized values are also accepted.
The ‘Package’, ‘Version’, ‘License’, ‘Description’, ‘Title’,
‘Author’, and ‘Maintainer’ fields are mandatory, all other fields are optional.
Fields ‘Author’ and ‘Maintainer’ can be auto-generated from ‘Authors@R’,
and may be omitted if the latter is provided: however if they are not ASCII we
recommend that they are provided.
The mandatory ‘Package’ field gives the name of the package. This should
contain only (ASCII) letters, numbers and dot, have at least two characters and
start with a letter and not end in a dot. If it needs explaining, this should be done in
the ‘Description’ field (and not the ‘Title’ field).
The mandatory ‘Version’ field gives the version of the package. This is a
sequence of at least two (and usually three) non-negative integers separated by
single ‘.’ or ‘-’ characters. The canonical form is as shown in the example, and a
version such as ‘0.01’ or ‘0.01.0’ will be handled as if it were ‘0.1-0’. It
is not a decimal number, so for example 0.9 < 0.75 since 9 < 75.
The mandatory ‘License’ field is discussed in the next subsection.
The mandatory ‘Title’ field should give a short description of the package.
Some package listings may truncate the title to 65 characters. It should use title
case (that is, use capitals for the principal words: tools::toTitleCase can help you
with this), not use any markup, not have any continuation lines, and not end in a
period (unless part of …). Do not repeat the package name: it is often used prefixed
by the name. Refer to other packages and external software in single quotes, and to
book titles (and similar) in double quotes.
The mandatory ‘Description’ field should give a comprehensive description of
what the package does. One can use several (complete) sentences, but only one
paragraph. It should be intelligible to all the intended readership (e.g. for
a CRAN package to all CRAN users). It is good practice not to start with the
package name, ‘This package’ or similar. As with the ‘Title’ field, double
quotes should be used for quotations (including titles of books and articles), and
single quotes for non-English usage, including names of other packages and
external software. This field should also be used for explaining the package name
if necessary. URLs should be enclosed in angle brackets, e.g.
‘<[Link] see also Specifying URLs.
The mandatory ‘Author’ field describes who wrote the package. It is a plain text
field intended for human readers, but not for automatic processing (such as
extracting the email addresses of all listed contributors: for that use
‘Authors@R’). Note that all significant contributors must be included: if you
wrote an R wrapper for the work of others included in the src directory, you are
not the sole (and maybe not even the main) author.
The mandatory ‘Maintainer’ field should give a single name followed by
a valid (RFC 2822) email address in angle brackets. It should not end in a period or
comma. This field is what is reported by the maintainer function and used
by [Link]. For a CRAN package it should be a person, not a mailing list and
not a corporate entity: do ensure that it is valid and will remain valid for the
lifetime of the package.
Note that the display name (the part before the address in angle brackets) should be
enclosed in double quotes if it contains non-alphanumeric characters such as
comma or period. (The current standard, RFC 5322, allows periods but RFC 2822
did not.)
Both ‘Author’ and ‘Maintainer’ fields can be omitted if a suitable
‘Authors@R’ field is given. This field can be used to provide a refined and
machine-readable description of the package “authors” (in particular specifying
their precise roles), via suitable R code. It should create an object of
class "person", by either a call to person or a series of calls (one per “author”)
concatenated by c(): see the example DESCRIPTION file above. The roles can
include ‘"aut"’ (author) for full authors, ‘"cre"’ (creator) for the package
maintainer, and ‘"ctb"’ (contributor) for other contributors, ‘"cph"’ (copyright
holder, which should be the legal name for an institution or corporate body),
among others. See ?person for more information. Note that no role is assumed by
default. Auto-generated package citation information takes advantage of this
specification. The ‘Author’ and ‘Maintainer’ fields are auto-generated from it
if needed when building5 or installing.
An optional ‘Copyright’ field can be used where the copyright holder(s) are not
the authors. If necessary, this can refer to an installed file: the convention is to use
file inst/COPYRIGHTS.
The optional ‘Date’ field gives the release date of the current version of the
package. It is strongly recommended6 to use the ‘yyyy-mm-dd’ format
conforming to the ISO 8601 standard.
The ‘Depends’, ‘Imports’, ‘Suggests’, ‘Enhances’, ‘LinkingTo’ and
‘Additional_repositories’ fields are discussed in a later subsection.
Dependencies external to the R system should be listed in the
‘SystemRequirements’ field, possibly amplified in a separate README file.
This includes specifying a non-default C++ standard and the need for GNU make.
The ‘URL’ field may give a list of URLs separated by commas or whitespace, for
example the homepage of the author or a page where additional material describing
the software can be found. These URLs are converted to active hyperlinks
in CRAN package listings. See Specifying URLs.
The ‘BugReports’ field may contain a single URL to which bug reports about
the package should be submitted. This URL will be used by [Link] instead of
sending an email to the maintainer. A browser is opened for a ‘[Link] or
‘[Link] URL. To specify another email address for bug reports, use
‘Contact’ instead: however [Link] will try to extract an email address
(preferably from a ‘[Link] URL or enclosed in angle brackets) from
‘BugReports’.
Base and recommended packages (i.e., packages contained in the R source
distribution or available from CRAN and recommended to be included in every
binary distribution of R) have a ‘Priority’ field with value ‘base’ or
‘recommended’, respectively. These priorities must not be used by other
packages.
A ‘Collate’ field can be used for controlling the collation order for the R code
files in a package when these are processed for package installation. The default is
to collate according to the ‘C’ locale. If present, the collate specification must
list all R code files in the package (taking possible OS-specific subdirectories into
account, see Package subdirectories) as a whitespace separated list of file paths
relative to the R subdirectory. Paths containing white space or quotes need to be
quoted. An OS-specific collation field (‘[Link]’ or
‘[Link]’) will be used in preference to ‘Collate’.
The ‘LazyData’ logical field controls whether the R datasets use lazy-loading. A
‘LazyLoad’ field was used in versions prior to 2.14.0, but now is ignored.
The ‘KeepSource’ logical field controls if the package code is sourced
using [Link] = TRUE or FALSE: it might be needed exceptionally for a package
designed to always be used with [Link] = TRUE.
The ‘ByteCompile’ logical field controls if the package R code is to be byte-
compiled on installation: the default is to byte-compile. This can be overridden by
installing with flag --no-byte-compile.
The ‘UseLTO’ logical field is used to indicate if source code in the package7 is to
be compiled with Link-Time Optimization (see Using Link-time Optimization) if
R was installed with --enable-lto (default true) or --enable-
lto=R (default false) (or on Windows if LTO_OPT is set in MkRules). This can be
overridden by the flags --use-LTO and --no-use-LTO. LTO is said to give
most size and performance improvements for large and complex (heavily
templated) C++ projects.
The ‘StagedInstall’ logical field controls if package installation is ‘staged’,
that is done to a temporary location and moved to the final location when
successfully completed. This field was introduced in R 3.6.0 and it true by default:
it is considered to be a temporary measure which may be withdrawn in future.
The ‘ZipData’ logical field has been ignored since R 2.13.0.
The ‘Biarch’ logical field is used on Windows to select the INSTALL option --
force-biarch for this package.
The ‘BuildVignettes’ logical field can be set to a false value to stop R CMD
8
build from attempting to build the vignettes, as well as preventing R CMD
check from testing this. This should only be used exceptionally, for example if the
PDFs include large figures which are not part of the package sources (and hence
only in packages which do not have an Open Source license).
The ‘VignetteBuilder’ field names (in a comma-separated list) packages that
provide an engine for building vignettes. These may include the current package,
or ones listed in ‘Depends’, ‘Suggests’ or ‘Imports’. The utils package is
always implicitly appended. See Non-Sweave vignettes for details. Note that if, for
example, a vignette has engine ‘knitr::rmarkdown’, then knitr provides the
engine but both knitr and rmarkdown are needed for using it, so both these
packages need to be in the ‘VignetteBuilder’ field and at least suggested
(as rmarkdown is only suggested by knitr, and hence not available automatically
along with it). Many packages using knitr also need the package formatR which it
suggests and so the user package needs to do so too and include this in
‘VignetteBuilder’.
If the DESCRIPTION file is not entirely in ASCII it should contain an
‘Encoding’ field specifying an encoding. This is used as the encoding of
the DESCRIPTION file itself and of the R and NAMESPACE files, and as the
default encoding of .Rd files. The examples are assumed to be in this encoding
when running R CMD check, and it is used for the encoding of the CITATION file.
Only encoding names latin1, latin2 and UTF-8 are known to be portable. (Do not
specify an encoding unless one is actually needed: doing so makes the
package less portable. If a package has a specified encoding, you should run R CMD
build etc in a locale using that encoding.)

The ‘NeedsCompilation’ field should be set to "yes" if the package contains

native code which needs to be compiled, otherwise "no" (when the package could
be installed from source on any platform without additional tools). This is used
by [Link](type = "both") in R >= 2.15.2 on platforms where binary
packages are the norm: it is normally set by R CMD build or the repository
assuming compilation is required if and only if the package has a src directory.
The ‘OS_type’ field specifies the OS(es) for which the package is intended. If
present, it should be one of unix or windows, and indicates that the package can
only be installed on a platform with ‘.Platform$[Link]’ having that value.
The ‘Type’ field specifies the type of the package: see Package types.
One can add subject classifications for the content of the package using the fields
‘Classification/ACM’ or ‘Classification/ACM-2012’ (using the
Computing Classification System of the Association for Computing
Machinery, [Link] the former refers to the
1998 version), ‘Classification/JEL’ (the Journal of Economic Literature
Classification System, [Link] or
‘Classification/MSC’ or ‘Classification/MSC-2010’ (the
Mathematics Subject Classification of the American Mathematical
Society, [Link] the former refers to the
2000 version). The subject classifications should be comma-separated lists of the
respective classification codes, e.g., ‘Classification/ACM: G.4,
H.2.8, I.5.1’.
A ‘Language’ field can be used to indicate if the package documentation is not in
English: this should be a comma-separated list of standard (not private use or
grandfathered) IETF language tags as currently defined by RFC 5646
([Link] see
also [Link] i.e., use language subtags
which in essence are 2-letter ISO 639-1 ([Link]
or 3-letter ISO 639-3 ([Link] language codes.
An ‘RdMacros’ field can be used to hold a comma-separated list of packages
from which the current package will import Rd macro definitions. These package
should also be listed in ‘Imports’ (or ‘Depends’). The macros in these
packages will be imported after the system macros, in the order listed in the
‘RdMacros’ field, before any macro definitions in the current package are loaded.
Macro definitions in individual .Rd files in the man directory are loaded last, and
are local to later parts of that file. In case of duplicates, the last loaded definition
will be used.9 Both R CMD Rd2pdf and R CMD Rdconv have an optional flag --
RdMacros=pkglist. The option is also a comma-separated list of package
names, and has priority over the value given in DESCRIPTION. Packages
using Rd macros should depend on R 3.2.0 or later.
Note: There should be no ‘Built’ or ‘Packaged’ fields, as these are added by
the package management tools.
There is no restriction on the use of other fields not mentioned here (but using
other capitalizations of these field names would cause confusion).
Fields Note, Contact (for contacting the authors/developers10) and MailingList are
in common use. Some repositories (including CRAN and R-forge) add their own
fields.

Next: Package Dependencies, Previous: The DESCRIPTION file, Up: Package

structure [Contents][Index]
1.1.2 Licensing

Licensing for a package which might be distributed is an important but potentially

complex subject.
It is very important that you include license information! Otherwise, it may not
even be legally correct for others to distribute copies of the package, let alone use
it.
The package management tools use the concept of ‘free or open source software’
(FOSS, e.g., [Link] licenses: the idea being that some
users of R and its packages want to restrict themselves to such software. Others
need to ensure that there are no restrictions stopping them using a package, e.g.
forbidding commercial or military use. It is a central tenet of FOSS software that
there are no restrictions on users nor usage.
Do not use the ‘License’ field for information on copyright holders: if needed,
use a ‘Copyright’ field.
The mandatory ‘License’ field in the DESCRIPTION file should specify the
license of the package in a standardized form. Alternatives are
indicated via vertical bars. Individual specifications must be one of
 One of the “standard” short specifications
 GPL-2 GPL-3 LGPL-2 LGPL-2.1 LGPL-3 AGPL-3 Artistic-2.0
 BSD_2_clause BSD_3_clause MIT
as made available via [Link] and contained in
subdirectory share/licenses of the R source or home directory.
 The names or abbreviations of other licenses contained in the license data
base in file share/licenses/[Link] in the R source or home
directory, possibly (for versioned licenses) followed by a version restriction
of the form ‘(op v)’ with ‘op’ one of the comparison operators ‘<’, ‘<=’,
‘>’, ‘>=’, ‘==’, or ‘!=’ and ‘v’ a numeric version specification (strings of
non-negative integers separated by ‘.’), possibly combined via ‘,’ (see
below for an example). For versioned licenses, one can also specify the
name followed by the version, or combine an existing abbreviation and the
version with a ‘-’.
Abbreviations GPL and LGPL are ambiguous and usually11 taken to mean any
version of the license: but it is better not to use them.
  One of the strings ‘file LICENSE’ or ‘file LICENCE’ referring to a
file named LICENSE or LICENCE in the package (source and installation)
top-level directory.
 The string ‘Unlimited’, meaning that there are no restrictions on
distribution or use other than those imposed by relevant laws (including
copyright laws).
Multiple licences can be specified separated by ‘|’ (surrounded by spaces) in
which case the user can choose any of the alternatives.
If a package license restricts a base license (where permitted, e.g., using GPL-3 or
AGPL-3 with an attribution clause), the additional terms should be placed in
file LICENSE (or LICENCE), and the string ‘+ file LICENSE’ (or ‘+ file
LICENCE’, respectively) should be appended to the corresponding individual
license specification (preferably with the ‘+’ surrounded by spaces). Note that
several commonly used licenses do not permit restrictions: this includes GPL-2 and
hence any specification which includes it.
Examples of standardized specifications include
License: GPL-2
License: LGPL (>= 2.0, < 3) | Mozilla Public License
License: GPL-2 | file LICENCE
License: GPL (>= 2) | BSD_3_clause + file LICENSE
License: Artistic-2.0 | AGPL-3 + file LICENSE
Please note in particular that “Public domain” is not a valid license, since it is not
recognized in some jurisdictions.
Please ensure that the license you choose also covers any dependencies (including
system dependencies) of your package: it is particularly important that any
restrictions on the use of such dependencies are evident to people reading
your DESCRIPTION file.
Fields ‘License_is_FOSS’ and ‘License_restricts_use’ may be added
by repositories where information cannot be computed from the name of the
license. ‘License_is_FOSS: yes’ is used for licenses which are known to be
FOSS, and ‘License_restricts_use’ can have values ‘yes’ or ‘no’ if
the LICENSE file is known to restrict users or usage, or known not to. These are
used by, e.g., the [Link] filters.
The optional file LICENSE/LICENCE contains a copy of the license of the
package. To avoid any confusion only include such a file if it is referred to in the
‘License’ field of the DESCRIPTION file.
Whereas you should feel free to include a license file in your source distribution,
please do not arrange to install yet another copy of
the GNU COPYING or [Link] files but refer to the copies
on [Link] and included in the R distribution (in
directory share/licenses). Since files named LICENSE or LICENCE will be
installed, do not use these names for standard license files. To include comments
about the licensing rather than the body of a license, use a file named something
like [Link].
A few “standard” licenses are rather license templates which need additional
information to be completed via ‘+ file LICENSE’ (with the ‘+’ surrounded
by spaces)

Next: The INDEX file, Previous: Licensing, Up: Package structure [Contents]
[Index]
1.1.3 Package Dependencies

The ‘Depends’ field gives a comma-separated list of package names which this
package depends on. Those packages will be attached before the current package
when library or require is called. Each package name may be optionally followed
by a comment in parentheses specifying a version requirement. The comment
should contain a comparison operator, whitespace and a valid version number, e.g.
‘MASS (>= 3.1-20)’.
The ‘Depends’ field can also specify a dependence on a certain version of R —
e.g., if the package works only with R version 4.0.0 or later, include ‘R (>=
4.0)’ in the ‘Depends’ field. (As here, trailing zeroes can be dropped and it is
recommended that they are.) You can also require a certain SVN revision for R-
devel or R-patched, e.g. ‘R (>= 2.14.0), R (>= r56550)’ requires a
version later than R-devel of late July 2011 (including released versions of 2.14.0).
It makes no sense to declare a dependence on R without a version specification, nor
on the package base: this is an R package and package base is always available.
A package or ‘R’ can appear more than once in the ‘Depends’ field, for example
to give upper and lower bounds on acceptable versions.
It is inadvisable to use a dependence on R with patchlevel (the third digit) other
than zero. Doing so with packages which others depend on will cause the other
packages to become unusable under earlier versions in the series, and e.g. versions
4.x.1 are widely used throughout the Northern Hemisphere academic year.
Both library and the R package checking facilities use this field: hence it is an
error to use improper syntax or misuse the ‘Depends’ field for comments on
other software that might be needed. The R INSTALL facilities check if the version
of R used is recent enough for the package being installed, and the list of packages
which is specified will be attached (after checking version requirements) before the
current package.
The ‘Imports’ field lists packages whose namespaces are imported from (as
specified in the NAMESPACE file) but which do not need to be attached.
Namespaces accessed by the ‘::’ and ‘:::’ operators must be listed here, or in
‘Suggests’ or ‘Enhances’ (see below). Ideally this field will include all the
standard packages that are used, and it is important to include S4-using packages
(as their class definitions can change and the DESCRIPTION file is used to decide
which packages to re-install when this happens). Packages declared in the
‘Depends’ field should not also be in the ‘Imports’ field. Version requirements
can be specified and are checked when the namespace is loaded.
The ‘Suggests’ field uses the same syntax as ‘Depends’ and lists packages that
are not necessarily needed. This includes packages used only in examples, tests or
vignettes (see Writing package vignettes), and packages loaded in the body of
functions. E.g., suppose an example12 from package foo uses a dataset from
package bar. Then it is not necessary to have bar use foo unless one wants to
execute all the examples/tests/vignettes: it is useful to have bar, but not necessary.
Version requirements can be specified but should be checked by the code which
uses the package.
Finally, the ‘Enhances’ field lists packages “enhanced” by the package at hand,
e.g., by providing methods for classes from these packages, or ways to handle
objects from these packages (so several packages have ‘Enhances: chron’
because they can handle datetime objects from chron even though they prefer R’s
native datetime functions). Version requirements can be specified, but are currently
not used. Such packages cannot be required to check the package: any tests which
use them must be conditional on the presence of the package. (If your tests use e.g.
a dataset from another package it should be in ‘Suggests’ and not
‘Enhances’.)
The general rules are
 A package should be listed in only one of these fields.
 Packages whose namespace only is needed to load the package
using library(pkgname) should be listed in the ‘Imports’ field and not in
the ‘Depends’ field. Packages listed in import or importFrom directives in
the NAMESPACE file should almost always be in ‘Imports’ and not
‘Depends’.
 Packages that need to be attached to successfully load the package
using library(pkgname) must be listed in the ‘Depends’ field.
 All packages that are needed13 to successfully run R CMD check on the
package must be listed in one of ‘Depends’ or ‘Suggests’ or
‘Imports’. Packages used to run examples or tests conditionally
(e.g. via if(require(pkgname))) should be listed in ‘Suggests’ or
‘Enhances’. (This allows checkers to ensure that all the packages needed
for a complete check are installed.)
 Packages needed to use datasets from the package should be in ‘Imports’:
this includes those needed to define S4 classes used.
In particular, packages providing “only” data for examples or vignettes should be
listed in ‘Suggests’ rather than ‘Depends’ in order to make lean installations
possible.
Version dependencies in the ‘Depends’ and ‘Imports’ fields are used
by library when it loads the package, and [Link] checks versions for
the ‘Depends’, ‘Imports’ and (for dependencies = TRUE) ‘Suggests’ fields.
It is important that the information in these fields is complete and accurate: it is for
example used to compute which packages depend on an updated package and
which packages can safely be installed in parallel.
This scheme was developed before all packages had namespaces (R 2.14.0 in
October 2011), and good practice changed once that was in place.
Field ‘Depends’ should nowadays be used rarely, only for packages which are
intended to be put on the search path to make their facilities available to the end
user (and not to the package itself): for example it makes sense that a user of
package latticeExtra would want the functions of package lattice made available.
Almost always packages mentioned in ‘Depends’ should also be imported from
in the NAMESPACE file: this ensures that any needed parts of those packages are
available when some other package imports the current package.
The ‘Imports’ field should not contain packages which are not imported from
(via the NAMESPACE file or :: or ::: operators), as all the packages listed in that
field need to be installed for the current package to be installed. (This is checked
by R CMD check.)
R code in the package should call library or require only exceptionally. Such
calls are never needed for packages listed in ‘Depends’ as they will already be on
the search path. It used to be common practice to use require calls for packages
listed in ‘Suggests’ in functions which used their functionality, but nowadays it
is better to access such functionality via :: calls.
A package that wishes to make use of header files in other packages to compile its
C/C++ code needs to declare them as a comma-separated list in the field
‘LinkingTo’ in the DESCRIPTION file. For example
LinkingTo: link1, link2
The ‘LinkingTo’ field can have a version requirement which is checked at
installation.
Specifying a package in ‘LinkingTo’ suffices if these are C/C++ headers
containing source code or static linking is done at installation: the packages do not
need to be (and usually should not be) listed in the ‘Depends’ or ‘Imports’
fields. This includes CRAN package BH and almost all users
of RcppArmadillo and RcppEigen. Note that ‘LinkingTo’ applies only to
installation: if a packages wishes to use headers to compile code in tests or
vignettes the package providing them needs to be listed in ‘Suggests’ or perhaps
‘Depends’.
For another use of ‘LinkingTo’ see Linking to native routines in other packages.
The ‘Additional_repositories’ field is a comma-separated list of
repository URLs where the packages named in the other fields may be found. It is
currently used by R CMD check to check that the packages can be found, at least as
source packages (which can be installed on any platform).
 Suggested packages

Previous: Package Dependencies, Up: Package Dependencies [Contents][Index]

[Link] Suggested packages

Note that someone wanting to run the examples/tests/vignettes may not have a
suggested package available (and it may not even be possible to install it for that
platform). The recommendation used to be to make their use
conditional via if(require("pkgname")): this is OK if that conditioning is done in
examples/tests/vignettes, although using if(requireNamespace("pkgname")) is
preferred, if possible.
However, using require for conditioning in package code is not good practice as it
alters the search path for the rest of the session and relies on functions in that
package not being masked by other require or library calls. It is better practice to
use code like
if (requireNamespace("rgl", quietly = TRUE)) {
rgl::plot3d(...)
} else {
## do something else not involving rgl.
}
Note the use of rgl:: as that object would not necessarily be visible (and if it is, it
need not be the one from that namespace: plot3d occurs in several other packages).
If the intention is to give an error if the suggested package is not available, simply
use e.g. rgl::plot3d.
If the conditional code produces print output, function withAutoprint can be
useful.
Note that the recommendation to use suggested packages conditionally in tests
does also apply to packages used to manage test suites: a notorious example
was testthat which in version 1.0.0 contained illegal C++ code and hence could
not be installed on standards-compliant platforms.
Some people have assumed that a ‘recommended’ package in ‘Suggests’ can
safely be used unconditionally, but this is not so. (R can be installed without
recommended packages, and which packages are ‘recommended’ may change.)
As noted above, packages in ‘Enhances’ must be used conditionally and hence
objects within them should always be accessed via ::.
On most systems, R CMD check can be run with only those packages declared in
‘Depends’ and ‘Imports’ by setting environment
variable _R_CHECK_DEPENDS_ONLY_=true, whereas
setting _R_CHECK_SUGGESTS_ONLY_=true also allows suggested packages, but not
those in ‘Enhances’ nor those not mentioned in the DESCRIPTION file. It is
recommended that a package is checked with each of these set, as well as with
neither.
WARNING: Be extremely careful if you do things which would be run at
installation time depending on whether suggested packages are available or not—
this includes top-level code in R code files, .onLoad functions and the definitions of
S4 classes and methods. The problem is that once a namespace of a suggested
package is loaded, references to it may be captured in the installed package (most
commonly in S4 methods), but the suggested package may not be available when
the installed package is used (which especially for binary packages might be on a
different machine). Even worse, the problems might not be confined to your
package, for the namespaces of your suggested packages will also be loaded
whenever any package which imports yours is installed and so may be captured
there.

Next: Package subdirectories, Previous: Package Dependencies, Up: Package

structure [Contents][Index]
1.1.4 The INDEX file

The optional file INDEX contains a line for each sufficiently interesting object in
the package, giving its name and a description (functions such as print methods not
usually called explicitly might not be included). Normally this file is missing and
the corresponding information is automatically generated from the documentation
sources (using tools::Rdindex()) when installing from source.
The file is part of the information given by library(help = pkgname).

Rather than editing this file, it is preferable to put customized information about
the package into an overview help page (see Documenting packages) and/or a
vignette (see Writing package vignettes).

Next: Data in packages, Previous: The INDEX file, Up: Package structure
[Contents][Index]
1.1.5 Package subdirectories
The R subdirectory contains R code files, only. The code files to be installed must
start with an ASCII (lower or upper case) letter or digit and have one of the
extensions14 .R, .S, .q, .r, or .s. We recommend using .R, as this extension
seems to be not used by any other software. It should be possible to read in the
files using source(), so R objects must be created by assignments. Note that there
need be no connection between the name of the file and the R objects created by it.
Ideally, the R code files should only directly assign R objects and definitely should
not call functions with side effects such as require and options. If computations
are required to create objects these can use code ‘earlier’ in the package (see the
‘Collate’ field) plus functions in the ‘Depends’ packages provided that the
objects created do not depend on those packages except via namespace imports.
Extreme care is needed if top-level computations are made to depend on
availability or not of other packages. In particular this applies
to setMethods and setClass calls. Nor should they depend on the availability of
external resources such as downloads.
Two exceptions are allowed: if the R subdirectory contains a
file [Link] (a saved image of one or more R objects: please use suitable
compression as suggested by tools::resaveRdaFiles, and see also the
‘SysDataCompression’ DESCRIPTION field.) this will be lazy-loaded into
the namespace environment – this is intended for system datasets that are not
intended to be user-accessible via data. Also, files ending in ‘.in’ will be allowed
in the R directory to allow a configure script to generate suitable files.
Only ASCII characters (and the control characters tab, formfeed, LF and CR)
should be used in code files. Other characters are accepted in comments15, but then
the comments may not be readable in e.g. a UTF-8 locale. Non-ASCII characters
in object names will normally16 fail when the package is installed. Any byte will be
allowed in a quoted character string but ‘\uxxxx’ escapes should be used for non-
ASCII characters. However, non-ASCII character strings may not be usable in
some locales and may display incorrectly in others.
Various R functions in a package can be used to initialize and clean up. See Load
hooks.
The man subdirectory should contain (only) documentation files for the objects in
the package in R documentation (Rd) format. The documentation filenames must
start with an ASCII (lower or upper case) letter or digit and have the
extension .Rd (the default) or .rd. Further, the names must be valid in
‘[Link] URLs, which means17 they must be entirely ASCII and not contain
‘%’. See Writing R documentation files, for more information. Note that all user-
level objects in a package should be documented; if a package pkg contains user-
level objects which are for “internal” use only, it should provide a file pkg-
[Link] which documents all such objects, and clearly states that these are
not meant to be called by the user. See e.g. the sources for package grid in the R
distribution. Note that packages which use internal objects extensively should not
export those objects from their namespace, when they do not need to be
documented (see Package namespaces).
Having a man directory containing no documentation files may give an installation
error.
The man subdirectory may contain a subdirectory named macros; this will
contain source for user-defined Rd macros. (See User-defined macros.) These use
the Rd format, but may not contain anything but macro definitions, comments and
whitespace.
The R and man subdirectories may contain OS-specific subdirectories
named unix or windows.
The sources and headers for the compiled code are in src, plus optionally a
file Makevars or Makefile (or for use on Windows, with
extension .win or .ucrt). When a package is installed using R CMD
INSTALL, make is used to control compilation and linking into a shared object for
loading into R. There are default make variables and rules for this (determined
when R is configured and recorded in R_HOME/etcR_ARCH/Makeconf),
providing support for C, C++, fixed- or free-form Fortran, Objective C and
Objective C++18 with associated
extensions .c, .cc or .cpp, .f, .f90 or .f95, .m, and .mm, respectively. We
recommend using .h for headers, also for C++19 or Fortran 9x include files. (Use
of extension .C for C++ is no longer supported.) Files in the src directory should
not be hidden (start with a dot), and hidden files will under some versions of R be
ignored.
It is not portable (and may not be possible at all) to mix all these languages in a
single package. Because R itself uses it, we know that C and fixed-form Fortran
can be used together, and mixing C, C++ and Fortran usually work for the
platform’s native compilers.
If your code needs to depend on the platform there are certain defines which can
used in C or C++. On all Windows builds (even 64-bit ones) ‘_WIN32’ will be
defined: on 64-bit Windows builds also ‘_WIN64’. On macOS ‘__APPLE__’ is
defined20; for an ‘Apple Silicon’ platform, test for both ‘__APPLE__’ and
‘__arm64__’.
The default rules can be tweaked by setting macros21 in a
file src/Makevars (see Using Makevars). Note that this mechanism should
be general enough to eliminate the need for a package-specific src/Makefile.
If such a file is to be distributed, considerable care is needed to make it general
enough to work on all R platforms. If it has any targets at all, it should have an
appropriate first target named ‘all’ and a (possibly empty) target ‘clean’ which
removes all files generated by running make (to be used by ‘R CMD INSTALL
--clean’ and ‘R CMD INSTALL --preclean’). There are platform-specific
file names on Windows: src/[Link] takes precedence
over src/Makevars and src/[Link] must be used. Since R
4.2.0, src/[Link] takes precedence
over src/[Link] and src/[Link] takes precedence
over src/[Link]. src/[Link] and src/[Link]
rt will be ignored by earlier versions of R, and hence can be used to provide
content specific to UCRT or Rtools42 and newer, but the support for .ucrt files
may be removed in the future when building packages from source on the older
versions of R will no longer be needed, and hence the files may be renamed back
to .win. Some make programs require makefiles to have a complete final line,
including a newline.
A few packages use the src directory for purposes other than making a shared
object (e.g. to create executables). Such packages should have
files src/Makefile and src/[Link] or src/[Link] (u
nless intended for only Unix-alikes or only Windows). Note that on Unix such
makefiles are included after R_HOME/etc/R_ARCH/Makeconf so all the usual
R macros and make rules are available – for example C compilation will by default
use the C compiler and flags with which R was configured. This also applies on
Windows as from R 4.3.0: packages intended to be used with earlier versions
should include that file themselves.
The order of inclusion of makefiles for a package which does not have
a src/Makefile file is
Unix-alike Windows
src/Makevars src/[Link], src/[Link]
R_HOME/etc/R_ARCH/
R_HOME/etc/R_ARCH/Makeconf
Makeconf
R_MAKEVARS_SITE, R_HOME/ R_MAKEVARS_SITE, R_HOME/etc/R_ARCH/
etc/R_ARCH/[Link] [Link]
R_HOME/share/make/
R_HOME/share/make/[Link]
[Link]
R_MAKEVARS_USER, ~/.R/
R_MAKEVARS_USER,
~/.R/[Link], ~/.R/
Makevars-platform, ~/.R/
Makevars.win64, ~/.R/[Link]
Makevars
For those which do, it is
R_HOME/etc/R_ARCH/
R_HOME/etc/R_ARCH/Makeconf
Makeconf
R_MAKEVARS_SITE, R_HOME/ R_MAKEVARS_SITE, R_HOME/etc/R_ARCH/
etc/R_ARCH/[Link] [Link]
src/Makefile src/[Link], src/[Link]
R_MAKEVARS_USER, ~/.R/ R_MAKEVARS_USER, ~/.R/[Link], ~/.R/
Makevars-platform, ~/.R/ Makevars.win64, ~/.R/[Link]
Makevars
Items in capitals are environment variables: those separated by commas are
alternatives looked for in the order shown.
In very special cases packages may create binary files other than the shared
objects/DLLs in the src directory. Such files will not be installed in a multi-
architecture setting since R CMD INSTALL --libs-only is used to merge multiple
sub-architectures and it only copies shared objects/DLLs. If a package wants to
install other binaries (for example executable programs), it should provide an R
script src/[Link].R which will be run as part of the installation in
the src build directory instead of copying the shared objects/DLLs. The script is
run in a separate R environment containing the following
variables: R_PACKAGE_NAME (the name of the package), R_PACKAGE_SOURCE (the path to
the source directory of the package), R_PACKAGE_DIR (the path of the target
installation directory of the package), R_ARCH (the arch-dependent part of the path,
often empty), SHLIB_EXT (the extension of shared objects) and WINDOWS (TRUE on
Windows, FALSE elsewhere). Something close to the default behavior could be
replicated with the following src/[Link].R file:
files <- [Link](paste0("*", SHLIB_EXT))
dest <- [Link](R_PACKAGE_DIR, paste0('libs', R_ARCH))
[Link](dest, recursive = TRUE, showWarnings = FALSE)
[Link](files, dest, overwrite = TRUE)
if([Link]("[Link]"))
[Link]("[Link]", dest, overwrite = TRUE)
On the other hand, executable programs could be installed along the lines of
execs <- c("one", "two", "three")
if(WINDOWS) execs <- paste0(execs, ".exe")
if ( any([Link](execs)) ) {
dest <- [Link](R_PACKAGE_DIR, paste0('bin', R_ARCH))
[Link](dest, recursive = TRUE, showWarnings = FALSE)
[Link](execs, dest, overwrite = TRUE)
}
Note the use of architecture-specific subdirectories of bin where needed.
(Executables should installed under a bin directory and not under libs. It is
good practice to check that they can be executed as part of the installation script, so
a broken package is not installed.)
The data subdirectory is for data files: See Data in packages.
The demo subdirectory is for R scripts (for running via demo()) that demonstrate
some of the functionality of the package. Demos may be interactive and are not
checked automatically, so if testing is desired use code in the tests directory to
achieve this. The script files must start with a (lower or upper case) letter and have
one of the extensions .R or .r. If present, the demo subdirectory should also have
a 00Index file with one line for each demo, giving its name and a description
separated by a tab or at least three spaces. (This index file is not generated
automatically.) Note that a demo does not have a specified encoding and so should
be an ASCII file (see Encoding issues). Function demo() will use the package
encoding if there is one, but this is mainly useful for non-ASCII comments.
The contents of the inst subdirectory will be copied recursively to the installation
directory. Subdirectories of inst should not interfere with those used by R
(currently, R, data, demo, exec, libs, man, help, html and Meta, and
earlier versions used latex, R-ex). The copying of the inst happens
after src is built so its Makefile can create files to be installed. To exclude files
from being installed, one can specify a list of exclude patterns in
file .Rinstignore in the top-level source directory. These patterns should be
Perl-like regular expressions (see the help for regexp in R for the precise details),
one per line, to be matched case-insensitively against the file and directory paths,
e.g. doc/.*[.]png$ will exclude all PNG files in inst/doc based on the
extension.
Note that with the exceptions of INDEX, LICENSE/LICENCE and NEWS,
information files at the top level of the package will not be installed and so not be
known to users of Windows and macOS compiled packages (and not seen by those
who use R CMD INSTALL or [Link]() on the tarball). So any information
files you wish an end user to see should be included in inst. Note that if the
named exceptions also occur in inst, the version in inst will be that seen in the
installed package.
Things you might like to add to inst are a CITATION file for use by
the citation function, and a [Link] file for use by the news function. See its
help page for the specific format restrictions of the [Link] file.
Another file sometimes needed in inst is AUTHORS or COPYRIGHTS to specify
the authors or copyright holders when this is too complex to put in
the DESCRIPTION file.
Subdirectory tests is for additional package-specific test code, similar to the
specific tests that come with the R distribution. Test code can either be provided
directly in a .R (or .r as from R 3.4.0) file, or via a .Rin file containing code
which in turn creates the corresponding .R file (e.g., by collecting all function
objects in the package and then calling them with the strangest arguments). The
results of running a .R file are written to a .Rout file. If there is a
corresponding22 .[Link] file, these two are compared, with differences
being reported but not causing an error. The directory tests is copied to the
check area, and the tests are run with the copy as the working directory and
with R_LIBS set to ensure that the copy of the package installed during testing will
be found by library(pkg_name). Note that the package-specific tests are run in a
vanilla R session without setting the random-number seed, so tests which use
random numbers will need to set the seed to obtain reproducible results (and it can
be helpful to do so in all cases, to avoid occasional failures when tests are run).
If directory tests has a subdirectory Examples containing a file pkg-
[Link], this is compared to the output file for running the examples when
the latter are checked. Reference output should be produced without having the --
timings option set (and note that --as-cran sets it).
If reference output is included for examples, tests or vignettes do make sure that it
is fully reproducible, as it will be compared verbatim to that produced in a check
run, unless the ‘IGNORE_RDIFF’ markup is used. Things which trip up
maintainers include displayed version numbers from loading other packages,
printing numerical results to an unreproducibly high precision and printing timings.
Another trap is small values which are in fact rounding error from zero: consider
using zapsmall.
Subdirectory exec could contain additional executable scripts the package needs,
typically scripts for interpreters such as the shell, Perl, or Tcl. NB: only files (and
not directories) under exec are installed (and those with names starting with a dot
are ignored), and they are all marked as executable (mode 755, moderated by
‘umask’) on POSIX platforms. Note too that this is not suitable for
executable programs since some platforms (including Windows) support multiple
architectures using the same installed package directory.
Subdirectory po is used for files related to localization: see Internationalization.
Subdirectory tools is the preferred place for auxiliary files needed during
configuration, and also for sources need to re-create scripts (e.g. M4 files
for autoconf: some prefer to put those in a subdirectory m4 of tools).

Next: Non-R scripts in packages, Previous: Package subdirectories, Up: Package

structure [Contents][Index]
1.1.6 Data in packages

The data subdirectory is for data files, either to be made available via lazy-
loading or for loading using data(). (The choice is made by the ‘LazyData’ field
in the DESCRIPTION file: the default is not to do so.) It should not be used for
other data files needed by the package, and the convention has grown up to use
directory inst/extdata for such files.
Data files can have one of three types as indicated by their extension: plain R code
(.R or .r), tables (.tab, .txt, or .csv, see ?data for the file formats, and note
that .csv is not the standard23 CSV format), or save() images
(.RData or .rda). The files should not be hidden (have names starting with a
dot). Note that R code should be if possible “self-sufficient” and not make use of
extra functionality provided by the package, so that the data file can also be used
without having to load the package or its namespace: it should run as silently as
possible and not change the search() path by attaching packages or other
environments.
Images (extensions .RData24 or .rda) can contain references to the namespaces
of packages that were used to create them. Preferably there should be no such
references in data files, and in any case they should only be to packages listed in
the Depends and Imports fields, as otherwise it may be impossible to install the
package. To check for such references, load all the images into a vanilla R session,
run str() on all the datasets, and look at the output of loadedNamespaces().
Particular care is needed where a dataset or one of its components is of an S4 class,
especially if the class is defined in a different package. First, the package
containing the class definition has to be available to do useful things with the
dataset, so that package must be listed in Imports or Depends (even if this gives a
check warning about unused imports). Second, the definition of an S4 class can
change, and often is unnoticed when in a package with a different author. So it may
be wiser to use the .R form and use that to create the dataset object when needed
(loading package namespaces but not attaching them by
using requireNamespace(pkg, quietly = TRUE) and using pkg:: to refer to objects
in the namespace).
If you are not using ‘LazyData’ and either your data files are large or e.g., you
use data/foo.R scripts to produce your data, loading your namespace, you can
speed up installation by providing a file datalist in the data subdirectory.
This should have one line per topic that data() will find, in the format ‘foo’
if data(foo) provides ‘foo’, or ‘foo: bar bah’ if data(foo) provides ‘bar’
and ‘bah’. R CMD build will automatically add a datalist file
to data directories of over 1Mb, using the function tools::add_datalist.
Tables (.tab, .txt, or .csv files) can be compressed by gzip, bzip2 or xz,
optionally with additional extension .gz, .bz2 or .xz.
If your package is to be distributed, do consider the resource implications of large
datasets for your users: they can make packages very slow to download and use up
unwelcome amounts of storage space, as well as taking many seconds to load. It is
normally best to distribute large datasets as .rda images prepared by save(,
compress = TRUE) (the default). Using bzip2 or xz compression will usually reduce
the size of both the package tarball and the installed package, in some cases by a
factor of two or more.
Package tools has a couple of functions to help with data
images: checkRdaFiles reports on the way the image was saved,
and resaveRdaFiles will re-save with a different type of compression, including
choosing the best type for that particular image.
Many packages using ‘LazyData’ will benefit from using a form of compression
other than gzip in the installed lazy-loading database. This can be selected by
the --data-compress option to R CMD INSTALL or by using the
‘LazyDataCompression’ field in the DESCRIPTION file. Useful values
are bzip2, xz and the default, gzip: value none is also accepted. The only way to
discover which is best is to try them all and look at the size of
the pkgname/data/[Link] file. A function to do that (quoting sizes in
KB) is
CheckLazyDataCompression <- function(pkg)
{
pkg_name <- sub("_.*", "", pkg)
lib <- tempfile(); [Link](lib)
zs <- c("gzip", "bzip2", "xz")
res <- integer(3); names(res) <- zs
for (z in zs) {
opts <- c(paste0("--data-compress=", z),
"--no-libs", "--no-help", "--no-demo", "--no-exec", "--
no-test-load")
[Link](pkg, lib, INSTALL_opts = opts, repos = NULL, quiet
= TRUE)
res[z] <- [Link]([Link](lib, pkg_name, "data", "[Link]"))
}
ceiling(res/1024)
}
(applied to a source package without any ‘LazyDataCompression’ field). R
CMD check will warn if it finds a pkgname/data/[Link] file of more than
5MB without ‘LazyDataCompression’ being set. If you see that,
run CheckLazyDataCompression() and set the field – to gzip in the unlikely
event25 that is the best choice.
The analogue for [Link] is field ‘SysDataCompression’: the default
is xz for files bigger than 1MB otherwise gzip.
Lazy-loading is not supported for very large datasets (those which when serialized
exceed 2GB, the limit for the format on 32-bit platforms).

Next: Specifying URLs, Previous: Data in packages, Up: Package structure

[Contents][Index]
1.1.7 Non-R scripts in packages

Code which needs to be compiled (C, C++, Fortran …) is included in

the src subdirectory and discussed elsewhere in this document.
Subdirectory exec could be used for scripts for interpreters such as the shell,
BUGS, JavaScript, Matlab, Perl, php (amap), Python or Tcl (Simile), or even R.
However, it seems more common to use the inst directory, for
example WriteXLS/inst/Perl, NMF/inst/m-files, RnavGraph/ins
t/tcl, RProtoBuf/inst/python and emdbook/inst/BUGS and gridS
VG/inst/js.
Java code is a special case: except for very small programs, .java files should be
byte-compiled (to a .class file) and distributed as part of a .jar file: the
conventional location for the .jar file(s) is inst/java. It is desirable (and
required under an Open Source license) to make the Java source files available:
this is best done in a top-level java directory in the package—the source files
should not be installed.
If your package requires one of these interpreters or an extension then this should
be declared in the ‘SystemRequirements’ field of its DESCRIPTION file.
(Users of Java most often do so via rJava, when depending on/importing that
suffices unless there is a version requirement on Java code in the package.)
Windows and Mac users should be aware that the Tcl extensions ‘BWidget’ and
‘Tktable’ (which have sometimes been included in the Windows26 and macOS R
installers) are extensions and do need to be declared (and that ‘Tktable’ is less
widely available than it used to be, including not in the main repositories for major
Linux distributions). ‘BWidget’ needs to be installed by the user on other OSes.
This is fairly easy to do: first find the Tcl search path:
library(tcltk)
strsplit(tclvalue('auto_path'), " ")[[1]]
then download the sources
from [Link] and in a terminal run
something like
tar xf [Link]
sudo mv bwidget-1.9.14 /usr/local/lib
substituting a location on the Tcl search path for /usr/local/lib if needed. (If
no location on that search path is writeable, you will need to add one each time
BWidget is to be used with tcltk::addTclPath().)
To (silently) test for the presence of ‘Tktable’ one can use
library(tcltk)
have_tktable <- !isFALSE(suppressWarnings(tclRequire('Tktable')))
Installing ‘Tktable’ needs a C compiler and the Tk headers (not necessarily
installed with Tcl/Tk). At the time of writing the latest sources (from 2008) were
available
from [Link]
download, but needed patching for current Tk (8.6.11, but not 8.6.10) – a patch can
be found at [Link] For a system installation
of Tk you may need to install Tktable as ‘root’ as on e.g. Fedora all the locations
on auto_path are owned by ‘root’.

Previous: Non-R scripts in packages, Up: Package structure [Contents][Index]

1.1.8 Specifying URLs
URLs in many places in the package documentation will be converted to clickable
hyperlinks in at least some of their renderings. So care is needed that their forms
are correct and portable.
The full URL should be given, including the scheme (often ‘[Link] or
‘[Link] and a final ‘/’ for references to directories.
Spaces in URLs are not portable and how they are handled does vary by HTTP
server and by client. There should be no space in the host part of an ‘[Link]
URL, and spaces in the remainder should be encoded, with each space replaced by
‘%20’.
Other characters may benefit from being encoded: see the help on URLencode().
The canonical URL for a CRAN package is
[Link]
and not a version starting
‘[Link]

Next: Checking and building packages, Previous: Package structure, Up: Creating
R packages [Contents][Index]

1.2 Configure and cleanup

Note that most of this section is specific to Unix-alikes: see the comments later on
about the Windows port of R.
If your package needs some system-dependent configuration before installation
you can include an executable (Bourne27 shell script configure in your package
which (if present) is executed by R CMD INSTALL before any other action is
performed. This can be a script created by the Autoconf mechanism, but may also
be a script written by yourself. Use this to detect if any nonstandard libraries are
present such that corresponding code in the package can be disabled at install time
rather than giving error messages when the package is compiled or used. To
summarize, the full power of Autoconf is available for your extension package
(including variable substitution, searching for libraries, etc.). Background and
useful tips on Autoconf and related tools (including pkg-config described below)
can be found at [Link]
A configure script is run in an environment which has all the environment
variables set for an R session (see R_HOME/etc/Renviron)
plus R_PACKAGE_NAME (the name of the package), R_PACKAGE_DIR (the path of the
target installation directory of the package, a temporary location for staged installs)
and R_ARCH (the arch-dependent part of the path, often empty).
Under a Unix-alike only, an executable (Bourne shell) script cleanup is executed as
the last thing by R CMD INSTALL if option --clean was given, and by R CMD
build when preparing the package for building from its source.

As an example consider we want to use functionality provided by a (C or Fortran)

library foo. Using Autoconf, we can create a configure script which checks for the
library, sets variable HAVE_FOO to TRUE if it was found and to FALSE otherwise, and
then substitutes this value into output files (by replacing instances of
‘@HAVE_FOO@’ in input files with the value of HAVE_FOO). For example, if a
function named bar is to be made available by linking against library foo (i.e.,
using -lfoo), one could use
AC_CHECK_LIB(foo, fun, [HAVE_FOO=TRUE], [HAVE_FOO=FALSE])
AC_SUBST(HAVE_FOO)
......
AC_CONFIG_FILES([foo.R])
AC_OUTPUT
in [Link] (assuming Autoconf 2.50 or later).
The definition of the respective R function in [Link] could be
foo <- function(x) {
if(!@HAVE_FOO@)
stop("Sorry, library ‘foo’ is not available")
...
From this file configure creates the actual R source file foo.R looking like
foo <- function(x) {
if(!FALSE)
stop("Sorry, library ‘foo’ is not available")
...
if library foo was not found (with the desired functionality). In this case, the above
R code effectively disables the function.
One could also use different file fragments for available and missing functionality,
respectively.
You will very likely need to ensure that the same C compiler and compiler flags
are used in the configure tests as when compiling R or your package. Under a
Unix-alike, you can achieve this by including the following fragment early
in [Link] (before calling AC_PROG_CC or anything which calls it)
: ${R_HOME=`R RHOME`}
if test -z "${R_HOME}"; then
echo "could not determine R_HOME"
exit 1
fi
CC=`"${R_HOME}/bin/R" CMD config CC`
CFLAGS=`"${R_HOME}/bin/R" CMD config CFLAGS`
CPPFLAGS=`"${R_HOME}/bin/R" CMD config CPPFLAGS`
(Using ‘${R_HOME}/bin/R’ rather than just ‘R’ is necessary in order to use the
correct version of R when running the script as part of R CMD INSTALL, and the
quotes since ‘${R_HOME}’ might contain spaces.)
If your code does load checks (for example, to check for an entry point in a library
or to run code) then you will also need
LDFLAGS=`"${R_HOME}/bin/R" CMD config LDFLAGS`
Packages written with C++ need to pick up the details for the C++ compiler and
switch the current language to C++ by something like
CXX=`"${R_HOME}/bin/R" CMD config CXX`
if test -z "$CXX"; then
AC_MSG_ERROR([No C++ compiler is available])
fi
CXXFLAGS=`"${R_HOME}/bin/R" CMD config CXXFLAGS`
CPPFLAGS=`"${R_HOME}/bin/R" CMD config CPPFLAGS`
AC_LANG(C++)
The latter is important, as for example C headers may not be available to C++
programs or may not be written to avoid C++ name-mangling. Note that an R
installation is not required to have a C++ compiler so ‘CXX’ may be empty. If the
package specifies a non-default C++ standard, use the config variable names (such
as CXX17) appropriate to the standard, but still set CXX and CXXFLAGS.
You can use R CMD config to get the value of the basic configuration variables, and
also the header and library flags necessary for linking a front-end executable
program against R, see R CMD config --help for details. If you do, it is essential
that you use both the command and the appropriate flags, so that for example ‘CC’
must always be used with ‘CFLAGS’ and (for code to be linked into a shared
library) ‘CPICFLAGS’. For Fortran, be careful to use ‘FC FFLAGS
FPICFLAGS’ for fixed-form Fortran and ‘FC FCFLAGS FPICFLAGS’ for free-
form Fortran.
As from R 4.3.0, variables
CC CFLAGS CXX CXXFLAGS CPPFLAGS LDFLAGS FC FCFLAGS
are set in the environment (if not already set) when configure is called from R CMD
INSTALL, in case the script forgets to set them as described above. This includes
making use of the selected C standard (but not the C++ standard as that is selected
at a later stage by R CMD SHLIB).
To check for an external BLAS library using the AX_BLAS macro from the official
Autoconf Macro Archive28, one can use
FC=`"${R_HOME}/bin/R" CMD config FC`
FCLAGS=`"${R_HOME}/bin/R" CMD config FFLAGS`
AC_PROG_FC
FLIBS=`"${R_HOME}/bin/R" CMD config FLIBS`
AX_BLAS([], AC_MSG_ERROR([could not find your BLAS library], 1))
Note that FLIBS as determined by R must be used to ensure that Fortran code works
on all R platforms.
N.B.: If the configure script creates files, e.g. src/Makevars, you do need
a cleanup script to remove them. Otherwise R CMD build may ship the files that are
created. For example, package RODBC has
#!/bin/sh

rm -f config.* src/Makevars src/config.h

As this example shows, configure often creates working files such
as [Link]. If you use a hand-crafted script rather than one created
by autoconf, it is highly recommended that you log its actions to
file [Link].
If your configure script needs auxiliary files, it is recommended that you ship them
in a tools directory (as R itself does).
You should bear in mind that the configure script will not be used on Windows
systems. If your package is to be made publicly available, please give enough
information for a user on a non-Unix-alike platform to configure it manually, or
provide a [Link] script (or [Link]) to be used on that
platform. (Optionally, there can be a [Link] script (or [Link]).
Both should be shell scripts to be executed by ash, which is a minimal version of
Bourne-style sh. As from R 4.2.0, bash is used.
When [Link] (or [Link]) is run the environment
variables R_HOME (which uses ‘/’ as the file separator), R_ARCH and R_ARCH_BIN will
be set. Use R_ARCH to decide if this is a 64-bit build (its value there is ‘/x64’) and
to install DLLs to the correct place (${R_HOME}/libs${R_ARCH}).
Use R_ARCH_BIN to find the correct place under the bin directory, e.g. $
{R_HOME}/bin${R_ARCH_BIN}/[Link]. If
a [Link] script does compilation (including calling R CMD SHLIB), most
of the considerations above apply.
As the scripts on Windows are executed as sh ./[Link] and similar, any
’shebang’ first line (such as #! /bin/bash) is treated as a comment.
In some rare circumstances, the configuration and cleanup scripts need to know the
location into which the package is being installed. An example of this is a package
that uses C code and creates two shared object/DLLs. Usually, the object that is
dynamically loaded by R is linked against the second, dependent, object. On some
systems, we can add the location of this dependent object to the object that is
dynamically loaded by R. This means that each user does not have to set the value
of the LD_LIBRARY_PATH (or equivalent) environment variable, but that the
secondary object is automatically resolved. Another example is when a package
installs support files that are required at run time, and their location is substituted
into an R data structure at installation time. The names of the top-level library
directory (i.e., specifiable via the ‘-l’ argument) and the directory of the package
itself are made available to the installation scripts via the two shell/environment
variables R_LIBRARY_DIR and R_PACKAGE_DIR. Additionally, the name of the package
(e.g. ‘survival’ or ‘MASS’) being installed is available from the environment
variable R_PACKAGE_NAME. (Currently the value of R_PACKAGE_DIR is always $
{R_LIBRARY_DIR}/${R_PACKAGE_NAME}, but this used not to be the case when
versioned installs were allowed. Its main use is
in [Link] (or [Link]) scripts for the installation path of
external software’s DLLs.) Note that the value of R_PACKAGE_DIR may contain
spaces and other shell-unfriendly characters, and so should be quoted in makefiles
and configure scripts.
One of the more tricky tasks can be to find the headers and libraries of external
software. One tool which is increasingly available on Unix-alikes (but not by
default29 on macOS) to do this is pkg-config. The configure script will need to
test for the presence of the command itself30 (see for example package tiff), and if
present it can be asked if the software is installed, of a suitable version and for
compilation/linking flags by e.g.
$ pkg-config --exists ‘libtiff-4 >= 4.1.0’ --print-errors # check the
status
$ pkg-config --modversion libtiff-4
4.3.0
$ pkg-config --cflags libtiff-4
-I/usr/local/include
$ pkg-config --libs libtiff-4
-L/usr/local/lib -ltiff
$ pkg-config --static --libs libtiff-4
-L/usr/local/lib -ltiff -lwebp -llzma -ljpeg -lz
Note that pkg-config --libs gives the information required to link against the
default version31 of that library (usually the dynamic one), and pkg-config --
static --libs may be needed if the static library is to be used.

Static libraries are commonly used on macOS (and Windows) to facilitate bundling
external software with binary distributions of packages. This means that portable
(source) packages need to allow for this. It is not safe to just use pkg-config --
static --libs, as that will often include further libraries that are not necessarily
installed on the user’s system (or maybe only the versioned library such
as [Link].2.1 is installed and not [Link] which would be needed
to use -ljbig sometimes included in pkg-config --static --libs libtiff-4).
Another issue is that pkg-config --exists may not be reliable. It checks not only
that the ‘module’ is available but all of the dependencies, including those in
principle needed for static linking. (XQuartz 2.8.x only distributed dynamic
libraries and not some of the .pc files needed for --exists.)
Sometimes the name by which the software is known to pkg-config is not what one
might expect (e.g. ‘libxml-2.0’ even for 2.9.x). To get a complete list use
pkg-config --list-all | sort
Some external software provides a -config command to do a similar job to pkg-
config, including
curl-config freetype-config gdal-config geos-config
gsl-config iodbc-config libpng-config nc-config
pcre-config pcre2-config xml2-config xslt-config
(curl-config is for libcurl not curl. nc-config is for netcdf.) Most have an option
to use static libraries.
N.B. These commands indicate what header paths and libraries are needed, but
they do not obviate the need to check that the recipes they give actually work.
(This is especially necessary for platforms which use static linking.)
If using Autoconf it is good practice to include all the Autoconf sources in the
package (and required for an Open Source package and tested by R CMD check --
32
as-cran). This will include the file [Link] in the top-level directory of
the package. If extensions written in m4 are needed, these should be included under
the directory tools and included from [Link] via e.g.,
m4_include([tools/ax_pthread.m4])
Alternatively, Autoconf can be asked to search all .m4 files in a directory by
including something like33
AC_CONFIG_MACRO_DIR([tools/m4])
One source of such extensions is the ‘Autoconf Archive’
([Link] It is not safe to assume this is
installed on users’ machines, so the extension should be shipped with the package
(taking care to comply with its licence).
 Using Makevars
 Configure example
 Using F9x code
 Using C++ code
 C standards
 Using cmake

Next: Configure example, Previous: Configure and cleanup, Up: Configure and
cleanup [Contents][Index]
1.2.1 Using Makevars

Sometimes writing your own configure script can be avoided by supplying a

file Makevars: also one of the most common uses of a configure script is to
make Makevars from [Link].
A Makevars file is a makefile and is used as one of several makefiles by R CMD
SHLIB (which is called by R CMD INSTALL to compile code in the src directory). It
should be written if at all possible in a portable style, in particular (except
for [Link] and [Link]) without the use of GNU extensions.
The most common use of a Makevars file is to set additional preprocessor
options (for example include paths and definitions) for C/C++
files via PKG_CPPFLAGS, and additional compiler flags by
setting PKG_CFLAGS, PKG_CXXFLAGS or PKG_FFLAGS, for C, C++ or Fortran respectively
(see Creating shared objects).
N.B.: Include paths are preprocessor options, not compiler options, and must be
set in PKG_CPPFLAGS as otherwise platform-specific paths (e.g.
‘-I/usr/local/include’) will take precedence. PKG_CPPFLAGS should contain
‘-I’, ‘-D’, ‘-U’ and (where supported) ‘-include’ and ‘-pthread’ options:
everything else should be a compiler flag. The order of flags matters, and using ‘-
I’ in PKG_CFLAGS or PKG_CXXFLAGS has led to hard-to-debug platform-specific errors.
Makevars can also be used to set flags for the linker, for example ‘-L’ and ‘-l’
options, via PKG_LIBS.
When writing a Makevars file for a package you intend to distribute, take care to
ensure that it is not specific to your compiler: flags such as -O2 -Wall -
pedantic (and all other -W flags: for the Oracle compilers these were used to
pass arguments to compiler phases) are all specific to GCC (and compilers such
as clang which aim to be options-compatible with it).
Also, do not set variables such as CPPFLAGS, CFLAGS etc.: these should be settable by
users (sites) through appropriate personal (site-wide) Makevars files.
See Customizing package compilation in R Installation and Administration,
There are some macros34 which are set whilst configuring the building of R itself
and are stored in R_HOME/etcR_ARCH/Makeconf. That makefile is included
as a Makefile after Makevars[.win], and the macros it defines can be used
in macro assignments and make command lines in the latter. These include
FLIBS
A macro containing the set of libraries need to link Fortran code. This may
need to be included in PKG_LIBS: it will normally be included automatically
if the package contains Fortran source files in the src directory.
BLAS_LIBS
A macro containing the BLAS libraries used when building R. This may
need to be included in PKG_LIBS. Beware that if it is empty then the R
executable will contain all the double-precision and double-complex BLAS
routines, but no single-precision nor complex routines. If BLAS_LIBS is
included, then FLIBS also needs to be35 included following it, as most BLAS
libraries are written at least partially in Fortran.
LAPACK_LIBS
A macro containing the LAPACK libraries (and paths where appropriate)
used when building R. This may need to be included in PKG_LIBS. It may
point to a dynamic library libRlapack which contains the main double-
precision LAPACK routines as well as those double-complex LAPACK
routines needed to build R, or it may point to an external LAPACK library,
or may be empty if an external BLAS library also contains LAPACK.
 [libRlapack includes all the double-precision LAPACK routines which were
current in 2003: a list of which routines are included is in
file src/modules/lapack/README. Note that an external
LAPACK/BLAS library need not do so, as some were ‘deprecated’ (and not
compiled by default) in LAPACK 3.6.0 in late 2015.]
For portability, the macros BLAS_LIBS and FLIBS should always be
included after LAPACK_LIBS (and in that order).
SAFE_FFLAGS
A macro containing flags which are needed to circumvent over-optimization
of FORTRAN code: it is might be ‘-g -O2 -ffloat-store’ or ‘-g -
O2 -msse2 -mfpmath=sse’ on ‘ix86’ platforms using gfortran.
Note that this is not an additional flag to be used as part of PKG_FFLAGS, but a
replacement for FFLAGS. See the example later in this section.
Setting certain macros in Makevars will prevent R CMD SHLIB setting them: in
particular if Makevars sets ‘OBJECTS’ it will not be set on the make command
line. This can be useful in conjunction with implicit rules to allow other types of
source code to be compiled and included in the shared object. It can also be used to
control the set of files which are compiled, either by excluding some files
in src or including some files in subdirectories. For example
OBJECTS = 4dfp/endianio.o 4dfp/Getifh.o R4dfp-object.o
Note that Makevars should not normally contain targets, as it is included before
the default makefile and make will call the first target, intended to be all in the
default makefile. If you really need to circumvent that, use a suitable (phony)
target all before any actual targets in Makevars.[win]: for example
package fastICA used to have
PKG_LIBS = @BLAS_LIBS@

SLAMC_FFLAGS=$(R_XTRA_FFLAGS) $(FPICFLAGS) $(SHLIB_FFLAGS) $(SAFE_FFLAGS)

all: $(SHLIB)

slamc.o: slamc.f
$(FC) $(SLAMC_FFLAGS) -c -o slamc.o slamc.f
needed to ensure that the LAPACK routines find some constants without infinite
looping. The Windows equivalent was
all: $(SHLIB)

slamc.o: slamc.f
$(FC) $(SAFE_FFLAGS) -c -o slamc.o slamc.f
(since the other macros are all empty on that platform, and R’s internal BLAS was
not used). Note that the first target in Makevars will be called, but for back-
compatibility it is best named all.
If you want to create and then link to a library, say using code in a subdirectory,
use something like
.PHONY: all mylibs

all: $(SHLIB)
$(SHLIB): mylibs

mylibs:
(cd subdir; $(MAKE))
Be careful to create all the necessary dependencies, as there is no guarantee that the
dependencies of all will be run in a particular order (and some of the CRAN build
machines use multiple CPUs and parallel makes). In particular,
all: mylibs
does not suffice. GNU make does allow the construct
.NOTPARALLEL: all
all: mylibs $(SHLIB)
but that is not portable. dmake and pmake allow the similar .NO_PARALLEL, also not
portable: some variants of pmake accept .NOTPARALLEL as an alias for .NO_PARALLEL.
Note that on Windows it is required that Makevars[.win, .ucrt] does
create a DLL: this is needed as it is the only reliable way to ensure that building a
DLL succeeded. If you want to use the src directory for some purpose other than
building a DLL, use a [Link] or [Link] file.
It is sometimes useful to have a target ‘clean’
in Makevars, [Link] or [Link]: this will be used by R
CMD build to clean up (a copy of) the package sources. When it is run by build it
will have fewer macros set, in particular not $(SHLIB), nor $(OBJECTS) unless set in
the file itself. It would also be possible to add tasks to the target ‘shlib-clean’
which is run by R CMD INSTALL and R CMD SHLIB with options --clean and --
preclean.
An unfortunately common error is to have
all: $(SHLIB) clean
which asks make to clean in parallel with compiling the code. Not only does this
lead to hard-to-debug installation errors, it wipes out all the evidence of any error
(from a parallel make or not). It is much better to leave cleaning to the end user
using the facilities in the previous paragraph.
If you want to run R code in Makevars, e.g. to find configuration information,
please do ensure that you use the correct copy of R or Rscript: there might not be
one in the path at all, or it might be the wrong version or architecture. The correct
way to do this is via
"$(R_HOME)/bin$(R_ARCH_BIN)/Rscript" filename
"$(R_HOME)/bin$(R_ARCH_BIN)/Rscript" -e ‘R expression’
where $(R_ARCH_BIN) is only needed currently on Windows.
Environment or make variables can be used to select different macros for 32- and
64-bit code, for example (GNU make syntax, allowed on Windows)
ifeq "$(WIN)" "64"
PKG_LIBS = value for 64-bit Windows
else
PKG_LIBS = value for 32-bit Windows
endif
On Windows there is normally a choice between linking to an import library or
directly to a DLL. Where possible, the latter is much more reliable: import libraries
are tied to a specific toolchain, and in particular on 64-bit Windows two different
conventions have been commonly used. So for example instead of
PKG_LIBS = -L$(XML_DIR)/lib -lxml2
one can use
PKG_LIBS = -L$(XML_DIR)/bin -lxml2
since on Windows -lxxx will look in turn for
[Link].a
[Link].a
libxxx.a
[Link]
[Link]
[Link]
where the first and second are conventionally import libraries, the third and fourth
often static libraries (with .lib intended for Visual C++), but might be import
libraries. See for
example [Link]
The fly in the ointment is that the DLL might not be named [Link], and in
fact on 32-bit Windows there is a [Link] whereas on one build for 64-bit
Windows the DLL is called [Link]. Using import libraries can cover
over these differences but can cause equal difficulties.
If static libraries are available they can save a lot of problems with run-time finding
of DLLs, especially when binary packages are to be distributed and even more
when these support both architectures. Where using DLLs is unavoidable we
normally arrange (via [Link] or [Link]) to ship them in
the same directory as the package DLL.
 OpenMP support
 Using pthreads
 Compiling in sub-directories

Next: Using pthreads, Previous: Using Makevars, Up: Using Makevars

[Contents][Index]
[Link] OpenMP support
There is some support for packages which wish to use OpenMP36. The make macros
SHLIB_OPENMP_CFLAGS
SHLIB_OPENMP_CXXFLAGS
SHLIB_OPENMP_FFLAGS
are available for use
in src/Makevars, src/[Link] or [Link]. Include the
appropriate macro in PKG_CFLAGS, PKG_CXXFLAGS and so on, and also
in PKG_LIBS (but see below for Fortran). C/C++ code that needs to be conditioned
on the use of OpenMP can be used inside #ifdef _OPENMP: note that some
toolchains used for R (including Apple’s for macOS37 and some others
using clang38) have no OpenMP support at all, not even omp.h.
For example, a package with C code written for OpenMP should have
in src/Makevars the lines
PKG_CFLAGS = $(SHLIB_OPENMP_CFLAGS)
PKG_LIBS = $(SHLIB_OPENMP_CFLAGS)
Note that the macro SHLIB_OPENMP_CXXFLAGS applies to the default C++ compiler
and not necessarily to the C++17/20/23 compiler: users of the latter should do their
own configure checks. If you do use your own checks, make sure that OpenMP
support is complete by compiling and linking an OpenMP-using program: on some
platforms the runtime library is optional and on others that library depends on other
optional libraries.
Some care is needed when compilers are from different families which may use
different OpenMP runtimes (e.g. clang vs GCC including gfortran, although it is
often possible to use the clang runtime with GCC but not vice versa:
however gfortran >= 9 may generate calls not in the clang runtime). For a package
with Fortran code using OpenMP the appropriate lines are
PKG_FFLAGS = $(SHLIB_OPENMP_FFLAGS)
PKG_LIBS = $(SHLIB_OPENMP_CFLAGS)
as the C compiler will be used to link the package code. There are platforms on
which this does not work for some OpenMP-using code and installation will fail.
Since R >= 3.6.2 the best alternative for a package with only Fortran sources using
OpenMP is to use
USE_FC_TO_LINK =
PKG_FFLAGS = $(SHLIB_OPENMP_FFLAGS)
PKG_LIBS = $(SHLIB_OPENMP_FFLAGS)
in src/Makevars, src/[Link] or [Link]. Note
however, that when this is used $(FLIBS) should not be included in PKG_LIBS since
it is for linking Fortran-compiled code by the C compiler.
Common platforms may inline all OpenMP calls and so tolerate the omission of
the OpenMP flag from PKG_LIBS, but this usually results in an installation failure
with a different compiler or compilation flags. So cross-check that e.g. -
fopenmp appears in the linking line in the installation logs.
It is not portable to use OpenMP with more than one of C, C++ and Fortran in a
single package since it is not uncommon that the compilers are of different
families.
For portability, any C/C++ code using the omp_* functions should include
the omp.h header: some compilers (but not all) include it when OpenMP mode is
switched on (e.g. via flag -fopenmp).
There is nothing39 to say what version of OpenMP is supported: version 4.0 (and
much of 4.5 or 5.0) is supported by recent versions of the Linux and Windows
platforms, but portable packages cannot assume that end users have recent
versions. Apple clang on macOS has no OpenMP
support. [Link] gives some
idea of what compilers support what versions.
Rarely, using OpenMP with clang on Linux generates calls in libatomic, resulting
in loading messages like
undefined symbol: __atomic_compare_exchange
undefined symbol: __atomic_load
The workaround is to link with -latomic (having checked it exists).
The performance of OpenMP varies substantially between platforms. The
Windows implementation has substantial overheads, so is only beneficial if quite
substantial tasks are run in parallel. Also, on Windows new threads are started with
the default40 FPU control word, so computations done on OpenMP threads will not
make use of extended-precision arithmetic which is the default for the main
process.
Do not include these macros unless your code does make use of OpenMP (possibly
for C++ via included external headers): this can result in the OpenMP runtime
being linked in, threads being started, ….
Calling any of the R API from threaded code is ‘for experts only’ and strongly
discouraged. Many functions in the R API modify internal R data structures and
might corrupt these data structures if called simultaneously from multiple threads.
Most R API functions can signal errors, which must only happen on the R main
thread. Also, external libraries (e.g. LAPACK) may not be thread-safe.
Packages are not standard-alone programs, and an R process could contain more
than one OpenMP-enabled package as well as other components (for example, an
optimized BLAS) making use of OpenMP. So careful consideration needs to be
given to resource usage. OpenMP works with parallel regions, and for most
implementations the default is to use as many threads as ‘CPUs’ for such regions.
Parallel regions can be nested, although it is common to use only a single thread
below the first level. The correctness of the detected number of ‘CPUs’ and the
assumption that the R process is entitled to use them all are both dubious
assumptions. One way to limit resources is to limit the overall number of threads
available to OpenMP in the R process: this can be done via environment
variable OMP_THREAD_LIMIT, where implemented.41 Alternatively, the number of
threads per region can be limited by the environment variable OMP_NUM_THREADS or
API call omp_set_num_threads, or, better, for the regions in your code as part of
their specification. E.g. R uses42
#pragma omp parallel for num_threads(nthreads) …
That way you only control your own code and not that of other OpenMP users.
Note that setting environment variables to control OpenMP is implementation-
dependent and may need to be done outside the R process or before any use of
OpenMP (which might be by another process or R itself). Also, implementation-
specific variables such as KMP_THREAD_LIMIT might take precedence.

