.C and .Fortrandyn.load and dyn.unload.Call and .External
Next: Acknowledgements, Previous: (dir), Up: (dir) [Contents][Index]
This is a guide to extending R, with modifications for pqR. It describes the process of creating R add-on packages, writing R documentation, R’s system and foreign language interfaces, and the R API.
This document is based on the version for R 2.15.0 (2012-03-30).
ISBN 3-900051-11-9
Modifications for pqR are for pqR version 2.15.1 (2020-07-23).
Next: Creating R packages, Previous: Top, Up: Top [Contents][Index]
The contributions of Saikat DebRoy (who wrote the first draft of a guide
to using .Call and .External) and of Adrian Trapletti (who
provided information on the C++ interface) are gratefully acknowledged.
Next: Writing R documentation files, Previous: Acknowledgements, Up: Top [Contents][Index]
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 lib.loc 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.
A computing environment including a number of tools is assumed; the “R Installation and Administration” manual describes what is needed. Under a Unix-alike most of the tools are likely to be present by default, but Microsoft Windows may require careful setup.
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, either 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 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. The first is 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). The second sense is that used by the operating system, as a shared library 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 most Unix-alikes as a shared object and on Windows as a DLL (and used to be called a shared library on some Unix-alikes). The concept of a shared library (dynamic library on Mac OS X) as a collection of compiled code to which a package might link is also used, especially for R itself on some platforms.
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
install.packages. Source packages can be built, a
distinct concept. This involves taking a source directory and creating
a tarball ready for distribution, including cleaning it up and creating
PDF 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. As from R 2.13.0 there is also the possibility of (‘byte’) compiling the R code in a package (using the facilities of package compiler): at some future time this might be done routinely when compiling a package may come to mean compiling its R code.
It used to be unambiguous to talk about loading an installed
package using library(), but since the advent of package name
spaces 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 option of lazy loading of code or data is mentioned at several points. This is part of the installation, always selected for R code (since R 2.14.0) 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 run faster and use less (virtual) memory. (For technical details, see Lazy loading in R Internals.)
Next: Configure and cleanup, Previous: Creating R packages, Up: Creating R packages [Contents][Index]
The sources of an R package consists of a subdirectory containing a file DESCRIPTION and the subdirectories R, data, demo, exec, inst, man, po, src, and tests (some of which can be missing, but which should not be empty). The package subdirectory may also contain files INDEX, NAMESPACE, configure, cleanup, LICENSE, LICENCE and NEWS. Other files such as INSTALL (for non-standard installation instructions), README or ChangeLog will be ignored by R, but may be useful to end users.
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) script files which are, respectively, executed before and (provided that option --clean was given) after installation on Unix-alikes, see Configure and cleanup. The analogues on Windows are configure.win and cleanup.win.
The optional file LICENSE/LICENCE contains a copy of the license to the package. 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 COPYING.LIB files but refer to the copies on http://www.r-project.org/Licenses/ 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 licence files.
For the conventions for files NEWS and ChangeLog in the GNU project see http://www.gnu.org/prep/standards/standards.html#Documentation.
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 Mac OS X) 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 system platforms, 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$’, ‘nul’, ‘com1’ to ‘com9’, and
‘lpt1’ to ‘lpt9’ after conversion to lower case and stripping
possible “extensions” (e.g., ‘lpt5.foo.bar’), are disallowed.
Also, file names in the same directory must not differ only by case (see
the previous paragraph). In addition, the basenames of ‘.Rd’ files
may be used in URLs and so must be ASCII and not contain
%. For maximal portability filenames should only contain only
ASCII characters not excluded already (that is
A-Za-z0-9._!#$%&+,;=@^(){}'[] — 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
(){}'[]$.
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 check will warn about
them2 unless they are listed (one filepath per line) in a file
BinaryFiles at the top level of the package. Note that
CRAN will no longer accept submissions containing binary files
even if they are listed.
The R function package.skeleton can help to create the
structure for a new package: see its help page for details.
| • The DESCRIPTION file | ||
| • The INDEX file | ||
| • Package subdirectories | ||
| • Package bundles | ||
| • Data in packages | ||
| • Non-R scripts in packages |
Next: The INDEX file, Previous: Package structure, Up: Package structure [Contents][Index]
The DESCRIPTION file contains basic information about the package in the following format:
Package: pkgname Version: 0.5-1 Date: 2004-01-01 Title: My First Collection of Functions Authors@R: c(person("Joe", "Developer", role = c("aut", "cre"), email = "Joe.Developer@some.domain.net"), person("Pat", "Developer", role = "aut"), person("A.", "User", role = "ctb", email = "A.User@whereever.net")) Author: Joe Developer and Pat Developer, with contributions from A. User Maintainer: Joe Developer <Joe.Developer@some.domain.net> Depends: R (>= 1.8.0), nlme Suggests: MASS Description: A short (one paragraph) description of what the package does and why it may be useful. License: GPL (>= 2) URL: http://www.r-project.org, http://www.another.url BugReports: http://pkgname.bugtracker.url
The format is that of a ‘Debian Control File’ (see the help for
‘read.dcf’ and
http://www.debian.org/doc/debian-policy/ch-controlfields.html:
R does not require encoding in UTF-8). Continuation lines (for
example, for descriptions longer than one line) start with a space or
tab. The ‘Package’, ‘Version’, ‘License’,
‘Description’, ‘Title’, ‘Author’, and ‘Maintainer’
fields are mandatory, all other fields are optional. For R 2.14.0 or
later, ‘Author’ and ‘Maintainer’ can be auto-generated from
‘Authors@R’, and should be omitted if the latter is provided (and
the package depends on R (>= 2.14): see below for details).
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).
The mandatory ‘Package’ field gives the name of the package. This should contain only letters, numbers and dot, have at least two characters and start with a letter and not end in a dot. (Translation packages are allowed names of the form ‘Translation-ll’.)
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’.
The mandatory ‘License’ field should specify the license of the package in a standardized form. Alternatives are indicated via vertical bars. Individual specifications must be one of
GPL-2 GPL-3 LGPL-2 LGPL-2.1 LGPL-3 AGPL-3 Artistic-1.0 Artistic-2.0
as made available via http://www.r-project.org/Licenses/ and contained in subdirectory share/licenses of the R source or home directory.
If a package license extends a base FOSS license (e.g., using GPL-3 or AGPL-3 with an attribution clause), the extension 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.
Examples for standardized specifications include
License: GPL-2 License: GPL (>= 2) | BSD License: LGPL (>= 2.0, < 3) | Mozilla Public License License: GPL-2 | file LICENCE License: Artistic-1.0 | AGPL-3 + file LICENSE
Please note in particular that “Public domain” is not a valid license, since it is not recognized in some jurisdictions.
It is very important that you include this license information! Otherwise, it may not even be legally correct for others to distribute copies of the package. Do not use the ‘License’ field for copyright information: if needed, use a ‘Copyright’ field.
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.
The mandatory ‘Description’ field should give a comprehensive description of what the package does. One can use several (complete) sentences, but only one paragraph.
The mandatory ‘Title’ field should give a short description of the package. Some package listings may truncate the title to 65 characters. It should be capitalized, not use any markup, not have any continuation lines, and not end in a period.
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 with a valid (RFC 2822) email address in angle brackets (for sending bug reports etc.). It should not end in a period or comma. For a public 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.
Both ‘Author’ and ‘Maintainer’ fields can be omitted (as from
R 2.14.0) if a suitable ‘Authors@R’ field is given. This field
can be used to provide a refined, machine-readable description of the
package “authors” (in particular specifying their precise
roles), via suitable R code. The roles can include
‘"aut"’ (author) for full authors, ‘"cre"’ (creator) for the
package maintainer, and ‘"ctb"’ (contributor) for other
contributors, 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; in R
2.14.0 or later, the ‘Author’ and ‘Maintainer’ fields are
auto-generated from it if needed when building or installing.
Several optional fields take logical values: these can be specified as ‘yes’, ‘true’, ‘no’ or ‘false’: capitalized values are also accepted.
The ‘Date’ field gives the release date of the current version of the package. It is strongly recommended to use the yyyy-mm-dd format conforming to the ISO 8601 standard.
The ‘Depends’ field gives a comma-separated list of package names
which this package depends on. The package name may be optionally
followed by a comment in parentheses. The comment should contain a
comparison operator, whitespace and a valid version number. You can
also use the special package name ‘R’ if your package depends on a
certain version of R — e.g., if the package works only with R
version 2.11.0 or later, include ‘R (>= 2.11.0)’ in the
‘Depends’ field. 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). 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. Other dependencies (external to the R system)
should be listed in the ‘SystemRequirements’ field, possibly
amplified in a separate README file. 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, both when library is called and when preparing
for lazy-loading during installation.
A package (or ‘R’) can appear more than once in the ‘Depends’, but only the first occurrence was used in versions of R prior to 2.7.0: these are now very unlikely to be encountered.
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 base is always available.
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, but will not be checked when the namespace is
loaded (whereas they are checked by R CMD check).
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 example 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, and will be used by R CMD check. 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), so it is helpful if the use of suggested packages
is made conditional via if(require(pkgname))).
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
library(pkgname) must be listed in the ‘Imports’
field and not in the ‘Depends’ field.
library(pkgname) must be listed in the ‘Depends’
field, only.
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.)
In particular, large 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’ field are used by
library when it loads the package, and install.packages
checks versions for the ‘Imports’ and (for dependencies =
TRUE) ‘Suggests’ fields.
It is increasingly 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.
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.
The ‘BugReports’ field may contain a single
URL to which bug reports about the package should be
submitted. This URL will be used by bug.reports
instead of sending an email to the maintainer.
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.
An ‘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 (‘Collate.unix’ or ‘Collate.windows’) will be used instead of ‘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 keep.source = TRUE or FALSE: it might be needed
exceptionally for a package designed to always be used with
keep.source = TRUE.
The ‘ByteCompile’ logical field controls if the package code is
byte-compiled on installation: the default is currently not to, so this
may be useful for a package known to benefit particularly from
byte-compilation (which can take quite a long time and increases the
installed size of the package). However, in pqR, byte compilation of
packages is never done, regardless of this setting, unless the environment
variable R_PKG_BYTECOMPILE is set to TRUE.
The ‘ZipData’ logical field used to control whether the automatic Windows build would zip up the data directory or not: set this to ‘no’ if your package will not work with a zipped data directory. (Setting to any other value is deprecated, and it is unused from R 2.13.0: but it might still be needed if the package can be installed under earlier versions of R.)
The ‘BuildVignettes’ logical field can be set to a false value to stop
R CMD build from attempting to rebuild the vignettes, as well
as preventing R CMD check from testing this. This should only
be used exceptionally, for example if the PDFs need large figures which
are not part of the package sources.
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.)
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$OS.type’ having that value.
The ‘Type’ field specifies the type of the package: see Package types.
Note: There should be no ‘Built’ or ‘Packaged’ fields, as these are added by the package management tools.
One can add subject classifications for the content of the package using the fields ‘Classification/ACM’ (using the Computing Classification System of the Association for Computing Machinery, http://www.acm.org/class/), ‘Classification/JEL’ (the Journal of Economic Literature Classification System, http://www.aeaweb.org/journal/jel_class_system.html), or ‘Classification/MSC’ (the Mathematics Subject Classification of the American Mathematical Society, http://www.ams.org/msc/). 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’.
Finally, an ‘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 (http://tools.ietf.org/html/rfc5646, see also http://en.wikipedia.org/wiki/IETF_language_tag), i.e., use language subtags which in essence are 2-letter ISO 639-1 (http://en.wikipedia.org/wiki/ISO_639-1) or 3-letter ISO 639-3 (http://en.wikipedia.org/wiki/ISO_639-3) language codes.
Next: Package subdirectories, Previous: The DESCRIPTION file, Up: Package structure [Contents][Index]
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.
Rather than editing this file, it is preferable to put customized information about the package into an overview man page (see Documenting packages) and/or a vignette (see Writing package vignettes).
Next: Package bundles, Previous: The INDEX file, Up: Package structure [Contents][Index]
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 extensions4 .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.
Two exceptions are allowed: if the R subdirectory contains a file
sysdata.rda (a saved image of R objects: please use suitable
compression as suggested by tools::resaveRdaFiles) this will be
lazy-loaded into the namespace/package 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 comments, but then the comments may not be readable in
e.g. a UTF-8 locale. Non-ASCII characters in object names
will normally5 fail when the package is installed. Any byte will be allowed
in a quoted character string but \uxxxx escapes should be
used6 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.7
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 ‘file://’ URLs, which means8 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-internal.Rd 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 for an example. 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 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. 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++, FORTRAN 77, Fortran 9x9, Objective C and Objective
C++10 with associated extensions .c, .cc or
.cpp, .f, .f90 or .f95, .m, and
.mm or .M, respectively. We recommend using .h for
headers, also for C++11 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, and we do not support using both C++ and Fortran 9x. Because R itself uses it, we know that C and FORTRAN 77 can be used together and mixing C and C++ seems to be widely successful.
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’, and on Mac OS X ‘__APPLE__’ and ‘__APPLE_CC__’ are defined.
The default rules can be tweaked by setting macros12 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/Makevars.win takes precedence over src/Makevars and
src/Makefile.win must be used. 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/Makefile.win (unless intended for only Unix-alikes or only Windows).
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 multi-arch setting since R CMD INSTALL --libs-only
is used to merge multiple architectures and it only copies shared
objects/DLLs. If a package wants to install other binaries (for example
executable programs), it should to provide an R script
src/install.libs.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), 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/install.libs.R file:
files <- Sys.glob(paste("*", SHLIB_EXT, sep=''))
libarch <- if (nzchar(R_ARCH)) paste('libs', R_ARCH, sep='') else 'libs'
dest <- file.path(R_PACKAGE_DIR, libarch)
dir.create(dest, recursive = TRUE, showWarnings = FALSE)
file.copy(files, dest, overwrite = TRUE)
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 white
space. (Note that it is not possible to generate this index file
automatically.)
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. Prior
to R 2.12.2, the files were installed on POSIX platforms with the
permissions in the package sources, so care should be taken to ensure
these are not too restrictive: R CMD build will make suitable
adjustments. 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 matched13 against the file and directory paths, e.g.
doc/.*[.]png$ will exclude all PNG files in inst/doc based on
the (lower-case) 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 Mac OS X compiled packages (and not seen
by those who use R CMD INSTALL or install.packages
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 versions in inst will be that seen
in the installed package.
One thing you might like to add to inst is a CITATION file
for use by the citation function.
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 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 corresponding14 .Rout.save
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 tests has a subdirectory Examples containing a file
pkg-Ex.Rout.save, this is compared to the output file for
running the examples when the latter are checked.
Subdirectory exec could contain additional executable scripts the
package needs, typically scripts for interpreters such as the shell,
Perl, or Tcl. This mechanism is currently used only by a very few
packages, and still experimental. 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 may not be suitable for executable programs since some
platforms (including Mac OS X and Windows) support multiple
architectures using the same installed package directory.
Subdirectory po is used for files related to localization: see Internationalization.
Next: Data in packages, Previous: Package subdirectories, Up: Package structure [Contents][Index]
Support for package bundles was removed in R 2.11.0.
Next: Non-R scripts in packages, Previous: Package bundles, Up: Package structure [Contents][Index]
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 standard15 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 “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.
Images (extensions .RData 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, and look at the output of
loadedNamespaces().
If your data files are large and you are not using ‘LazyData’ 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. However, such files can only be used with R 2.10.0 or
later, and so the package should have an appropriate ‘Depends’
entry in its DESCRIPTION file.
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): there is no excuse for distributing ASCII saves.
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. However, such compression can only be
used with R 2.10.0 or later, and so the package should have an
appropriate ‘Depends’ entry in its DESCRIPTION file.
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.
Some 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. The only way to discover which
is best is to try them all and look at the size of the
pkgname/data/Rdata.rdb file.
Lazy-loading is not supported for very large datasets (those which when serialized exceed 2GB).
Previous: Data in packages, Up: Package structure [Contents][Index]
Code which needs to be compiled (C, C++, FORTRAN, Fortran 95 …) 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 (e.g. arulesSequences), BUGS, Java, JavaScript, Matlab, Perl (FEST), php (amap), Python or Tcl, or even R. However, it seems more common to use the inst directory, for example AMA/inst/java, WriteXLS/inst/Perl, Amelia/inst/tklibs, CGIwithR/inst/cgi-bin, NMF/inst/matlab and emdbook/inst/BUGS.
If your package requires one of these interpreters or an extension then this should be declared in the ‘SystemRequirements’ field of its DESCRIPTION file. Windows users should be aware that the Tcl extensions ‘BWidget’ and ‘Tktable’ which are included with the R for Windows installer are extensions and do need to be declared. ‘Tktable’ does ship as part of the Tcl/Tk provided on CRAN for Mac OS X, but you will need to tell your users how to make use of it:
> addTclPath('/usr/local/lib/Tktable2.9')
> tclRequire('Tktable')
<Tcl> 2.9
Next: Checking and building packages, Previous: Package structure, Up: Creating R packages [Contents][Index]
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 (Bourne 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.).
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. It can be used to
clean up the package source tree: in particular, it should remove all
files created by configure.
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 configure.ac (assuming Autoconf 2.50 or later).
The definition of the respective R function in foo.R.in 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 configure.ac
: ${R_HOME=`R RHOME`}
if test -z "${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 ‘${R_HOME}’
might contain spaces.)
If your code does load checks then you may also need
LDFLAGS=`"${R_HOME}/bin/R" CMD config LDFLAGS`
and packages written with C++ need to pick up the details for the C++ compiler and switch the current language to C++ by
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.
You can use R CMD config for getting the value of the basic
configuration variables, or the header and library flags necessary for
linking against R, see R CMD config --help for details.