Next: Compiling in sub-directories, Previous: OpenMP support,

Up: Using Makevars [Contents][Index]

[Link] Using pthreads

There is no direct support for the POSIX threads (more commonly known
as pthreads): by the time we considered adding it several packages were using it
unconditionally so it seems that nowadays it is universally available on POSIX
operating systems (hence not Windows).
For reasonably recent versions of gcc and clang the correct specification is
PKG_CPPFLAGS = -pthread
PKG_LIBS = -pthread
(and the plural version is also accepted on some systems/versions). For other
platforms the specification is
PKG_CPPFLAGS = -D_REENTRANT
PKG_LIBS = -lpthread
(and note that the library name is singular). This is what -pthread does on all
known current platforms (although earlier versions of OpenBSD used a different
library name).
For a tutorial see [Link]
POSIX threads are not normally used on Windows, which has its own native
concepts of threads. However, there are two projects implementing pthreads on top
of Windows, pthreads-w32 and winpthreads (part of the MinGW-w64 project).
Whether Windows toolchains implement pthreads is up to the toolchain provider.
A make variable SHLIB_PTHREAD_FLAGS is available for use
in src/[Link] or [Link]: this should be included in
both PKG_CPPFLAGS (or the Fortran compiler flags) and PKG_LIBS.
The presence of a working pthreads implementation cannot be unambiguously
determined without testing for yourself: however, that ‘_REENTRANT’ is
defined43 in C/C++ code is a good indication.
Note that not all pthreads implementations are equivalent as parts are optional
(see [Link]
for example, macOS lacks the ‘Barriers’ option.
See also the comments on thread-safety and performance under OpenMP: on all
known R platforms OpenMP is implemented via pthreads and the known
performance issues are in the latter.

Previous: Using pthreads, Up: Using Makevars [Contents][Index]

[Link] Compiling in sub-directories

Package authors fairly often want to organize code in sub-directories of src, for
example if they are including a separate piece of external software to which this is
an R interface.
One simple way is simply to set OBJECTS to be all the objects that need to be
compiled, including in sub-directories. For example, CRAN package RSiena has
SOURCES = $(wildcard data/*.cpp network/*.cpp utils/*.cpp model/*.cpp
model/*/*.cpp model/*/*/*.cpp)

OBJECTS = siena07utilities.o siena07internals.o siena07setup.o

siena07models.o $(SOURCES:.cpp=.o)
One problem with that approach is that unless GNU make extensions are used, the
source files need to be listed and kept up-to-date. As in the following
from CRAN package lossDev:
[Link] = samplers/ExpandableArray.o samplers/Knots.o \
samplers/RJumpSpline.o samplers/RJumpSplineFactory.o \
samplers/RealSlicerOV.o samplers/SliceFactoryOV.o samplers/MNorm.o
[Link] = distributions/DSpline.o \
distributions/DChisqrOV.o distributions/DTOV.o \
distributions/DNormOV.o distributions/DUnifOV.o
distributions/RScalarDist.o
[Link] = RJump.o

OBJECTS = $([Link]) $([Link]) $([Link])

Where the subdirectory is self-contained code with a suitable makefile, the best
approach is something like
PKG_LIBS = -LCsdp/lib -lsdp $(LAPACK_LIBS) $(BLAS_LIBS) $(FLIBS)

$(SHLIB): Csdp/lib/libsdp.a

Csdp/lib/libsdp.a:
@(cd Csdp/lib && $(MAKE) libsdp.a \
CC="$(CC)" CFLAGS="$(CFLAGS) $(CPICFLAGS)" AR="$(AR)" RANLIB="$
(RANLIB)")
Note the quotes: the macros can contain spaces, e.g. CC = "gcc -m64 -std=gnu99".
Several authors have forgotten about parallel makes: the static library in the
subdirectory must be made before the shared object ($(SHLIB)) and so the latter
must depend on the former. Others forget the need44 for position-independent code.
We really do not recommend using src/Makefile instead of src/Makevars,
and as the example above shows, it is not necessary.

Next: Using F9x code, Previous: Using Makevars, Up: Configure and cleanup
[Contents][Index]
1.2.2 Configure example

It may be helpful to give an extended example of using a configure script to

create a src/Makevars file: this is based on that in the RODBC package.
The [Link] file follows: configure is created from this by
running autoconf in the top-level package directory
(containing [Link]).
AC_INIT([RODBC], 1.1.8) dnl package name, version

dnl A user-specifiable option

odbc_mgr=""
AC_ARG_WITH([odbc-manager],
AC_HELP_STRING([--with-odbc-manager=MGR],
[specify the ODBC manager, e.g. odbc or iodbc]),
[odbc_mgr=$withval])

if test "$odbc_mgr" = "odbc" ; then

AC_PATH_PROGS(ODBC_CONFIG, odbc_config)
fi

dnl Select an optional include path, from a configure option

dnl or from an environment variable.
AC_ARG_WITH([odbc-include],
AC_HELP_STRING([--with-odbc-include=INCLUDE_PATH],
[the location of ODBC header files]),
[odbc_include_path=$withval])
RODBC_CPPFLAGS="-I."
if test [ -n "$odbc_include_path" ] ; then
RODBC_CPPFLAGS="-I. -I${odbc_include_path}"
else
if test [ -n "${ODBC_INCLUDE}" ] ; then
RODBC_CPPFLAGS="-I. -I${ODBC_INCLUDE}"
fi
fi

dnl ditto for a library path

AC_ARG_WITH([odbc-lib],
AC_HELP_STRING([--with-odbc-lib=LIB_PATH],
[the location of ODBC libraries]),
[odbc_lib_path=$withval])
if test [ -n "$odbc_lib_path" ] ; then
LIBS="-L$odbc_lib_path ${LIBS}"
else
if test [ -n "${ODBC_LIBS}" ] ; then
LIBS="-L${ODBC_LIBS} ${LIBS}"
else
if test -n "${ODBC_CONFIG}"; then
odbc_lib_path=`odbc_config --libs | sed s/-lodbc//`
LIBS="${odbc_lib_path} ${LIBS}"
fi
fi
fi

dnl Now find the compiler and compiler flags to use

: ${R_HOME=`R RHOME`}
if test -z "${R_HOME}"; then
echo "could not determine R_HOME"
exit 1
fi
CC=`"${R_HOME}/bin/R" CMD config CC`
CFLAGS=`"${R_HOME}/bin/R" CMD config CFLAGS`
CPPFLAGS=`"${R_HOME}/bin/R" CMD config CPPFLAGS`

if test -n "${ODBC_CONFIG}"; then

RODBC_CPPFLAGS=`odbc_config --cflags`
fi
CPPFLAGS="${CPPFLAGS} ${RODBC_CPPFLAGS}"

dnl Check the headers can be found

AC_CHECK_HEADERS(sql.h sqlext.h)
if test "${ac_cv_header_sql_h}" = no ||
test "${ac_cv_header_sqlext_h}" = no; then
AC_MSG_ERROR("ODBC headers sql.h and sqlext.h not found")
fi

dnl search for a library containing an ODBC function

if test [ -n "${odbc_mgr}" ] ; then
AC_SEARCH_LIBS(SQLTables, ${odbc_mgr}, ,
AC_MSG_ERROR("ODBC driver manager ${odbc_mgr} not found"))
else
AC_SEARCH_LIBS(SQLTables, odbc odbc32 iodbc, ,
AC_MSG_ERROR("no ODBC driver manager found"))
fi

dnl for 64-bit ODBC need SQL[U]LEN, and it is unclear where they are
defined.
AC_CHECK_TYPES([SQLLEN, SQLULEN], , , [# include <sql.h>])
dnl for unixODBC header
AC_CHECK_SIZEOF(long, 4)

dnl substitute RODBC_CPPFLAGS and LIBS

AC_SUBST(RODBC_CPPFLAGS)
AC_SUBST(LIBS)
AC_CONFIG_HEADERS([src/config.h])
dnl and do substitution in the src/[Link] and src/config.h
AC_CONFIG_FILES([src/Makevars])
AC_OUTPUT

where src/[Link] would be simply

PKG_CPPFLAGS = @RODBC_CPPFLAGS@
PKG_LIBS = @LIBS@
A user can then be advised to specify the location of the ODBC driver manager
files by options like (lines broken for easier reading)
R CMD INSTALL \
--configure-args='--with-odbc-include=/opt/local/include \
--with-odbc-lib=/opt/local/lib --with-odbc-manager=iodbc' \
RODBC
or by setting the environment variables ODBC_INCLUDE and ODBC_LIBS.

Next: Using C++ code, Previous: Configure example, Up: Configure and cleanup
[Contents][Index]
1.2.3 Using F9x code

R assumes that source files with extension .f are fixed-form Fortran 90 (which
includes Fortran 77), and passes them to the compiler specified by macro ‘FC’. On
known platforms the Fortran compiler will also accept free-form Fortran 90/95
code with extension .f90 or .f95, but those are not used by R itself so this is not
required.
The same compiler is used45 for both fixed-form and free-form Fortran code (with
different file extensions and possibly different flags). Macro PKG_FFLAGS can be
used for package-specific flags: for the un-encountered case that both are included
in a single package and that different flags are needed for the two forms,
macro PKG_FCFLAGS is also available for free-form Fortran.
The code used to build R allows a ‘Fortran 90’ compiler to be selected as ‘FC’, so
platforms might be encountered which only support Fortran 90. However, Fortran
95 is widely supported.
Some compilers specified by ‘FC’ will accept Fortran 2003, 2008 or 2018 code:
such code should still use file extension .f90 or .f95. Almost all current
platforms use gfortran where you may need to include -std=f2003, -
std=f2008 or (from version 8) -std=f2018 in PKG_FFLAGS or PKG_FCFLAGS: the
default is ‘GNU Fortran’, Fortran 95 with non-standard extensions. Intel Fortran
had full Fortran 2008 support from version 17.0, and some 2018 support in version
16.0 and more in version 19.0. It is good practice to describe the requirement
in DESCRIPTION’s ‘SystemRequirements’ field.
Modern versions of Fortran support modules, whereby compiling one source file
creates a module file which is then included in others. (Module files typically have
a .mod extension: they do depend on the compiler used and so should never be
included in a package.) This creates a dependence which make will not know about
and often causes installation with a parallel make to fail. Thus it is necessary to add
explicit dependencies to src/Makevars to tell make the constraints on the order
of compilation. For example, if file iface.f90 creates a module ‘iface’ used
by files cmi.f90 and dmi.f90 then src/Makevars needs to contain
something like
cmi.o dmi.o: iface.o
Note that it is not portable (although some platforms do accept it) to define a
module of the same name in multiple source files.

Next: C standards, Previous: Using F9x code, Up: Configure and cleanup
[Contents][Index]
1.2.4 Using C++ code

R can be built without a C++ compiler although one is available (but not
necessarily installed) on all known R platforms. As from R 4.0.0 a C++ compiler
will be selected only if it conforms to the 2011 standard (‘C++11’). A minor
update46 (‘C++14’) was published in December 2014 and was used by default as
from R 4.1.0 if supported. Further revisions ‘C++17’ (in December 2017) and ‘C+
+20’ (with many new features in December 2020) have been published since. The
next revision, ‘C++23’, is expected in 2023 and several compilers already have
extensive partial support for the current drafts.
The default standard for compiling R packages was changed to C++17 in R 4.3.0 if
supported (and for rather old compilers, C++14 or even C++11 would be used as
the default).
What standard a C++ compiler aims to support can be hard to determine: the
value47 of __cplusplus may help but some compilers use it to denote a standard
which is partially supported and some the latest standard which is (almost) fully
supported. On a Unix-alike configure will try to identify a compiler and flags for
each of the standards: this relies heavily on the reported values of __cplusplus.
The webpage [Link] gives some
information on which compilers are known to support recent C++ features.
C++ standards have deprecated and later removed features. Be aware that some
current compilers still accept removed features in C++17 mode, such
as std::unary_function (deprecated in C++11, removed in C++17).
Different versions of R have used different default C++ standards, so for maximal
portability a package should specify the standard it requires. In order to specify C+
+14 code in a package with a Makevars file
(or [Link] or [Link] on Windows) should include the line
CXX_STD = CXX14
Compilation and linking will then be done with the C++14 compiler (if any).
Analogously for other standards (details below). On the other hand, specifying C+
+1148 when the code is valid under C++14 or C++17 reduces future portability.
Packages without a src/Makevars or src/Makefile file may specify a C++
standard for code in the src directory by including something like ‘C++14’ in the
‘SystemRequirements’ field of the DESCRIPTION file, e.g.
SystemRequirements: C++14
If a package does have a src/Makevars[.win] file then also setting the make
variable ‘CXX_STD’ there is recommended, as it allows R CMD SHLIB to work
correctly in the package’s src directory.
A requirement of C++17 or later should always be declared in the
‘SystemRequirements’ field (as well as
in src/Makevars or src/Makefile) so this is shown on the package’s
summary pages on CRAN or similar. This is also good practice for a requirement
of C++14. Note that support of C++14 or C++17 is only available from R 3.4.0, so
if the package has an R version requirement it needs to take that into account.
Essentially complete C++14 support is available from GCC 5, LLVM clang 3.4
and currently-used versions of Apple clang (10.0.0 for High Sierra).
Code needing C++14 features can check for their presence via ‘SD-6 feature
tests’49. Such a check could be
#include <memory> // header where this is defined
#if defined(__cpp_lib_make_unique) && (__cpp_lib_make_unique >= 201304)
using std::make_unique;
#else
// your emulation
#endif
C++17 (as from R 3.4.0), C++20 (as from R 4.0.0) and C++23 (as from R 4.3.0)
can be specified in an analogous way (replacing 14 by 17, 20 or 23) but
compiler/OS support is platform-dependent. Some C++17 and C++20 support is
available with the default builds of R on macOS and Windows as from R 4.0.0.
Much of g++’s support for C++17 needs version 7 or later: that is more recent than
some still-current Linux distributions but often packages for later compilers are
available: for RHEL/Centos 7 look for ‘devtoolset’.
Note that C++17 or later ‘support’ does not mean complete support: use feature
tests as well as resources such
as [Link] [Link]
projects/[Link] and [Link] to see if the
features you want to use are widely implemented.
Attempts to specify an unknown C++ standard are silently ignored: recent versions
of R throw an error for C++98 and for known standards for which no
compiler+flags has been detected.
If a package using C++ has a configure script it is essential that the script selects
the correct C++ compiler and standard, via something like
CXX17=`"${R_HOME}/bin/R" CMD config CXX17`
if test -z "$CXX17"; then
 AC_MSG_ERROR([No C++17 compiler is available])
fi
CXX17STD=`"${R_HOME}/bin/R" CMD config CXX17STD`
CXX="${CXX17} ${CXX17STD}"
CXXFLAGS=`"${R_HOME}/bin/R" CMD config CXX17FLAGS`
## for an [Link] file
AC_LANG(C++)
if C++17 was specified, but using
CXX=`"${R_HOME}/bin/R" CMD config CXX`
CXXFLAGS=`"${R_HOME}/bin/R" CMD config CXXFLAGS`
## for an [Link] file
AC_LANG(C++)
if no standard was specified.
If you want to compile C++ code in a subdirectory, make sure you pass down the
macros to specify the appropriate compiler, e.g. in src/Makevars
sublibs:
@(cd libs && $(MAKE) \
CXX="$(CXX17) $(CXX17STD)" CXXFLAGS="$(CXX17FLAGS) $
(CXX17PICFLAGS)")
The discussion above is about the standard R ways of compiling C++: it will not
apply to packages using src/Makefile or building in a subdirectory that do not
set the C++ standard. And compilers’ default C++ standards varies widely and gets
changed frequently by vendors – for example Apple clang 14 defaults to C++98,
LLVM clang 14–15 to C++14, LLVM clang 16 to C++17 and g++ 11–13 to C+
+17.
For a package with a src/Makefile (or a Windows analogue), a non-default
C++ compiler can be selected by including something like
CXX14 = `"${R_HOME}/bin/R" CMD config CXX14`
CXX14STD = `"${R_HOME}/bin/R" CMD config CXX14STD`
CXX = ${CXX14} ${CXX14STD}
CXXFLAGS = `"${R_HOME}/bin/R" CMD config CXX14FLAGS`
CXXPICFLAGS = `"${R_HOME}/bin/R" CMD config CXX14PICFLAGS`
SHLIB_LD = "${R_HOME}/bin/R" CMD config SHLIB_CXX14LD`
SHLIB_LDFLAGS = "${R_HOME}/bin/R" CMD config SHLIB_CXX14LDFLAGS`
and ensuring these values are used in relevant compilations, after checking they are
non-empty. A common use of src/Makefile is to compile an executable, when
likely something like (for example for C++14)
CXX14 = `"${R_HOME}/bin/R" CMD config CXX14`
CXX14STD = `"${R_HOME}/bin/R" CMD config CXX14STD`
CXX = ${CXX14} ${CXX14STD}
CXXFLAGS = `"${R_HOME}/bin/R" CMD config CXX14FLAGS`
suffices. On Unix (and on Windows from R 4.3.0) this can be simplified to
CXX = ${CXX14} ${CXX14STD}
CXXFLAGS = ${CXX14FLAGS}
On a Unix-alike C++ compilation defaulted to C++11 from R 3.6.0, to C++14
from R 4.1.0 and to C++17 from R 4.3.0. However, only ‘if available’, so
platforms using very old OSes might have used the previous default. Even older
versions of R defaulted to the compiler’s default, almost certainly C++98 for
compilers of comparable vintage.
On Windows the default was changed from C++98 to C++11 in R 3.6.2, to C++14
in R 4.2.3 and to C++17 in R 4.3.0.
The C++11 standard could be specified as from R 3.1.0 and C++14 or C++17 as
from R 3.4.0, for C++20 from R 4.0.0 and for C++23 from R 4.3.0 (although they
may not be supported by the compilers in use). C++11 support became mandatory
in R 4.0.0.

Next: Using cmake, Previous: Using C++ code, Up: Configure and cleanup
[Contents][Index]
1.2.5 C standards

C has had standards C89/C90, C99, C11, C17 (also known as C18) and C23 is in
final draft and expected to be publishedd in early 2024. C11 was a minor change to
C99 which introduced some new features and made others optional, and C17 is a
‘bug-fix’ update to C11. On the other hand, C23 makes extensive changes,
including making bool, true and false reserved words, finally disallowing K&R-
style function declarations and clarifying the formerly deprecated meaning of
function declarations with an empty parameter list to mean zero parameters. (There
are many other additions: see for example [Link]
The configure script in recent versions of R aims to choose a C compiler which
supports C11: as the default in recent versions of gcc, LLVM clang and
Apple clang is C17, that is what is likely to be chosen. On the other hand, until R
4.3.0 the makefiles for the Windows build specified C99. They now use the
compiler default which for the recommended compiler is C17.
Packages may want to either avoid or embrace the changes in C23, and can do
so via specifying ‘USE_Cnn’ for 17, 23, 90 or 99 in the
‘SystemRequirements’ field of their DESCRIPTION file of a package
depending on ‘R (>= 4.3.0)’. Those using a configure script should set the
corresponding compiler and flags, for example using
CC=`"${R_HOME}/bin/R" CMD config CC23`
CFLAGS=`"${R_HOME}/bin/R" CMD config C23FLAGS`
CPPFLAGS=`"${R_HOME}/bin/R" CMD config CPPFLAGS`
LDFLAGS=`"${R_HOME}/bin/R" CMD config LDFLAGS`
The (claimed) C standard in use can be checked by the macro __STDC_VERSION__.
This is undefined in C89/C90 and should have
values 199901L, 201112L and 201710L for C99, C11 and C17. As C23 is not yet
published there is as yet no definitive value: compilers are currently using 202000L.
C23 has macros similar to C++ ‘feature tests’ for many of its changes, for
example __STDC_VERSION_LIMITS_H__.
However, note the ‘claimed’ as no compiler had 100% conformance, and it is
better to use configure to test for the feature you want to use than to condition on
the value of __STDC_VERSION__. In particular, C11 alignment functionality such
as _Alignas and aligned_alloc is not implemented on Windows.
End users can specify a standard by something like R CMD INSTALL --use-C17. This
overrides the ‘SystemRequirements’ field, but not for any configure file.

Previous: C standards, Up: Configure and cleanup [Contents][Index]

1.2.6 Using cmake

Packages often wish to include the sources of other software and compile that for
inclusion in their .so or .dll, which is normally done by including (or
unpacking) the sources in a subdirectory of src, as considered above.
Further issues arise when the external software uses another build system such
as cmake, principally to ensure that all the settings for compilers, include and load
paths etc are made. This section has already mentioned the need to set at least
some of
CC CFLAGS CXX CXXFLAGS CPPFLAGS LDFLAGS
CFLAGS and CXXFLAGS will need to include CPICFLAGS and CXXPICFLAGS respectively
unless (as below) cmake is asked to generate PIC code.
Setting these (and more) as environment variables controls the behaviour
of cmake ([Link]
[Link]#manual:cmake-env-variables(7)), but it may be desirable to
translate these into native settings such as
CMAKE_C_COMPILER
CMAKE_C_FLAGS
CMAKE_CXX_COMPILER
CMAKE_CXX_FLAGS
CMAKE_INCLUDE_PATH
CMAKE_LIBRARY_PATH
CMAKE_SHARED_LINKER_FLAGS_INIT
CMAKE_OSX_DEPLOYMENT_TARGET
and it is often necessary to ensure a static library of PIC code is built by
-DBUILD_SHARED_LIBS:bool=OFF
-DCMAKE_POSITION_INDEPENDENT_CODE:bool=ON
If R is to be detected or used, this must be the build being used for package
installation – "${R_HOME}"/bin/R.
To fix ideas, consider a package with sources for a
library myLib under src/libs. Two approaches have been used. It is often
most convenient to build the external software in a directory other than its sources
(particularly during development when the build directory can be removed between
builds rather than attempting to clean the sources) – this is illustrated in the first
approach.
1. Use the package’s configure script to create a static
library src/build/libmyLib.a. This can then be treated in the same
way as external software, for example having in src/Makevars
2. PKG_CPPFLAGS = -Ilibs/include
3. PKG_LIBS = build/libmyLib.a
(-Lbuild -lmyLib could also be used but this explicit specification avoids
any confusion with dynamic libraries of the same name.)
The configure script will need to contain something like (for C code)
: ${R_HOME=`R RHOME`}
if test -z "${R_HOME}"; then
echo "could not determine R_HOME"
exit 1
fi
CC=`"${R_HOME}/bin/R" CMD config CC`
CFLAGS=`"${R_HOME}/bin/R" CMD config CFLAGS`
CPPFLAGS=`"${R_HOME}/bin/R" CMD config CPPFLAGS`
LDFLAGS=`"${R_HOME}/bin/R" CMD config LDFLAGS`

cd src
mkdir build && cd build
cmake ../libs \
-DCMAKE_BUILD_TYPE=Release \
-DBUILD_SHARED_LIBS:bool=OFF \
-DCMAKE_POSITION_INDEPENDENT_CODE:bool=ON
${MAKE}
4. Use src/Makevars (or src/[Link] or [Link])
to build within the subdirectory. This could be something like (for C code)
5. PKG_CPPFLAGS = -Ilibs/include
6. PKG_LIBS = libs/libmyLib.a
7.
8. $(SHLIB): mylibs
9.
10. mylibs:
11. (cd libs; \
12. CC="$(CC)" CFLAGS="$(CFLAGS)" \
13. CPPFLAGS="$(CPPFLAGS)" LDFLAGS="$(LDFLAGS)" \
14. cmake . \
15. -DCMAKE_BUILD_TYPE=Release \
16. -DBUILD_SHARED_LIBS:bool=OFF \
17. -DCMAKE_POSITION_INDEPENDENT_CODE:bool=ON; \
18. $(MAKE))
19.
the compiler and other settings having been set as Make variables by an R
makefile included by INSTALL before src/Makevars.
A complication is that on macOS cmake (where installed) is commonly not on the
path but at /Applications/[Link]/Contents/bin/cmake. One
way to work around this is for the package’s configure script to include
if test -z "$CMAKE"; then CMAKE="`which cmake`"; fi
if test -z "$CMAKE"; then CMAKE=/Applications/[Link]/Contents/bin/cmake;
fi
if test -f "$CMAKE"; then echo "no ‘cmake’ command found"; exit 1; fi
and for the second approach to substitute CMAKE into src//Makevars.

Next: Writing package vignettes, Previous: Configure and cleanup, Up: Creating R
packages [Contents][Index]

1.3 Checking and building packages

Before using these tools, please check that your package can be installed. R CMD
check will inter alia do this, but you may get more detailed error messages doing
the install directly.
If your package specifies an encoding in its DESCRIPTION file, you should run
these tools in a locale which makes use of that encoding: they may not work at all
or may work incorrectly in other locales (although UTF-8 locales will most likely
work).
Note: R CMD check and R CMD build run R processes with --vanilla in which
none of the user’s startup files are read. If you need R_LIBS set (to find packages in
a non-standard library) you can set it in the environment: also you can use the
check and build environment files (as specified by the environment
variables R_CHECK_ENVIRON and R_BUILD_ENVIRON; if unset,
files50 ~/.R/[Link] and ~/.R/[Link] are used) to
set environment variables when using these utilities.
Note to Windows users: R CMD build may make use of the Windows toolset (see
the “R Installation and Administration” manual) if present and in your path, and it
is required for packages which need it to install (including those
with [Link], [Link], [Link] or [Link]
rt scripts or a src directory) and e.g. need vignettes built.
You may need to set the environment variable TMPDIR to point to a suitable writable
directory with a path not containing spaces – use forward slashes for the separators.
Also, the directory needs to be on a case-honouring file system (some network-
mounted file systems are not).
 Checking packages
 Building package tarballs
 Building binary packages

Next: Building package tarballs, Previous: Checking and building packages,

Up: Checking and building packages [Contents][Index]
1.3.1 Checking packages
Using R CMD check, the R package checker, one can test whether source R
packages work correctly. It can be run on one or more directories, or compressed
package tar archives with extension .[Link], .tgz, .tar.bz2 or .[Link].
It is strongly recommended that the final checks are run on a tar archive prepared
by R CMD build.
This runs a series of checks, including
1. The package is installed. This will warn about missing cross-references and
duplicate aliases in help files.
2. The file names are checked to be valid across file systems and supported
operating system platforms.
3. The files and directories are checked for sufficient permissions (Unix-alikes
only).
4. The files are checked for binary executables, using a suitable version
of file if available51. (There may be rare false positives.)
5. The DESCRIPTION file is checked for completeness, and some of its
entries for correctness. Unless installation tests are skipped, checking is
aborted if the package dependencies cannot be resolved at run time. (You
may need to set R_LIBS in the environment if dependent packages are in a
separate library tree.) One check is that the package name is not that of a
standard package, nor one of the defunct standard packages (‘ctest’,
‘eda’, ‘lqs’, ‘mle’, ‘modreg’, ‘mva’, ‘nls’, ‘stepfun’ and ‘ts’).
Another check is that all packages mentioned in library or requires or from
which the NAMESPACE file imports or are called via :: or ::: are listed (in
‘Depends’, ‘Imports’, ‘Suggests’): this is not an exhaustive check of
the actual imports.
6. Available index information (in particular, for demos and vignettes) is
checked for completeness.
7. The package subdirectories are checked for suitable file names and for not
being empty. The checks on file names are controlled by the option --
check-subdirs=value. This defaults to ‘default’, which runs the
checks only if checking a tarball: the default can be overridden by
specifying the value as ‘yes’ or ‘no’. Further, the check on
the src directory is only run if the package does not contain
a configure script (which corresponds to the value ‘yes-maybe’) and
there is no src/Makefile or src/[Link].
To allow a configure script to generate suitable files, files ending in
‘.in’ will be allowed in the R directory.
A warning is given for directory names that look like R package check
directories – many packages have been submitted to CRAN containing
these.
8. The R files are checked for syntax errors. Bytes which are non-ASCII are
reported as warnings, but these should be regarded as errors unless it is
known that the package will always be used in the same locale.
9. It is checked that the package can be loaded, first with the usual default
packages and then only with package base already loaded. It is checked that
the namespace can be loaded in an empty session with only
the base namespace loaded. (Namespaces and packages can be loaded very
early in the session, before the default packages are available, so packages
should work then.)
[Link] R files are checked for correct calls to [Link]. Package startup
functions are checked for correct argument lists and (incorrect) calls to
functions which modify the search path or inappropriately generate
messages. The R code is checked for possible problems using codetools. In
addition, it is checked whether S3 methods have all the arguments of the
corresponding generic, and whether the final argument of replacement
functions is called ‘value’. All foreign function calls
(.C, .Fortran, .Call and .External calls) are tested to see if they have
a PACKAGE argument, and if not, whether the appropriate DLL might be
deduced from the namespace of the package. Any other calls are reported.
(The check is generous, and users may want to supplement this by
examining the output of tools::checkFF("mypkg", verbose=TRUE),
especially if the intention were to always use a PACKAGE argument)
[Link] Rd files are checked for correct syntax and metadata, including the
presence of the mandatory fields (\name, \alias, \title and \description).
The Rd name and title are checked for being non-empty, and there is a
check for missing cross-references (links).
12.A check is made for missing documentation entries, such as undocumented
user-level objects in the package.
[Link] for functions, data sets, and S4 classes is checked for
consistency with the corresponding code.
[Link] is checked whether all function arguments given in \usage sections
of Rd files are documented in the corresponding \arguments section.
[Link] data directory is checked for non-ASCII characters and for the use of
reasonable levels of compression.
16.C, C++ and Fortran source and header files52 are tested for portable (LF-
only) line endings. If there is
a Makefile or [Link] or Makevars or [Link] file
under the src directory, it is checked for portable line endings and the
correct use of ‘$(BLAS_LIBS)’ and ‘$(LAPACK_LIBS)’
Compiled code is checked for symbols corresponding to functions which
might terminate R or write to stdout/stderr instead of the console.
Note that the latter might give false positives in that the symbols might be
pulled in with external libraries and could never be called. Windows53 users
 should note that the Fortran and C++ runtime libraries are examples of such
external libraries.
[Link] checks are made of the contents of the inst/doc directory. These
always include checking for files that look like leftovers, and if suitable
tools (such as qpdf) are available, checking that the PDF documentation is of
minimal size.
[Link] examples provided by the package’s documentation are run.
(see Writing R documentation files, for information on using \examples to
create executable example code.) If there is a
file tests/Examples/[Link], the output of running the
examples is compared to that file.
Of course, released packages should be able to run at least their own
examples. Each example is run in a ‘clean’ environment (so earlier examples
cannot be assumed to have been run), and with the
variables T and F redefined to generate an error unless they are set in the
example: See Logical vectors in An Introduction to R.
[Link] the package sources contain a tests directory then the tests specified in
that directory are run. (Typically they will consist of a set of .R source files
and target output files .[Link].) Please note that the comparison will
be done in the end user’s locale, so the target output files should be ASCII if
at all possible. (The command line option --test-dir=foo may be used to
specify tests in a non-standard location. For example, unusually slow tests
could be placed in inst/slowTests and then R CMD check --test-
dir=inst/slowTests would be used to run them. Other names that have been
suggested are, for example, inst/testWithOracle for tests that
require Oracle to be installed, inst/randomTests for tests which use
random values and may occasionally fail by chance, etc.)
[Link] R code in package vignettes (see Writing package vignettes) is
executed, and the vignettes re-made from their sources as a check of
completeness of the sources (unless there is a ‘BuildVignettes’ field in
the package’s DESCRIPTION file with a false value). If there is a target
output file .[Link] in the vignette source directory, the output from
running the code in that vignette is compared with the target output file and
any differences are reported (but not recorded in the log file). (If the vignette
sources are in the deprecated location inst/doc, do mark such target
output files to not be installed in .Rinstignore.)
If there is an error54 in executing the R code in vignette [Link], a log
file [Link] is created in the check directory. The vignettes are re-
made in a copy of the package sources in the vign_test subdirectory of
the check directory, so for further information on errors look in
directory pkgname/vign_test/vignettes. (It is only retained if
 there are errors or if environment variable _R_CHECK_CLEAN_VIGN_TEST_ is set
to a false value.)
[Link] PDF version of the package’s manual is created (to check that
the Rd files can be converted successfully). This needs LaTeX and suitable
fonts and LaTeX packages to be installed. See Making the manuals in R
Installation and Administration.
[Link] (including by R CMD check --as-cran) the HTML version of the
manual is created and checked for compliance with the HTML5 standard.
This requires a recent version55 of ‘HTML Tidy’, either on the path or at a
location specified by environment variable R_TIDYCMD. Up-to-date versions
can be installed from [Link]
All these tests are run with collation set to the C locale, and for the examples and
tests with environment variable LANGUAGE=en: this is to minimize differences
between platforms.
Use R CMD check --help to obtain more information about the usage of the R
package checker. A subset of the checking steps can be selected by adding
command-line options. It also allows customization by setting environment
variables _R_CHECK_*_ as described in Tools in R Internals: a set of these
customizations similar to those used by CRAN can be selected by the option --
as-cran (which works best if Internet access is available). Some Windows users
may need to set environment variable R_WIN_NO_JUNCTIONS to a non-empty value.
The test of cyclic declarations56in DESCRIPTION files needs repositories
(including CRAN) set: do this in ~/.Rprofile, by e.g.
options(repos = c(CRAN="[Link]
One check customization which can be revealing is
_R_CHECK_CODETOOLS_PROFILE_="suppressLocalUnused=FALSE"
which reports unused local assignments. Not only does this point out computations
which are unnecessary because their results are unused, it also can uncover errors.
(Two such are to intend to update an object by assigning a value but mistype its
name or assign in the wrong scope, for example using <- where <<- was intended.)
This can give false positives, most commonly because of non-standard evaluation
for formulae and because the intention is to return objects in the environment of a
function for later use.
Complete checking of a package which contains a file [Link] needs a
reasonably current version of pandoc installed:
see [Link]
You do need to ensure that the package is checked in a suitable locale if it contains
non-ASCII characters. Such packages are likely to fail some of the checks in
a C locale, and R CMD check will warn if it spots the problem. You should be able to
check any package in a UTF-8 locale (if one is available). Beware that although
a C locale is rarely used at a console, it may be the default if logging in remotely or
for batch jobs.
Often R CMD check will need to consult a CRAN repository to check details of
uninstalled packages. Normally this defaults to the CRAN main site, but a mirror
can be specified by setting environment variables R_CRAN_WEB and (rarely
needed) R_CRAN_SRC to the URL of a CRAN mirror.

Next: Building binary packages, Previous: Checking packages, Up: Checking and
building packages [Contents][Index]
1.3.2 Building package tarballs

Packages may be distributed in source form as “tarballs” (.[Link] files) or in

binary form. The source form can be installed on all platforms with suitable tools
and is the usual form for Unix-like systems; the binary form is platform-specific,
and is the more common distribution form for the Windows and macOS platforms.
Using R CMD build, the R package builder, one can build R package tarballs from
their sources (for example, for subsequent release). It is recommended that
packages are built for release by the current release version of R or ‘r-patched’,
to avoid inadvertently picking up new features of a development version of R.
Prior to actually building the package in the standard gzipped tar file format, a few
diagnostic checks and cleanups are performed. In particular, it is tested whether
object indices exist and can be assumed to be up-to-date, and C, C++ and Fortran
source files and relevant makefiles in a src directory are tested and converted to
LF line-endings if necessary.
Run-time checks whether the package works correctly should be performed using R
CMD check prior to invoking the final build procedure.

To exclude files from being put into the package, one can specify a list of exclude
patterns in file .Rbuildignore in the top-level source directory. These patterns
should be Perl-like regular expressions (see the help for regexp in R for the precise
details), one per line, to be matched case-insensitively against the file and directory
names relative to the top-level package source directory. In addition, directories
from source control systems57 or from eclipse58, directories with
names check, chm, or ending .Rcheck or Old or old and
files GNUMakefile59, Read-and-delete-me or with base names starting
with ‘.#’, or starting and ending with ‘#’, or ending in ‘~’, ‘.bak’ or ‘.swp’, are
excluded by default60. In addition, same-package tarballs (from previous builds)
and their binary forms will be excluded from the top-level directory, as well as
those files in the R, demo and man directories which are flagged by R CMD
check as having invalid names.
Use R CMD build --help to obtain more information about the usage of the R
package builder.
Unless R CMD build is invoked with the --no-build-vignettes option (or
the package’s DESCRIPTION contains ‘BuildVignettes: no’ or similar), it
will attempt to (re)build the vignettes (see Writing package vignettes) in the
package. To do so it installs the current package into a temporary library tree, but
any dependent packages need to be installed in an available library tree (see the
Note: at the top of this section).
Similarly, if the .Rd documentation files contain any \Sexpr macros (see Dynamic
pages), the package will be temporarily installed to execute them. Post-execution
binary copies of those pages containing build-time macros will be saved
in build/[Link]. If there are any install-time or render-time macros,
a .pdf version of the package manual will be built and installed in
the build subdirectory. (This allows CRAN or other repositories to display the
manual even if they are unable to install the package.) This can be suppressed by
the option --no-manual or if package’s DESCRIPTION contains
‘BuildManual: no’ or similar.
One of the checks that R CMD build runs is for empty source directories. These are
in most (but not all) cases unintentional, if they are intentional use the option --
keep-empty-dirs (or set the environment
variable _R_BUILD_KEEP_EMPTY_DIRS_ to ‘TRUE’, or have a ‘BuildKeepEmpty’
field with a true value in the DESCRIPTION file).
The --resave-data option allows saved images (.rda and .RData files) in
the data directory to be optimized for size. It will also compress tabular files and
convert .R files to saved images. It can take values no, gzip (the default if this
option is not supplied, which can be changed by setting the environment
variable _R_BUILD_RESAVE_DATA_) and best (equivalent to giving it without a value),
which chooses the most effective compression. Using best adds a dependence on R
(>= 2.10) to the DESCRIPTION file if bzip2 or xz compression is selected for any
of the files. If this is thought undesirable, --resave-data=gzip (which is the
default if that option is not supplied) will do what compression it can with gzip. A
package can control how its data is resaved by supplying a ‘BuildResaveData’
field (with one of the values given earlier in this paragraph) in
its DESCRIPTION file.
The --compact-vignettes option will run tools::compactPDF over the PDF
files in inst/doc (and its subdirectories) to losslessly compress them. This is not
enabled by default (it can be selected by environment
variable _R_BUILD_COMPACT_VIGNETTES_) and
needs qpdf ([Link] to be available.
It can be useful to run R CMD check --check-subdirs=yes on the built tarball as a
final check on the contents.
Where a non-POSIX file system is in use which does not utilize execute
permissions, some care is needed with permissions. This applies on Windows and
to e.g. FAT-formatted drives and SMB-mounted file systems on other OSes. The
‘mode’ of the file recorded in the tarball will be whatever [Link]() returns. On
Windows this will record only directories as having execute permission and on
other OSes it is likely that all files have reported ‘mode’ 0777. A particular issue is
packages being built on Windows which are intended to contain executable scripts
such as configure and cleanup: R CMD build ensures those two are recorded
with execute permission.
Directory build of the package sources is reserved for use by R CMD build: it
contains information which may not easily be created when the package is
installed, including index information on the vignettes and, rarely, information on
the help pages and perhaps a copy of the PDF reference manual (see above).

Previous: Building package tarballs, Up: Checking and building packages

[Contents][Index]
1.3.3 Building binary packages

Binary packages are compressed copies of installed versions of packages. They

contain compiled shared libraries rather than C, C++ or Fortran source code, and
the R functions are included in their installed form. The format and filename are
platform-specific; for example, a binary package for Windows is usually supplied
as a .zip file, and for the macOS platform the default binary package file
extension is .tgz.
The recommended method of building binary packages is to use
R CMD INSTALL --build pkg where pkg is either the name of a source tarball (in
the usual .[Link] format) or the location of the directory of the package source
to be built. This operates by first installing the package and then packing the
installed binaries into the appropriate binary package file for the particular
platform.
By default, R CMD INSTALL --build will attempt to install the package into the
default library tree for the local installation of R. This has two implications:
 If the installation is successful, it will overwrite any existing installation of
the same package.
 The default library tree must have write permission; if not, the package will
not install and the binary will not be created.
To prevent changes to the present working installation or to provide an install
location with write access, create a suitably located directory with write access and
use the -l option to build the package in the chosen location. The usage is then
R CMD INSTALL -l location --build pkg

where location is the chosen directory with write access. The package will be
installed as a subdirectory of location, and the package binary will be created
in the current directory.
Other options for R CMD INSTALL can be found using R CMD INSTALL --help, and
platform-specific details for special cases are discussed in the platform-specific
FAQs.
Finally, at least one web-based service is available for building binary packages
from (checked) source code: WinBuilder (see [Link] is
able to build Windows binaries. Note that this is intended for developers on other
platforms who do not have access to Windows but wish to provide binaries for the
Windows platform.

Next: Package namespaces, Previous: Checking and building packages,

Up: Creating R packages [Contents][Index]

1.4 Writing package vignettes

In addition to the help files in Rd format, R packages allow the inclusion of
documents in arbitrary other formats. The standard location for these is
subdirectory inst/doc of a source package, the contents will be copied to
subdirectory doc when the package is installed. Pointers from package help
indices to the installed documents are automatically created. Documents
in inst/doc can be in arbitrary format, however we strongly recommend
providing them in PDF format, so users on almost all platforms can easily read
them. To ensure that they can be accessed from a browser (as an HTML index is
provided), the file names should start with an ASCII letter and be comprised
entirely of ASCII letters or digits or hyphen or underscore.
A special case is package vignettes. Vignettes are documents in PDF
or HTML format obtained from plain-text literate source files from which R knows
how to extract R code and create output (in PDF/HTML or intermediate LaTeX).
Vignette engines do this work, using “tangle” and “weave” functions respectively.
Sweave, provided by the R distribution, is the default engine. Other vignette
engines besides Sweave are supported; see Non-Sweave vignettes.
Package vignettes have their sources in subdirectory vignettes of the package
sources. Note that the location of the vignette sources only affects R CMD
build and R CMD check: the tarball built by R CMD build includes in inst/doc the
components intended to be installed.
Sweave vignette sources are normally given the file extension .Rnw or .Rtex,
but for historical reasons extensions61 .Snw and .Stex are also recognized.
Sweave allows the integration of LaTeX documents: see the Sweave help page in R
and the Sweave vignette in package utils for details on the source document format.
Package vignettes are tested by R CMD check by executing all R code chunks they
contain (except those marked for non-evaluation, e.g., with option eval=FALSE for
Sweave). The R working directory for all vignette tests in R CMD check is a copy of
the vignette source directory. Make sure all files needed to run the R code in the
vignette (data sets, …) are accessible by either placing them in
the inst/doc hierarchy of the source package or by using calls to [Link]().
All other files needed to re-make the vignettes (such as LaTeX style files, BibTeX
input files and files for any figures not created by running the code in the vignette)
must be in the vignette source directory. R CMD check will check that vignette
production has succeeded by comparing modification times of output files
in inst/doc with the source in vignettes.
R CMD build will automatically62 create the (PDF or HTML versions of the)
vignettes in inst/doc for distribution with the package sources. By including the
vignette outputs in the package sources it is not necessary that these can be re-built
at install time, i.e., the package author can use private R packages, screen
snapshots and LaTeX extensions which are only available on their machine.63
By default R CMD build will run Sweave on all Sweave vignette source files
in vignettes. If Makefile is found in the vignette source directory, then R
CMD build will try to run make after the Sweave runs, otherwise texi2pdf is run on
each .tex file produced.
The first target in the Makefile should take care of both creation of
PDF/HTML files and cleaning up afterwards (including after Sweave), i.e., delete
all files that shall not appear in the final package archive. Note that if the make step
runs R it needs to be careful to respect the environment values
of R_LIBS and R_HOME64. Finally, if there is a Makefile and it has a ‘clean:’
target, make clean is run.
All the usual caveats about including a Makefile apply. It must be portable
(no GNU extensions), use LF line endings and must work correctly with a
parallel make: too many authors have written things like
## BAD EXAMPLE
all: pdf clean

pdf: [Link] [Link]

%.pdf: %.tex
texi2dvi --pdf $*

clean:
rm *.tex ABC-details-*.pdf
which will start removing the source files whilst pdflatex is working.
Metadata lines can be placed in the source file, preferably in LaTeX comments in
the preamble. One such is a \VignetteIndexEntry of the form
%\VignetteIndexEntry{Using Animal}
Others you may see are \VignettePackage (currently ignored), \VignetteDepends (a
comma-separated list of package names) and \VignetteKeyword (which replaced \
VignetteKeywords). These are processed at package installation time to create the
saved data frame Meta/[Link]. The \VignetteEngine statement is
described in Non-Sweave vignettes. Vignette metadata can be extracted from a
source file using tools::vignetteInfo.
At install time an HTML index for all vignettes in the package is automatically
created from the \VignetteIndexEntry statements unless a
file [Link] exists in directory inst/doc. This index is linked from
the HTML help index for the package. If you do supply
a inst/doc/[Link] file it should contain relative links only to files
under the installed doc directory, or perhaps (not really an index) to HTML help
files or to the DESCRIPTION file, and be valid HTML as confirmed via the W3C
Markup Validation Service or [Link].
Sweave/Stangle allows the document to specify the split=TRUE option to create a
single R file for each code chunk: this will not work for vignettes where it is
assumed that each vignette source generates a single file with the vignette
extension replaced by .R.
Do watch that PDFs are not too large – one in a CRAN package was 72MB! This
is usually caused by the inclusion of overly detailed figures, which will not render
well in PDF viewers. Sometimes it is much better to generate fairly high resolution
bitmap (PNG, JPEG) figures and include those in the PDF document.
When R CMD build builds the vignettes, it copies these and the vignette sources
from directory vignettes to inst/doc. To install any other files from
the vignettes directory, include a
file vignettes/.install_extras which specifies these as Perl-like regular
expressions on one or more lines. (See the description of the .Rinstignore file
for full details.)
 Encodings and vignettes
 Non-Sweave vignettes

Next: Non-Sweave vignettes, Previous: Writing package vignettes, Up: Writing

package vignettes [Contents][Index]
1.4.1 Encodings and vignettes
Vignettes will in general include descriptive text, R input, R output and figures,
LaTeX include files and bibliographic references. As any of these may contain
non-ASCII characters, the handling of encodings can become very complicated.
The vignette source file should be written in ASCII or contain a declaration of the
encoding (see below). This applies even to comments within the source file, since
vignette engines process comments to look for options and metadata lines. When
an engine’s weave and tangle functions are called on the vignette source, it will be
converted to the encoding of the current R session.
Stangle()will produce an R code file in the current locale’s encoding: for a non-
ASCII vignette what that is is recorded in a comment at the top of the file.
Sweave() will produce a .tex file in the current encoding, or in UTF-8 if that is
declared. Non-ASCII encodings need to be declared to LaTeX via a line like
\usepackage[utf8]{inputenc}
(It is also possible to use the more recent ‘inputenx’ LaTeX package.) For files
where this line is not needed (e.g. chapters included within the body of a larger
document, or non-Sweave vignettes), the encoding may be declared using a
comment like
%\VignetteEncoding{UTF-8}
If the encoding is UTF-8, this can also be declared using the declaration
%\SweaveUTF8
If no declaration is given in the vignette, it will be assumed to be in the encoding
declared for the package. If there is no encoding declared in either place, then it is
an error to use non-ASCII characters in the vignette.
In any case, be aware that LaTeX may require the ‘usepackage’ declaration.
Sweave() will also parse and evaluate the R code in each chunk. The R output will
also be in the current locale (or UTF-8 if so declared), and should be covered by
the ‘inputenc’ declaration. One thing people often forget is that the R output
may not be ASCII even for ASCII R sources, for many possible reasons. One
common one is the use of ‘fancy’ quotes: see the R help on sQuote: note carefully
that it is not portable to declare UTF-8 or CP1252 to cover such quotes, as their
encoding will depend on the locale used to run Sweave(): this can be circumvented
by setting options(useFancyQuotes="UTF-8") in the vignette.
The final issue is the encoding of figures – this applies only to PDF figures and not
PNG etc. The PDF figures will contain declarations for their encoding, but the
Sweave option [Link] may need to be set appropriately: see the help for
the pdf() graphics device.
As a real example of the complexities, consider the fortunes package version
‘1.4-0’. That package did not have a declared encoding, and its vignette was
in ASCII. However, the data it displays are read from a UTF-8 CSV file and will
be assumed to be in the current encoding, so [Link] will be in UTF-8 in
any locale. Had [Link] been told the data were UTF-
8, [Link] would have been in the locale’s encoding.

Previous: Encodings and vignettes, Up: Writing package vignettes [Contents]

[Index]
1.4.2 Non-Sweave vignettes

Vignettes in formats other than Sweave are supported via “vignette engines”. For
example knitr version 1.1 or later can create .tex files from a variation on
Sweave format, and .html files from a variation on “markdown” format. These
engines replace the Sweave() function with other functions to convert vignette
source files into LaTeX files for processing into .pdf, or directly
into .pdf or .html files. The Stangle() function is replaced with a function that
extracts the R source from a vignette.
R recognizes non-Sweave vignettes using filename extensions specified by the
engine. For example, the knitr package supports the extension .Rmd (standing for
“R markdown”). The user indicates the vignette engine within the vignette source
using a \VignetteEngine line, for example
%\VignetteEngine{knitr::knitr}
This specifies the name of a package and an engine to use in place of Sweave in
processing the vignette. As Sweave is the only engine supplied with the R
distribution, the package providing any other engine must be specified in the
‘VignetteBuilder’ field of the package DESCRIPTION file, and also
specified in the ‘Suggests’, ‘Imports’ or ‘Depends’ field (since its
namespace must be available to build or check your package). If more than one
package is specified as a builder, they will be searched in the order given there.
The utils package is always implicitly appended to the list of builder packages, but
may be included earlier to change the search order.
Note that a package with non-Sweave vignettes should always have a
‘VignetteBuilder’ field in the DESCRIPTION file, since this is how R CMD
check recognizes that there are vignettes to be checked: packages listed there are
required when the package is checked.
The vignette engine can produce .tex, .pdf, or .html files as output. If it
produces .tex files, R will call texi2pdf to convert them to .pdf for display to
the user (unless there is a Makefile in the vignettes directory).
Package writers who would like to supply vignette engines need to register those
engines in the package .onLoad function. For example, that function could make
the call
tools::vignetteEngine("knitr", weave = vweave, tangle = vtangle,
 pattern = "[.]Rmd$", package = "knitr")
(The actual registration in knitr is more complicated, because it supports other
input formats.) See the ?tools::vignetteEngine help topic for details on engine
registration.

Next: Writing portable packages, Previous: Writing package vignettes,

Up: Creating R packages [Contents][Index]

1.5 Package namespaces

R has a namespace management system for code in packages. This system allows
the package writer to specify which variables in the package should be exported to
make them available to package users, and which variables should
be imported from other packages.
The namespace for a package is specified by the NAMESPACE file in the top level
package directory. This file contains namespace directives describing the imports
and exports of the namespace. Additional directives register any shared objects to
be loaded and any S3-style methods that are provided. Note that although the file
looks like R code (and often has R-style comments) it is not processed as R code.
Only very simple conditional processing of if statements is implemented.
Packages are loaded and attached to the search path by calling library or require.
Only the exported variables are placed in the attached frame. Loading a package
that imports variables from other packages will cause these other packages to be
loaded as well (unless they have already been loaded), but they will not be placed
on the search path by these implicit loads. Thus code in the package can only
depend on objects in its own namespace and its imports (including
the base namespace) being visible65.
Namespaces are sealed once they are loaded. Sealing means that imports and
exports cannot be changed and that internal variable bindings cannot be changed.
Sealing allows a simpler implementation strategy for the namespace mechanism
and allows code analysis and compilation tools to accurately identify the definition
corresponding to a global variable reference in a function body.
The namespace controls the search strategy for variables used by functions in the
package. If not found locally, R searches the package namespace first, then the
imports, then the base namespace and then the normal search path (so the base
namespace precedes the normal search rather than being at the end of it).
 Specifying imports and exports
 Registering S3 methods
 Load hooks
 useDynLib
 An example
  Namespaces with S4 classes and methods

Next: Registering S3 methods, Previous: Package namespaces, Up: Package

namespaces [Contents][Index]
1.5.1 Specifying imports and exports

Exports are specified using the export directive in the NAMESPACE file. A
directive of the form
export(f, g)
specifies that the variables f and g are to be exported. (Note that variable names
may be quoted, and reserved words and non-standard names such
as [<-.fractions must be.)
For packages with many variables to export it may be more convenient to specify
the names to export with a regular expression using exportPattern. The directive
exportPattern("^[^\\.]")
exports all variables that do not start with a period. However, such broad patterns
are not recommended for production code: it is better to list all exports or use
narrowly-defined groups. (This pattern applies to S4 classes.) Beware of patterns
which include names starting with a period: some of these are internal-only
variables and should never be exported, e.g. ‘.__S3MethodsTable__.’ (and
loading excludes known cases).
Packages implicitly import the base namespace. Variables exported from other
packages with namespaces need to be imported explicitly using the
directives import and importFrom. The import directive imports all exported
variables from the specified package(s). Thus the directives
import(foo, bar)
specifies that all exported variables in the packages foo and bar are to be imported.
If only some of the exported variables from a package are needed, then they can be
imported using importFrom. The directive
importFrom(foo, f, g)
specifies that the exported variables f and g of the package foo are to be imported.
Using importFrom selectively rather than import is good practice and recommended
notably when importing from packages with more than a dozen exports and
especially from those written by others (so what they export can change in future).
To import every symbol from a package but for a few exceptions, pass
the except argument to import. The directive
import(foo, except=c(bar, baz))
imports every symbol from foo except bar and baz. The value of except should
evaluate to something coercible to a character vector, after substituting each
symbol for its corresponding string.
It is possible to export variables from a namespace which it has imported from
other namespaces: this has to be done explicitly and not via exportPattern.
If a package only needs a few objects from another package it can use a fully
qualified variable reference in the code instead of a formal import. A fully-
qualified reference to the function f in package foo is of the form foo::f. This is
slightly less efficient than a formal import and also loses the advantage of
recording all dependencies in the NAMESPACE file (but they still need to be
recorded in the DESCRIPTION file). Evaluating foo::f will cause package foo to
be loaded, but not attached, if it was not loaded already—this can be an advantage
in delaying the loading of a rarely used package. However, if foo is listed only in
‘Suggests’ or ‘Enhances’ this also delays the check that it is installed: it is
good practice to use such imports conditionally (e.g. via requireNamespace("foo",
quietly = TRUE)).

Using the foo::f form will be necessary when a package needs to use a function of
the same name from more than one namespace.
Using foo:::f instead of foo::f allows access to unexported objects. This is
generally not recommended, as the existence or semantics of unexported objects
may be changed by the package author in routine maintenance.

Next: Load hooks, Previous: Specifying imports and exports, Up: Package
namespaces [Contents][Index]
1.5.2 Registering S3 methods

The standard method for S3-style UseMethod dispatching might fail to locate
methods defined in a package that is imported but not attached to the search path.
To ensure that these methods are available the packages defining the methods
should ensure that the generics are imported and register the methods
using S3method directives. If a package defines a function [Link] intended to be
used as a print method for class foo, then the directive
S3method(print, foo)
ensures that the method is registered and available for UseMethod dispatch, and the
function [Link] does not need to be exported. Since the generic print is defined
in base it does not need to be imported explicitly.
(Note that function and class names may be quoted, and reserved words and non-
standard names such as [<- and function must be.)
It is possible to specify a third argument to S3method, the function to be used as
the method, for example
S3method(print, check_so_symbols, .[Link])
when print.check_so_symbols is not needed.
As from R 3.6.0 one can also use S3method() directives to
perform delayed registration. With
if(getRversion() >= "3.6.0") {
S3method(pkg::gen, cls)
}
function [Link] will get registered as an S3 method for class cls and
generic gen from package pkg only when the namespace of pkg is loaded. This can
be employed to deal with situations where the method is not “immediately”
needed, and having to pre-load the namespace of pkg (and all its strong
dependencies) in order to perform immediate registration is considered too
onerous.

Next: useDynLib, Previous: Registering S3 methods, Up: Package namespaces

[Contents][Index]
1.5.3 Load hooks

There are a number of hooks called as packages are loaded, attached, detached, and
unloaded. See help(".onLoad") for more details.
Since loading and attaching are distinct operations, separate hooks are provided for
each. These hook functions are called .onLoad and .onAttach. They both take
arguments66 libname and pkgname; they should be defined in the namespace but not
exported.
Packages can use a .onDetach or .[Link] function (provided the latter is exported
from the namespace) when detach is called on the package. It is called with a
single argument, the full path to the installed package. There is also a
hook .onUnload which is called when the namespace is unloaded (via a call
to unloadNamespace, perhaps called by detach(unload = TRUE)) with argument the
full path to the installed package’s directory.
Functions .onUnload and .onDetach should be defined in the namespace and not
exported, but .[Link] does need to be exported.
Packages are not likely to need .onAttach (except perhaps for a start-up banner);
code to set options and load shared objects should be placed in a .onLoad function,
or use made of the useDynLib directive described next.
User-level hooks are also available: see the help on function setHook.
These hooks are often used incorrectly. People forget to export .[Link].
Compiled code should be loaded in .onLoad (or via a useDynLb directive: see
below) and unloaded in .onUnload. Do remember that a package’s namespace can
be loaded without the namespace being attached (e.g. by pkgname::fun) and that a
package can be detached and re-attached whilst its namespace remains loaded.
It is good practice for these functions to be quiet. Any messages should
use packageStartupMessage so users (include check scripts) can suppress them if
desired.

Next: An example, Previous: Load hooks, Up: Package namespaces [Contents]

[Index]
1.5.4 useDynLib

A NAMESPACE file can contain one or more useDynLib directives which allows
shared objects that need to be loaded.67 The directive
useDynLib(foo)
registers the shared object foo68 for loading with [Link]. Loading of
registered object(s) occurs after the package code has been loaded and before
running the load hook function. Packages that would only need a load hook
function to load a shared object can use the useDynLib directive instead.
The useDynLib directive also accepts the names of the native routines that are to be
used in R via the .C, .Call, .Fortran and .External interface functions. These are
given as additional arguments to the directive, for example,
useDynLib(foo, myRoutine, myOtherRoutine)
By specifying these names in the useDynLib directive, the native symbols are
resolved when the package is loaded and R variables identifying these symbols are
added to the package’s namespace with these names. These can be used in
the .C, .Call, .Fortran and .External calls in place of the name of the routine and
the PACKAGE argument. For instance, we can call the routine myRoutine from R with
the code
.Call(myRoutine, x, y)
rather than
.Call("myRoutine", x, y, PACKAGE = "foo")
There are at least two benefits to this approach. Firstly, the symbol lookup is done
just once for each symbol rather than each time the routine is invoked. Secondly,
this removes any ambiguity in resolving symbols that might be present in more
than one DLL. However, this approach is nowadays deprecated in favour of
supplying registration information (see below).
In some circumstances, there will already be an R variable in the package with the
same name as a native symbol. For example, we may have an R function in the
package named myRoutine. In this case, it is necessary to map the native symbol to
a different R variable name. This can be done in the useDynLib directive by using
named arguments. For instance, to map the native symbol name myRoutine to the R
variable myRoutine_sym, we would use
useDynLib(foo, myRoutine_sym = myRoutine, myOtherRoutine)
We could then call that routine from R using the command
.Call(myRoutine_sym, x, y)
Symbols without explicit names are assigned to the R variable with that name.
In some cases, it may be preferable not to create R variables in the package’s
namespace that identify the native routines. It may be too costly to compute these
for many routines when the package is loaded if many of these routines are not
likely to be used. In this case, one can still perform the symbol resolution correctly
using the DLL, but do this each time the routine is called. Given a reference to the
DLL as an R variable, say dll, we can call the routine myRoutine using the
expression
.Call(dll$myRoutine, x, y)
The $ operator resolves the routine with the given name in the DLL using a call
to getNativeSymbol. This is the same computation as above where we resolve the
symbol when the package is loaded. The only difference is that this is done each
time in the case of dll$myRoutine.
In order to use this dynamic approach (e.g., dll$myRoutine), one needs the
reference to the DLL as an R variable in the package. The DLL can be assigned to
a variable by using the variable = dllName format used above for mapping
symbols to R variables. For example, if we wanted to assign the DLL reference for
the DLL foo in the example above to the variable myDLL, we would use the
following directive in the NAMESPACE file:
myDLL = useDynLib(foo, myRoutine_sym = myRoutine, myOtherRoutine)
Then, the R variable myDLL is in the package’s namespace and available for calls
such as myDLL$dynRoutine to access routines that are not explicitly resolved at load
time.
If the package has registration information (see Registering native routines), then
we can use that directly rather than specifying the list of symbols again in
the useDynLib directive in the NAMESPACE file. Each routine in the registration
information is specified by giving a name by which the routine is to be specified
along with the address of the routine and any information about the number and
type of the parameters. Using the .registration argument of useDynLib, we can
instruct the namespace mechanism to create R variables for these symbols. For
example, suppose we have the following registration information for a DLL
named myDLL:
static R_NativePrimitiveArgType foo_t[] = {
REALSXP, INTSXP, STRSXP, LGLSXP
};

static const R_CMethodDef cMethods[] = {

{"foo", (DL_FUNC) &foo, 4, foo_t},
{"bar_sym", (DL_FUNC) &bar, 0},
{NULL, NULL, 0, NULL}
};
static const R_CallMethodDef callMethods[] = {
{"R_call_sym", (DL_FUNC) &R_call, 4},
{"R_version_sym", (DL_FUNC) &R_version, 0},
{NULL, NULL, 0}
};
Then, the directive in the NAMESPACE file
useDynLib(myDLL, .registration = TRUE)
causes the DLL to be loaded and also for the R
variables foo, bar_sym, R_call_sym and R_version_sym to be defined in the
package’s namespace.
Note that the names for the R variables are taken from the entry in the registration
information and do not need to be the same as the name of the native routine. This
allows the creator of the registration information to map the native symbols to non-
conflicting variable names in R, e.g. R_version to R_version_sym for use in an R
function such as
R_version <- function()
{
.Call(R_version_sym)
}
Using argument .fixes allows an automatic prefix to be added to the registered
symbols, which can be useful when working with an existing package. For
example, package KernSmooth has
useDynLib(KernSmooth, .registration = TRUE, .fixes = "F_")
which makes the R variables corresponding to the Fortran symbols F_bkde and so
on, and so avoid clashes with R code in the namespace.
NB: Using these arguments for a package which does not register native symbols
merely slows down the package loading (although many CRAN packages have
done so). Once symbols are registered, check that the corresponding R variables
are not accidentally exported by a pattern in the NAMESPACE file.

Next: Namespaces with S4 classes and methods, Previous: useDynLib,

Up: Package namespaces [Contents][Index]
1.5.5 An example

As an example consider two packages named foo and bar. The R code for
package foo in file foo.R is
x <- 1
f <- function(y) c(x,y)
foo <- function(x) .Call("foo", x, PACKAGE="foo")
[Link] <- function(x, ...) cat("<a foo>\n")

Some C code defines a C function compiled into DLL foo (with an appropriate
extension). The NAMESPACE file for this package is
useDynLib(foo)
export(f, foo)
S3method(print, foo)

The second package bar has code file bar.R

c <- function(...) sum(...)
g <- function(y) f(c(y, 7))
h <- function(y) y+9

and NAMESPACE file

import(foo)
export(g, h)

Calling library(bar) loads bar and attaches its exports to the search path.
Package foo is also loaded but not attached to the search path. A call to g produces
> g(6)
[1] 1 13
This is consistent with the definitions of c in the two settings: in bar the
function c is defined to be equivalent to sum, but in foo the variable c refers to the
standard function c in base.

Previous: An example, Up: Package namespaces [Contents][Index]

1.5.6 Namespaces with S4 classes and methods

Some additional steps are needed for packages which make use of formal (S4-
style) classes and methods (unless these are purely used internally). The package
should have Depends: methods in
its DESCRIPTION and import(methods) or importFrom(methods, ...) plus any
classes and methods which are to be exported need to be declared in
the NAMESPACE file. For example, the stats4 package has
export(mle) # exporting methods implicitly exports the generic
importFrom("stats", approx, optim, pchisq, predict, qchisq, qnorm, spline)
## For these, we define methods or (AIC, BIC, nobs) an implicit generic:
importFrom("stats", AIC, BIC, coef, confint, logLik, nobs, profile,
update, vcov)
exportClasses(mle, [Link], [Link])
## All methods for imported generics:
exportMethods(coef, confint, logLik, plot, profile, summary,
show, update, vcov)
## implicit generics which do not have any methods here
export(AIC, BIC, nobs)
All S4 classes to be used outside the package need to be listed in
an exportClasses directive. Alternatively, they can be specified
using exportClassPattern69 in the same style as for exportPattern. To export
methods for generics from other packages an exportMethods directive can be used.
Note that exporting methods on a generic in the namespace will also export the
generic, and exporting a generic in the namespace will also export its methods. If
the generic function is not local to this package, either because it was imported as a
generic function or because the non-generic version has been made generic solely
to add S4 methods to it (as for functions such as coef in the example above), it can
be declared via either or both of export or exportMethods, but the latter is clearer
(and is used in the stats4 example above). In particular, for primitive functions
there is no generic function, so export would export the primitive, which makes no
sense. On the other hand, if the generic is local to this package, it is more natural to
export the function itself using export(), and this must be done if an implicit
generic is created without setting any methods for it (as is the case
for AIC in stats4).
A non-local generic function is only exported to ensure that calls to the function
will dispatch the methods from this package (and that is not done or required when
the methods are for primitive functions). For this reason, you do not need to
document such implicitly created generic functions, and undoc in
package tools will not report them.
If a package uses S4 classes and methods exported from another package, but does
not import the entire namespace of the other package70, it needs to import the
classes and methods explicitly, with directives
importClassesFrom(package, ...)
importMethodsFrom(package, ...)
listing the classes and functions with methods respectively. Suppose we had two
small packages A and B with B using A. Then they could have NAMESPACE files
export(f1, ng1)
exportMethods("[")
exportClasses(c1)

and
importFrom(A, ng1)
importClassesFrom(A, c1)
importMethodsFrom(A, f1)
export(f4, f5)
exportMethods(f6, "[")
exportClasses(c1, c2)

respectively.
Note that importMethodsFrom will also import any generics defined in the
namespace on those methods.
It is important if you export S4 methods that the corresponding generics are
available. You may for example need to import coef from stats to make visible a
function to be converted into its implicit generic. But it is better practice to make
use of the generics exported by stats4 as this enables multiple packages to
unambiguously set methods on those generics.

Next: Diagnostic messages, Previous: Package namespaces, Up: Creating R

packages [Contents][Index]

1.6 Writing portable packages

This section contains advice on writing packages to be used on multiple platforms
or for distribution (for example to be submitted to a package repository such
as CRAN).
Portable packages should have simple file names: use only
alphanumeric ASCII characters and period (.), and avoid those names not allowed
under Windows (see Package structure).
Many of the graphics devices are platform-specific: even X11() (aka x11()) which
although emulated on Windows may not be available on a Unix-alike (and is not
the preferred screen device on OS X). It is rarely necessary for package code or
examples to open a new device, but if essential,71 use [Link]().
Use R CMD build to make the release .[Link] file.
R CMD checkprovides a basic set of checks, but often further problems emerge
when people try to install and use packages submitted to CRAN – many of these
involve compiled code. Here are some further checks that you can do to make your
package more portable.
 If your package has a configure script, provide
a [Link] or [Link] script to be used on Windows
(an empty [Link] file if no actions are needed).
 If your package has a Makevars or Makefile file, make sure that you
use only portable make features. Such files should be LF-
terminated72 (including the final line of the file) and not make use of GNU
extensions. (The POSIX specification is available
at [Link]
anything not documented there should be regarded as an extension to be
avoided. Further advice can be found
at [Link]
Make. ) Commonly misused GNU extensions are conditional inclusions
(ifeq and the like), ${shell ...}, ${wildcard ...} and similar, and the use
of +=73 and :=. Also, the use of $< other than in implicit rules is a GNU
extension, as is the $^ macro. As is the use of .PHONY (some other makes
ignore it). Unfortunately makefiles which use GNU extensions often run on
other platforms but do not have the intended results.
 Note that the -C flag for make is not included in the POSIX specification and
is not implemented by some of the makes which have been used with R.
The use of ${shell ...} can be avoided by using backticks, e.g.
PKG_CPPFLAGS = `gsl-config --cflags`
which works in all versions of make known74 to be used with R.
If you really must require GNU make, declare it in the DESCRIPTION file
by
SystemRequirements: GNU make
and ensure that you use the value of environment variable MAKE (and not
just make) in your scripts. (On some platforms GNU make is available under
a name such as gmake, and there SystemRequirements is used to set MAKE.)
If you only need GNU make for parts of the package which are rarely
needed (for example to create bibliography files under vignettes), use a
file called GNUmakefile rather than Makefile as GNU make (only)
will use the former.
macOS has used GNU make for many years (it previously used BSD make),
but the version has been frozen at 3.81 (from 2006).
Since the only viable make for Windows is GNU make, it is permissible to
use GNU extensions in
files [Link], [Link], [Link] or Makefil
[Link].
 If you use src/Makevars to compile code in a subdirectory, ensure that
you have followed all the advice above. In particular
 Anticipate a parallel make. See Using Makevars.
 Pass macros down to the makefile in the subdirectory,
including all the needed compiler flags (including PIC and visibility
flags). If they are used in the subdirectory’s Makefile, this includes
macros ‘AR’ and ‘RANLIB’. See Compiling in sub-directories, which
has a C example. A C++ example:
 pkg/libpkg.a:
 (cd pkg && $(MAKE) -f make_pkg libpkg.a \
 CXX="$(CXX)" CXXFLAGS="$(CXXFLAGS) $
(CXXPICFLAGS) $(C_VISIBILITY)" \
 AR="$(AR)" RANLIB="$(RANLIB)")
 Ensure that cleanup will be performed by R CMD build, for example in
a cleanup script or a ‘clean’ target.
 If your package uses a src/Makefile file to compile code to be linked
into R, ensure that it uses exactly the same compiler and flag settings that R
uses when compiling such code: people often forget ‘PIC’ flags. If R CMD
config is used, this needs something like (for C++)
 RBIN = `"${R_HOME}/bin/R"`
  CXX = `"${RBIN}" CMD config CXX`
 CXXFLAGS = `"${RBIN}" CMD config CXXFLAGS` `"${RBIN}" CMD
config CXXPICFLAGS`
 Names of source files including = (such as src/complex_Sig=gen.c)
will confuse some make programs and should be avoided.
 Bash extensions also need to be avoided in shell scripts, including
expressions in Makefiles (which are passed to the shell for processing).
Some R platforms use strict75 Bourne shells: an earlier R toolset on
Windows76 and some Unix-alike OSes
use ash ([Link] a ‘lightweight shell
with few builtins) or derivatives such as dash. Beware of assuming that all
the POSIX command-line utilities are available, especially on Windows
where only a subset (which has changed by version of Rtools) is provided
for use with R. One particular issue is the use of echo, for which two
behaviours are allowed
([Link] and
both have occurred as defaults on R platforms: portable applications should
use neither -n (as the first argument) nor escape sequences. The
recommended replacement for echo -n is the command printf. Another
common issue is the construction
 export FOO=value
which is bash-specific (first set the variable then export it by name).
Using test -e (or [ -e ]) in shell scripts is not fully portable77: -f is
normally what is intended. Flags -a and -o are nowadays declared
obsolescent by POSIX and should not be used.
Use of ‘brace expansion’, e.g.,
rm -f src/*.{o,so,d}
is not portable.
The -o flag for set in shell scripts is optional in POSIX and not supported
on all the platforms R is used on.
The variable ‘OSTYPE’ is shell-specific and its values are rather
unpredictable and may include a version such as
‘darwin19.0’: `uname` is often what is intended (with common values
‘Darwin’, ‘Linux’ and ‘SunOS’).
On macOS which shell /bin/sh invokes is user- and platform-dependent:
it might be bash version 3.2, dash or zsh (for new accounts it is zsh, for
accounts ported from Mojave or earlier it is usually bash).
 Make use of the abilities of your compilers to check the standards-
conformance of your code. For example, gcc and gfortran78 can be used
with options -Wall -pedantic to alert you to potential problems. This
is particularly important for C++, where g++ -Wall -pedantic will alert you
 to the use of some of the GNU extensions which fail to compile on most
other C++ compilers. If R was not configured accordingly, one can achieve
this via personal Makevars files. See Customizing package
compilation in R Installation and Administration,
Portable C++ code needs to follow both the 2011 and 2014 standards or to
specify C+11/14/17/20 where available (which is not the case on all R
platforms). Currently C++17/20 support is patchy across R platforms.
If using Fortran with the GNU compiler, use the flags -std=f95 -Wall
-pedantic which reject most GNU extensions and features from later
standards. (Although R only requires Fortran 90, gfortran does not have a
way to specify that standard.)
R has tested that DOUBLE COMPLEX works and so is preferred to COMPLEX*16.
(One can also use something like COMPLEX(KIND=KIND(0.0D0)).)
The use of Fortran types such as REAL(KIND=8) is very far from portable.
According of the standards this merely enumerates different supported
types, so DOUBLE PRECISION might be REAL(KIND=3) (and is on an actual
compiler). Even if for a particular compiler the value indicates the size in
bytes, which values are supported is platform-specific — for
example gfortran supports values of 4 and 8 on all current platforms and 10
and 16 on a few (but not for example on ‘arm’ CPUs).
Not all common R platforms conform to the expected standards, e.g. C99 for
C code. One common area of problems is the *printf functions where
Windows did not support %lld, %Lf and similar formats (and has its own
formats such as %I64d for 64-bit integers). It is very rare to need to output
such types, and 64-bit integers can usually be converted to doubles for
output. However, the C11 standard (section 7.8.1)
includes PRIxNN macros79 in C header inttypes.h (for example PRId64)
so the portable approach is to test for these and if not available provide
emulations in the package.
As from macOS 11 (late 2020), its C compiler sets the flag -
Werror=implicit-function-declaration by default which
forces stricter conformance to C99. This can be used on other platforms
with gcc or clang. If your package has a (autoconf-generated) configure
script, try installing it whilst using this flag, and read through
the [Link] file — compilation warnings and errors can lead to
features which are present not being detected. (If possible do this on several
platforms.)
 R CMD check performs some checks for non-portable compiler/linker flags
in src/Makevars. However, it cannot check the meaning of such flags,
and some are commonly accepted but with compiler-specific meanings.
There are other non-portable flags which are not checked, nor
 are src/Makefile files and makefiles in sub-directories. As a comment
in the code says
It is hard to think of anything apart from -I* and -D* that is safe for
general use …
although -pthread is pretty close to portable. (Option -U is portable but
little use on the command line as it will only cancel built-in defines (not
portable) and those defined earlier on the command line (R does not use
any).)
People have used configure to customize src/Makevars, including for
specific compilers. This is unsafe for several reasons. First, unintended
compilers might meet the check—for example, several compilers other than
GCC identify themselves as ‘GCC’ whilst being only partially conformant.
Second, future versions of compilers may behave differently (including
updates to quite old series) so for example -Werror (and specializations)
can make a package non-installable under a future version. Third, using
flags to suppress diagnostic messages can hide important information for
debugging on a platform not tested by the package maintainer. (R CMD
check can optionally report on unsafe flags which were used.)

Avoid the use of -march and especially -march=native. This allows

the compiler to generate code that will only run on a particular class of
CPUs (that of the compiling machine for ‘native’). People assume this is
a ‘minimum’ CPU specification, but that is not how it is documented
for gcc (it is accepted by clang but apparently it is undocumented what
precisely it does, and it can be accepted and may be ignored for other
compilers). (For personal use -mtune is safer, but still not portable enough
to be used in a public package.) Not even gcc supports ‘native’ for all
CPUs, and it can do surprising things if it finds a CPU released later than its
version.
 Do be very careful with passing arguments between R, C and Fortran code.
In particular, long in C will be 32-bit on some R platforms (including 64-bit
Windows), but 64-bit on most modern Unix and Linux platforms. It is rather
unlikely that the use of long in C code has been thought through: if you need
a longer type than int you should use a configure test for a C99/C++11 type
such as int_fast64_t (and failing that, long long) and typedef your own
type, or use another suitable type (such as size_t, but beware that is
unsigned and ssize_t is not portable).
It is not safe to assume that long and pointer types are the same size, and
they are not on 64-bit Windows. If you need to convert pointers to and from
integers use the C99/C++11 integer types intptr_t and uintptr_t (in the
headers <stdint.h> and <cstdint>: they are not required to be implemented
by the standards but are used in C code by R itself).
 Note that integer in Fortran corresponds to int in C on all R platforms.
 Under no circumstances should your compiled code ever
call abort or exit80: these terminate the user’s R process, quite possibly
losing all unsaved work. One usage that could call abort is the assert macro
in C or C++ functions, which should never be active in production code. The
normal way to ensure that is to define the macro NDEBUG, and R CMD
INSTALL does so as part of the compilation flags. Beware of including
headers (including from other packages) which could undefine it, now or in
future versions. If you wish to use assert during development. you can
include -UNDEBUG in PKG_CPPFLAGS or #undef it in your headers or code files.
Note that your own src/Makefile or makefiles in sub-directories may
also need to define NDEBUG.
This applies not only to your own code but to any external software you
compile in or link to.
 Compiled code should not write to stdout or stderr and C++ and
Fortran I/O should not be used. As with the previous item such calls may
come from external software and may never be called, but package authors
are often mistaken about that.
 Compiled code should not call the system random number generators such
as rand, drand48 and random81, but rather use the interfaces to R’s RNGs
described in Random number generation. In particular, if more than one
package initializes a system RNG (e.g. via srand), they will interfere with
each other.
Nor should the C++11 random number library be used, nor any other third-
party random number generators such as those in GSL.
 Use of sprintf and vsprintf is regarded as a potential security risk and
warned about on some platforms.82 R CMD check reports if any calls are
found.
 Errors in memory allocation and reading/writing outside arrays are very
common causes of crashes (e.g., segfaults) on some machines. See Checking
memory access for tools which can be used to look for this.
 Many platforms will allow unsatisfied entry points in compiled code, but
will crash the application (here R) if they are ever used. Some (notably
Windows) will not. Looking at the output of
 nm -pg [Link]
and checking if any of the symbols marked U is unexpected is a good way to
avoid this.
 Linkers have a lot of freedom in how to resolve entry points in dynamically-
loaded code, so the results may differ by platform. One area that has caused
grief is packages including copies of standard system software such
as libz (especially those already linked into R). In the case in point, entry
 point gzgets was sometimes resolved against the old version compiled into
the package, sometimes against the copy compiled into R and sometimes
against the system dynamic library. The only safe solution is to rename the
entry points in the copy in the package. We have even seen problems with
entry point name myprintf, which is a system entry point83 on some Linux
systems.
A related issue is the naming of libraries built as part of the package
installation. macOS and Windows have case-insensitive file systems, so
using
-L. -lLZ4
in PKG_LIBS will match liblz4. And -L. only appends to the list of searched
locations, and liblz4 might be found in an earlier-searched location (and
has been). The only safe way is to give an explicit path, for example
./libLZ4.a
 Conflicts between symbols in DLLs are handled in very platform-specific
ways. Good ways to avoid trouble are to make as many symbols as possible
static (check with nm -pg), and to use names which are clearly tied to your
package (which also helps users if anything does go wrong). Note that
symbol names starting with R_ are regarded as part of R’s namespace and
should not be used in packages.
 It is good practice for DLLs to register their symbols (see Registering native
routines), restrict visibility (see Controlling visibility) and not allow symbol
search (see Registering native routines). It should be possible for a DLL to
have only one visible symbol, R_init_pkgname, on suitable platforms84,
which would completely avoid symbol conflicts.
 It is not portable to call compiled code in R or other
packages via .Internal, .C, .Fortran, .Call or .External, since such
interfaces are subject to change without notice and will probably result in
your code terminating the R process.
 Do not use (hard or symbolic) file links in your package sources. Where
possible R CMD build will replace them by copies.
 If you do not yourself have a Windows system, consider submitting your
source package to WinBuilder ([Link] before
distribution. If you need to check on an M1 Mac, there is a check service
at [Link]
 It is bad practice for package code to alter the search path
using library, require or attach and this often does not work as intended.
For alternatives, see Suggested packages and with().
 Examples can be run interactively via example as well as in batch mode
when checking. So they should behave appropriately in both scenarios,
conditioning by interactive() the parts which need an operator or observer.
For instance, progress bars85 are only appropriate in interactive use, as is
displaying help pages or calling View() (see below).
 Be careful with the order of entries in macros such as PKG_LIBS. Some
linkers will re-order the entries, and behaviour can differ between dynamic
and static libraries. Generally -L options should precede86 the libraries
(typically specified by -l options) to be found from those directories, and
libraries are searched once in the order they are specified. Not all linkers
allow a space after -L .
 Care is needed with the use of LinkingTo. This puts one or more directories
on the include search path ahead of system headers but (prior to R 3.4.0)
after those specified in the CPPFLAGS macro of the R build (which normally
includes -I/usr/local/include, but most platforms ignore that and include
it with the system headers).
Any confusion would be avoided by having LinkingTo headers in a directory
named after the package. In any case, name conflicts of headers and
directories under package include directories should be avoided, both
between packages and between a package and system and third-party
software.
 The ar utility is often used in makefiles to make static libraries. Its
modifier u is defined by POSIX but is disabled in GNU ar on some Linux
distributions which use ‘deterministic mode’. The safest way to make a
static library is to first remove any existing file of that name then use ar -
cr and then ranlib if needed (which is system-dependent: on most
systems87 ar always maintains a symbol table). The POSIX standard says
options should be preceded by a hyphen (as in -cr), although most OSes
accept them without. Note that on some systems ar -cr must have at least
one file specified.
The s modifier (to replace a separate call to ranlib) is required by X/OPEN
but not POSIX, so ar -crs is not portable.
 The strip utility is platform-specific (and CRAN prohibits removing debug
symbols). For example the options --strip-debug and --strip-
unneeded of the GNU version are not supported on macOS: the POSIX
standard for strip does not mention any options, and what calling it without
options does is platform-dependent. Stripping a .so file could even prevent
it being dynamically loaded into R on an untested platform.
ld -S invokes strip --strip-debug on GNU ld but is not portable: in
particular on Solaris it did something completely different and took an
argument.
 Some people have a need to set a locale. Locale names are not portable, and
e.g. ‘fr_FR.utf8’ is commonly used on Linux but not accepted on
macOS. ‘fr_FR.UTF-8’ is more portable, being accepted on recent Linux,
AIX, FreeBSD, macOS and Solaris (at least). However, some Linux
 distributions micro-package, so locales defined by glibc (including these
examples) may not be installed.
 Avoid spaces in file names, not least as they can cause difficulties for
external tools. An example was a package with a knitr vignette that used
spaces in plot names: this caused some older versions of pandoc to fail with
a baffling error message.
Non-ASCII filenames can also cause problems (particularly in non-UTF-8
locales).
 Take care in naming LaTeX macros (also known as ‘commands’) in vignette
sources: if these are also defined in a future version of one of the LaTeX
packages used there will be a fatal error. One instance in 2021 was package
‘hyperref’ newly defining ‘\C’, ‘\F’, ‘\G’, ‘\U’ and ‘\textapprox’.
If you are confident that your definitions will be the only ones relevant you
can use ‘\renewcommand’ but it is better to use names clearly associated
with your package.
 Make sure that any version requirement for Java code is both declared in the
‘SystemRequirements’ field88 and tested at runtime (not least as the
Java installation when the package is installed might not be the same as
when the package is run and will not be for binary packages).
When specifying a minimum Java version please use the official version
names, which are (confusingly)
1.1 1.2 1.3 1.4 5.0 6 7 8 9 10 11 12 13 14 15 16 17 18 19 20
(announced 21)
and as from 2018 a [Link] scheme such as ‘18.9’ is also in use.
Fortunately only the integer values are likely to be relevant. If at all
possible, use one of the LTS versions (8, 11, 17, 21 …) as the minimum
version. The preferred form of version specification is
SystemRequirements: Java (>= 11)
A suitable test for Java at least version 8 for packages using rJava would be
something like
.jinit()
jv <- .jcall("java/lang/System", "S", "getProperty",
"[Link]")
if(substr(jv, 1L, 2L) == "1.") {
jvn <- [Link](paste0(strsplit(jv, "[.]")[[1L]][1:2],
collapse = "."))
if(jvn < 1.8) stop("Java >= 8 is needed for this package but
not available")
}
Java 9 changed the format of this string (which used to be something like
‘1.8.0_292-b10’); Java 11 gave jv as ‘11+28’ whereas Java 11.0.11
gave ‘11.0.11+9’. ([Link] details the current
scheme. Note that it is necessary to allow for pre-releases like ‘11-
ea+22’.)
 Note too that the compiler used to produce a jar can impose a minimum
Java version, often resulting in an arcane message like
[Link]: ... Unsupported
[Link] version 52.0
(Where [Link] maps class-file version
numbers to Java versions.) Compile with something like javac -target
11 to ensure this is avoided. Note this also applies to packages distributing
(or even downloading) compiled Java code produced by others, so their
requirements need to be checked (they are often not documented accurately)
and accounted for. It should be possible to check the class-file
version via command-line utility javap, if necessary after extracting
the .class files from a .jar archive.
Some packages have stated a requirement on a particular JDK, but a
package should only be requiring a JRE unless providing its own Java
interface.
Java 8 is still in widespread use (and may remain so because of licence
changes and support on older OSes: OpenJDK has security support until
March 2026). On the other hand, newer platforms may only have support for
recent versions of Java: for ‘arm64’ macOS the first officially supported
version was 17.
 A package with a hard-to-satisfy system requirement is by definition not
portable, annoyingly so if this is not declared in the
‘SystemRequirements’ field. The most common example is the use
of pandoc, which is only available for a very limited range of platforms (and
has onerous requirements to install from source) and has capabilities89 that
vary by build but are not documented. Several recent versions of pandoc for
macOS did not work on R’s target of High Sierra (and this too was
undocumented). Another example is the Rust compilation system
(cargo and rustc).
Usage of external commands should always be conditional on a test for
presence (perhaps using [Link]), as well as declared in the
‘SystemRequirements’ field. A package should pass its checks without
warnings nor errors without the external command being present.
An external command can be a (possibly optional) requirement for an
imported or suggested package but needed for examples, tests or vignettes in
the package itself. Such usages should always be declared and conditional.
Interpreters for scripting languages such as Perl, Python and Ruby need to
be declared as system requirements and used conditionally: for example
macOS 10.16 was announced not to have them (but released as macOS 11
with them); later it was announced that macOS 12.3 does not have Python 2
and only a minimal install of Python 3 is included. Python 2 has passed end-
 of-life and been removed from many major distributions. Support for Rust
cannot be assumed.
Command cmake is not commonly installed, and where it is, it might not be
on the path. In particular, the most common location on macOS
is /Applications/[Link]/Contents/bin/cmake and that
should be looked for if cmake is not found on the path.
 Be sure to use portable encoding names: none of utf8, mac and macroman is
portable. See the help for file for more details.
 Do not invoke R by plain R, Rscript or (on Windows) Rterm in your
examples, tests, vignettes, makefiles or other scripts. As pointed out in
several places earlier in this manual, use something like
 "$(R_HOME)/bin/Rscript"
 "$(R_HOME)/bin$(R_ARCH_BIN)/Rterm"
with appropriate quotes (as, although not recommended, R_HOME can contain
spaces).
 Do not use R_HOME in makefiles except when passing them to the shell.
Specifically, do not use R_HOME in the argument to include, as R_HOME can
contain spaces. Quoting the argument to include does not help. A portable
and the recommended way to avoid the problem of spaces in ${R_HOME} is
using option -f of make. This is easy to do with recursive invocation of make,
which is also the only usual situation when R_HOME is needed in the argument
for include.
 $(MAKE) -f "${R_HOME}/etc${R_ARCH}/Makeconf" -f [Link]
 If distributing datasets involving date-times, consider if a time zone needs to
be specified. The most portable way to distribute date-times is as objects of
class "POSIXct" and as these record the time in UTC, the time represented is
independent of the time zone: but how it is printed may not be. Objects of
class "POSIXlt" should have a "tzone" attribute. Dates (e.g, birthdays) are
conventionally considered independently of time zone.
Do be careful in what your tests (and examples) actually test. Bad practice seen in
distributed packages include:
 It is not reasonable to test the time taken by a command: you cannot know
how fast or how heavily loaded an R platform might be. At best you can test
a ratio of times, and even that is fraught with difficulties and not advisable:
for example, the garbage collector may trigger at unpredictable times
following heuristics that may change without notice.
 Do not test the exact format of R messages (from R itself or from other
packages): They change, and they can be translated.
Packages have even tested the exact format of system error messages, which
are platform-dependent and perhaps locale-dependent. For example, in late
2021 libcurl changed its warning/error messages, including when URLs are
not found.
 If you use functions such as View, remember that in testing there is no one to
look at the output. It is better to use something like one of
 if(interactive()) View(obj) else print(head(obj))
 if(interactive()) View(obj) else str(obj)
 Be careful when comparing file paths. There can be multiple paths to a
single file, and some of these can be very long character strings. If possible
canonicalize paths before comparisons, but study ?normalizePath to be
aware of the pitfalls.
 Only test the accuracy of results if you have done a formal error analysis.
Things such as checking that probabilities numerically sum to one are silly:
numerical tests should always have a tolerance. That the tests on your
platform achieve a particular tolerance says little about other platforms. R is
configured by default to make use of long doubles where available, but they
may not be available or be too slow for routine use. Most R platforms use
‘ix86’ or ‘x86_64’ CPUs: these may use extended precision registers on
some but not all of their FPU instructions. Thus the achieved precision can
depend on the compiler version and optimization flags—our experience is
that 32-bit builds tend to be less precise than 64-bit ones. But not all
platforms use those CPUs, and not all90 which use them configure them to
allow the use of extended precision. In particular, current ARM CPUs do
not have extended precision nor long doubles, and clang currently has long
double the same as double on all ARM CPUs. On the other hand some
CPUs have higher-precision modes which may be used for long double,
notably 64-bit PowerPC and Sparc.
If you must try to establish a tolerance empirically, configure and build R
with --disable-long-double and use appropriate compiler flags
(such as -ffloat-store and -fexcess-
precision=standard for gcc, depending on the CPU type91) to
mitigate the effects of extended-precision calculations. The platform most
often seen to give different numerical results is ‘arm64’ macOS, so be sure
to include that in any empirical determination.
Tests which involve random inputs or non-deterministic algorithms should
normally set a seed or be tested for many seeds.
 Tests should use options(warn= 1) as reporting
 There were 22 warnings (use warnings() to see them)
is pointless, especially for automated checking systems.
 If your package uses dates/times, ensure that it works in all timezones,
especially those near boundaries (problems have most often be seen in
‘Europe/London’ (zero offset in Winter) and ‘Pacific/Auckland’,
near enough the International Date line) and with offsets not in whole hours
(Adelaide, Chatham Islands, …). More extreme examples are
‘Africa/Conakry’ (permanent UTC), ‘Asia/Calcutta’ (no DST,
 permanent half-hour offset) and ‘Pacific/Kiritimati’(no DST, more
than 12 hours ahead of UTC).
 PDF size
 Check timing
 Encoding issues
 Portable C and C++ code
 Binary distribution

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1.6.1 PDF size

There are a several tools available to reduce the size of PDF files: often the size
can be reduced substantially with no or minimal loss in quality. Not only do large
files take up space: they can stress the PDF viewer and take many minutes to print
(if they can be printed at all).
qpdf ([Link] can compress losslessly. It is fairly readily
available (e.g. it has binaries for Windows and packages in Debian/Ubuntu/Fedora,
and is installed as part of the CRAN macOS distribution of R). R CMD build has an
option to run qpdf over PDF files under inst/doc and replace them if at least
10Kb and 10% is saved. The full path to the qpdf command can be supplied as
environment variable R_QPDF (and is on the CRAN binary of R for macOS). It
seems MiKTeX does not use PDF object compression and so qpdf can reduce
considerably the sizes of files it outputs: MiKTeX’s defaults can be overridden by
code in the preamble of an Sweave or LaTeX file — see how this is done for the R
reference manual at [Link]
Other tools can reduce the size of PDFs containing bitmap images at excessively
high resolution. These are often best re-generated (for example Sweave defaults to
300 ppi, and 100–150 is more appropriate for a package manual). These tools
include Adobe Acrobat (not Reader), Apple’s Preview92 and Ghostscript (which
converts PDF to PDF by
ps2pdf options -dAutoRotatePages=/None -dPrinted=false [Link] [Link]
and suitable options might be
-dPDFSETTINGS=/ebook
-dPDFSETTINGS=/screen
See [Link] for more such
and consider all the options for image downsampling). There have been examples
in CRAN packages for which current versions of Ghostscript produced much
bigger reductions than earlier ones (e.g. at the upgrades from 9.50 to 9.52,
from 9.55 to 9.56 and then to 10.00.0).
We come across occasionally large PDF files containing excessively complicated
figures using PDF vector graphics: such figures are often best redesigned or failing
that, output as PNG files.
Option --compact-vignettes to R CMD build defaults to value ‘qpdf’: use
‘both’ to try harder to reduce the size, provided you have Ghostscript available
(see the help for tools::compactPDF).

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[Contents][Index]
1.6.2 Check timing

There are several ways to find out where time is being spent in the check process.
Start by setting the environment variable _R_CHECK_TIMINGS_ to ‘0’. This will report
the total CPU times (not Windows) and elapsed times for installation and running
examples, tests and vignettes, under each sub-architecture if appropriate. For tests
and vignettes, it reports the time for each as well as the total.
Setting _R_CHECK_TIMINGS_ to a positive value sets a threshold (in seconds elapsed
time) for reporting timings.
If you need to look in more detail at the timings for examples, use option --
timings to R CMD check (this is set by --as-cran). This adds a summary to
the check output for all the examples with CPU or elapsed time of more than 5
seconds. It produces a file [Link]/[Link] containing
timings for each help file: it is a tab-delimited file which can be read into R for
further analysis.
Timings for the tests and vignette runs are given at the bottom of the corresponding
log file: note that log files for successful vignette runs are only retained if
environment variable _R_CHECK_ALWAYS_LOG_VIGNETTE_OUTPUT_ is set to a true value.

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1.6.3 Encoding issues

The issues in this subsection have been much alleviated by the change in R 4.2.0 to
running the Windows port of R in a UTF-8 locale where available. However,
Windows users might be running an earlier version of R on an earlier version of
Windows which does not support UTF-8 locales.
Care is needed if your package contains non-ASCII text, and in particular if it is
intended to be used in more than one locale. It is possible to mark the encoding
used in the DESCRIPTION file and in .Rd files, as discussed elsewhere in this
manual.
First, consider carefully if you really need non-ASCII text. Some users of R will
only be able to view correctly text in their native language group (e.g. Western
European, Eastern European, Simplified Chinese) and ASCII.93. Other characters
may not be rendered at all, rendered incorrectly, or cause your R code to give an
error. For .Rd documentation, marking the encoding and
including ASCII transliterations is likely to do a reasonable job. The set of
characters which is commonly supported is wider than it used to be around 2000,
but non-Latin alphabets (Greek, Russian, Georgian, …) are still often problematic
and those with double-width characters (Chinese, Japanese, Korean, emoji) often
need specialist fonts to render correctly.
Several CRAN packages have messages in their R code in French (and a few in
German). A better way to tackle this is to use the internationalization facilities
discussed elsewhere in this manual.
Function showNonASCIIfile in package tools can help in finding non-ASCII bytes
in files.
There is a portable way to have arbitrary text in character strings (only) in your R
code, which is to supply them in Unicode as ‘\uxxxx’ escapes (or, rarely needed
except for emojis, ‘\Uxxxxxxxx’ escapes). If there are any characters not in the
current encoding the parser will encode the character string as UTF-8 and mark it
as such. This applies also to character strings in datasets: they can be prepared
using ‘\uxxxx’ escapes or encoded in UTF-8 in a UTF-8 locale, or even
converted to UTF-8 via iconv(). If you do this, make sure you have ‘R (>=
2.10)’ (or later) in the ‘Depends’ field of the DESCRIPTION file.
R sessions running in non-UTF-8 locales will if possible re-encode such strings for
display (and this is done by RGui on older versions of Windows, for example).
Suitable fonts will need to be selected or made available94 both for the
console/terminal and graphics devices such as ‘X11()’ and ‘windows()’. Using
‘postscript’ or ‘pdf’ will choose a default 8-bit encoding depending on the
language of the UTF-8 locale, and your users would need to be told how to select
the ‘encoding’ argument.
Note that the previous two paragraphs only apply to character strings in R code.
Non-ASCII characters are particularly prevalent in comments (in the R code of the
package, in examples, tests, vignettes and even in the NAMESPACE file) but should
be avoided there. Most commonly people use the Windows extensions to Latin-1
(often directional single and double quotes, ellipsis, bullet and en and em dashes)
which are not supported in strict Latin-1 locales nor in CJK locales on Windows. A
surprisingly common misuse is to use a right quote in ‘don't’ instead of the
correct apostrophe.
Datasets can include marked UTF-8 or Latin-1 character strings. As R is nowadays
unlikely to be run in a Latin-1 or Windows’ CP1252 locale, for performance
reasons these should be converted to UTF-8.
If you want to run R CMD check on a Unix-alike over a package that sets a package
encoding in its DESCRIPTION file and do not use a UTF-8 locale you may need
to specify a suitable locale via environment variable R_ENCODING_LOCALES. The
default is equivalent to the value
"latin1=en_US:latin2=pl_PL:UTF-8=en_US.UTF-8:latin9=fr_FR.iso885915@euro"
(which is appropriate for a system based on glibc: macOS
requires latin9=fr_FR.ISO8859-15) except that if the current locale is UTF-8 then
the package code is translated to UTF-8 for syntax checking, so it is strongly
recommended to check in a UTF-8 locale.

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packages [Contents][Index]
1.6.4 Portable C and C++ code

Writing portable C and C++ code is mainly a matter of observing the standards
(C99, C++14 or where declared C++11/17/20) and testing that extensions (such as
POSIX functions) are supported. Do make maximal use of your compiler
diagnostics — this typically means using flags -Wall and -pedantic for both
C and C++ and additionally -Werror=implicit-function-
declaration and -Wstrict-prototypes for C (on some platforms and
compiler versions) these are part of -Wall or -pedantic).
C++ standards: From version 3.6.0 (3.6.2 on Windows), R defaulted to C++11
where available95; R 4.1.0 and later default to C++14 (where available). However,
in earlier versions the default standard was that of the compiler used, often C++98
or C++14, and the default is likely to change in future. For maximal portability a
package should either specify a standard (see Using C++ code) or be tested under
all of C++11, C++98 and C++14. (Specifying C++14 will limit portability.)
Note that the ‘TR1’ C++ extensions are not part of any of these standards and
the <tr1/name> headers are not supplied by some of the compilers used for R,
including on macOS. (Use the C++11 versions instead.)
A common error is to assume recent versions of compilers or OSes. In production
environments ‘long term support’ versions of OSes may be in use for many
years,96 and their compilers may not be updated during that time. For example,
GCC 4.8 was still in use in 2022 and could be (in RHEL 7) until 2028: that
supports neither C++14 nor C++17.
The POSIX standards only require recently-defined functions to be declared if
certain macros are defined with large enough values, and on some compiler/OS
combinations97 they are not declared otherwise. So you may need to include
something like one of
#define _XOPEN_SOURCE 600
or
#ifdef __GLIBC__
# define _POSIX_C_SOURCE 200809L
#endif
before any headers. (strdup, strncasecmp and strnlen are such functions – there
were several older platforms which did not have the POSIX 2008
function strnlen.)
However, some common errors are worth pointing out here. It can be helpful to
look up functions
at [Link] or [Link] and compare
what is defined in the various standards.
More care is needed for functions such as mallinfo which are not specified by any
of these standards—hopefully the man page on your system will tell you so.
Searching online for such pages for various OSes (preferably at least Linux and
macOS, and the FreeBSD manual pages
at [Link] allow you to select many OSes) should
reveal useful information but a configure script is likely to be needed to check
availability and functionality.
Both the compiler and OS (via system header files, which may differ by
architecture even for nominally the same OS) affect the compilability of C/C++
code. Compilers from the GCC, clang, Intel and Oracle Developer Studio suites
have been used with R, and both LLVM clang and Oracle have more than one
implementation of C++ headers and library. The range of possibilities makes
comprehensive empirical checking impossible, and regrettably compilers are
patchy at best on warning about non-standard code.
 Mathematical functions such as sqrt are defined in C++11 for floating-point
arguments: float, double, long double and possibly more. The standard
specifies what happens with an argument of integer type but this is not
always implemented, resulting in a report of ‘overloading ambiguity’: this
was commonly seen on Solaris, but for pow also seen on macOS and other
platforms using clang++.
A not-uncommonly-seen problem is to mistakenly
call floor(x/y) or ceil(x/y) for int arguments x and y. Since x/y does
integer division, the result is of type int and ‘overloading ambiguity’ may
be reported. Some people have (pointlessly) called floor and ceil on
arguments of integer type, which may have an ‘overloading ambiguity’.
A surprising common misuse is things like pow(10, -3): this should be the
constant 1e-3. Note that there are constants such
 as M_SQRT2 defined via Rmath.h98 for sqrt(2.0), frequently mis-coded
as sqrt(2).
 Function fabs is defined only for floating-point types, except in C++11 and
later which have overloads for std::fabs in <cmath> for integer types.
Function abs is defined in C99’s <stdlib.h> for int and in C+
+’s <cstdlib> for integer types, overloaded in <cmath> for floating-
point types. C++11 has additional overloads for std::abs in <cmath> for
integer types. The effect of calling abs with a floating-point type is
implementation-specific: it may truncate to an integer. For clarity and to
avoid compiler warnings, use abs for integer types and fabs for double
values, and when using C++ include <cmath> and use the std:: prefix.
 It is an error (and make little sense, although has been seen) to call
macros/functions isnan, isinf and isfinite for integer arguments: a few
compilers give a compilation error. Function finite is obsolete, and some
compilers will warn about its use99.
 The GNU C/C++ compilers support a large number of non-portable
extensions. For example, INFINITY (which is a float value in C99 and C+
+11), for which R provides the portable double
value R_PosInf (and R_NegInf for -INFINITY). And NAN100 is just one
NaN float value: for use with R, NA_REAL is often what is intended,
but R_NaN is also available.
Some (but not all) extensions are listed
at [Link] and https://
[Link]/onlinedocs/gcc/C_002b_002b-[Link].
Other GNU extensions which have bitten package writers are the use of
non-portable characters such as ‘$’ in identifiers and use of C++ headers
under ext.
The GNU Fortran compiler also supports a large number of non-portable
extensions, the most commonly encountered one being ISNAN101. Some are
listed at [Link]
[Link]. One that frequently catches package writers is that it
allows out-of-order declarations: in standard-conformant Fortran variables
must be declared (explicitly or implicitly) before use in other declarations
such as dimensions.
GNU Fortran 10 and later give a compilation error for the previously
widespread practice of passing a Fortran array element where an array is
expected, or a scalar instead of a length-one array.
See [Link]
 Including C-style headers in C++ code is not portable. Including the legacy
header102 math.h in C++ code may conflict with cmath which may be
included by other headers. In C++11, functions like sqrt and isnan are
 defined for double arguments in math.h and for a range of types
including double in cmath. Similar issues have been seen
for stdlib.h and cstdlib. Including the C++ header first used to be a
sufficient workaround but for some 2016 compilers only one could be
included.
 Be careful to include the headers which define the functions you use. Some
compilers/OSes include other system headers in their headers which are not
required by the standards, and so code may compile on such systems and not
on others. (A prominent example is the C++ header <random> which is
indirectly included by <algorithm> by g++. Another issue is the C
header <time.h> which is included by other headers on Linux and Windows
but not macOS.) g++ 11 often needs explicit inclusion of the C++
headers <limits> (for numeric_limits)
or <exception> (for set_terminate and similar), whereas earlier versions
included these in other headers. g++ 13 requires the explicit inclusion
of <cstdint> for types such as uint32_t which was previously included
implicitly. (For more such, see [Link]
Note that malloc, calloc, realloc and free are defined by C99 in the
header stdlib.h and (in the std:: namespace) by C++ header cstdlib.
Some earlier implementations used a header malloc.h, but that is not
portable and does not exist on macOS.
This also applies to types such as ssize_t. The POSIX standards say that is
declared in headers unistd.h and sys/types.h, and the latter is often
included indirectly by other headers on some but not all systems.
Similarly for constants: for example SIZE_MAX is defined
in stdint.h alongside size_t.
 Some headers are not portable: we have just mentioned malloc.h and
often CRAN submissions attempt to use endian.h. The latter is
a glibc extension: some OSs
have machine/endian.h or sys/endian.h but some have neither.
 Use #include "my.h" not #include <my.h> for headers in your package. The
second form is intended for system headers and the search order for such
headers is platform-dependent (and may not include the current directory).
For extra safety, name headers in a way that cannot be confused with a
system header so not, for example, types.h.
 For C++ code, be careful to specify namespaces where needed. Many
functions are defined by the standards to be in the std namespace, but g+
+ puts many such also in the C++ main namespace. One way to do so is to
use declarations such as
 using std::floor;
but it is usually preferable to use explicit namespace prefixes in the code.
 Examples seen in CRAN packages include
abs acos atan bind calloc ceil div exp fabs floor fmod free
log malloc
memcpy memset pow printf qsort round sin sprintf sqrt strcmp
strcpy
strerror strlen strncmp strtol tan trunc
This problem is less common than it used to be, but in 2019
LLVM clang did not have bind in the main namespace. Also seen has been
type size_t defined only in the std namespace.
NB: These functions are only guaranteed to be in the std namespace if the
correct C++ header is included, e.g. <cmath> rather than <math.h>.
If you define functions in C++ which are inspired by later standards, put
them in a namespace and refer to them using the namespace. We have seen
conflicts with std::make_unique from C++14
and std::byte, std::data, std::sample and std::size from C++17.
 In C++ code
 using namesapace std;
is not good practice, and has caused platform-dependent errors if included
before headers, especially system headers (which may be included by other
headers). The best practice is to use explicit std:: prefixes for all functions
declared by the C++ standard to be in that namespace.
 Some C++ compilers refuse to compile constructs such as
 if(ptr > 0) { ....}
which compares a pointer to the integer 0. This could just
use if(ptr) (pointer addresses cannot be negative) but if needed pointers
can be tested against nullptr (C++11) or NULL.
 Macros defined by the compiler/OS can cause problems. Identifiers starting
with an underscore followed by an upper-case letter or another underscore
are reserved for system macros and should not be used in portable code
(including not as guards in C/C++ headers). Other macros, typically upper-
case, may be defined by the compiler or system headers and can cause
problems. Some of these can be avoided by defining _POSIX_C_SOURCE before
including any system headers, but it is better to only use all-upper-case
names which have a unique prefix such as the package name.
 typedefs in OS headers can conflict with those in the package: examples
have included ulong, index_t, single and thread. (Note that these may
conflict with other uses as identifiers, e.g. defining a C++ function
called single.) The POSIX standard reserves (in §2.2.2) all identifiers
ending in _t.
 Some compilers do not allow a space between -D and the macro to be
defined. Similarly for -U.
 If you use OpenMP, check carefully that you have followed the advice in
the subsection on OpenMP support. In particular, any use of OpenMP in
C/C++ code will need to use
 #ifdef _OPENMP
 # include <omp.h>
 #endif
Any use of OpenMP functions, e.g. omp_set_num_threads, also needs to be
conditioned. To avoid incessant warnings such as
warning: ignoring #pragma omp parallel [-Wunknown-pragmas]
uses of such pragmas should also be conditioned (or commented out if they
are used in code in a package not enabling OpenMP on any platform).
Do not hardcode -lgomp: not only is that specific to the GCC family of
compilers, using the correct linker flag often sets up the run-time path to the
library.
 Package authors commonly assume things are part of C/C++ when they are
not: the most common example is POSIX103 function strdup. The most
common C library on Linux, glibc, will hide the declarations of such
extensions unless a ‘feature-test macro’ is defined before (almost) any
system header is included. So for strdup you need
 #define _POSIX_C_SOURCE 200809L
 ...
 #include <string.h>
 ...
 strdup call(s)
where the appropriate value can be found by man strdup on Linux. (Use
of strncasecmp is similar.)
However, modes of gcc with ‘GNU EXTENSIONS’ (which are the default,
either -std=gnu99 or -std=gnu11) declare enough macros to ensure
that missing declarations are rarely seen.
This applies also to constants such as M_PI and M_LN2, which are part of the
X/Open standard: to use these define _XOPEN_SOURCE before including any
headers, or include the R header Rmath.h.
 Using alloca portably is tricky: it is neither an ISO C/C++ nor a POSIX
function. An adequately portable preamble is
 #ifdef __GNUC__
 /* Includes GCC, clang and Intel compilers */
 # undef alloca
 # define alloca(x) __builtin_alloca((x))
 #elif defined(__sun) || defined(_AIX)
 /* this was necessary (and sufficient) for Solaris 10 and AIX
6: */
 # include <alloca.h>
 #endif
 Compiler writers feel free to implement features from later standards than
the one specified, so for example they may implement or warn on C+
 +14/17/20 features when C++11 is specified. Portable code will not use such
features – it can be hard to know what they are but the most common
warnings are
 'register' storage class specifier is deprecated and
incompatible with C++17

 ISO C++11 does not allow conversion from string literal to
‘char *’
(where conversion should be to const char *). Keyword register was not
mentioned in C++98, deprecated in C++11 and removed in C++17.
There are quite a lot of other C++98 features deprecated in C++11 and
removed in C++17, and LLVM clang 9 and later warn about them.
Examples include bind1st/bind2nd (use std::bind or
lambdas104) std::auto_ptr (replaced
by std::unique_ptr), std::mem_fun_ref and std::ptr_fun.
 Later versions of standards may add reserved words: for
example bool, false and true became keywords in C23 and are no longer
available as variable names. As noted above, C++17
uses byte, data, sample and size.
So avoid common words and keywords in other programming languages.
 Be careful about including C headers in C++ code. Issues include
 Use of the register storage class specifier (see the previous but one
item).
105
 The C99 keyword restrict is not part of any C++ standard and is
rejected by some C++ compilers.
 Inclusion by such headers of C-style headers such as math.h (see
above).
The most portable way to interface to other software with a C API is to use
C code (which can normally be mixed with C++ code in a package).
 reinterpret_cast in C++ is not safe for pointers: for example the types may
have different alignment requirements. Use memcpy to copy the contents to a
fresh variable of the destination type.
 Avoid platform-specific code if at all possible, but if you need to test for a
platform ensure that all platforms are covered. For example, __unix__ is not
defined on all Unix-alikes, in particular not on macOS. A reasonably
portable way to condition code for a Unix-alike is
 #if defined (__unix__) || (defined (__APPLE__) && defined
(__MACH__))
 #endif
but
#ifdef _WIN32
// Windows-specific code
#else
// Unix-alike code
 #endif
would be better. For a Unix-alike it is much better to use configure to test
for the functionality needed than make assumptions about OSes (and people
all too frequently forget R is used on platforms other than Linux, Windows
and macOS — and some forget macOS).
 Headers in subdirectories are often not portable. For C++, this
includes bits/, tr1/ and tr2/, none of which exist on macOS
(and ext/ exists there but with different content from g++-based platforms).
Header bits/stdc++.h is both not portable and not recommended for
end-user code even on platforms which include it.
 Be careful if using malloc or calloc. First, their return value must always be
checked to see if the allocation succeeded – it is almost always easier to use
R’s R_Calloc, which does check. Second, the first argument is of
type size_t and recent compilers are warning about passing signed
arguments (which could get promoted to ridiculously large values).
 For C code, consider using the flag -Wstrict-prototypes which is
supported by gcc and LLVM and Apple clang. This has found quite a
number of errors where functions have been declared without arguments and
is likely to become the default in future compilers. (It already is for
LLVM clang in C23 mode.) Note that using f() for a function without any
parameters was deprecated in C99 and C11, but it expected to be non-
deprecated in C23. However, f(void) is supported by all standards and
avoids any uncertainty.
LLVM clang has a separate warning -Wdeprecated-non-
prototype which is enabled by -Wstrict-prototypes. This warns
on K&R-style usage, which will not be accepted in C23.
 Several C entry points are warned against in their man pages on most
systems, often in very strong terms such as ’Do not use these functions’.
macOS has started to warn106 if these are used
for sprintf, vsprintf, gets, mktemp, tempmam and tmpnam. It is highly
recommended that you use safer alternatives (on any platform) but the
warning can be avoided by defining ‘_POSIX_C_SOURCE’ to for example
‘200809L’ before including the (C or C++) header which defines them.
(However, this may hide other extensions.)
Some additional information for C++ is available
at [Link] by
Martyn Plummer.
 Common symbols
 C++17 issues
Next: C++17 issues, Previous: Portable C and C++ code, Up: Portable C and C++
code [Contents][Index]
[Link] Common symbols

Most OSes (including all those commonly used for R) have the concept of
‘tentative definitions’ where global C variables are defined without an initializer.
Traditionally the linker resolves all tentative definitions of the same variable in
different object files to the same object, or to a non-tentative definition.
However, gcc 10107 and LLVM clang 11108 changed their default so that tentative
definitions cannot be merged and the linker will give an error if the same variable
is defined in more than one object file. To avoid this, all but one of the C source
files should declare the variable extern — which means that any such variables
included in header files need to be declared extern. A commonly used idiom
(including by R itself) is to define all global variables as extern in a header,
say globals.h (and nowhere else), and then in one (and one only) source file
use
#define extern
# include "globals.h"
#undef extern
A cleaner approach is not to have global variables at all, but to place in a single file
common variables (declared static) followed by all the functions which make use
of them: this may result in more efficient code.
The ‘modern’ behaviour can be seen109 by using compiler flag -fno-common as
part of ‘CFLAGS’ in earlier versions of gcc and clang.
-fno-common is said to be particularly beneficial for ARM cpus.
This is not pertinent to C++ which does not permit tentative definitions.

Previous: Common symbols, Up: Portable C and C++ code [Contents][Index]

[Link] C++17 issues

R 4.3.0 and later default to C++17 when compiling C++, and that finally removed
many C++98 features which were deprecated as long ago as C++11.
Compiler/runtime authors have been slow to remove these, but LLVM clang with
its libc++ runtime library finally started to do so in 2023 – some others warn but
some do not.
The principal offender is the ‘Boost’ collection of C++ headers and libraries. There
are two little-documented ways to work around aspects of its outdated code. One is
to add
-D_HAS_AUTO_PTR_ETC=0
to PKG_CPPLAGS in src/Makevars, src/[Link] and src/
[Link]. This covers the removal of
std::auto_ptr
std::unary_function
std::binary_function
std::random_shuffle
std::binder1st
std::binder2nd
with most issues seen with code that includes boost/[Link],
usually indirectly.
A rarer issue is the use of illegal values for enum types, usually negative ones such
as
BOOST_MPL_AUX_STATIC_CAST(AUX_WRAPPER_VALUE_TYPE, (value - 1));
in boost/mpl/aux_/integral_wrapper.hpp. Adding
-Wno-error=enum-constexpr-conversion
to PKG_CXXFLAGS will allow this, but that flag is only accepted by recent versions of
LLVM clang so needs a configure test.
Pre=built versions of current clang/libc++ are usually available
from [Link] for a wide range of platforms
(but the Windows builds there are not compatible with Rtools and the macOS ones
are unsigned). To select libc++ add -stdlib=libc++ to CXX, for example by
having
CXX="/path/to/clang/clang++ -std=gnu++17 -stdlib=libc++"
in ~/.R/Makevars.
Another build for Windows which may be sufficiently compatible with Rtools can
be found at [Link] this uses libc++.

Previous: Portable C and C++ code, Up: Writing portable packages [Contents]
[Index]
1.6.5 Binary distribution

If you want to distribute a binary version of a package on Windows or macOS,

there are further checks you need to do to check it is portable: it is all too easy to
depend on external software on your own machine that other users will not have.
For Windows, check what other DLLs your package’s DLL depends on (‘imports’
from in the DLL tools’ parlance). A convenient GUI-based tool to do so is
‘Dependency Walker’ ([Link] for both 32-bit and
64-bit DLLs – note that this will report as missing links to R’s own DLLs such
as [Link] and [Link]. The command-line tool objdump in the appropriate
toolchain will also reveal what DLLs are imported from. If you use a toolchain
other than one provided by the R developers or use your own makefiles, watch out
in particular for dependencies on the toolchain’s runtime DLLs such
as libgfortran, libstdc++ and libgcc_s.
For macOS, using R CMD otool -L on the package’s shared object(s) in
the libs directory will show what they depend on: watch for any dependencies
in /usr/local/lib or /usr/local/gfortran/lib,
notably libgfortran.?.dylib and [Link]. (For ways
to fix these, see Building binary-packages in R Installation and Administration.)
Many people (including the CRAN package repository) will not accept source
packages containing binary files as the latter are a security risk. If you want to
distribute a source package which needs external software on Windows or macOS,
options include
 To arrange for installation of the package to download the additional
software from a URL, as e.g. package Cairo does.
 (For CRAN.) To negotiate with Uwe Ligges to host the additional
components on WinBuilder, and write a [Link] file to install
them.
Be aware that license requirements you may require you to supply the sources for
the additional components (and will if your package has a GPL-like license).

Next: Internationalization, Previous: Writing portable packages, Up: Creating R

packages [Contents][Index]

1.7 Diagnostic messages

Diagnostic messages can be made available for translation, so it is important to
write them in a consistent style. Using the tools described in the next section to
extract all the messages can give a useful overview of your consistency (or lack of
it). Some guidelines follow.
 Messages are sentence fragments, and not viewed in isolation. So it is
conventional not to capitalize the first word and not to end with a period (or
other punctuation).
 Try not to split up messages into small pieces. In C error messages use a
single format string containing all English words in the messages.
In R error messages do not construct a message with paste (such messages
will not be translated) but via multiple arguments to stop or warning,
or via gettextf.
 Do not use colloquialisms such as “can’t” and “don’t”.
 Conventionally single quotation marks are used for quotations such as
 'ord' must be a positive integer, at most the number of knots
 and double quotation marks when referring to an R character string or a
class, such as
'format' must be "normal" or "short" - using "normal"
Since ASCII does not contain directional quotation marks, it is best to use
‘'’ and let the translator (including automatic translation) use directional
quotations where available. The range of quotation styles is immense:
unfortunately we cannot reproduce them in a portable texinfo document.
But as a taster, some languages use ‘up’ and ‘down’ (comma) quotes rather
than left or right quotes, and some use guillemets (and some use what
Adobe calls ‘guillemotleft’ to start and others use it to end).
In R messages it is also possible to use sQuote or dQuote as in
stop(gettextf("object must be of class %s or %s",
dQuote("manova"), dQuote("maov")),
domain = NA)
 Occasionally messages need to be singular or plural (and in other languages
there may be no such concept or several plural forms – Slovenian has four).
So avoid constructions such as was once used in library
 if((length(nopkgs) > 0) && !missing([Link])) {
 if(length(nopkgs) > 1)
 warning("libraries ",
 paste(sQuote(nopkgs), collapse = ", "),
 " contain no packages")
 else
 warning("library ", paste(sQuote(nopkgs)),
 " contains no package")
 }
and was replaced by
if((length(nopkgs) > 0) && !missing([Link])) {
pkglist <- paste(sQuote(nopkgs), collapse = ", ")
msg <- sprintf(ngettext(length(nopkgs),
"library %s contains no packages",
"libraries %s contain no
packages",
domain = "R-base"),
pkglist)
warning(msg, domain=NA)
}
Note that it is much better to have complete clauses as here, since in another
language one might need to say ‘There is no package in library %s’ or
‘There are no packages in libraries %s’.

Next: CITATION files, Previous: Diagnostic messages, Up: Creating R packages

[Contents][Index]

1.8 Internationalization
There are mechanisms to translate the R- and C-level error and warning messages.
There are only available if R is compiled with NLS support (which is requested
by configure option --enable-nls, the default).
The procedures make use of msgfmt and xgettext which are part
of GNU gettext and this will need to be installed: Windows users can find pre-
compiled binaries at [Link]
[Link].
 C-level messages
 R messages
 Preparing translations

Next: R messages, Previous: Internationalization, Up: Internationalization

[Contents][Index]
1.8.1 C-level messages

The process of enabling translations is

 In a header file that will be included in all the C (or C++ or Objective C/C+
+) files containing messages that should be translated, declare
 #include <R.h> /* to include Rconfig.h */

 #ifdef ENABLE_NLS
 #include <libintl.h>
 #define _(String) dgettext ("pkg", String)
 /* replace pkg as appropriate */
 #else
 #define _(String) (String)
 #endif
 For each message that should be translated, wrap it in _(...), for example
 error(_("'ord' must be a positive integer"));
If you want to use different messages for singular and plural forms, you
need to add
#ifndef ENABLE_NLS
#define dngettext(pkg, String, StringP, N) (N == 1 ? String :
StringP)
#endif
and mark strings by
dngettext("pkg", <singular string>, <plural string>, n)
 In the package’s src directory run
 xgettext --keyword=_ -o [Link] *.c
The file src/[Link] is the template file, and conventionally this is shipped
as po/[Link].
Next: Preparing translations, Previous: C-level messages, Up: Internationalization
[Contents][Index]
1.8.2 R messages

Mechanisms are also available to support the automatic translation of

R stop, warning and message messages. They make use of message catalogs in the
same way as C-level messages, but using domain R-pkg rather than pkg. Translation
of character strings inside stop, warning and message calls is automatically enabled,
as well as other messages enclosed in calls to gettext or gettextf. (To suppress
this, use argument domain=NA.)
Tools to prepare the [Link] file are provided in
package tools: xgettext2pot will prepare a file from all strings occurring
inside gettext/gettextf, stop, warning and message calls. Some of these are likely
to be spurious and so the file is likely to need manual editing. xgettext extracts the
actual calls and so is more useful when tidying up error messages.
The R function ngettext provides an interface to the C function of the same name:
see example in the previous section. It is safest to use domain="R-pkg" explicitly in
calls to ngettext, and necessary for earlier versions of R unless they are calls
directly from a function in the package.

Previous: R messages, Up: Internationalization [Contents][Index]

1.8.3 Preparing translations

Once the template files have been created, translations can be made. Conventional
translations have file extension .po and are placed in the po subdirectory of the
package with a name that is either ‘[Link]’ or ‘[Link]’ for translations of the
C and R messages respectively to language with code ‘ll’.
See Localization of messages in R Installation and Administration, for details of
language codes.
There is an R function, update_pkg_po in package tools, to automate much of the
maintenance of message translations. See its help for what it does in detail.
If this is called on a package with no existing translations, it creates the
directory pkgdir/po, creates a template file of R messages, pkgdir/po/R-
[Link], within it, creates the ‘en@quot’ translation and installs that. (The
‘en@quot’ pseudo-language interprets quotes in their directional forms in suitable
(e.g. UTF-8) locales.)
If the package has C source files in its src directory that are marked for
translation, use
touch pkgdir/po/[Link]
to create a dummy template file, then call update_pkg_po again (this can also be
done before it is called for the first time).
When translations to new languages are added in the pkgdir/po directory,
running the same command will check and then install the translations.
If the package sources are updated, the same command will update the template
files, merge the changes into the translation .po files and then installed the
updated translations. You will often see that merging marks translations as ‘fuzzy’
and this is reported in the coverage statistics. As fuzzy translations are not used,
this is an indication that the translation files need human attention.
The merged translations are run through tools::checkPofile to check that C-style
formats are used correctly: if not the mismatches are reported and the broken
translations are not installed.
This function needs the GNU gettext-tools installed and on the path: see its help
page.

Next: Package types, Previous: Internationalization, Up: Creating R packages

[Contents][Index]

1.9 CITATION files

An installed file named CITATION will be used by the citation() function. (It
should be in the inst subdirectory of the package sources.)
The CITATION file is parsed as R code (in the package’s declared encoding, or
in ASCII if none is declared). It will contain calls to function bibentry. Here is that
for nlme:
## R package reference generated from DESCRIPTION metadata
citation(auto = meta)

## NLME book
bibentry(bibtype = "Book",
title = "Mixed-Effects Models in S and S-PLUS",
author = c(person(c("José", "C."), "Pinheiro"),
person(c("Douglas", "M."), "Bates")),
year = "2000", publisher = "Springer", address = "New York",
doi = "10.1007/b98882")
Note how the first call auto-generates citation information from object meta, a
parsed version of the DESCRIPTION file – it is tempting to hardcode such
information, but it normally then gets outdated. How the first entry would look like
as a bibentry call can be seen from print(citation("pkgname", auto = TRUE),
style = "R") for any installed package. Auto-generated information is returned by
default if no CITATION file is present.
See ?bibentry for further details of the information which can be provided. In case
a bibentry contains LaTeX markup (e.g., for accented characters or mathematical
symbols), it may be necessary to provide a text representation to be used for
printing via the textVersion argument to bibentry. E.g., earlier versions
of nlme additionally used something like
textVersion =
paste0("Jose Pinheiro, Douglas Bates, Saikat DebRoy, ",
"Deepayan Sarkar and the R Core Team (",
sub("-.*", "", meta$Date),
"). nlme: Linear and Nonlinear Mixed Effects Models. ",
sprintf("R package version %s", meta$Version), ".")
The CITATION file should itself produce no output when source-d.
It is desirable (and essential for CRAN) that the CITATION file does not contain
calls to functions such as packageDescription which assume the package is
installed in a library tree on the package search path.

Next: Services, Previous: CITATION files, Up: Creating R packages [Contents]

[Index]

1.10 Package types

The DESCRIPTION file has an optional field Type which if missing is assumed to
be ‘Package’, the sort of extension discussed so far in this chapter. Currently one
other type is recognized; there used also to be a ‘Translation’ type.
 Frontend

Previous: Package types, Up: Package types [Contents][Index]

1.10.1 Frontend

This is a rather general mechanism, designed for adding new front-ends such as the
former gnomeGUI package (see the Archive area on CRAN). If
a configure file is found in the top-level directory of the package it is executed,
and then if a Makefile is found (often generated by configure), make is
called. If R CMD INSTALL --clean is used make clean is called. No other action is
taken.
R CMD build can package up this type of extension, but R CMD check will check the
type and skip it.
Many packages of this type need write permission for the R installation directory.