To check for an external BLAS library using the ACX_BLAS macro
from the official Autoconf Macro Archive, one can simply do
F77=`"${R_HOME}/bin/R" CMD config F77`
AC_PROG_F77
FLIBS=`"${R_HOME}/bin/R" CMD config FLIBS`
ACX_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 77 code works on all R platforms. Calls to the Autoconf macro
AC_F77_LIBRARY_LDFLAGS, which would overwrite FLIBS, must
not be used (and hence e.g. removed from ACX_BLAS). (Recent
versions of Autoconf in fact allow an already set FLIBS to
override the test for the FORTRAN linker flags. Also, recent versions
of R can detect external BLAS and LAPACK libraries.)
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 configure.win script to be
used on that platform. (Optionally, there can be a cleanup.win
script. Both should be shell scripts to be executed by ash,
which is a minimal version of Bourne-style sh.) When
configure.win is run the environment variables R_HOME
(which uses ‘/’ as the file separator) and R_ARCH 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}/Rscript.exe.
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. (This happens with the Java Archive
files in the Omegahat SJava package.)
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
configure.win 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 Mac OS X) to do this is pkg-config. The
configure script will need to test for the presence of the
command itself (see for example package Cairo), 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 'QtCore >= 4.0.0' # check the status $ pkg-config --modversion QtCore 4.7.1 $ pkg-config --cflags QtCore -DQT_SHARED -I/usr/include/QtCore $ pkg-config --libs QtCore -lQtCore
Note that pkg-config --libs gives the information
required to link against the default version of that library (usually
the dynamic one), and pkg-config --static is needed if the
static library is to be used.
Sometimes the name by which the software is known to
pkg-config is not what one might expect (e.g.
‘gtk+-2.0’ even for 2.22). To get a complete list use
pkg-config --list-all | sort
| • Using Makevars | ||
| • Configure example | ||
| • Using F95 code |
Next: Configure example, Previous: Configure and cleanup, Up: Configure and cleanup [Contents][Index]
| • OpenMP support | ||
| • Using pthreads | ||
| • Compiling in sub-directories |
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 Makevars.in.
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 Makevars.win) without the use of GNU extensions.
The most common use of a Makevars file is to set additional
preprocessor options (for example include paths) for C/C++ files
via PKG_CPPFLAGS, and additional compiler flags by setting
PKG_CFLAGS, PKG_CXXFLAGS, PKG_FFLAGS or
PKG_FCFLAGS, for C, C++, FORTRAN or Fortran 9x respectively
(see Creating shared objects).
NB: 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.
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 are all specific to GCC.
There are some macros16 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
FLIBSA 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.
BLAS_LIBSA 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 or complex
routines. If BLAS_LIBS is included, then FLIBS also needs
to be17 included following it, as most BLAS
libraries are written at least partially in FORTRAN.
LAPACK_LIBSA 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 all the double-precision LAPACK routines as well as those
double-complex LAPACK and BLAS 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.
[There is no guarantee that the LAPACK library will provide more than all the double-precision and double-complex routines, and some do not provide all the auxiliary routines.]
For portability, the macros BLAS_LIBS and FLIBS should
always be included after LAPACK_LIBS (and in that order).
SAFE_FFLAGSA macro containing flags which are needed to circumvent
over-optimization of FORTRAN code: it is typically ‘-g -O2
-ffloat-store’ 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, and that it is
intended for the FORTRAN 77 compiler ‘F77’ and not necessarily for
the Fortran 90/95 compiler ‘FC’. 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 has
PKG_LIBS = @BLAS_LIBS@
SLAMC_FFLAGS=$(R_XTRA_FFLAGS) $(FPICFLAGS) $(SHLIB_FFLAGS) $(SAFE_FFLAGS)
all: $(SHLIB)
slamc.o: slamc.f
$(F77) $(SLAMC_FFLAGS) -c -o slamc.o slamc.f
needed to ensure that the LAPACK routines find some constants without infinite looping. The Windows equivalent is
all: $(SHLIB)
slamc.o: slamc.f
$(F77) $(SAFE_FFLAGS) -c -o slamc.o slamc.f
(since the other macros are all empty on that platform, and R’s
internal BLAS is 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 a 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).
Note that on Windows it is required that Makevars[.win] 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 Makefile.win file.
It is sometimes useful to have a target ‘clean’ in Makevars
or Makevars.win: 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 $(OBJECTS) unless set in the file itself.
It would also be possible to add tasks to the target ‘shlib-clean’
which is run by R CMD INSTALL and R CMD SHLIB with
options --clean and --preclean.
If you want to run R code in Makevars, e.g. to find
configuration information, please do ensure that you use the correct
copy of R or Rscript: there might not be one in the path
at all, or it might be the wrong version or architecture. The correct
way to do this is via
"$(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
libxxx.dll.a xxx.dll.a libxxx.a xxx.lib libxxx.dll xxx.dll
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
http://sourceware.org/binutils/docs-2.20/ld/WIN32.html#WIN32.
The fly in the ointment is that the DLL might not be named libxxx.dll, and in fact on 32-bit Windows there is a libxml2.dll whereas on one build for 64-bit Windows the DLL is called libxml2-2.dll. 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 configure.win) to ship them in the same directory as the package DLL.
Next: Using pthreads, Previous: Using Makevars, Up: Using Makevars [Contents][Index]
As from R 2.13.0 there is some support for packages which wish to use
OpenMP18. The
make macros
SHLIB_OPENMP_CFLAGS SHLIB_OPENMP_CXXFLAGS SHLIB_OPENMP_FCFLAGS SHLIB_OPENMP_FFLAGS
are available for use in src/Makevars or
src/Makevars.win.19
Include the appropriate macro in PKG_CFLAGS, PKG_CPPFLAGS
and so on, and also in PKG_LIBS. C/C++ code that needs to be
conditioned on the use of OpenMP can be used inside #ifdef
SUPPORT_OPENMP, a macro defined in the header Rconfig.h
(see Platform and version information): however the use of OpenMP is
most often indicated by ‘#pragma’ statements.
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)
There is nothing to say what version of OpenMP is supported: version 3.0 (May 2008) is supported by recent versions of the main platforms (but note that Mac OS X binaries are currently built for 10.5 using compilers which support version 2.5), but portable packages cannot assume that end users have recent versions (there are some years-old versions of Linux in use), and it may be safest to assume version 2.5.
OpenMP support is expected to be available on Windows in the toolchain
used for R 2.15.0 and these macros will be set appropriately. It
is not available on Windows prior to R 2.14.2. WARNING: With the
Windows toolchain, OpenMP threads may be initialized with the floating
point unit’s state set so that long double arithmetic is the same as
double arithmetic; use __asm__("fninit") in C to reset the FPU so
that long double arithmetic will work.
The performance of OpenMP varies substantially between platforms. Both the Mac OS X and Windows implementations have substantial overheads and are only beneficial if quite substantial tasks are run in parallel.
Calling any of the R API from threaded code is ‘for experts only’: they will need to read the source code to determine if it is thread-safe.
Next: Compiling in sub-directories, Previous: OpenMP support, Up: Using Makevars [Contents][Index]
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 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 version of OpenBSD used a different library name).
For a tutorial see https://computing.llnl.gov/tutorials/pthreads/.
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 (a recent part of the MinGW-w64 project). Both
implement libptheads as an import library for a DLL.
Whether Windows toolchains implement pthreads is up to the
toolchain provider. One issue has been licenses: pthreads-w32 is
licensed under LGPL which requires source code to be made available.
The toolchains used to compile R prior to version 2.14.2 do not
contain pthreads, although in some cases pthreads-w32
could be retro-fitted. As from R 2.14.2 a make variable
SHLIB_PTHREAD_FLAGS is available: this should be included in both
PKG_CPPFLAGS (or the Fortran or F9x equivalents) and
PKG_LIBS.
The presence of a working pthreads implementation cannot be
unambiguously determined without testing for yourself: however, that
‘_REENTRANT’ is defined20 in C/C++ code is a good indication.
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]
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:
OBJECTS.samplers = samplers/ExpandableArray.o samplers/Knots.o \ samplers/RJumpSpline.o samplers/RJumpSplineFactory.o \ samplers/RealSlicerOV.o samplers/SliceFactoryOV.o samplers/MNorm.o OBJECTS.distributions = distributions/DSpline.o \ distributions/DChisqrOV.o distributions/DTOV.o \ distributions/DNormOV.o distributions/DUnifOV.o distributions/RScalarDist.o OBJECTS.root = RJump.o OBJECTS = $(OBJECTS.samplers) $(OBJECTS.distributions) $(OBJECTS.root)
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="$(RANLIB)")
Note the quotes: the macros can contain spaces, e.g. gcc -m64
-std=gnu99. Several authors have forgotten about parallel makes: the
static library in the subdirectory must be made before the shared
library and so must depend on the latter. Others forget the need for
position-independent code.
We really do not recommend using a src/Makefile instead on src/Makevars, and as the example above shows, it is not necessary.
Next: Using F95 code, Previous: Using Makevars, Up: Configure and cleanup [Contents][Index]
It may be helpful to give an extended example of using a configure script to create a src/Makevars file: this is based on that in the RODBC package.
The configure.ac file follows: configure is created from
this by running autoconf in the top-level package directory
(containing configure.ac).
AC_INIT([RODBC], 1.1.8) dnl package name, version dnl A user-specifiable option odbc_mgr="" AC_ARG_WITH([odbc-manager], AC_HELP_STRING([--with-odbc-manager=MGR], [specify the ODBC manager, e.g. odbc or iodbc]), [odbc_mgr=$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=`"${R_HOME}/bin/R" CMD config CC` CPP=`"${R_HOME}/bin/R" CMD config CPP` CFLAGS=`"${R_HOME}/bin/R" CMD config CFLAGS` CPPFLAGS=`"${R_HOME}/bin/R" CMD config CPPFLAGS` AC_PROG_CC AC_PROG_CPP 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/Makevars.in and src/config.h AC_CONFIG_FILES([src/Makevars]) AC_OUTPUT
where src/Makevars.in 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.
Previous: Configure example, Up: Configure and cleanup [Contents][Index]
R assumes that source files with extension .f are FORTRAN 77, and passes them to the compiler specified by ‘F77’. On most but not all platforms that compiler will accept Fortran 90/95 code: some platforms have a separate Fortran 90/95 compiler and a few (by now quite rare21) platforms have no Fortran 90/95 support.
This means that portable packages need to be written in correct FORTRAN 77, which will also be valid Fortran 95. See http://developer.r-project.org/Portability.html for reference resources. In particular, free source form F95 code is not portable.
On some systems an alternative F95 compiler is available: from the
gcc family this might be gfortran or g95.
Configuring R will try to find a compiler which (from its name)
appears to be a Fortran 90/95 compiler, and set it in macro ‘FC’.
Note that it does not check that such a compiler is fully (or even
partially) compliant with Fortran 90/95. Packages making use of Fortran
90/95 features should use file extension .f90 or .f95 for
the source files: the variable PKG_FCFLAGS specifies any special
flags to be used. There is no guarantee that compiled Fortran 90/95
code can be mixed with any other type of compiled code, nor that a build
of R will have support for such packages.
Some (but not) all compilers specified by the ‘FC’ macro will
accept Fortran 2003 or 2008 code. For platforms using
gfortran, you may need to include -std=f2003 or
-std=f2008 in PKG_FCFLAGS: the default is ‘GNU Fortran’,
Fortran 95 with non-standard extensions. The Solaris f95
compiler ‘accepts some Fortran 2003 features’. Such code should still
use file extension .f90 or .f95.
Next: Writing package vignettes, Previous: Configure and cleanup, Up: Creating R packages [Contents][Index]
Before using these tools, please check that your package can be
installed and loaded. R CMD check will inter alia do
this, but you may get more detailed error messages doing the checks
directly.
| • Checking packages | ||
| • Building package tarballs | ||
| • Building binary packages |
Note:
R CMD checkandR CMD buildrun R with --vanilla, so none of the user’s startup files are read. If you needR_LIBSset (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 variablesR_CHECK_ENVIRONandR_BUILD_ENVIRON; if unset, files22 ~/.R/check.Renviron and ~/.R/build.Renviron are used) to set environment variables when using these utilities.
Note to Windows users:
R CMD buildmay require you to have installed the Windows toolset (see the “R Installation and Administration” manual) and have it in your path, andR CMD checkwill make use of it if present. You may need to setTMPDIRto 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).
Next: Building package tarballs, Previous: Checking and building packages, Up: Checking and building packages [Contents][Index]
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 gzipped package tar
archives23 with
extension .tar.gz or .tgz. (Some platforms may allow
other forms of compression and extensions .tar.bz2 and
.tar.xz.)
This runs a series of checks, including
file if available24. (There may be rare false positives.)
R_LIBS 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’ or ‘Contains’): this is not an exhaustive check of
the actual imports.
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.
library.dynam.
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 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)
\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).
\usage
sections of Rd files are documented in the corresponding
\arguments section.
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. Windows25 users should note that the Fortran and C++ runtime libraries are examples of such external libraries.
qpdf) are available, checking that the
PDF documentation is of minimal size.
\examples to create executable example code.) If there is a file
tests/Examples/pkg-Ex.Rout.save, 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.
If there is an error26 in executing the R code in vignette foo.ext, a log
file foo.ext.log is created in the check directory. The
vignette PDFs 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/inst/doc. (It is only retained if there
are errors or if environment variable _R_CHECK_CLEAN_VIGN_TEST_ is
set to a false value.)
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 available27).
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.
Multiple sub-architectures: On systems which support multiple sub-architectures (principally Windows and Mac OS X),
R CMD checkwill install and check a package which contains compiled code under all available sub-architectures. (Use option --force-multiarch to force this for packages without compiled code, which are otherwise only checked under the main sub-architecture.) This will run the loading tests, examples and tests directory under each installed sub-architecture in turn, and give an error if any fail. Where environment variables (including perhapsPATH) need to be set differently for each sub-architecture, these can be set in architecture-specific files such as R_HOME/etc/i386/Renviron.site.An alternative approach is to use
R CMD check --no-multiarchto check the primary sub-architecture, and then to use something likeR --arch=x86_64 CMD check --extra-archor (Windows)/path/to/R/bin/x64/Rcmd check --extra-archto run for each additional sub-architecture just the checks28 which differ by sub-architecture.
Next: Building binary packages, Previous: Checking packages, Up: Checking and building packages [Contents][Index]
Packages may be distributed in source form as “tarballs” (.tar.gz 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 more common distribution form for the Windows and Mac platforms.
Using R CMD build, the R package builder, one can build R
package tarballs from their sources (for example, for subsequent release).
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 make files 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 matched29 against the
file names30 relative
to the top-level package source directory. In addition, directories
from source control systems31,
directories with names ending .Rcheck or Old or old
and files GNUMakefile, Read-and-delete-me or with base
names starting with ‘.#’, or starting and ending with ‘#’, or
ending in ‘~’, ‘.bak’ or ‘.swp’, are excluded by default.
In addition, those files in the R, demo and man
directories which are flagged by R CMD check as having invalid
names will be excluded.
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-vignettes option32, it will attempt to rebuild 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/partial.rdb. 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
(http://qpdf.sourceforge.net/) 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.
Note that prior to R 2.13.0, R CMD build did some cleaning in
the supplied source directory, but this was undocumented and is no
longer done.
R CMD build requires a suitable tar program that can
produce a compressed tarball: almost certainly one will have been found
when R was configured on a Unix-alike (and the Windows toolset
contains one), but if there are problems, set the environment variable
TAR to the path to a suitable program or to "internal" if
none is available.
Previous: Building package tarballs, Up: Checking and building packages [Contents][Index]
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 Mac 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
.tar.gz format) or the location of the directory of the package
source to be built.
R CMD INSTALL --build 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:
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 (e.g. handling Fortran sources on Mac OS X) are discussed in the
platform-specific FAQs.
In earlier versions of R, R CMD build --binary could build
a binary version of a package, but this approach is now deprecated in
favour of R CMD INSTALL --build.
Finally, at least one web-based service is available for building binary packages from (checked) source code: WinBuilder (see http://win-builder.r-project.org/) 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: Submitting a package to CRAN, Previous: Checking and building packages, Up: Creating R packages [Contents][Index]
| • Encodings and 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 are PDF documents with sources in Sweave format, which we call package vignettes. As from R 2.14.0 the preferred location for the Sweave sources is the subdirectory vignettes of the source packages, but for compatibility with earlier versions of R, vignette sources will be looked for in inst/doc if vignettes does not exist.
Vignette sources are normally given the file extension .Rnw or
.Rtex, but for historical reasons extensions33 .Snw and .Stex are also
recognized as vignettes. 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 document format.
Package vignettes are tested by R CMD check by executing all R
code chunks they contain (except those with option eval=FALSE).
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 system.file(). All other
files needed to re-make the vignette PDFs (such as LaTeX style files,
BiBTeX input files and files for any figures not created by running the
code in the vignette) must in the vignette source directory.
R CMD build will automatically34 create PDF
versions of the vignettes in inst/doc for distribution with the
package sources. By including the PDF version in the package sources it
is not necessary that the vignette PDFs 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 his
machine.35
By default R CMD build will run Sweave on all files in
Sweave format in vignettes, or if that does not exist,
inst/doc (but not in sub-directories). If no Makefile is
found in directory inst/doc, then tools::texi2dvi(pdf =
TRUE) is run on all processed vignettes. Whenever a Makefile is
found, then R CMD build will try to run make after the
Sweave runs. The first target in the Makefile should take
care of both creation of PDF 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_HOME36. 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) and must work
correctly with a parallel make: too many authors have written
things like
## BAD EXAMPLE
all: pdf clean
pdf: ABC-intro.pdf ABC-details.pdf
%.pdf: %.tex
texi2dvi --pdf $*
clean:
rm *.tex ABC-details-*.pdf
which will start removing the source files whilst pdflatex is working.