Previous: Package types, Up: Creating R packages [Contents][Index]

1.11 Services
Several members of the R project have set up services to assist those writing R
packages, particularly those intended for public distribution.
[Link] offers the automated preparation of (32/64-bit) Windows
binaries from well-tested source packages.
R-Forge ([Link]) and RForge ([Link]) are similar services
with similar names. Both provide source-code management through SVN, daily
building and checking, mailing lists and a repository that can be
accessed via [Link] (they can be selected by setRepositories and the
GUI menus that use it). Package developers have the opportunity to present their
work on the basis of project websites or news announcements. Mailing lists,
forums or wikis provide useRs with convenient instruments for discussions and for
exchanging information between developers and/or interested useRs.

Next: Tidying and profiling R code, Previous: Creating R packages, Up: Writing R
Extensions [Contents][Index]

2 Writing R documentation files

 Rd format
 Sectioning
 Marking text
 Lists and tables
 Cross-references
 Mathematics
 Figures
 Insertions
 Indices
 Platform-specific documentation
 Conditional text
 Dynamic pages
 User-defined macros
 Encoding
 Processing documentation files
 Editing Rd files

Next: Sectioning, Previous: Writing R documentation files, Up: Writing R

documentation files [Contents][Index]
2.1 Rd format
R objects are documented in files written in “R documentation” (Rd) format, a
simple markup language much of which closely resembles (La)TeX, which can be
processed into a variety of formats, including LaTeX, HTML and plain text. The
translation is carried out by functions in the tools package called by the
script Rdconv in R_HOME/bin and by the installation scripts for packages.
The R distribution contains more than 1400 such files which can be found in
the src/library/pkg/man directories of the R source tree, where pkg stands
for one of the standard packages which are included in the R distribution.
As an example, let us look at a simplified version
of src/library/base/man/[Link] which documents the R function load.
% File src/library/base/man/[Link]
\name{load}
\alias{load}
\title{Reload Saved Datasets}
\description{
Reload the datasets written to a file with the function
\code{save}.
}
\usage{
load(file, envir = [Link]())
}
\arguments{
\item{file}{a connection or a character string giving the
name of the file to load.}
\item{envir}{the environment where the data should be
loaded.}
}
\seealso{
\code{\link{save}}.
}
\examples{
## save all data
save(list = ls(), file= "[Link]")

## restore the saved values to the current environment

load("[Link]")

## restore the saved values to the workspace

load("[Link]", .GlobalEnv)
}
\keyword{file}

An Rd file consists of three parts. The header gives basic information about the
name of the file, the topics documented, a title, a short textual description and R
usage information for the objects documented. The body gives further information
(for example, on the function’s arguments and return value, as in the above
example). Finally, there is an optional footer with keyword information. The
header is mandatory.
Information is given within a series of sections with standard names (and user-
defined sections are also allowed). Unless otherwise specified110 these should occur
only once in an Rd file (in any order), and the processing software will retain only
the first occurrence of a standard section in the file, with a warning.
See “Guidelines for Rd files” for guidelines for writing documentation
in Rd format which should be useful for package writers. The R generic
function prompt is used to construct a bare-bones Rd file ready for manual editing.
Methods are defined for documenting functions (which fill in the proper function
and argument names) and data frames. There are also
functions promptData, promptPackage, promptClass, and promptMethods for other
types of Rd file.
The general syntax of Rd files is summarized below. For a detailed technical
discussion of current Rd syntax, see “Parsing Rd files”.
Rd files consist of four types of text input. The most common is LaTeX-like, with
the backslash used as a prefix on markup (e.g. \alias), and braces used to indicate
arguments (e.g. {load}). The least common type of text is ‘verbatim’ text, where
no markup other than the comment marker (%) is processed. There is also a rare
variant of ‘verbatim’ text (used in \eqn, \deqn, \figure, and \newcommand) where
comment markers need not be escaped. The final type is R-like, intended for R
code, but allowing some embedded macros. Quoted strings within R-like text are
handled specially: regular character escapes such as \n may be entered as-is. Only
markup starting with \l (e.g. \link) or \v (e.g. \var) will be recognized within
quoted strings. The rarely used vertical tab \v must be entered as \\v.
Each macro defines the input type for its argument. For example, the file initially
uses LaTeX-like syntax, and this is also used in the \description section, but the \
usage section uses R-like syntax, and the \alias macro uses ‘verbatim’ syntax.
Comments run from a percent symbol % to the end of the line in all types of text
except the rare ‘verbatim’ variant (as on the first line of the load example).
Because backslashes, braces and percent symbols have special meaning, to enter
them into text sometimes requires escapes using a backslash. In general balanced
braces do not need to be escaped, but percent symbols always do, except in the
‘verbatim’ variant. For the complete list of macros and rules for escapes,
see “Parsing Rd files”.
 Documenting functions
 Documenting data sets
 Documenting S4 classes and methods
 Documenting packages

Next: Documenting data sets, Previous: Rd format, Up: Rd format [Contents]

[Index]
2.1.1 Documenting functions

The basic markup commands used for documenting R objects (in particular,
functions) are given in this subsection.
\name{name}
name typically111 is the basename of the Rd file containing the
documentation. It is the “name” of the Rd object represented by the file and
has to be unique in a package. To avoid problems with indexing the package
manual, it may not contain ‘!’ ‘|’ nor ‘@’, and to avoid possible problems
with the HTML help system it should not contain ‘/’ nor a space. (LaTeX
special characters are allowed, but may not be collated correctly in the
index.) There can only be one \name entry in a file, and it must not contain
any markup. Entries in the package manual will be in alphabetic112 order of
the \name entries.
\alias{topic}
The \alias sections specify all “topics” the file documents. This information
is collected into index data bases for lookup by the on-line (plain text
and HTML) help systems. The topic can contain spaces, but (for historical
reasons) leading and trailing spaces will be stripped. Percent and left brace
need to be escaped by a backslash.
There may be several \alias entries. Quite often it is convenient to
document several R objects in one file. For example,
file [Link] documents the density, distribution function, quantile
function and generation of random variates for the normal distribution, and
hence starts with
\name{Normal}
\alias{Normal}
\alias{dnorm}
\alias{pnorm}
\alias{qnorm}
\alias{rnorm}
Also, it is often convenient to have several different ways to refer to an R
object, and an \alias does not need to be the name of an object.
Note that the \name is not necessarily a topic documented, and if so desired it
needs to have an explicit \alias entry (as in this example).
\title{Title}
Title information for the Rd file. This should be capitalized and not end in a
period; try to limit its length to at most 65 characters for widest
compatibility.
Markup is supported in the text, but use of characters other than English text
and punctuation (e.g., ‘<’) may limit portability.
There must be one (and only one) \title section in a help file.
\description{…}
A short description of what the function(s) do(es) (one paragraph, a few
lines only). (If a description is too long and cannot easily be shortened, the
file probably tries to document too much at once.) This is mandatory except
for package-overview files.
\usage{fun(arg1, arg2, …)}
One or more lines showing the synopsis of the function(s) and variables
documented in the file. These are set in typewriter font. This is an R-like
command.
The usage information specified should match the function
definition exactly (such that automatic checking for consistency between
code and documentation is possible).
To indicate that a function can be used in several different ways, depending
on the named arguments specified, use section \details.
E.g., [Link] contains
\details{
Typical usages are
\preformatted{abline(a, b, ...)
......
}
Use \method{generic}{class} to indicate the name of an S3 method for the
generic function generic for objects inheriting from class "class". In the
printed versions, this will come out as generic (reflecting the understanding
that methods should not be invoked directly but via method dispatch),
but codoc() and other QC tools always have access to the full name.
For example, [Link] contains
\usage{
\method{print}{ts}(x, calendar, \dots)
}
which will print as
Usage:

## S3 method for class ‘ts’:

print(x, calendar, ...)
Usage for replacement functions should be given in the style of dim(x) <-
value rather than explicitly indicating the name of the replacement function
("dim<-" in the above). Similarly, one can use \method{generic}{class}
(arglist) <- value to indicate the usage of an S3 replacement method for
the generic replacement function "generic<-" for objects inheriting from
class "class".
Usage for S3 methods for extracting or replacing parts of an object, S3
methods for members of the Ops group, and S3 methods for user-defined
 (binary) infix operators (‘%xxx%’) follows the above rules, using the
appropriate function names. E.g., [Link] contains
\usage{
\method{[}{factor}(x, \dots, drop = FALSE)
\method{[[}{factor}(x, \dots)
\method{[}{factor}(x, \dots) <- value
}
which will print as
Usage:

## S3 method for class ‘factor’:

x[..., drop = FALSE]
## S3 method for class ‘factor’:
x[[...]]
## S3 replacement method for class ‘factor’:
x[...] <- value
\S3method is accepted as an alternative to \method.
\arguments{…}
Description of the function’s arguments, using an entry of the form
\item{arg_i}{Description of arg_i.}
for each element of the argument list. (Note that there is no whitespace
between the three parts of the entry.) There may be optional text outside
the \item entries, for example to give general information about groups of
parameters.
\details{…}
A detailed if possible precise description of the functionality provided,
extending the basic information in the \description slot.
\value{…}
Description of the function’s return value.
If a list with multiple values is returned, you can use entries of the form
\item{comp_i}{Description of comp_i.}
for each component of the list returned. Optional text may precede113 this list
(see for example the help for rle). Note that \value is implicitly a \
describe environment, so that environment should not be used for listing
components, just individual \item{}{} entries.
\references{…}
A section with references to the literature. Use \url{} or \href{}{} for web
pointers, and \doi{} for DOIs (this needs R >= 3.3, see User-defined
macros for more info).
\note{...}
Use this for a special note you want to have pointed out. Multiple \
note sections are allowed, but might be confusing to the end users.
 For example, [Link] contains
\note{
Pie charts are a very bad way of displaying information.
The eye is good at judging linear measures and bad at
judging relative areas.
......
}
\author{…}
Information about the author(s) of the Rd file. Use \email{} without extra
delimiters (such as ‘( )’ or ‘< >’) to specify email addresses, or \
url{} or \href{}{} for web pointers.
\seealso{…}
Pointers to related R objects, using \code{\link{...}} to refer to them (\
code is the correct markup for R object names, and \link produces
hyperlinks in output formats which support this. See Marking text,
and Cross-references).
\examples{…}
Examples of how to use the function. Code in this section is set in typewriter
font without reformatting and is run by example() unless marked otherwise
(see below).
Examples are not only useful for documentation purposes, but also provide
test code used for diagnostic checking of R code. By default, text inside \
examples{} will be displayed in the output of the help page and run
by example() and by R CMD check. You can use \dontrun{} for text that
should only be shown, but not run, and \dontshow{} for extra commands for
testing that should not be shown to users, but will be run by example().
(Previously this was called \testonly, and that is still accepted.)
Text inside \dontrun{} is ‘verbatim’, but the other parts of the \
examples section are R-like text.

For example,
x <- runif(10) # Shown and run.
\dontrun{plot(x)} # Only shown.
\dontshow{log(x)} # Only run.
Thus, example code not included in \dontrun must be executable! In
addition, it should not use any system-specific features or require special
facilities (such as Internet access or write permission to specific directories).
Text included in \dontrun is indicated by comments in the processed help
files: it need not be valid R code but the escapes must still be used
for %, \ and unpaired braces as in other ‘verbatim’ text.
Example code must be capable of being run by example, which uses source.
This means that it should not access stdin, e.g. to scan() data from the
example file.
 Data needed for making the examples executable can be obtained by random
number generation (for example, x <- rnorm(100)), or by using standard
data sets listed by data() (see ?data for more info).
Finally, there is \donttest, used (at the beginning of a separate line) to mark
code that should be run by example() but not by R CMD check (by default: the
option --run-donttest can be used). This should be needed only
occasionally but can be used for code which might fail in circumstances that
are hard to test for, for example in some locales. (Use
e.g. capabilities() or nzchar([Link]("someprogram")) to test for
features needed in the examples wherever possible, and you can also
use try() or tryCatch(). Use interactive() to condition examples which
need someone to interact with.) Note that code included in \donttest must
be correct R code, and any packages used should be declared in
the DESCRIPTION file. It is good practice to include a comment in the \
donttest section explaining why it is needed.

Output from code between comments

## IGNORE_RDIFF_BEGIN
## IGNORE_RDIFF_END
is ignored when comparing check output to reference output (a -
[Link] file). This markup can also be used for scripts
under tests.
\keyword{key}
There can be zero or more \keyword sections per file. Each \keyword section
should specify a single keyword, preferably one of the standard keywords as
listed in file KEYWORDS in the R documentation directory
(default R_HOME/doc). Use e.g. RShowDoc("KEYWORDS") to inspect the
standard keywords from within R. There can be more than one \
keyword entry if the R object being documented falls into more than one
category, or none.
Do strongly consider using \concept (see Indices) instead of \keyword if you
are about to use more than very few non-standard keywords.
The special keyword ‘internal’ marks a page of internal objects that are
not part of the package’s API. If the help page for object foo has keyword
‘internal’, then help(foo) gives this help page, but foo is excluded from
several object indices, including the alphabetical list of objects in
the HTML help system.
[Link]() can search by keyword, including user-defined values:
however the ‘Search Engine & Keywords’ HTML page
accessed via [Link]() provides single-click access only to a pre-defined
list of keywords.
Next: Documenting S4 classes and methods, Previous: Documenting functions,
Up: Rd format [Contents][Index]
2.1.2 Documenting data sets

The structure of Rd files which document R data sets is slightly different. Sections
such as \arguments and \value are not needed but the format and source of the data
should be explained.
As an example, let us look
at src/library/datasets/man/[Link] which documents the
standard R data set rivers.
\name{rivers}
\docType{data}
\alias{rivers}
\title{Lengths of Major North American Rivers}
\description{
This data set gives the lengths (in miles) of 141 \dQuote{major}
rivers in North America, as compiled by the US Geological
Survey.
}
\usage{rivers}
\format{A vector containing 141 observations.}
\source{World Almanac and Book of Facts, 1975, page 406.}
\references{
McNeil, D. R. (1977) \emph{Interactive Data Analysis}.
New York: Wiley.
}
\keyword{datasets}

This uses the following additional markup commands.

\docType{…}
Indicates the “type” of the documentation object. Always ‘data’ for data
sets, and ‘package’ for [Link] overview files.
Documentation for S4 methods and classes uses ‘methods’
(from promptMethods()) and ‘class’ (from promptClass()).
\format{…}
A description of the format of the data set (as a vector, matrix, data frame,
time series, …). For matrices and data frames this should give a description
of each column, preferably as a list or table. See Lists and tables, for more
information.
\source{…}
Details of the original source (a reference or URL, see Specifying URLs). In
addition, section \references could give secondary sources and usages.
Note also that when documenting data set bar,
  The \usage entry is always bar or (for packages which do not use lazy-
loading of data) data(bar). (In particular, only document a single data object
per Rd file.)
 The \keyword entry should always be ‘datasets’.
If bar is a data frame, documenting it as a data set can be initiated via prompt(bar).
Otherwise, the promptData function may be used.

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[Contents][Index]
2.1.3 Documenting S4 classes and methods

There are special ways to use the ‘?’ operator, namely ‘class?topic’ and
‘methods?topic’, to access documentation for S4 classes and methods,
respectively. This mechanism depends on conventions for the topic names used
in \alias entries. The topic names for S4 classes and methods respectively are of
the form
class-class
generic,signature_list-method
where signature_list contains the names of the classes in the signature of the
method (without quotes) separated by ‘,’ (without whitespace), with ‘ANY’ used
for arguments without an explicit specification. E.g., ‘genericFunction-
class’ is the topic name for documentation for the S4 class "genericFunction",
and ‘coerce,ANY,NULL-method’ is the topic name for documentation for the
S4 method for coerce for signature c("ANY", "NULL").
Skeletons of documentation for S4 classes and methods can be generated by using
the functions promptClass() and promptMethods() from package methods. If it is
necessary or desired to provide an explicit function declaration (in a \
usage section) for an S4 method (e.g., if it has “surprising arguments” to be
mentioned explicitly), one can use the special markup
\S4method{generic}{signature_list}(argument_list)
(e.g., ‘\S4method{coerce}{ANY,NULL}(from, to)’).
To make full use of the potential of the on-line documentation system, all user-
visible S4 classes and methods in a package should at least have a suitable \
alias entry in one of the package’s Rd files. If a package has methods for a
function defined originally somewhere else, and does not change the underlying
default method for the function, the package is responsible for documenting the
methods it creates, but not for the function itself or the default method.
An S4 replacement method is documented in the same way as an S3 one: see the
description of \method in Documenting functions.
See help("Documentation", package = "methods") for more information on using
and creating on-line documentation for S4 classes and methods.

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2.1.4 Documenting packages

Packages may have an overview help page with an \alias pkgname-package, e.g.
‘utils-package’ for the utils package, when package?pkgname will open that
help page. If a topic named pkgname does not exist in another Rd file, it is helpful to
use this as an additional \alias.
Skeletons of documentation for a package can be generated using the
function promptPackage(). If the final = LIBS argument is used, then the Rd file
will be generated in final form, containing the information that would be produced
up to library(help = pkgname). Otherwise (the default) comments will be inserted
giving suggestions for content.
Apart from the mandatory \name and \title and the pkgname-package alias, the
only requirement for the package overview page is that it include a \
docType{package} statement. All other content is optional. We suggest that it
should be a short overview, to give a reader unfamiliar with the package enough
information to get started. More extensive documentation is better placed into a
package vignette (see Writing package vignettes) and referenced from this page, or
into individual man pages for the functions, datasets, or classes.

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2.2 Sectioning
To begin a new paragraph or leave a blank line in an example, just insert an empty
line (as in (La)TeX). To break a line, use \cr.
In addition to the predefined sections (such as \description{}, \value{}, etc.), you
can “define” arbitrary ones by \section{section_title}{…}. For example
\section{Warning}{
You must not call this function unless …
}
For consistency with the pre-assigned sections, the section name (the first
argument to \section) should be capitalized (but not all upper case). Whitespace
between the first and second braced expressions is not allowed. Markup (e.g. \
code) within the section title may cause problems with the latex conversion
(depending on the version of macro packages such as ‘hyperref’) and so should
be avoided.
The \subsection macro takes arguments in the same format as \section, but is
used within a section, so it may be used to nest subsections within sections or other
subsections. There is no predefined limit on the nesting level, but formatting is not
designed for more than 3 levels (i.e. subsections within subsections within
sections).
Note that additional named sections are always inserted at a fixed position in the
output (before \note, \seealso and the examples), no matter where they appear in
the input (but in the same order amongst themselves as in the input).

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[Contents][Index]

2.3 Marking text

The following logical markup commands are available for emphasizing or quoting
text.
\emph{text}
\strong{text}
Emphasize text using italic and bold font if possible; \strong is regarded as
stronger (more emphatic).
\bold{text}
Set text in bold font where possible.
\sQuote{text}
\dQuote{text}
Portably single or double quote text (without hard-wiring the characters used
for quotation marks).
Each of the above commands takes LaTeX-like input, so other macros may be used
within text.
The following logical markup commands are available for indicating specific kinds
of text. Except as noted, these take ‘verbatim’ text input, and so other macros may
not be used within them. Some characters will need to be escaped (see Insertions).
\code{text}
Indicate text that is a literal example of a piece of an R program, e.g., a
fragment of R code or the name of an R object. Text is entered in R-like
syntax, and displayed using typewriter font where possible. Macros \
var and \link are interpreted within text.
\preformatted{text}
Indicate text that is a literal example of a piece of a program. Text is
displayed using typewriter font where possible. Formatting, e.g. line
breaks, is preserved. (Note that this includes a line break after the initial {,
so typically text should start on the same line as the command.)
 Due to limitations in LaTeX as of this writing, this macro may not be nested
within other markup macros other than \dQuote and \sQuote, as errors or bad
formatting may result.
\kbd{keyboard-characters}
Indicate keyboard input, using slanted typewriter font if possible, so users
can distinguish the characters they are supposed to type from computer
output. Text is entered ‘verbatim’.
\samp{text}
Indicate text that is a literal example of a sequence of characters, entered
‘verbatim’, to be included within word-wrapped text. Displayed within
single quotation marks and using typewriter font where possible.
\verb{text}
Indicate text that is a literal example of a sequence of characters, entered
‘verbatim’. No wrapping or reformatting will occur. Displayed
using typewriter font where possible.
\pkg{package_name}
Indicate the name of an R package. LaTeX-like.
\file{file_name}
Indicate the name of a file. Text is LaTeX-like, so backslash needs to be
escaped. Displayed using a distinct font where possible.
\email{email_address}
Indicate an electronic mail address. LaTeX-like, will be rendered as a
hyperlink in HTML and PDF conversion. Displayed using typewriter font
where possible.
\url{uniform_resource_locator}
Indicate a uniform resource locator (URL) for the World Wide Web. The
argument is handled as ‘verbatim’ text (with percent and braces escaped by
backslash), and rendered as a hyperlink in HTML and PDF conversion.
Linefeeds are removed, and leading and trailing whitespace114 is removed.
See Specifying URLs.
Displayed using typewriter font where possible.
\href{uniform_resource_locator}{text}
Indicate a hyperlink to the World Wide Web. The first argument is handled
as ‘verbatim’ text (with percent and braces escaped by backslash) and is
used as the URL in the hyperlink, with the second argument of LaTeX-like
text displayed to the user. Linefeeds are removed from the first argument,
and leading and trailing whitespace is removed.
Note that RFC3986-encoded URLs (e.g. using ‘%28VS.85%29’ in place of
‘(VS.85)’) may not work correctly in versions of R before 3.1.3 and are
best avoided—use URLdecode() to decode them.
\var{metasyntactic_variable}
Indicate a metasyntactic variable. In some cases this will be rendered
distinctly, e.g. in italic, but not in all115. LaTeX-like.
\env{environment_variable}
Indicate an environment variable. ‘Verbatim’. Displayed
using typewriter font where possible
\option{option}
Indicate a command-line option. ‘Verbatim’. Displayed
using typewriter font where possible.
\command{command_name}
Indicate the name of a command. LaTeX-like, so \var is interpreted.
Displayed using typewriter font where possible.
\dfn{term}
Indicate the introductory or defining use of a term. LaTeX-like.
\cite{reference}
Indicate a reference without a direct cross-reference via \link (see Cross-
references), such as the name of a book. LaTeX-like.
\acronym{acronym}
Indicate an acronym (an abbreviation written in all capital letters), such
as GNU. LaTeX-like.

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files [Contents][Index]

2.4 Lists and tables

The \itemize and \enumerate commands take a single argument, within which
there may be one or more \item commands. The text following each \item is
formatted as one or more paragraphs, suitably indented and with the first paragraph
marked with a bullet point (\itemize) or a number (\enumerate).
Note that unlike argument lists, \item in these formats is followed by a space and
the text (not enclosed in braces). For example
\enumerate{
\item A database consists of one or more records, each with one or
more named fields.
\item Regular lines start with a non-whitespace character.
\item Records are separated by one or more empty lines.
}
\itemize and \enumerate commands may be nested.
The \describe command is similar to \itemize but allows initial labels to be
specified. Each \item takes two arguments, the label and the body of the item, in
exactly the same way as an argument or value \item. \describe commands are
mapped to <DL> lists in HTML and \description lists in LaTeX.
Using these without any \items may cause problems with some conversions and
makes little sense.
The \tabular command takes two arguments. The first gives for each of the
columns the required alignment (‘l’ for left-justification, ‘r’ for right-justification
or ‘c’ for centring.) The second argument consists of an arbitrary number of lines
separated by \cr, and with fields separated by \tab. For example:
\tabular{rlll}{
[,1] \tab Ozone \tab numeric \tab Ozone (ppb)\cr
[,2] \tab Solar.R \tab numeric \tab Solar R (lang)\cr
[,3] \tab Wind \tab numeric \tab Wind (mph)\cr
[,4] \tab Temp \tab numeric \tab Temperature (degrees F)\cr
[,5] \tab Month \tab numeric \tab Month (1--12)\cr
[,6] \tab Day \tab numeric \tab Day of month (1--31)
}
There must be the same number of fields on each line as there are alignments in the
first argument, and they must be non-empty (but can contain only spaces). (There
is no whitespace between \tabular and the first argument, nor between the two
arguments.)

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[Contents][Index]

2.5 Cross-references
The markup \link{foo} (usually in the combination \code{\link{foo}}) produces
a hyperlink to the help for foo. Here foo is a topic, that is the argument of \
alias markup in another Rd file (possibly in another package). Hyperlinks are
supported in some of the formats to which Rd files are converted, for
example HTML and PDF, but ignored in others, e.g. the text format.
One main usage of \link is in the \seealso section of the help page, see Rd format.
Note that whereas leading and trailing spaces are stripped when extracting a topic
from a \alias, they are not stripped when looking up the topic of a \link.
You can specify a link to a different topic than its name by \link[=dest]
{name} which links to topic dest with name name. This can be used to refer to the
documentation for S3/4 classes, for example \code{"\link[=abc-class]
{abc}"} would be a way to refer to the documentation of an S4 class "abc" defined
in your package, and \code{"\link[=[Link]]{terms}"} to the
S3 "terms" class (in package stats). To make these easy to read in the source file, \
code{"\linkS4class{abc}"} expands to the form given above.
There are two other forms with an optional argument, specified as \link[pkg]
{foo} and \link[pkg:bar]{foo}, to link to topics foo and bar respectively in the
package pkg. They are currently only used in HTML help (and ignored for
hyperlinks in LaTeX conversions of help pages). One should be careful about
topics containing special characters (such as arithmetic operators) as they may
result in unresolvable links, and preferably use a safer alias in the same help page.
Historically (before R version 4.1.0), links of the form \link[pkg]{foo} and \
link[pkg:bar]{foo} used to be interpreted as links
to files [Link] and [Link] in package pkg, respectively. For this reason,
the HTML help system looks for file [Link] in package pkg if it does not find
topic foo, and then searches for the topic in other installed packages. To test that
links work both with both old and new systems, the pre-4.1.0 behaviour can be
restored by setting the environment variable _R_HELP_LINKS_TO_TOPICS_=false.
Packages referred to by these ‘other forms’ should be declared in
the DESCRIPTION file, in the ‘Depends’, ‘Imports’, ‘Suggests’ or
‘Enhances’ fields.

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[Contents][Index]

2.6 Mathematics
Mathematical formulae should be set beautifully for printed documentation yet we
still want something useful for text and HTML online help. To this end, the two
commands \eqn{latex}{ascii} and \deqn{latex}{ascii} are used. Whereas \
eqn is used for “inline” formulae (corresponding to TeX’s $…$), \deqn gives
“displayed equations” (as in LaTeX’s displaymath environment, or TeX’s $$…$$).
Both arguments are treated as ‘verbatim’ text.
Both commands can also be used as \eqn{latexascii} (only one argument) which
then is used for both latex and ascii. No whitespace is allowed between command
and the first argument, nor between the first and second arguments.
The following example is from [Link]:
\deqn{p(x) = \frac{\lambda^x e^{-\lambda}}{x!}}{%
p(x) = \lambda^x exp(-\lambda)/x!}
for \eqn{x = 0, 1, 2, \ldots}.
For text on-line help we get
p(x) = lambda^x exp(-lambda)/x!

for x = 0, 1, 2, ....
Greek letters (both cases) will be rendered in HTML if preceded by a backslash, \
dots and \ldots will be rendered as ellipses and \sqrt, \ge and \le as
mathematical symbols.
Note that only basic LaTeX can be used, there being no provision to specify
LaTeX style files such as the AMS extensions.

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2.7 Figures
To include figures in help pages, use the \figure markup. There are three forms.
The two commonly used simple forms are \figure{filename} and \
figure{filename}{alternate text}. This will include a copy of the figure in
either HTML or LaTeX output. In text output, the alternate text will be displayed
instead. (When the second argument is omitted, the filename will be used.) Both
the filename and the alternate text will be parsed verbatim, and should not include
special characters that are significant in HTML or LaTeX.
The expert form is \figure{filename}{options: string}. (The word ‘options:’
must be typed exactly as shown and followed by at least one space.) In this form,
the string is copied into the HTML img tag as attributes following the src attribute,
or into the second argument of the \Figure macro in LaTeX, which by default is
used as options to an \includegraphics call. As it is unlikely that any single string
would suffice for both display modes, the expert form would normally be wrapped
in conditionals. It is up to the author to make sure that legal HTML/LaTeX is used.
For example, to include a logo in both HTML (using the simple form) and LaTeX
(using the expert form), the following could be used:
\if{html}{\figure{[Link]}{options: width=100 alt="R logo"}}
\if{latex}{\figure{[Link]}{options: width=0.5in}}
The files containing the figures should be stored in the directory man/figures.
Files with extensions .jpg, .jpeg, .pdf, .png and .svg from that directory
will be copied to the help/figures directory at install time. (Figures in PDF
format will not display in most HTML browsers, but might be the best choice in
reference manuals.) Specify the filename relative to man/figures in the \
figure directive.

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[Index]

2.8 Insertions
Use \R for the R system itself. Use \dots for the dots in function argument lists ‘…’,
and \ldots for ellipsis dots in ordinary text.116 These can be followed by {}, and
should be unless followed by whitespace.
After an unescaped ‘%’, you can put your own comments regarding the help text.
The rest of the line (but not the newline at the end) will be completely disregarded.
Therefore, you can also use it to make part of the “help” invisible.
You can produce a backslash (‘\’) by escaping it by another backslash. (Note
that \cr is used for generating line breaks.)
The “comment” character ‘%’ and unpaired braces117 almost always need to be
escaped by ‘\’, and ‘\\’ can be used for backslash and needs to be when there are
two or more adjacent backslashes. In R-like code quoted strings are handled
slightly differently; see “Parsing Rd files” for details – in particular braces should
not be escaped in quoted strings.
All of ‘% { } \’ should be escaped in LaTeX-like text.
Text which might need to be represented differently in different encodings should
be marked by \enc, e.g. \enc{Jöreskog}{Joreskog} (with no whitespace between
the braces) where the first argument will be used where encodings are allowed and
the second should be ASCII (and is used for e.g. the text conversion in locales that
cannot represent the encoded form). (This is intended to be used for individual
words, not whole sentences or paragraphs.)

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documentation files [Contents][Index]

2.9 Indices
The \alias command (see Documenting functions) is used to specify the “topics”
documented, which should include all R objects in a package such as functions and
variables, data sets, and S4 classes and methods (see Documenting S4 classes and
methods). The on-line help system searches the index data base consisting of all
alias topics.
In addition, it is possible to provide “concept index entries” using \concept, which
can be used for [Link]() lookups. E.g., file [Link] in the standard
package stats contains
\concept{Kendall correlation coefficient}
\concept{Pearson correlation coefficient}
\concept{Spearman correlation coefficient}
so that e.g. ??Spearman will succeed in finding the help page for the test for
association between paired samples using Spearman’s rho.
(Note that [Link]() only uses “sections” of documentation objects with no
additional markup.)
Each \concept entry should give a single index term (word or phrase), and not use
any Rd markup.
If you want to cross reference such items from other help files via \link, you need
to use \alias and not \concept.

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2.10 Platform-specific documentation

Sometimes the documentation needs to differ by platform. Currently two OS-
specific options are available, ‘unix’ and ‘windows’, and lines in the help source
file can be enclosed in
#ifdef OS
...
#endif
or
#ifndef OS
...
#endif
for OS-specific inclusion or exclusion. Such blocks should not be nested, and
should be entirely within a block (that, is between the opening and closing brace of
a section or item), or at top-level contain one or more complete sections.
If the differences between platforms are extensive or the R objects documented are
only relevant to one platform, platform-specific Rd files can be put in
a unix or windows subdirectory.

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documentation files [Contents][Index]

2.11 Conditional text

Occasionally the best content for one output format is different from the best
content for another. For this situation, the \if{format}{text} or \ifelse{format}
{text}{alternate} markup is used. Here format is a comma separated list of
formats in which the text should be rendered. The alternate will be rendered if the
format does not match. Both text and alternate may be any sequence of text and
markup.
Currently the following formats are recognized: example, html, latex and text.
These select output for the corresponding targets. (Note that example refers to
extracted example code rather than the displayed example in some other format.)
Also accepted are TRUE (matching all formats) and FALSE (matching no formats).
These could be the output of the \Sexpr macro (see Dynamic pages).
The \out{literal} macro would usually be used within the text part of \
if{format}{text}. It causes the renderer to output the literal text exactly, with no
attempt to escape special characters. For example, use the following to output the
markup necessary to display the Greek letter in LaTeX or HTML, and the text
string alpha in other formats:
\ifelse{latex}{\out{$\alpha$}}{\ifelse{html}{\out{&alpha;}}{alpha}}

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documentation files [Contents][Index]

2.12 Dynamic pages

Two macros supporting dynamically generated man pages are \Sexpr and \RdOpts.
These are modelled after Sweave, and are intended to contain executable R
expressions in the Rd file.
The main argument to \Sexpr must be valid R code that can be executed. It may
also take options in square brackets before the main argument. Depending on the
options, the code may be executed at package build time, package install time, or
man page rendering time.
The options follow the same format as in Sweave, but different options are
supported. Currently the allowed options and their defaults are:
 eval=TRUE Whether the R code should be evaluated.
 echo=FALSE Whether the R code should be echoed. If TRUE, a display will be
given in a preformatted block. For example, \Sexpr[echo=TRUE]{ x <-
1 } will be displayed as
 > x <- 1
 [Link]=TRUE Whether to keep the author’s formatting when displaying
the code, or throw it away and use a deparsed version.
 results=text How should the results be displayed? The possibilities are:
 results=text Apply [Link]() to the result of the code, and
insert it as a text element.
 results=verbatim Print the results of the code just as if it was
executed at the console, and include the printed results verbatim.
(Invisible results will not print.)
 results=rd The result is assumed to be a character vector containing
markup to be passed to parse_Rd(), with the result inserted in place.
This could be used to insert computed aliases, for
 instance. parse_Rd() is called first with fragment = FALSE to allow a
single Rd section macro to be inserted. If that fails, it is called again
with fragment = TRUE, the older behavior.
 results=hide Insert no output.
 [Link]=true Remove leading and trailing blank lines in verbatim
output if [Link]=true (or TRUE). With [Link]=all, remove all
blank lines.
 stage=install Control when this macro is run. Possible values are
 stage=build The macro is run when building a source tarball.
 stage=install The macro is run when installing from source.
 stage=render The macro is run when displaying the help page.
Conditionals such as #ifdef (see Platform-specific documentation) are
applied after the build macros but before the install macros. In some
situations (e.g. installing directly from a source directory without a tarball,
or building a binary package) the above description is not literally accurate,
but authors can rely on the sequence being build, #ifdef, install, render,
with all stages executed.
Code is only run once in each stage, so a \Sexpr[results=rd] macro can
output an \Sexpr macro designed for a later stage, but not for the current one
or any earlier stage.
 width, height, fig These options are currently allowed but ignored.
The \RdOpts macro is used to set new defaults for options to apply to following
uses of \Sexpr.
For more details, see the online document “Parsing Rd files”.

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2.13 User-defined macros

The \newcommand and \renewcommand macros allow new macros to be defined within
an Rd file. These are similar but not identical to the same-named LaTeX macros.
They each take two arguments which are parsed verbatim. The first is the name of
the new macro including the initial backslash, and the second is the macro
definition. As in LaTeX, \newcommand requires that the new macro not have been
previously defined, whereas \renewcommand allows existing macros (including all
built-in ones) to be replaced. (This test is disabled by default, but may be enabled
by setting the environment variable _R_WARN_DUPLICATE_RD_MACROS_ to a true value.)
Also as in LaTeX, the new macro may be defined to take arguments, and numeric
placeholders such as #1 are used in the macro definition. However, unlike LaTeX,
the number of arguments is determined automatically from the highest placeholder
number seen in the macro definition. For example, a macro definition
containing #1 and #3 (but no other placeholders) will define a three argument
macro (whose second argument will be ignored). As in LaTeX, at most 9
arguments may be defined. If the # character is followed by a non-digit it will have
no special significance. All arguments to user-defined macros will be parsed as
verbatim text, and simple text-substitution will be used to replace the place-
holders, after which the replacement text will be parsed.
A number of macros are defined in the file share/Rd/macros/[Link] of
the R source or home directory, and these will normally be available in
all .Rd files. For example, that file contains the definition
\newcommand{\PR}{\Sexpr[results=rd]{tools:::Rd_expr_PR(#1)}}
which defines \PR to be a single argument macro; then code (typically used in
the [Link] file) like
\PR{1234}
will expand to
\Sexpr[results=rd]{tools:::Rd_expr_PR(1234)}
when parsed.
Some macros that might be of general use are:
\CRANpkg{pkg}
A package on CRAN
\sspace
A single space (used after a period that does not end a sentence).
\doi{numbers}
A digital object identifier (DOI).
See the [Link] file in share/Rd/macros for more details and macro
definitions, including macros \packageTitle, \packageDescription, \
packageAuthor, \packageMaintainer, \packageDESCRIPTION and \packageIndices.

Packages may also define their own common macros; these would be stored in
an .Rd file in man/macros in the package source and will be installed
into help/macros when the package is installed. A package may also use the
macros from a different package by listing the other package in the ‘RdMacros’
field in the DESCRIPTION file.

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R documentation files [Contents][Index]

2.14 Encoding
Rd files are text files and so it is impossible to deduce the encoding they are
written in unless ASCII: files with 8-bit characters could be UTF-8, Latin-1, Latin-
9, KOI8-R, EUC-JP, etc. So an \encoding{} section must be used to specify the
encoding if it is not ASCII. (The \encoding{} section must be on a line by itself,
and in particular one containing no non-ASCII characters. The encoding declared
in the DESCRIPTION file will be used if none is declared in the file.) The Rd files
are converted to UTF-8 before parsing and so the preferred encoding for the files
themselves is now UTF-8.
Wherever possible, avoid non-ASCII chars in Rd files, and even symbols such as
‘<’, ‘>’, ‘$’, ‘^’, ‘&’, ‘|’, ‘@’, ‘~’, and ‘*’ outside ‘verbatim’ environments (since
they may disappear in fonts designed to render text).
(Function showNonASCIIfile in package tools can help in finding non-ASCII bytes
in the files.)
For convenience, encoding names ‘latin1’ and ‘latin2’ are always
recognized: these and ‘UTF-8’ are likely to work fairly widely. However, this
does not mean that all characters in UTF-8 will be recognized, and the coverage of
non-Latin characters118 is fairly low. Using LaTeX inputenx (see ?Rd2pdf in R) will
give greater coverage of UTF-8.
The \enc command (see Insertions) can be used to provide transliterations which
will be used in conversions that do not support the declared encoding.
The LaTeX conversion converts the file to UTF-8 from the declared encoding, and
includes a
\inputencoding{utf8}
command, and this needs to be matched by a suitable invocation of the \
usepackage{inputenc} command. The R utility R CMD Rd2pdf looks at the converted
code and includes the encodings used: it might for example use
\usepackage[utf8]{inputenc}
(Use of utf8 as an encoding requires LaTeX dated 2003/12/01 or later. Also, the
use of Cyrillic characters in ‘UTF-8’ appears to also need ‘\
usepackage[T2A]{fontenc}’, and R CMD Rd2pdf includes this conditionally
on the file [Link] being present and environment
variable _R_CYRILLIC_TEX_ being set.)
Note that this mechanism works best with Latin letters: the coverage of UTF-8 in
LaTeX is quite low.

Next: Editing Rd files, Previous: Encoding, Up: Writing R documentation files

[Contents][Index]

2.15 Processing documentation files

There are several commands to process Rd files from the system command line.
Using R CMD Rdconv one can convert R documentation format to other formats, or
extract the executable examples for run-time testing. The currently supported
conversions are to plain text, HTML and LaTeX as well as extraction of the
examples.
R CMD Rd2pdf generates PDF output from documentation in Rd files, which can be
specified either explicitly or by the path to a directory with the sources of a
package. In the latter case, a reference manual for all documented objects in the
package is created, including the information in the DESCRIPTION files.
R CMD Sweave and R CMD Stangle process vignette-like documentation files (e.g.
Sweave vignettes with extension ‘.Snw’ or ‘.Rnw’, or other non-Sweave
vignettes). R CMD Stangle is used to extract the R code fragments.
The exact usage and a detailed list of available options for all of these commands
can be obtained by running R CMD command --help, e.g., R CMD Rdconv --help. All
available commands can be listed using R --help (or Rcmd --help under Windows).
All of these work under Windows. You may need to have installed the the tools to
build packages from source as described in the “R Installation and Administration”
manual, although typically all that is needed is a LaTeX installation.

Previous: Processing documentation files, Up: Writing R documentation files

[Contents][Index]

2.16 Editing Rd files

It can be very helpful to prepare .Rd files using a editor which knows about their
syntax and will highlight commands, indent to show the structure and detect mis-
matched braces, and so on.
The system most commonly used for this is some version
of Emacs (including XEmacs) with the ESS package ([Link] it is
often is installed with Emacs but may need to be loaded, or even installed,
separately).
Another is the Eclipse IDE with the Stat-ET plugin
([Link] and (on Windows only) Tinn-R
([Link]
People have also used LaTeX mode in a editor, as .Rd files are rather similar to
LaTeX files.
Some R front-ends provide editing support for .Rd files, for example RStudio
([Link]
Next: Debugging, Previous: Writing R documentation files, Up: Writing R
Extensions [Contents][Index]

3 Tidying and profiling R code

R code which is worth preserving in a package and perhaps making available for
others to use is worth documenting, tidying up and perhaps optimizing. The last
two of these activities are the subject of this chapter.
 Tidying R code
 Profiling R code for speed
 Profiling R code for memory use
 Profiling compiled code

Next: Profiling R code for speed, Previous: Tidying and profiling R code,
Up: Tidying and profiling R code [Contents][Index]

3.1 Tidying R code

R treats function code loaded from packages and code entered by users differently.
By default code entered by users has the source code stored internally, and when
the function is listed, the original source is reproduced. Loading code from a
package (by default) discards the source code, and the function listing is re-created
from the parse tree of the function.
Normally keeping the source code is a good idea, and in particular it avoids
comments being removed from the source. However, we can make use of the
ability to re-create a function listing from its parse tree to produce a tidy version of
the function, for example with consistent indentation and spaces around operators.
If the original source does not follow the standard format this tidied version can be
much easier to read.
We can subvert the keeping of source in two ways.
1. The option [Link] can be set to FALSE before the code is loaded into R.
2. The stored source code can be removed by calling
the removeSource() function, for example by
3. myfun <- removeSource(myfun)
In each case if we then list the function we will get the standard layout.
Suppose we have a file of functions myfuns.R that we want to tidy up. Create a
file tidy.R containing
source("myfuns.R", [Link] = FALSE)
dump(ls([Link] = TRUE), file = "[Link].R")
and run R with this as the source file, for example by R --vanilla < tidy.R or by
pasting into an R session. Then the file [Link].R will contain the
functions in alphabetical order in the standard layout. Warning: comments in your
functions will be lost.
The standard format provides a good starting point for further tidying. Although
the deparsing cannot do so, we recommend the consistent use of the preferred
assignment operator ‘<-’ (rather than ‘=’) for assignment. Many package authors
use a version of Emacs (on a Unix-alike or Windows) to edit R code, using the
ESS[S] mode of the ESS Emacs package. See R coding standards in R Internals for
style options within the ESS[S] mode recommended for the source code of R itself.

Next: Profiling R code for memory use, Previous: Tidying R code, Up: Tidying
and profiling R code [Contents][Index]

3.2 Profiling R code for speed

It is possible to profile R code on Windows and most119 Unix-alike versions of R.
The command Rprof is used to control profiling, and its help page can be consulted
for full details. Profiling works by recording at fixed intervals120 (by default every
20 msecs) which line in which R function is being used, and recording the results
in a file (default [Link] in the working directory). Then the
function summaryRprof or the command-line utility R CMD Rprof [Link] can be
used to summarize the activity.
As an example, consider the following code (from Venables & Ripley, 2002, pp.
225–6).
library(MASS); library(boot)
[Link] <- nls(Time ~ b*Viscosity/(Wt - c), stormer,
start = c(b=30.401, c=2.2183))
st <- cbind(stormer, fit=fitted([Link]))
[Link] <- function(rs, i) {
st$Time <- st$fit + rs[i]
tmp <- nls(Time ~ (b * Viscosity)/(Wt - c), st,
start = coef([Link]))
tmp$m$getAllPars()
}
rs <- scale(resid([Link]), scale = FALSE) # remove the mean
Rprof("[Link]")
[Link] <- boot(rs, [Link], R = 4999) # slow enough to profile
Rprof(NULL)
Having run this we can summarize the results by
R CMD Rprof [Link]

Each sample represents 0.02 seconds.

Total run time: 22.52 seconds.

Total seconds: time spent in function and callees.

Self seconds: time spent in function alone.
 % total % self
total seconds self seconds name
100.0 25.22 0.2 0.04 "boot"
99.8 25.18 0.6 0.16 "statistic"
96.3 24.30 4.0 1.02 "nls"
33.9 8.56 2.2 0.56 "<Anonymous>"
32.4 8.18 1.4 0.36 "eval"
31.8 8.02 1.4 0.34 ".Call"
28.6 7.22 0.0 0.00 "[Link]"
28.5 7.18 0.3 0.08 "[Link]"
28.1 7.10 3.5 0.88 "[Link]"
17.4 4.38 0.7 0.18 "sapply"
15.0 3.78 3.2 0.80 "nlsModel"
12.5 3.16 1.8 0.46 "lapply"
12.3 3.10 2.7 0.68 "assign"
...

% self % total
self seconds total seconds name
5.7 1.44 7.5 1.88 "inherits"
4.0 1.02 96.3 24.30 "nls"
3.6 0.92 3.6 0.92 "$"
3.5 0.88 28.1 7.10 "[Link]"
3.2 0.80 15.0 3.78 "nlsModel"
2.8 0.70 9.8 2.46 "[Link]"
2.7 0.68 12.3 3.10 "assign"
2.5 0.64 2.5 0.64 ".Fortran"
2.5 0.62 7.1 1.80 "[Link]"
2.2 0.56 33.9 8.56 "<Anonymous>"
2.1 0.54 5.9 1.48 "unlist"
2.1 0.52 7.9 2.00 "FUN"
...
This often produces surprising results and can be used to identify bottlenecks or
pieces of R code that could benefit from being replaced by compiled code.
Two warnings: profiling does impose a small performance penalty, and the output
files can be very large if long runs are profiled at the default sampling interval.
Profiling short runs can sometimes give misleading results. R from time to time
performs garbage collection to reclaim unused memory, and this takes an
appreciable amount of time which profiling will charge to whichever function
happens to provoke it. It may be useful to compare profiling code immediately
after a call to gc() with a profiling run without a preceding call to gc.
More detailed analysis of the output can be achieved by the tools in
the CRAN packages proftools and profr: in particular these allow call graphs to
be studied.

Next: Profiling compiled code, Previous: Profiling R code for speed, Up: Tidying
and profiling R code [Contents][Index]

3.3 Profiling R code for memory use

Measuring memory use in R code is useful either when the code takes more
memory than is conveniently available or when memory allocation and copying of
objects is responsible for slow code. There are three ways to profile memory use
over time in R code. The second and third require R to have been compiled
with --enable-memory-profiling, which is not the default, but is
currently used for the macOS and Windows binary distributions. All can be
misleading, for different reasons.
In understanding the memory profiles it is useful to know a little more about R’s
memory allocation. Looking at the results of gc() shows a division of memory
into Vcells used to store the contents of vectors and Ncells used to store
everything else, including all the administrative overhead for vectors such as type
and length information. In fact the vector contents are divided into two pools.
Memory for small vectors (by default 128 bytes or less) is obtained in large chunks
and then parcelled out by R; memory for larger vectors is obtained directly from
the operating system.
Some memory allocation is obvious in interpreted code, for example,
y <- x + 1
allocates memory for a new vector y. Other memory allocation is less obvious and
occurs because R is forced to make good on its promise of ‘call-by-value’ argument
passing. When an argument is passed to a function it is not immediately copied.
Copying occurs (if necessary) only when the argument is modified. This can lead
to surprising memory use. For example, in the ‘survey’ package we have
[Link] <- function (x, ...)
{
print(x$[Link], varnames = FALSE, [Link] = FALSE, ...)
x$call <- x$printcall
NextMethod()
}
It may not be obvious that the assignment to x$call will cause the entire object x to
be copied. This copying to preserve the call-by-value illusion is usually done by
the internal C function duplicate.
The main reason that memory-use profiling is difficult is garbage collection.
Memory is allocated at well-defined times in an R program, but is freed whenever
the garbage collector happens to run.
 Memory statistics from Rprof
 Tracking memory allocations
 Tracing copies of an object

Next: Tracking memory allocations, Previous: Profiling R code for memory use,
Up: Profiling R code for memory use [Contents][Index]
3.3.1 Memory statistics from Rprof
The sampling profiler Rprof described in the previous section can be given the
option [Link]=TRUE. It then writes out the total R memory allocation in
small vectors, large vectors, and cons cells or nodes at each sampling interval. It
also writes out the number of calls to the internal function duplicate, which is
called to copy R objects. summaryRprof provides summaries of this information.
The main reason that this can be misleading is that the memory use is attributed to
the function running at the end of the sampling interval. A second reason is that
garbage collection can make the amount of memory in use decrease, so a function
appears to use little memory. Running under gctorture helps with both problems:
it slows down the code to effectively increase the sampling frequency and it makes
each garbage collection release a smaller amount of memory.

Next: Tracing copies of an object, Previous: Memory statistics from Rprof,

Up: Profiling R code for memory use [Contents][Index]
3.3.2 Tracking memory allocations

The second method of memory profiling uses a memory-allocation

profiler, Rprofmem(), which writes out a stack trace to an output file every time a
large vector is allocated (with a user-specified threshold for ‘large’) or a new page
of memory is allocated for the R heap. Summary functions for this output are still
being designed.
Running the example from the previous section with
> Rprofmem("[Link]",threshold=1000)
> [Link] <- boot(rs, [Link], R = 4999)
> Rprofmem(NULL)
shows that apart from some initial and final work in boot there are no vector
allocations over 1000 bytes.

Previous: Tracking memory allocations, Up: Profiling R code for memory use
[Contents][Index]
3.3.3 Tracing copies of an object

The third method of memory profiling involves tracing copies made of a specific
(presumably large) R object. Calling tracemem on an object marks it so that a
message is printed to standard output when the object is copied via duplicate or
coercion to another type, or when a new object of the same size is created in
arithmetic operations. The main reason that this can be misleading is that copying
of subsets or components of an object is not tracked. It may be helpful to
use tracemem on these components.
In the example above we can run tracemem on the data frame st
> tracemem(st)
[1] "<0x9abd5e0>"
> [Link] <- boot(rs, [Link], R = 4)
memtrace[0x9abd5e0->0x92a6d08]: statistic boot
memtrace[0x92a6d08->0x92a6d80]: $<-.[Link] $<- statistic boot
memtrace[0x92a6d80->0x92a6df8]: $<-.[Link] $<- statistic boot
memtrace[0x9abd5e0->0x9271318]: statistic boot
memtrace[0x9271318->0x9271390]: $<-.[Link] $<- statistic boot
memtrace[0x9271390->0x9271408]: $<-.[Link] $<- statistic boot
memtrace[0x9abd5e0->0x914f558]: statistic boot
memtrace[0x914f558->0x914f5f8]: $<-.[Link] $<- statistic boot
memtrace[0x914f5f8->0x914f670]: $<-.[Link] $<- statistic boot
memtrace[0x9abd5e0->0x972cbf0]: statistic boot
memtrace[0x972cbf0->0x972cc68]: $<-.[Link] $<- statistic boot
memtrace[0x972cc68->0x972cd08]: $<-.[Link] $<- statistic boot
memtrace[0x9abd5e0->0x98ead98]: statistic boot
memtrace[0x98ead98->0x98eae10]: $<-.[Link] $<- statistic boot
memtrace[0x98eae10->0x98eae88]: $<-.[Link] $<- statistic boot
The object is duplicated fifteen times, three times for each of the R+1 calls
to [Link]. This is surprising, since none of the duplications happen inside nls.
Stepping through [Link] in the debugger shows that all three happen in the line
st$Time <- st$fit + rs[i]
Data frames are slower than matrices and this is an example of why.
Using tracemem(st$Viscosity) does not reveal any additional copying.

Previous: Profiling R code for memory use, Up: Tidying and profiling R code
[Contents][Index]

3.4 Profiling compiled code

Profiling compiled code is highly system-specific, but this section contains some
hints gleaned from various R users. Some methods need to be different for a
compiled executable and for dynamic/shared libraries/objects as used by R
packages. We know of no good way to profile DLLs on Windows.
This chapter is based on reports from users and the information may not be current.
 Linux
 macOS

Next: macOS, Previous: Profiling compiled code, Up: Profiling compiled code
[Contents][Index]
3.4.1 Linux

Options include using sprof for a shared object,

and oprofile (see [Link]
and perf (see [Link] for any executable or
shared object. These seem less widely supplied than they used to be (for example
Fedora 36 only has perf).
  oprofile and operf
 sprof
[Link] oprofile and operf

The oprofile project has two modes of operation. In what is now called ‘legacy’
mode, it is uses a daemon to collect information on a process (see below). Since
version 0.9.8 (August 2012), the preferred mode is to use operf, so we discuss that
first. The modes differ in how the profiling data is collected: it is analysed by tools
such as opreport and oppannote in both.
Here is an example on x86_64 Linux using R 3.0.2. File pvec.R contains the part
of the examples from pvec in package parallel:
library(parallel)
N <- 1e6
dates <- sprintf('%04d-%02d-%02d', [Link](2000+rnorm(N)),
[Link](runif(N, 1, 12)), [Link](runif(N, 1, 28)))
[Link](a <- [Link](dates, format = "%Y-%m-%d"))
with timings from the final step
user system elapsed
0.371 0.237 0.612
R-level profiling by Rprof shows
[Link] [Link] [Link] [Link]
"strptime" 1.70 41.06 1.70 41.06
"[Link]" 1.40 33.82 1.42 34.30
"sprintf" 0.74 17.87 0.98 23.67
...
so the conversion from character to POSIXlt takes most of the time.
This can be run under operf and analysed by
operf R -f pvec.R
opreport
opreport -l /path/to/R_HOME/bin/exec/R
opannotate --source /path/to/R_HOME/bin/exec/R
## And for the system time
opreport -l /lib64/[Link].6
The first report shows where (which library etc) the time was spent:
CPU_CLK_UNHALT...|
samples| %|
------------------
166761 99.9161 Rdev
CPU_CLK_UNHALT...|
samples| %|
------------------
70586 42.3276 no-vmlinux
56963 34.1585 [Link]
36922 22.1407 R
1584 0.9499 [Link]
624 0.3742 [Link]
...
The rest of the output is voluminous, and only extracts are shown below.
Most of the time within R is spent in
samples % image name symbol name
10397 28.5123 R R_gc_internal
5683 15.5848 R do_sprintf
3036 8.3258 R do_asPOSIXct
2427 6.6557 R do_strptime
2421 6.6392 R Rf_mkCharLenCE
1480 4.0587 R w_strptime_internal
1202 3.2963 R Rf_qnorm5
1165 3.1948 R unif_rand
675 1.8511 R mktime0
617 1.6920 R makelt
617 1.6920 R validate_tm
584 1.6015 R day_of_the_week
...
opannotate shows that 31% of the time in R is spent in memory.c, 21%
in datetime.c and 7% in Rstrptime.h. The analysis for libc showed that
calls to wcsftime dominated, so those calls were cached for R 3.0.3: the time spent
in no-vmlinux (the kernel) was reduced dramatically.
On platforms which support it, call graphs can be produced by opcontrol --
callgraph if collected via operf --callgraph.

The profiling data is by default stored in sub-directory oprofile_data of the

current directory, which can be removed at the end of the session.
Another way to use this is to run operf -s as root, run the R session in another
terminal then shut down operf and analyse as above.
Another example, from sm version 2.2-5.4. The example for [Link] took a
long time:
[Link](example([Link]))
...
user system elapsed
5.543 3.202 8.785
including a lot of system time. Profiling just the slow part, the second plot, showed
samples| %|
------------------
381845 99.9885 R
CPU_CLK_UNHALT...|
samples| %|
------------------
187484 49.0995 [Link]
169627 44.4230 no-vmlinux
12636 3.3092 [Link].3.0.0
6455 1.6905 R
so the system time was almost all in the Linux kernel. It is possible to dig deeper if
you have a matching uncompressed kernel with debug symbols to specify via --
vmlinux: we did not.
In ‘legacy’ mode oprofile works by running a daemon which collects information.
The daemon must be started as root, e.g.
% su
% opcontrol --no-vmlinux
% (optional, some platforms) opcontrol --callgraph=5
% opcontrol --start
% exit
Then as a user
% R
... run the boot example
% opcontrol --dump
% opreport -l /path/to/R_HOME/library/stats/libs/[Link]
...
samples % symbol name
1623 75.5939 anonymous symbol from section .plt
349 16.2552 numeric_deriv
113 5.2632 nls_iter
62 2.8878 getListElement
% opreport -l /path/to/R_HOME/bin/exec/R
...
samples % symbol name
76052 11.9912 Rf_eval
54670 8.6198 Rf_findVarInFrame3
37814 5.9622 Rf_allocVector
31489 4.9649 Rf_duplicate
28221 4.4496 Rf_protect
26485 4.1759 Rf_cons
23650 3.7289 Rf_matchArgs
21088 3.3250 Rf_findFun
19995 3.1526 findVarLocInFrame
14871 2.3447 Rf_evalList
13794 2.1749 R_Newhashpjw
13522 2.1320 R_gc_internal
...
Shutting down the profiler and clearing the records needs to be done as root.
[Link] sprof

You can select shared objects to be profiled with sprof by setting the environment
variable LD_PROFILE. For example
% setenv LD_PROFILE /path/to/R_HOME/library/stats/libs/[Link]
R
... run the boot example
% sprof /path/to/R_HOME/library/stats/libs/[Link] \
/var/tmp/path/to/R_HOME/library/stats/libs/[Link]

Flat profile:

Each sample counts as 0.01 seconds.

% cumulative self self total
time seconds seconds calls us/call us/call name
76.19 0.32 0.32 0 0.00 numeric_deriv
16.67 0.39 0.07 0 0.00 nls_iter
7.14 0.42 0.03 0 0.00 getListElement

rm /var/tmp/path/to/R_HOME/library/stats/libs/[Link]
... to clean up ...
It is possible that root access is needed to create the directories used for the profile
data.

Previous: Linux, Up: Profiling compiled code [Contents][Index]

3.4.2 macOS

Developers have recommended sample (or [Link], which is a GUI

version), Shark (in version of Xcode up to those for Snow Leopard),
and Instruments (part of Xcode,
see [Link]

Next: System and foreign language interfaces, Previous: Tidying and profiling R
code, Up: Writing R Extensions [Contents][Index]

4 Debugging
This chapter covers the debugging of R extensions, starting with the ways to get
useful error information and moving on to how to deal with errors that crash R.
 Browsing
 Debugging R code
 Checking memory access
 Debugging compiled code
 Using Link-time Optimization

Next: Debugging R code, Previous: Debugging, Up: Debugging [Contents]

[Index]

4.1 Browsing
Most of the R-level debugging facilities are based around the built-in browser. This
can be used directly by inserting a call to browser() into the code of a function (for
example, using fix(my_function) ). When code execution reaches that point in the
function, control returns to the R console with a special prompt. For example
> fix([Link]) ## insert browser() call after for() loop
> summary(women)
Called from: [Link](women)
Browse[1]> ls()
[1] "digits" "i" "lbs" "lw" "maxsum" "nm" "nr" "nv"
[9] "object" "sms" "z"
Browse[1]> maxsum
[1] 7
Browse[1]>
 height weight
Min. :58.0 Min. :115.0
1st Qu.:61.5 1st Qu.:124.5
Median :65.0 Median :135.0
Mean :65.0 Mean :136.7
3rd Qu.:68.5 3rd Qu.:148.0
Max. :72.0 Max. :164.0
> rm([Link])
At the browser prompt one can enter any R expression, so for example ls() lists
the objects in the current frame, and entering the name of an object will121 print it.
The following commands are also accepted
 n
Enter ‘step-through’ mode. In this mode, hitting return executes the next line
of code (more precisely one line and any continuation lines). Typing c will
continue to the end of the current context, e.g. to the end of the current loop
or function.
 c
In normal mode, this quits the browser and continues execution, and just
return works in the same way. cont is a synonym.
 where
This prints the call stack. For example
> summary(women)
Called from: [Link](women)
Browse[1]> where
where 1: [Link](women)
where 2: summary(women)

Browse[1]>
 Q
Quit both the browser and the current expression, and return to the top-level
prompt.
Errors in code executed at the browser prompt will normally return control to the
browser prompt. Objects can be altered by assignment, and will keep their changed
values when the browser is exited. If really necessary, objects can be assigned to
the workspace from the browser prompt (by using <<- if the name is not already in
scope).