Note that it is pointless (and potentially misleading since the files might be outdated) to include in inst/doc R code files which would be generated from vignettes, as these will be re-generated when the package is installed (unless the vignette does not generate any R code, in which case it is also pointless/misleading).
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 and \VignetteKeyword (which replaced
\VignetteKeywords). These are processed at package installation
time to create the saved data frame Meta/vignette.rds, but only
the \VignetteIndexEntry and \VignetteKeyword statements
are currently used.
At install time an HTML index for all vignettes in the package is
automatically created from the \VignetteIndexEntry statements
unless a file index.html exists in directory
inst/doc. This index is linked from the HTML help index for
the package. If you do supply a inst/doc/index.html 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.
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 vignette PDFs, 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.)
Previous: Writing package vignettes, Up: Writing package vignettes [Contents][Index]
Vignette PDFs 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 Sweave() processes comments to look
for options and metadata lines. When Sweave() or
Stangle() is called on the vignette source, it will be
converted37 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 recorded in a comment at
the top of the file.
Sweave() will produce a .tex file in the current locale’s
encoding. That needs to be declared to LaTeX via a line like
\usepackage[utf8]{inputenc}
R CMD check will warn about any non-ASCII vignettes it finds
which do not have such a declaration.
The problem is that this cannot be known in advance, so vignette PDFs
may only be re-createable on the author’s own machine. R CMD
check will report on any non-ASCII vignettes it finds which do not have
such a declaration. (It is also possible to use the more recent
‘inputenx’ LaTeX package.)
Sweave() will also parse and evaluate the R code in each
chunk. The R output will also be in the current locale, 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 pdf.encoding 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 fortunes.tex will be in UTF-8 in any locale. Had
read.table been told the data were UTF-8, fortunes.tex
would have been in the locale’s encoding.
Next: Package namespaces, Previous: Writing package vignettes, Up: Creating R packages [Contents][Index]
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.
Before submitting a package mypkg, do run the following steps to test it is complete and will install properly. (Run from the directory containing mypkg as a subdirectory.)
R CMD build to make the release .tar.gz file.
R CMD check --as-cran on the .tar.gz file to check
that the package will install and will run its examples, and that the
documentation is complete and can be processed. If the package contains
code that needs to be compiled, try to enable a reasonable amount of
diagnostic messaging (“warnings”) when compiling, such as e.g.
-Wall -pedantic for tools from GCC, the GNU Compiler
Collection. If R was not configured accordingly, one can achieve
this via personal Makevars files.
See Customizing package compilation in R Installation and Administration,
Note that it is particularly important to use -Wall -pedantic with C++ code: the GNU C++ compiler has many extensions which are not supported by other compilers, and this will report some of them (such as the misuse of variable-length arrays). If possible, check C++ code on a standards-conformant compiler.
Although there is now a 2011 version of the C++ standard, it is not yet implemented (nor is it likely to be widely available for some years) and portable C++ code needs to follow the 1998 standard (and not use features from C99).
Similarly, the 2011 C standard is unlikely to be widely implemented for several years.
If your package has tests or vignettes, study their output too.
R CMD check at
mypkg.Rcheck/mypkg-manual.pdf, or produce another copy by
R CMD Rd2pdf mypkg.
Many aspects of help rendering changed in R 2.10.0, and in particular the interpretation of comment lines (which are rendered as blank lines, so do not put comment lines in the middle of a paragraph of text).
R CMD check will report38 on installed packages of
more than 5Mb, detailing directories of more than 1Mb. It warns about
inefficient compression of data: R CMD build --resave-data
will compact data as best it can.
Watch out for unnecessary files in inst/doc: R CMD
check will note files of types that probably should be installed, but
it cannot distinguish PDF figures from PDF documents. If files need to
be in inst/doc but not installed, use a .Rinstignore file.
The CRAN policy is that doc directories should not exceed 5Mb, and where data directories need to be more than 5–10Mb, consideration should be given to a separate package containing just the data. (Similarly for external data directories, large jar files and other libraries that need to be installed.)
See below for ways to reduce the size of PDF files such as vignettes.
See below for ways to find out where your package checks are taking significant time.
Please ensure that you can run through the complete procedure with only
warnings that you understand and have reasons not to eliminate. In
principle, packages must pass R CMD check without warnings or
significant notes to be admitted to the main CRAN package
area. If there are warnings you cannot eliminate (for example because
you believe them to be spurious) send an explanatory note as part of
your covering email.
Also read the CRAN policies linked from http://cran.r-project.org/web/packages/ and note that by submitting a package you are confirming that your package complies with them.
When all the testing is done, upload the .tar.gz file, using ‘anonymous’ as log-in name and your e-mail address as password, to ftp://CRAN.R-project.org/incoming/ (note: use ‘ftp’39 and not ‘sftp’ to connect to this server, and passive ‘ftp’ is more often successful) and send a message to CRAN@R-project.org about it (with your package name and version in the subject line, and please do not submit a package by email). For a new submission, please note in the message that you have read and agreed to the CRAN policies.
The CRAN maintainers will run these tests before putting a submission online. (They will use the latest development version of R, so if at all possible so should you.)
Please note that submissions without an accompanying email to CRAN@R-project.org will not be processed, and that emails should not be sent personally to members of the CRAN team.
Note also that for running LaTeX, the Debian GNU/Linux CRAN check systems use the Debian TeXLive40 distribution (http://packages.debian.org/en/sid/texlive); the Fedora and Solaris check systems use current TexLive; the Windows CRAN builder uses a reasonably recent version of MikTeX (including all packages available directly for MikTeX); the Mac OS X builders use a current full version of MacTeX, which includes all of the current TeXLive. Developers wanting to have their vignettes use TeX packages or style files not (yet) included in these distributions should add41 the style files to the vignettes (or for the legacy layout, inst/doc) subdirectory of their package.
| • PDF size | ||
| • Package timing | ||
| • Windows external software |
Next: Package timing, Previous: Submitting a package to CRAN, Up: Submitting a package to CRAN [Contents][Index]
There are a several tools available to reduce the size of PDF files,
including Adobe Acrobat (not Reader), Apple’s Preview42,
qpdf (http://qpdf.sourceforge.net/), and Ghostscript
(which converts PDF to PDF by
ps2pdf options -dAutoRotatePages=/None in.pdf out.pdf
and suitable options might be
-dPDFSETTINGS=/ebook -dPDFSETTINGS=/screen
; see http://www.ghostscript.com/doc/9.04/Ps2pdf.htm for
more such and consider all the options for image downsampling) as well
as numerous commercial and shareware Windows programs. Note that these
do not all try the same size-reduction strategies, and Acrobat and
ps2pdf can sometimes do much better at reducing the size of
embedded bitmap images, and ps2pdf does not use PDF object
compression (see below).
Since qpdf is fairly readily available (e.g. it has binaries
for Windows and packages in Debian/Ubuntu, and is installed as part of
the CRAN Mac OS X distribution of R), there is an option
--compact-vignettes to R CMD build 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 Mac OS X). This option can take values
‘qpdf’ (the default) as well as ‘gs’ or ‘both’ to try
harder to reduce the size. These should definitely be tried before
submission to CRAN for packages with more than 250Kb of PDF files: as
‘gs’ may make lossy changes such as downsampling bitmap images, do
examine the results and if necessary use ps2pdf or
tools::compactPDF directly.
Most of the large PDFs we have encountered have been large because of
the inclusion of figures, for example complex figures from R (where
.png versions may be more appropriate, and PDF compression was
not used by pdf() prior to R 2.14.0, so it may help to
re-generate them) and screendumps. However, some have been
unnecessarily large due to pdftex settings. The modern
default is to use both PDF compression and PDF object compression (which
needs PDF version 1.5 from 2003): this is the default in most TeX
distributions but not MiKTeX. It 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
https://svn.r-project.org/R/trunk/doc/manual/refman.top.
Next: Windows external software, Previous: PDF size, Up: Submitting a package to CRAN [Contents][Index]
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 non-zero 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 generates a
file called mypkg.Rcheck/mypkg-Ex.timings
containing timings for each help files (as given by
system.time()). 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 _R_CHECK_ALWAYS_LOG_VIGNETTE_OUTPUT_ is set
to a true value.
Previous: Package timing, Up: Submitting a package to CRAN [Contents][Index]
Note that CRAN does not accept submissions of precompiled binaries due to security concerns, and does not allow binary executables in source packages. Maintainers who need additional software for the Windows binaries of their packages on CRAN have three options
Be aware that in all cases license requirements will need to be met so you may need to supply the sources for the additional components (and will if your package has a GPL-like license).
Also be aware that there are both 32- and 64-bit builds of R for Windows with a combined distribution of binary packages, so the CRAN team will be unwilling to support a package that works under just one of the architectures.
Next: Writing portable packages, Previous: Submitting a package to CRAN, Up: Creating R packages [Contents][Index]
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 mechanism for specifying a namespace for a package is to place a
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.
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. Sealing also 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.
If a NAMESPACE file is not present, then one is generated automatically when the package is built or installed, all objects are exported, and all packages listed in the Imports or Depends fields in the DESCRIPTION file are imported. This is only intended as a temporary measure whilst packages are converted to have a NAMESPACE file and will be removed in due course. A hand-crafted NAMESPACE should be added to any existing package which does not have one.
Prior to version 2.14.0, namespaces were optional in packages. In such packages searches for non-local variables started with the search path, so a package’s own functions could be masked by those of a package appearing earlier.
As from R 2.14.0 all packages have a namespace, and a default NAMESPACE file is generated on installation if there is not one in the sources. However, not all versions of R will read the NAMESPACE file if the package contains not R code.
| • Specifying imports and exports | ||
| • Registering S3 methods | ||
| • Load hooks | ||
| • An example | ||
| • Summary -- converting an existing package | ||
| • Namespaces with S4 classes and methods |
Next: Registering S3 methods, Previous: Package namespaces, Up: Package namespaces [Contents][Index]
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. (As from R 2.13.0 this pattern applies to S4 classes, but did not in earlier versions of R.) 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__.’ . (Such objects are excluded from pattern matches in recent versions of R, so such patterns are safer for packages only to be used with R 2.14.0 or later.)
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.
It is possible to export variables from a namespace that it has imported from other namespaces.
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, so this approach is usually
not recommended. 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.
Using foo:::f instead of foo::f allows access to
unexported objects. This is generally not recommended, as the
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]
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 print.foo 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 print.foo 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.)
Next: An example, Previous: Registering S3 methods, Up: Package namespaces [Contents][Index]
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 arguments43 libname and
pkgname; they should be defined in the namespace but not
exported.
Packages use the .Last.lib function (provided it 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. .onUnload should be defined in
the name space and not exported, but .Last.lib 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.
There can be one or more useDynLib directives which allows shared
objects that need to be loaded to be specified in the NAMESPACE
file.44 The directive
useDynLib(foo)
registers the shared object foo45 for loading with library.dynam.
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.
User-level hooks are also available: see the help on function
setHook.
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 several compiled DLLs.
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:
R_CMethodDef cMethods[] = {
{"foo", (DL_FUNC) &foo, 4, {REALSXP, INTSXP, STRSXP, LGLSXP}},
{"bar_sym", (DL_FUNC) &bar, 0},
{NULL, NULL, 0}
};
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 name
space.
More information about this symbol lookup, along with some approaches for customizing it, is available from http://www.omegahat.org/examples/RDotCall.
Next: Summary -- converting an existing package, Previous: Load hooks, Up: Package namespaces [Contents][Index]
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") print.foo <- 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
The second package bar has code file bar.R
and NAMESPACE file
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.
Next: Namespaces with S4 classes and methods, Previous: An example, Up: Package namespaces [Contents][Index]
To summarize, converting a pre-2.14.0 package to use a namespace involves several simple steps:
export directives.
S3method declarations.
require calls by
import directives (and make appropriate changes in the
Depends and Imports fields of the DESCRIPTION
file).
.First.lib functions with .onLoad/.onAttach
functions or use a useDynLib directive in the NAMESPACE
file.
The first two of these are done automatically, but a package author can usually improve on R’s guesswork.
R CMD build will add a basic NAMESPACE file to a
package. If this is edited, do remove the first line (as the comment in
the file says).
Previous: Summary -- converting an existing package, Up: Package namespaces [Contents][Index]
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 file and 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)
importFrom("graphics", plot)
importFrom("stats", optim, qchisq)
## 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, profile.mle, summary.mle)
## 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 exportClassPattern.46 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 plot 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 package, 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
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: the requirements on this are stricter as from R
2.15.0. You may for example need to import plot from
graphics 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]
| • Encoding issues | ||
| • Binary distribution |
Portable packages should have simple file names: use only alphanumeric
ASCII characters and ., and avoid those names not
allowed under Windows which are mentioned above.
R CMD check provides 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.
ifeq and the like), ${shell ...} and
${wildcard ...}, and the use of += and :=. Also,
the use of $< other than in implicit rules is a GNU extension.
Unfortunately makefiles which use GNU extensions often run on other
platforms but do not have the intended results.
The use of ${shell ...} can be avoided by using backticks, e.g.
PKG_CPPFLAGS = `gsl-config --cflags`
which works in all versions of make known47 to be used with R.
If you really must assume GNU make, declare it in the DESCRIPTON file by
SystemRequirements: GNU make
Since the only viable make for Windows is GNU make, it is permissible to use GNU extensions in files Makevars.win or Makefile.win.
gcc 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 GNU extensions which fail to
compile on most other C++ compilers. R assumes a C99 compiler as
from version 2.12.0, but if you want your package to be portable to
earlier versions you should write in C90. (In practice C99 has been
available on most platforms since ca 2007 but old versions of
gcc were still in use for R 2.11.x.)
If you use FORTRAN 77, ftnchek
(http://www.dsm.fordham.edu/~ftnchek/) provides thorough testing
of conformance to the standard.
long in C will be 32-bit
on most R platforms (including those mostly used by the
CRAN maintainers), but 64-bit on many 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 type such as int_fast64_t
(and failing that, long long 48) and typedef your own type to be long or
long long, or use another suitable type (such as size_t).
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 integer types intptr_t
and uintptr_t (which are defined in the header <stdint.h>
and are not required to be implemented by the C99 standard).
Note that integer in FORTRAN corresponds to int
in C on all R platforms.
abort
or exit: these terminate the user’s R process, quite possibly
including all his 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 as from R 2.15.0 R CMD INSTALL
does so as part of the compilation flags. If you wish to use
assert during development. you can include -UNDEBUG in
PKG_CPPFLAGS. 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. Such code may contain references
to abort or exit that can never be called, but if any are
found in the package’s shared object/DLL, they are reported by
R CMD check.
R CMD check can
detect this in the package’s shared object/DLL it will report it: as
with the previous item such calls may come from external software and
may never be called. (This seems particularly common on Mac OS X and
Windows with static libraries: however on Windows the use of Fortran I/O
usually results in the detection of _assert and exit.)
nm -pg mypkg.so # or other extension such as .sl
and checking if any of the symbols marked U is unexpected is a
good way to avoid this.
nm -pg), and to use unusual names, as
well as ensuring you have used the PACKAGE argument that R
CMD check checks for.
R CMD build packages the tarball with the -h
tar flag which is documented to dereference links so this is
not usually a problem, but versions 1.24 and later of GNU tar
dereference some links to hard links which may not be handled correctly
by R CMD INSTALL.
Next: Binary distribution, Previous: Writing portable packages, Up: Writing portable packages [Contents][Index]
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. Many 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. Other characters may not be rendered at all, rendered incorrectly, or cause your R code to give an error. For 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) 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.
From R 2.10.0 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. 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 Windows,
for example). Suitable fonts will need to be selected or made
available49 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.
If you want to run R CMD check on a Unix-alike over a package
that sets a package encoding in its DESCRIPTION file 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) except that if
the current locale is UTF-8 then the package code is translated to UTF-8
for syntax checking.
Previous: Encoding issues, Up: Writing portable packages [Contents][Index]
If you want to distribute a binary version of a package on Windows or Mac OS X, 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’
(http://www.dependencywalker.com/) for both 32-bit and 64-bit
DLLs – note that this will report as missing links to R’s own DLLs
such as R.dll and Rblas.dll. For 32-bit DLLs only, the
command-line tool pedump.exe -i (in Rtools*.exe) can be
used, and for the brave, the objdump tool 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 Mac OS X, using R CMD otool -L on the package’s shared
objects under libs will show what they depend on: watch for any
dependencies in /usr/local/lib, notably libgfortran.2.dylib.
Next: Internationalization, Previous: Writing portable packages, Up: Creating R packages [Contents][Index]
Now that diagnostic messages can be made available for translation, 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.
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.
sQuote or dQuote except where the argument is a
variable.
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 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).
library
if((length(nopkgs) > 0) && !missing(lib.loc)) {
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(lib.loc)) {
pkglist <- paste(sQuote(nopkgs), collapse = ", ")
msg <- sprintf(ngettext(length(nopkgs),
"library %s contains no packages",
"libraries %s contain no packages"),
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]
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 the GNU
archive mirrors and packaged with the poEdit package
(http://poedit.sourceforge.net/download.php#win32).
| • C-level messages | ||
| • R messages | ||
| • Installing translations | ||
| • Makefile support |
Next: R messages, Previous: Internationalization, Up: Internationalization [Contents][Index]
The process of enabling translations is
#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 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 ? StringP: String) #endif
and mark strings by
dngettext(("pkg", <singular string>, <plural string>, n)
(This is only supported from R 2.10.0, so packages which use it need
to depend on R (>= 2.10).)
xgettext --keyword=_ -o pkg.pot *.c
The file src/pkg.pot is the template file, and
conventionally this is shipped as po/pkg.pot. A translator
to another language makes a copy of this file and edits it (see the
gettext manual) to produce say ll.po, where ll
is the code for the language in which the translation is to be used.
(This file would be shipped in the po directory.) Next run
msgfmt on ll.po to produce ll.mo, and
copy that to inst/po/ll/LC_MESSAGES/pkg.mo. Now when
the package is loaded after installation it will look for translations
of its messages in the po/lang/LC_MESSAGES/pkg.mo file
for any language lang that matches the user’s preferences (via the
setting of the LANGUAGE environment variable or from the locale
settings).
Next: Installing translations, Previous: C-level messages, Up: Internationalization [Contents][Index]
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 R-pkg.pot 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.
Translation of messages which might be singular or plural can be very
intricate: languages can have up to four different forms. The R
function ngettext provides an interface to the C function of the
same name, and will choose an appropriate singular or plural form for
the selected language depending on the value of its first argument
n. It is safest to use domain="R-pkg" explicitly in
calls to ngettext, and necessary unless they are calls directly
from a function in the package.
Next: Makefile support, Previous: R messages, Up: Internationalization [Contents][Index]
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 ‘ll.po’ or ‘R-ll.po’ 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.
Translations need to be prepared and installed in inst/po/ to be usable once the package is installed. To do this use the appropriate lines of
mkdir -p inst/po/ll/LC_MESSAGES msgfmt -c --statistics -o inst/po/ll/LC_MESSAGES/R-pkg.mo po/R-ll.po msgfmt -c --statistics -o inst/po/ll/LC_MESSAGES/pkg.mo po/ll.po
from the package’s top-level directory. Using -c does some useful validity checks, and --statistics notes the coverage.
Previous: Installing translations, Up: Internationalization [Contents][Index]
There is some makefile support in the po directory of the R sources. To use this to create the template files, use
mkdir -p pkgdir/po
where pkgdir is the top-level directory of the package sources. If the package has C source files in its src directory that are marked for translation, use
touch pkgdir/po/pkg.pot
to create a dummy template file. Then
cd R_BUILD_DIR/po make pkg-update PKG=pkg PKGDIR=pkgdir
will create a template file of R messages and update any template of C messages. It will also prepare and install a translation for the ‘en@quot’ pseudo-language, which if selected interprets (single and double) quotes in their directional forms in suitable (e.g. UTF-8) locales.
If translations to new languages are added in the pkgdir/po
directory, running the same make command will check and then
install the translations.
If the package sources are updated, the same make 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.
This support is only for Unix-alikes, and the tools did not work correctly on at least one Mac OS X system.
Next: Package types, Previous: Internationalization, Up: Creating R packages [Contents][Index]
An installed file named CITATION will be used by the
citation() function. (To be installed, it needed to 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). If no such file is
present, citation auto-generates citation information from the
package DESCRIPTION metadata, and an example of what that would
look like as a CITATION file can be seen in recommended package
nlme (see below): recommended packages boot,
cluster and mgcv have further examples.
A CITATION file will contain calls to function bibentry
(new style, only works with R 2.12.0 or later), or to the functions
citHeader, citEntry and (optionally) citFooter (old
style).
Here is that for nlme, re-formatted:
citHeader("To cite package 'nlme' in publications use:")
year <- sub(".*(2[[:digit:]]{3})-.*", "\\1", meta$Date, perl = TRUE)
vers <- paste("R package version", meta$Version)
citEntry(entry="Manual",
title = "nlme: Linear and Nonlinear Mixed Effects Models",
author = personList(as.person("Jose Pinheiro"),
as.person("Douglas Bates"),
as.person("Saikat DebRoy"),
as.person("Deepayan Sarkar"),
person("R Core Team")),
year = year,
note = vers,
textVersion =
paste("Jose Pinheiro, Douglas Bates, Saikat DebRoy,",
"Deepayan Sarkar and the R Core Team (",
year,
"). nlme: Linear and Nonlinear Mixed Effects Models. ",
vers, ".", sep=""))
Note the way that information that may need to be updated is picked up
from the DESCRIPTION file – it is tempting to hardcode such
information, but it normally then gets outdated. See ?bibentry
for further details of the information which can be provided.
The CITATION file should itself produce no output when
source-d.
Next: Services, Previous: CITATION files, Up: Creating R packages [Contents][Index]
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 two other types are recognized, both
of which need write permission in the R installation tree.
| • Frontend | ||
| • Translation |
Next: Translation, Previous: Package types, Up: Package types [Contents][Index]
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.
Previous: Frontend, Up: Package types [Contents][Index]
Conventionally, a translation package for language ll is called
Translation-ll and has Type: Translation. It needs
to contain the directories share/locale/ll and
library/pkgname/po/ll, or at least those for
which translations are available. The files .mo are installed in
the parallel places in the R installation tree.
For example, a package Translation-it might be prepared from an installed (and tested) version of R by
mkdir Translation-it cd Translation-it (cd "$R_HOME"; tar cf - share/locale/it library/*/po/it) | tar xf - # the next step is not needed on Windows msgfmt -c -o share/locale/it/LC_MESSAGES/RGui.mo $R_SRC_HOME/po/RGui-it.gmo # create a DESCRIPTION file cd .. R CMD build Translation-it
It is probably appropriate to give the package a version number based on the version of R which has been translated. So the DESCRIPTION file might look like
Package: Translation-it Type: Translation Version: 2.2.1-1 Title: Italian Translations for R 2.2.1 Description: Italian Translations for R 2.2.1 Author: The translators Maintainer: Some Body <somebody@some.where.net> License: GPL (>= 2)
Previous: Package types, Up: Creating R packages [Contents][Index]
Several members of the R project have set up services to assist those writing R packages, particularly those intended for public distribution.
win-builder.r-project.org offers the automated preparation of (32/64-bit) Windows binaries from well-tested source packages.
R-Forge (R-Forge.r-project.org) and
RForge (www.rforge.net) 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 install.packages (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: Top [Contents][Index]
Next: Sectioning, Previous: Writing R documentation files, Up: Writing R documentation files [Contents][Index]
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 1300 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/load.Rd which documents the R function
load.
% File src/library/base/man/load.Rd \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 = parent.frame()) } \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= "all.RData") ## restore the saved values to the current environment load("all.RData") ## restore the saved values to the workspace load("all.RData", .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 specified50 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”. Note that there have been a number of changes to the Rd format over the years, which can be important if a package is intended to be used with earlier versions of R: see earlier versions of this manual if a package is intended to be used with R before 2.10.0.
Rd files consists of three 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 is processed. The third 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 (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. 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]
The basic markup commands used for documenting R objects (in particular, functions) are given in this subsection.
\name{name}name typically51 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 alphabetic52 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 Normal.Rd 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.
Since R version 2.12.0 markup has been 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).
It is no longer advisable to use \synopsis for the actual
synopsis and show modified synopses in the \usage. Support for
\synopsis will be removed eventually. To indicate that a
function can be used in several different ways, depending on the named
arguments specified, use section \details. E.g.,
abline.Rd contains
\details{
Typical usages are
\preformatted{
abline(a, b, untf = FALSE, \dots)
......
}
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, print.ts.Rd 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., Extract.factor.Rd 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
precede53 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.
\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, pie.Rd 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 examples() but not by
R CMD check. 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() to
test for features needed in the examples wherever possible, and you can
also use try() or trycatch().)
\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.
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.
help.search() can search by keyword, including user-defined
values: however the ‘Search Engine & Keywords’ HTML page accessed
via help.start() 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]
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/rivers.Rd
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 pkg-package.Rd
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). In
addition, section \references could give secondary sources and
usages.
Note also that when documenting data set bar,
\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.)
\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.
Next: Documenting packages, Previous: Documenting data sets, Up: Rd format [Contents][Index]
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.
Previous: Documenting S4 classes and methods, Up: Rd format [Contents][Index]
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 = TRUE 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.
Next: Marking text, Previous: Rd format, Up: Writing R documentation files [Contents][Index]
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).
Next: Lists and tables, Previous: Sectioning, Up: Writing R documentation files [Contents][Index]
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 if 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
if 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 if possible. Formatting,
e.g. line breaks, is preserved.
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. No wrapping or reformatting will occur. Displayed
using typewriter font if possible.
\verb{text}Indicate text that is a literal example of a sequence of characters,
with no interpretation of e.g. \var, but which will be included
within word-wrapped text. Displayed using typewriter font if
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 if 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 if possible.
\url{uniform_resource_locator}Indicate a uniform resource locator (URL) for the World Wide
Web. The argument is handled verbatim, and rendered as a hyperlink in
HTML and PDF conversion. Displayed using typewriter font if
possible.
\href{uniform_resource_locator}{text}Indicate a hyperlink to the World Wide Web. The first argument is handled verbatim, and is used as the URL in the hyperlink, with the second argument of LaTeX-like text displayed to the user.
\var{metasyntactic_variable}Indicate a metasyntactic variable. In some cases this will be rendered distinctly, e.g. in italic, but not in all54. LaTeX-like.
\env{environment_variable}Indicate an environment variable. Verbatim.
Displayed using typewriter font if possible
\option{option}Indicate a command-line option. Verbatim.
Displayed using typewriter font if possible.
\command{command_name}Indicate the name of a command. LaTeX-like, so \var is
interpreted. Displayed using typewriter font if 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.
Next: Cross-references, Previous: Marking text, Up: Writing R documentation files [Contents][Index]
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.
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.)
Next: Mathematics, Previous: Lists and tables, Up: Writing R documentation files [Contents][Index]
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[=terms.object]{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 of optional argument specified as
\link[pkg]{foo} and
\link[pkg:bar]{foo} to link to the package
pkg, to files foo.html and
bar.html respectively. These are rarely needed, perhaps to
refer to not-yet-installed packages (but there the HTML help system
will resolve the link at run time) or in the normally undesirable event
that more than one package offers help on a topic55 (in
which case the present package has precedence so this is only needed to
refer to other packages). They are currently only used in HTML help
(and ignored for hyperlinks in LaTeX conversions of help pages), and
link to the file rather than the topic (since there is no way to know
which topics are in which files in an uninstalled package). The
only reason to use these forms for base and recommended
packages is to force a reference to a package that might be further down
the search path. Because they have been frequently misused, the HTML
help system looks for topic foo in package pkg
if it does not find file foo.html.
Next: Figures, Previous: Cross-references, Up: Writing R documentation files [Contents][Index]
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 Poisson.Rd:
\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
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.
Next: Insertions, Previous: Mathematics, Up: Writing R documentation files [Contents][Index]
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{logo.jpg}{Our logo}}
\if{latex}{\figure{logo.jpg}{options: width=0.5in}}
The files containing the figures should be stored in the directory
man/figures. Files with extensions .jpg, .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.
Next: Indices, Previous: Figures, Up: Writing R documentation files [Contents][Index]
Use \R for the R system itself. Use \dots
for the dots in function argument lists ‘…’, and
\ldots
for ellipsis dots in ordinary text.56 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 braces57 almost always need to be escaped by ‘\’, and ‘\\’ can be used for backslash and needs to be when there 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.)
Next: Platform-specific sections, Previous: Insertions, Up: Writing R documentation files [Contents][Index]
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 help.search() lookups.
E.g., file cor.test.Rd 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 help.search() only uses “sections” of documentation
objects with no additional markup.)
If you want to cross reference such items from other help files via
\link, you need to use \alias and not \concept.
Next: Conditional text, Previous: Indices, Up: Writing R documentation files [Contents][Index]
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.
Next: Dynamic pages, Previous: Platform-specific sections, Up: Writing R documentation files [Contents][Index]
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:
\if{latex}{\out{\alpha}}\ifelse{html}{\out{α}}{alpha}
Next: User-defined macros, Previous: Conditional text, Up: Writing R documentation files [Contents][Index]
Two new macros supporting dynamically generated man pages were
introduced in R 2.10.0, \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
keep.source=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 as.character() 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.
As of R 2.13.1-patched, 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.
strip.white=TRUE
Remove leading and trailing white space from each line of
output if strip.white=TRUE. With
strip.white=all, also remove 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 sections) 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”.
Next: Encoding, Previous: Dynamic pages, Up: Writing R documentation files [Contents][Index]
Two new macros supporting user-defined macros were introduced in
R 2.12.0. 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.
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.
For example, the NEWS.Rd file currently uses the definition
\newcommand{\PR}{\Sexpr[results=rd]{tools:::Rd_expr_PR(#1)}}
which defines \PR to be a single argument macro; then code like
\PR{1234}
will expand to
\Sexpr[results=rd]{tools:::Rd_expr_PR(1234)}
when parsed.
Next: Processing Rd format, Previous: User-defined macros, Up: Writing R documentation files [Contents][Index]
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 characters58 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 t2aenc.def 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]
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 ‘Sweave’
documentation files (usually with extension ‘.Snw’ or ‘.Rnw’):
R CMD Stangle is use 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 Rd format, Up: Writing R documentation files [Contents][Index]
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 (http://ess.r-project.org/: 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 (http://www.walware.de/goto/statet), and (on Windows only) Tinn-R (http://sourceforge.net/projects/tinn-r/).
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 (http://rstudio.org/).
Next: Debugging, Previous: Writing R documentation files, Up: Top [Contents][Index]
| • Tidying R code | ||
| • Profiling R code for speed | ||
| • Profiling R code for memory use | ||
| • Profiling compiled 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.
Next: Profiling R code for speed, Previous: Tidying and profiling R code, Up: Tidying and profiling R code [Contents][Index]
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.
keep.source can be set to FALSE before the code
is loaded into R.
removeSource()
function, for example by
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", keep.source = FALSE)
dump(ls(all = TRUE), file = "new.myfuns.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 new.myfuns.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]
It is possible to profile R code on Windows and most59 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 intervals60 (by default every 20 msecs)
which R function is being used, and recording the results in a file
(default Rprof.out in the working directory). Then the function
summaryRprof or the command-line utility R CMD Rprof
Rprof.out 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)
storm.fm <- nls(Time ~ b*Viscosity/(Wt - c), stormer,
start = c(b=30.401, c=2.2183))
st <- cbind(stormer, fit=fitted(storm.fm))
storm.bf <- function(rs, i) {
st$Time <- st$fit + rs[i]
tmp <- nls(Time ~ (b * Viscosity)/(Wt - c), st,
start = coef(storm.fm))
tmp$m$getAllPars()
}
rs <- scale(resid(storm.fm), scale = FALSE) # remove the mean
Rprof("boot.out")
storm.boot <- boot(rs, storm.bf, R = 4999) # slow enough to profile
Rprof(NULL)
Having run this we can summarize the results by
R CMD Rprof boot.out Each sample represents 0.02 seconds. Total run time: 22.52 seconds. Total seconds: time spent in function and callees. Self seconds: time spent in function alone.
% total % self total seconds self seconds name 100.0 25.22 0.2 0.04 "boot" 99.8 25.18 0.6 0.16 "statistic" 96.3 24.30 4.0 1.02 "nls" 33.9 8.56 2.2 0.56 "<Anonymous>" 32.4 8.18 1.4 0.36 "eval" 31.8 8.02 1.4 0.34 ".Call" 28.6 7.22 0.0 0.00 "eval.parent" 28.5 7.18 0.3 0.08 "model.frame" 28.1 7.10 3.5 0.88 "model.frame.default" 17.4 4.38 0.7 0.18 "sapply" 15.0 3.78 3.2 0.80 "nlsModel" 12.5 3.16 1.8 0.46 "lapply" 12.3 3.10 2.7 0.68 "assign" ...
% self % total self seconds total seconds name 5.7 1.44 7.5 1.88 "inherits" 4.0 1.02 96.3 24.30 "nls" 3.6 0.92 3.6 0.92 "$" 3.5 0.88 28.1 7.10 "model.frame.default" 3.2 0.80 15.0 3.78 "nlsModel" 2.8 0.70 9.8 2.46 "qr.coef" 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 "qr.default" 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" ...
(Function names are not quoted on Windows.) 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]
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. All except Rprofmem
require R to have been compiled with --enable-memory-profiling,
which is not the default, but is currently used for the Mac OS X 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 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
print.svycoxph <- function (x, ...)
{
print(x$survey.design, varnames = FALSE, design.summaries = FALSE,
...)
x$call <- x$printcall
NextMethod()
}
It may not be obvious whether or not the assignment to x$call will
cause the entire object x to be copied, as might (or might not)
be needed to preserve the call-by-value illusion.
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 |
Next: Tracking memory allocations, Previous: Profiling R code for memory use, Up: Profiling R code for memory use [Contents][Index]
RprofThe sampling profiler Rprof described in the previous section can
be given the option memory.profiling=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.
Changing the memory limits with mem.limits() may also be useful,
to see how the code would run under different memory conditions.
Previous: Memory statistics from Rprof, Up: Profiling R code for memory use [Contents][Index]
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. In pqR, Rprofmem is enhanced to allow
output to the terminal (interspersed with other output, allowing
better understanding), more detailed output, and better control
of which allocations are displayed.
Running the example from the previous section with
> Rprofmem("boot.memprof",threshold=1000)
> storm.boot <- boot(rs, storm.bf, R = 4999)
> Rprofmem(NULL)
shows that apart from some initial and final work in boot there
are no vector allocations over 1000 bytes.
Previous: Profiling R code for memory use, Up: Tidying and profiling R code [Contents][Index]
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.
| • Linux | ||
| • Solaris | ||
| • Mac OS X |
Next: Solaris, Previous: Profiling compiled code, Up: Profiling compiled code [Contents][Index]
Options include using sprof for a shared object, and
oprofile (see http://oprofile.sourceforge.net/) for any
executable or shared object.