Next: Checking memory access, Previous: Browsing, Up: Debugging [Contents]

[Index]

4.2 Debugging R code

Suppose your R program gives an error message. The first thing to find out is what
R was doing at the time of the error, and the most useful tool is traceback(). We
suggest that this is run whenever the cause of the error is not immediately obvious.
Errors are often reported to the R mailing lists as being in some package
when traceback() would show that the error was being reported by some other
package or base R. Here is an example from the regression suite.
> success <- c(13,12,11,14,14,11,13,11,12)
> failure <- c(0,0,0,0,0,0,0,2,2)
> resp <- cbind(success, failure)
> predictor <- c(0, 5^(0:7))
> glm(resp ~ 0+predictor, family = binomial(link="log"))
Error: no valid set of coefficients has been found: please supply starting
values
> traceback()
3: stop("no valid set of coefficients has been found: please supply
starting values", call. = FALSE)
2: [Link](x = X, y = Y, weights = weights, start = start, etastart =
etastart,
mustart = mustart, offset = offset, family = family, control =
control,
intercept = attr(mt, "intercept") > 0)
1: glm(resp ~ 0 + predictor, family = binomial(link ="log"))
The calls to the active frames are given in reverse order (starting with the
innermost). So we see the error message comes from an explicit check in [Link].
(traceback() shows you all the lines of the function calls, which can be limited by
setting option "[Link]".)
Sometimes the traceback will indicate that the error was detected inside compiled
code, for example (from ?nls)
Error in nls(y ~ a + b * x, start = list(a = 0.12345, b = 0.54321), trace =
TRUE) :
step factor 0.000488281 reduced below ‘minFactor’ of 0.000976563
> traceback()
2: .Call(R_nls_iter, m, ctrl, trace)
1: nls(y ~ a + b * x, start = list(a = 0.12345, b = 0.54321), trace = TRUE)
This will be the case if the innermost call is
to .C, .Fortran, .Call, .External or .Internal, but as it is also possible for such
code to evaluate R expressions, this need not be the innermost call, as in
> traceback()
9: gm(a, b, x)
8: .Call(R_numeric_deriv, expr, theta, rho, dir)
7: numericDeriv(form[[3]], names(ind), env)
6: getRHS()
5: assign("rhs", getRHS(), envir = thisEnv)
4: assign("resid", .swts * (lhs - assign("rhs", getRHS(), envir =
thisEnv)),
envir = thisEnv)
3: function (newPars)
{
setPars(newPars)
assign("resid", .swts * (lhs - assign("rhs", getRHS(), envir =
thisEnv)),
envir = thisEnv)
assign("dev", sum(resid^2), envir = thisEnv)
assign("QR", qr(.swts * attr(rhs, "gradient")), envir = thisEnv)
return(QR$rank < min(dim(QR$qr)))
}(c(-0.00760232418963883, 1.00119632515036))
2: .Call(R_nls_iter, m, ctrl, trace)
1: nls(yeps ~ gm(a, b, x), start = list(a = 0.12345, b = 0.54321))
Occasionally traceback() does not help, and this can be the case if S4 method
dispatch is involved. Consider the following example
> xyd <- new("xyloc", x=runif(20), y=runif(20))
Error in [Link](pkg) : no item called "package:S4nswv"
on the search list
Error in initialize(value, ...) : S language method selection got
an error when called from internal dispatch for function ‘initialize’
> traceback()
2: initialize(value, ...)
1: new("xyloc", x = runif(20), y = runif(20))
which does not help much, as there is no call to [Link] in initialize (and
the note “called from internal dispatch” tells us so). In this case we searched the R
sources for the quoted call, which occurred in only one
place, methods:::.asEnvironmentPackage. So now we knew where the error was
occurring. (This was an unusually opaque example.)
The error message
evaluation nested too deeply: infinite recursion / options(expressions=)?
can be hard to handle with the default value (5000). Unless you know that there
actually is deep recursion going on, it can help to set something like
options(expressions=500)
and re-run the example showing the error.
Sometimes there is warning that clearly is the precursor to some later error, but it is
not obvious where it is coming from. Setting options(warn = 2) (which turns
warnings into errors) can help here.
Once we have located the error, we have some choices. One way to proceed is to
find out more about what was happening at the time of the crash by looking a post-
mortem dump. To do so, set options(error=[Link]) and run the code again.
Then invoke debugger() and explore the dump. Continuing our example:
> options(error = [Link])
> glm(resp ~ 0 + predictor, family = binomial(link ="log"))
Error: no valid set of coefficients has been found: please supply starting
values
which is the same as before, but an object called [Link] has appeared in the
workspace. (Such objects can be large, so remove it when it is no longer needed.)
We can examine this at a later time by calling the function debugger.
> debugger()
Message: Error: no valid set of coefficients has been found: please supply
starting values
Available environments had calls:
1: glm(resp ~ 0 + predictor, family = binomial(link = "log"))
2: [Link](x = X, y = Y, weights = weights, start = start, etastart =
etastart, mus
3: stop("no valid set of coefficients has been found: please supply
starting values
Enter an environment number, or 0 to exit Selection:
which gives the same sequence of calls as traceback, but in outer-first order and
with only the first line of the call, truncated to the current width. However, we can
now examine in more detail what was happening at the time of the error. Selecting
an environment opens the browser in that frame. So we select the function call
which spawned the error message, and explore some of the variables (and execute
two function calls).
Enter an environment number, or 0 to exit Selection: 2
Browsing in the environment with call:
[Link](x = X, y = Y, weights = weights, start = start, etas
Called from: [Link](ind)
Browse[1]> ls()
[1] "aic" "boundary" "coefold" "control" "conv"
[6] "dev" "[Link]" "devold" "EMPTY" "eta"
[11] "etastart" "family" "fit" "good" "intercept"
[16] "iter" "linkinv" "mu" "[Link]" "[Link]"
[21] "mustart" "n" "ngoodobs" "nobs" "nvars"
[26] "offset" "start" "valideta" "validmu" "variance"
[31] "varmu" "w" "weights" "x" "xnames"
[36] "y" "ynames" "z"
Browse[1]> eta
1 2 3 4 5
0.000000e+00 -2.235357e-06 -1.117679e-05 -5.588393e-05 -2.794197e-04
6 7 8 9
-1.397098e-03 -6.985492e-03 -3.492746e-02 -1.746373e-01
Browse[1]> valideta(eta)
[1] TRUE
Browse[1]> mu
1 2 3 4 5 6 7
8
1.0000000 0.9999978 0.9999888 0.9999441 0.9997206 0.9986039 0.9930389
0.9656755
9
0.8397616
Browse[1]> validmu(mu)
[1] FALSE
Browse[1]> c
Available environments had calls:
1: glm(resp ~ 0 + predictor, family = binomial(link = "log"))
2: [Link](x = X, y = Y, weights = weights, start = start, etastart =
etastart
3: stop("no valid set of coefficients has been found: please supply
starting v

Enter an environment number, or 0 to exit Selection: 0

> rm([Link])
Because [Link] can be looked at later or even in another R session, post-
mortem debugging is possible even for batch usage of R. We do need to arrange
for the dump to be saved: this can be done either using the command-line flag --
save to save the workspace at the end of the run, or via a setting such as
> options(error = quote({[Link]([Link]=TRUE); q()}))
See the help on [Link] for further options and a worked example.
An alternative error action is to use the function recover():
> options(error = recover)
> glm(resp ~ 0 + predictor, family = binomial(link = "log"))
Error: no valid set of coefficients has been found: please supply starting
values

Enter a frame number, or 0 to exit

1: glm(resp ~ 0 + predictor, family = binomial(link = "log"))

2: [Link](x = X, y = Y, weights = weights, start = start, etastart =
etastart

Selection:
which is very similar to [Link]. However, we can examine the state of the
program directly, without dumping and re-loading the dump. As its help page
says, recover can be routinely used as the error action in place
of [Link] and [Link], since it behaves like [Link] in non-interactive
use.
Post-mortem debugging is good for finding out exactly what went wrong, but not
necessarily why. An alternative approach is to take a closer look at what was
happening just before the error, and a good way to do that is to use debug. This
inserts a call to the browser at the beginning of the function, starting in step-
through mode. So in our example we could use
> debug([Link])
> glm(resp ~ 0 + predictor, family = binomial(link ="log"))
debugging in: [Link](x = X, y = Y, weights = weights, start = start,
etastart = etastart,
mustart = mustart, offset = offset, family = family, control = control,
intercept = attr(mt, "intercept") > 0)
debug: {
## lists the whole function
Browse[1]>
debug: x <- [Link](x)
...
Browse[1]> start
[1] -2.235357e-06
debug: eta <- drop(x %*% start)
Browse[1]> eta
1 2 3 4 5
0.000000e+00 -2.235357e-06 -1.117679e-05 -5.588393e-05 -2.794197e-04
6 7 8 9
-1.397098e-03 -6.985492e-03 -3.492746e-02 -1.746373e-01
Browse[1]>
debug: mu <- linkinv(eta <- eta + offset)
Browse[1]> mu
1 2 3 4 5 6 7
8
1.0000000 0.9999978 0.9999888 0.9999441 0.9997206 0.9986039 0.9930389
0.9656755
9
0.8397616
(The prompt Browse[1]> indicates that this is the first level of browsing: it is
possible to step into another function that is itself being debugged or contains a call
to browser().)
debug can be used for hidden functions and S3 methods by
e.g. debug(stats:::[Link]). (It cannot be used for S4 methods, but an
alternative is given on the help page for debug.) Sometimes you want to debug a
function defined inside another function, e.g. the function arimafn defined
inside arima. To do so, set debug on the outer function (here arima) and step
through it until the inner function has been defined. Then call debug on the inner
function (and use c to get out of step-through mode in the outer function).
To remove debugging of a function, call undebug with the argument previously
given to debug; debugging otherwise lasts for the rest of the R session (or until the
function is edited or otherwise replaced).
trace can be used to temporarily insert debugging code into a function, for
example to insert a call to browser() just before the point of the error. To return to
our running example
## first get a numbered listing of the expressions of the function
> page([Link](body([Link])), method="print")
> trace([Link], browser, at=22)
Tracing function "[Link]" in package "stats"
[1] "[Link]"
> glm(resp ~ 0 + predictor, family = binomial(link ="log"))
Tracing [Link](x = X, y = Y, weights = weights, start = start,
etastart = etastart, .... step 22
Called from: eval(expr, envir, enclos)
Browse[1]> n
## and single-step from here.
> untrace([Link])
For your own functions, it may be as easy to use fix to insert temporary code,
but trace can help with functions in a namespace (as can fixInNamespace).
Alternatively, use trace(,edit=TRUE) to insert code visually.

Next: Debugging compiled code, Previous: Debugging R code, Up: Debugging

[Contents][Index]

4.3 Checking memory access

Errors in memory allocation and reading/writing outside arrays are very common
causes of crashes (e.g., segfaults) on some machines. Often the crash appears long
after the invalid memory access: in particular damage to the structures which R
itself has allocated may only become apparent at the next garbage collection (or
even at later garbage collections after objects have been deleted).
Note that memory access errors may be seen with LAPACK, BLAS, OpenMP and
Java-using packages: some at least of these seem to be intentional, and some are
related to passing characters to Fortran.
Some of these tools can detect mismatched allocation and deallocation. C++
programmers should note that memory allocated by new [] must be freed
by delete [], other uses of new by delete, and memory allocated
by malloc, calloc and realloc by free. Some platforms will tolerate mismatches
(perhaps with memory leaks) but others will segfault.
 Using gctorture
 Using valgrind
 Using the Address Sanitizer
 Using the Undefined Behaviour Sanitizer
 Other analyses with ‘clang’
 Other analyses with ‘gcc’
 Using ‘Dr. Memory’
 Fortran array bounds checking

Next: Using valgrind, Previous: Checking memory access, Up: Checking memory
access [Contents][Index]
4.3.1 Using gctorture

We can help to detect memory problems in R objects earlier by running garbage

collection as often as possible. This is achieved by gctorture(TRUE), which as
described on its help page
Provokes garbage collection on (nearly) every memory allocation. Intended to
ferret out memory protection bugs. Also makes R run very slowly, unfortunately.
The reference to ‘memory protection’ is to missing C-level calls
to PROTECT/UNPROTECT (see Handling the effects of garbage collection) which if
missing allow R objects to be garbage-collected when they are still in use. But it
can also help with other memory-related errors.
Normally running under gctorture(TRUE) will just produce a crash earlier in the R
program, hopefully close to the actual cause. See the next section for how to
decipher such crashes.
It is possible to run all the examples, tests and vignettes covered by R CMD
check under gctorture(TRUE) by using the option --use-gct.

The function gctorture2 provides more refined control over the GC torture
process. Its arguments step, wait and inhibit_release are documented on its help
page. Environment variables can also be used at the start of the R session to turn on
GC torture: R_GCTORTURE corresponds to the step argument
to gctorture2, R_GCTORTURE_WAIT to wait,
and R_GCTORTURE_INHIBIT_RELEASE to inhibit_release.
If R is configured with --enable-strict-barrier then a variety of tests for
the integrity of the write barrier are enabled. In addition tests to help detect protect
issues are enabled:
  All GCs are full GCs.
 New nodes in small node pages are marked as NEWSXP on creation.
 After a GC all free nodes that are not of type NEWSXP are marked as
type FREESXP and their previous type is recorded.
 Most calls to accessor functions check their SEXP inputs and SEXP outputs
and signal an error if a FREESXP is found. The address of the node and the old
type are included in the error message.
R CMD check --use-gct can be set to use gctorture2(n) rather
than gctorture(TRUE) by setting environment variable _R_CHECK_GCT_N_ to a
positive integer value to be used as n.
Used with a debugger and with gctorture or gctorture2 this mechanism can be
helpful in isolating memory protect problems.

Next: Using the Address Sanitizer, Previous: Using gctorture, Up: Checking
memory access [Contents][Index]
4.3.2 Using valgrind

If you have access to Linux on a common CPU type or supported versions of

FreeBSD or Solaris122 you can use valgrind ([Link] pronounced to
rhyme with ‘tinned’) to check for possible problems. To run some examples
under valgrind use something like
R -d valgrind --vanilla < mypkg-Ex.R
R -d "valgrind --tool=memcheck --leak-check=full" --vanilla < mypkg-Ex.R
where mypkg-Ex.R is a set of examples, e.g. the file created
in [Link] by R CMD check. Occasionally this reports memory reads of
‘uninitialised values’ that are the result of compiler optimization, so can be worth
checking under an unoptimized compile: for maximal information use a build with
debugging symbols. We know there will be some small memory leaks
from readline and R itself — these are memory areas that are in use right up to the
end of the R session. Expect this to run around 20x slower than without valgrind,
and in some cases much slower than that. Several versions of valgrind were not
happy with some optimized BLASes that use CPU-specific instructions so you
may need to build a version of R specifically to use with valgrind.
On platforms where valgrind is installed you can build a version of R with extra
instrumentation to help valgrind detect errors in the use of memory allocated from
the R heap. The configure option is --with-valgrind-
instrumentation=level, where level is 0, 1 or 2. Level 0 is the default and
does not add anything. Level 1 will detect some uses123 of uninitialised memory
and has little impact on speed (compared to level 0). Level 2 will detect many
other memory-use bugs124 but make R much slower when running under valgrind.
Using this in conjunction with gctorture can be even more effective (and even
slower).
It is highly recommended that the valgrind headers (sometimes packaged
separately, for example as valgrind-devel) are installed to build an
instrumented R: this will be required in future.
An example of valgrind output is
==12539== Invalid read of size 4
==12539== at 0x1CDF6CBE: csc_compTr (Mutils.c:273)
==12539== by 0x1CE07E1E: tsc_transpose (dtCMatrix.c:25)
==12539== by 0x80A67A7: do_dotcall (dotcode.c:858)
==12539== by 0x80CACE2: Rf_eval (eval.c:400)
==12539== by 0x80CB5AF: R_execClosure (eval.c:658)
==12539== by 0x80CB98E: R_execMethod (eval.c:760)
==12539== by 0x1B93DEFA: R_standardGeneric (methods_list_dispatch.c:624)
==12539== by 0x810262E: do_standardGeneric (objects.c:1012)
==12539== by 0x80CAD23: Rf_eval (eval.c:403)
==12539== by 0x80CB2F0: Rf_applyClosure (eval.c:573)
==12539== by 0x80CADCC: Rf_eval (eval.c:414)
==12539== by 0x80CAA03: Rf_eval (eval.c:362)
==12539== Address 0x1C0D2EA8 is 280 bytes inside a block of size 1996
alloc'd
==12539== at 0x1B9008D1: malloc (vg_replace_malloc.c:149)
==12539== by 0x80F1B34: GetNewPage (memory.c:610)
==12539== by 0x80F7515: Rf_allocVector (memory.c:1915)
...
This example is from an instrumented version of R, while tracking down a bug in
the Matrix package in 2006. The first line indicates that R has tried to read 4 bytes
from a memory address that it does not have access to. This is followed by a C
stack trace showing where the error occurred. Next is a description of the memory
that was accessed. It is inside a block allocated by malloc, called from GetNewPage,
that is, in the internal R heap. Since this memory all belongs to R, valgrind would
not (and did not) detect the problem in an uninstrumented build of R. In this
example the stack trace was enough to isolate and fix the bug, which was
in tsc_transpose, and in this example running under gctorture() did not provide
any additional information.
valgrind is good at spotting the use of uninitialized values: use option --track-
origins=yes to show where these originated from. What it cannot detect is the
misuse of arrays allocated on the stack: this includes C automatic variables and
some125 Fortran arrays.
It is possible to run all the examples, tests and vignettes covered by R CMD
check under valgrind by using the option --use-valgrind. If you do this you
will need to select the valgrind options some other way, for example by having
a ~/.valgrindrc file containing
--leak-check=full
--track-origins=yes
or setting the environment variable VALGRIND_OPTS. As from R 4.2.0, --use-
valgrind also uses valgrind when re-building the vignettes.
This section has described the use of memtest, the default (and most useful)
of valgrind’s tools. There are others described in its documentation: helgrind can
be useful for threaded programs.

Next: Using the Undefined Behaviour Sanitizer, Previous: Using valgrind,

Up: Checking memory access [Contents][Index]
4.3.3 Using the Address Sanitizer

AddressSanitizer (‘ASan’) is a tool with similar aims to the memory checker

in valgrind. It is available with suitable builds126 of gcc and clang on common
Linux and macOS platforms.
See [Link] htt
ps://[Link]/docs/[Link] and [Link]
sanitizers.
More thorough checks of C++ code are done if the C++ library has been
‘annotated’: at the time of writing this applied to std::vector in libc++ for use
with clang and gives rise to ‘container-overflow’127 reports.
It requires code to have been compiled and linked with -
fsanitize=address and compiling with -fno-omit-frame-pointer will give
more legible reports. It has a runtime penalty of 2–3x, extended compilation times
and uses substantially more memory, often 1–2GB, at run time. On 64-bit
platforms it reserves (but does not allocate) 16–20TB of virtual memory: restrictive
shell settings can cause problems. It can be helpful to increase the stack size, for
example to 40MB.
By comparison with valgrind, ASan can detect misuse of stack and global
variables but not the use of uninitialized memory.
Recent versions return symbolic addresses for the location of the error
provided llvm-symbolizer128 is on the path: if it is available but not on the path or
has been renamed129, one can use an environment variable, e.g.
ASAN_SYMBOLIZER_PATH=/path/to/llvm-symbolizer
An alternative is to pipe the output through asan_symbolize.py130 and perhaps then
(for compiled C++ code) c++filt. (On macOS, you may need to run dsymutil to
get line-number reports.)
The simplest way to make use of this is to build a version of R with something like
CC="gcc -std=gnu99 -fsanitize=address"
CFLAGS="-fno-omit-frame-pointer -g -O2 -Wall -pedantic -mtune=native"
which will ensure that the libasan run-time library is compiled into the R
executable. However this check can be enabled on a per-package basis by using
a ~/.R/Makevars file like
CC = gcc -std=gnu99 -fsanitize=address -fno-omit-frame-pointer
CXX = g++ -fsanitize=address -fno-omit-frame-pointer
FC = gfortran -fsanitize=address
(Note that -fsanitize=address has to be part of the compiler specification to
ensure it is used for linking. These settings will not be honoured by packages
which ignore ~/.R/Makevars.) It will be necessary to build R with
MAIN_LDFLAGS = -fsanitize=address
to link the runtime libraries into the R executable if it was not specified as part of
‘CC’ when R was built. (For some builds without OpenMP, -pthread is also
required.)
For options available via the environment
variable ASAN_OPTIONS see [Link]
AddressSanitizerFlags. With gcc additional control is available via the --
param flag: see its man page.
For more detailed information on an error, R can be run under a debugger with a
breakpoint set before the address sanitizer report is produced: for gdb or lldb you
could use
break __asan_report_error
(See [Link]
More recent versions131 added the flag -fsanitize-address-use-after-
scope:
see [Link]
One of the checks done by ASan is that malloc/free and in C+
+ new/delete and new[]/delete[] are used consistently (rather than say free being
used to dealloc memory allocated by new[]). This matters on some systems but not
all: unfortunately on some of those where it does not matter, system libraries132 are
not consistent. The check can be suppressed by including
‘alloc_dealloc_mismatch=0’ in ASAN_OPTIONS.
ASan also checks system calls and sometimes reports can refer to problems in the
system software and not the package nor R. A couple of reports have been of
‘heap-use-after-free’ errors in the X11 libraries called from Tcl/Tk.
 Using the Leak Sanitizer

Previous: Using the Address Sanitizer, Up: Using the Address Sanitizer
[Contents][Index]
[Link] Using the Leak Sanitizer
For x86_64 Linux there is a leak sanitizer, ‘LSan’:
see [Link] This
is available on recent versions of gcc and clang, and where available is compiled in
as part of ASan.
One way to invoke this from an ASan-enabled build is by the environment variable
ASAN_OPTIONS='detect_leaks=1'
However, this was made the default as from clang 3.5 and gcc 5.1.0.
When LSan is enabled, leaks give the process a failure error status (by default 23).
For an R package this means the R process, and as the parser retains some memory
to the end of the process, if R itself was built against ASan all runs will have a
failure error status (which may include running R as part of building R itself).
To disable this, allocation-mismatch checking and some strict C++ checking use
setenv ASAN_OPTIONS
‘alloc_dealloc_mismatch=0:detect_leaks=0:detect_odr_violation=0’
LSan also has a ‘stand-alone’ mode where it is compiled in using -
fsanitize=leak and avoids the run-time overhead of ASan.

Next: Other analyses with ‘clang’, Previous: Using the Address Sanitizer,
Up: Checking memory access [Contents][Index]
4.3.4 Using the Undefined Behaviour Sanitizer

‘Undefined behaviour’ is where the language standard does not require particular
behaviour from the compiler. Examples include division by zero (where for
doubles R requires the ISO/IEC 60559 behaviour but C/C++ do not), use of zero-
length arrays, shifts too far for signed types (e.g. int x, y; y = x << 31;), out-of-
range coercion, invalid C++ casts and mis-alignment. Not uncommon examples of
out-of-range coercion in R packages are attempts to coerce a NaN or infinity to
type int or NA_INTEGER to an unsigned type such as size_t. Also common is y[x -
1] forgetting that x might be NA_INTEGER.

‘UBSanitizer’ is a tool for C/C++ source code selected by -

fsanitize=undefined in suitable builds133 of clang and GCC. Its (main)
runtime library is linked into each package’s DLL, so it is less often needed to be
included in MAIN_LDFLAGS. Platforms supported by clang are listed
at [Link]
platforms: CRAN uses it for C/C++ with both GCC and clang on ‘x86_64’
Linux: the two toolchains often highlight different things with more reports
from clang than GCC.
This sanitizer can be combined with the Address Sanitizer by -
fsanitize=undefined,address (where both are supported).
Finer control of what is checked can be achieved by other options.
For clang see [Link]
checks. The current set is (on a single line):
-fsanitize=alignment,bool,bounds,builtin,enum,float-cast-overflow,
float-divide-by-zero,function,implicit-unsigned-integer-truncation,
implicit-signed-integer-truncation,implicit-integer-sign-change,
integer-divide-by-zero,nonnull-attribute,null,object-size,
pointer-overflow,return,returns-nonnull-attribute,shift,
signed-integer-overflow,unreachable,unsigned-integer-overflow,
unsigned-shift-base,vla-bound,vptr
(plus the more specific versions shift-base and shift-exponent) a subset of which
could be combined with address, or use something like
-fsanitize=undefined -fno-sanitize=float-divide-by-zero
Options function, return and vptr apply only to C++: to use vptr its run-time
library needs to be linked into the main R executable by building the latter with
something like
MAIN_LD="clang++ -fsanitize=undefined"
Option float-divide-by-zero is undesirable for use with R which allow such
divisions as part of IEC 60559 arithmetic, and in versions of clang since June 2019
it is no longer part of -fsanitize=undefined.
For GCC see [Link] (or
the manual for your version of GCC, installed
or via [Link] look for ‘Program Instrumentation Options’)
for the options supported by GCC: 10 supported
-fsanitize=alignment,bool,bounds,builtin,enum,integer-divide-by-zero,
nonnull-attribute,null,object-size,pointer-overflow,return,
returns-nonnull-attribute,shift,signed-integer-overflow,
unreachable,vla-bound,vptr
plus the more specific versions shift-base and shift-exponent and non-default
options
bound-strict,float-cast-overflow,float-divide-by-zero
where float-divide-by-zero is not desirable for R uses and bounds-strict is an
extension of bounds.
Other useful flags include
-no-fsanitize-recover
which causes the first report to be fatal (it always is for
the unreachable and return suboptions). For more detailed information on where
the runtime error occurs, using
setenv UBSAN_OPTIONS ‘print_stacktrace=1’
will include a traceback in the report. Beyond that, R can be run under a debugger
with a breakpoint set before the sanitizer report is produced: for gdb or lldb you
could use
break __ubsan_handle_float_cast_overflow
break __ubsan_handle_float_cast_overflow_abort
or similar (there are handlers for each type of undefined behaviour).
There are also the compiler flags -fcatch-undefined-behavior and -
ftrapv, said to be more reliable in clang than gcc.
For more details on the topic
see [Link] and [Link]
[Link] (which has 3 parts).
It may or may not be possible to build R itself with -fsanitize=undefined:
problems have been seen with OpenMP-using code with gcc but there has been
success with clang.

Next: Other analyses with ‘gcc’, Previous: Using the Undefined Behaviour
Sanitizer, Up: Checking memory access [Contents][Index]
4.3.5 Other analyses with ‘clang’

Recent versions of clang on ‘x86_64’ Linux have ‘ThreadSanitizer’

([Link] a ‘data race detector
for C/C++ programs’, and ‘MemorySanitizer’
([Link] [Link]
sanitizers) for the detection of uninitialized memory. Both are based on and
provide similar functionality to tools in valgrind.
clanghas a ‘Static Analyzer’ which can be run on the source files during
compilation: see [Link]

Next: Using ‘Dr. Memory’, Previous: Other analyses with ‘clang’, Up: Checking
memory access [Contents][Index]
4.3.6 Other analyses with ‘gcc’

GCC 10 introduced a new flag -fanalyzer which does static analysis during
compilation, currently for C code. It is regarded as experimental and it may slow
down computation considerably when problems are found (and use many GB of
resident memory). There is some overlap with problems detected by the Undefined
Behaviour sanitizer, but some issues are only reported by this tool and as it is a
static analysis, it does not rely on code paths being exercised.
See [Link] (o
r the documentation for your version of gcc if later)
and [Link]
Next: Fortran array bounds checking, Previous: Other analyses with ‘gcc’,
Up: Checking memory access [Contents][Index]
4.3.7 Using ‘Dr. Memory’

‘Dr. Memory’ from [Link] is a memory checker for (currently) 32-

bit Windows, Linux and macOS with similar aims to valgrind. It works with
unmodified executables134 and detects memory access errors, uninitialized reads
and memory leaks.

Previous: Using ‘Dr. Memory’, Up: Checking memory access [Contents][Index]

4.3.8 Fortran array bounds checking

Most of the Fortran compilers used with R allow code to be compiled with
checking of array bounds: for example gfortran has option -fbounds-check.
This will give an error when the upper or lower bound is exceeded, e.g.
At line 97 of file .../src/appl/dqrdc2.f
Fortran runtime error: Index ‘1’ of dimension 1 of array ‘x’ above upper
bound of 0
One does need to be aware that lazy programmers often specify Fortran dimensions
as 1 rather than * or a real bound and these will be reported (as may * dimensions)
It is easy to arrange to use this check on just the code in your package: add
to ~/.R/Makevars something like (for gfortran)
FFLAGS = -g -O2 -mtune=native -fbounds-check
when you run R CMD check.

This may report errors with the way that Fortran character variables are passed,
particularly when Fortran subroutines are called from C code and character lengths
are not passed (see Fortran character strings).

Next: Using Link-time Optimization, Previous: Checking memory access,

Up: Debugging [Contents][Index]

4.4 Debugging compiled code

Sooner or later programmers will be faced with the need to debug compiled code
loaded into R. This section is geared to platforms using gdb with code compiled
by gcc, but similar things are possible with other debuggers such
as lldb ([Link] used on macOS) and Sun’s dbx: some debuggers
have graphical front-ends available.
Consider first ‘crashes’, that is when R terminated unexpectedly with an illegal
memory access (a ‘segfault’ or ‘bus error’), illegal instruction or similar. Unix-
alike versions of R use a signal handler which aims to give some basic information.
For example
*** caught segfault ***
address 0x20000028, cause ‘memory not mapped’

Traceback:
1: .identC(class1[[1]], class2)
2: possibleExtends(class(sloti), classi, ClassDef2 = getClassDef(classi,
where = where))
3: validObject(t(cu))
4: stopifnot(validObject(cu <- as(tu, "dtCMatrix")), validObject(t(cu)),
validObject(t(tu)))

Possible actions:
1: abort (with core dump)
2: normal R exit
3: exit R without saving workspace
4: exit R saving workspace
Selection: 3
Since the R process may be damaged, the only really safe options are the first or
third. (Note that a core dump is only produced where enabled: a common default in
a shell is to limit its size to 0, thereby disabling it.)
A fairly common cause of such crashes is a package which uses .C or .Fortran and
writes beyond (at either end) one of the arguments it is passed. There is a good way
to detect this: using options(CBoundsCheck = TRUE) (which can be selected via the
environment variable R_C_BOUNDS_CHECK=yes) changes the
way .C and .Fortran work to check if the compiled code writes in the 64 bytes at
either end of an argument.
Another cause of a ‘crash’ is to overrun the C stack. R tries to track that in its own
code, but it may happen in third-party compiled code. For modern POSIX-
compliant OSes R can safely catch that and return to the top-level prompt, so one
gets something like
> .C("aaa")
Error: segfault from C stack overflow
>
However, C stack overflows are fatal under Windows and normally defeat attempts
at debugging on that platform. Further, the size of the stack is set when R is
compiled on Windows, whereas on POSIX OSes it can be set in the shell from
which R is launched.
If you have a crash which gives a core dump you can use something like
gdb /path/to/R/bin/exec/R core.12345
to examine the core dump. If core dumps are disabled or to catch errors that do not
generate a dump one can run R directly under a debugger by for example
$ R -d gdb --vanilla
...
gdb> run
at which point R will run normally, and hopefully the debugger will catch the error
and return to its prompt. This can also be used to catch infinite loops or interrupt
very long-running code. For a simple example
> for(i in 1:1e7) x <- rnorm(100)
[hit Ctrl-C]
Program received signal SIGINT, Interrupt.
0x00397682 in _int_free () from /lib/tls/[Link].6
(gdb) where
#0 0x00397682 in _int_free () from /lib/tls/[Link].6
#1 0x00397eba in free () from /lib/tls/[Link].6
#2 0xb7cf2551 in R_gc_internal (size_needed=313)
at /users/ripley/R/svn/R-devel/src/main/memory.c:743
#3 0xb7cf3617 in Rf_allocVector (type=13, length=626)
at /users/ripley/R/svn/R-devel/src/main/memory.c:1906
#4 0xb7c3f6d3 in PutRNGstate ()
at /users/ripley/R/svn/R-devel/src/main/RNG.c:351
#5 0xb7d6c0a5 in do_random2 (call=0x94bf7d4, op=0x92580e8, args=0x9698f98,
rho=0x9698f28) at /users/ripley/R/svn/R-devel/src/main/random.c:183
...
In many cases it is possible to attach a debugger to a running process: this is
helpful if an alternative front-end is in use or to investigate a task that seems to be
taking far too long. This is done by something like
gdb -p pid
where pid is the id of the R executable or front-end process and can be found from
within a running R process by calling [Link]() or from a process monitor.
This stops the process so its state can be examined: use continue to resume
execution.
Some “tricks” worth knowing follow:
 Finding entry points in dynamically loaded code
 Inspecting R objects when debugging
 Debugging on macOS

Next: Inspecting R objects when debugging, Previous: Debugging compiled code,

Up: Debugging compiled code [Contents][Index]
4.4.1 Finding entry points in dynamically loaded code

Under most compilation environments, compiled code dynamically loaded into R

cannot have breakpoints set within it until it is loaded. To use a symbolic debugger
on such dynamically loaded code under Unix-alikes use
 Call the debugger on the R executable, for example by R -d gdb.
 Start R.
 At the R prompt, use [Link] or library to load your shared object.
 Send an interrupt signal. This will put you back to the debugger prompt.
 Set the breakpoints in your code.
 Continue execution of R by typing signal 0RET.
Under Windows signals may not be able to be used, and if so the procedure is more
complicated. See the rw-FAQ.

Next: Debugging on macOS, Previous: Finding entry points in dynamically loaded

code, Up: Debugging compiled code [Contents][Index]
4.4.2 Inspecting R objects when debugging

The key to inspecting R objects from compiled code is the

function PrintValue(SEXP s) which uses the normal R printing mechanisms to
print the R object pointed to by s, or the safer version R_PV(SEXP s) which will
only print ‘objects’.
One way to make use of PrintValue is to insert suitable calls into the code to be
debugged.
Another way is to call R_PV from the symbolic debugger. (PrintValue is hidden
as Rf_PrintValue.) For example, from gdb we can use
(gdb) p R_PV(ab)
using the object ab from the convolution example, if we have placed a suitable
breakpoint in the convolution C code.
To examine an arbitrary R object we need to work a little harder. For example, let
R> DF <- [Link](a = 1:3, b = 4:6)
By setting a breakpoint at do_get and typing get("DF") at the R prompt, one can
find out the address in memory of DF, for example
Value returned is $1 = (SEXPREC *) 0x40583e1c
(gdb) p *$1
$2 = {
sxpinfo = {type = 19, obj = 1, named = 1, gp = 0,
mark = 0, debug = 0, trace = 0, = 0},
attrib = 0x40583e80,
u = {
vecsxp = {
length = 2,
type = {c = 0x40634700 "0>X@D>X@0>X@", i = 0x40634700,
f = 0x40634700, z = 0x40634700, s = 0x40634700},
truelength = 1075851272,
},
primsxp = {offset = 2},
symsxp = {pname = 0x2, value = 0x40634700, internal = 0x40203008},
listsxp = {carval = 0x2, cdrval = 0x40634700, tagval = 0x40203008},
envsxp = {frame = 0x2, enclos = 0x40634700},
closxp = {formals = 0x2, body = 0x40634700, env = 0x40203008},
promsxp = {value = 0x2, expr = 0x40634700, env = 0x40203008}
}
}
(Debugger output reformatted for better legibility).
Using R_PV() one can “inspect” the values of the various elements of the SEXP, for
example,
(gdb) p R_PV($1->attrib)
$names
[1] "a" "b"

$[Link]
[1] "1" "2" "3"

$class
[1] "[Link]"

$3 = void
To find out where exactly the corresponding information is stored, one needs to go
“deeper”:
(gdb) set $a = $1->attrib
(gdb) p $a->[Link]->[Link]->[Link].c
$4 = 0x405d40e8 "names"
(gdb) p $a->[Link]->[Link].s[1]->[Link].c
$5 = 0x40634378 "b"
(gdb) p $1->[Link].s[0]->[Link].i[0]
$6 = 1
(gdb) p $1->[Link].s[1]->[Link].i[1]
$7 = 5
Another alternative is the R_inspect function which shows the low-level structure
of the objects recursively (addresses differ from the above as this example is
created on another machine):
(gdb) p R_inspect($1)
@100954d18 19 VECSXP g0c2 [OBJ,NAM(2),ATT] (len=2, tl=0)
@100954d50 13 INTSXP g0c2 [NAM(2)] (len=3, tl=0) 1,2,3
@100954d88 13 INTSXP g0c2 [NAM(2)] (len=3, tl=0) 4,5,6
ATTRIB:
@102a70140 02 LISTSXP g0c0 []
TAG: @10083c478 01 SYMSXP g0c0 [MARK,NAM(2),gp=0x4000] "names"
@100954dc0 16 STRSXP g0c2 [NAM(2)] (len=2, tl=0)
@10099df28 09 CHARSXP g0c1 [MARK,gp=0x21] "a"
@10095e518 09 CHARSXP g0c1 [MARK,gp=0x21] "b"
TAG: @100859e60 01 SYMSXP g0c0 [MARK,NAM(2),gp=0x4000] "[Link]"
@102a6f868 13 INTSXP g0c1 [NAM(2)] (len=2, tl=1) -2147483648,-3
TAG: @10083c948 01 SYMSXP g0c0 [MARK,gp=0x4000] "class"
@102a6f838 16 STRSXP g0c1 [NAM(2)] (len=1, tl=1)
@1008c6d48 09 CHARSXP g0c2 [MARK,gp=0x21,ATT] "[Link]"
In general the representation of each object follows the format:
@<address> <type-nr> <type-name> <gc-info> [<flags>] ...
For a more fine-grained control over the depth of the recursion and the output of
vectors R_inspect3 takes additional two character() parameters: maximum depth
and the maximal number of elements that will be printed for scalar vectors. The
defaults in R_inspect are currently -1 (no limit) and 5 respectively.

Previous: Inspecting R objects when debugging, Up: Debugging compiled code

[Contents][Index]
4.4.3 Debugging on macOS

To debug code in a package it is easiest to unpack it in a directory and install it

with
R CMD INSTALL --dsym pkgname
as macOS does not store debugging symbols in the .so file. (It is not necessary to
have R built with debugging symbols, although compiling the package should be
done including -g in CFLAGS / CXXFLAGS / FFLAGS / FCFLAGS as appropriate.)
Security measures may prevent running a CRAN binary distribution of R
under lldb or attaching this as a debugger
([Link]
debugger-to-R), although both were possible on High Sierra and are again from R
4.2.0. This can also affect locally compiled builds, where attaching to an
interactive R session under Big Sur or Monterey worked in 2022 after giving
administrator permission via a popup-up. (To debug in what Apple deems a non-
interactive session, e.g. logged in remotely, see man DevToolsSecurity.)
Debugging a local build of R on macOS can raise additional hurdles as
environment variables such as DYLD_FALLBACK_LIBRARY_PATH are not usually passed
through135 the lldb process, resulting in messages like
R -d lldb
...
(lldb) run
Process 16828 launched: ‘/path/to/bin/exec/R’ (x86_64)
dyld: Library not loaded: [Link]
Referenced from: /path/to/bin/exec/R
A quick workaround is to symlink the dylibs under R_HOME/lib to somewhere
where they will be found such as the current working directory. It would be
possible to do as the distribution does136 and use install_name_tool, but that would
have to be done for all the dylibs including those in packages.
It may be simplest to attach the debugger to a running process (see above).
Specifically, run R and when it is at the prompt just before a command that is to be
debugged, at a terminal
ps -ef | grep exec/R
# identify the pid pid for the next command: it is the second item
lldb -p pid
(lldb) continue
and then return to the R console.
For non-interactive use, one may need lldb --batch.

Previous: Debugging compiled code, Up: Debugging [Contents][Index]

4.5 Using Link-time Optimization

Where supported, link time optimization provides a comprehensive way to check
the consistency of calls between Fortran files or between C and Fortran. Use
this via R CMD INSTALL --use-LTO (but that does not apply if there is
a src/Makefile file or a Windows analogue).
To set up support on a Unix-alike, See Link-Time Optimization in R Installation
and Administration. On Linux using GCC without building R with LTO support, it
should suffice to set
LTO_OPT = -flto
LTO_FC_OPT = -flto
AR = gcc-ar
NM = gcc-nm
in a personal (or site) Makevars file: See Customizing package compilation in R
Installation and Administration,
For Windows, first edit file etc/${R_ARCH}/Makeconf to give LTO_OPT the
value -flto or do so in a personal/site Makevars file; see also
file src/gnuwin32/[Link] in the sources.
For example:
boot.f:61: warning: type of ‘ddot’ does not match original declaration [-
Wlto-type-mismatch]
y(j,i)=ddot(p,x(j,1),n,b(1,j,i),1)
crq.f:1023: note: return value type mismatch
where the package author forgot to declare
double precision ddot
external ddot
in boot.f. That package had its own copy of ddot: to detect misuse of the one in
R’s BLAS library would have needed R configured with --enable-
lto=check.
Further examples:
rkpk2.f:77:5: warning: type of ‘dstup’ does not match original declaration
[-Wlto-type-mismatch]
*info, wk)
rkpk1.f:2565:5: note: type mismatch in parameter 14
subroutine dstup (s, lds, nobs, nnull, qraux, jpvt, y, q, ldqr,
rkpk1.f:2565:5: note: ‘dstup’ was previously declared here
where the fourteenth argument dum was missing in the call.
reg.f:78:33: warning: type of ‘dqrdc’ does not match original declaration
[-Wlto-type-mismatch]
call dqrdc (sr, nobs, nobs, nnull, wk, dum, dum, 0)
dstup.f:20: note: ‘dqrdc’ was previously declared here
call dqrdc (s, lds, nobs, nnull, qraux, jpvt, work, 1)
dqrdc is a LINPACK routine from R, jpvt is an integer array and work is a double
precision one so dum cannot match both. (If --enable-lto=check had been
used the comparison would have been with the definition in R.)
For Fortran files all in the package, most inconsistencies can be detected by
concatenating the Fortran files and compiling the result, sometimes with clearer
diagnostics than provided by LTO. For our last two examples this gives
all.f:2966:72:

*info, work1)
1
Warning: Missing actual argument for argument ‘dum’ at (1)
and
all.f:1663:72:

*ipvtwk), wk(ikwk), wk(iwork1), wk(iwork2), info)

1
Warning: Type mismatch in argument ‘jpvt’ at (1); passed REAL(8) to
INTEGER(4)
On a Unix-alike for a package with a src/Makefile file, LTO can be enabled
by including suitable flags in that file, for example
LTO = $(LTO_OPT)
LTO_FC = $(LTO_FC_OPT)
and ensuring these are used for compilation, for example as part
of CFLAGS, CXXFLAGS or FCFLAGS. If R CMD SHLIB is used for compilation, add --
use-LTO to its call.
On Windows for a package with
a src/[Link] or src/[Link] file which includes ‘"$
{R_HOME}/etc${R_ARCH}/Makeconf"’, include
LTO = $(LTO_OPT)
or to always use LTO however R was built,
LTO = -flto

Next: The R API: entry points for C code, Previous: Debugging, Up: Writing R
Extensions [Contents][Index]

5 System and foreign language

interfaces
 Operating system access
 Interface functions .C and .Fortran
 [Link] and [Link]
 Registering native routines
 Creating shared objects
 Interfacing C++ code
 Fortran I/O
  Linking to other packages
 Handling R objects in C
 Interface functions .Call and .External
 Evaluating R expressions from C
 Parsing R code from C
 External pointers and weak references
 Vector accessor functions
 Character encoding issues

Next: Interface functions .C and .Fortran, Previous: System and foreign language
interfaces, Up: System and foreign language interfaces [Contents][Index]

5.1 Operating system access

Access to operating system functions is via the R
functions system and system2. The details will differ by platform (see the on-line
help), and about all that can safely be assumed is that the first argument will be a
string command that will be passed for execution (not necessarily by a shell) and the
second argument to system will be internal which if true will collect the output of
the command into an R character vector.
On POSIX-compliant OSes these commands pass a command-line to a shell:
Windows is not POSIX-compliant and there is a separate function shell to do so.
The function [Link] is available for timing. Timing on child processes is only
available on Unix-alikes, and may not be reliable there.

Next: [Link] and [Link], Previous: Operating system access, Up: System
and foreign language interfaces [Contents][Index]

5.2 Interface functions .C and .Fortran

These two functions provide an interface to compiled code that has been linked
into R, either at build time or via [Link] (see [Link] and [Link]). They are
primarily intended for compiled C and Fortran code respectively, but
the .C function can be used with other languages which can generate C interfaces,
for example C++ (see Interfacing C++ code).
The first argument to each function is a character string specifying the symbol
name as known137 to C or Fortran, that is the function or subroutine name. (That the
symbol is loaded can be tested by, for example, [Link]("cg"). Use the name
you pass to .C or .Fortran rather than the translated symbol name.)
There can be up to 65 further arguments giving R objects to be passed to compiled
code. Normally these are copied before being passed in, and copied again to an R
list object when the compiled code returns. If the arguments are given names, these
are used as names for the components in the returned list object (but not passed to
the compiled code).
The following table gives the mapping between the modes of R atomic vectors and
the types of arguments to a C function or Fortran subroutine.
R storage mode C type Fortran type
logical int * INTEGER
integer int * INTEGER
double double * DOUBLE PRECISION
complex Rcomplex * DOUBLE COMPLEX
character char ** CHARACTER(255)
raw unsigned char * none
On all R platforms int and INTEGER are 32-bit. Code ported from S-PLUS (which
uses long * for logical and integer) will not work on all 64-bit platforms
(although it may appear to work on some, including Windows). Note also that if
your compiled code is a mixture of C functions and Fortran subprograms the
argument types must match as given in the table above.
C type Rcomplex is a structure with double members r and i defined in the header
file R_ext/Complex.h.138 (On most platforms this is stored in a way compatible
with the C99 double complex type: however, it may not be possible to
pass Rcomplex to a C99 function expecting a double complex argument. Nor need it
be compatible with a C++ complex type. Moreover, the compatibility can depend
on the optimization level set for the compiler.)
Only a single character string of fixed length can be passed to or from Fortran (the
length is not passed), and the success of this is compiler-dependent: its use was
formally deprecated in 2019. Other R objects can be passed to .C, but it is much
better to use one of the other interfaces.
It is possible to pass numeric vectors of storage mode double to C as float * or to
Fortran as REAL by setting the attribute Csingle, most conveniently by using the R
functions [Link], single or mode. This is intended only to be used to aid
interfacing existing C or Fortran code.
Logical values are sent as 0 (FALSE), 1 (TRUE) or INT_MIN = -2147483648 (NA, but
only if NAOK is true), and the compiled code should return one of these three values.
(Non-zero values other than INT_MIN are mapped to TRUE.) Note that the use of int
* for Fortran logical is not guaranteed to be portable (although people have gotten
away with it for many years): it is better to pass integers and convert to/from
Fortran logical in a Fortran wrapper.
Unless formal argument NAOK is true, all the other arguments are checked for
missing values NA and for the IEEE special values NaN, Inf and -Inf, and the
presence of any of these generates an error. If it is true, these values are passed
unchecked.
Argument PACKAGE confines the search for the symbol name to a specific shared
object (or use "base" for code compiled into R). Its use is highly desirable, as there
is no way to avoid two package writers using the same symbol name, and such
name clashes are normally sufficient to cause R to crash. (If it is not present and
the call is from the body of a function defined in a package namespace, the shared
object loaded by the first (if any) useDynLib directive will be used.)
Note that the compiled code should not return anything except through its
arguments: C functions should be of type void and Fortran subprograms should be
subroutines.
To fix ideas, let us consider a very simple example which convolves two finite
sequences. (This is hard to do fast in interpreted R code, but easy in C code.) We
could do this using .C by
void convolve(double *a, int *na, double *b, int *nb, double *ab)
{
int nab = *na + *nb - 1;

for(int i = 0; i < nab; i++)

ab[i] = 0.0;
for(int i = 0; i < *na; i++)
for(int j = 0; j < *nb; j++)
ab[i + j] += a[i] * b[j];
}
called from R by
conv <- function(a, b)
.C("convolve",
[Link](a),
[Link](length(a)),
[Link](b),
[Link](length(b)),
ab = double(length(a) + length(b) - 1))$ab
Note that we take care to coerce all the arguments to the correct R storage mode
before calling .C; mistakes in matching the types can lead to wrong results or hard-
to-catch errors.
Special care is needed in handling character vector arguments in C (or C++). On
entry the contents of the elements are duplicated and assigned to the elements of
a char ** array, and on exit the elements of the C array are copied to create new
elements of a character vector. This means that the contents of the character strings
of the char ** array can be changed, including to \0 to shorten the string, but the
strings cannot be lengthened. It is possible139 to allocate a new
string via R_alloc and replace an entry in the char ** array by the new string.
However, when character vectors are used other than in a read-only way,
the .Call interface is much to be preferred.
Passing character strings to Fortran code needs even more care, is deprecated and
should be avoided where possible. Only the first element of the character vector is
passed in, as a fixed-length (255) character array. Up to 255 characters are passed
back to a length-one character vector. How well this works (or even if it works at
all) depends on the C and Fortran compilers on each platform (including on their
options). Often what is being passed to Fortran is one of a small set of possible
values (a factor in R terms) which could alternatively be passed as an integer code:
similarly Fortran code that wants to generate diagnostic messages could pass an
integer code to a C or R wrapper which would convert it to a character string.
It is possible to pass some R objects other than atomic vectors via .C, but this is
only supported for historical compatibility: use the .Call or .External interfaces
for such objects. Any C/C++ code that includes Rinternals.h should be
called via .Call or .External.
.Fortran is primarily intended for Fortran 77 code, and long precedes any support
for Fortran 9x. Now current implementations of Fortran 9x support the Fortran
2003 module iso_c_binding, a better way to interface modern Fortran code to R is
to use .C and write a C interface using use iso_c_binding.

Next: Registering native routines, Previous: Interface functions .C and .Fortran,

Up: System and foreign language interfaces [Contents][Index]

5.3 [Link] and [Link]

Compiled code to be used with R is loaded as a shared object (Unix-alikes

including macOS, see Creating shared objects for more information) or DLL
(Windows).
The shared object/DLL is loaded by [Link] and unloaded by [Link].
Unloading is not normally necessary and is not safe in general, but it is needed to
allow the DLL to be re-built on some platforms, including Windows. Unloading a
DLL and then re-loading a DLL of the same name may not work: Solaris used the
first version loaded. A DLL that registers C finalizers, but fails to unregister them
when unloaded, may cause R to crash after unloading.
The first argument to both functions is a character string giving the path to the
object. Programmers should not assume a specific file extension for the
object/DLL (such as .so) but use a construction like
[Link](path1, path2, paste0("mylib", .Platform$[Link]))
for platform independence. On Unix-alike systems the path supplied
to [Link] can be an absolute path, one relative to the current directory or, if it
starts with ‘~’, relative to the user’s home directory.
Loading is most often done automatically based on the useDynLib() declaration in
the NAMESPACE file, but may be done explicitly via a call to [Link]. This
has the form
[Link]("libname", package, [Link])
where libname is the object/DLL name with the extension omitted. Note that the
first argument, chname, should not be package since this will not work if the
package is installed under another name.
Under some Unix-alike systems there is a choice of how the symbols are resolved
when the object is loaded, governed by the arguments local and now. Only use
these if really necessary: in particular using now=FALSE and then calling an
unresolved symbol will terminate R unceremoniously.
R provides a way of executing some code automatically when a object/DLL is
either loaded or unloaded. This can be used, for example, to register native routines
with R’s dynamic symbol mechanism, initialize some data in the native code, or
initialize a third party library. On loading a DLL, R will look for a routine within
that DLL named R_init_lib where lib is the name of the DLL file with the
extension removed. For example, in the command
[Link]("mylib", package, [Link])
R looks for the symbol named R_init_mylib. Similarly, when unloading the object,
R looks for a routine named R_unload_lib, e.g., R_unload_mylib. In either case, if
the routine is present, R will invoke it and pass it a single argument describing the
DLL. This is a value of type DllInfo which is defined in the Rdynload.h file in
the R_ext directory.
Note that there are some implicit restrictions on this mechanism as the basename of
the DLL needs to be both a valid file name and valid as part of a C entry point (e.g.
it cannot contain ‘.’): for portable code it is best to confine DLL names to
be ASCII alphanumeric plus underscore. If entry point R_init_lib is not found it is
also looked for with ‘.’ replaced by ‘_’.
The following example shows templates for the initialization and unload routines
for the mylib DLL.
#include <R_ext/Rdynload.h>

void
R_init_mylib(DllInfo *info)
{
/* Register routines,
allocate resources. */
}

void
R_unload_mylib(DllInfo *info)
{
/* Release resources. */
}

If a shared object/DLL is loaded more than once the most recent version is
used.140 More generally, if the same symbol name appears in several shared
objects, the most recently loaded occurrence is used. The PACKAGE argument and
registration (see the next section) provide good ways to avoid any ambiguity in
which occurrence is meant.
On Unix-alikes the paths used to resolve dynamically linked dependent libraries
are fixed (for security reasons) when the process is launched, so [Link] will only
look for such libraries in the locations set by the R shell script
(via etc/ldpaths) and in the OS-specific defaults.
Windows allows more control (and less security) over where dependent DLLs are
looked for. On all versions this includes the PATH environment variable, but with
lowest priority: note that it does not include the directory from which the DLL was
loaded. It is possible to add a single path with quite high
priority via the DLLpath argument to [Link]. This is (by default) used
by [Link] to include the package’s libs/x64 directory in the DLL search
path.

Next: Creating shared objects, Previous: [Link] and [Link], Up: System and
foreign language interfaces [Contents][Index]

5.4 Registering native routines

By ‘native’ routine, we mean an entry point in compiled code.
In calls to .C, .Call, .Fortran and .External, R must locate the specified native
routine by looking in the appropriate shared object/DLL. By default, R uses the
operating-system-specific dynamic loader to lookup the symbol in all141 loaded
DLLs and the R executable or libraries it is linked to. Alternatively, the author of
the DLL can explicitly register routines with R and use a single, platform-
independent mechanism for finding the routines in the DLL. One can use this
registration mechanism to provide additional information about a routine,
including the number and type of the arguments, and also make it available to R
programmers under a different name.
Registering routines has two main advantages: it provides a faster142 way to find
the address of the entry point via tables stored in the DLL at compilation time, and
it provides a run-time check that the entry point is called with the right number of
arguments and, optionally, the right argument types.
To register routines with R, one calls the C routine R_registerRoutines. This is
typically done when the DLL is first loaded within the initialization
routine R_init_dll name described
in [Link] and [Link]. R_registerRoutines takes 5 arguments. The first is
the DllInfo object passed by R to the initialization routine. This is where R stores
the information about the methods. The remaining 4 arguments are arrays
describing the routines for each of the 4 different
interfaces: .C, .Call, .Fortran and .External. Each argument is a NULL-terminated
array of the element types given in the following table:
.C R_CMethodDef
.Call R_CallMethodDef
.Fortran R_FortranMethodDef
.External R_ExternalMethodDef

Currently, the R_ExternalMethodDef type is the same as R_CallMethodDef type and

contains fields for the name of the routine by which it can be accessed in R, a
pointer to the actual native symbol (i.e., the routine itself), and the number of
arguments the routine expects to be passed from R. For example, if we had a
routine named myCall defined as
SEXP myCall(SEXP a, SEXP b, SEXP c);
we would describe this as
static const R_CallMethodDef callMethods[] = {
{"myCall", (DL_FUNC) &myCall, 3},
{NULL, NULL, 0}
};
along with any other routines for the .Call interface. For routines with a variable
number of arguments invoked via the .External interface, one specifies -1 for the
number of arguments which tells R not to check the actual number passed.
Routines for use with the .C and .Fortran interfaces are described with similar data
structures, which have one optional additional field for describing the type of each
argument. If specified, this field should be an array with the SEXP types describing
the expected type of each argument of the routine. (Technically, the elements of
the types array are of type R_NativePrimitiveArgType which is just an unsigned
integer.) The R types and corresponding type identifiers are provided in the
following table:
numeric REALSXP
integer INTSXP
logical LGLSXP
single SINGLESXP
character STRSXP
list VECSXP

Consider a C routine, myC, declared as

void myC(double *x, int *n, char **names, int *status);
We would register it as
static R_NativePrimitiveArgType myC_type[] = {
REALSXP, INTSXP, STRSXP, LGLSXP
};

static const R_CMethodDef cMethods[] = {

{"myC", (DL_FUNC) &myC, 4, myC_type},
{NULL, NULL, 0, NULL}
};
If registering types, check carefully that the number of types matches the number
of arguments: as the type array (here myC_type) is passed as a pointer in C, the
registration mechanism cannot check this for you.
Note that .Fortran entry points are mapped to lowercase, so registration should use
lowercase only.
Having created the arrays describing each routine, the last step is to actually
register them with R. We do this by calling R_registerRoutines. For example, if
we have the descriptions above for the routines accessed by the .C and .Call we
would use the following code:
void
R_init_myLib(DllInfo *info)
{
R_registerRoutines(info, cMethods, callMethods, NULL, NULL);
}
This routine will be invoked when R loads the shared object/DLL named myLib.
The last two arguments in the call to R_registerRoutines are for the routines
accessed by .Fortran and .External interfaces. In our example, these are given
as NULL since we have no routines of these types.
When R unloads a shared object/DLL, its registrations are removed. There is no
other facility for unregistering a symbol.
Examples of registering routines can be found in the different packages in the R
source tree (e.g., stats and graphics). Also, there is a brief, high-level introduction
in R News (volume 1/3, September 2001, pages 20–
23, [Link]
Once routines are registered, they can be referred to as R objects if this is arranged
in the useDynLib call in the package’s NAMESPACE file (see useDynLib). So for
example the stats package has
# Refer to all C/Fortran routines by their name prefixed by C_
useDynLib(stats, .registration = TRUE, .fixes = "C_")
in its NAMESPACE file, and then [Link]’s default methods can contain
pansari <- function(q, m, n)
.C(C_pansari, [Link](length(q)), p = [Link](q),
[Link](m), [Link](n))$p
This avoids the overhead of looking up an entry point each time it is used, and
ensures that the entry point in the package is the one used (without a PACKAGE =
"pkg" argument).

R_init_ routines are often of the form

void attribute_visible R_init_mypkg(DllInfo *dll)
{
R_registerRoutines(dll, CEntries, CallEntries, FortEntries,
ExternalEntries);
R_useDynamicSymbols(dll, FALSE);
R_forceSymbols(dll, TRUE);
...
}
The R_useDynamicSymbols call says the DLL is not to be searched for entry points
specified by character strings so .C etc calls will only find registered symbols:
the R_forceSymbols call only allows .C etc calls which specify entry points by R
objects such as C_pansari (and not by character strings). Each provides some
protection against accidentally finding your entry points when people supply a
character string without a package, and avoids slowing down such searches. (For
the visibility attribute see Controlling visibility.)
In more detail, if a package mypkg contains entry points reg and unreg and the first
is registered as a 0-argument .Call routine, we could use (from code in the
package)
.Call("reg")
.Call("unreg")
Without or with registration, these will both work.
If R_init_mypkg calls R_useDynamicSymbols(dll, FALSE), only the first will work. If
in addition to registration the NAMESPACE file contains
useDynLib(mypkg, .registration = TRUE, .fixes = "C_")
then we can call .Call(C_reg). Finally, if R_init_mypkg also
calls R_forceSymbols(dll, TRUE), only .Call(C_reg) will work (and
not .Call("reg")). This is usually what we want: it ensures that all of our
own .Call calls go directly to the intended code in our package and that no one
else accidentally finds our entry points. (Should someone need to call our code
from outside the package, for example for debugging, they can
use .Call(mypkg:::C_reg).)
 Speed considerations
 Example: converting a package to use registration
 Linking to native routines in other packages

Next: Example: converting a package to use registration, Previous: Registering

native routines, Up: Registering native routines [Contents][Index]
5.4.1 Speed considerations

Sometimes registering native routines or using a PACKAGE argument can make a

large difference. The results can depend quite markedly on the OS (and even if it is
32- or 64-bit), on the version of R and what else is loaded into R at the time.
To fix ideas, first consider x86_64 OS 10.7 and R 2.15.2. A simple .Call function
might be
foo <- function(x) .Call("foo", x)
with C code
#include <Rinternals.h>
SEXP foo(SEXP x)
{
return x;
}
If we compile with by R CMD SHLIB foo.c, load the code
by [Link]("[Link]") and run foo(pi) it took around 22 microseconds (us).
Specifying the DLL by
foo2 <- function(x) .Call("foo", x, PACKAGE = "foo")
reduced the time to 1.7 us.
Now consider making these functions part of a package whose NAMESPACE file
uses useDynlib(foo). This immediately reduces the running time as "foo" will be
preferentially looked for [Link]. Without specifying PACKAGE it took about 5 us
(it needs to fathom out the appropriate DLL each time it is invoked but it does not
need to search all DLLs), and with the PACKAGE argument it is again about 1.7 us.
Next suppose the package has registered the native routine foo. Then foo() still has
to find the appropriate DLL but can get to the entry point in the DLL faster, in
about 4.2 us. And foo2() now takes about 1 us. If we register the symbols in
the NAMESPACE file and use
foo3 <- function(x) .Call(C_foo, x)
then the address for the native routine is looked up just once when the package is
loaded, and foo3(pi) takes about 0.8 us.
Versions using .C() rather than .Call() took about 0.2 us longer.
These are all quite small differences, but C routines are not uncommonly invoked
millions of times for run times of a few microseconds each, and those doing such
things may wish to be aware of the differences.
On Linux and Solaris there is a smaller overhead in looking up symbols.
Symbol lookup on Windows used to be far slower, so R maintains a small cache. If
the cache is currently empty enough that the symbol can be stored in the cache then
the performance is similar to Linux and Solaris: if not it may be slower. R’s own
code always uses registered symbols and so these never contribute to the cache:
however many other packages do rely on symbol lookup.
In more recent versions of R all the standard packages register native symbols and
do not allow symbol search, so in a new session foo() can only look
in [Link] and may be as fast as foo2(). This will no longer apply when many
contributed packages are loaded, and generally those last loaded are searched first.
For example, consider R 3.3.2 on x86_64 Linux. In an empty R session,
both foo() and foo2() took about 0.75 us; however after
packages igraph and spatstat had been loaded (which loaded another 12
DLLs), foo() took 3.6 us but foo2() still took about 0.80 us. Using registration in a
package reduced this to 0.55 us and foo3() took 0.40 us, times which were
unchanged when further packages were loaded.

Next: Linking to native routines in other packages, Previous: Speed considerations,

Up: Registering native routines [Contents][Index]
5.4.2 Example: converting a package to use registration

The splines package was converted to use symbol registration in 2001, but we can
use it as an example143 of what needs to be done for a small package.
 Find the relevant entry points. This is somewhat OS-specific, but something
like the following should be possible at the OS command-line
 nm -g /path/to/[Link] | grep " T "
 0000000000002670 T _spline_basis
 0000000000001ec0 T _spline_value
This indicates that there are two relevant entry points. (They may or may not
have a leading underscore, as here. Fortran entry points will have a trailing
underscore.) Check in the R code that they are called by the package and
how: in this case they are used by .Call.
Alternatively, examine the package’s R code for
all .C, .Fortran, .Call and .External calls.
 Construct the registration table. First write skeleton registration code,
conventionally in file src/init.c (or at the end of the only C source file
in the package: if included in a C++ file the ‘R_init’ function would need
to be declared extern "C"):
 #include <stdlib.h> // for NULL
 #include <R_ext/Rdynload.h>

 #define CALLDEF(name, n) {#name, (DL_FUNC) &name, n}

 static const R_CallMethodDef R_CallDef[] = {
 CALLDEF(spline_basis, ?),
 CALLDEF(spline_value, ?),
 {NULL, NULL, 0}
 };

 void R_init_splines(DllInfo *dll)
 {
 R_registerRoutines(dll, NULL, R_CallDef, NULL, NULL);
 }
and then replace the ? in the skeleton with the actual numbers of arguments.
You will need to add declarations (also known as ‘prototypes’) of the
functions unless appending to the only C source file. Some packages will
already have these in a header file, or you could create one and include it
in init.c, for example splines.h containing
#include <Rinternals.h> // for SEXP
 extern SEXP spline_basis(SEXP knots, SEXP order, SEXP xvals,
SEXP derivs);
extern SEXP spline_value(SEXP knots, SEXP coeff, SEXP order,
SEXP x, SEXP deriv);
Tools are available to extract declarations, at least for C and C++ code: see
the help file for package_native_routine_registration_skeleton in
package tools. Here we could have used
cproto -I/path/to/R/include -e splines.c
For examples of registering other types of calls, see
packages graphics and stats. In particular, when registering entry points
for .Fortran one needs declarations as if called from C, such as
#include <R_ext/RS.h>
void F77_NAME(supsmu)(int *n, double *x, double *y,
double *w, int *iper, double *span,
double *alpha,
double *smo, double *sc, double *edf);
gfortran 8.4, 9.2 and later can help generate such prototypes with its flag -
fc-prototypes-external (although one will need to replace the
hard-coded trailing underscore with the F77_NAME macro).
One can get away with inaccurate argument lists in the declarations: it is
easy to specify the arguments for .Call (all SEXP) and .External (one SEXP)
and as the arguments for .C and .Fortran are all pointers, specifying them
as void * suffices. (For most platforms one can omit all the arguments,
although link-time optimization will warn, as will compilers set up to warn
on strict prototypes – and C23 will require correct arguments.)
Using -fc-prototypes-external will give a prototype
using int_least32_t *lgl for Fortran LOGICAL LGL, but this is not portable
and traditionally it has been assumed that the C/C++ equivalent was int
*lgl. If adding a declaration just to register a .Fortran call, the most
portable version is void *lgl.
 (Optional but highly recommended.) Restrict .Call etc to use the symbols
you chose to register by editing src/init.c to contain
 void R_init_splines(DllInfo *dll)
 {
 R_registerRoutines(dll, NULL, R_CallDef, NULL, NULL);
 R_useDynamicSymbols(dll, FALSE);
 }
A skeleton for the steps so far can be made
using package_native_routine_registration_skeleton in package tools. This will
optionally create declarations based on the usage in the R code.
The remaining steps are optional but recommended.
 Edit the NAMESPACE file to create R objects for the registered symbols:
 useDynLib(splines, .registration = TRUE, .fixes = "C_")
 Find all the relevant calls in the R code and edit them to use the R objects.
This entailed changing the lines
 temp <- .Call("spline_basis", knots, ord, x, derivs, PACKAGE =
"splines")
 y[accept] <- .Call("spline_value", knots, coeff, ord,
x[accept], deriv, PACKAGE = "splines")
 y = .Call("spline_value", knots, coef(object), ord, x, deriv,
PACKAGE = "splines")
to
temp <- .Call(C_spline_basis, knots, ord, x, derivs)
y[accept] <- .Call(C_spline_value, knots, coeff, ord,
x[accept], deriv)
y = .Call(C_spline_value, knots, coef(object), ord, x, deriv)
Check that there is no exportPattern directive which unintentionally exports
the newly created R objects.
 Restrict .Call to use the R symbols by editing src/init.c to contain
 void R_init_splines(DllInfo *dll)
 {
 R_registerRoutines(dll, NULL, R_CallDef, NULL, NULL);
 R_useDynamicSymbols(dll, FALSE);
 R_forceSymbols(dll, TRUE);
 }
 Consider visibility. On some OSes we can hide entry points from the loader,
which precludes any possible name clashes and calling them accidentally
(usually with incorrect arguments and crashing the R process). If we repeat
the first step we now see
 nm -g /path/to/[Link] | grep " T "
 0000000000002e00 T _R_init_splines
 00000000000025e0 T _spline_basis
 0000000000001e20 T _spline_value
If there were any entry points not intended to be used by the package we
should try to avoid exporting them, for example by making them static.
Now that the two relevant entry points are only accessed via the registration
table, we can hide them. There are two ways to do so on some Unix-alikes.
We can hide individual entry points via
#include <R_ext/Visibility.h>

SEXP attribute_hidden
spline_basis(SEXP knots, SEXP order, SEXP xvals, SEXP derivs)
…

SEXP attribute_hidden
spline_value(SEXP knots, SEXP coeff, SEXP order, SEXP x, SEXP
deriv)
…
Alternatively, we can change the default visibility for all C symbols by
including
PKG_CFLAGS = $(C_VISIBILITY)
 in src/Makevars, and then we need to allow registration by
declaring R_init_splines to be visible:
#include <R_ext/Visibility.h>

void attribute_visible
R_init_splines(DllInfo *dll)
…
See Controlling visibility for more details, including using Fortran code and
ways to restrict visibility on Windows.
 We end up with a file src/init.c containing
#include <stdlib.h>
#include <R_ext/Rdynload.h>
#include <R_ext/Visibility.h> // optional

#include "splines.h"

#define CALLDEF(name, n) {#name, (DL_FUNC) &name, n}

static const R_CallMethodDef R_CallDef[] = {

CALLDEF(spline_basis, 4),
CALLDEF(spline_value, 5),
{NULL, NULL, 0}
};

void
attribute_visible // optional
R_init_splines(DllInfo *dll)
{
R_registerRoutines(dll, NULL, R_CallDef, NULL, NULL);
R_useDynamicSymbols(dll, FALSE);
R_forceSymbols(dll, TRUE);
}

Previous: Example: converting a package to use registration, Up: Registering

native routines [Contents][Index]
5.4.3 Linking to native routines in other packages

In addition to registering C routines to be called by R, it can at times be useful for

one package to make some of its C routines available to be called by C code in
another package. The interface consists of two routines declared in
header R_ext/Rdynload.h as
void R_RegisterCCallable(const char *package, const char *name,
DL_FUNC fptr);
DL_FUNC R_GetCCallable(const char *package, const char *name);
A package packA that wants to make a C routine myCfun available to C code in
other packages would include the call
R_RegisterCCallable("packA", "myCfun", myCfun);
in its initialization function R_init_packA. A package packB that wants to use this
routine would retrieve the function pointer with a call of the form
p_myCfun = R_GetCCallable("packA", "myCfun");
As the type DL_FUNC is only appropriate for functions with no arguments, other
users will need to cast to an appropriate type. For example
typedef SEXP (*na_omit_xts_func) (SEXP x);
...
na_omit_xts_func fun = (na_omit_xts_func) R_GetCCallable("xts",
"na_omit_xts");
return fun(x);
The author of packB is responsible for ensuring that p_myCfun has an appropriate
declaration. In the future R may provide some automated tools to simplify
exporting larger numbers of routines.
A package that wishes to make use of header files in other packages needs to
declare them as a comma-separated list in the field ‘LinkingTo’ in
the DESCRIPTION file. This then arranges for the include directories in the
installed linked-to packages to be added to the include paths for C and C++ code.
It must specify144 ‘Imports’ or ‘Depends’ of those packages, for they have to
be loaded145 prior to this one (so the path to their compiled code has been
registered).
CRAN examples of the use of this mechanism include coxme linking
to bdsmatrix and xts linking to zoo.
NB: this mechanism is fragile, as changes to the interface provided by packA have
to be recognised by packB. The consequences of not doing so have included
serious corruption to the memory pool of the R session. Either packB has to
depend on the exact version of packA or there needs to be a mechanism
for packB to test at runtime the version of packA it is linked to matches that it was
compiled against.

Next: Interfacing C++ code, Previous: Registering native routines, Up: System and
foreign language interfaces [Contents][Index]

5.5 Creating shared objects

Shared objects for loading into R can be created using R CMD SHLIB. This accepts as
arguments a list of files which must be object files (with extension .o) or sources
for C, C++, Fortran, Objective C or Objective C++ (with
extensions .c, .cc or .cpp, .f (fixed-form Fortran), .f90 or .f95 (free-
form), .m, and .mm or .M, respectively), or commands to be passed to the linker.
See R CMD SHLIB --help (or the R help for SHLIB) for usage information. Note that
files intended for the Fortran pre-processor with extension .F are not accepted.
If compiling the source files does not work “out of the box”, you can specify
additional flags by setting some of the variables PKG_CPPFLAGS (for the C/C++
preprocessor, mainly ‘-I’, ‘-D’ and ‘-U’
flags), PKG_CFLAGS, PKG_CXXFLAGS, PKG_FFLAGS, PKG_OBJCFLAGS,
and PKG_OBJCXXFLAGS (for the C, C++, Fortran, Objective C, and Objective C++
compilers, respectively) in the file Makevars in the compilation directory (or, of
course, create the object files directly from the command line). Similarly,
variable PKG_LIBS in Makevars can be used for additional ‘-l’ and ‘-L’ flags to
be passed to the linker when building the shared object. (Supplying linker
commands as arguments to R CMD SHLIB will take precedence
over PKG_LIBS in Makevars.)
It is possible to arrange to include compiled code from other languages by setting
the macro ‘OBJECTS’ in file Makevars, together with suitable rules to make the
objects.
Flags that are already set (for example in file etcR_ARCH/Makeconf) can be
overridden by the environment variable MAKEFLAGS (at least for systems using a
POSIX-compliant make), as in (Bourne shell syntax)
MAKEFLAGS="CFLAGS=-O3" R CMD SHLIB *.c
It is also possible to set such variables in personal Makevars files, which are read
after the local Makevars and the system makefiles or in a site-
wide [Link] file. See Customizing package compilation in R
Installation and Administration,
Note that as R CMD SHLIB uses Make, it will not remake a shared object just because
the flags have changed, and if test.c and test.f both exist in the current
directory
R CMD SHLIB test.f
will compile test.c!
If the src subdirectory of an add-on package contains source code with one of the
extensions listed above or a file Makevars but not a file Makefile, R CMD
INSTALL creates a shared object (for loading into R through useDynlib in
the NAMESPACE, or in the .onLoad function of the package) using the R CMD
SHLIB mechanism. If file Makevars exists it is read first, then the system makefile
and then any personal Makevars files.
If the src subdirectory of package contains a file Makefile, this is used by R
CMD INSTALL in place of the R CMD SHLIB mechanism. make is called with
makefiles R_HOME/etcR_ARCH/Makeconf, src/Makefile and any
personal Makevars files (in that order). The first target found
in src/Makefile is used.
It is better to make use of a Makevars file rather than a Makefile: the latter
should be needed only exceptionally.
Under Windows the same commands work, but [Link] will be used in
preference to Makevars, and only src/[Link] will be used by R CMD
INSTALL with src/Makefile being ignored. Since R
4.2.0, [Link] will be used in preference
to [Link] and src/[Link] will be used in preference
to src/[Link]. For past experiences of building DLLs with a variety of
compilers, see file ‘[Link]’. Under Windows you can supply an
exports definitions file called [Link]: otherwise all entry points in
objects (but not libraries) supplied to R CMD SHLIB will be exported from the DLL.
An example is [Link] for the stats package: a CRAN example in
package fastICA.
If you feel tempted to read the source code and subvert these mechanisms, please
resist. Far too much developer time has been wasted in chasing down errors caused
by failures to follow this documentation, and even more by package authors
demanding explanations as to why their packages no longer work. In particular,
undocumented environment or make variables are not for use by package writers
and are subject to change without notice.

Next: Fortran I/O, Previous: Creating shared objects, Up: System and foreign
language interfaces [Contents][Index]

5.6 Interfacing C++ code

Suppose we have the following hypothetical C++ library, consisting of the two
files X.h and [Link], and implementing the two classes X and Y which we want to
use in R.
// X.h

class X {
public: X (); ~X ();
};

class Y {
public: Y (); ~Y ();
};

// [Link]

#include <R.h>
#include "X.h"

static Y y;

X::X() { REprintf("constructor X\n"); }

X::~X() { REprintf("destructor X\n"); }
Y::Y() { REprintf("constructor Y\n"); }
Y::~Y() { REprintf("destructor Y\n"); }

To use with R, the only thing we have to do is writing a wrapper function and
ensuring that the function is enclosed in
extern "C" {

}
For example,
// X_main.cpp:

#include "X.h"

extern "C" {

void X_main () {
X x;
}

} // extern "C"

Compiling and linking should be done with the C++ compiler-linker (rather than
the C compiler-linker or the linker itself); otherwise, the C++ initialization code
(and hence the constructor of the static variable Y) are not called. On a properly
configured system, one can simply use
R CMD SHLIB [Link] X_main.cpp
to create the shared object, typically [Link] (the file name extension may be
different on your platform). Now starting R yields
R version 2.14.1 Patched (2012-01-16 r58124)
Copyright (C) 2012 The R Foundation for Statistical Computing
...
Type "q()" to quit R.

R> [Link](paste("X", .Platform$[Link], sep = ""))

constructor Y
R> .C("X_main")
constructor X
destructor X
list()
R> q()
Save workspace image? [y/n/c]: y
destructor Y
The R for Windows FAQ (rw-FAQ) contains details of how to compile this
example under Windows.
Earlier versions of this example used C++ iostreams: this is best avoided. There is
no guarantee that the output will appear in the R console, and indeed it will not on
the R for Windows console. Use R code or the C entry points (see Printing) for all
I/O if at all possible. Examples have been seen where merely loading a DLL that
contained calls to C++ I/O upset R’s own C I/O (for example by resetting buffers
on open files).
Most R header files can be included within C++ programs but they should not be
included within an extern "C" block (as they include system headers146).
 External C++ code
5.6.1 External C++ code

Quite a lot of external C++ software is header-only (e.g. most of the Boost
‘libraries’ including all those supplied by package BH, and most of Armadillo as
supplied by package RcppArmadillo) and so is compiled when an R package
which uses it is installed. This causes few problems.
A small number of external libraries used in R packages have a C++ interface to a
library of compiled code, e.g. packages sf and rjags. This raises many more
problems! The C++ interface uses name-mangling and the ABI147 may depend on
the compiler, version and even C++ defines148, so requires the package C++ code to
be compiled in exactly the same way as the library (and what that was is often
undocumented).
Even fewer external libraries use C++ internally but present a C interface, such
as rgeos. These require the C++ runtime library to be linked into the package’s
shared object/DLL, and this is best done by including a dummy C++ file in the
package sources.
There is a trend to link to the C++ interfaces offered by C software such
as hdf5, pcre and ImageMagick. Their C interfaces are much preferred for
portability (and can be used from C++ code). Also, the C++ interfaces are often
optional in the software build or packaged separately and so users installing from
package sources are less likely to already have them installed.

Next: Linking to other packages, Previous: Interfacing C++ code, Up: System and
foreign language interfaces [Contents][Index]

5.7 Fortran I/O

We have already warned against the use of C++ iostreams not least because output
is not guaranteed to appear on the R console, and this warning applies equally to
Fortran output to units * and 6. See Printing from Fortran, which describes
workarounds.
In the past most Fortran compilers implemented I/O on top of the C I/O system and
so the two interworked successfully. This was true of g77, but it is less true
of gfortran as used in gcc 4 and later. In particular, any package that makes use of
Fortran I/O will when compiled on Windows interfere with C I/O: when the
Fortran I/O support code is initialized (typically when the package is loaded) the
C stdout and stderr are switched to LF line endings. (Function init in
file src/modules/lapack/init_win.c shows how to mitigate this. In a
package this would look something like
#ifdef _WIN32
# include <fcntl.h>
#endif

void R_init_mypkgname(DllInfo *dll)

{
// Native symbol registration calls

#ifdef _WIN32
// gfortran I/O initialization sets these to _O_BINARY
setmode(1, _O_TEXT); /* stdout */
setmode(2, _O_TEXT); /* stderr */
#endif
}
in the file used for native symbol registration.)

Next: Handling R objects in C, Previous: Fortran I/O, Up: System and foreign
language interfaces [Contents][Index]

5.8 Linking to other packages

It is not in general possible to link a DLL in package packA to a DLL provided by
package packB (for the security reasons mentioned in [Link] and [Link],
and also because some platforms distinguish between shared objects and dynamic
libraries), but it is on Windows.
Note that there can be tricky versioning issues here, as package packB could be re-
installed after package packA — it is desirable that the API provided by
package packB remains backwards-compatible.
Shipping a static library in package packB for other packages to link to avoids
most of the difficulties.
 Unix-alikes
 Windows

Next: Windows, Previous: Linking to other packages, Up: Linking to other

packages [Contents][Index]
5.8.1 Unix-alikes

It is possible to link a shared object in package packA to a library provided by

package packB under limited circumstances on a Unix-alike OS. There are severe
portability issues, so this is not recommended for a distributed package.
This is easiest if packB provides a static library packB/lib/libpackB.a.
(Note using directory lib rather than libs is conventional, and architecture-
specific sub-directories may be needed and are assumed in the sample code below.
The code in the static library will need to be compiled with PIC flags on platforms
where it matters.) Then as the code from package packB is incorporated when
package packA is installed, we only need to find the static library at install time
for package packA. The only issue is to find package packB, and for that we can
ask R by something like (long lines broken for display here)
PKGB_PATH=‘echo ’library(packB);
cat([Link]("lib", package="packB", mustWork=TRUE))' \
| "${R_HOME}/bin/R" --vanilla --no-echo`
PKG_LIBS="$(PKGB_PATH)$(R_ARCH)/libpackB.a"
For a dynamic
library packB/lib/[Link] (packB/lib/[Link] on
macOS: note that you cannot link to a shared object, .so, on that platform) we
could use
PKGB_PATH=‘echo ’library(packB);
cat([Link]("lib", package="packB", mustWork=TRUE))' \
| "${R_HOME}/bin/R" --vanilla --no-echo`
PKG_LIBS=-L"$(PKGB_PATH)$(R_ARCH)" -lpackB
This will work for installation, but very likely not when package packB is loaded,
as the path to package packB’s lib directory is not in the ld.so149 search path.
You can arrange to put it there before R is launched by setting (on some
platforms) LD_RUN_PATH or LD_LIBRARY_PATH or adding to the [Link] cache (see man
ldconfig). On platforms that support it, the path to the directory containing the
dynamic library can be hardcoded at install time (which assumes that the location
of package packB will not be changed nor the package updated to a changed API).
On systems with the gcc or clang and the GNU linker (e.g. Linux) and some others
this can be done by e.g.
PKGB_PATH=‘echo ’library(packB);
cat([Link]("lib", package="packB", mustWork=TRUE)))' \
| "${R_HOME}/bin/R" --vanilla --no-echo`
PKG_LIBS=-L"$(PKGB_PATH)$(R_ARCH)" -Wl,-rpath,"$(PKGB_PATH)$(R_ARCH)" -
lpackB
Some other systems (e.g. Solaris with its native linker) use -Rdir rather than -
rpath,dir (and this is accepted by the compiler as well as the linker).
It may be possible to figure out what is required semi-automatically from the result
of R CMD libtool --config (look for ‘hardcode’).
Making headers provided by package packB available to the code to be compiled
in package packA can be done by the LinkingTo mechanism (see Registering
native routines).

Previous: Unix-alikes, Up: Linking to other packages [Contents][Index]

5.8.2 Windows

Suppose package packA wants to make use of compiled code provided

by packB in DLL packB/libs/[Link], possibly the package’s
DLL packB/libs/[Link]. (This can be extended to linking to more than
one package in a similar way.) There are three issues to be addressed:
 Making headers provided by package packB available to the code to be
compiled in package packA.
This is done by the LinkingTo mechanism (see Registering native routines).
 preparing [Link] to link to packB/libs/[Link].
This needs an entry in [Link] or [Link] of the form
PKG_LIBS= -L<something> -lexB
and one possibility is that <something> is the path to the
installed pkgB/libs directory. To find that we need to ask R where it is
by something like
PKGB_PATH=‘echo ’library(packB);
cat([Link]("libs", package="packB", mustWork=TRUE))' \
| rterm --vanilla --no-echo`
PKG_LIBS= -L"$(PKGB_PATH)$(R_ARCH)" -lexB
Another possibility is to use an import library, shipping with
package packA an exports file [Link].
Then [Link] (or [Link]) could contain
PKG_LIBS= -L. -lexB

all: $(SHLIB) before

before: [Link].a
[Link].a: [Link]
and then installing package packA will make and use the import library
for [Link]. (One way to prepare the exports file is to
use [Link].)
 loading [Link] which depends on [Link].
If [Link] was used by package packB (because it is in
fact [Link] or [Link] depends on it) and packB has been
loaded before packA, then nothing more needs to be done as [Link] will
already be loaded into the R executable. (This is the most common
scenario.)
More generally, we can use the DLLpath argument to [Link] to
ensure that [Link] is found, for example by setting
[Link]("packA", pkg, lib,
DLLpath = [Link]("libs", package="packB"))
 Note that DLLpath can only set one path, and so for linking to two or more
packages you would need to resort to setting environment variable PATH.

Next: Interface functions .Call and .External, Previous: Linking to other

packages, Up: System and foreign language interfaces [Contents][Index]

5.9 Handling R objects in C

Using C code to speed up the execution of an R function is often very fruitful.
Traditionally this has been done via the .C function in R. However, if a user wants
to write C code using internal R data structures, then that can be done using
the .Call and .External functions. The syntax for the calling function in R in each
case is similar to that of .C, but the two functions have different C interfaces.
Generally the .Call interface is simpler to use, but .External is a little more
general.
A call to .Call is very similar to .C, for example
.Call("convolve2", a, b)
The first argument should be a character string giving a C symbol name of code
that has already been loaded into R. Up to 65 R objects can passed as arguments.
The C side of the interface is
#include <R.h>
#include <Rinternals.h>

SEXP convolve2(SEXP a, SEXP b)

...
A call to .External is almost identical
.External("convolveE", a, b)
but the C side of the interface is different, having only one argument
#include <R.h>
#include <Rinternals.h>

SEXP convolveE(SEXP args)

...
Here args is a LISTSXP, a Lisp-style pairlist from which the arguments can be
extracted.
In each case the R objects are available for manipulation via a set of functions and
macros defined in the header file Rinternals.h or some S-compatibility
macros150 See Interface functions .Call and .External for details
on .Call and .External.
Before you decide to use .Call or .External, you should look at other alternatives.
First, consider working in interpreted R code; if this is fast enough, this is normally
the best option. You should also see if using .C is enough. If the task to be
performed in C is simple enough involving only atomic vectors and requiring no
call to R, .C suffices. A great deal of useful code was written using
just .C before .Call and .External were available. These interfaces allow much
more control, but they also impose much greater responsibilities so need to be used
with care. Neither .Call nor .External copy their arguments: you should treat
arguments you receive through these interfaces as read-only.
To handle R objects from within C code we use the macros and functions that have
been used to implement the core parts of R. A public151 subset of these is defined in
the header file Rinternals.h in the
directory R_INCLUDE_DIR (default R_HOME/include) that should be
available on any R installation.
A substantial amount of R, including the standard packages, is implemented using
the functions and macros described here, so the R source code provides a rich
source of examples and “how to do it”: do make use of the source code for
inspirational examples.
It is necessary to know something about how R objects are handled in C code. All
the R objects you will deal with will be handled with the type SEXP152, which is a
pointer to a structure with typedef SEXPREC. Think of this structure as a variant
type that can handle all the usual types of R objects, that is vectors of various
modes, functions, environments, language objects and so on. The details are given
later in this section and in R Internal Structures in R Internals, but for most
purposes the programmer does not need to know them. Think rather of a model
such as that used by Visual Basic, in which R objects are handed around in C code
(as they are in interpreted R code) as the variant type, and the appropriate part is
extracted for, for example, numerical calculations, only when it is needed. As in
interpreted R code, much use is made of coercion to force the variant object to the
right type.
 Handling the effects of garbage collection
 Allocating storage
 Details of R types
 Attributes
 Classes
 Handling lists
 Handling character data
 Finding and setting variables
 Some convenience functions
 Named objects and copying

Next: Allocating storage, Previous: Handling R objects in C, Up: Handling R

objects in C [Contents][Index]
5.9.1 Handling the effects of garbage collection
We need to know a little about the way R handles memory allocation. The memory
allocated for R objects is not freed by the user; instead, the memory is from time to
time garbage collected. That is, some or all of the allocated memory not being
used is freed or marked as re-usable.
The R object types are represented by a C structure defined by a
typedef SEXPREC in Rinternals.h. It contains several things among which are
pointers to data blocks and to other SEXPRECs. A SEXP is simply a pointer to
a SEXPREC.
If you create an R object in your C code, you must tell R that you are using the
object by using the PROTECT macro on a pointer to the object. This tells R that the
object is in use so it is not destroyed during garbage collection. Notice that it is the
object which is protected, not the pointer variable. It is a common mistake to
believe that if you invoked PROTECT(p) at some point then p is protected from then
on, but that is not true once a new object is assigned to p.
Protecting an R object automatically protects all the R objects pointed to in the
corresponding SEXPREC, for example all elements of a protected list are
automatically protected.
The programmer is solely responsible for housekeeping the calls to PROTECT. There
is a corresponding macro UNPROTECT that takes as argument an int giving the
number of objects to unprotect when they are no longer needed. The protection
mechanism is stack-based, so UNPROTECT(n) unprotects the last n objects which
were protected. The calls to PROTECT and UNPROTECT must balance when the user’s
code returns and should balance in all functions. R will warn about "stack
imbalance in .Call" (or .External) if the housekeeping is wrong.

Here is a small example of creating an R numeric vector in C code:

#include <R.h>
#include <Rinternals.h>

SEXP ab;
....
ab = PROTECT(allocVector(REALSXP, 2));
REAL(ab)[0] = 123.45;
REAL(ab)[1] = 67.89;
UNPROTECT(1);
Now, the reader may ask how the R object could possibly get removed during
those manipulations, as it is just our C code that is running. As it happens, we can
do without the protection in this example, but in general we do not know (nor want
to know) what is hiding behind the R macros and functions we use, and any of
them might cause memory to be allocated, hence garbage collection and hence our
object ab to be removed. It is usually wise to err on the side of caution and assume
that any of the R macros and functions might remove the object.
In some cases it is necessary to keep better track of whether protection is really
needed. Be particularly aware of situations where a large number of objects are
generated. The pointer protection stack has a fixed size (default 10,000) and can
become full. It is not a good idea then to just PROTECT everything in sight
and UNPROTECT several thousand objects at the end. It will almost invariably be
possible to either assign the objects as part of another object (which automatically
protects them) or unprotect them immediately after use.
There is a less-used macro UNPROTECT_PTR(s) that unprotects the object pointed to
by the SEXP s, even if it is not the top item on the pointer protection stack. This
macro was introduced for use in the parser, where the code interfacing with the R
heap is generated and the generator cannot be configured to insert proper calls
to PROTECT and UNPROTECT. However, UNPROTECT_PTR is dangerous to use in
combination with UNPROTECT when the same object has been protected multiple
times. It has been superseded by multi-set based
functions R_PreserveInMSet and R_ReleaseFromMSet, which protect objects in a
multi-set created by R_NewPreciousMSet and typically itself protected
using PROTECT. These functions should not be needed outside parsers.
Sometimes an object is changed (for example duplicated, coerced or grown) yet the
current value needs to be protected. For these cases PROTECT_WITH_INDEX saves an
index of the protection location that can be used to replace the protected value
using REPROTECT. For example (from the internal code for optim)
PROTECT_INDEX ipx;

....
PROTECT_WITH_INDEX(s = eval(OS->R_fcall, OS->R_env), &ipx);
REPROTECT(s = coerceVector(s, REALSXP), ipx);
Note that it is dangerous to mix UNPROTECT_PTR also with PROTECT_WITH_INDEX, as
the former changes the protection locations of objects that were protected after the
one being unprotected.
There is another way to avoid the effects of garbage collection: a call
to R_PreserveObject adds an object to an internal list of objects not to be collects,
and a subsequent call to R_ReleaseObject removes it from that list. This provides a
way for objects which are not returned as part of R objects to be protected across
calls to compiled code: on the other hand it becomes the user’s responsibility to
release them when they are no longer needed (and this often requires the use of a
finalizer). It is less efficient than the normal protection mechanism, and should be
used sparingly.
For functions from packages as well as R to safely co-operate in protecting objects,
certain rules have to be followed:
 Pointer-protection balance. Calls to PROTECT and UNPROTECT should balance in
each function. A function may only call UNPROTECT or REPROTECT on objects it
has itself protected. Note that the pointer protection stack balance is restored
automatically on non-local transfer of control (See Condition handling and
cleanup code.), as if a call to UNPROTECT was invoked with the right
argument.
  Caller protection. It is the responsibility of the caller that all arguments
passed to a function are protected and will stay protected for the whole
execution of the callee. Typically this is achieved
by PROTECT and UNPROTECT calls.
 Protecting return values. Any R objects returned from a function are
unprotected (the callee must maintain pointer-protection balance), and hence
should be protected immediately by the caller. To be safe against future
code changes, assume that any R object returned from any function may
need protection. Note that even when conceptually returning an existing
protected object, that object may be duplicated.
 All functions/macros allocate. To be safe against future code changes,
assume that any function or macro may allocate and hence garbage collector
may run and destroy unprotected objects.
It is always safe and recommended to follow those rules. In fact, several R
functions and macros protect their own arguments and some functions do not
allocate or do not allocate when used in a certain way, but that is subject to change,
so relying on that may be fragile. PROTECT and PROTECT_WITH_INDEX can be safely
called with unprotected arguments and UNPROTECT does not allocate.

Next: Details of R types, Previous: Handling the effects of garbage collection,

Up: Handling R objects in C [Contents][Index]
5.9.2 Allocating storage

For many purposes it is sufficient to allocate R objects and manipulate those. There
are quite a few allocXxx functions defined in Rinternals.h—you may want to
explore them.
One that is commonly used is allocVector, the C-level equivalent of R-
level vector() and its wrappers such as integer() and character(). One
distinction is that whereas the R functions always initialize the elements of the
vector, allocVector only does so for lists, expressions and character vectors (the
cases where the elements are themselves R objects).
If storage is required for C objects during the calculations this is best allocating by
calling R_alloc; see Memory allocation. All of these memory allocation routines
do their own error-checking, so the programmer may assume that they will raise an
error and not return if the memory cannot be allocated.

Next: Attributes, Previous: Allocating storage, Up: Handling R objects in C

[Contents][Index]
5.9.3 Details of R types
Users of the Rinternals.h macros will need to know how the R types are
known internally. The different R data types are represented in C by SEXPTYPE.
Some of these are familiar from R and some are internal data types. The usual R
object modes are given in the table.
SEXPTYPE R equivalent
REALSXP numeric with storage mode double
INTSXP integer
CPLXSXP complex
LGLSXP logical
STRSXP character
VECSXP list (generic vector)
LISTSXP pairlist
DOTSXP a ‘…’ object
NILSXP NULL
SYMSXP name/symbol
CLOSXP function or function closure
ENVSXP environment
Among the important internal SEXPTYPEs are LANGSXP, CHARSXP, PROMSXP, etc. (N.B.:
although it is possible to return objects of internal types, it is unsafe to do so as
assumptions are made about how they are handled which may be violated at user-
level evaluation.) More details are given in R Internal Structures in R Internals.
Unless you are very sure about the type of the arguments, the code should check
the data types. Sometimes it may also be necessary to check data types of objects
created by evaluating an R expression in the C code. You can use functions
like isReal, isInteger and isString to do type checking. Other such functions
declared in the header
file Rinternals.h include isNull, isSymbol, isLogical, isComplex, isExpressio
n, and isEnvironment. All of these take a SEXP as argument and return 1 or 0 to
indicate TRUE or FALSE.
What happens if the SEXP is not of the correct type? Sometimes you have no other
option except to generate an error. You can use the function error for this. It is
usually better to coerce the object to the correct type. For example, if you find that
an SEXP is of the type INTEGER, but you need a REAL object, you can change the type
by using
newSexp = PROTECT(coerceVector(oldSexp, REALSXP));
Protection is needed as a new object is created; the object formerly pointed to by
the SEXP is still protected but now unused.153
All the coercion functions do their own error-checking, and generate NAs with a
warning or stop with an error as appropriate.
Note that these coercion functions are not the same as calling [Link] (and so
on) in R code, as they do not dispatch on the class of the object. Thus it is normally
preferable to do the coercion in the calling R code.
So far we have only seen how to create and coerce R objects from C code, and how
to extract the numeric data from numeric R vectors. These can suffice to take us a
long way in interfacing R objects to numerical algorithms, but we may need to
know a little more to create useful return objects.

Next: Classes, Previous: Details of R types, Up: Handling R objects in C

[Contents][Index]
5.9.4 Attributes

Many R objects have attributes: some of the most useful are classes and
the dim and dimnames that mark objects as matrices or arrays. It can also be helpful
to work with the names attribute of vectors.
To illustrate this, let us write code to take the outer product of two vectors
(which outer and %o% already do). As usual the R code is simple
out <- function(x, y)
{
[Link](x) <- [Link](y) <- "double"
.Call("out", x, y)
}
where we expect x and y to be numeric vectors (possibly integer), possibly with
names. This time we do the coercion in the calling R code.
C code to do the computations is
#include <R.h>
#include <Rinternals.h>

SEXP out(SEXP x, SEXP y)

{
int nx = length(x), ny = length(y);
SEXP ans = PROTECT(allocMatrix(REALSXP, nx, ny));
double *rx = REAL(x), *ry = REAL(y), *rans = REAL(ans);
for(int i = 0; i < nx; i++) {
double tmp = rx[i];
for(int j = 0; j < ny; j++)
rans[i + nx*j] = tmp * ry[j];
}
UNPROTECT(1);
return ans;
}
Note the way REAL is used: as it is a function call it can be considerably faster to
store the result and index that.
However, we would like to set the dimnames of the result. We can use
#include <R.h>
#include <Rinternals.h>
SEXP out(SEXP x, SEXP y)
{
int nx = length(x), ny = length(y);
SEXP ans = PROTECT(allocMatrix(REALSXP, nx, ny));
double *rx = REAL(x), *ry = REAL(y), *rans = REAL(ans);

for(int i = 0; i < nx; i++) {

double tmp = rx[i];
for(int j = 0; j < ny; j++)
rans[i + nx*j] = tmp * ry[j];
}

SEXP dimnames = PROTECT(allocVector(VECSXP, 2));

SET_VECTOR_ELT(dimnames, 0, getAttrib(x, R_NamesSymbol));
SET_VECTOR_ELT(dimnames, 1, getAttrib(y, R_NamesSymbol));
setAttrib(ans, R_DimNamesSymbol, dimnames);

UNPROTECT(2);
return ans;
}
This example introduces several new features.
The getAttrib and setAttrib functions get and set individual attributes. Their
second argument is a SEXP defining the name in the symbol table of the attribute we
want; these and many such symbols are defined in the header
file Rinternals.h.
There are shortcuts here too: the
functions namesgets, dimgets and dimnamesgets are the internal versions of the
default methods of names<-, dim<- and dimnames<- (for vectors and arrays), and
there are functions such
as GetColNames, GetRowNames, GetMatrixDimnames and GetArrayDimnames.
What happens if we want to add an attribute that is not pre-defined? We need to
add a symbol for it via a call to install. Suppose for illustration we wanted to add
an attribute "version" with value 3.0. We could use
SEXP version;
version = PROTECT(allocVector(REALSXP, 1));
REAL(version)[0] = 3.0;
setAttrib(ans, install("version"), version);
UNPROTECT(1);
Using install when it is not needed is harmless and provides a simple way to
retrieve the symbol from the symbol table if it is already installed. However, the
lookup takes a non-trivial amount of time, so consider code such as
static SEXP VerSymbol = NULL;
...
if (VerSymbol == NULL) VerSymbol = install("version");
if it is to be done frequently.
This example can be simplified by another convenience function:
SEXP version = PROTECT(ScalarReal(3.0));
setAttrib(ans, install("version"), version);
 UNPROTECT(1);

Next: Handling lists, Previous: Attributes, Up: Handling R objects in C

[Contents][Index]
5.9.5 Classes

In R the class is just the attribute named "class" so it can be handled as such, but
there is a shortcut classgets. Suppose we want to give the return value in our
example the class "mat". We can use
#include <R.h>
#include <Rinternals.h>
....
SEXP ans, dim, dimnames, class;
....
class = PROTECT(allocVector(STRSXP, 1));
SET_STRING_ELT(class, 0, mkChar("mat"));
classgets(ans, class);
UNPROTECT(4);
return ans;
}
As the value is a character vector, we have to know how to create that from a C
character array, which we do using the function mkChar.

Next: Handling character data, Previous: Classes, Up: Handling R objects in C

[Contents][Index]
5.9.6 Handling lists

Some care is needed with lists, as R moved early on from using LISP-like lists
(now called “pairlists”) to S-like generic vectors. As a result, the appropriate test
for an object of mode list is isNewList, and we need allocVector(VECSXP, n)
and not allocList(n).
List elements can be retrieved or set by direct access to the elements of the generic
vector. Suppose we have a list object
a <- list(f = 1, g = 2, h = 3)
Then we can access a$g as a[[2]] by
double g;
....
g = REAL(VECTOR_ELT(a, 1))[0];
This can rapidly become tedious, and the following function (based on one in
package stats) is very useful:
/* get the list element named str, or return NULL */

SEXP getListElement(SEXP list, const char *str)

{
SEXP elmt = R_NilValue, names = getAttrib(list, R_NamesSymbol);
 for (int i = 0; i < length(list); i++)
if(strcmp(CHAR(STRING_ELT(names, i)), str) == 0) {
elmt = VECTOR_ELT(list, i);
break;
}
return elmt;
}
and enables us to say
double g;
g = REAL(getListElement(a, "g"))[0];

Next: Finding and setting variables, Previous: Handling lists, Up: Handling R
objects in C [Contents][Index]
5.9.7 Handling character data

R character vectors are stored as STRSXPs, a vector type like VECSXP where every
element is of type CHARSXP. The CHARSXP elements of STRSXPs are accessed
using STRING_ELT and SET_STRING_ELT.
CHARSXPs are read-only objects and must never be modified. In particular, the C-
style string contained in a CHARSXP should be treated as read-only and for this
reason the CHAR function used to access the character data of
a CHARSXP returns (const char *) (this also allows compilers to issue warnings
about improper use). Since CHARSXPs are immutable, the same CHARSXP can be
shared by any STRSXP needing an element representing the same string. R maintains
a global cache of CHARSXPs so that there is only ever one CHARSXP representing a
given string in memory.
You can obtain a CHARSXP by calling mkChar and providing a nul-terminated C-style
string. This function will return a pre-existing CHARSXP if one with a matching
string already exists, otherwise it will create a new one and add it to the cache
before returning it to you. The variant mkCharLen can be used to create
a CHARSXP from part of a buffer and will ensure null-termination.
Note that R character strings are restricted to 2^31 - 1 bytes, and hence so should
the input to mkChar be (C allows longer strings on 64-bit platforms).

Next: Some convenience functions, Previous: Handling character data,

Up: Handling R objects in C [Contents][Index]
5.9.8 Finding and setting variables

It will be usual that all the R objects needed in our C computations are passed as
arguments to .Call or .External, but it is possible to find the values of R objects
from within the C given their names. The following code is the equivalent
of get(name, envir = rho).
SEXP getvar(SEXP name, SEXP rho)
{
SEXP ans;

if(!isString(name) || length(name) != 1)
error("name is not a single string");
if(!isEnvironment(rho))
error("rho should be an environment");
ans = findVar(installChar(STRING_ELT(name, 0)), rho);
Rprintf("first value is %f\n", REAL(ans)[0]);
return R_NilValue;
}
The main work is done by findVar, but to use it we need to install name as a name
in the symbol table. As we wanted the value for internal use, we return NULL.
Similar functions with syntax
void defineVar(SEXP symbol, SEXP value, SEXP rho)
void setVar(SEXP symbol, SEXP value, SEXP rho)
can be used to assign values to R variables. defineVar creates a new binding or
changes the value of an existing binding in the specified environment frame; it is
the analogue of assign(symbol, value, envir = rho, inherits = FALSE), but
unlike assign, defineVar does not make a copy of the
object value.154 setVar searches for an existing binding for symbol in rho or its
enclosing environments. If a binding is found, its value is changed to value.
Otherwise, a new binding with the specified value is created in the global
environment. This corresponds to assign(symbol, value, envir = rho, inherits
= TRUE).

At times it may also be useful to create a new environment frame in C

code. R_NewEnv is a C version of the R function [Link]:
SEXP R_NewEnv(SEXP enclos, int hash, int size)

Next: Named objects and copying, Previous: Finding and setting variables,
Up: Handling R objects in C [Contents][Index]
5.9.9 Some convenience functions

Some operations are done so frequently that there are convenience functions to
handle them. (All these are provided via the header file Rinternals.h.)
Suppose we wanted to pass a single logical argument ignore_quotes: we could use
int ign = asLogical(ignore_quotes);
if(ign == NA_LOGICAL) error("'ignore_quotes' must be TRUE or FALSE");
which will do any coercion needed (at least from a vector argument), and
return NA_LOGICAL if the value passed was NA or coercion failed. There are
also asInteger, asReal and asComplex. The function asChar returns a CHARSXP. All
of these functions ignore any elements of an input vector after the first.
To return a length-one real vector we can use
 double x;

...
return ScalarReal(x);
and there are versions of this for all the atomic vector types (those for a length-one
character vector being ScalarString with argument a CHARSXP and mkString with
argument const char *).
SEXP ScalarReal(double);
SEXP ScalarInteger(int);
SEXP ScalarLogical(int)
SEXP ScalarRaw(Rbyte);
SEXP ScalarComplex(Rcomplex);
SEXP ScalarString(SEXP);
SEXP mkString(const char *);
Some of the isXXXX functions differ from their apparent R-level counterparts: for
example isVector is true for any atomic vector type (isVectorAtomic) and for lists
and expressions (isVectorList) (with no check on attributes). isMatrix is a test of
a length-2 "dim" attribute.
Rboolean isVector(SEXP);
Rboolean isVectorAtomic(SEXP);
Rboolean isVectorList(SEXP);
Rboolean isMatrix(SEXP);
Rboolean isPairList(SEXP);
Rboolean isPrimitive(SEXP);
Rboolean isTs(SEXP);
Rboolean isNumeric(SEXP);
Rboolean isArray(SEXP);
Rboolean isFactor(SEXP);
Rboolean isObject(SEXP);
Rboolean isFunction(SEXP);
Rboolean isLanguage(SEXP);
Rboolean isNewList(SEXP);
Rboolean isList(SEXP);
Rboolean isOrdered(SEXP);
Rboolean isUnordered(SEXP);
There are a series of small macros/functions to help construct pairlists and
language objects (whose internal structures just differ by SEXPTYPE).
Function CONS(u, v) is the basic building block: it constructs a pairlist
from u followed by v (which is a pairlist or R_NilValue). LCONS is a variant that
constructs a language object. Functions list1 to list6 construct a pairlist from one
to six items, and lang1 to lang6 do the same for a language object (a function to
call plus zero to five arguments). Functions elt and lastElt find the ith element
and the last element of a pairlist, and nthcdr returns a pointer to the nth position in
the pairlist (whose CAR is the nth item).
Functions str2type and type2str map R length-one character strings to and
from SEXPTYPE numbers, and type2char maps numbers to C character strings.
 Semi-internal convenience functions
Previous: Some convenience functions, Up: Some convenience functions
[Contents][Index]
[Link] Semi-internal convenience functions

There is quite a collection of functions that may be used in your C code if you are
willing to adapt to rare “API” changes. These typically contain “workhorses” of
their R counterparts.
Functions any_duplicated and any_duplicated3 are fast versions of
R’s any(duplicated(.)).
Function R_compute_identical corresponds to R’s identical function.

Previous: Some convenience functions, Up: Handling R objects in C [Contents]

[Index]
5.9.10 Named objects and copying

[The NAMED mechanism has been replaced by reference counting.]

When assignments are done in R such as
x <- 1:10
y <- x
the named object is not necessarily copied, so after those two
assignments y and x are bound to the same SEXPREC (the structure a SEXP points to).
This means that any code which alters one of them has to make a copy before
modifying the copy if the usual R semantics are to apply. Note that
whereas .C and .Fortran do copy their arguments (unless the dangerous dup =
FALSE is used), .Call and .External do not. So duplicate is commonly called on
arguments to .Call before modifying them.
However, at least some of this copying is unneeded. In the first assignment
shown, x <- 1:10, R first creates an object with value 1:10 and then assigns it
to x but if x is modified no copy is necessary as the temporary object with
value 1:10 cannot be referred to again. R distinguishes between named and
unnamed objects via a field in a SEXPREC that can be accessed via the
macros NAMED and SET_NAMED. This can take values
0
The object is not bound to any symbol
1
The object has been bound to exactly one symbol
>= 2
 The object has potentially been bound to two or more symbols, and one
should act as if another variable is currently bound to this value. The
maximal value is NAMEDMAX.
Note the past tenses: R does not do currently do full reference counting and there
may currently be fewer bindings.
It is safe to modify the value of any SEXP for which NAMED(foo) is zero, and
if NAMED(foo) is two or more, the value should be duplicated (via a call
to duplicate) before any modification. Note that it is the responsibility of the
author of the code making the modification to do the duplication, even if it
is x whose value is being modified after y <- x.
The case NAMED(foo) == 1 allows some optimization, but it can be ignored (and
duplication done whenever NAMED(foo) > 0). (This optimization is not currently
usable in user code.) It is intended for use within replacement functions. Suppose
we used
x <- 1:10
foo(x) <- 3
which is computed as
x <- 1:10
x <- "foo<-"(x, 3)
Then inside "foo<-" the object pointing to the current value of x will
have NAMED(foo) as one, and it would be safe to modify it as the only symbol bound
to it is x and that will be rebound immediately. (Provided the remaining code
in "foo<-" make no reference to x, and no one is going to attempt a direct call such
as y <- "foo<-"(x).)
This mechanism was replaced in R 4.0.0. To support future changes, package code
should use the macros MAYBE_REFERENCED, MAYBE_SHARED, and MARK_NOT_MUTABLE.
These currently correspond to
MAYBE_REFERENCED(x)
NAMED(x) > 0
MAYBE_SHARED(x)
NAMED(x) > 1
MARK_NOT_MUTABLE(x)
SET_NAMED(x, NAMEDMAX)

Next: Evaluating R expressions from C, Previous: Handling R objects in C,

Up: System and foreign language interfaces [Contents][Index]

5.10 Interface functions .Call and .External

In this section we consider the details of the R/C interfaces.

These two interfaces have almost the same functionality. .Call is based on the
interface of the same name in S version 4, and .External is based on
R’s .Internal. .External is more complex but allows a variable number of
arguments.
 Calling .Call
 Calling .External
 Missing and special values

Next: Calling .External, Previous: Interface functions .Call and .External,

Up: Interface functions .Call and .External [Contents][Index]

5.10.1 Calling .Call

Let us convert our finite convolution example to use .Call. The calling function in
R is
conv <- function(a, b) .Call("convolve2", a, b)
which could hardly be simpler, but as we shall see all the type coercion is
transferred to the C code, which is
#include <R.h>
#include <Rinternals.h>

SEXP convolve2(SEXP a, SEXP b)

{
int na, nb, nab;
double *xa, *xb, *xab;
SEXP ab;

a = PROTECT(coerceVector(a, REALSXP));
b = PROTECT(coerceVector(b, REALSXP));
na = length(a); nb = length(b); nab = na + nb - 1;
ab = PROTECT(allocVector(REALSXP, nab));
xa = REAL(a); xb = REAL(b); xab = REAL(ab);
for(int i = 0; i < nab; i++) xab[i] = 0.0;
for(int i = 0; i < na; i++)
for(int j = 0; j < nb; j++) xab[i + j] += xa[i] * xb[j];
UNPROTECT(3);
return ab;
}

Next: Missing and special values, Previous: Calling .Call, Up: Interface
functions .Call and .External [Contents][Index]

5.10.2 Calling .External

We can use the same example to illustrate .External. The R code changes only by
replacing .Call by .External
conv <- function(a, b) .External("convolveE", a, b)
but the main change is how the arguments are passed to the C code, this time as a
single SEXP. The only change to the C code is how we handle the arguments.
#include <R.h>
#include <Rinternals.h>

SEXP convolveE(SEXP args)

{
int i, j, na, nb, nab;
double *xa, *xb, *xab;
SEXP a, b, ab;

a = PROTECT(coerceVector(CADR(args), REALSXP));
b = PROTECT(coerceVector(CADDR(args), REALSXP));
...
}
Once again we do not need to protect the arguments, as in the R side of the
interface they are objects that are already in use. The macros
first = CADR(args);
second = CADDR(args);
third = CADDDR(args);
fourth = CAD4R(args);
fifth = CAD5R(args);
provide convenient ways to access the first four arguments. More generally we can
use the CDR and CAR macros as in
args = CDR(args); a = CAR(args);
args = CDR(args); b = CAR(args);
which clearly allows us to extract an unlimited number of arguments
(whereas .Call has a limit, albeit at 65 not a small one).
More usefully, the .External interface provides an easy way to handle calls with a
variable number of arguments, as length(args) will give the number of arguments
supplied (of which the first is ignored). We may need to know the names (‘tags’)
given to the actual arguments, which we can by using the TAG macro and using
something like the following example, that prints the names and the first value of
its arguments if they are vector types.
SEXP showArgs(SEXP args)
{
args = CDR(args); /* skip ‘name’ */
for(int i = 0; args != R_NilValue; i++, args = CDR(args)) {
const char *name =
isNull(TAG(args)) ? "" : CHAR(PRINTNAME(TAG(args)));
SEXP el = CAR(args);
if (length(el) == 0) {
Rprintf("[%d] ‘%s’ R type, length 0\n", i+1, name);
continue;
}
switch(TYPEOF(el)) {
case REALSXP:
Rprintf("[%d] ‘%s’ %f\n", i+1, name, REAL(el)[0]);
break;
case LGLSXP:
case INTSXP:
Rprintf("[%d] ‘%s’ %d\n", i+1, name, INTEGER(el)[0]);
 break;
case CPLXSXP:
{
Rcomplex cpl = COMPLEX(el)[0];
Rprintf("[%d] ‘%s’ %f + %fi\n", i+1, name, cpl.r, cpl.i);
}
break;
case STRSXP:
Rprintf("[%d] ‘%s’ %s\n", i+1, name,
CHAR(STRING_ELT(el, 0)));
break;
default:
Rprintf("[%d] ‘%s’ R type\n", i+1, name);
}
}
return R_NilValue;
}
This can be called by the wrapper function
showArgs <- function(...) invisible(.External("showArgs", ...))
Note that this style of programming is convenient but not necessary, as an
alternative style is
showArgs1 <- function(...) invisible(.Call("showArgs1", list(...)))
The (very similar) C code is in the scripts.
Additional functions for accessing pairlist components are CAAR, CDAR, CDDR,
and CDDDR. These components can be modified
with SETCAR, SETCDR, SETCADR, SETCADDR, SETCADDDR, and SETCAD4R.

Previous: Calling .External, Up: Interface functions .Call and .External

[Contents][Index]
5.10.3 Missing and special values

One piece of error-checking the .C call does (unless NAOK is true) is to check for
missing (NA) and IEEE special values (Inf, -Inf and NaN) and give an error if any
are found. With the .Call interface these will be passed to our code. In this
example the special values are no problem, as IEC60559 arithmetic will handle
them correctly. In the current implementation this is also true of NA as it is a type
of NaN, but it is unwise to rely on such details. Thus we will re-write the code to
handle NAs using macros defined in R_ext/Arith.h included by R.h.
The code changes are the same in any of the versions of convolve2 or convolveE:
...
for(int i = 0; i < na; i++)
for(int j = 0; j < nb; j++)
if(ISNA(xa[i]) || ISNA(xb[j]) || ISNA(xab[i + j]))
xab[i + j] = NA_REAL;
else
xab[i + j] += xa[i] * xb[j];
...
Note that the ISNA macro, and the similar macros ISNAN (which checks
for NaN or NA) and R_FINITE (which is false for NA and all the special values), only
apply to numeric values of type double. Missingness of integers, logicals and
character strings can be tested by equality to the
constants NA_INTEGER, NA_LOGICAL and NA_STRING. These and NA_REAL can be used to
set elements of R vectors to NA.
The constants R_NaN, R_PosInf and R_NegInf can be used to set doubles to the
special values.

Next: Parsing R code from C, Previous: Interface functions .Call and .External,
Up: System and foreign language interfaces [Contents][Index]

5.11 Evaluating R expressions from C

The main function we will use is
SEXP eval(SEXP expr, SEXP rho);
the equivalent of the interpreted R code eval(expr, envir = rho) (so rho must be
an environment), although we can also make use
of findVar, defineVar and findFun (which restricts the search to functions).
To see how this might be applied, here is a simplified internal version of lapply for
expressions, used as
a <- list(a = 1:5, b = rnorm(10), test = runif(100))
.Call("lapply", a, quote(sum(x)), [Link]())
with C code
SEXP lapply(SEXP list, SEXP expr, SEXP rho)
{
int n = length(list);
SEXP ans;

if(!isNewList(list)) error("'list' must be a list");

if(!isEnvironment(rho)) error("'rho' should be an environment");
ans = PROTECT(allocVector(VECSXP, n));
for(int i = 0; i < n; i++) {
defineVar(install("x"), VECTOR_ELT(list, i), rho);
SET_VECTOR_ELT(ans, i, eval(expr, rho));
}
setAttrib(ans, R_NamesSymbol, getAttrib(list, R_NamesSymbol));
UNPROTECT(1);
return ans;
}
It would be closer to lapply if we could pass in a function rather than an
expression. One way to do this is via interpreted R code as in the next example, but
it is possible (if somewhat obscure) to do this in C code. The following is based on
the code in src/main/optimize.c.
SEXP lapply2(SEXP list, SEXP fn, SEXP rho)
{
 int n = length(list);
SEXP R_fcall, ans;

if(!isNewList(list)) error("'list' must be a list");

if(!isFunction(fn)) error("'fn' must be a function");
if(!isEnvironment(rho)) error("'rho' should be an environment");
R_fcall = PROTECT(lang2(fn, R_NilValue));
ans = PROTECT(allocVector(VECSXP, n));
for(int i = 0; i < n; i++) {
SETCADR(R_fcall, VECTOR_ELT(list, i));
SET_VECTOR_ELT(ans, i, eval(R_fcall, rho));
}
setAttrib(ans, R_NamesSymbol, getAttrib(list, R_NamesSymbol));
UNPROTECT(2);
return ans;
}
used by
.Call("lapply2", a, sum, [Link]())
Function lang2 creates an executable pairlist of two elements, but this will only be
clear to those with a knowledge of a LISP-like language.
As a more comprehensive example of constructing an R call in C code and
evaluating, consider the following fragment
of printAttributes in src/main/print.c.
/* Need to construct a call to
print(CAR(a), digits=digits)
based on the R_print structure, then eval(call, env).
See do_docall for the template for this sort of thing.
*/
SEXP s, t;
t = s = PROTECT(allocList(3));
SET_TYPEOF(s, LANGSXP);
SETCAR(t, install("print")); t = CDR(t);
SETCAR(t, CAR(a)); t = CDR(t);
SETCAR(t, ScalarInteger(digits));
SET_TAG(t, install("digits"));
eval(s, env);
UNPROTECT(1);
At this point CAR(a) is the R object to be printed, the current attribute. There are
three steps: the call is constructed as a pairlist of length 3, the list is filled in, and
the expression represented by the pairlist is evaluated.
A pairlist is quite distinct from a generic vector list, the only user-visible form of
list in R. A pairlist is a linked list (with CDR(t) computing the next entry), with
items (accessed by CAR(t)) and names or tags (set by SET_TAG). In this call there are
to be three items, a symbol (pointing to the function to be called) and two
argument values, the first unnamed and the second named. Setting the type
to LANGSXP makes this a call which can be evaluated.
Customarily, the evaluation environment is passed from the calling R code
(see rho above). In special cases it is possible that the C code may need to obtain
the current evaluation environment which can be done
via R_GetCurrentEnv() function.
  Zero-finding
 Calculating numerical derivatives

Next: Calculating numerical derivatives, Previous: Evaluating R expressions from

C, Up: Evaluating R expressions from C [Contents][Index]
5.11.1 Zero-finding

In this section we re-work the example of Becker, Chambers & Wilks (1988,
pp.~205–10) on finding a zero of a univariate function. The R code and an example
are
zero <- function(f, guesses, tol = 1e-7) {
[Link] <- function(x) {
x <- f(x)
if() stop("Need a numeric result")
[Link](x)
}
.Call("zero", body([Link]), [Link](guesses), [Link](tol),
[Link]())
}

cube1 <- function(x) (x^2 + 1) * (x - 1.5)

zero(cube1, c(0, 5))
where this time we do the coercion and error-checking in the R code. The C code is
SEXP mkans(double x)
{
// no need for PROTECT() here, as REAL(.) does not allocate:
SEXP ans = allocVector(REALSXP, 1);
REAL(ans)[0] = x;
return ans;
}

double feval(double x, SEXP f, SEXP rho)

{
// a version with (too) much PROTECT()ion .. "better safe than sorry"
SEXP symbol, value;
PROTECT(symbol = install("x"));
PROTECT(value = mkans(x));
defineVar(symbol, value, rho);
UNPROTECT(2);
return(REAL(eval(f, rho))[0]);
}

SEXP zero(SEXP f, SEXP guesses, SEXP stol, SEXP rho)

{
double x0 = REAL(guesses)[0], x1 = REAL(guesses)[1],
tol = REAL(stol)[0];
double f0, f1, fc, xc;

if(tol <= 0.0) error("non-positive tol value");

f0 = feval(x0, f, rho); f1 = feval(x1, f, rho);
if(f0 == 0.0) return mkans(x0);
if(f1 == 0.0) return mkans(x1);
if(f0*f1 > 0.0) error("x[0] and x[1] have the same sign");
 for(;;) {
xc = 0.5*(x0+x1);
if(fabs(x0-x1) < tol) return mkans(xc);
fc = feval(xc, f, rho);
if(fc == 0) return mkans(xc);
if(f0*fc > 0.0) {
x0 = xc; f0 = fc;
} else {
x1 = xc; f1 = fc;
}
}
}

Previous: Zero-finding, Up: Evaluating R expressions from C [Contents][Index]

5.11.2 Calculating numerical derivatives

We will use a longer example (by Saikat DebRoy) to illustrate the use of
evaluation and .External. This calculates numerical derivatives, something that
could be done as effectively in interpreted R code but may be needed as part of a
larger C calculation.
An interpreted R version and an example are
[Link] <- function(expr, theta, rho=[Link]([Link]()))
{
eps <- sqrt(.Machine$[Link])
ans <- eval(substitute(expr), rho)
grad <- matrix(, length(ans), length(theta),
dimnames=list(NULL, theta))
for (i in seq_along(theta)) {
old <- get(theta[i], envir=rho)
delta <- eps * max(1, abs(old))
assign(theta[i], old+delta, envir=rho)
ans1 <- eval(substitute(expr), rho)
assign(theta[i], old, envir=rho)
grad[, i] <- (ans1 - ans)/delta
}
attr(ans, "gradient") <- grad
ans
}
omega <- 1:5; x <- 1; y <- 2
[Link](sin(omega*x*y), c("x", "y"))
where expr is an expression, theta a character vector of variable names and rho the
environment to be used.
For the compiled version the call from R will be
.External("numeric_deriv", expr, theta, rho)
with example usage
.External("numeric_deriv", quote(sin(omega*x*y)),
c("x", "y"), .GlobalEnv)
Note the need to quote the expression to stop it being evaluated in the caller.
Here is the complete C code which we will explain section by section.
#include <R.h>
#include <Rinternals.h>
#include <float.h> /* for DBL_EPSILON */

SEXP numeric_deriv(SEXP args)

{
SEXP theta, expr, rho, ans, ans1, gradient, par, dimnames;
double tt, xx, delta, eps = sqrt(DBL_EPSILON), *rgr, *rans;
int i, start;

expr = CADR(args);
if(!isString(theta = CADDR(args)))
error("theta should be of type character");
if(!isEnvironment(rho = CADDDR(args)))
error("rho should be an environment");

ans = PROTECT(coerceVector(eval(expr, rho), REALSXP));

gradient = PROTECT(allocMatrix(REALSXP, LENGTH(ans), LENGTH(theta)));
rgr = REAL(gradient); rans = REAL(ans);

for(i = 0, start = 0; i < LENGTH(theta); i++, start += LENGTH(ans)) {

par = PROTECT(findVar(installChar(STRING_ELT(theta, i)), rho));
tt = REAL(par)[0];
xx = fabs(tt);
delta = (xx < 1) ? eps : xx*eps;
REAL(par)[0] += delta;
ans1 = PROTECT(coerceVector(eval(expr, rho), REALSXP));
for(int j = 0; j < LENGTH(ans); j++)
rgr[j + start] = (REAL(ans1)[j] - rans[j])/delta;
REAL(par)[0] = tt;
UNPROTECT(2); /* par, ans1 */
}

dimnames = PROTECT(allocVector(VECSXP, 2));

SET_VECTOR_ELT(dimnames, 1, theta);
dimnamesgets(gradient, dimnames);
setAttrib(ans, install("gradient"), gradient);
UNPROTECT(3); /* ans gradient dimnames */
return ans;
}
The code to handle the arguments is
expr = CADR(args);
if(!isString(theta = CADDR(args)))
error("theta should be of type character");
if(!isEnvironment(rho = CADDDR(args)))
error("rho should be an environment");
Note that we check for correct types of theta and rho but do not check the type
of expr. That is because eval can handle many types of R objects other
than EXPRSXP. There is no useful coercion we can do, so we stop with an error
message if the arguments are not of the correct mode.
The first step in the code is to evaluate the expression in the environment rho, by
ans = PROTECT(coerceVector(eval(expr, rho), REALSXP));
We then allocate space for the calculated derivative by
gradient = PROTECT(allocMatrix(REALSXP, LENGTH(ans), LENGTH(theta)));
The first argument to allocMatrix gives the SEXPTYPE of the matrix: here we want it
to be REALSXP. The other two arguments are the numbers of rows and columns.
(Note that LENGTH is intended to be used for vectors: length is more generally
applicable.)
for(i = 0, start = 0; i < LENGTH(theta); i++, start += LENGTH(ans)) {
par = PROTECT(findVar(installChar(STRING_ELT(theta, i)), rho));
Here, we are entering a for loop. We loop through each of the variables. In
the for loop, we first create a symbol corresponding to the i’th element of
the STRSXP theta. Here, STRING_ELT(theta, i) accesses the i’th element of
the STRSXP theta. Macro CHAR() extracts the actual character representation155 of it:
it returns a pointer. We then install the name and use findVar to find its value.
tt = REAL(par)[0];
xx = fabs(tt);
delta = (xx < 1) ? eps : xx*eps;
REAL(par)[0] += delta;
ans1 = PROTECT(coerceVector(eval(expr, rho), REALSXP));
We first extract the real value of the parameter, then calculate delta, the increment
to be used for approximating the numerical derivative. Then we change the value
stored in par (in environment rho) by delta and evaluate expr in
environment rho again. Because we are directly dealing with original R memory
locations here, R does the evaluation for the changed parameter value.
for(int j = 0; j < LENGTH(ans); j++)
rgr[j + start] = (REAL(ans1)[j] - rans[j])/delta;
REAL(par)[0] = tt;
UNPROTECT(2);
}
Now, we compute the i’th column of the gradient matrix. Note how it is accessed:
R stores matrices by column (like Fortran).
dimnames = PROTECT(allocVector(VECSXP, 2));
SET_VECTOR_ELT(dimnames, 1, theta);
dimnamesgets(gradient, dimnames);
setAttrib(ans, install("gradient"), gradient);
UNPROTECT(3);
return ans;
}
First we add column names to the gradient matrix. This is done by allocating a list
(a VECSXP) whose first element, the row names, is NULL (the default) and the second
element, the column names, is set as theta. This list is then assigned as the
attribute having the symbol R_DimNamesSymbol. Finally we set the gradient matrix as
the gradient attribute of ans, unprotect the remaining protected locations and return
the answer ans.

Next: External pointers and weak references, Previous: Evaluating R expressions

from C, Up: System and foreign language interfaces [Contents][Index]

5.12 Parsing R code from C

Suppose an R extension want to accept an R expression from the user and evaluate
it. The previous section covered evaluation, but the expression will be entered as
text and needs to be parsed first. A small part of R’s parse interface is declared in
header file R_ext/Parse.h156.
An example of the usage can be found in the (example) Windows
package windlgs included in the R source tree. The essential part is
#include <R.h>
#include <Rinternals.h>
#include <R_ext/Parse.h>

SEXP menu_ttest3()
{
char cmd[256];
SEXP cmdSexp, cmdexpr, ans = R_NilValue;
ParseStatus status;
...
if(done == 1) {
cmdSexp = PROTECT(allocVector(STRSXP, 1));
SET_STRING_ELT(cmdSexp, 0, mkChar(cmd));
cmdexpr = PROTECT(R_ParseVector(cmdSexp, -1, &status, R_NilValue));
if (status != PARSE_OK) {
UNPROTECT(2);
error("invalid call %s", cmd);
}
/* Loop is needed here as EXPSEXP will be of length > 1 */
for(int i = 0; i < length(cmdexpr); i++)
ans = eval(VECTOR_ELT(cmdexpr, i), R_GlobalEnv);
UNPROTECT(2);
}
return ans;
}
Note that a single line of text may give rise to more than one R expression.
R_ParseVector is essentially the code used to implement parse(text=) at R level.
The first argument is a character vector (corresponding to text) and the second the
maximal number of expressions to parse (corresponding to n). The third argument
is a pointer to a variable of an enumeration type, and it is normal (as parse does) to
regard all values other than PARSE_OK as an error. Other values which might be
returned are PARSE_INCOMPLETE (an incomplete expression was found)
and PARSE_ERROR (a syntax error), in both cases the value returned
being R_NilValue. The fourth argument is a length one character vector to be used
as a filename in error messages, a srcfile object or the R NULL object (as in the
example above). If a srcfile object was used, a srcref attribute would be attached
to the result, containing a list of srcref objects of the same length as the
expression, to allow it to be echoed with its original formatting.
 Accessing source references

Previous: Parsing R code from C, Up: Parsing R code from C [Contents][Index]

5.12.1 Accessing source references
The source references added by the parser are recorded by R’s evaluator as it
evaluates code. Two functions make these available to debuggers running C code:
SEXP R_GetCurrentSrcref(int skip);
This function checks R_Srcref and the current evaluation stack for entries that
contain source reference information. The skip argument tells how many source
references to skip before returning the SEXP of the srcref object, counting from the
top of the stack. If skip < 0, abs(skip) locations are counted up from the bottom
of the stack. If too few or no source references are found, NULL is returned.
SEXP R_GetSrcFilename(SEXP srcref);
This function extracts the filename from the source reference for display, returning
a length 1 character vector containing the filename. If no name is found, "" is
returned.

Next: Vector accessor functions, Previous: Parsing R code from C, Up: System and
foreign language interfaces [Contents][Index]

5.13 External pointers and weak

references
The SEXPTYPEs EXTPTRSXP and WEAKREFSXP can be encountered at R level, but are
created in C code.
External pointer SEXPs are intended to handle references to C structures such as
‘handles’, and are used for this purpose in package RODBC for example. They are
unusual in their copying semantics in that when an R object is copied, the external
pointer object is not duplicated. (For this reason external pointers should only be
used as part of an object with normal semantics, for example an attribute or an
element of a list.)
An external pointer is created by
SEXP R_MakeExternalPtr(void *p, SEXP tag, SEXP prot);
where p is the pointer (and hence this cannot portably be a function pointer),
and tag and prot are references to ordinary R objects which will remain in
existence (be protected from garbage collection) for the lifetime of the external
pointer object. A useful convention is to use the tag field for some form of type
identification and the prot field for protecting the memory that the external pointer
represents, if that memory is allocated from the R heap. Both tag and prot can
be R_NilValue, and often are.
An alternative way to create an external pointer from a function pointer is
typedef void * (*R_DL_FUNC)();
SEXP R_MakeExternalPtrFn(R_DL_FUNC p, SEXP tag, SEXP prot);
The elements of an external pointer can be accessed and set via
void *R_ExternalPtrAddr(SEXP s);
DL_FUNC R_ExternalPtrAddrFn(SEXP s);
SEXP R_ExternalPtrTag(SEXP s);
SEXP R_ExternalPtrProtected(SEXP s);
void R_ClearExternalPtr(SEXP s);
void R_SetExternalPtrAddr(SEXP s, void *p);
void R_SetExternalPtrTag(SEXP s, SEXP tag);
void R_SetExternalPtrProtected(SEXP s, SEXP p);
Clearing a pointer sets its value to the C NULL pointer.
An external pointer object can have a finalizer, a piece of code to be run when the
object is garbage collected. This can be R code or C code, and the various
interfaces are, respectively.
void R_RegisterFinalizer(SEXP s, SEXP fun);
void R_RegisterFinalizerEx(SEXP s, SEXP fun, Rboolean onexit);

typedef void (*R_CFinalizer_t)(SEXP);

void R_RegisterCFinalizer(SEXP s, R_CFinalizer_t fun);
void R_RegisterCFinalizerEx(SEXP s, R_CFinalizer_t fun, Rboolean onexit);
The R function indicated by fun should be a function of a single argument, the
object to be finalized. R does not perform a garbage collection when shutting
down, and the onexit argument of the extended forms can be used to ask that the
finalizer be run during a normal shutdown of the R session. It is suggested that it is
good practice to clear the pointer on finalization.
The only R level function for interacting with external pointers
is [Link] which can be used to set a finalizer.
It is probably not a good idea to allow an external pointer to be saved and then
reloaded, but if this happens the pointer will be set to the C NULL pointer.
Finalizers can be run at many places in the code base and much of it, including the
R interpreter, is not re-entrant. So great care is needed in choosing the code to be
run in a finalizer. Finalizers are marked to be run at garbage collection but only run
at a somewhat safe point thereafter.
Weak references are used to allow the programmer to maintain information on
entities without preventing the garbage collection of the entities once they become
unreachable.
A weak reference contains a key and a value. The value is reachable is if it either
reachable directly or via weak references with reachable keys. Once a value is
determined to be unreachable during garbage collection, the key and value are set
to R_NilValue and the finalizer will be run later in the garbage collection.
Weak reference objects are created by one of
SEXP R_MakeWeakRef(SEXP key, SEXP val, SEXP fin, Rboolean onexit);
SEXP R_MakeWeakRefC(SEXP key, SEXP val, R_CFinalizer_t fin,
Rboolean onexit);
where the R or C finalizer are specified in exactly the same way as for an external
pointer object (whose finalization interface is implemented via weak references).
The parts can be accessed via
SEXP R_WeakRefKey(SEXP w);
SEXP R_WeakRefValue(SEXP w);
void R_RunWeakRefFinalizer(SEXP w);
A toy example of the use of weak references can be found
at [Link] but that is
used to add finalizers to external pointers which can now be done more directly. At
the time of writing no CRAN or Bioconductor package uses weak references.
 An example

Previous: External pointers and weak references, Up: External pointers and weak
references [Contents][Index]
5.13.1 An example

Package RODBC uses external pointers to maintain its channels, connections to

databases. There can be several connections open at once, and the status
information for each is stored in a C structure (pointed to by thisHandle in the code
extract below) that is returned via an external pointer as part of the RODBC
‘channel’ (as the "handle_ptr" attribute). The external pointer is created by
SEXP ans, ptr;
ans = PROTECT(allocVector(INTSXP, 1));
ptr = R_MakeExternalPtr(thisHandle, install("RODBC_channel"),
R_NilValue);
PROTECT(ptr);
R_RegisterCFinalizerEx(ptr, chanFinalizer, TRUE);
...
/* return the channel no */
INTEGER(ans)[0] = nChannels;
/* and the connection string as an attribute */
setAttrib(ans, install("[Link]"), constr);
setAttrib(ans, install("handle_ptr"), ptr);
UNPROTECT(3);
return ans;
Note the symbol given to identify the usage of the external pointer, and the use of
the finalizer. Since the final argument when registering the finalizer is TRUE, the
finalizer will be run at the end of the R session (unless it crashes). This is used to
close and clean up the connection to the database. The finalizer code is simply
static void chanFinalizer(SEXP ptr)
{
if(!R_ExternalPtrAddr(ptr)) return;
inRODBCClose(R_ExternalPtrAddr(ptr));
R_ClearExternalPtr(ptr); /* not really needed */
}
Clearing the pointer and checking for a NULL pointer avoids any possibility of
attempting to close an already-closed channel.
R’s connections provide another example of using external pointers, in that case
purely to be able to use a finalizer to close and destroy the connection if it is no
longer is use.