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/stats.so R ... run the boot example % sprof /path/to/R_HOME/library/stats/libs/stats.so \ /var/tmp/path/to/R_HOME/library/stats/libs/stats.so.profile 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 /path/to/R_HOME/library/stats/libs/stats.so.profile ... to clean up ...
It is possible that root access is needed to create the directories used for the profile data.
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/stats.so ... 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. You can use opannotate to annotate the source code with
the times spent in each section, if the appropriate source code was
compiled with debugging support, and opreport -c to generate a
callgraph (if collection was enabled and the platform supports this).
Next: Mac OS X, Previous: Linux, Up: Profiling compiled code [Contents][Index]
On 64-bit (only) Solaris, the standard profiling tool gprof
collects information from shared objects compiled with -pg.
Previous: Solaris, Up: Profiling compiled code [Contents][Index]
Developers have recommended sample (or Sampler.app,
which is a GUI version) and Shark (see
http://developer.apple.com/tools/sharkoptimize.html and
http://developer.apple.com/tools/shark_optimize.html).
Next: System and foreign language interfaces, Previous: Tidying and profiling R code, Up: Top [Contents][Index]
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. For those who prefer other styles there are contributed packages such as debug on CRAN (described in an article in R-News 3/3). (There are notes from 2002 provided by Roger Peng at http://www.biostat.jhsph.edu/~rpeng/docs/R-debug-tools.pdf which provide complementary examples to those given here.)
| • Browsing | ||
| • Debugging R code | ||
| • Using gctorture and valgrind | ||
| • Debugging compiled code |
Next: Debugging R code, Previous: Debugging, Up: Debugging [Contents][Index]
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(summary.data.frame) ## insert browser() call after for() loop
> summary(women)
Called from: summary.data.frame(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(summary.data.frame)
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 will61 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: summary.data.frame(women) Browse[1]> where where 1: summary.data.frame(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: Using gctorture and valgrind, Previous: Browsing, Up: Debugging [Contents][Index]
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. Daily, errors are
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: glm.fit(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 glm.fit. (traceback() shows you all the lines of
the function calls, which can be limited by setting option
"deparse.max.lines".)
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 as.environment(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 as.environment
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=dump.frames) and run the code again. Then invoke
debugger() and explore the dump. Continuing our example:
> options(error = dump.frames) > 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 last.dump 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: glm.fit(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:
glm.fit(x = X, y = Y, weights = weights, start = start, etas
Called from: debugger.look(ind)
Browse[1]> ls()
[1] "aic" "boundary" "coefold" "control" "conv"
[6] "dev" "dev.resids" "devold" "EMPTY" "eta"
[11] "etastart" "family" "fit" "good" "intercept"
[16] "iter" "linkinv" "mu" "mu.eta" "mu.eta.val"
[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: glm.fit(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(last.dump)
Because last.dump 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({dump.frames(to.file=TRUE); q()}))
See the help on dump.frames 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: glm.fit(x = X, y = Y, weights = weights, start = start, etastart = etastart Selection:
which is very similar to dump.frames. 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 dump.calls and dump.frames,
since it behaves like dump.frames 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(glm.fit)
> glm(resp ~ 0 + predictor, family = binomial(link ="log"))
debugging in: glm.fit(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 <- as.matrix(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:::predict.Arima). (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(as.list(body(glm.fit)), method="print") > trace(glm.fit, browser, at=22) Tracing function "glm.fit" in package "stats" [1] "glm.fit" > glm(resp ~ 0 + predictor, family = binomial(link ="log")) Tracing glm.fit(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(glm.fit)
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]
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).
| • Using gctorture | ||
| • Using valgrind |
Next: Using valgrind, Previous: Using gctorture and valgrind, Up: Using gctorture and valgrind [Contents][Index]
We can help to detect memory problems 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 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 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.
Previous: Using gctorture, Up: Using gctorture and valgrind [Contents][Index]
If you have access to Linux on an ‘ix86’, ‘x86_64’,
‘ppc32’, ‘ppc64’ or ‘s390x’ platform, or Mac OS
10.5/6/7 on ‘i386’ or ‘x86_64’ you can use
valgrind (http://www.valgrind.org/, 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
mypkg.Rcheck 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 even slower than that. Earlier
versions (at least) of valgrind are not happy with many optimized
BLASes that use CPU-specific instructions (3D now, SSE, SSE2,
SSE3 and similar) so you may need to build a version of R
specifically to use with valgrind.
On platforms supported by valgrind 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 any anything.
Level 1 will detect use of uninitialised memory and has little impact on
speed. Level 2 will detect many other memory-use bugs but makes R
much slower when running under valgrind. Using this in
conjunction with gctorture can be even more effective (and even
slower).
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 January, 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. When the
stack trace is not sufficiently informative the option
--db-attach=yes to valgrind may be helpful. This starts
a post-mortem debugger (by default gdb) so that variables in the
C code can be inspected (see Inspecting R objects).
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
--tool=memcheck --memcheck:leak-check=full
or setting the environment variable VALGRIND_OPTS.
On Mac OS X you may need to ensure that debugging symbols are made
available (so valgrind reports line numbers in files). This
can usually be done with the valgrind option
--dysmutil=yes to ask for the symbols to be dumped when the
.so file is loaded. This will not work where packages are
installed into a system area (such as the R.framework) and can be
slow. Installing packages with R CMD INSTALL --dsym installs
the dumped symbols. (This can also be done by setting environment
variable PKG_MAKE_DSYM to a non-empty value.)
Previous: Using gctorture and valgrind, Up: Debugging [Contents][Index]
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 front-ends to gdb such as ddd and
insight, and other debuggers such as Sun’s dbx.
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 option is the first.
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.
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/libc.so.6
(gdb) where
#0 0x00397682 in _int_free () from /lib/tls/libc.so.6
#1 0x00397eba in free () from /lib/tls/libc.so.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
...
Some “tricks” worth knowing follow:
| • Finding entry points | ||
| • Inspecting R objects |
Next: Inspecting R objects, Previous: Debugging compiled code, Up: Debugging compiled code [Contents][Index]
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
dyn.load or library to load your
shared object.
Under Windows signals may not be able to be used, and if so the procedure is
more complicated. See the rw-FAQ and
www.stats.uwo.ca/faculty/murdoch/software/debuggingR/gdb.shtml.
Previous: Finding entry points, Up: Debugging compiled code [Contents][Index]
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 <- data.frame(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" $row.names [1] "1" "2" "3" $class [1] "data.frame" $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->u.listsxp.tagval->u.symsxp.pname->u.vecsxp.type.c $4 = 0x405d40e8 "names" (gdb) p $a->u.listsxp.carval->u.vecsxp.type.s[1]->u.vecsxp.type.c $5 = 0x40634378 "b" (gdb) p $1->u.vecsxp.type.s[0]->u.vecsxp.type.i[0] $6 = 1 (gdb) p $1->u.vecsxp.type.s[1]->u.vecsxp.type.i[1] $7 = 5
Another alternative available from R 2.13.0 on 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] "row.names"
@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] "data.frame"
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 the depth of the recursion
and the output of vectors R_inspect3 takes additional two integer
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.
Next: Interface functions .C and .Fortran, Previous: System and foreign language interfaces, Up: System and foreign language interfaces [Contents][Index]
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.
The function system.time
is available for timing. Timing on child processes is only available on
Unix-alikes, and may not be reliable there.
Next: dyn.load and dyn.unload, Previous: Operating system access, Up: System and foreign language interfaces [Contents][Index]
.C and .FortranThese two functions provide an interface to compiled code that has been
linked into R, either at build time or via dyn.load
(see dyn.load and dyn.unload). They are primarily intended for
compiled C and FORTRAN 77 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 known62 to C or
FORTRAN, that is the function or subroutine name. (That the symbol is
loaded can be tested by, for example, is.loaded("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 logicalint *INTEGERintegerint *INTEGERdoubledouble *DOUBLE PRECISIONcomplexRcomplex *DOUBLE COMPLEXcharacterchar **CHARACTER*255rawunsigned char *none
Do please note the first two. On the 64-bit Unix/Linux/OS X platforms,
long is 64-bit whereas 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
included by R.h. (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 depends on the
optimization level set for the compiler.)
Only a single character string can be passed to or from FORTRAN, and the
success of this is compiler-dependent. 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
as.single, 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.)
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 DUP can be used to suppress copying. It is dangerous:
see the on-line help for arguments against its use. It is not possible
to pass numeric vectors as float * or REAL if
DUP = FALSE, and character vectors cannot be used.
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)
{
R_len_t i, j, nab = *na + *nb - 1;
for(i = 0; i < nab; i++)
ab[i] = 0.0;
for(i = 0; i < *na; i++)
for(j = 0; j < *nb; j++)
ab[i + j] += a[i] * b[j];
}
called from R by
conv <- function(a, b)
.C("convolve",
as.double(a),
as.integer(length(a)),
as.double(b),
as.integer(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++). Since only DUP = TRUE is allowed, 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 possible 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, 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.
It is possible to pass 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.
Next: Registering native routines, Previous: Interface functions .C and .Fortran, Up: System and foreign language interfaces [Contents][Index]
dyn.load and dyn.unloadCompiled code to be used with R is loaded as a shared object (Unix-alikes including Mac OS X, see Creating shared objects for more information) or DLL (Windows).
The shared object/DLL is loaded by dyn.load and unloaded by
dyn.unload. Unloading is not normally necessary, but it is
needed to allow the DLL to be re-built on some platforms, including
Windows.
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
file.path(path1, path2, paste0("mylib", .Platform$dynlib.ext))
for platform independence. On Unix-alike systems the path supplied to
dyn.load 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 library.dynam.
This has the form
library.dynam("libname", package, lib.loc)
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
library.dynam("mylib", package, lib.loc)
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. As from R 2.15.0, 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.h> #include <Rinternals.h> #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. 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 dyn.load 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 dyn.load. This is (by default) used by
library.dynam to include the package’s libs/i386 or
libs/x64 directory in the DLL search path.
Next: Creating shared objects, Previous: dyn.load and dyn.unload, Up: System and foreign language interfaces [Contents][Index]
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 all
loaded DLLs and elsewhere. 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. In
the future, registration may be used to implement a form of “secure”
or limited native access.
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 dyn.load and dyn.unload. 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:
.CR_CMethodDef.CallR_CallMethodDef.FortranR_FortranMethodDef.ExternalR_ExternalMethodDef
Currently, the R_ExternalMethodDef 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. 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. For example, if we had a routine named myCall defined as
SEXP myCall(SEXP a, SEXP b, SEXP c);
we would describe this as
R_CallMethodDef callMethods[] = {
{"myCall", (DL_FUNC) &myCall, 3},
{NULL, NULL, 0}
};
along with any other routines for the .Call interface.
Routines for use with the .C and .Fortran interfaces are
described with similar data structures, but which have two additional
fields for describing the type and “style” of each argument. Each of
these can be omitted. However, if specified, each should be an array
with the same number of elements as the number of parameters for the
routine. The types array should contain the SEXP types
describing the expected type of the argument. (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:
numericREALSXPintegerINTSXPlogicalLGLSXPsingleSINGLESXPcharacterSTRSXPlistVECSXP
Consider a C routine, myC, declared as
void myC(double *x, int *n, char **names, int *status);
We would register it as
R_CMethodDef cMethods[] = {
{"myC", (DL_FUNC) &myC, 4, {REALSXP, INTSXP, STRSXP, LGLSXP}},
{NULL, NULL, 0}
};
One can also specify whether each argument is used simply as input, or as output, or as both input and output. The style field in the description of a method is used for this. The purpose is to allow R to transfer values more efficiently across the R-C/FORTRAN interface by avoiding copying values when it is not necessary. This information is often omitted.
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 automatically 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). Also, there is a brief, high-level introduction in R News (volume 1/3, September 2001, pages 20–23, http://www.r-project.org/doc/Rnews/Rnews_2001-3.pdf).
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. An interface to support this has been provided since R 2.4.0. The interface consists of two routines declared 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");
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. For example
Depends: link2, link3 LinkingTo: link2, link3
It must also ‘Depends’ on those packages for they have to be installed prior to this one, and loaded prior to this one (so the path to their compiled code can be found).
This then arranges that the include directories in the installed linked-to packages are added to the include paths for C and C++ code.
A CRAN example of the use of this mechanism is package lme4, which links to Matrix.
Next: Interfacing C++ code, Previous: Registering native routines, Up: System and foreign language interfaces [Contents][Index]
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 77,
Fortran 9x, Objective C or Objective C++ (with extensions .c,
.cc or .cpp, .f, .f90 or .f95,
.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.
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 preprocessor, typically ‘-I’ flags),
PKG_CFLAGS, PKG_CXXFLAGS, PKG_FFLAGS,
PKG_FCFLAGS, and PKG_OBJCFLAGS (for the C, C++, FORTRAN
77, Fortran 9x, 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 which 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 Makevars.site 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 Makevars.win will be
used in preference to Makevars, and only src/Makefile.win
will be used by R CMD INSTALL with src/Makefile being
ignored. For past experiences of building DLLs with a variety of
compilers, see file ‘README.packages’ and
http://www.stats.uwo.ca/faculty/murdoch/software/compilingDLLs/
. Under Windows you can supply an exports definitions file called
dllname-win.def: otherwise all entry points in objects (but
not libraries) supplied to R CMD SHLIB will be exported from the
DLL. An example is stats-win.def 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 not 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]
Suppose we have the following hypothetical C++ library, consisting of
the two files X.h and X.cpp, 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 (); };
// X.cpp #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 X.cpp X_main.cpp
to create the shared object, typically X.so (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> dyn.load(paste("X", .Platform$dynlib.ext, 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 version 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, and they
should not be included within an extern "C" block (as
they include C++ system headers). It may not be possible to include
some R headers as they in turn include C header files that may cause
conflicts—if this happens, define ‘NO_C_HEADERS’ before including
the R headers, and include C++ versions (such as ‘cmath’) of the
appropriate headers yourself before the R headers.
Next: Linking to other packages, Previous: Interfacing C++ code, Up: System and foreign language interfaces [Contents][Index]
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 (77 or 9x) 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.y.z. 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 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.) Even worse, prior to R 2.6.2 using Fortran output
when running under the Windows GUI console (Rgui) would hang the
R session. This is now avoided by ensuring that the Fortran output
is written to a file (fort.6 in the working directory).
Next: Handling R objects in C, Previous: Fortran I/O, Up: System and foreign language interfaces [Contents][Index]
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 dyn.load and dyn.unload, 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.
| • Unix-alikes | ||
| • Windows |
Next: Windows, Previous: Linking to other packages, Up: Linking to other packages [Contents][Index]
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/libs/libpackB.a. (This 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 packB. The only issue is to find package packB, and
for that we can ask R by something like
PKGB_PATH=`echo 'cat(system.file("libs", .Platform$r_arch, package="packB", mustWork=TRUE))' \
| "${R_HOME}/bin/R" --vanilla --slave`
PKG_LIBS="$(PKGB_PATH)/libpackB.a"
which will give an empty path component if sub-architectures are not in use (but that works on current platforms).
For a dynamic library packB/libs/libpackB.so (packB/libs/libpackB.dylib on Mac OS X) we could use
PKGB_PATH=`echo 'cat(system.file("libs", .Platform$r_arch, package="packB", mustWork=TRUE))' \
| "${R_HOME}/bin/R" --vanilla --slave`
PKG_LIBS=-L"$(PKGB_PATH)" -lpackB
This will work for installation, but very likely not when package
packB is loaded, as the path to package packB’s libs
directory is not in the ld.so63 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 ld.so cache (see man ldconfig). On platforms
that support it, the path to 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 GNU
linker (e.g. Linux) and some others (e.g. Mac OS X) this can be done
by
PKGB_PATH=`echo 'library(packB); cat(system.file("libs", package="packB"))' \
| "${R_HOME}/bin/R" --vanilla --slave`
PKG_LIBS=-L"$(PKGB_PATH)" -rpath "$(PKGB_PATH)" -lpackB
and on some other systems (e.g. Solaris with its native linker) use
-R rather than -rpath.
It may be possible to figure out what is required semi-automatically
from the result of R CMD libtool --config (look for
‘hardcode’).
Making headers provided by package packB available to the code to
be compiled in package packA can be done by the LinkingTo
mechanism (see Registering native routines).
Previous: Unix-alikes, Up: Linking to other packages [Contents][Index]
Suppose package packA wants to make use of compiled code provided by packB in DLL packB/libs/exB.dll, possibly the package’s DLL packB/libs/packB.dll. (This can be extended to linking to more than one package in a similar way.) There are three issues to be addressed:
This is done by the LinkingTo mechanism (see Registering native routines).
packA.dll to link to packB/libs/exB.dll.
This needs an entry in Makevars.win of the form
PKG_LIBS= -L<something> -lexB
and one possibility is that <something> is the path to the
installed pkgB/libs directory. To find that we need to ask R
where it is by something like
PKGB_PATH=`echo 'library(packB); cat(system.file("libs", package="packB"))' \
| rterm --vanilla --slave`
PKG_LIBS= -L"$(PKGB_PATH)" -lexB
Another possibility is to use an import library, shipping with package packA an exports file exB.def. Then Makevars.win could contain
PKG_LIBS= -L. -lexB all: $(SHLIB) before before: libexB.dll.a libexB.dll.a: exB.def
and then installing package packA will make and use the import library for exB.dll. (One way to prepare the exports file is to use pexports.exe.)
If exB.dll was used by package packB (because it is in fact
packB.dll or packB.dll depends on it) and packB has
been loaded before packA, then nothing more needs to be done as
exB.dll will already be loaded into the R executable. (This
is the most common scenario).
More generally, we can use the DLLpath argument to
library.dynam to ensure that exB.dll is found, for example
by setting
library.dynam("packA", pkg, lib,
DLLpath = system.file("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 PATH.
Next: Interface functions .Call and .External, Previous: Linking to other packages, Up: System and foreign language interfaces [Contents][Index]
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. But before you decide to
use these, 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.
The new interfaces are relatively recent additions to S and R,
and a great deal of useful code has been written using just .C
before they were available. The .Call and .External
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, unless you have a thorough understanding of how to check
whether modifications are safe, using the NAMED field of
objects.
The syntax for the calling function in R with .Call and
.External is similar to that of .C, but the two
functions have different C interfaces. Generally the .Call
interface (which is modelled on the interface of the same name in
S version 4) is a little 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 S4-compatibility macros defined in Rdefines.h. See
Interface functions .Call and .External for details on
.Call and .External.
There are two approaches that can be taken to handling R objects from
within C code. The first (historically) is to use the macros and
functions that have been used to implement the core parts of R
through .Internal calls. A public64 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.
Another approach is to use R versions of the macros and functions
defined for the S version 4 interface .Call, which are
defined in the header file Rdefines.h. This is a somewhat
simpler approach, and is to be preferred if the code is intended to be
shared with S. However, it is less well documented and even less
tested. Note too that some idiomatic S4 constructions with these macros
(such as assigning elements of character vectors or lists) are invalid
in R.
A substantial amount of R 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.
The C type SEXP65 is central
to how C code manipulates R objects. All the R objects you will
deal with will be handled with the type, whose nature will vary
depending on the platform and configuration options used. It may be a
C pointer to a C structure, or it may be a “compressed pointer”, by
which such a structure can be located indirectly. Either way, it can
handle all the usual types of R objects — that is, vectors of
various modes, functions, environments, language objects and so on.
R objects are handed around in C code (as they are in interpreted
R code) as SEXP values, and the appropriate part is
extracted, for example for numerical calculations, only when it is
needed. As in interpreted R code, much use is made of coercion to
force the object to the right type.
Details regarding SEXP 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 — and indeed should not pay any attention to them, since
they may change, and will differ depending on whether compressed
pointers are used.
Next: Allocating storage, Previous: Handling R objects in C, Up: Handling R objects in C [Contents][Index]
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, in one of several ways. This is a very important responsibility of the programmer, since failing to “protect” all objects in use at a point when new memory is allocated can lead to arbitrarily bizarre behaviour of the program, manifesting at times that may seem unrelated to when the error actually occurred.
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.
One method of telling R not to garbage collect an object is to use
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. If you want this behaviour, you should use instead
the BEGIN_PROTECT family of macros described below.
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. 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. First we use the macros in Rinternals.h:
#include <R.h>
#include <Rinternals.h>
SEXP ab;
....
PROTECT(ab = allocVector(REALSXP, 2));
REAL(ab)[0] = 123.45;
REAL(ab)[1] = 67.89;
UNPROTECT(1);
and then those in Rdefines.h:
#include <R.h>
#include <Rdefines.h>
SEXP ab;
....
PROTECT(ab = NEW_NUMERIC(2));
NUMERIC_POINTER(ab)[0] = 123.45;
NUMERIC_POINTER(ab)[1] = 67.89;
UNPROTECT(1);
Now, the reader may ask how the ab object could possibly be
affected by these manipulations, since 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 destroyed. It is usually wise to err on the
side of caution and assume that any of the R macros and functions
might destroy an unprotected 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 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.
Protection is not needed for objects which R already knows are in
use. In particular, this applies to the arguments of .Call or
.External.
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. For this to
be reliable, it must be the only means used to unprotect pointers,
since it would be difficult to guarantee that another PROTECT
for the same pointer will not be done, rendering the effect of
mixtures of UNPROTECT and UNPROTECT_PTR unpredictable.
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);
This must not be done in conjunction with use of UNPROTECT_PTR,
since it may change the location where a pointer resides on the
protect stack.
A newer alternative approach to protecting objects from garbage
collection is to tell R that certain variables contain pointers to
objects that must not be garbage collected. Note that these variables
must always contain valid pointers to R objects, and hence must not be
declared and then left uninitialized. R must be told when these
variables should no longer be looked at, and this must be done before
the variables disappear (as local variables do when the block within
which they are declared is exited). This will happen naturally if the
BEGIN/END macros below are used properly.
A C function that uses this method for protection should normally start and end with macro calls such as shown below:
void func (void)
{
BEGIN_PROTECT3 (var1, var2, var3);
...
END_PROTECT;
}
The BEGIN_PROTECT3 macro will declare var1, var2,
and var3 as local variables of type SEXP (in a block
that starts with BEGIN_PROTECT3), initialize them to
R_NilValue, and tell R that the objects they point to should not be
garbage collected. The END_PROTECT macro will close the block
begun by BEGIN_PROTECT3, so the variables will not exist
afterwards, and will tell R that these (now non-existent) variables
should no longer be looked at. In between, any object pointed to by
var1, var2, or var3 will not be garbage
collected.
There are ten macros, called BEGIN_PROTECT0 to
BEGIN_PROTECT9, which allow for a BEGIN_PROTECT block to
be started in which from 0 to 9 variables are declared. (There is
only one END_PROTECT macro that goes with any of them.) Only a
single BEGIN_PROTECT / END_PROTECT pair may appear in a
function, and the BEGIN_PROTECT and END_PROTECT must be
at the same block level (normally the outermost level for the
function).
Most functions take one or more arguments, which are often of type SEXP,
and return a value, again often a SEXP. The following example
illustrates how this can be handled:
SEXP func (SEXP arg1, SEXP arg2, int flag)
{
BEGIN_PROTECT3 (var1, var2, var3);
ALSO_PROTECT2 (arg1, arg2);
...
RETURN_SEXP_INSIDE_PROTECT (var2);
END_PROTECT;
}
This code protects all the SEXP arguments at the start of the
function. There are some functions that are specified as not
protecting their arguments, with that being the caller’s
responsibility, but unless the slight performance advantage of
foregoing protection is paramount, protecting all SEXP
arguments is recommended. However, arguments cannot be protected by
listing them as variables in a BEGIN_PROTECT call, since that
would declare new variables of those names in the inner block (and
initialize them to R_NilValue). The ALSO_PROTECT2 macro (which has
forms protecting 1 to 9 arguments/variables) tells R to not collect
objects pointed to by the named SEXP arguments or variables,
which must already exist and must be initialized to valid SEXP
values. The protection of objects pointed to by these variables lasts
until the END_PROTECT or until the function exits with
one of the RETURN_... macros.
Variables mentioned in an ALSO_PROTECT call must exist at the
outermost block level within the BEGIN_PROTECT /
END_PROTECT pair, since variables that exist only in an inner
block will have disappeared while R is still looking at them, which
could cause arbitrarily bizarre behaviour. This will be ensured if
ALSO_PROTECT is used only immediately after
BEGIN_PROTECT.
In the example above, the function returns with var2 as its
value when it reaches the RETURN_SEXP_INSIDE_PROTECT macro before
END_PROTECT. Using END_PROTECT followed by
return(var2) would not work here, since var2 will not
exist after the END_PROTECT. If the value returned was, say,
arg2 (whose value might have been changed), END_PROTECT
followed immediately by return(arg2) would work, but it is
generally a good idea for END_PROTECT to be the last statement
in a function, so that it is clear that variables are always protected when
necessary.
There is also a RETURN_OUTSIDE_PROTECT macro, which can be used
to return a value of any type from within a BEGIN_PROTECT /
END_PROTECT block, but the expression for the return value will
be evaluated after the protection for all variables protected
by any BEGIN_PROTECT, BEGIN_INNER_PROTECT, and
ALSO_PROTECT macros has been removed. This macro should
normally be used only for returning values that are not of SEXP
type.
Note that any return from a function within a BEGIN_PROTECT /
END_PROTECT block must be done with
RETURN_SEXP_INSIDE_PROTECT or RETURN_OUTSIDE_PROTECT.
Using a simple return statement will result in the actions
done by END_PROTECT being bypassed, with possibly disastrous
consequences, since R will then be looking at variables that no
longer exist. Similarly, a BEGIN_PROTECT / END_PROTECT
block must not be exited via a C break, continue, or
goto statement. But exiting these blocks via R’s error
signaling mechanism is allowed.
BEGIN_INNER_PROTECT0 through BEGIN_INNER_PROTECT9 may be
used to create inner blocks with protected variables, which are ended
with END_INNER_PROTECT. Here is an example using this, which
also shows how RETURN_SEXP_INSIDE_PROTECT can be used to exit in the
middle of a function:
SEXP func (SEXP arg1, SEXP arg2)
{
BEGIN_PROTECT3 (var1, var2, var3);
ALSO_PROTECT2 (arg1, arg2);
...
while (var3 != R_NilValue)
BEGIN_INNER_PROTECT1 (ivar);
...
RETURN_SEXP_INSIDE_PROTECT (list2(list1(var1),ivar));
...
END_INNER_PROTECT;
...
RETURN_SEXP_INSIDE_PROTECT (R_NilValue);
END_PROTECT;
}
Note that BEGIN_INNER_PROTECT and END_INNER_PROTECT
together form what is syntactically a C statement, which may be the direct
object of a while statement.
If ALSO_PROTECT is used within a BEGIN_INNER_PROTECT
block, the variables it protects must exist at the outermost block
level within the BEGIN_INNER_PROTECT / END_INNER_PROTECT
pair. The variables will be protected only until after the
END_INNER_PROTECT.
As seen in the example above, the value returned by a function may be
an object that has just been allocated (here, by list2), which
will of course not be protected. The caller must protect the value
returned if necessary. Also note that an argument passed to a
function can be unprotected (as is the case for
list1(var1) above) only if the function to which it is
passed protects its arguments when necesary (as list2 does),
and only if this is the sole argument of the function that may
allocate memory. So, for example, the following is not allowed:
list2 (list2(var1,var2), list2(var3,ivar))
but the following is allowed (though may be ill-advised, due to the danger that future careless modifications might produce a form that is not allowed):
list2 (var1, list2 (var2, list2(var3,ivar)))
In this respect, note that C does not specify the order in which arguments to a function are evaluated, so one cannot assume that leaving the last argument unprotected is OK when earlier arguments may allocate memory.
Also note that the following is not allowed:
BEGIN_PROTECT5 (u, v, w, x, y);
...
y = list2 (u = list1(w), v = list1(x));
...
END_PROTECT;
The arguments of list2 are not properly protected above, because
the C standard allows the assignments to u and v
to be done only just before the call of list2, so the result
of whichever list1 call happens first may be unprotected when
the second list1 call occurs. One should instead
write this as below:
BEGIN_PROTECT5 (u, v, w, x, y);
...
u = list1(w);
v = list1(x);
y = list2(u,v);
...
END_PROTECT;
A third way of protecting an object is to call R_PreserveObject
passing it a pointer to the object, which prevents it from being
garbage collected indefinitely, until R_ReleaseObject is called
for it. This should be used sparingly, since it has higher overhead
than the other mechanisms, and it is easy to fail to ever call
R_ReleaseObject (such as, if an error exit occurs).
Note that these three methods for preventing objects from being garbage collected are separate, and may be combined and intermixed. An object will be preserved for as long as it is preserved by at least one of these mechanisms. However, mixing these mechanisms may well make your program hard to read.
Next: Details of R types, Previous: Garbage Collection, Up: Handling R objects in C [Contents][Index]
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. These
allocate R objects of various types, and for the standard vector
types there are equivalent NEW_XXX macros defined in
Rdefines.h.
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]
Users of the Rinternals.h macros will need to know how the R types are known internally: if the Rdefines.h macros are used then S4-compatible names are used.
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 REALSXPnumeric with storage mode doubleINTSXPinteger CPLXSXPcomplex LGLSXPlogical STRSXPcharacter VECSXPlist (generic vector) LISTSXPpairlist DOTSXPa ‘…’ object NILSXPNULL SYMSXPname/symbol CLOSXPfunction or function closure ENVSXPenvironment
Among the important internal SEXPTYPEs are LANGSXP,
CHARSXP, PROMSXP, etc. (Note: 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. See the header file
Rinternals.h for definitions of other such functions. All of
these take a SEXP as argument and return 1 or 0 to indicate
TRUE or FALSE. Once again there are two ways to do this,
and Rdefines.h has macros such as IS_NUMERIC.
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, equivalently,
PROTECT(newSexp = coerceVector(oldSexp, REALSXP));
or
PROTECT(newSexp = AS_NUMERIC(oldSexp));
Protection is needed as a new object is created; the object
formerly pointed to by the SEXP is still protected but now
unused.
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
as.numeric (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]
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)
{
storage.mode(x) <- storage.mode(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)
{
R_len_t i, j, nx = length(x), ny = length(y);
double tmp, *rx = REAL(x), *ry = REAL(y), *rans;
SEXP ans;
PROTECT(ans = allocMatrix(REALSXP, nx, ny));
rans = REAL(ans);
for(i = 0; i < nx; i++) {
tmp = rx[i];
for(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.
Although allocMatrix provides a short cut, we will show how to
set the dim attribute directly.
#include <R.h> #include <Rinternals.h>
SEXP out(SEXP x, SEXP y)
{
R_len_t i, j, nx = length(x), ny = length(y);
double tmp, *rx = REAL(x), *ry = REAL(y), *rans;
SEXP ans, dim, dimnames;
PROTECT(ans = allocVector(REALSXP, nx*ny));
rans = REAL(ans);
for(i = 0; i < nx; i++) {
tmp = rx[i];
for(j = 0; j < ny; j++)
rans[i + nx*j] = tmp * ry[j];
}
PROTECT(dim = allocVector(INTSXP, 2));
INTEGER(dim)[0] = nx; INTEGER(dim)[1] = ny;
setAttrib(ans, R_DimSymbol, dim);
PROTECT(dimnames = 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(3);
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
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;
PROTECT(version = 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.
Next: Handling lists, Previous: Attributes, Up: Handling R objects in C [Contents][Index]
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 <Rdefines.h>
....
SEXP ans, dim, dimnames, class;
....
PROTECT(class = 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]
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 (R_len_t 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]
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): the function itself did not check
prior to R 2.15.1.
Next: Some convenience functions, Previous: Handling character data, Up: Handling R objects in C [Contents][Index]
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(install(CHAR(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 adjust the count of references to
value.66 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), except as for defineVar, it does not
adjust the count of references to value.
Next: Named objects and copying, Previous: Finding and setting variables, Up: Handling R objects in C [Contents][Index]
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 *).
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.
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: is 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
list5 construct a pairlist from one to five 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]
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]
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
0The object is not bound to any symbol
1The object has been bound to exactly one symbol
2The object has potentially been bound to two or more symbols, and one should act as if another variable is currently bound to this value.
Note the past tenses: R does not 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, 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).)
Currently all arguments to a .Call call will have NAMED
set to 2, and so users must assume that they need to be duplicated
before alteration.
User code may also deal with objects that are encountered as elements
of lists, or as attributes. Such references to an object also count
as it being “named”, and will normally be included in the count seen
with NAMED. However, NAMED for such objects is
sometimes left at zero — hence, any object obtained from a list that
has NAMED greater than zero must be regarded as having
NAMED of at least one (and hence, recursively, elements within
this object must also be regarded as having NAMED of at least
one).
See the section on “Reference counts and the nmcnt field” in the
“R Internals” manual for more details on conventions regarding NAMED.
Next: Evaluating R expressions from C, Previous: Handling R objects in C, Up: System and foreign language interfaces [Contents][Index]
.Call and .ExternalIn 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 .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]
.CallLet us convert our finite convolution example to use .Call, first
using the Rdefines.h macros. 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 checking must be transferred to the C code, which is
#include <R.h>
#include <Rdefines.h>
SEXP convolve2(SEXP a, SEXP b)
{
R_len_t i, j, na, nb, nab;
double *xa, *xb, *xab;
SEXP ab;
PROTECT(a = AS_NUMERIC(a));
PROTECT(b = AS_NUMERIC(b));
na = LENGTH(a); nb = LENGTH(b); nab = na + nb - 1;
PROTECT(ab = NEW_NUMERIC(nab));
xa = NUMERIC_POINTER(a); xb = NUMERIC_POINTER(b);
xab = NUMERIC_POINTER(ab);
for(i = 0; i < nab; i++) xab[i] = 0.0;
for(i = 0; i < na; i++)
for(j = 0; j < nb; j++) xab[i + j] += xa[i] * xb[j];
UNPROTECT(3);
return(ab);
}
Now for the version in Rinternals.h style. Only the C code changes.
#include <R.h>
#include <Rinternals.h>
SEXP convolve2(SEXP a, SEXP b)
{
R_len_t i, j, na, nb, nab;
double *xa, *xb, *xab;
SEXP ab;
PROTECT(a = coerceVector(a, REALSXP));
PROTECT(b = coerceVector(b, REALSXP));
na = length(a); nb = length(b); nab = na + nb - 1;
PROTECT(ab = allocVector(REALSXP, nab));
xa = REAL(a); xb = REAL(b);
xab = REAL(ab);
for(i = 0; i < nab; i++) xab[i] = 0.0;
for(i = 0; i < na; i++)
for(j = 0; j < nb; j++) xab[i + j] += xa[i] * xb[j];
UNPROTECT(3);
return(ab);
}
This is called in exactly the same way.
Next: Missing and special values, Previous: Calling .Call, Up: Interface functions .Call and .External [Contents][Index]
.ExternalWe 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)
{
R_len_t i, j, na, nb, nab;
double *xa, *xb, *xab;
SEXP a, b, ab;
PROTECT(a = coerceVector(CADR(args), REALSXP));
PROTECT(b = 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);
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.
#include <R_ext/PrtUtil.h>
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.
Previous: Calling .External, Up: Interface functions .Call and .External [Contents][Index]
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_exts/Arith.h included by R.h.