Next: Character encoding issues, Previous: External pointers and weak references,
Up: System and foreign language interfaces [Contents][Index]

5.14 Vector accessor functions

The vector accessors like REAL, INTEGER, LOGICAL, RAW, COMPLEX,
and VECTOR_ELT are functions when used in R extensions. (For efficiency they may
be macros or inline functions when used in the R source code, apart
from SET_STRING_ELT and SET_VECTOR_ELT which are always functions.)
The accessor functions check that they are being used on an appropriate type
of SEXP.
Formerly it was possible for packages to obtain internal versions of some accessors
by defining ‘USE_RINTERNALS’ before including Rinternals.h. This is no
longer the case. Defining ‘USE_RINTERNALS’ now has no effect.

Previous: Vector accessor functions, Up: System and foreign language interfaces
[Contents][Index]

5.15 Character encoding issues

CHARSXPs can be marked as coming from a known encoding (Latin-1 or UTF-8).
This is mainly intended for human-readable output, and most packages can just
treat such CHARSXPs as a whole. However, if they need to be interpreted as
characters or output at C level then it would normally be correct to ensure that they
are converted to the encoding of the current locale: this can be done by accessing
the data in the CHARSXP by translateChar rather than by CHAR. If re-encoding is
needed this allocates memory with R_alloc which thus persists to the end of
the .Call/.External call unless vmaxset is used (see Transient storage allocation).
There is a similar function translateCharUTF8 which converts to UTF-8: this has
the advantage that a faithful translation is almost always possible (whereas only a
few languages can be represented in the encoding of the current locale unless that
is UTF-8).
Both translateChar and translateCharUTF8 will translate any input, using escapes
such as ‘<A9>’ and ‘<U+0093>’ to represent untranslatable parts of the input.
There is a public interface to the encoding marked on CHARSXPs via
typedef enum {CE_NATIVE, CE_UTF8, CE_LATIN1, CE_BYTES, CE_SYMBOL, CE_ANY}
cetype_t;
cetype_t getCharCE(SEXP);
SEXP mkCharCE(const char *, cetype_t);
Only CE_UTF8 and CE_LATIN1 are marked on CHARSXPs (and so Rf_getCharCE will
only return one of the first three), and these should only be used on non-
ASCII strings. Value CE_BYTES is used to make CHARSXPs which should be regarded
as a set of bytes and not translated. Value CE_SYMBOL is used internally to indicate
Adobe Symbol encoding. Value CE_ANY is used to indicate a character string that
will not need re-encoding – this is used for character strings known to be in ASCII,
and can also be used as an input parameter where the intention is that the string is
treated as a series of bytes. (See the comments under mkChar about the length of
input allowed.)
Function
const char *reEnc(const char *x, cetype_t ce_in, cetype_t ce_out,
int subst);
can be used to re-encode character strings: like translateChar it returns a string
allocated by R_alloc. This can translate from CE_SYMBOL to CE_UTF8, but not
conversely. Argument subst controls what to do with untranslatable characters or
invalid input: this is done byte-by-byte with 1 indicates to output hex of the
form <a0>, and 2 to replace by ., with any other value causing the byte to produce
no output.
There is also
SEXP mkCharLenCE(const char *, size_t, cetype_t);
to create marked character strings of a given length.

Next: Generic functions and methods, Previous: System and foreign language
interfaces, Up: Writing R Extensions [Contents][Index]

6 The R API: entry points for C

code
There are a large number of entry points in the R executable/DLL that can be
called from C code (and some that can be called from Fortran code). Only those
documented here are stable enough that they will only be changed with
considerable notice.
The recommended procedure to use these is to include the header file R.h in your
C code by
#include <R.h>
This will include several other header files from the
directory R_INCLUDE_DIR/R_ext, and there are other header files there that
can be included too, but many of the features they contain should be regarded as
undocumented and unstable.
Most of these header files, including all those included by R.h, can be used from
C++ code.
Note: Because R re-maps many of its external names to avoid clashes with system
or user code, it is essential to include the appropriate header files when using these
entry points.
This remapping can cause problems157, and can be eliminated by
defining R_NO_REMAP (before including any R headers) and prepending ‘Rf_’
to all the function names used from Rinternals.h and R_ext/Error.h.
These problems can usually be avoided by including other headers (such as system
headers and those for external software used by the package) before any R headers.
(Headers from other packages may include R headers directly or via inclusion from
further packages, and may define R_NO_REMAP with or without
including Rinternals.h.)
We can classify the entry points as
API
Entry points which are documented in this manual and declared in an
installed header file. These can be used in distributed packages and will only
be changed after deprecation.
public
Entry points declared in an installed header file that are exported on all R
platforms but are not documented and subject to change without notice.
private
Entry points that are used when building R and exported on all R platforms
but are not declared in the installed header files. Do not use these in
distributed code.
hidden
Entry points that are where possible (Windows and some modern Unix-alike
compilers/loaders when using R as a shared library) not exported.
 Memory allocation
 Error signaling
 Random number generation
 Missing and IEEE special values
 Printing
 Calling C from Fortran and vice versa
 Numerical analysis subroutines
 Optimization
  Integration
 Utility functions
 Re-encoding
 Condition handling and cleanup code
 Allowing interrupts
 Platform and version information
 Inlining C functions
 Controlling visibility
 Using these functions in your own C code
 Organization of header files

Next: Error signaling, Previous: The R API: entry points for C code, Up: The
R API: entry points for C code [Contents][Index]

6.1 Memory allocation

There are two types of memory allocation available to the C programmer, one in
which R manages the clean-up and the other in which user has full control (and
responsibility).
These functions are declared in header R_exts/RS.h which is included by R.h.
 Transient storage allocation
 User-controlled memory

Next: User-controlled memory, Previous: Memory allocation, Up: Memory

allocation [Contents][Index]
6.1.1 Transient storage allocation

Here R will reclaim the memory at the end of the call to .C, .Call or .External.
Use
char *R_alloc(size_t n, int size)
which allocates n units of size bytes each. A typical usage (from package stats) is
x = (int *) R_alloc(nrows(merge)+2, sizeof(int));
(size_t is defined in stddef.h which the header defining R_alloc includes.)
There is a similar call, S_alloc (named for compatibility with older versions of S)
which zeroes the memory allocated,
char *S_alloc(long n, int size)
and
char *S_realloc(char *p, long new, long old, int size)
which (for new > old) changes the allocation size from old to new units, and zeroes
the additional units. NB: these calls are best avoided as long is insufficient for
large memory allocations on 64-bit Windows (where it is limited to 2^31-1 bytes).
This memory is taken from the heap, and released at the end of
the .C, .Call or .External call. Users can also manage it, by noting the current
position with a call to vmaxget and subsequently clearing memory allocated by a
call to vmaxset. An example might be
void *vmax = vmaxget()
// a loop involving the use of R_alloc at each iteration
vmaxset(vmax)
This is only recommended for experts.
Note that this memory will be freed on error or user interrupt (if allowed:
see Allowing interrupts).
The memory returned is only guaranteed to be aligned as required
for double pointers: take precautions if casting to a pointer which needs more.
There is also
long double *R_allocLD(size_t n)
which is guaranteed to have the 16-byte alignment needed for long double pointers
on some platforms.
These functions should only be used in code called by .C etc, never from front-
ends. They are not thread-safe.

Previous: Transient storage allocation, Up: Memory allocation [Contents][Index]

6.1.2 User-controlled memory

The other form of memory allocation is an interface to malloc, the interface

providing R error signaling. This memory lasts until freed by the user and is
additional to the memory allocated for the R workspace.
The interface macros are
type* R_Calloc(size_t n, type)
type* R_Realloc(any *p, size_t n, type)
void R_Free(any *p)
providing analogues of calloc, realloc and free. If there is an error during
allocation it is handled by R, so if these return the memory has been successfully
allocated or freed. R_Free will set the pointer p to NULL. (Some but not all versions
of S did so.)
Users should arrange to R_Free this memory when no longer needed, including on
error or user interrupt. This can often be done most conveniently from
an [Link] action in the calling R function – see pwilcox for an example.
Do not assume that memory allocated by R_Calloc/R_Realloc comes from the same
pool as used by malloc:158 in particular do not use free or strdup with it.
Memory obtained by these macros should be aligned in the same way as malloc,
that is ‘suitably aligned for any kind of variable’.
Historically the macros Calloc, Free and Realloc were used, and these remain
available unless STRICT_R_HEADERS was defined prior to the inclusion of the header.
char * CallocCharBuf(size_t n)
void * Memcpy(p, q, n)
void * Memzero(p, m)
CallocCharBuf is shorthand for R_Calloc(n+1, char) to allow for
the nul terminator. Memcpy and Memzero take n items from array p and copy them to
array p or zero them respectively.

Next: Random number generation, Previous: Memory allocation, Up: The R API:
entry points for C code [Contents][Index]

6.2 Error signaling

The basic error signaling routines are the equivalents of stop and warning in R
code, and use the same interface.
void error(const char * format, ...);
void warning(const char * format, ...);
void errorcall(SEXP call, const char * format, ...);
void warningcall(SEXP call, const char * format, ...);
void warningcall_immediate(SEXP call, const char * format, ...);
These have the same call sequences as calls to printf, but in the simplest case can
be called with a single character string argument giving the error message. (Don’t
do this if the string contains ‘%’ or might otherwise be interpreted as a format.)
These are defined in header R_ext/Error.h included by R.h.
 Error signaling from Fortran

Previous: Error signaling, Up: Error signaling [Contents][Index]

6.2.1 Error signaling from Fortran

There are two interface function provided to call error and warning from Fortran
code, in each case with a simple character string argument. They are defined as
subroutine rexit(message)
subroutine rwarn(message)
Messages of more than 255 characters are truncated, with a warning.
Next: Missing and IEEE special values, Previous: Error signaling, Up: The R API:
entry points for C code [Contents][Index]

6.3 Random number generation

The interface to R’s internal random number generation routines is
double unif_rand();
double norm_rand();
double exp_rand();
double R_unif_index(double);
giving one uniform, normal or exponential pseudo-random variate. However,
before these are used, the user must call
GetRNGstate();
and after all the required variates have been generated, call
PutRNGstate();
These essentially read in (or create) .[Link] and write it out after use.
These are defined in header R_ext/Random.h.
The random number generator is private to R; there is no way to select the kind of
RNG nor set the seed except by evaluating calls to the R functions.
The C code behind R’s rxxx functions can be accessed by including the header
file Rmath.h; See Distribution functions. Those calls should also be preceded and
followed by calls to GetRNGstate and PutRNGstate.

Next: Printing, Previous: Random number generation, Up: The R API: entry points
for C code [Contents][Index]

6.4 Missing and IEEE special values

A set of functions is provided to test for NA, Inf, -Inf and NaN. These functions are
accessed via macros:
ISNA(x) True for R’s NA only
ISNAN(x) True for R’s NA and IEEE NaN
R_FINITE(x) False for Inf, -Inf, NA, NaN
and via function R_IsNaN which is true for NaN but not NA.
Do use R_FINITE rather than isfinite or finite; the latter is often mendacious
and isfinite is only available on a some platforms, on which R_FINITE is a macro
expanding to isfinite.
Currently in C code ISNAN is a macro calling isnan. (Since this gives problems on
some C++ systems, if the R headers is called from C++ code a function call is
used.)
You can check for Inf or -Inf by testing equality to R_PosInf or R_NegInf, and set
(but not test) an NA as NA_REAL.
All of the above apply to double variables only. For integer variables there is a
variable accessed by the macro NA_INTEGER which can used to set or test for
missingness.
These are defined in header R_ext/Arith.h included by R.h.

Next: Calling C from Fortran and vice versa, Previous: Missing and IEEE special
values, Up: The R API: entry points for C code [Contents][Index]

6.5 Printing
The most useful function for printing from a C routine compiled into R is Rprintf.
This is used in exactly the same way as printf, but is guaranteed to write to R’s
output (which might be a GUI console rather than a file, and can be re-directed
by sink). It is wise to write complete lines (including the "\n") before returning to
R. It is defined in R_ext/Print.h.
The function REprintf is similar but writes on the error stream (stderr) which may
or may not be different from the standard output stream.
Functions Rvprintf and REvprintf are analogues using the vprintf interface.
Because that is a C99159 interface, they are only defined by R_ext/Print.h in
C++ code if the macro R_USE_C99_IN_CXX is defined before it is included or (as
from R 4.0.0) a C++11 compiler is used.
Another circumstance when it may be important to use these functions is when
using parallel computation on a cluster of computational nodes, as their output will
be re-directed/logged appropriately.
 Printing from Fortran

Previous: Printing, Up: Printing [Contents][Index]

6.5.1 Printing from Fortran

On many systems Fortran write and print statements can be used, but the output
may not interleave well with that of C, and may be invisible on GUI interfaces.
They are not portable and best avoided.
Some subroutines are provided to ease the output of information from Fortran
code.
subroutine dblepr(label, nchar, data, ndata)
subroutine realpr(label, nchar, data, ndata)
subroutine intpr (label, nchar, data, ndata)
and from R 4.0.0,
subroutine labelpr(label, nchar)
subroutine dblepr1(label, nchar, var)
subroutine realpr1(label, nchar, var)
subroutine intpr1 (label, nchar, var)
Here label is a character label of up to 255 characters, nchar is its length (which
can be -1 if the whole label is to be used), data is an array of length at
least ndata of the appropriate type (double
precision, real and integer respectively) and var is a (scalar) variable. These
routines print the label on one line and then print data or var as if it were an R
vector on subsequent line(s). Note that some compilers will give an error or
warning unless data is an array: others will accept a scalar when ndata has value
one or zero. NB: There is no check on the type of data or var, so
using real (including a real constant) instead of double precision will give
incorrect answers.
intpr works with zero ndata so can be used to print a label in earlier versions of R.

Next: Numerical analysis subroutines, Previous: Printing, Up: The R API: entry
points for C code [Contents][Index]

6.6 Calling C from Fortran and vice versa

Naming conventions for symbols generated by Fortran differ by platform: it is not
safe to assume that Fortran names appear to C with a trailing underscore. To help
cover up the platform-specific differences there is a set of macros160 that should be
used.
F77_SUB(name)
to define a function in C to be called from Fortran
F77_NAME(name)
to declare a Fortran routine in C before use
F77_CALL(name)
to call a Fortran routine from C
F77_COMDECL(name)
to declare a Fortran common block in C
F77_COM(name)
to access a Fortran common block from C
On most current platforms these are all the same, but it is unwise to rely on this.
Note that names containing underscores were not legal in Fortran 77, and are not
portably handled by the above macros. (Also, all Fortran names for use by R are
lower case, but this is not enforced by the macros.)
For example, suppose we want to call R’s normal random numbers from Fortran.
We need a C wrapper along the lines of
#include <R.h>

void F77_SUB(rndstart)(void) { GetRNGstate(); }

void F77_SUB(rndend)(void) { PutRNGstate(); }
double F77_SUB(normrnd)(void) { return norm_rand(); }
to be called from Fortran as in
subroutine testit()
double precision normrnd, x
call rndstart()
x = normrnd()
call dblepr("X was", 5, x, 1)
call rndend()
end
Note that this is not guaranteed to be portable, for the return conventions might not
be compatible between the C and Fortran compilers used. (Passing
values via arguments is safer.)
The standard packages, for example stats, are a rich source of further examples.
Where supported, link time optimization provides a reliable way to check the
consistency of calls to C from Fortran or vice versa. See Using Link-time
Optimization. One place where this occurs is the registration of .Fortran calls in C
code (see Registering native routines). For example
init.c:10:13: warning: type of ‘vsom_’ does not match original
declaration [-Wlto-type-mismatch]
extern void F77_NAME(vsom)(void *, void *, void *, void *,
void *, void *, void *, void *, void *);
vsom.f90:20:33: note: type mismatch in parameter 9
subroutine vsom(neurons,dt,dtrows,dtcols,xdim,ydim,alpha,train)
vsom.f90:20:33: note: ‘vsom’ was previously declared here
shows that a subroutine has been registered with 9 arguments (as that is what
the .Fortran call used) but only has 8.
 Fortran character strings
 Fortran LOGICAL
 Passing functions

Next: Fortran LOGICAL, Previous: Calling C from Fortran and vice versa,
Up: Calling C from Fortran and vice versa [Contents][Index]
6.6.1 Fortran character strings

Passing character strings from C to Fortran or vice versa is not portable, but can be
done with care. The internal representations are different: a character array in C (or
C++) is nul-terminated so its length can be computed by strlen. Fortran character
arrays are typically stored as an array of bytes and a length. This matters when
passing strings from C to Fortran or vice versa: in many cases one has been able to
get away with passing the string but not the length. However, in 2019 this changed
for gfortran, starting with version 9 but backported to versions 7 and 8. Several
months later, gfortran 9.2 introduced an option
-ftail-call-workaround
and made it the current default but said it might be withdrawn in future.
Suppose we want a function to report a message from Fortran to R’s console (one
could use labelpr, or intpr with dummy data, but this might be the basis of a
custom reporting function). Suppose the equivalent in Fortran would be
subroutine rmsg(msg)
character*(*) msg
print *.msg
end
in file rmsg.f. Using gfortran 9.2 and later we can extract the C view by
gfortran -c -fc-prototypes-external rmsg.f
which gives
void rmsg_ (char *msg, size_t msg_len);
(where size_t applies to version 8 and later). We could re-write that portably in C
as
#ifndef USE_FC_LEN_T
# define USE_FC_LEN_T
#endif
#include <Rconfig.h> // included by R.h, so define USE_FC_LEN_T early

void F77_NAME(rmsg)(char *msg, FC_LEN_T msg_len)

{
char cmsg[msg_len+1];
strncpy(cmsg, msg, msg_len);
cmsg[msg_len] = ‘\0’; // nul-terminate the string, to be sure
// do something with ‘cmsg’
}
in code depending on R(>= 3.6.2). For earlier versions of R we could just assume
that msg is nul-terminated (not guaranteed, but people have been getting away with
it for many years), so the complete C side might be
#ifndef USE_FC_LEN_T
# define USE_FC_LEN_T
#endif
#include <Rconfig.h>

#ifdef FC_LEN_T
void F77_NAME(rmsg)(char *msg, FC_LEN_T msg_len)
{
char cmsg[msg_len+1];
strncpy(cmsg, msg, msg_len);
cmsg[msg_len] = ‘\0’;
// do something with ‘cmsg’
}
#else
void F77_NAME(rmsg)(char *msg)
{
// do something with ‘msg’
}
#endif
(USE_FC_LEN_T is the default as from R 4.3.0.)
An alternative is to use Fortran 2003 features to set up the Fortran routine to pass a
C-compatible character string. We could use something like
module cfuncs
use iso_c_binding, only: c_char, c_null_char
interface
subroutine cmsg(msg) bind(C, name = ‘cmsg’)
use iso_c_binding, only: c_char
character(kind = c_char):: msg(*)
end subroutine cmsg
end interface
end module

subroutine rmsg(msg)
use cfuncs
character(*) msg
call cmsg(msg//c_null_char) ! need to concatenate a nul terminator
end subroutine rmsg
where the C side is simply
void cmsg(const char *msg)
{
// do something with nul-terminated string ‘msg’
}
If you use bind to a C function as here, the only way to check that the bound
definition is correct is to compile the package with LTO (which requires
compatible C and Fortran compilers, usually gcc and gfortran).
Passing a variable-length string from C to Fortran is trickier,
but [Link]
guide-reference/2023-0/[Link] provides a recipe. However, all the uses in
BLAS and LAPACK are of a single character, and for these we can write a
wrapper in Fortran along the lines of
subroutine c_dgemm(transa, transb, m, n, k, alpha,
+ a, lda, b, ldb, beta, c, ldc)
+ bind(C, name = ‘Cdgemm’)
use iso_c_binding, only : c_char, c_int, c_double
character(c_char), intent(in) :: transa, transb
integer(c_int), intent(in) :: m, n, k, lda, ldb, ldc
real(c_double), intent(in) :: alpha, beta, a(lda, *), b(ldb, *)
real(c_double), intent(out) :: c(ldc, *)
call dgemm(transa, transb, m, n, k, alpha,
+ a, lda, b, ldb, beta, c, ldc)
end subroutine c_dgemm
which is then called from C with declaration
void
Cdgemm(const char *transa, const char *transb, const int *m,
const int *n, const int *k, const double *alpha,
const double *a, const int *lda, const double *b, const int *ldb,
const double *beta, double *c, const int *ldc);
Alternatively, do as R does as from version 3.6.2 and pass the character length(s)
from C to Fortran. A portable way to do this is
// before any R headers, or define in PKG_CPPFLAGS
#ifndef USE_FC_LEN_T
# define USE_FC_LEN_T
#endif
#include <Rconfig.h>
#include <R_ext/BLAS.h>
#ifndef FCONE
# define FCONE
#endif
...
F77_CALL(dgemm)("N", "T", &nrx, &ncy, &ncx, &one, x,
&nrx, y, &nry, &zero, z, &nrx FCONE FCONE);
(Note there is no comma before or between the FCONE invocations.) It is strongly
recommended that packages which call from C/C++ BLAS/LAPACK routines
with character arguments adopt this approach: packages not using will fail to
install as from R 4.3.0.

Next: Passing functions, Previous: Fortran character strings, Up: Calling C from
Fortran and vice versa [Contents][Index]
6.6.2 Fortran LOGICAL

Passing Fortran LOGICAL variables to/from C/C++ is potentially compiler-

dependent. Fortran compilers have long used a 32-bit integer type so it is pretty
portable to use int * on the C/C++ side. However, recent versions
of gfortran via the option -fc-prototypes-external say the C equivalent
is int_least32_t *: ‘Link-Time Optimization’ will report int * as a mismatch. It
is possible to use iso_c_binding in Fortran to map LOGICAL variables to the C99
type _Bool, but it is usually simpler to pass integers to and fro.

Previous: Fortran LOGICAL, Up: Calling C from Fortran and vice versa
[Contents][Index]
6.6.3 Passing functions

A number of packages call C functions passed as arguments to Fortran code along

the lines of
c subroutine fcn(m,n,x,fvec,iflag)
c integer m,n,iflag
c double precision x(n),fvec(m)
...
subroutine lmdif(fcn, ...
where the C declaration and call are
void fcn_lmdif(int *m, int *n, double *par, double *fvec, int *iflag);
void F77_NAME(lmdif)(void (*fcn_lmdif)(int *m, int *n, double *par,
double *fvec, int *iflag), ...

F77_CALL(lmdif)(&fcn_lmdif, ...
This works on most platforms but depends on the C and Fortran compilers
agreeing on calling conventions: this have been seen to fail. The most portable
solution seems to be to convert the Fortran code to C, perhaps using f2c.

Next: Optimization, Previous: Calling C from Fortran and vice versa, Up: The
R API: entry points for C code [Contents][Index]

6.7 Numerical analysis subroutines

R contains a large number of mathematical functions for its own use, for example
numerical linear algebra computations and special functions.
The header
files R_ext/BLAS.h, R_ext/Lapack.h and R_ext/Linpack.h contains
declarations of the BLAS, LAPACK and LINPACK linear algebra functions
included in R. These are expressed as calls to Fortran subroutines, and they will
also be usable from users’ Fortran code. Although not part of the official API, this
set of subroutines is unlikely to change (but might be supplemented).
The header file Rmath.h lists many other functions that are available and
documented in the following subsections. Many of these are C interfaces to the
code behind R functions, so the R function documentation may give further details.
 Distribution functions
 Mathematical functions
 Numerical Utilities
 Mathematical constants

Next: Mathematical functions, Previous: Numerical analysis subroutines,

Up: Numerical analysis subroutines [Contents][Index]
6.7.1 Distribution functions

The routines used to calculate densities, cumulative distribution functions and

quantile functions for the standard statistical distributions are available as entry
points.
The arguments for the entry points follow the pattern of those for the normal
distribution:
double dnorm(double x, double mu, double sigma, int give_log);
double pnorm(double x, double mu, double sigma, int lower_tail,
int give_log);
double qnorm(double p, double mu, double sigma, int lower_tail,
 int log_p);
double rnorm(double mu, double sigma);
That is, the first argument gives the position for the density and CDF and
probability for the quantile function, followed by the distribution’s parameters.
Argument lower_tail should be TRUE (or 1) for normal use, but can be FALSE (or 0)
if the probability of the upper tail is desired or specified.
Finally, give_log should be non-zero if the result is required on log scale,
and log_p should be non-zero if p has been specified on log scale.
Note that you directly get the cumulative (or “integrated”) hazard function, H(t) =
- log(1 - F(t)), by using
- pdist(t, ..., /*lower_tail = */ FALSE, /* give_log = */ TRUE)
or shorter (and more cryptic) - pdist(t, ..., 0, 1).

The random-variate generation routine rnorm returns one normal variate.

See Random number generation, for the protocol in using the random-variate
routines.
Note that these argument sequences are (apart from the names and that rnorm has
no n) mainly the same as the corresponding R functions of the same name, so the
documentation of the R functions can be used. Note that the exponential and
gamma distributions are parametrized by scale rather than rate.
For reference, the following table gives the basic name (to be prefixed by ‘d’, ‘p’,
‘q’ or ‘r’ apart from the exceptions noted) and distribution-specific arguments for
the complete set of distributions.
beta beta a, b
non-central beta nbeta a, b, ncp
binomial binom n, p
Cauchy cauchy location, scale
chi-squared chisq df
non-central chi-squared nchisq df, ncp
exponential exp scale (and not rate)
F f n1, n2
non-central F nf n1, n2, ncp
gamma gamma shape, scale
geometric geom p
hypergeometric hyper NR, NB, n
logistic logis location, scale
lognormal lnorm logmean, logsd
negative binomial nbinom size, prob
normal norm mu, sigma
Poisson pois lambda
Student’s t t n
non-central t nt df, delta
Studentized range tukey (*) rr, cc, df
uniform unif a, b
Weibull weibull shape, scale
Wilcoxon rank sum wilcox m, n
Wilcoxon signed rank signrank n

Entries marked with an asterisk only have ‘p’ and ‘q’ functions available, and
none of the non-central distributions have ‘r’ functions.
(If remapping is suppressed, the Normal distribution names
are Rf_dnorm4, Rf_pnorm5 and Rf_qnorm5.)
Additionally, a multivariate RNG for the multinomial distribution is
void rmultinom(int n, double* prob, int K, int* rN)
where K = length(prob), sum(prob[.]) == 1 and rN must point to a length-K integer
vector n1 n2 .. nK where each entry nj=rN[j] is “filled” by a random binomial
from Bin(n; prob[j]), constrained to sum(rN[.]) == n.
After calls to dwilcox, pwilcox or qwilcox the function wilcox_free() should be
called, and similarly signrank_free() for the signed rank
functions. Since wilcox_free() and signrank_free() were only added
to Rmath.h in R 4.2.0, their use requires something like
#include "Rmath.h"
#include "Rversion.h"

#if R_VERSION < R_Version(4, 2, 0)

extern void wilcox_free(void);
extern void signrank_free(void);
#endif
For the negative binomial distribution (‘nbinom’), in addition to the (size,
prob) parametrization, the alternative (size, mu) parametrization is provided as
well by functions ‘[dpqr]nbinom_mu()’, see ?NegBinomial in R.
Functions dpois_raw(x, *) and dbinom_raw(x, *) are versions of the Poisson and
binomial probability mass functions which work continuously in x,
whereas dbinom(x,*) and dpois(x,*) only return non zero values for integer x.
double dbinom_raw(double x, double n, double p, double q, int give_log)
double dpois_raw (double x, double lambda, int give_log)
Note that dbinom_raw() returns both p and q = 1-p which may be advantageous
when one of them is close to 1.

Next: Numerical Utilities, Previous: Distribution functions, Up: Numerical

analysis subroutines [Contents][Index]
6.7.2 Mathematical functions

Function: double gammafn (double x)

Function: double lgammafn (double x)

Function: double digamma (double x)

Function: double trigamma (double x)

Function: double tetragamma (double x)

Function: double pentagamma (double x)

Function: double psigamma (double x, double deriv)

Function: void dpsifn (double x, int n, int kode, int m, double* ans,
int* nz, int* ierr)
The Gamma function, the natural logarithm of its absolute value and first
four derivatives and the n-th derivative of Psi, the digamma function, which
is the derivative of lgammafn. In other words, digamma(x) is the same
as psigamma(x,0), trigamma(x) == psigamma(x,1), etc. The underlying
workhorse, dpsifn(), is useful, e.g., when several derivatives of log
Gamma=lgammafn are desired. It computes and returns in ans[] the length-
m sequence (-1)^(k+1) / gamma(k+1) * psi(k;x) for k = n ... n+m-1, where
psi(k;x) is the k-th derivative of Psi(x), i.e., psigamma(x,k). For more details,
see the comments in src/nmath/polygamma.c.

Function: double beta (double a, double b)

Function: double lbeta (double a, double b)

The (complete) Beta function and its natural logarithm.
Function: double choose (double n, double k)

Function: double lchoose (double n, double k)

The number of combinations of k items chosen from n and the natural
logarithm of its absolute value, generalized to arbitrary real n. k is rounded
to the nearest integer (with a warning if needed).
Function: double bessel_i (double x, double nu, double expo)

Function: double bessel_j (double x, double nu)

Function: double bessel_k (double x, double nu, double expo)

Function: double bessel_y (double x, double nu)

Bessel functions of types I, J, K and Y with index nu.
For bessel_i and bessel_k there is the option to return exp(-x) I(x; nu) or
exp(x) K(x; nu) if expo is 2. (Use expo == 1 for unscaled values.)

Next: Mathematical constants, Previous: Mathematical functions, Up: Numerical

analysis subroutines [Contents][Index]
6.7.3 Numerical Utilities
There are a few other numerical utility functions available as entry points.
Function: double R_pow (double x, double y)

Function: double R_pow_di (double x, int i)

R_pow(x, y) and R_pow_di(x, i) compute x^y and x^i, respectively
using R_FINITE checks and returning the proper result (the same as R) for the
cases where x, y or i are 0 or missing or infinite or NaN.

Function: double log1p (double x)

Computes log(1 + x) (log 1 plus x), accurately even for small x, i.e., |x| <<
1.
This should be provided by your platform, in which case it is not included
in Rmath.h, but is (probably) in math.h which Rmath.h includes
(except under C++, so it may not be declared for C++98).
Function: double log1pmx (double x)
Computes log(1 + x) - x (log 1 plus x minus x), accurately even for
small x, i.e., |x| << 1.
Function: double log1pexp (double x)
Computes log(1 + exp(x)) (log 1 plus exp), accurately, notably for large x,
e.g., x > 720.
Function: double log1mexp (double x)
Computes log(1 - exp(-x)) (log 1 minus exp), accurately, carefully for
two regions of x, optimally cutting off at log 2 (= 0.693147..), using ((-x) >
-M_LN2 ? log(-expm1(-x)) : log1p(-exp(-x))).

Function: double expm1 (double x)

Computes exp(x) - 1 (exp x minus 1), accurately even for small x, i.e., |x|
<< 1.
This should be provided by your platform, in which case it is not included
in Rmath.h, but is (probably) in math.h which Rmath.h includes
(except under C++, so it may not be declared for C++98).
Function: double lgamma1p (double x)
Computes log(gamma(x + 1)) (log(gamma(1 plus x))), accurately even for
small x, i.e., 0 < x < 0.5.
Function: double cospi (double x)
Computes cos(pi * x) (where pi is 3.14159...), accurately, notably for half
integer x.
 This might be provided by your platform161, in which case it is not included
in Rmath.h, but is in math.h which Rmath.h includes. (Ensure that
neither math.h nor cmath is included before Rmath.h or define
#define __STDC_WANT_IEC_60559_FUNCS_EXT__ 1
before the first inclusion.)
Function: double sinpi (double x)
Computes sin(pi * x) accurately, notably for (half) integer x.
This might be provided by your platform, in which case it is not included
in Rmath.h, but is in math.h which Rmath.h includes (but see the
comments for cospi).

Function: double Rtanpi (double x)

Computes tan(pi * x) accurately, notably for integer x, giving NaN for half
integer x and exactly +1 or -1 for (non half) quarter integers.
Function: double tanpi (double x)
Computes tan(pi * x) accurately for integer x with possibly platform
dependent behavior for half (and quarter) integers. This might be provided
by your platform, in which case it is not included in Rmath.h, but is
in math.h which Rmath.h includes (but see the comments for cospi).

Function: double logspace_add (double logx, double logy)

Function: double logspace_sub (double logx, double logy)

Function: double logspace_sum (const double* logx, int n)

Compute the log of a sum or difference from logs of terms, i.e., “x + y”
as log (exp(logx) + exp(logy)) and “x - y” as log (exp(logx) -
exp(logy)), and “sum_i x[i]” as log (sum[i = 1:n exp(logx[i])] ) without
causing unnecessary overflows or throwing away too much accuracy.
Function: int imax2 (int x, int y)

Function: int imin2 (int x, int y)

Function: double fmax2 (double x, double y)

Function: double fmin2 (double x, double y)

Return the larger (max) or smaller (min) of two integer or double numbers,
respectively. Note that fmax2 and fmin2 differ from C99/C+
+11’s fmax and fmin when one of the arguments is a NaN: these versions
return NaN.

Function: double sign (double x)

 Compute the signum function, where sign(x) is 1, 0, or -1, when x is
positive, 0, or negative, respectively, and NaN if x is a NaN.

Function: double fsign (double x, double y)

Performs “transfer of sign” and is defined as |x| * sign(y).
Function: double fprec (double x, double digits)
Returns the value of x rounded to digits decimal digits (after the decimal
point).
This is the function used by R’s signif().

Function: double fround (double x, double digits)

Returns the value of x rounded to digits significant decimal digits.
This is the function used by R’s round(). (Note that C99/C++11 provide
a round function but C++98 need not.)

Function: double ftrunc (double x)

Returns the value of x truncated (to an integer value) towards zero.

Previous: Numerical Utilities, Up: Numerical analysis subroutines [Contents]

[Index]
6.7.4 Mathematical constants

R has a set of commonly used mathematical constants encompassing constants

defined by POSIX and usually found in headers math.h and cmath, as well as
further ones that are used in statistical computations. These are defined to (at least)
30 digits accuracy in Rmath.h. The following definitions use ln(x) for the
natural logarithm (log(x) in R).
Name Definition (ln = log) round(value, 7)
M_E e 2.7182818
M_LOG2E log2(e) 1.4426950
M_LOG10E log10(e) 0.4342945
M_LN2 ln(2) 0.6931472
M_LN10 ln(10) 2.3025851
M_PI pi 3.1415927
M_PI_2 pi/2 1.5707963
M_PI_4 pi/4 0.7853982
M_1_PI 1/pi 0.3183099
M_2_PI 2/pi 0.6366198
M_2_SQRTPI 2/sqrt(pi) 1.1283792
M_SQRT2 sqrt(2) 1.4142136
M_SQRT1_2 1/sqrt(2) 0.7071068
 Name Definition (ln = log) round(value, 7)
M_SQRT_3 sqrt(3) 1.7320508
M_SQRT_32 sqrt(32) 5.6568542
M_LOG10_2 log10(2) 0.3010300
M_2PI 2*pi 6.2831853
M_SQRT_PI sqrt(pi) 1.7724539
M_1_SQRT_2PI 1/sqrt(2*pi) 0.3989423
M_SQRT_2dPI sqrt(2/pi) 0.7978846
M_LN_SQRT_PI ln(sqrt(pi)) 0.5723649
M_LN_SQRT_2PI ln(sqrt(2*pi)) 0.9189385
M_LN_SQRT_PId2 ln(sqrt(pi/2)) 0.2257914
There are a set of constants (PI, DOUBLE_EPS) (and so on) defined
(unless STRICT_R_HEADERS is defined) in the included
header R_ext/Constants.h, mainly for compatibility with S. All but PI are
deprecated and should be replaced by the C99/C++11 versions used in that file.
Further, the included header R_ext/Boolean.h has enumeration
constants TRUE and FALSE of type Rboolean in order to provide a way of using
“logical” variables in C consistently. This can conflict with other software: for
example it conflicts with the headers in IJG’s jpeg-9 (but not earlier versions).

Next: Integration, Previous: Numerical analysis subroutines, Up: The R API: entry
points for C code [Contents][Index]

6.8 Optimization
The C code underlying optim can be accessed directly. The user needs to supply a
function to compute the function to be minimized, of the type
typedef double optimfn(int n, double *par, void *ex);
where the first argument is the number of parameters in the second argument. The
third argument is a pointer passed down from the calling routine, normally used to
carry auxiliary information.
Some of the methods also require a gradient function
typedef void optimgr(int n, double *par, double *gr, void *ex);
which passes back the gradient in the gr argument. No function is provided for
finite-differencing, nor for approximating the Hessian at the result.
The interfaces (defined in header R_ext/Applic.h) are
 Nelder Mead:
 void nmmin(int n, double *xin, double *x, double *Fmin,
optimfn fn,
 int *fail, double abstol, double intol, void *ex,
 double alpha, double beta, double gamma, int trace,
 int *fncount, int maxit);
  BFGS:
 void vmmin(int n, double *x, double *Fmin,
 optimfn fn, optimgr gr, int maxit, int trace,
 int *mask, double abstol, double reltol, int
nREPORT,
 void *ex, int *fncount, int *grcount, int *fail);
 Conjugate gradients:
 void cgmin(int n, double *xin, double *x, double *Fmin,
 optimfn fn, optimgr gr, int *fail, double abstol,
 double intol, void *ex, int type, int trace,
 int *fncount, int *grcount, int maxit);
 Limited-memory BFGS with bounds:
 void lbfgsb(int n, int lmm, double *x, double *lower,
 double *upper, int *nbd, double *Fmin, optimfn fn,
 optimgr gr, int *fail, void *ex, double factr,
 double pgtol, int *fncount, int *grcount,
 int maxit, char *msg, int trace, int nREPORT);
 Simulated annealing:
 void samin(int n, double *x, double *Fmin, optimfn fn, int
maxit,
 int tmax, double temp, int trace, void *ex);
Many of the arguments are common to the various methods. n is the number of
parameters, x or xin is the starting parameters on entry and x the final parameters
on exit, with final value returned in Fmin. Most of the other parameters can be
found from the help page for optim: see the source
code src/appl/lbfgsb.c for the values of nbd, which specifies which bounds
are to be used.

Next: Utility functions, Previous: Optimization, Up: The R API: entry points for C
code [Contents][Index]

6.9 Integration
The C code underlying integrate can be accessed directly. The user needs to
supply a vectorizing C function to compute the function to be integrated, of the
type
typedef void integr_fn(double *x, int n, void *ex);
where x[] is both input and output and has length n, i.e., a C function, say fn, of
type integr_fn must basically do for(i in 1:n) x[i] := f(x[i], ex). The
vectorization requirement can be used to speed up the integrand instead of calling
it n times. Note that in the current implementation built on QUADPACK, n will be
either 15 or 21. The ex argument is a pointer passed down from the calling routine,
normally used to carry auxiliary information.
There are interfaces (defined in header R_ext/Applic.h) for integrals over
finite and infinite intervals (or “ranges” or “integration boundaries”).
 Finite:
  void Rdqags(integr_fn f, void *ex, double *a, double *b,
 double *epsabs, double *epsrel,
 double *result, double *abserr, int *neval, int
*ier,
 int *limit, int *lenw, int *last,
 int *iwork, double *work);
 Infinite:
 void Rdqagi(integr_fn f, void *ex, double *bound, int *inf,
 double *epsabs, double *epsrel,
 double *result, double *abserr, int *neval, int
*ier,
 int *limit, int *lenw, int *last,
 int *iwork, double *work);
Only the 3rd and 4th argument differ for the two integrators; for the finite range
integral using Rdqags, a and b are the integration interval bounds, whereas for an
infinite range integral using Rdqagi, bound is the finite bound of the integration (if
the integral is not doubly-infinite) and inf is a code indicating the kind of
integration range,
inf = 1
corresponds to (bound, +Inf),
inf = -1
corresponds to (-Inf, bound),
inf = 2
corresponds to (-Inf, +Inf),
f and ex define the integrand function, see above; epsabs and epsrel specify the
absolute and relative accuracy requested, result, abserr and last are the output
components value, [Link] and subdivisions of the R function integrate,
where neval gives the number of integrand function evaluations, and the error
code ier is translated to R’s integrate() $ message, look at that function
definition. limit corresponds to integrate(..., subdivisions = *). It seems you
should always define the two work arrays and the length of the second one as
lenw = 4 * limit;
iwork = (int *) R_alloc(limit, sizeof(int));
work = (double *) R_alloc(lenw, sizeof(double));
The comments in the source code in src/appl/integrate.c give more
details, particularly about reasons for failure (ier >= 1).

Next: Re-encoding, Previous: Integration, Up: The R API: entry points for C code
[Contents][Index]

6.10 Utility functions

R has a fairly comprehensive set of sort routines which are made available to users’
C code. The following is declared in header file Rinternals.h.
Function: void R_orderVector (int* indx, int n, SEXP arglist,
Rboolean nalast, Rboolean decreasing)
Function: void R_orderVector1 (int* indx, int n, SEXP x,
Rboolean nalast, Rboolean decreasing)
R_orderVector() corresponds to R’s order(..., [Link], decreasing).
More specifically, indx <- order(x, y, [Link], decreasing) corresponds
to R_orderVector(indx, n, Rf_lang2(x, y), nalast, decreasing) and for
three vectors, Rf_lang3(x,y,z) is used as arglist.
Both R_orderVector and R_orderVector1 assume the vector indx to be
allocated to length >= n. On return, indx[] contains a permutation of 0:(n-
1), i.e., 0-based C indices (and not 1-based R indices, as R’s order()).

When ordering only one vector, R_orderVector1 is faster and corresponds

(but is 0-based) to R’s indx <- order(x, [Link], decreasing). It was
added in R 3.3.0.
All other sort routines are declared in header file R_ext/Utils.h (included
by R.h) and include the following.

Function: void R_isort (int* x, int n)

Function: void R_rsort (double* x, int n)

Function: void R_csort (Rcomplex* x, int n)

Function: void rsort_with_index (double* x, int* index, int n)

The first three sort integer, real (double) and complex data respectively.
(Complex numbers are sorted by the real part first then the imaginary
part.) NAs are sorted last.
rsort_with_index sorts on x, and applies the same permutation to index. NAs
are sorted last.
Function: void revsort (double* x, int* index, int n)
Is similar to rsort_with_index but sorts into decreasing order, and NAs are
not handled.
Function: void iPsort (int* x, int n, int k)

Function: void rPsort (double* x, int n, int k)

Function: void cPsort (Rcomplex* x, int n, int k)

These all provide (very) partial sorting: they permute x so that x[k] is in the
correct place with smaller values to the left, larger ones to the right.
Function: void R_qsort (double *v, size_t i, size_t j)

Function: void R_qsort_I (double *v, int *I, int i, int j)

Function: void R_qsort_int (int *iv, size_t i, size_t j)

Function: void R_qsort_int_I (int *iv, int *I, int i, int j)
These routines sort v[i:j] or iv[i:j] (using 1-indexing, i.e., v[1] is the first
element) calling the quicksort algorithm as used by R’s sort(v, method =
"quick") and documented on the help page for the R function sort.
The ..._I() versions also return the [Link]() vector in I. Note that the
ordering is not stable, so tied values may be permuted.
Note that NAs are not handled (explicitly) and you should use different
sorting functions if NAs can be present.

Function: subroutine qsort4 (double precision v, integer indx, integer ii,

integer jj)
Function: subroutine qsort3 (double precision v, integer ii, integer jj)
The Fortran interface routines for sorting double precision vectors
are qsort3 and qsort4, equivalent to R_qsort and R_qsort_I, respectively.

Function: void R_max_col (double* matrix, int* nr, int* nc, int* maxes,
int* ties_meth)
Given the nr by nc matrix matrix in column-major (“Fortran”)
order, R_max_col() returns in maxes[i-1] the column number of the maximal
element in the i-th row (the same as R’s [Link]() function). In the case of
ties (multiple maxima), *ties_meth is an integer code in 1:3 determining the
method: 1 = “random”, 2 = “first” and 3 = “last”. See R’s help page ?
[Link].

Function: int findInterval (double* xt, int n, double x,

Rboolean rightmost_closed, Rboolean all_inside, int ilo, int* mflag)
Function: int findInterval2(double* xt, int n, double x,
Rboolean rightmost_closed, Rboolean all_inside, Rboolean left_open,
int ilo, int* mflag)
Given the ordered vector xt of length n, return the interval or index
of x in xt[], typically max(i; 1 <= i <= n & xt[i] <= x) where we use 1-
indexing as in R and Fortran (but not C). If rightmost_closed is true, also
returns n-1 if x equals xt[n]. If all_inside is not 0, the result is coerced to lie
in 1:(n-1) even when x is outside the xt[] range. On return, *mflag equals -
1 if x < xt[1], +1 if x >= xt[n], and 0 otherwise.
The algorithm is particularly fast when ilo is set to the last result
of findInterval() and x is a value of a sequence which is increasing or
decreasing for subsequent calls.
findInterval2() is a generalization of findInterval(), with an
extra Rboolean argument left_open. Setting left_open = TRUE basically
replaces all left-closed right-open intervals t) by left-open ones t], see the
help page of R function findInterval for details.
 There is also an F77_CALL(interv)() version of findInterval() with the
same arguments, but all pointers.
A system-independent interface to produce the name of a temporary file is
provided as
Function: char * R_tmpnam (const char *prefix, const char *tmpdir)
Function: char * R_tmpnam2 (const char *prefix, const char *tmpdir,
const char *fileext)
Function: void R_free_tmpnam (char *name)
Return a pathname for a temporary file with name beginning with prefix and
ending with fileext in directory tmpdir. A NULL prefix or extension is
replaced by "". Note that the return value is dynamically allocated and
should be freed using R_free_tmpnam when no longer needed (unlike the
system call tmpnam). Freeing the result using free is no longer
recommended.
There is also the internal function used to expand file names in several R functions,
and called directly by [Link].

Function: const char * R_ExpandFileName (const char *fn)

Expand a path name fn by replacing a leading tilde by the user’s home
directory (if defined). The precise meaning is platform-specific; it will
usually be taken from the environment variable HOME if this is defined.
For historical reasons there are Fortran interfaces to functions D1MACH and I1MACH.
These can be called from C code as e.g. F77_CALL(d1mach)(4). Note that these are
emulations of the original functions by Fox, Hall and Schryer on NetLib
at [Link] for IEC 60559 arithmetic (required by R).

Next: Condition handling and cleanup code, Previous: Utility functions, Up: The
R API: entry points for C code [Contents][Index]

6.11 Re-encoding
R has its own C-level interface to the encoding conversion capabilities provided
by iconv because there are incompatibilities between the declarations in different
implementations of iconv.
These are declared in header file R_ext/Riconv.h.

Function: void * Riconv_open (const char *to, const char *from)

Set up a pointer to an encoding object to be used to convert between two
encodings: "" indicates the current locale.
Function: size_t Riconv (void *cd, const char **inbuf, size_t
*inbytesleft, char **outbuf, size_t *outbytesleft)
Convert as much as possible of inbuf to outbuf. Initially the size_t variables
indicate the number of bytes available in the buffers, and they are updated (and
the char pointers are updated to point to the next free byte in the buffer). The return
value is the number of characters converted, or (size_t)-1 (beware: size_t is
usually an unsigned type). It should be safe to assume that an error condition
sets errno to one of E2BIG (the output buffer is full), EILSEQ (the input cannot be
converted, and might be invalid in the encoding specified) or EINVAL (the input
does not end with a complete multi-byte character).
Function: int Riconv_close (void * cd)

Free the resources of an encoding object.

Next: Allowing interrupts, Previous: Re-encoding, Up: The R API: entry points for
C code [Contents][Index]

6.12 Condition handling and cleanup code

Three functions are available for establishing condition handlers from within C
code:
#include <Rinternals.h>

SEXP R_tryCatchError(SEXP (*fun)(void *data), void *data,

SEXP (*hndlr)(SEXP cond, void *hdata), void *hdata);

SEXP R_tryCatch(SEXP (*fun)(void *data), void *data,

SEXP,
SEXP (*hndlr)(SEXP cond, void *hdata), void *hdata,
void (*clean)(void *cdata), void *cdata);
SEXP R_withCallingErrorHandler(SEXP (*fun)(void *data), void *data,
SEXP (*hndlr)(SEXP cond, void *hdata), void
*hdata)
R_tryCatchError establishes an exiting handler for conditions inheriting form
class error.
R_tryCatch can be used to establish a handler for other conditions and to register a
cleanup action. The conditions to be handled are specified as a character vector
(STRSXP). A NULL pointer can be passed as fun or clean if condition handling or
cleanup are not needed.
These are currently implemented using the R-level tryCatch mechanism so are
subject to some overhead.
R_withCallingErrorHandler establishes a calling handler for conditions inheriting
form class error. It establishes the handler without calling back into R and will
therefore be more efficient.
The function R_UnwindProtect can be used to ensure that a cleanup action takes
place on ordinary return as well as on a non-local transfer of control, which R
implements as a longjmp.
SEXP R_UnwindProtect(SEXP (*fun)(void *data), void *data,
void (*clean)(void *data, Rboolean jump), void *cdata,
SEXP cont);
R_UnwindProtect can be used in two ways. The simper usage, suitable for use in C
code, passes NULL for the cont argument. R_UnwindProtect will call fun(data).
If fun returns a value, then R_UnwindProtect calls clean(cleandata, FALSE) before
returning the value returned by fun. If fun executes a non-local transfer of control,
then clean(cleandata, TRUE) is called, and the non-local transfer of control is
resumed.
The second use pattern, suitable to support C++ stack unwinding, uses two
additional functions:
SEXP R_MakeUnwindCont();
NORET void R_ContinueUnwind(SEXP cont);
R_MakeUnwindCont allocates a continuation token cont to pass to R_UnwindProtect.
This token should be protected with PROTECT before calling R_UnwindProtect. When
the clean function is called with jump == TRUE, indicating that R is executing a
non-local transfer of control, it can throw a C++ exception to a C++ catch outside
the C++ code to be unwound, and then use the continuation token in the a
call R_ContinueUnwind(cont) to resume the non-local transfer of control within R.

Next: Platform and version information, Previous: Condition handling and cleanup
code, Up: The R API: entry points for C code [Contents][Index]

6.13 Allowing interrupts

No part of R can be interrupted whilst running long computations in compiled
code, so programmers should make provision for the code to be interrupted at
suitable points by calling from C
#include <R_ext/Utils.h>

void R_CheckUserInterrupt(void);
and from Fortran
subroutine rchkusr()
These check if the user has requested an interrupt, and if so branch to R’s error
signaling functions.
Note that it is possible that the code behind one of the entry points defined here if
called from your C or Fortran code could be interruptible or generate an error and
so not return to your code.
Next: Inlining C functions, Previous: Allowing interrupts, Up: The R API: entry
points for C code [Contents][Index]

6.14 Platform and version information

The header files define USING_R, which can be used to test if the code is indeed
being used with R.
Header file Rconfig.h (included by R.h) is used to define platform-specific
macros that are mainly for use in other header files. The macro WORDS_BIGENDIAN is
defined on big-endian162 systems (e.g. most OSes on Sparc and PowerPC
hardware) and not on little-endian systems (nowadays all the commoner R
platforms). It can be useful when manipulating binary files. NB: these macros
apply only to the C compiler used to build R, not necessarily to another C or C++
compiler.
Header file Rversion.h (not included by R.h) defines a
macro R_VERSION giving the version number encoded as an integer, plus a
macro R_Version to do the encoding. This can be used to test if the version of R is
late enough, or to include back-compatibility features. For protection against very
old versions of R which did not have this macro, use a construction such as
#if defined(R_VERSION) && R_VERSION >= R_Version(3, 1, 0)
...
#endif
More detailed information is available in the
macros R_MAJOR, R_MINOR, R_YEAR, R_MONTH and R_DAY: see the header
file Rversion.h for their format. Note that the minor version includes the
patchlevel (as in ‘2.2’).
Packages which use alloca need to ensure it is defined: as it is part of neither C nor
POSIX there is no standard way to do so. One can use
#include <Rconfig.h> // for HAVE_ALLOCA_H
#ifdef __GNUC__
// this covers gcc, clang, icc
# undef alloca
# define alloca(x) __builtin_alloca((x))
#elif defined(HAVE_ALLOCA_H)
// needed for native compilers on Solaris and AIX
# include <alloca.h>
#endif
(and this should be included before standard C headers such as stdlib.h, since
on some platforms these include malloc.h which may have a conflicting
definition), which suffices for known R platforms.

Next: Controlling visibility, Previous: Platform and version information, Up: The
R API: entry points for C code [Contents][Index]
6.15 Inlining C functions
The C99 keyword inline should be recognized by all compilers nowadays used to
build R. Portable code which might be used with earlier versions of R can be
written using the macro R_INLINE (defined in file Rconfig.h included by R.h),
as for example from package cluster
#include <R.h>

static R_INLINE int ind_2(int l, int j)

{
...
}
Be aware that using inlining with functions in more than one compilation unit is
almost impossible to do portably,
see [Link] so this usage is
for static functions as in the example. All the R configure code has checked is
that R_INLINE can be used in a single C file with the compiler used to build R. We
recommend that packages making extensive use of inlining include their own
configure code.

Next: Using these functions in your own C code, Previous: Inlining C functions,
Up: The R API: entry points for C code [Contents][Index]

6.16 Controlling visibility

Header R_ext/Visibility.h has some definitions for controlling the
visibility of entry points. These are only effective when
‘HAVE_VISIBILITY_ATTRIBUTE’ is defined – this is checked when R is
configured and recorded in header Rconfig.h (included
by R_ext/Visibility.h). It is often defined on modern Unix-alikes with a
recent compiler163, but not supported on macOS nor Windows. Minimizing the
visibility of symbols in a shared library will both speed up its loading (unlikely to
be significant) and reduce the possibility of linking to other entry points of the
same name.
C/C++ entry points prefixed by attribute_hidden will not be visible in the shared
object. There is no comparable mechanism for Fortran entry points, but there is a
more comprehensive scheme used by, for example package stats. Most compilers
which allow control of visibility will allow control of visibility for all
symbols via a flag, and where known the flag is encapsulated in the macros
‘C_VISIBILITY’, ‘CXX_VISIBILITY’164 and ‘F_VISIBILITY’ for C, C++
and Fortran compilers.165 These are defined in etc/Makeconf and so available
for normal compilation of package code. For example, src/Makevars could
include some of
PKG_CFLAGS=$(C_VISIBILITY)
PKG_CXXFLAGS=$(CXX_VISIBILITY)
PKG_FFLAGS=$(F_VISIBILITY)
This would end up with no visible entry points, which would be pointless.
However, the effect of the flags can be overridden by using
the attribute_visible prefix. A shared object which registers its entry points
needs only for have one visible entry point, its initializer, so for example
package stats has
void attribute_visible R_init_stats(DllInfo *dll)
{
R_registerRoutines(dll, CEntries, CallEntries, FortEntries, NULL);
R_useDynamicSymbols(dll, FALSE);
...
}
Because the ‘C_VISIBILITY’ mechanism is only useful in conjunction
with attribute_visible, it is not enabled unless
‘HAVE_VISIBILITY_ATTRIBUTE’ is defined. The usual visibility flag is -
fvisibility=hidden: some compilers also support -fvisibility-
inlines-hidden which can be used by overriding ‘C_VISIBILITY’ and
‘CXX_VISIBILITY’ in [Link] when building R, or
editing etc/Makeconf in the R installation.
Note that configure only checks that visibility attributes and flags are accepted, not
that they actually hide symbols.
The visibility mechanism is not available on Windows, but there is an equally
effective way to control which entry points are visible, by supplying a definitions
file pkgnme/src/[Link]: only entry points listed in that file will
be visible. Again using stats as an example, it has
LIBRARY [Link]
EXPORTS
R_init_stats

Next: Organization of header files, Previous: Controlling visibility, Up: The

R API: entry points for C code [Contents][Index]

6.17 Using these functions in your own C

code
It is possible to build Mathlib, the R set of mathematical functions documented
in Rmath.h, as a standalone library libRmath under both Unix-alikes and
Windows. (This includes the functions documented in Numerical analysis
subroutines as from that header file.)
The library is not built automatically when R is installed, but can be built in the
directory src/nmath/standalone in the R sources: see the
file README there. To use the code in your own C program include
#define MATHLIB_STANDALONE
#include <Rmath.h>
and link against ‘-lRmath’ (and perhaps ‘-lm’). There is an example
file test.c.
A little care is needed to use the random-number routines. You will need to supply
the uniform random number generator
double unif_rand(void)
or use the one supplied (and with a dynamic library or DLL you will have to use
the one supplied, which is the Marsaglia-multicarry with an entry points
set_seed(unsigned int, unsigned int)
to set its seeds and
get_seed(unsigned int *, unsigned int *)
to read the seeds).

Previous: Using these functions in your own C code, Up: The R API: entry points
for C code [Contents][Index]

6.18 Organization of header files

The header files which R installs are in
directory R_INCLUDE_DIR (default R_HOME/include). This currently
includes
R.h includes many other files
Rinternals.h definitions for using R’s internal structures
Rdefines.h macros for an S-like interface to the above (no longer
maintained)
Rmath.h standalone math library
Rversion.h R version information
Rinterface.h for add-on front-ends (Unix-alikes only)
Rembedded.h for add-on front-ends
R_ext/Applic.h optimization and integration
R_ext/BLAS.h C definitions for BLAS routines
R_ext/Callbacks.h C (and R function) top-level task handlers
R_ext/GetX11Image.h X11Image interface used by package trkplot
R_ext/Lapack.h C definitions for some LAPACK routines
R_ext/Linpack.h C definitions for some LINPACK routines, not all of which
are included in R
R_ext/Parse.h a small part of R’s parse interface: not part of the stable
API.
R_ext/RStartup.h for add-on front-ends
R_ext/Rdynload.h needed to register compiled code in packages
R_ext/Riconv.h interface to iconv
R_ext/Visibility.h definitions controlling visibility
R_ext/eventloop.h for add-on front-ends and for packages that need to share in
the R event loops (not Windows)
The following headers are included by R.h:
Rconfig.h configuration info that is made available
R_ext/Arith.h handling for NAs, NaNs, Inf/-Inf
R_ext/Boolean.h TRUE/FALSE type
R_ext/Complex.h C typedefs for R’s complex
R_ext/Constants.h constants
R_ext/Error.h error signaling
R_ext/Memory.h memory allocation
R_ext/Print.h Rprintf and variations.
definitions common to R.h and the former S.h,
R_ext/RS.h
including F77_CALL etc.
R_ext/Random.h random number generation
R_ext/Utils.h sorting and other utilities
R_ext/libextern.h definitions for exports from [Link] on Windows.
The graphics systems are exposed in
headers R_ext/GraphicsEngine.h, R_ext/GraphicsDevice.h (which
it includes) and R_ext/QuartzDevice.h. Facilities for defining custom
connection implementations are provided in R_ext/Connections.h, but
make sure you consult the file before use.
Let us re-iterate the advice to include system headers before the R header files,
especially Rinternals.h (included by Rdefines.h) and Rmath.h, which
redefine names which may be used in system headers (fewer if ‘R_NO_REMAP’ is
defined before inclusion, or ‘R_NO_REMAP_RMATH’ for Rmath.h).

Next: Linking GUIs and other front-ends to R, Previous: The R API: entry points
for C code, Up: Writing R Extensions [Contents][Index]

7 Generic functions and methods

R programmers will often want to add methods for existing generic functions, and
may want to add new generic functions or make existing functions generic. In this
chapter we give guidelines for doing so, with examples of the problems caused by
not adhering to them.
This chapter only covers the ‘informal’ class system copied from S3, and not with
the S4 (formal) methods of package methods.
First, a caveat: a function named [Link] will be invoked by the generic gen for
class cl, so do not name functions in this style unless they are intended to be
methods.
The key function for methods is NextMethod, which dispatches the next method. It
is quite typical for a method function to make a few changes to its arguments,
dispatch to the next method, receive the results and modify them a little. An
example is
[Link] <- function(x)
{
x <- [Link](x)
NextMethod("t")
}
Note that the example above works because there is a next method, the default
method, not that a new method is selected when the class is changed.
Any method a programmer writes may be invoked from another method
by NextMethod, with the arguments appropriate to the previous method. Further,
the programmer cannot predict which method NextMethod will pick (it might be one
not yet dreamt of), and the end user calling the generic needs to be able to pass
arguments to the next method. For this to work
A method must have all the arguments of the generic, including … if the generic
does.
It is a grave misunderstanding to think that a method needs only to accept the
arguments it needs. The original S version of [Link] did not have
a … argument, although predict did. It soon became clear that [Link] needed
an argument dispersion to handle over-dispersion. As [Link] had neither
a dispersion nor a … argument, NextMethod could no longer be used. (The legacy,
two direct calls to [Link], lives on in [Link] in R, which is based on the
workaround for S3 written by Venables & Ripley.)
Further, the user is entitled to use positional matching when calling the generic,
and the arguments to a method called by UseMethod are those of the call to the
generic. Thus
A method must have arguments in exactly the same order as the generic.
To see the scale of this problem, consider the generic function scale, defined as
scale <- function (x, center = TRUE, scale = TRUE)
UseMethod("scale")
Suppose an unthinking package writer created methods such as
[Link] <- function(x, scale = FALSE, ...) { }
Then for x of class "foo" the calls
scale(x, , TRUE)
scale(x, scale = TRUE)
would most likely do different things, to the justifiable consternation of the end
user.
To add a further twist, which default is used when a user calls scale(x) in our
example? What if
[Link] <- function(x, center, scale = TRUE) NextMethod("scale")
and x has class c("bar", "foo")? It is the default specified in the method that is
used, but the default specified in the generic may be the one the user sees. This
leads to the recommendation:
If the generic specifies defaults, all methods should use the same defaults.
An easy way to follow these recommendations is to always keep generics simple,
e.g.
scale <- function(x, ...) UseMethod("scale")
Only add parameters and defaults to the generic if they make sense in all possible
methods implementing it.
 Adding new generics

Previous: Generic functions and methods, Up: Generic functions and methods
[Contents][Index]

7.1 Adding new generics

When creating a new generic function, bear in mind that its argument list will be
the maximal set of arguments for methods, including those written elsewhere years
later. So choosing a good set of arguments may well be an important design issue,
and there need to be good arguments not to include a … argument.
If a … argument is supplied, some thought should be given to its position in the
argument sequence. Arguments which follow … must be named in calls to the
function, and they must be named in full (partial matching is suppressed after …).
Formal arguments before … can be partially matched, and so may ‘swallow’ actual
arguments intended for …. Although it is commonplace to make the … argument the
last one, that is not always the right choice.
Sometimes package writers want to make generic a function in the base package,
and request a change in R. This may be justifiable, but making a function generic
with the old definition as the default method does have a small performance cost. It
is never necessary, as a package can take over a function in the base package and
make it generic by something like
foo <- function(object, ...) UseMethod("foo")
[Link] <- function(object, ...) base::foo(object)
Earlier versions of this manual suggested assigning [Link] <- base::foo.
This is not a good idea, as it captures the base function at the time of installation
and it might be changed as R is patched or updated.
The same idea can be applied for functions in other packages.
Next: Function and variable index, Previous: Generic functions and methods,
Up: Writing R Extensions [Contents][Index]

8 Linking GUIs and other front-

ends to R
There are a number of ways to build front-ends to R: we take this to mean a GUI or
other application that has the ability to submit commands to R and perhaps to
receive results back (not necessarily in a text format). There are other routes
besides those described here, for example the package Rserve (from CRAN, see
also [Link] and connections to Java in ‘JRI’ (part of
the rJava package on CRAN).
Note that the APIs described in this chapter are only intended to be used in an
alternative front-end: they are not part of the API made available for R packages
and can be dangerous to use in a conventional package (although packages may
contain alternative front-ends). Conversely some of the functions from the API
(such as R_alloc) should not be used in front-ends.
 Embedding R under Unix-alikes
 Embedding R under Windows

Next: Embedding R under Windows, Previous: Linking GUIs and other front-ends
to R, Up: Linking GUIs and other front-ends to R [Contents][Index]

8.1 Embedding R under Unix-alikes

R can be built as a shared library166 if configured with --enable-R-shlib.
This shared library can be used to run R from alternative front-end programs. We
will assume this has been done for the rest of this section. Also, it can be built as a
static library if configured with --enable-R-static-lib, and that can be
used in a very similar way (at least on Linux: on other platforms one needs to
ensure that all the symbols exported by libR.a are linked into the front-end).
The command-line R front-end, R_HOME/bin/exec/R, is one such example,
and the former GNOME (see package gnomeGUI on CRAN’s ‘Archive’ area)
and macOS consoles are others. The source for R_HOME/bin/exec/R is in
file src/main/Rmain.c and is very simple
int Rf_initialize_R(int ac, char **av); /* in ../unix/system.c */
void Rf_mainloop(); /* in main.c */

extern int R_running_as_main_program; /* in ../unix/system.c */

int main(int ac, char **av)

{
 R_running_as_main_program = 1;
Rf_initialize_R(ac, av);
Rf_mainloop(); /* does not return */
return 0;
}
indeed, misleadingly simple. Remember that R_HOME/bin/exec/R is run from
a shell script R_HOME/bin/R which sets up the environment for the executable,
and this is used for
 Setting R_HOME and checking it is valid, as well as the
path R_SHARE_DIR and R_DOC_DIR to the installed share and doc directory
trees. Also setting R_ARCH if needed.
 Setting LD_LIBRARY_PATH to include the directories used in linking R. This is
recorded as the default setting of R_LD_LIBRARY_PATH in the shell
script R_HOME/etcR_ARCH/ldpaths.
 Processing some of the arguments, for example to run R under a debugger
and to launch alternative front-ends to provide GUIs.
The first two of these can be achieved for your front-end by running it via R CMD.
So, for example
R CMD /usr/local/lib/R/bin/exec/R
R CMD exec/R
will both work in a standard R installation. (R CMD looks first for executables
in R_HOME/bin. These command-lines need modification if a sub-architecture is
in use.) If you do not want to run your front-end in this way, you need to ensure
that R_HOME is set and LD_LIBRARY_PATH is suitable. (The latter might well be, but
modern Unix/Linux systems do not normally
include /usr/local/lib (/usr/local/lib64 on some architectures), and
R does look there for system components.)
The other senses in which this example is too simple are that all the internal
defaults are used and that control is handed over to the R main loop. There are a
number of small examples167 in the tests/Embedding directory. These make
use of Rf_initEmbeddedR in src/main/Rembedded.c, and essentially use
#include <Rembedded.h>

int main(int ac, char **av)

{
/* do some setup */
Rf_initEmbeddedR(argc, argv);
/* do some more setup */

/* submit some code to R, which is done interactively via

run_Rmainloop();

A possible substitute for a pseudo-console is

R_ReplDLLinit();
while(R_ReplDLLdo1() > 0) {
/* add user actions here if desired */
 }

*/
Rf_endEmbeddedR(0);
/* final tidying up after R is shutdown */
return 0;
}
If you do not want to pass R arguments, you can fake an argv array, for example by
char *argv[]= {"REmbeddedPostgres", "--silent"};
Rf_initEmbeddedR(sizeof(argv)/sizeof(argv[0]), argv);
However, to make a GUI we usually do want to run run_Rmainloop after setting up
various parts of R to talk to our GUI, and arranging for our GUI callbacks to be
called during the R mainloop.
One issue to watch is that on some
platforms Rf_initEmbeddedR and Rf_endEmbeddedR change the settings of the FPU
(e.g. to allow errors to be trapped and to make use of extended precision registers).
The standard code sets up a session temporary directory in the usual
way, unless R_TempDir is set to a non-NULL value before Rf_initEmbeddedR is
called. In that case the value is assumed to contain an existing writable directory,
and it is not cleaned up when R is shut down.
Rf_initEmbeddedR sets R to be in interactive mode: you can
set R_Interactive (defined in Rinterface.h) subsequently to change this.
Note that R expects to be run with the locale category ‘LC_NUMERIC’ set to its
default value of C, and so should not be embedded into an application which
changes that.
It is the user’s responsibility to attempt to initialize only once. To protect the R
interpreter, Rf_initialize_R will exit the process if re-initialization is attempted.
 Compiling against the R library
 Setting R callbacks
 Registering symbols
 Meshing event loops
 Threading issues

Next: Setting R callbacks, Previous: Embedding R under Unix-alikes,

Up: Embedding R under Unix-alikes [Contents][Index]
8.1.1 Compiling against the R library

Suitable flags to compile and link against the R (shared or static) library can be
found by
R CMD config --cppflags
R CMD config --ldflags
(These apply only to an uninstalled copy or a standard install.)
If R is installed, pkg-config is available and neither sub-architectures nor a macOS
framework have been used, alternatives for a shared R library are
pkg-config --cflags libR
pkg-config --libs libR
and for a static R library
pkg-config --cflags libR
pkg-config --static --libs libR
(This may work for an installed OS framework if pkg-config is taught where to
look for [Link]: it is installed inside the framework.)
However, a more comprehensive way is to set up a Makefile to compile the
front-end. Suppose file myfe.c is to be compiled to myfe. A
suitable Makefile might be
## WARNING: does not work when ${R_HOME} contains spaces
include ${R_HOME}/etc${R_ARCH}/Makeconf
all: myfe

## The following is not needed, but avoids PIC flags.

myfe.o: myfe.c
$(CC) $(ALL_CPPFLAGS) $(CFLAGS) -c myfe.c -o $@

## replace $(LIBR) $(LIBS) by $(STATIC_LIBR) if R was build with a static

libR
myfe: myfe.o
$(MAIN_LINK) -o $@ myfe.o $(LIBR) $(LIBS)
invoked as
R CMD make
R CMD myfe
Even though not recommended, ${R_HOME} may contain spaces. In that case, it
cannot be passed as an argument to include in the makefile. Instead, one can
instruct make using the -f option to include Makeconf, for example via recursive
invocation of make, see Writing portable packages.
all:
$(MAKE) -f "${R_HOME}/etc${R_ARCH}/Makeconf" -f [Link]
Additional flags which $(MAIN_LINK) includes are, amongst others, those to select
OpenMP and --export-dynamic for the GNU linker on some platforms. In
principle $(LIBS) is not needed when using a shared R library as libR is linked
against those libraries, but some platforms need the executable also linked against
them.