The code changes are the same in any of the versions of convolve2
or convolveE:
...
for(i = 0; i < na; i++)
for(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]
The main function we will use is
SEXP eval(SEXP expr, SEXP rho);
the equivalent of the interpreted R code eval(expr, envir =
rho), 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)), new.env())
with C code
SEXP lapply(SEXP list, SEXP expr, SEXP rho)
{
R_len_t i, n = length(list);
SEXP ans;
if(!isNewList(list)) error("'list' must be a list");
if(!isEnvironment(rho)) error("'rho' should be an environment");
PROTECT(ans = allocVector(VECSXP, n));
for(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)
{
R_len_t i, 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");
PROTECT(R_fcall = lang2(fn, R_NilValue));
PROTECT(ans = allocVector(VECSXP, n));
for(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, new.env())
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;
PROTECT(t = s = 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 vector list, which is the most
commonly-seen type of list at the R level. 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.
| • Zero-finding | ||
| • Calculating numerical derivatives |
Next: Calculating numerical derivatives, Previous: Evaluating R expressions from C, Up: Evaluating R expressions from C [Contents][Index]
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) {
f.check <- function(x) {
x <- f(x)
if(!is.numeric(x)) stop("Need a numeric result")
as.double(x)
}
.Call("zero", body(f.check), as.double(guesses), as.double(tol),
new.env())
}
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)
{
SEXP ans;
PROTECT(ans = allocVector(REALSXP, 1));
/* This PROTECT is not essential with this code, but would become so if
we added anything below that could allocate memory, so let's be safe. */
REAL(ans)[0] = x;
UNPROTECT(1);
return ans;
}
double feval(double x, SEXP f, SEXP rho)
{
SEXP ansx;
PROTECT(ansx = mkans(x));
defineVar(install("x"), ansx, rho);
UNPROTECT(1);
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]
We will use a longer example (by Saikat DebRoy, with bug fixed by
Radford Neal) 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
numeric.deriv <- function(expr, theta, rho=sys.frame(sys.parent()))
{
eps <- sqrt(.Machine$double.eps)
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
numeric.deriv(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> /* for DOUBLE_EPS */
#include <Rinternals.h>
SEXP numeric_deriv(SEXP args)
{
SEXP theta, expr, rho, ans, ans1, gradient, par, dimnames;
double tt, xx, delta, eps = sqrt(DOUBLE_EPS), *rgr, *rans;
R_len_t start, i, j;
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");
PROTECT(ans = coerceVector(eval(expr, rho), REALSXP));
PROTECT(gradient = allocMatrix(REALSXP, LENGTH(ans), LENGTH(theta)));
rgr = REAL(gradient); rans = REAL(ans);
for(i = 0, start = 0; i < LENGTH(theta); i++, start += LENGTH(ans)) {
PROTECT(par = findVar(install(CHAR(STRING_ELT(theta, i))), rho));
if (NAMED(par) > 1) {
par = duplicate(par);
UNPROTECT(1); /* old value of par */
PROTECT(par);
defineVar(install(CHAR(STRING_ELT(theta, i))), par, rho);
SET_NAMED(par,1);
}
tt = REAL(par)[0];
xx = fabs(tt);
delta = (xx < 1) ? eps : xx*eps;
REAL(par)[0] += delta;
PROTECT(ans1 = coerceVector(eval(expr, rho), REALSXP));
for(j = 0; j < LENGTH(ans); j++)
rgr[j + start] = (REAL(ans1)[j] - rans[j])/delta;
REAL(par)[0] = tt;
UNPROTECT(2); /* par, ans1 */
}
PROTECT(dimnames = 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
PROTECT(ans = coerceVector(eval(expr, rho), REALSXP));
We then allocate space for the calculated derivative by
PROTECT(gradient = 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.
for(i = 0, start = 0; i < LENGTH(theta); i++, start += LENGTH(ans)) {
PROTECT(par = findVar(install(CHAR(STRING_ELT(theta, i))), rho));
if (NAMED(par) > 1) {
par = duplicate(par);
UNPROTECT(1); /* old value of par */
PROTECT(par);
defineVar(install(CHAR(STRING_ELT(theta, i))), par, rho);
SET_NAMED(par,1);
}
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
representation67 of it: it returns a pointer. We then
install the name and use findVar to find its value.
It’s possible the value of this variable is shared with other
variables (or perhaps an element of a list). We need to check for
this, by seeing if NAMED is greater than one, and if so,
duplicate the value and store this value (which will not be shared)
back in the variable, since we will shortly be changing it. (Although
we restore the changed value later, that’s not enough, since it’s
possible that the changed value will incorrectly be seen in the
meantime.)
tt = REAL(par)[0];
xx = fabs(tt);
delta = (xx < 1) ? eps : xx*eps;
REAL(par)[0] += delta;
PROTECT(ans1 = 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(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).
PROTECT(dimnames = 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]
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.h68.
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) {
PROTECT(cmdSexp = 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(R_len_t 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 srcfile object or the R NULL
object (as in the example above). In the former case 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]
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]
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.
The elements of an external pointer can be accessed and set via
void *R_ExternalPtrAddr(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_RegisterFinalizerEx(SEXP s, SEXP fun, Rboolean onexit); typedef void (*R_CFinalizer_t)(SEXP); 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
reg.finalizer 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.
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
www.stat.uiowa.edu/~luke/R/references/weakfinex.html,
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 external pointer example |
Previous: External pointers and weak references, Up: External pointers and weak references [Contents][Index]
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 this_handle) 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;
PROTECT(ans = 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("connection.string"), 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 the 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]
The vector accessors like REAL and INTEGER and
VECTOR_ELT are functions when used in R extensions.
(For efficiency they are macros 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.
If efficiency is essential, the macro versions of the accessors can be obtained by defining ‘USE_RINTERNALS’ before including Rinternals.h. If you find it necessary to do so, please do test that your code compiles without ‘USE_RINTERNALS’ defined, as this provides a stricter test that the accessors have been used correctly.
Previous: Vector accessor functions, Up: System and foreign language interfaces [Contents][Index]
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.
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).
There is a public interface to the encoding marked on CHARXSXPs
via
typedef enum {CE_NATIVE, CE_UTF8, CE_LATIN1, 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_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: Top [Contents][Index]
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.
An alternative is to include the header file S.h, which may be
useful when porting code from S. This includes rather less than
R.h, and has some extra compatibility definitions (for example
the S_complex type from S).
The defines used for compatibility with S sometimes causes
conflicts (notably with Windows headers), and the known
problematic defines can be removed by defining STRICT_R_HEADERS.
Most of these header files, including all those included by R.h,
can be used from C++ code. Some others need to be included within an
extern "C" declaration, and for clarity this is advisable for all
R header files.
Note: Because R re-maps many of its external names to avoid clashes with user code, it is essential to include the appropriate header files when using these entry points.
This remapping can cause problems69, and can
be eliminated by defining R_NO_REMAP and prepending ‘Rf_’ to
all the function names used from Rinternals.h and
R_ext/Error.h.
We can classify the entry points as
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.
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.
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.
Entry points that are where possible (Windows and some modern Unix-alike compilers/loaders when using R as a shared library) not exported.
Next: Error handling, Previous: The R API, Up: The R API [Contents][Index]
| • Transient | ||
| • User-controlled |
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).
Next: User-controlled, Previous: Memory allocation, Up: Memory allocation [Contents][Index]
Here R will reclaim the memory at the end of the call to .C.
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 (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 changes the allocation size from old to new units, and zeroes the additional units.
For compatibility with current versions of S, header S.h (only) defines wrapper macros equivalent to
type* Salloc(long n, int type) type* Srealloc(char *p, long new, long old, int type)
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
clearing memory allocated subsequently by a call to vmaxset.
This is only recommended for experts.
Note that this memory will be freed on error or user interrupt (if allowed: see Allowing interrupts).
Note that although n is long, there are limits imposed by
R’s internal allocation mechanism. These will only come into play on
64-bit systems, where the current limit for n is just under 16Gb.
Previous: Transient, Up: Memory allocation [Contents][Index]
The other form of memory allocation is an interface to malloc,
the interface providing R error handling. This memory lasts until
freed by the user and is additional to the memory allocated for the R
workspace.
The interface functions are
type* Calloc(size_t n, type) type* Realloc(any *p, size_t n, type) void 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 routines return the memory has been successfully allocated or
freed. Free will set the pointer p to NULL. (Some
but not all versions of S do so.)
Users should arrange to Free this memory when no longer needed,
including on error or user interrupt. This can often be done most
conveniently from an on.exit action in the calling R function
– see pwilcox for an example.
Do not assume that memory allocated by Calloc/Realloc
comes from the same pool as used by malloc: in particular do not
use free or strdup with it.
These entry points need to be prefixed by R_ if
STRICT_R_HEADERS has been defined.
Next: Random numbers, Previous: Memory allocation, Up: The R API [Contents][Index]
The basic error handling 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, ...);
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.)
If STRICT_R_HEADERS is not defined there is also an
S-compatibility interface which uses calls of the form
PROBLEM ...... ERROR MESSAGE ...... WARN PROBLEM ...... RECOVER(NULL_ENTRY) MESSAGE ...... WARNING(NULL_ENTRY)
the last two being the forms available in all S versions. Here
‘......’ is a set of arguments to printf, so can be a string
or a format string followed by arguments separated by commas.
| • Error handling from FORTRAN |
Previous: Error handling, Up: Error handling [Contents][Index]
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 values, Previous: Error handling, Up: The R API [Contents][Index]
The interface to R’s internal random number generation routines is
double unif_rand(); double norm_rand(); double exp_rand();
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) .Random.seed and write it
out after use.
File S.h defines seed_in and seed_out for
S-compatibility rather than GetRNGstate and
PutRNGstate. These take a long * argument which is
ignored.
The random number generator is private to R; there is no way to select the kind of RNG or 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 generate a single variate and should also be
enclosed in calls to GetRNGstate and PutRNGstate.
In addition, there is an interface (defined in header R_ext/Applic.h) to the generation of random 2-dimensional tables with given row and column totals using Patefield’s algorithm.
Here, nrow and ncol give the numbers nr and nc of rows and columns and nrowt and ncolt the corresponding row and column totals, respectively, ntotal gives the sum of the row (or columns) totals, jwork is a workspace of length nc, and on output matrix a contains the nr * nc generated random counts in the usual column-major order.
Next: Printing, Previous: Random numbers, Up: The R API [Contents][Index]
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’sNAonly ISNAN(x) True for R’sNAand IEEENaNR_FINITE(x) False forInf,-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.
Next: Calling C from FORTRAN and vice versa, Previous: Missing and IEEE values, Up: The R API [Contents][Index]
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 C99 interface, they are
only defined by R_ext/Print.h in C++ code if the macro
R_USE_C99_IN_CXX is defined when it is included.
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 |
On many systems FORTRAN write and print statements can be
used, but the output may not interleave well with that of C, and will be
invisible on GUI interfaces. They are not portable and best
avoided.
Three 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)
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), and data is an array of length at least ndata
of the appropriate type (double precision, real and
integer respectively). These routines print the label on one
line and then print data as if it were an R vector on
subsequent line(s). They work with zero ndata, and so can be used
to print a label alone.
Next: Numerical analysis subroutines, Previous: Printing, Up: The R API [Contents][Index]
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 macros 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 with underscores are 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.
Next: Optimization, Previous: Calling C from FORTRAN and vice versa, Up: The R API [Contents][Index]
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/EISPACK 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]
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 numbers, 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 betaa,bnon-central beta nbetaa,b,ncpbinomial binomn,pCauchy cauchylocation,scalechi-squared chisqdfnon-central chi-squared nchisqdf,ncpexponential expscale(and notrate)F fn1,n2non-central F nfn1,n2,ncpgamma gammashape,scalegeometric geomphypergeometric hyperNR,NB,nlogistic logislocation,scalelognormal lnormlogmean,logsdnegative binomial nbinomsize,probnormal normmu,sigmaPoisson poislambdaStudent’s t tnnon-central t ntdf,deltaStudentized range tukey(*)rr,cc,dfuniform unifa,bWeibull weibullshape,scaleWilcoxon rank sum wilcoxm,nWilcoxon signed rank signrankn
Entries marked with an asterisk only have ‘p’ and ‘q’
functions available, and none of the non-central distributions have
‘r’ functions. After a call to dwilcox, pwilcox or
qwilcox the function wilcox_free() should be called, and
similarly for the signed rank functions.
Next: Numerical Utilities, Previous: Distribution functions, Up: Numerical analysis subroutines [Contents][Index]
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 (complete) Beta function and its natural logarithm.
The number of combinations of k items chosen from 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).
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]
There are a few other numerical utility functions available as entry points.
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.
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.
Computes log(1 + x) - x (log 1 plus x minus x),
accurately even for small x, i.e., |x| << 1.
Computes log(1 + exp(x)) (log 1 plus exp),
accurately, notably for large x, e.g., x > 720.
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.
Computes log(gamma(x + 1)) (log(gamma(1 plus x))),
accurately even for small x, i.e., 0 < x < 0.5.
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)), without causing
unnecessary overflows or throwing away too much accuracy.
Return the larger (max) or smaller (min) of two integer or
double numbers, respectively. Note that fmax2 and fmin2
differ from C99’s fmax and fmin when one of the arguments
is a NaN: these versions return NaN.
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.
Performs “transfer of sign” and is defined as |x| * sign(y).
Returns the value of x rounded to digits decimal digits (after the decimal point).
This is the function used by R’s round().
Returns the value of x rounded to digits significant decimal digits.
This is the function used by R’s signif().
Returns the value of x truncated (to an integer value) towards zero.
Previous: Numerical Utilities, Up: Numerical analysis subroutines [Contents][Index]
R has a set of commonly used mathematical constants encompassing
constants usually found math.h and contains further ones that are
used in statistical computations. All 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_Ee 2.7182818 M_LOG2Elog2(e) 1.4426950 M_LOG10Elog10(e) 0.4342945 M_LN2ln(2) 0.6931472 M_LN10ln(10) 2.3025851 M_PIpi 3.1415927 M_PI_2pi/2 1.5707963 M_PI_4pi/4 0.7853982 M_1_PI1/pi 0.3183099 M_2_PI2/pi 0.6366198 M_2_SQRTPI2/sqrt(pi) 1.1283792 M_SQRT2sqrt(2) 1.4142136 M_SQRT1_21/sqrt(2) 0.7071068 M_SQRT_3sqrt(3) 1.7320508 M_SQRT_32sqrt(32) 5.6568542 M_LOG10_2log10(2) 0.3010300 M_2PI2*pi 6.2831853 M_SQRT_PIsqrt(pi) 1.7724539 M_1_SQRT_2PI1/sqrt(2*pi) 0.3989423 M_SQRT_2dPIsqrt(2/pi) 0.7978846 M_LN_SQRT_PIln(sqrt(pi)) 0.5723649 M_LN_SQRT_2PIln(sqrt(2*pi)) 0.9189385 M_LN_SQRT_PId2ln(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.
Further, the included header R_ext/Boolean.h has constants
TRUE and FALSE = 0 of type Rboolean in order to
provide a way of using “logical” variables in C consistently.
Next: Integration, Previous: Numerical analysis subroutines, Up: The R API [Contents][Index]
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
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);
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);
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);
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);
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 [Contents][Index]
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 definite and for indefinite integrals. ‘Indefinite’ means that at least one of the integration boundaries is not 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);
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
definite integral, using Rdqags, a and b are the
integration interval bounds, whereas for an indefinite 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 = 1corresponds to (bound, +Inf),
inf = -1corresponds to (-Inf, bound),
inf = 2corresponds 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, abs.err 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 [Contents][Index]
R has a fairly comprehensive set of sort routines which are made available to users’ C code. These are declared in header file R_ext/Utils.h (included by R.h) and include the following.
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.
Is similar to rsort_with_index but sorts into decreasing order,
and NAs are not handled.
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.
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 sort.index() 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.
The FORTRAN interface routines for sorting double precision vectors are
qsort3 and qsort4, equivalent to R_qsort and
R_qsort_I, respectively.
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 max.col() 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 ?max.col.
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.
There is also an F77_CALL(interv)() version of
findInterval() with the same arguments, but all pointers.
The following two functions do numerical colorspace conversion from HSV to RGB and back. Note that all colours must be in [0,1].
A system-independent interface to produce the name of a temporary file is provided as
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 malloced and should be freed when no
longer needed (unlike the system call tmpnam).
There is also the internal function used to expand file names in several
R functions, and called directly by path.expand.
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.
Next: Allowing interrupts, Previous: Utility functions, Up: The R API [Contents][Index]
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.
Set up a pointer to an encoding object to be used to convert between two
encodings: "" indicates the current locale.
Convert as much as possible of inbuf to outbuf. Initially
the int 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).
Free the resources of an encoding object.
Next: Platform and version information, Previous: Re-encoding, Up: The R API [Contents][Index]
No port 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 handling 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 [Contents][Index]
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-endian70
systems (e.g. most OSes on Sparc and PowerPC hardware) and not on
little-endian systems (such as i686 and x86_64 on all
OSes, and Linux on Alpha and Itanium). It can be useful when
manipulating binary files. The macro SUPPORT_OPENMP is defined
on suitable systems as from R 2.13.0, and can be used in conjunction
with the SUPPORT_OPENMP_* macros in packages that want to make
use of OpenMP.
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(1, 9, 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 ‘9.0’).
Next: Controlling visibility, Previous: Platform and version information, Up: The R API [Contents][Index]
The C99 keyword inline should be recognized by all compilers now
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
http://www.greenend.org.uk/rjk/2003/03/inline.html, 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: Standalone Mathlib, Previous: Inlining C functions, Up: The R API [Contents][Index]
Header R_ext/Visibility 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 generally defined on modern
Unix-alikes with a recent compiler (e.g. gcc4), but not
supported on 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 the wrong 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’ and F77_VISIBILITY for C and FORTRAN
compilers. These are defined in etc/Makeconf and so available
for normal compilation of package code. For example,
src/Makevars could include
PKG_CFLAGS=$(C_VISIBILITY) PKG_FFLAGS=$(F77_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);
...
}
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/pkgname-win.def: only entry points listed in that file will be visible. Again using stats as an example, it has
LIBRARY stats.dll EXPORTS R_init_stats
In addition, a call
R_forceSymbols(dll, TRUE);
can be added to an initializer function to specify that calls via .C,
etc. can only be made via R variables, not by character strings.
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).)
Next: Organization of header files, Previous: Controlling visibility, Up: The R API [Contents][Index]
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: Standalone Mathlib, Up: The R API [Contents][Index]
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 S.h different version for code ported from S Rinternals.h definitions for using R’s internal structures Rdefines.h macros for an S-like interface to the above 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 R_ext/RConvertors.h R_ext/Rdynload.h needed to register compiled code in packages R_ext/R-ftp-http.h interface to internal method of download.fileR_ext/Riconv.h interface to iconvR_ext/RStartup.h for add-on front-ends 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 (on all platforms)
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/-InfR_ext/Boolean.h TRUE/FALSEtypeR_ext/Complex.h C typedefs for R’s complexR_ext/Constants.h constants R_ext/Error.h error handling R_ext/Memory.h memory allocation R_ext/Print.h Rprintfand variations.R_ext/Random.h random number generation R_ext/RS.h definitions common to R.h and S.h, including F77_CALLetc.R_ext/Utils.h sorting and other utilities R_ext/libextern.h definitions for exports from R.dll 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. Some entry points from the
stats package are in R_ext/stats_package.h (currently
related to the internals of nls and nlminb).
Next: Linking GUIs and other front-ends to R, Previous: The R API, Up: Top [Contents][Index]
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.
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
t.data.frame <- function(x)
{
x <- as.matrix(x)
NextMethod("t")
}
Also consider predict.glm: it happens that in R for historical
reasons it calls predict.lm directly, but in principle (and in S
originally and currently) it could use NextMethod.
(NextMethod seems under-used in the R sources. Do be aware
that there are S/R differences in this area, and 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
predict.lm did not have a … argument, although
predict did. It soon became clear that predict.glm needed
an argument dispersion to handle over-dispersion. As
predict.lm had neither a dispersion nor a …
argument, NextMethod could no longer be used. (The legacy, two
direct calls to predict.lm, lives on in predict.glm 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
scale.foo <- function(x, scale = FALSE, ...) { }
Then for x of class "foo" the calls
scale(x, , TRUE) scale(x, scale = TRUE)
would do 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
scale.bar <- 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]
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")
foo.default <- function(object, ...) base::foo(object)
Earlier versions of this manual suggested assigning foo.default <-
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 with namespaces.
Next: Function and variable index, Previous: Generic functions and methods, Up: Top [Contents][Index]
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 http://www.rforge.net/Rserve/) and connections to Java in ‘SJava’ (see http://www.omegahat.org/RSJava/) and ‘JRI’ (part of the rJava package on CRAN).
| • 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]
R can be built as a shared library71 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 this can be used in a very similar way.
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 Mac OS X 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
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.
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.
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.) 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 examples72 in the
tests/Embedding directory. These make use of
Rf_initEmbeddedR in src/main/Rembedded.c. Here is one
example, which mimics the usual Real-Eval-Print Loop, but using code
in which application-specific actions could be added at varous points:
#include <Rinternals.h>
#include <Rembedded.h>
int main(int argc, char **argv)
{
Rf_initEmbeddedR(argc, argv);
R_ReplDLLinit();
for (;;) {
int status;
status = R_ReplDLLdo1();
if (status < 0) /* EOF */
break;
else if (status == 2) /* error trapped at top level */
Rprintf("Oops!\n"); /* example of extra error action */
else if (TYPEOF(SYMVALUE(R_LastvalueSymbol)) == LGLSXP)
Rprintf("Logical!\n"); /* another example of an extra action */
}
Rf_endEmbeddedR(0);
return 0;
}
If you don’t 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 set 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 (no check is done), 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.
Finally, the deferred evaluation apparatus used for task merging and
helper threads is set up in run_Rmainloop (which is called from
Rf_mainloop) and goes away at the end of run_Rmainloop.
If run_Rmainloop is bypassed, with R_ReplDLLdo1 used
instead, there will be no helper threads and no task merging.
| • 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]
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
If R is installed, pkg-config is available and
sub-architectures have not 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 --libs --static libR
Next: Registering symbols, Previous: Compiling against the R library, Up: Embedding R under Unix-alikes [Contents][Index]
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);
which allow standard R callbacks to be redirected to your GUI. What these do is generally documented in the file src/unix/system.txt.
This should display the message, which may have multiple lines: it should be brought to the user’s attention immediately.
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).
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.
This function is used to display the contents of files.
Choose a file and return its name in buf of length len. Return value is 0 for success, > 0 otherwise.
Send a file to an editor window.
.Internal functions for loadhistory, savehistory
and timestamp: these are called after checking the number of
arguments.
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.
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", s);
R_ShowMessage(pp);
R_CleanUp(SA_SUICIDE, 2, 0);
}
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);
}
Next: Meshing event loops, Previous: Setting R callbacks, Up: Embedding R under Unix-alikes [Contents][Index]
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 cMethod 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]
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
locator()).
Sys.sleep().
Specifically, the Unix-alike command-line version of R runs separate event loops for
download.file() and for
direct socket access, in files
src/modules/internet/nanoftp.c,
src/modules/internet/nanohttp.c and
src/modules/internet/Rsock.c
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.
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. This is not handled very well in the existing examples. The GNOME front-end can run a own handler for polled events by setting
extern int (*R_timeout_handler)();
extern long R_timeout_val;
if (R_timeout_handler && R_timeout_val)
gtk_timeout_add(R_timeout_val, R_timeout_handler, NULL);
gtk_main ();
whilst it is waiting for console input. This obviously handles events
for Gtk windows (such as the graphics device in the gtkDevice
package), but not X11 events (such as the X11() device) or for
other event handlers that might have been registered with R. It does
not attempt to keep itself alive whilst R is waiting on sockets. 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]
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 a C99 type for which a substitute is
defined in R, so your code needs to define HAVE_UINTPTR_T
appropriately.
These will be set73 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, 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 8Mb 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.
Previous: Embedding R under Unix-alikes, Up: Linking GUIs and other front-ends to R [Contents][Index]
All Windows interfaces to R call entry points in the DLL R.dll, directly or indirectly. Simpler applications may find it easier to use the indirect route via (D)COM.
| • Using (D)COM | ||
| • Calling R.dll directly | ||
| • Finding R_HOME |
Next: Calling R.dll directly, Previous: Embedding R under Windows, Up: Embedding R under Windows [Contents][Index]
(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:
StatConnector written by Thomas
Baier available via
http://cran.r-project.org/other-software.html or
http://sunsite.univie.ac.at/rcom/, which works with package
rscproxy to support transfer of data to and from R and remote
execution of R commands, as well as embedding of an R graphics
window. The rcom package on CRAN provides a (D)COM
server in a running R session.
RDCOMServer, is available from
http://www.omegahat.org/. Its philosophy is discussed in
http://www.omegahat.org/RDCOMServer/Docs/Paradigm.html and is
very different from the purpose of this section.
Next: Finding R_HOME, Previous: Using (D)COM, Up: Embedding R under Windows [Contents][Index]
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 R.dll. Examples of its use (and a
suitable Makefile.win) 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 R.dll directly are provided in the directory src/gnuwin32/front-ends, including a simple command-line front end rtest.c whose code is
#define Win32
#define WIN32_LEAN_AND_MEAN 1
#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>
#include <Rinternals.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, char *buf, int len, int addtohistory)
{
fputs(prompt, stdout);
fflush(stdout);
if(fgets(buf, len, stdin)) return 1;
else return 0;
}
void myWriteConsoleEx(const char *buf, int len, int otype)
{
/* we could distinguish between ouput (type=0) and errors (otype=1) ... */
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)
{
/* The code below is very similar that in gnuwin32/embeddedR.c, but
illustrates how slight modifications could be made. */
structRstart rp;
Rstart Rp = &rp;
char Rversion[25], *RHome;
snprintf(Rversion, 25, "%s.%s", R_MAJOR, R_MINOR);
if(strcmp(getDLLVersion(), Rversion) != 0) {
fprintf(stderr, "Error: R.DLL version does not match\n");
exit(1);
}
R_setStartTime();
R_DefParams(Rp);
if((RHome = get_R_HOME()) == NULL) {
fprintf(stderr,
"R_HOME must be set in the environment or Registry\n");
exit(1);
}
Rp->rhome = RHome;
Rp->home = getRUser();
Rp->CharacterMode = LinkDLL;
Rp->ReadConsole = myReadConsole;
Rp->WriteConsole = NULL; /* for illustration purposes we use more flexible WriteConsoleEx */
Rp->WriteConsoleEx = myWriteConsoleEx;
Rp->CallBack = myCallBack;
Rp->ShowMessage = askok;
Rp->YesNoCancel = askyesnocancel;
Rp->Busy = myBusy;
Rp->R_Quiet = TRUE;
Rp->R_Interactive = TRUE;
Rp->RestoreAction = SA_RESTORE;
Rp->SaveAction = SA_NOSAVE;
R_SetParams(Rp);
R_set_command_line_arguments(argc, argv);
FlushConsoleInputBuffer(GetStdHandle(STD_INPUT_HANDLE));
signal(SIGBREAK, my_onintr);
GA_initapp(0, 0);
readconsolecfg();
setup_Rmainloop();
/* Now we implement a REPL, one way or another. */
#if 0 /* the simple case */
run_Rmainloop();
#else
R_ReplDLLinit();
for (;;) {
int status;
status = R_ReplDLLdo1();
/* Add other user actions here if desired. This is an illustration. */
if (status < 0) /* EOF */
break;
else if (status == 2) /* error trapped at top level */
printf("Oops!\n"); /* example of extra error action */
else if (TYPEOF(SYMVALUE(R_LastvalueSymbol)) == LGLSXP)
printf("Logical!\n"); /* another example of an extra action */
}
/* only get here on EOF (not q()) */
#endif
Rf_endEmbeddedR(0);
return 0;
}
The ideas are
HKEY_LOCAL_MACHINE\Software\pqR\R\InstallPath from an
administrative install and
HKEY_CURRENT_USER\Software\pqR\R\InstallPath otherwise, if
selected during installation (as it is by default).
Rstart structure.
R_DefParams sets the defaults, and R_SetParams sets
updated values.
R_set_command_line_arguments for use by the R function
commandArgs().
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();
}
#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 choose.file()
and select.list(). 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 RGui.exe shows) but it will normally be easier74 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.
Previous: Calling R.dll directly, Up: Embedding R under Windows [Contents][Index]
Both applications which embed R and those which use a system
call to invoke R (as Rscript.exe, Rterm.exe or
R.exe) 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\pqR\R. For an
administrative install this is under HKEY_LOCAL_MACHINE and on a
64-bit OS HKEY_LOCAL_MACHINE\Software\pqR\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\pqR\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\pqR\R32 and Software\pqR\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 2.11.0 or
2.11.0 patched or 2.12.0 Pre-release with a value for
InstallPath.
So a comprehensive algorithm to search to R_HOME is something
like
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.
Software\pqR\R32
or Software\pqR\R64, and if that does not exist or the
architecture is immaterial, in Software\pqR\R.
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.
Prior to R 2.12.0 R.dll and the various front-end executables are in R_HOME\bin, but they are now in R_HOME\bin\i386 or R_HOME\bin\x64. So you need to arrange to look first in the architecture-specific subdirectory and then in R_HOME\bin.
Next: Concept index, Previous: Linking GUIs and other front-ends to R, Up: Top [Contents][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 |
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although this is common 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.
false positives are possible, but only a handful have been seen so far.
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 will 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’.
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.
This is true for OSes which implement the ‘C’ locale: Windows’ idea of the ‘C’ locale uses the WinAnsi charset.
the package needs to depend on R (>= 2.10)
Prior to R
version 2.14.0, the .First.lib and .Last.lib functions
handled these tasks in packages without namespaces. (In current R
versions, all packages have namespaces.) To help with
conversion of old packages, here is how they were handled: It was
conventional to define these functions in a file called zzz.R.
If .First.lib was defined in a package, it was called with
arguments libname and pkgname after the package was
loaded and attached. A common use was to call library.dynam
inside .First.lib to load compiled code: another use was to
call some functions with side effects. If .Last.lib existed in
a package it was called (with argument the full path to the installed
package) just before the package was detached.
More precisely, they can contain the English alphanumeric characters and the symbols ‘$ - _ . + ! ' ( ) , ; = &’.
Note that Ratfor is not supported. If you have Ratfor source code, you need to convert it to FORTRAN. Only FORTRAN 77 (which we write in upper case) is supported on all platforms, but most also support Fortran-95 (for which we use title case). If you want to ship Ratfor source files, please do so in a subdirectory of src and not in the main subdirectory.
either or both of which may not be supported on particular platforms
Using .hpp, although somewhat popular, is not guaranteed to be portable.
the POSIX terminology, called ‘make variables’ by GNU make.
case-insensitively on Windows.
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 --slave and with environment variable
LANGUAGE=en set to get messages in English.
e.g http://tools.ietf.org/html/rfc4180.
in POSIX parlance: GNU make
calls these ‘make variables’.
at least on Unix-alikes: the Windows build currently resolves such dependencies to a static FORTRAN library when Rblas.dll is built.
http://www.openmp.org/, http://en.wikipedia.org/wiki/OpenMP, https://computing.llnl.gov/tutorials/openMP/
But OpenMP support is not available with the default toolchain used prior to R 2.14.2 on Windows.
some Windows toolchains have the typo ‘_REENTRANCE’ instead.
Cygwin used g77 up to 2011, and some pre-built
versions of R for Unix OSes still do.
On systems which use sub-architectures, architecture-specific versions such as ~/.R/check.Renviron.i386 take precedence.
This may require GNU tar: the
command used can be set with environment variable TAR.
A suitable file.exe is
part of the Windows toolset.
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.
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
Windows users behind proxies may
want to set environment variable R_WIN_INTERNET2 to a non-empty
value, e.g. in ~/.R/check_environ. Some Windows users may need
to set R_WIN_NO_JUNCTIONS to a non-empty value.
loading, examples, tests, vignettes
case-insensitively on Windows.
including directory names as from R 2.13.0: earlier versions accepted the names of non-empty directories.
called CVS or .svn or .arch-ids or .bzr or .git or .hg.
or the package’s description contains ‘BuildVignettes: no’ or similar.
and to avoid problems with case-insensitive file systems, lower-case versions of all these extensions.
unless inhibited by using ‘BuildVignettes: no’ in the DESCRIPTION file.
provided the conditions of the package’s licence are met: many would see these as incompatible with an Open Source licence.
As from R 2.13.0, R_HOME/bin is
prepended to the PATH so that references to R or
Rscript in the Makefile do make use of the currently
running version of R.
provided the encoding is known: currently if it is not, it is guessed to be Latin-1.
provided a
POSIX-compliant du program is found on the system: it is
possible that some other du programs will incorrectly report
double the actual size. This can be disabled by setting
_R_CHECK_PKG_SIZE_ to a false value.
for Windows users the simplest way may be to open that URL in Internet Explorer and (depending on the version) follow the instructions to view it as a folder, then copy the submission to the folder.
currently the long obsolete TeXLive 2009.
if their license allows: this often requires also including the corresponding .dtx file.
Select ‘Save as’, and select ‘Reduce file size’ from the ‘Quartz filter’ menu’: this can be accessed in other ways, for example by Automator.
they will be called with two unnamed arguments, in that order.
NB: this will only be read in all versions of R if the package contains R code in a R directory.
Note that this is the basename of the shared object, and the appropriate extension (.so or .dll) will be added.
As from R 2.13.0 this
defaults to the same pattern as exportPattern: use something like
exportClassPattern("^$") to override this.
GNU make,
BSD make as in FreeBSD and bsdmake on Darwin, AT&T make as
implemented on Solaris.
but note that long
long is not a standard C++ type, and C++ compilers set up for strict
checking will reject it.
Typically on a Unix-alike this is done by telling
fontconfig where to find suitable fonts to select glyphs
from.
e.g. \alias, \keyword and
\note sections.
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.
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.
Text between or after list items was discarded prior to R 2.10.0, and is discouraged.
Currently it is rendered differently only in HTML conversions, and LaTeX conversion outside ‘\usage’ and ‘\examples’ environments.
a common
example in CRAN packages is \link[mgcv]{gam}.
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.
See the examples section in the file Paren.Rd for an example.
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.
R has to be built to enable this, but the option --enable-R-profiling is the default.
For Unix-alikes these are intervals of CPU time, and for Windows of elapsed time.
With the exceptions of the commands
listed below: an object of such a name can be printed via an
explicit call to print.
possibly after some platform-specific translation, e.g. adding leading or trailing underscores.
dyld on Mac
OS X, and DYLD_LIBRARY_PATHS below.
see The R API: note that these are not all part of the API.
SEXP is an acronym for Simple EXPression, common in LISP-like language syntaxes.
You should therefore usually assign a copy
of the object in the environment frame rho using defineVar(symbol,
duplicate(value), rho)).
see Character encoding issues for why this might not be what is required.
This is only guaranteed to show the current interface: it is liable to change.
Known problems are redefining
error, length, vector and warning
http://en.wikipedia.org/wiki/Endianness.
In the parlance of Mac OS X this is a dynamic library, and is the normal way to build R on that platform.
but these are not part of the automated test procedures and so little tested.
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
Mac OS X.
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.