Next: Registering symbols, Previous: Compiling against the R library,

Up: Embedding R under Unix-alikes [Contents][Index]
8.1.2 Setting R callbacks
For Unix-alikes there is a public header file Rinterface.h that makes it
possible to change the standard callbacks used by R in a documented way. This
defines pointers (if R_INTERFACE_PTRS is defined)
extern void
(*ptr_R_Suicide)(const char *);
extern void
(*ptr_R_ShowMessage)(const char *);
extern int(*ptr_R_ReadConsole)(const char *, unsigned char *, int, int);
extern void
(*ptr_R_WriteConsole)(const char *, int);
extern void
(*ptr_R_WriteConsoleEx)(const char *, int, int);
extern void
(*ptr_R_ResetConsole)();
extern void
(*ptr_R_FlushConsole)();
extern void
(*ptr_R_ClearerrConsole)();
extern void
(*ptr_R_Busy)(int);
extern void
(*ptr_R_CleanUp)(SA_TYPE, int, int);
extern int(*ptr_R_ShowFiles)(int, const char **, const char **,
const char *, Rboolean, const char *);
extern int (*ptr_R_ChooseFile)(int, char *, int);
extern int (*ptr_R_EditFile)(const char *);
extern void (*ptr_R_loadhistory)(SEXP, SEXP, SEXP, SEXP);
extern void (*ptr_R_savehistory)(SEXP, SEXP, SEXP, SEXP);
extern void (*ptr_R_addhistory)(SEXP, SEXP, SEXP, SEXP);
extern int (*ptr_R_EditFiles)(int, const char **, const char **, const
char *);
extern SEXP (*ptr_do_selectlist)(SEXP, SEXP, SEXP, SEXP);
extern SEXP (*ptr_do_dataentry)(SEXP, SEXP, SEXP, SEXP);
extern SEXP (*ptr_do_dataviewer)(SEXP, SEXP, SEXP, SEXP);
extern void (*ptr_R_ProcessEvents)();
which allow standard R callbacks to be redirected to your GUI. What these do is
generally documented in the file src/unix/[Link].

Function: void R_ShowMessage (char *message)

This should display the message, which may have multiple lines: it should
be brought to the user’s attention immediately.
Function: void R_Busy (int which)
This function invokes actions (such as change of cursor) when R embarks
on an extended computation (which=1) and when such a state terminates
(which=0).

Function: int R_ReadConsole (const char *prompt, unsigned char *buf,

int buflen, int hist)
Function: void R_WriteConsole (const char *buf, int buflen)

Function: void R_WriteConsoleEx (const char *buf, int buflen,

int otype)
Function: void R_ResetConsole ()
Function: void R_FlushConsole ()
Function: void R_ClearerrConsole ()
These functions interact with a console.
 R_ReadConsole prints the given prompt at the console and then does
a fgets(3)–like operation, transferring up to buflen characters into the
buffer buf. The last two bytes should be set to ‘"\n\0"’ to preserve sanity.
If hist is non-zero, then the line should be added to any command history
which is being maintained. The return value is 0 is no input is available and
>0 otherwise.
R_WriteConsoleEx writes the given buffer to the console, otype specifies the
output type (regular output or warning/error). Call to R_WriteConsole(buf,
buflen) is equivalent to R_WriteConsoleEx(buf, buflen, 0). To ensure
backward compatibility of the callbacks, ptr_R_WriteConsoleEx is used only
if ptr_R_WriteConsole is set to NULL. To ensure
that stdout() and stderr() connections point to the console, set the
corresponding files to NULL via
R_Outputfile = NULL;
R_Consolefile = NULL;
R_ResetConsole is called when the system is reset after an
error. R_FlushConsole is called to flush any pending output to the system
console. R_ClearerrConsole clears any errors associated with reading from
the console.
Function: int R_ShowFiles (int nfile, const char **file, const char
**headers, const char *wtitle, Rboolean del, const char *pager)
This function is used to display the contents of files.
Function: int R_ChooseFile (int new, char *buf, int len)
Choose a file and return its name in buf of length len. Return value is 0 for
success, > 0 otherwise.
Function: int R_EditFile (const char *buf)

Send a file to an editor window.

Function: int R_EditFiles (int nfile, const char **file, const char
**title, const char *editor)
Send nfile files to an editor, with titles possibly to be used for the editor
window(s).
Function: SEXP R_loadhistory (SEXP, SEXP, SEXP, SEXP);

Function: SEXP R_savehistory (SEXP, SEXP, SEXP, SEXP);

Function: SEXP R_addhistory (SEXP, SEXP, SEXP, SEXP);

.Internal functions for loadhistory, savehistory and timestamp.

If the console has no history mechanism these can be as simple as

SEXP R_loadhistory (SEXP call, SEXP op, SEXP args, SEXP env)
{
 errorcall(call, "loadhistory is not implemented");
return R_NilValue;
}
SEXP R_savehistory (SEXP call, SEXP op , SEXP args, SEXP env)
{
errorcall(call, "savehistory is not implemented");
return R_NilValue;
}
SEXP R_addhistory (SEXP call, SEXP op , SEXP args, SEXP env)
{
return R_NilValue;
}
The R_addhistory function should return silently if no history mechanism is
present, as a user may be calling timestamp purely to write the time stamp to
the console.
Function: void R_Suicide (const char *message)
This should abort R as rapidly as possible, displaying the message. A
possible implementation is
void R_Suicide (const char *message)
{
char pp[1024];
snprintf(pp, 1024, "Fatal error: %s\n", message);
R_ShowMessage(pp);
R_CleanUp(SA_SUICIDE, 2, 0);
}
Function: void R_CleanUp (SA_TYPE saveact, int status, int RunLast)
This function invokes any actions which occur at system termination. It
needs to be quite complex:
#include <Rinterface.h>
#include <Rembedded.h> /* for Rf_KillAllDevices */

void R_CleanUp (SA_TYPE saveact, int status, int RunLast)

{
if(saveact == SA_DEFAULT) saveact = SaveAction;
if(saveact == SA_SAVEASK) {
/* ask what to do and set saveact */
}
switch (saveact) {
case SA_SAVE:
if(runLast) R_dot_Last();
if(R_DirtyImage) R_SaveGlobalEnv();
/* save the console history in R_HistoryFile */
break;
case SA_NOSAVE:
if(runLast) R_dot_Last();
break;
case SA_SUICIDE:
default:
break;
}

R_RunExitFinalizers();
/* clean up after the editor e.g. CleanEd() */
 R_CleanTempDir();

/* close all the graphics devices */

if(saveact != SA_SUICIDE) Rf_KillAllDevices();
fpu_setup(FALSE);

exit(status);
}
These callbacks should never be changed in a running R session (and hence cannot
be called from an extension package).
Function: SEXP R_dataentry (SEXP, SEXP, SEXP, SEXP);

Function: SEXP R_dataviewer (SEXP, SEXP, SEXP, SEXP);

Function: SEXP R_selectlist (SEXP, SEXP, SEXP, SEXP);

.External functions for dataentry (and edit on matrices and data
frames), View and [Link]. These can be changed if they are not
currently in use.

Next: Meshing event loops, Previous: Setting R callbacks, Up: Embedding R under
Unix-alikes [Contents][Index]
8.1.3 Registering symbols

An application embedding R needs a different way of registering symbols because

it is not a dynamic library loaded by R as would be the case with a package.
Therefore R reserves a special DllInfo entry for the embedding application such
that it can register symbols to be used with .C, .Call etc. This entry can be
obtained by calling getEmbeddingDllInfo, so a typical use is
DllInfo *info = R_getEmbeddingDllInfo();
R_registerRoutines(info, cMethods, callMethods, NULL, NULL);
The native routines defined by cMethods and callMethods should be present in the
embedding application. See Registering native routines for details on registering
symbols in general.

Next: Threading issues, Previous: Registering symbols, Up: Embedding R under

Unix-alikes [Contents][Index]
8.1.4 Meshing event loops

One of the most difficult issues in interfacing R to a front-end is the handling of

event loops, at least if a single thread is used. R uses events and timers for
 Running X11 windows such as the graphics device and data editor, and
interacting with them (e.g., using locator()).
  Supporting Tcl/Tk events for the tcltk package (for at least the X11 version
of Tk).
 Preparing input.
 Timing operations, for example for profiling R code and [Link]().
 Interrupts, where permitted.
Specifically, the Unix-alike command-line version of R runs separate event loops
for
 Preparing input at the console command-line, in file src/unix/sys-
unix.c.
 Waiting for a response from a socket in the internal functions for direct
socket access in file src/modules/internet/Rsock.c and for the
interface to libcurl.
 Mouse and window events when displaying the X11-based dataentry
window, in file src/modules/X11/dataentry.c. This is regarded
as modal, and no other events are serviced whilst it is active.
There is a protocol for adding event handlers to the first two types of event loops,
using types and functions declared in the header R_ext/eventloop.h and
described in comments in file src/unix/sys-std.c. It is possible to add (or
remove) an input handler for events on a particular file descriptor, or to set a
polling interval (via R_wait_usec) and a function to be called
periodically via R_PolledEvents: the polling mechanism is used by
the tcltk package.
It is not intended that these facilities are used by packages, but if they are needed
exceptionally, the package should ensure that it cleans up and removes its handlers
when its namespace is unloaded. Note that the header sys/select.h is
needed168: users should check this is available and define HAVE_SYS_SELECT_H before
including R_ext/eventloop.h. (It is often the case that another header will
include sys/select.h before eventloop.h is processed, but this should not
be relied on.)
An alternative front-end needs both to make provision for other R events whilst
waiting for input, and to ensure that it is not frozen out during events of the second
type. The ability to add a polled handler as R_timeout_handler is used by
the tcltk package.

Previous: Meshing event loops, Up: Embedding R under Unix-alikes [Contents]

[Index]
8.1.5 Threading issues

Embedded R is designed to be run in the main thread, and all the testing is done in
that context. There is a potential issue with the stack-checking mechanism where
threads are involved. This uses two variables declared
in Rinterface.h (if CSTACK_DEFNS is defined) as
extern uintptr_t R_CStackLimit; /* C stack limit */
extern uintptr_t R_CStackStart; /* Initial stack address */
Note that uintptr_t is an optional C99 type for which a substitute is defined in R,
so your code needs to define HAVE_UINTPTR_T appropriately. To do so, test if the
type is defined in C header stdint.h or C++ header cstdint and if so include
the header and define HAVE_UINTPTR_T before including Rinterface.h. (For C
code one can simply include Rconfig.h, possibly via R.h, and for C++11
code Rinterface.h will include the header cstdint.)
These will be set169 when Rf_initialize_R is called, to values appropriate to the
main thread. Stack-checking can be disabled by setting R_CStackLimit =
(uintptr_t)-1 immediately after Rf_initialize_R is called, but it is better to if
possible set appropriate values. (What these are and how to determine them are
OS-specific, and the stack size limit may differ for secondary threads. If you have a
choice of stack size, at least 10Mb is recommended.)
You may also want to consider how signals are handled: R sets signal handlers for
several signals, including SIGINT, SIGSEGV, SIGPIPE, SIGUSR1 and SIGUSR2, but these
can all be suppressed by setting the variable R_SignalHandlers (declared
in Rinterface.h) to 0.
Note that these variables must not be changed by an R package: a package should
not call R internals which makes use of the stack-checking mechanism on a
secondary thread.

Previous: Embedding R under Unix-alikes, Up: Linking GUIs and other front-ends
to R [Contents][Index]

8.2 Embedding R under Windows

All Windows interfaces to R call entry points in the DLL [Link], directly or
indirectly. Simpler applications may find it easier to use the indirect
route via (D)COM.
 Using (D)COM
 Calling [Link] directly
 Finding R_HOME

Next: Calling [Link] directly, Previous: Embedding R under Windows,

Up: Embedding R under Windows [Contents][Index]
8.2.1 Using (D)COM
(D)COM is a standard Windows mechanism used for communication between
Windows applications. One application (here R) is run as COM server which offers
services to clients, here the front-end calling application. The services are
described in a ‘Type Library’ and are (more or less) language-independent, so the
calling application can be written in C or C++ or Visual Basic or Perl or Python
and so on. The ‘D’ in (D)COM refers to ‘distributed’, as the client and server can
be running on different machines.
The basic R distribution is not a (D)COM server, but two addons are currently
available that interface directly with R and provide a (D)COM server:
 There is a (D)COM server called StatConnector written by Thomas Baier
available via [Link] which works with R packages to
support transfer of data to and from R and remote execution of R
commands, as well as embedding of an R graphics window.
Recent versions have usage restrictions.

Next: Finding R_HOME, Previous: Using (D)COM, Up: Embedding R under

Windows [Contents][Index]
8.2.2 Calling [Link] directly

The R DLL is mainly written in C and has _cdecl entry points. Calling it directly
will be tricky except from C code (or C++ with a little care).
There is a version of the Unix-alike interface calling
int Rf_initEmbeddedR(int ac, char **av);
void Rf_endEmbeddedR(int fatal);
which is an entry point in [Link]. Examples of its use (and a
suitable [Link]) can be found in the tests/Embedding directory of
the sources. You may need to ensure that R_HOME/bin is in your PATH so the R
DLLs are found.
Examples of calling [Link] directly are provided in the
directory src/gnuwin32/front-ends, including a simple command-line
front end rtest.c whose code is
#define Win32
#include <windows.h>
#include <stdio.h>
#include <Rversion.h>
#define LibExtern __declspec(dllimport) extern
#include <Rembedded.h>
#include <R_ext/RStartup.h>
/* for askok and askyesnocancel */
#include <graphapp.h>

/* for signal-handling code */

#include <psignal.h>
/* simple input, simple output */

/* This version blocks all events: a real one needs to call ProcessEvents
frequently. See rterm.c and ../system.c for one approach using
a separate thread for input.
*/
int myReadConsole(const char *prompt, unsigned char *buf, int len, int
addtohistory)
{
fputs(prompt, stdout);
fflush(stdout);
if(fgets((char *)buf, len, stdin)) return 1; else return 0;
}

void myWriteConsole(const char *buf, int len)

{
printf("%s", buf);
}

void myCallBack(void)
{
/* called during i/o, eval, graphics in ProcessEvents */
}

void myBusy(int which)

{
/* set a busy cursor ... if which = 1, unset if which = 0 */
}

static void my_onintr(int sig) { UserBreak = 1; }

int main (int argc, char **argv)

{
structRstart rp;
Rstart Rp = &rp;
char Rversion[25], *RHome, *RUser;

sprintf(Rversion, "%s.%s", R_MAJOR, R_MINOR);

if(strcmp(getDLLVersion(), Rversion) != 0) {
fprintf(stderr, "Error: [Link] version does not match\n");
exit(1);
}

R_setStartTime();
R_DefParamsEx(Rp, RSTART_VERSION);
if((RHome = get_R_HOME()) == NULL) {
fprintf(stderr, "R_HOME must be set in the environment or Registry\
n");
exit(1);
}
Rp->rhome = RHome;
RUser = getRUser();
Rp->home = RUser;
Rp->CharacterMode = LinkDLL;
Rp->EmitEmbeddedUTF8 = FALSE;
Rp->ReadConsole = myReadConsole;
Rp->WriteConsole = myWriteConsole;
Rp->CallBack = myCallBack;
Rp->ShowMessage = askok;
Rp->YesNoCancel = askyesnocancel;
Rp->Busy = myBusy;
 Rp->R_Quiet = TRUE; /* Default is FALSE */
Rp->R_Interactive = FALSE; /* Default is TRUE */
Rp->RestoreAction = SA_RESTORE;
Rp->SaveAction = SA_NOSAVE;
R_SetParams(Rp);
freeRUser(RUser);
free_R_HOME(RHome);
R_set_command_line_arguments(argc, argv);

FlushConsoleInputBuffer(GetStdHandle(STD_INPUT_HANDLE));

signal(SIGBREAK, my_onintr);
GA_initapp(0, 0);
readconsolecfg();
setup_Rmainloop();
#ifdef SIMPLE_CASE
run_Rmainloop();
#else
R_ReplDLLinit();
while(R_ReplDLLdo1() > 0) {
/* add user actions here if desired */
}
/* only get here on EOF (not q()) */
#endif
Rf_endEmbeddedR(0);
return 0;
}
The ideas are
 Check that the front-end and the linked [Link] match – other front-ends
may allow a looser match.
 Find and set the R home directory and the user’s home directory. The
former may be available from the Windows Registry: it will be
in HKEY_LOCAL_MACHINE\Software\R-core\R\InstallPath from an
administrative install and HKEY_CURRENT_USER\Software\R-core\R\
InstallPath otherwise, if selected during installation (as it is by default).
 Define startup conditions and
callbacks via the Rstart structure. R_DefParams sets the defaults,
and R_SetParams sets updated values. R_DefParamsEx takes an extra
argument, the version number of the Rstart structure provided
(RSTART_VERSION refers to the current version) and returns a non-zero status
when that version is not supported by R.
 Record the command-line arguments used
by R_set_command_line_arguments for use by the R function commandArgs().
 Set up the signal handler and the basic user interface.
 Run the main R loop, possibly with our actions intermeshed.
 Arrange to clean up.
An underlying theme is the need to keep the GUI ‘alive’, and this has not been
done in this example. The R callback R_ProcessEvents needs to be called
frequently to ensure that Windows events in R windows are handled expeditiously.
Conversely, R needs to allow the GUI code (which is running in the same process)
to update itself as needed – two ways are provided to allow this:
 R_ProcessEvents calls the callback registered by Rp->callback. A version of
this is used to run package Tcl/Tk for tcltk under Windows, for the code is
 void R_ProcessEvents(void)
 {
 while (peekevent()) doevent(); /* Windows events for
GraphApp */
 if (UserBreak) { UserBreak = FALSE; onintr(); }
 R_CallBackHook();
 if(R_tcldo) R_tcldo();
 }
 The mainloop can be split up to allow the calling application to take some
action after each line of input has been dealt with: see the alternative code
below #ifdef SIMPLE_CASE.
It may be that no R GraphApp windows need to be considered, although these
include pagers, the windows() graphics device, the R data and script editors and
various popups such as [Link]() and [Link](). It would be possible to
replace all of these, but it seems easier to allow GraphApp to handle most of them.
It is possible to run R in a GUI in a single thread (as [Link] shows) but it will
normally be easier170 to use multiple threads.
Note that R’s own front ends use a stack size of 10Mb, whereas MinGW
executables default to 2Mb, and Visual C++ ones to 1Mb. The latter stack sizes are
too small for a number of R applications, so general-purpose front-ends should use
a larger stack size.
Applications embedding R 4.2.0 and newer should use UCRT as the C runtime and
opt in for UTF-8 as the active code page in their manifest, as all frontends shipped
with R do. This will allow the embedded R to use UTF-8 as its native encoding on
recent Windows systems.

Previous: Calling [Link] directly, Up: Embedding R under Windows [Contents]

[Index]
8.2.3 Finding R_HOME

Both applications which embed R and those which use a system call to invoke R
(as [Link], [Link] or [Link]) need to be able to find the R bin directory.
The simplest way to do so is the ask the user to set an environment
variable R_HOME and use that, but naive users may be flummoxed as to how to do so
or what value to use.
The R for Windows installers have for a long time allowed the value of R_HOME to
be recorded in the Windows Registry: this is optional but selected by
default. Where it is recorded has changed over the years to allow for multiple
versions of R to be installed at once, and to allow 32- and 64-bit versions of R to
be installed on the same machine.
The basic Registry location is Software\R-core\R. For an administrative install this
is under HKEY_LOCAL_MACHINE and on a 64-bit OS HKEY_LOCAL_MACHINE\Software\R-
core\R is by default redirected for a 32-bit application, so a 32-bit application will
see the information for the last 32-bit install, and a 64-bit application that for the
last 64-bit install. For a personal install, the information is
under HKEY_CURRENT_USER\Software\R-core\R which is seen by both 32-bit and 64-
bit applications and so records the last install of either architecture. To circumvent
this, there are locations Software\R-core\R32 and Software\R-core\R64 which
always refer to one architecture.
When R is installed and recording is not disabled then two string values are written
at that location for keys InstallPath and Current Version, and these keys are
removed when R is uninstalled. To allow information about other installed
versions to be retained, there is also a key named something like 3.0.0 or 3.0.0
patched or 3.1.0 Pre-release with a value for InstallPath.

So a comprehensive algorithm to search for R_HOME is something like

 Decide which of personal or administrative installs should have precedence.
There are arguments both ways: we find that with roaming profiles
that HKEY_CURRENT_USER\Software often gets reverted to an earlier version.
Do the following for one or both
of HKEY_CURRENT_USER and HKEY_LOCAL_MACHINE.
 If the desired architecture is known, look in Software\R-core\
R32 or Software\R-core\R64, and if that does not exist or the architecture is
immaterial, in Software\R-core\R.
 If key InstallPath exists then this is R_HOME (recorded using backslashes). If
it does not, look for version-specific keys like 2.11.0 alpha, pick the latest
(which is of itself a complicated algorithm as 2.11.0 patched > 2.11.0 >
2.11.0 alpha > 2.8.1) and use its value for InstallPath.

Next: Concept index, Previous: Linking GUIs and other front-ends to R,

Up: Writing R Extensions [Contents][Index]

Function and variable index

. \
Jump to:
A B C D E F G I L M N O P Q R S T U V W
Index Entry Section

.
.C: Interface functions .C and .Fortran
.Call: Handling R objects in C
 .Call: Calling .Call
.External: Handling R objects in C
.External: Calling .External
.Fortran: Interface functions .C and .Fortran
.[Link]: Load hooks
.onAttach: Load hooks
.onDetach: Load hooks
.onLoad: Load hooks
.onUnload: Load hooks
.[Link]: Random numbers

\
\acronym: Marking text
\alias: Documenting functions
\arguments: Documenting functions
\author: Documenting functions
\bold: Marking text
\cite: Marking text
\code: Marking text
\command: Marking text
\concept: Indices
\cr: Sectioning
\CRANpkg{pkg}: User-defined macros
\deqn: Mathematics
\describe: Lists and tables
\description: Documenting functions
\details: Documenting functions
\dfn: Marking text
\doi{numbers}: User-defined macros
\dontrun: Documenting functions
\dontshow: Documenting functions
\dots: Insertions
\dQuote: Marking text
\email: Marking text
\emph: Marking text
\enc: Insertions
\enumerate: Lists and tables
\env: Marking text
\eqn: Mathematics
\examples: Documenting functions
\figure: Figures
\file: Marking text
\format: Documenting data sets
\href: Marking text
 \if: Conditional text
\ifelse: Conditional text
\itemize: Lists and tables
\kbd: Marking text
\keyword: Documenting functions
\ldots: Insertions
\link: Cross-references
\method: Documenting functions
\name: Documenting functions
\newcommand: User-defined macros
\note: Documenting functions
\option: Marking text
\out: Conditional text
\packageAuthor: User-defined macros
\packageDescription: User-defined macros
\packageDESCRIPTION: User-defined macros
\packageIndices: User-defined macros
\packageMaintainer: User-defined macros
\packageTitle: User-defined macros
\pkg: Marking text
\preformatted: Marking text
\R: Insertions
\RdOpts: Dynamic pages
\references: Documenting functions
\renewcommand: User-defined macros
\S3method: Documenting functions
\samp: Marking text
\section: Sectioning
\seealso: Documenting functions
\Sexpr: Dynamic pages
\source: Documenting data sets
\sQuote: Marking text
\sspace: User-defined macros
\strong: Marking text
\tabular: Lists and tables
\title: Documenting functions
\url: Marking text
\usage: Documenting functions
\value: Documenting functions
\var: Marking text
\verb: Marking text

A
allocList: Evaluating R expressions from C
 allocMatrix: Calculating numerical derivatives
allocVector: Allocating storage
any_duplicated: Semi-internal convenience functions
any_duplicated3: Semi-internal convenience functions
asChar: Some convenience functions
asComplex: Some convenience functions
asInteger: Some convenience functions
asLogical: Some convenience functions
asReal: Some convenience functions
AUTHORS: Package subdirectories

B
bessel_i: Mathematical functions
bessel_j: Mathematical functions
bessel_k: Mathematical functions
bessel_y: Mathematical functions
beta: Mathematical functions
BLAS_LIBS: Using Makevars
browser: Browsing

C
CAAR: Calling .External
CAD4R: Calling .External
CAD5R: Calling .External
CADDDR: Calling .External
CADDR: Calling .External
CADR: Calling .External
Calloc: User-controlled memory
CallocCharBuf: User-controlled memory
CAR: Calling .External
CDAR: Calling .External
CDDDR: Calling .External
CDDR: Calling .External
CDR: Calling .External
cgmin: Optimization
choose: Mathematical functions
CITATION: Package subdirectories
CITATION: Preparing translations
classgets: Classes
CleanEd: Setting R callbacks
coerceVector: Details of R types
COMPLEX: Vector accessor functions
CONS: Some convenience functions
cons: Some convenience functions
 COPYRIGHTS: The DESCRIPTION file
COPYRIGHTS: Package subdirectories
cospi: Numerical Utilities
cPsort: Utility functions

D
dblepr: Printing from Fortran
dblepr1: Printing from Fortran
debug: Debugging R code
debugger: Debugging R code
defineVar: Finding and setting variables
digamma: Mathematical functions
dimgets: Attributes
dimnamesgets: Attributes
dpsifn: Mathematical functions
[Link]: Debugging R code
duplicate: Named objects and copying
[Link]: [Link] and [Link]
[Link]: [Link] and [Link]

E
elt: Some convenience functions
error: Error signaling
errorcall: Error signaling
eval: Evaluating R expressions from C
expm1: Numerical Utilities
export: Specifying imports and exports
exportClasses: Namespaces with S4 classes and methods
exportClassPattern: Namespaces with S4 classes and methods
exportMethods: Namespaces with S4 classes and methods
exportPattern: Specifying imports and exports
exportPattern: Namespaces with S4 classes and methods
exp_rand: Random numbers

F
FALSE: Mathematical constants
findFun: Evaluating R expressions from C
findInterval: Utility functions
findInterval2(double*: Utility functions
findVar: Finding and setting variables
FLIBS: Using Makevars
fmax2: Numerical Utilities
fmin2: Numerical Utilities
fprec: Numerical Utilities
 fpu_setup: Setting R callbacks
Free: User-controlled memory
fround: Numerical Utilities
fsign: Numerical Utilities
ftrunc: Numerical Utilities

G
gammafn: Mathematical functions
gctorture: Using gctorture
GetArrayDimnames: Attributes
getAttrib: Attributes
getCharCE: Character encoding issues
GetColNames: Attributes
GetMatrixDimnames: Attributes
GetRNGstate: Random numbers
GetRowNames: Attributes

I
imax2: Numerical Utilities
imin2: Numerical Utilities
import: Specifying imports and exports
importClassesFrom: Namespaces with S4 classes and methods
importFrom: Specifying imports and exports
importMethodsFrom: Namespaces with S4 classes and methods
install: Attributes
installChar: Finding and setting variables
INTEGER: Vector accessor functions
integr_fn: Integration
intpr: Printing from Fortran
intpr1: Printing from Fortran
iPsort: Utility functions
isArray: Some convenience functions
isComplex: Details of R types
isEnvironment: Details of R types
isExpression: Details of R types
isFactor: Some convenience functions
isFunction: Some convenience functions
isInteger: Details of R types
isLanguage: Some convenience functions
isList: Some convenience functions
isLogical: Details of R types
isMatrix: Some convenience functions
ISNA: Missing and special values
ISNA: Missing and IEEE values
 ISNAN: Missing and special values
ISNAN: Missing and IEEE values
isNewList: Some convenience functions
isNull: Details of R types
isNumeric: Some convenience functions
isObject: Some convenience functions
isOrdered: Some convenience functions
isPairList: Some convenience functions
isPrimitive: Some convenience functions
isReal: Details of R types
isString: Details of R types
isSymbol: Details of R types
isTs: Some convenience functions
isUnordered: Some convenience functions
isVector: Some convenience functions
isVectorAtomic: Some convenience functions
isVectorList: Some convenience functions

L
labelpr: Printing from Fortran
lang1: Some convenience functions
lang2: Some convenience functions
lang3: Some convenience functions
lang4: Some convenience functions
lang5: Some convenience functions
lang6: Some convenience functions
LAPACK_LIBS: Using Makevars
lastElt: Some convenience functions
lbeta: Mathematical functions
lbfgsb: Optimization
lchoose: Mathematical functions
LCONS: Some convenience functions
lcons: Some convenience functions
lgamma1p: Numerical Utilities
lgammafn: Mathematical functions
[Link]: Package subdirectories
[Link]: [Link] and [Link]
list1: Some convenience functions
list2: Some convenience functions
list3: Some convenience functions
list4: Some convenience functions
list5: Some convenience functions
list6: Some convenience functions
log1mexp: Numerical Utilities
 log1p: Numerical Utilities
log1pexp: Numerical Utilities
log1pmx: Numerical Utilities
LOGICAL: Vector accessor functions
logspace_add: Numerical Utilities
logspace_sub: Numerical Utilities
logspace_sum: Numerical Utilities

M
MARK_NOT_MUTABLE: Named objects and copying
MAYBE_REFERENCED: Named objects and copying
MAYBE_SHARED: Named objects and copying
Memcpy: User-controlled memory
Memzero: User-controlled memory
mkChar: Handling character data
mkCharCE: Character encoding issues
mkCharLen: Handling character data
mkCharLenCE: Character encoding issues
mkString: Some convenience functions
M_E: Mathematical constants
M_PI: Mathematical constants

N
namesgets: Attributes
NA_REAL: Missing and IEEE values
[Link]: Package subdirectories
nmmin: Optimization
norm_rand: Random numbers
nrows: Transient storage allocation
nthcdr: Some convenience functions

O
OBJECTS: Using Makevars
OBJECTS: Creating shared objects
onintr: Calling [Link] directly
optimfn: Optimization
optimgr: Optimization

P
pentagamma: Mathematical functions
PKG_CFLAGS: Creating shared objects
PKG_CPPFLAGS: Creating shared objects
PKG_CXXFLAGS: Creating shared objects
PKG_FCFLAGS: Using F9x code
 PKG_FFLAGS: Creating shared objects
PKG_LIBS: Creating shared objects
PKG_OBJCFLAGS: Creating shared objects
PKG_OBJCXXFLAGS: Creating shared objects
PRINTNAME: Calling .External
PrintValue: Inspecting R objects
prompt: Rd format
PROTECT: Garbage Collection
protect: Garbage Collection
PROTECT_WITH_INDEX: Garbage Collection
psigamma: Mathematical functions
PutRNGstate: Random numbers

Q
qsort3: Utility functions
qsort4: Utility functions

R
R CMD build: Building package tarballs
R CMD check: Checking packages
R CMD config: Configure and cleanup
R CMD Rd2pdf: Processing documentation files
R CMD Rdconv: Processing documentation files
R CMD SHLIB: Creating shared objects
R CMD Stangle: Processing documentation files
R CMD Sweave: Processing documentation files
RAW: Vector accessor functions
rchkusr: Allowing interrupts
Rdqagi: Integration
Rdqags: Integration
REAL: Vector accessor functions
Realloc: User-controlled memory
realpr: Printing from Fortran
realpr1: Printing from Fortran
recover: Debugging R code
reEnc: Character encoding issues
REprintf: Printing
REPROTECT: Garbage Collection
REvprintf: Printing
revsort: Utility functions
Rf_endEmbeddedR: Embedding R under Unix-alikes
Rf_initEmbeddedR: Embedding R under Unix-alikes
Rf_initialize_R: Embedding R under Unix-alikes
Rf_KillAllDevices: Setting R callbacks
Rf_mainloop: Embedding R under Unix-alikes
Riconv: Re-encoding
Riconv_close: Re-encoding
Riconv_open: Re-encoding
Rprintf: Printing
Rprof: Profiling R code for speed
Rprof: Memory statistics from Rprof
Rprofmem: Tracking memory allocations
rPsort: Utility functions
rsort_with_index: Utility functions
Rtanpi: Numerical Utilities
run_Rmainloop: Embedding R under Unix-alikes
Rvprintf: Printing
R_addhistory: Setting R callbacks
R_alloc: Transient storage allocation
R_allocLD: Transient storage allocation
R_Busy: Setting R callbacks
R_Calloc: User-controlled memory
R_CheckUserInterrupt: Allowing interrupts
R_ChooseFile: Setting R callbacks
R_CleanTempDir: Setting R callbacks
R_CleanUp: Setting R callbacks
R_ClearerrConsole: Setting R callbacks
R_ClearExternalPtr: External pointers and weak references
R_compute_identical: Semi-internal convenience functions
R_ContinueUnwind: Condition handling and cleanup code
R_csort: Utility functions
R_dataentry: Setting R callbacks
R_dataviewer: Setting R callbacks
R_DefParams: Calling [Link] directly
R_DefParamsEx: Calling [Link] directly
R_dot_Last: Setting R callbacks
R_EditFile: Setting R callbacks
R_EditFiles: Setting R callbacks
R_ExpandFileName: Utility functions
R_ExternalPtrAddr: External pointers and weak references
R_ExternalPtrAddrFn: External pointers and weak references
R_ExternalPtrProtected: External pointers and weak references
R_ExternalPtrTag: External pointers and weak references
R_FINITE: Missing and IEEE values
R_FlushConsole: Setting R callbacks
R_forceSymbols: Registering native routines
R_Free: User-controlled memory
R_free_tmpnam: Utility functions
R_GetCCallable: Linking to native routines in other packages
R_GetCurrentEnv: Evaluating R expressions from C
R_GetCurrentSrcref: Accessing source references
R_getEmbeddingDllInfo: Registering symbols
R_GetSrcFilename: Accessing source references
R_INLINE: Inlining C functions
R_IsNaN: Missing and IEEE values
R_isort: Utility functions
R_LIBRARY_DIR: Configure and cleanup
R_loadhistory: Setting R callbacks
R_MakeExternalPtr: External pointers and weak references
R_MakeExternalPtrFn: External pointers and weak references
R_MakeUnwindCont: Condition handling and cleanup code
R_MakeWeakRef: External pointers and weak references
R_MakeWeakRefC: External pointers and weak references
R_max_col: Utility functions
R_NegInf: Missing and IEEE values
R_NewEnv: Finding and setting variables
R_NewPreciousMSet: Garbage Collection
R_orderVector: Utility functions
R_orderVector1: Utility functions
R_PACKAGE_DIR: Configure and cleanup
R_PACKAGE_DIR: Configure and cleanup
R_PACKAGE_NAME: Configure and cleanup
R_PACKAGE_NAME: Configure and cleanup
R_ParseVector: Parsing R code from C
R_PolledEvents: Meshing event loops
R_PosInf: Missing and IEEE values
R_pow: Numerical Utilities
R_pow_di: Numerical Utilities
R_PreserveInMSet: Garbage Collection
R_PreserveObject: Garbage Collection
R_ProcessEvents: Calling [Link] directly
R_ProtectWithIndex: Garbage Collection
R_PV: Inspecting R objects
R_qsort: Utility functions
R_qsort_I: Utility functions
R_qsort_int: Utility functions
R_qsort_int_I: Utility functions
R_ReadConsole: Setting R callbacks
R_Realloc: User-controlled memory
R_RegisterCCallable: Linking to native routines in other packages
R_RegisterCFinalizer: External pointers and weak references
R_RegisterCFinalizerEx: External pointers and weak references
 R_RegisterFinalizer: External pointers and weak references
R_RegisterFinalizerEx: External pointers and weak references
R_registerRoutines: Registering native routines
R_ReleaseFromMSet: Garbage Collection
R_ReleaseObject: Garbage Collection
R_ReplDLLdo1: Embedding R under Unix-alikes
R_ReplDLLinit: Embedding R under Unix-alikes
R_Reprotect: Garbage Collection
R_ResetConsole: Setting R callbacks
R_rsort: Utility functions
R_RunExitFinalizers: Setting R callbacks
R_RunWeakRefFinalizer: External pointers and weak references
R_SaveGlobalEnv: Setting R callbacks
R_savehistory: Setting R callbacks
R_selectlist: Setting R callbacks
R_SetExternalPtrAddr: External pointers and weak references
R_SetExternalPtrProtected: External pointers and weak references
R_SetExternalPtrTag: External pointers and weak references
R_SetParams: Calling [Link] directly
R_setStartTime: Calling [Link] directly
R_set_command_line_arguments: Calling [Link] directly
R_ShowFiles: Setting R callbacks
R_ShowMessage: Setting R callbacks
R_Srcref: Accessing source references
R_Suicide: Setting R callbacks
R_tmpnam: Utility functions
R_tmpnam2: Utility functions
R_tryCatch: Condition handling and cleanup code
R_tryCatchError: Condition handling and cleanup code
R_unif_index: Random numbers
R_UnwindProtect: Condition handling and cleanup code
R_useDynamicSymbols: Registering native routines
R_Version: Platform and version information
R_wait_usec: Meshing event loops
R_WeakRefKey: External pointers and weak references
R_WeakRefValue: External pointers and weak references
R_withCallingErrorHandler: Condition handling and cleanup code
R_WriteConsole: Setting R callbacks
R_WriteConsoleEx: Setting R callbacks

S
S3method: Registering S3 methods
SAFE_FFLAGS: Using Makevars
samin: Optimization
 ScalarComplex: Some convenience functions
ScalarInteger: Some convenience functions
ScalarLogical: Some convenience functions
ScalarRaw: Some convenience functions
ScalarReal: Some convenience functions
ScalarString: Some convenience functions
setAttrib: Attributes
SETCAD4R: Calling .External
SETCADDDR: Calling .External
SETCADDR: Calling .External
SETCADR: Calling .External
SETCAR: Calling .External
SETCDR: Calling .External
setup_Rmainloop: Calling [Link] directly
setVar: Finding and setting variables
SET_STRING_ELT: Handling character data
SET_TAG: Evaluating R expressions from C
SET_VECTOR_ELT: Vector accessor functions
sign: Numerical Utilities
signrank_free: Distribution functions
sinpi: Numerical Utilities
str2type: Some convenience functions
STRING_ELT: Handling character data
summaryRprof: Memory statistics from Rprof
system: Operating system access
[Link]: Operating system access
system2: Operating system access
S_alloc: Transient storage allocation
S_realloc: Transient storage allocation

T
TAG: Calling .External
tanpi: Numerical Utilities
tetragamma: Mathematical functions
trace: Debugging R code
traceback: Debugging R code
tracemem: Tracing copies of an object
translateChar: Character encoding issues
translateCharUTF8: Character encoding issues
trigamma: Mathematical functions
TRUE: Mathematical constants
type2char: Some convenience functions
type2str: Some convenience functions
TYPEOF: Calling .External
U
undebug: Debugging R code
unif_rand: Random numbers
UNPROTECT: Garbage Collection
unprotect: Garbage Collection
UNPROTECT_PTR: Garbage Collection
unprotect_ptr: Garbage Collection
untracemem: Tracing copies of an object
useDynLib: useDynLib

V
VECTOR_ELT: Vector accessor functions
vmaxget: Transient storage allocation
vmaxset: Transient storage allocation
vmmin: Optimization

W
warning: Error signaling
warningcall: Error signaling
warningcall_immediate: Error signaling
wilcox_free: Distribution functions

. \
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A B C D E F G I L M N O P Q R S T U V W

Previous: Function and variable index, Up: Writing R Extensions [Contents]

[Index]

Concept index
. \
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A B C D E F G H I L M N O P R S T U V W Z
Index Entry Section

.
.install_extras file: Writing package vignettes
.Rbuildignore file: Building package tarballs
.Rinstignore file: Package subdirectories

\
\linkS4class: Cross-references

A
 Allocating storage: Allocating storage
Attributes: Attributes

B
Bessel functions: Mathematical functions
Beta function: Mathematical functions
Building binary packages: Building binary packages
Building source packages: Building package tarballs

C
C++ code, interfacing: Interfacing C++ code
Calling C from Fortran and vice versa: Calling C from Fortran and vice versa
Checking packages: Checking packages
citation: Package subdirectories
citation: Preparing translations
Classes: Classes
Cleanup code: Condition handling and cleanup code
cleanup file: Package structure
Condition handling: Condition handling and cleanup code
conditionals: Conditional text
configure file: Package structure
Copying objects: Named objects and copying
CRAN: Creating R packages
Creating packages: Creating R packages
Creating shared objects: Creating shared objects
Cross-references in documentation: Cross-references
cumulative hazard: Distribution functions

D
Debugging: Debugging compiled code
DESCRIPTION file: The DESCRIPTION file
Details of R types: Details of R types
Distribution functions from C: Distribution functions
Documentation, writing: Writing R documentation files
Dynamic loading: [Link] and [Link]
dynamic pages: Dynamic pages

E
Editing Rd files: Editing Rd files
encoding: Encoding
Error handling: Condition handling and cleanup code
Error signaling from C: Error signaling
Error signaling from Fortran: Error signaling from Fortran
Evaluating R expressions from C: Evaluating R expressions from C
external pointer: External pointers and weak references
F
Figures in documentation: Figures
finalizer: External pointers and weak references
Finding variables: Finding and setting variables

G
Gamma function: Mathematical functions
Garbage collection: Garbage Collection
Generic functions: Generic functions and methods

H
handling character data: Handling character data
Handling lists: Handling lists
Handling R objects in C: Handling R objects in C

I
IEEE special values: Missing and special values
IEEE special values: Missing and IEEE values
INDEX file: The INDEX file
Indices: Indices
Inspecting R objects when debugging: Inspecting R objects
integration: Integration
Interfaces to compiled code: Interface functions .C and .Fortran
Interfaces to compiled code: Interface functions .Call and .External
Interfacing C++ code: Interfacing C++ code
Interrupts: Allowing interrupts

L
LICENCE file: Licensing
LICENSE file: Licensing
Lists and tables in documentation: Lists and tables

M
Marking text in documentation: Marking text
Mathematics in documentation: Mathematics
Memory allocation from C: Memory allocation
Memory use: Profiling R code for memory use
Method functions: Generic functions and methods
Missing values: Missing and special values
Missing values: Missing and IEEE values

N
namespaces: Package namespaces
news: Package subdirectories
 Numerical analysis subroutines from C: Numerical analysis subroutines
Numerical derivatives: Calculating numerical derivatives

O
OpenMP: OpenMP support
OpenMP: Platform and version information
Operating system access: Operating system access
optimization: Optimization

P
Package builder: Building package tarballs
Package structure: Package structure
Package subdirectories: Package subdirectories
Packages: Creating R packages
Parsing R code from C: Parsing R code from C
Platform-specific documentation: Platform-specific sections
Polygamma functions: Mathematical functions
Printing from C: Printing
Printing from Fortran: Printing from Fortran
Processing Rd format: Processing documentation files
Profiling: Profiling R code for speed
Profiling: Profiling R code for memory use
Profiling: Profiling compiled code

R
Random numbers in C: Random numbers
Random numbers in C: Distribution functions
Random numbers in Fortran: Calling C from Fortran and vice versa
Registering native routines: Registering native routines

S
Setting variables: Finding and setting variables
Sort functions from C: Utility functions
Sweave: Writing package vignettes

T
tarballs: Building package tarballs
Tidying R code: Tidying R code

U
user-defined macros: User-defined macros

V
Version information from C: Platform and version information
vignettes: Writing package vignettes
 Visibility: Controlling visibility

W
weak reference: External pointers and weak references

Z
Zero-finding: Zero-finding

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A B C D E F G H I L M N O P R S T U V W Z

Footnotes

(1)

although this is a persistent mis-usage. It seems to stem from S, whose analogues

of R’s packages were officially known as library sections and later as chapters, but
almost always referred to as libraries.
(2)

This seems to be commonly used for a file in ‘markdown’ format. Be aware that
most users of R will not know that, nor know how to view such a file: platforms
such as macOS and Windows do not have a default viewer set in their file
associations. The CRAN package web pages render such files in HTML: the
converter used expects the file to be encoded in UTF-8.
(3)

currently, top-level files .Rbuildignore and .Rinstignore,

and vignettes/.install_extras.

(4)

false positives are possible, but only a handful have been seen so far.
(5)

at least if this is done in a locale which matches the package encoding.

(6)

and required by CRAN, so checked by R CMD check --as-cran.

(7)

without a src/Makefile* file.

(8)

But it is checked for Open Source packages by R CMD check --as-cran.

(9)

Duplicate definitions may trigger a warning: see User-defined macros.

(10)

[Link] will try to extract an email address from a Contact field if there is
no BugReports field.
(11)

CRAN expands them to e.g. GPL-2 | GPL-3.

(12)

even one wrapped in \donttest.

(13)

This includes all packages directly called by library and require calls, as well as
data obtained via data(theirdata, package = "somepkg") calls: R CMD check will
warn about all of these. But there are subtler uses which it may not detect: e.g. if
package A uses package B and makes use of functionality in package B which uses
package C which package B suggests or enhances, then package C needs to be in
the ‘Suggests’ list for package A. Nor will undeclared uses in included files be
reported, nor unconditional uses of packages listed under ‘Enhances’. R CMD
check --as-cran will detect more of the subtler uses.

(14)

Extensions .S and .s arise from code originally written for S(-PLUS), but are
commonly used for assembler code. Extension .q was used for S, which at one
time was tentatively called QPE.
(15)

but they should be in the encoding declared in the DESCRIPTION file.

(16)

This is true for OSes which implement the ‘C’ locale: Windows’ idea of the ‘C’
locale uses the WinAnsi charset.
(17)
More precisely, they can contain the English alphanumeric characters and the
symbols ‘$ - _ . + ! ' ( ) , ; = &’.

(18)

either or both of which may not be supported on particular platforms. Their main
use is on macOS, but unfortunately recent versions of the macOS SDK have
removed much of the support for Objective C v1.0 and Objective C++.
(19)

Using .hpp is not guaranteed to be portable.

(20)

There is also ‘__APPLE_CC__’, but that indicates a compiler with Apple-specific

features not the OS, although for historical reasons is is defined by LLVM clang. It
is used in Rinlinedfuns.h.

(21)

the POSIX terminology, called ‘make variables’ by GNU make.

(22)

The best way to generate such a file is to copy the .Rout from a successful run
of R CMD check. If you want to generate it separately, do run R with options --
vanilla --no-echo and with environment variable LANGUAGE=en set to get
messages in English. Be careful not to use output with the option --
timings (and note that --as-cran sets it).

(23)

e.g. [Link]
(24)

People who have trouble with case are advised to use .rda as a common error is
to refer to [Link] as [Link]!

(25)

For all the CRAN packages tested, either gz or bzip2 provided a very substantial
reduction in installed size.
(26)

‘BWidget’ still is on Windows but ‘Tktable’ was not in R 4.0.0.

(27)

The script should only assume a POSIX-compliant /bin/sh –

see [Link]
In particular bash extensions must not be used, and not all R platforms have
a bash command, let alone one at /bin/bash. All known shells used with R
support the use of backticks, but not all support ‘$(cmd)’. However, real-world
shells are not fully POSIX-compliant and omissions and idiosyncrasies need to be
worked around—which Autoconf will do for you. Arithmetic expansion is a
known issue:
see [Link] f
or this and others. Some checks can be done by the checkbashisms Perl script
at [Link] also available in most
Linux distributions in a package named either ‘devscripts’ or
‘devscripts-checkbashisms’: a later version can be extracted from Debian
sources such as the most
recent [Link] in [Link] and has
been needed for recent versions of Perl.
(28)

[Link] If you include

macros from that archive you need to arrange for them to be included in the
package sources for use by autoreconf.
(29)

but it is available on the machines used to produce the CRAN binary packages:
however as Apple does not ship .pc files for its system libraries such
as expat, libcurl, libxml2, sqlite3 and ‘zlib’, it may well not find information
on these. Some substitutes are available
from [Link] and
are installed on the CRAN package builders.
(30)

It is not wise to check the version of pkg-config as it is sometimes a link

to pkgconf, a separate project with a different version series.
(31)

but not all projects get this right when only a static library is installed, so it is often
necessary to try in turn pkg-config --libs and pkg-config --static --libs.
(32)
a decade ago Autoconf used [Link]: this is still accepted but should be
renamed and autoreconf as used by R CMD check --as-cran will report as such.
(33)

For those using autoconf 2.70 or later there is also AC_CONFIG_MACRO_DIRS which
allows multiple directories to be specified.
(34)

in POSIX parlance: GNU make calls these ‘make variables’.

(35)

at least on Unix-alikes: the Windows build currently resolves such dependencies to

a static Fortran library when [Link] is built. Also, not if USE_FC_TO_LINK is
used.
(36)

[Link] [Link] [Link]

[Link]/openmp/
(37)

There are somewhat fragile workarounds: see [Link]

(38)

Default builds of LLVM clang 3.8.0 and later have support for OpenMP, but
the libomp run-time library may not be installed.
(39)

In most implementations the _OPENMP macro has value a date which can be mapped
to an OpenMP version: for example, value 201307 is the date of version 4.0 (July
2013). However this may be used to denote the latest version which is partially
supported, not that which is fully implemented.
(40)

Windows default, not MinGW-w64 default.

(41)

Which it was at the time of writing with GCC, Intel and Clang compilers. The
count may include the thread running the main process.
(42)
Be careful not to declare nthreads as const int: the Oracle compiler required it to
be ‘an lvalue’.
(43)

some Windows toolchains had the typo ‘_REENTRANCE’ instead.

(44)

A few OSes (AIX, Windows) do not need special flags for such code, but most do
—although compilers will often generate PIC code when not asked to do so.
(45)

for versions of R since 3.6.0.

(46)

Some changes are linked from [Link]

sg10-feature-test-recommendations: there were also additional deprecations.
(47)

Values 201103L, 201402L, 201703L and 202002L are most commonly used for C++11,
C++14, C++17 and C++20 respectively, but some compilers set 1L. For C++23 all
that can currently be assumed is a value greater than that for C++20: for
example g++ 12 uses 202100L and clang++ (LLVM 15, Apple 14) uses 202101L.
(48)

Often historically used to mean ‘not C++98’

(49)

See [Link]
recommendations or [Link]
It seems a reasonable assumption that any compiler promising some C++14
conformance will provide these—e.g. g++ 4.9.x did but 4.8.5 did not.
(50)

On systems which use sub-architectures, architecture-specific versions such

as ~/.R/[Link].x64 take precedence.

(51)

A suitable [Link] is part of the Windows toolset: it checks for gfile if a

suitable file is not found: the latter is available in the OpenCSW collection for
Solaris at [Link] The source repository
is [Link]
(52)

An exception is made for subdirectories with names starting ‘win’ or ‘Win’.

(53)

on most other platforms such runtime libraries are dynamic, but static libraries are
currently used on Windows because the toolchain is not a standard part of the OS.
(54)

or if option --use-valgrind is used or environment

variable _R_CHECK_ALWAYS_LOG_VIGNETTE_OUTPUT_ is set to a true value or if there are
differences from a target output file
(55)

for the most comprehensive checking this should be 5.8.0 or later: any for
which tidy --version does not report a version number will be too old – this
includes the 2006 version shipped with macOS.
(56)

For example, in early 2014 gdata declared ‘Imports: gtools’

and gtools declared ‘Imports: gdata’.

(57)

called CVS or .svn or .arch-ids or .bzr or .git (but not files called .git)
or .hg.

(58)

called .metadata.

(59)

which is an error: GNU make uses GNUmakefile.

(60)

see tools:::.hidden_file_exclusions and tools:::get_exclude_patterns() for

further excluded files and file patterns, respectively.
(61)
and to avoid problems with case-insensitive file systems, lower-case versions of all
these extensions.
(62)

unless inhibited by using ‘BuildVignettes: no’ in the DESCRIPTION file.

(63)

provided the conditions of the package’s license are met: many, including CRAN,
see the omission of source components as incompatible with an Open Source
license.
(64)

is prepended to the PATH so that references to R or Rscript in

R_HOME/bin
the Makefile do make use of the currently running version of R.

(65)

Note that lazy-loaded datasets are not in the package’s namespace so need to be
accessed via ::, e.g. survival::[Link].
(66)

they will be called with two unnamed arguments, in that order.

(67)

NB: this will only be read in all versions of R if the package contains R code in
a R directory.

(68)

Note that this is the basename of the shared object, and the appropriate extension
(.so or .dll) will be added.

(69)

This defaults to the same pattern as exportPattern: use something

like exportClassPattern("^$") to override this.
(70)

if it does, there will be opaque warnings about replacing imports if the

classes/methods are also imported.
(71)
People use [Link]() to open a device at a particular size: that is not portable but
using [Link](noRStudioGD = TRUE) helps.
(72)

Solaris make did not accept CRLF-terminated Makefiles; Solaris warned about and
some other makes ignore incomplete final lines.
(73)

This was apparently introduced in SunOS 4, and is available elsewhere provided it

is surrounded by spaces.
(74)

GNU make, BSD make and other variants of pmake in FreeBSD, NetBSD and
formerly in macOS, and formerly AT&T make as implemented on Solaris and
‘Distributed Make’ (dmake), part of Oracle Developer Studio and available in other
versions including from Apache OpenOffice.
(75)

For example, test options -a and -e are not portable, and not supported in the
AT&T Bourne shell used on Solaris 10/11, even though they are in the POSIX
standard. Nor did Solaris support ‘$(cmd)’.

(76)

as from R 4.0.0 the default is bash.

(77)

it was not in the Bourne shell, and was not supported by Solaris 10.
(78)

[Link] may help explain

some of the warnings from gfortran -Wall -pedantic.
(79)

These are optional because the corresponding types are, but must be provided if the
types are.
(80)

or where supported the variants _Exit and _exit.

(81)
This and srandom are in any case not portable. They are in POSIX but not in the
C99 standard, and not available on Windows.
(82)

including macOS as from version 13.

(83)

in libselinux.

(84)

At least Linux and Windows, but not macOS.

(85)

except perhaps the simplest kind as used by [Link]() in non-interactive

use.
(86)

Whereas the GNU linker reorders so -L options are processed first, the Solaris one
did not.
(87)

some versions of macOS did not.

(88)

If a Java interpreter is required directly (not via rJava) this must be declared and
its presence tested like any other external command.
(89)

For example, the ability to handle ‘[Link] URLs.

(90)

Not doing so is the default on Windows, overridden for the R executables.

(91)

These are not needed for the default compiler settings on ‘x86_64’ but are likely
to be needed on ‘ix86’.

(92)
Select ‘Save as’, and select ‘Reduce file size’ from the ‘Quartz filter’ menu’: this
can be accessed in other ways, for example by Automator.
(93)

except perhaps some special characters such as backslash and hash which may be
taken over for currency symbols.
(94)

Typically on a Unix-alike this is done by telling fontconfig where to find suitable

fonts to select glyphs from.
(95)

which it is on all known platforms, and is required as from R 4.0.0

(96)

Ubuntu provides 5 years of support (but people were running 14.04 after 7 years)
and RHEL provides 10 years full support and up to 14 with extended support.
(97)

This is seen on Linux, Solaris and FreeBSD, although each has other ways to turn
on all extensions, e.g. defining _GNU_SOURCE, __EXTENSIONS__ or _BSD_SOURCE: the
GCC compilers by default define _GNU_SOURCE unless a strict standard such as -
std=c99 is used. On macOS extensions are declared unless one of these macros
is given too small a value.
(98)

often taken from the toolchain’s headers.

(99)

at the time of writing ‘arm64’ macOS both warned and did not supply a prototype
in math.h which resulted in a compilation error.

(100)

also part of C++11 and later.

(101)

There is a portable way to do this in Fortran 2003 (ieee_is_nan() in

module ieee_arithmetic), but ironically that is not supported in the versions 4.x of
GNU Fortran. A pretty robust alternative is to test if(my_var /= my_var).
(102)

which often is the same as the header included by the C compiler, but some
compilers have wrappers for some of the C headers.
(103)

Although this is expected to be part of C23, full support of that is years away.
(104)

[Link]
(105)

it is allowed but ignored in system headers.

(106)

when using the macOS 13 SDK with a deployment target of macOS 13.
(107)

see [Link]
(108)

See [Link]
[Link]#modified-compiler-flags.
(109)

In principle this could depend on the OS, but has been checked on Linux and
macOS.
(110)

e.g. \alias, \keyword and \note sections.

(111)

There can be exceptions: for example Rd files are not allowed to start with a dot,
and have to be uniquely named on a case-insensitive file system.
(112)

in the current locale, and with special treatment for LaTeX special characters and
with any ‘pkgname-package’ topic moved to the top of the list.

(113)
Text between or after list items is discouraged.
(114)

as defined by the R function trimws.

(115)

Currently it is rendered differently only in HTML conversions, and LaTeX

conversion outside ‘\usage’ and ‘\examples’ environments.

(116)

There is only a fine distinction between \dots and \ldots. It is technically incorrect
to use \ldots in code blocks and tools::checkRd will warn about this—on the
other hand the current converters treat them the same way in code blocks, and
elsewhere apart from the small distinction between the two in LaTeX.
(117)

See the examples section in the file [Link] for an example.

(118)

R 2.9.0 added support for UTF-8 Cyrillic characters in LaTeX, but on some OSes
this will need Cyrillic support added to LaTeX, so environment
variable _R_CYRILLIC_TEX_ may need to be set to a non-empty value to enable this.
(119)

R has to be built to enable this, but the option --enable-R-profiling is the

default.
(120)

For Unix-alikes these are intervals of CPU time, and for Windows of elapsed time.
(121)

With the exceptions of the commands listed below: an object of such a name can
be printed via an explicit call to print.
(122)

The macOS support is for long-obsolete versions.

(123)
Those in some numeric, logical, integer, raw, complex vectors and in memory
allocated by R_alloc.
(124)

including using the data sections of R vectors after they are freed.
(125)

small fixed-size arrays by default in gfortran, for example.

(126)

currently on ‘x86_64’/‘ix86’ Linux and FreeBSD, with some support for Intel
macOS but not with the toolchain normally used with R. (There is a faster variant,
HWASAN, for ‘aarch64’ only.) On some platforms the runtime library, libasan,
needs to be installed separately, and for checking C++ you may also
need libubsan.
(127)

see [Link]
%202014%20--%20container%[Link].
(128)

part of the LLVM project and distributed in llvm RPMs and .debs on Linux. It is
not currently shipped by Apple.
(129)

as Ubuntu has been said to do.

(130)

installed on some Linux systems as asan_symbolize, and obtainable

from [Link]
asan_symbolize.py: it makes use of llvm-symbolizer if available.
(131)

including gcc 7.1 and clang 4.0.0: for gcc it is implied by -

fsanitize=address.

(132)
for example, X11/GL libraries on Linux, seen when checking package rgl and
some others using it—a workaround is to set environment
variable RGL_USE_NULL=true.
(133)

On some platforms the runtime library, libubsan, needs to be installed separately.

(134)

but works better if inlining and frame pointer optimizations are disabled.
(135)

By default as a security measure: see man dyld.

(136)

See [Link]
‘@executable_path’ could be used rather than absolute paths.

(137)

possibly after some platform-specific translation, e.g. adding leading or trailing

underscores.
(138)

This is currently included by R.h but may not be in future, so it should be

included by code needing the type.
(139)

Note that this is then not checked for over-runs by option CBoundsCheck = TRUE.

(140)

Strictly this is OS-specific, but no exceptions have been seen for many years.
(141)

For calls from within a namespace the search is confined to the DLL loaded for
that package.
(142)

For unregistered entry points the OS’s dlsym routine is used to find addresses. Its
performance varies considerably by OS and even in the best case it will need to
search a much larger symbol table than, say, the table of .Call entry points.
(143)

Because it is a standard package, one would need to rename it before attempting to

reproduce the account here.
(144)

whether or not ‘LinkingTo’ is used.

(145)

so there needs to be a corresponding import or importFrom entry in

the NAMESPACE file.

(146)

Even including C system headers in such a block has caused compilation errors.
(147)

[Link]
(148)

For example, ‘_GLIBCXX_USE_CXX11_ABI’ in g++ 5.1 and

later: [Link]
(149)

dyld on macOS, and DYLD_LIBRARY_PATHS below.

(150)

That is, similar to those defined in S version 4 from the 1990s: these are not kept
up to date and are not recommended for new projects.
(151)

see The R API: entry points for C code: note that these are not all part of the API.
(152)

SEXP is an acronym for Simple EXPression, common in LISP-like language

syntaxes.
(153)

If no coercion was required, coerceVector would have passed the old object
through unchanged.
(154)

You can assign a copy of the object in the environment

frame rho using defineVar(symbol, duplicate(value), rho)).

(155)

see Character encoding issues for why this might not be what is required.
(156)

This is only guaranteed to show the current interface: it is liable to change.

(157)

Known problems have been defining LENGTH, error, length, vector and warning:
whether these matter depends on the OS and toolchain, with many problem reports
involving clang++. As from LLVM clang 13.0.0, the remapping of match breaks
the subsequent inclusion of omp.h.

(158)

That was not the case on Windows prior to R 4.2.0.

(159)

also part of C++11.

(160)

The ‘F77_’ in the names is historical and dates back to usage in S.

(161)

It is an optional C11 extension.

(162)

[Link]
(163)

It is defined by the Intel compilers, but also hides unsatisfied references and so
cannot be used with R. It was not supported by the AIX nor Solaris compilers.
(164)

This applies to the compiler for the default C++ dialect (currently C++11) and not
necessarily to other dialects.
(165)

In some cases Fortran compilers accept the flag but do not actually hide their
symbols.
(166)

In the parlance of macOS this is a dynamic library, and is the normal way to build
R on that platform.
(167)

but these are not part of the automated test procedures and so little tested.
(168)

At least according to POSIX 2004 and later. Earlier standards

prescribed sys/time.h: R_ext/eventloop.h will include it
if HAVE_SYS_TIME_H is defined.
(169)

at least on platforms where the values are available, that is having getrlimit and
on Linux or having sysctl supporting KERN_USRSTACK, including FreeBSD and
macOS.
(170)

An attempt to use only threads in the late 1990s failed to work correctly under
Windows 95, the predominant version of Windows at that time.