Next: Obtaining R [Contents][Index]
This is a guide to installation and administration for R.
This manual is for R, version 4.0.2 (2020-06-22).
Copyright © 2001–2018 R Core Team
Permission is granted to make and distribute verbatim copies of this manual provided the copyright notice and this permission notice are preserved on all copies.
Permission is granted to copy and distribute modified versions of this manual under the conditions for verbatim copying, provided that the entire resulting derived work is distributed under the terms of a permission notice identical to this one.
Permission is granted to copy and distribute translations of this manual into another language, under the above conditions for modified versions, except that this permission notice may be stated in a translation approved by the R Core Team.
Next: Installing R under Unix-alikes, Previous: Top, Up: Top [Contents][Index]
Sources, binaries and documentation for R can be obtained via CRAN, the “Comprehensive R Archive Network” whose current members are listed at https://CRAN.R-project.org/mirrors.html.
• Getting and unpacking the sources | ||
• Getting patched and development versions |
Next: Getting patched and development versions, Previous: Obtaining R, Up: Obtaining R [Contents][Index]
The simplest way is to download the most recent R-x.y.z.tar.gz file, and unpack it with
tar -xf R-x.y.z.tar.gz
on systems that have a suitable1 tar
installed. On other systems you need to
have the gzip
program installed, when you can use
gzip -dc R-x.y.z.tar.gz | tar -xf -
The pathname of the directory into which the sources are unpacked should
not contain spaces, as most make
programs (and specifically
GNU make
) do not expect spaces.
If you want the build to be usable by a group of users, set umask
before unpacking so that the files will be readable by the target group
(e.g., umask 022
to be usable by all users). Keep this
setting of umask
whilst building and installing.
If you use a fairly recent GNU version of tar
and do
this as a root account (which on Windows includes accounts with
administrator privileges) you may see many warnings about changing
ownership. In which case you can use
tar --no-same-owner -xf R-x.y.z.tar.gz
and perhaps also include the option --no-same-permissions.
(These options can also be set in the TAR_OPTIONS
environment
variable: if more than one option is included they should be separated
by spaces.)
Previous: Getting and unpacking the sources, Up: Obtaining R [Contents][Index]
A patched version of the current release, ‘r-patched’, and the current development version, ‘r-devel’, are available as daily tarballs and via access to the R Subversion repository. (For the two weeks prior to the release of a minor (4.x.0) version, ‘r-patched’ tarballs may refer to beta/release candidates of the upcoming release, the patched version of the current release being available via Subversion.)
The tarballs are available from https://stat.ethz.ch/R/daily. Download R-patched.tar.gz or R-devel.tar.gz (or the .tar.bz2 versions) and unpack as described in the previous section. They are built in exactly the same way as distributions of R releases.
• Using Subversion and rsync |
Previous: Getting patched and development versions, Up: Getting patched and development versions [Contents][Index]
Sources are also available via https://svn.R-project.org/R/, the R Subversion repository. If you have a Subversion client (see https://subversion.apache.org/), you can check out and update the current ‘r-devel’ from https://svn.r-project.org/R/trunk/ and the current ‘r-patched’ from ‘https://svn.r-project.org/R/branches/R-x-y-branch/’ (where x and y are the major and minor number of the current released version of R). E.g., use
svn checkout https://svn.r-project.org/R/trunk/ path
to check out ‘r-devel’ into directory path (which will be created if necessary). The alpha, beta and RC versions of an upcoming x.y.0 release are available from ‘https://svn.r-project.org/R/branches/R-x-y-branch/’ in the four-week period prior to the release.
Note that ‘https:’ is required2, and that the SSL certificate for the Subversion server of the R project should be recognized as from a trusted source.
Note that retrieving the sources by e.g. wget -r
or
svn export
from that URL will not work (and will give a error
early in the make
process): the Subversion information is
needed to build R.
The Subversion repository does not contain the current sources for the
recommended packages, which can be obtained by rsync
or
downloaded from CRAN. To use rsync
to install the
appropriate sources for the recommended packages, run
./tools/rsync-recommended
from the top-level directory of the
R sources.
If downloading manually from CRAN, do ensure that you have the
correct versions of the recommended packages: if the number in the file
VERSION is ‘x.y.z’ you need to download
the contents of ‘https://CRAN.R-project.org/src/contrib/dir’,
where dir is ‘x.y.z/Recommended’ for
r-devel or x.y-patched/Recommended for r-patched,
respectively, to directory src/library/Recommended in the sources
you have unpacked. After downloading manually you need to execute
tools/link-recommended
from the top level of the sources to
make the requisite links in src/library/Recommended. A suitable
incantation from the top level of the R sources using wget
might be (for the correct value of dir)
wget -r -l1 --no-parent -A\*.gz -nd -P src/library/Recommended \ https://CRAN.R-project.org/src/contrib/dir ./tools/link-recommended
Next: Installing R under Windows, Previous: Obtaining R, Up: Top [Contents][Index]
R will configure and build under most common Unix and Unix-alike platforms including ‘cpu-*-linux-gnu’ for the ‘alpha’, ‘arm64’, ‘hppa’, ‘ix86’, ‘m68k’, ‘mips’, ‘mipsel’#, ‘ppc64’, ‘s390x’, ‘sparc64’, and ‘x86_64’ CPUs, ‘x86_64-apple-darwin’ and ‘i386-sun-solaris’ as well as perhaps (it is tested less frequently on these platforms) ‘i386-*-freebsd’, ‘x86_64-*-freebsd’, ‘i386-*-netbsd’, ‘x86_64-*-openbsd’ and ‘powerpc-ibm-aix6*’
In addition, binary distributions are available for some common Linux distributions and for macOS (formerly OS X and Mac OS). See the FAQ for current details. These are installed in platform-specific ways, so for the rest of this chapter we consider only building from the sources.
Cross-building is not possible: installing R builds a minimal version of R and then runs many R scripts to complete the build.
• Simple compilation | ||
• Help options | ||
• Making the manuals | ||
• Installation | ||
• Uninstallation | ||
• Sub-architectures | ||
• Other Options | ||
• Testing a Unix-alike Installation |
Next: Help options, Previous: Installing R under Unix-alikes, Up: Installing R under Unix-alikes [Contents][Index]
First review the essential and useful tools and libraries in
Essential and useful other programs under a Unix-alike, and install
those you
want or need. Ensure that either the environment variable TMPDIR
is either unset (and /tmp exists and can be written in and
scripts can be executed from) or points to the absolute path to a valid
temporary directory (one from which execution of scripts is allowed)
which does not contain spaces.3
Choose a directory to install the R tree (R is not just a binary, but has additional data sets, help files, font metrics etc). Let us call this place R_HOME. Untar the source code. This should create directories src, doc, and several more under a top-level directory: change to that top-level directory (At this point North American readers should consult Setting paper size.) Issue the following commands:
./configure make
(See Using make if your make is not called ‘make’.) Users of Debian-based 64-bit systems4 may need
./configure LIBnn=lib make
Then check the built system works correctly by
make check
Failures are not necessarily problems as they might be caused by missing
functionality, but you should look carefully at any reported
discrepancies. (Some non-fatal errors are expected in locales that do
not support Latin-1, in particular in true C
locales and
non-UTF-8 non-Western-European locales.) A failure in
tests/ok-errors.R may indicate inadequate resource limits
(see Running R).
More comprehensive testing can be done by
make check-devel
or
make check-all
see file tests/README and Testing a Unix-alike Installation for the possibilities of doing this in parallel. Note that these checks are only run completely if the recommended packages are installed.
If the configure
and make
commands execute
successfully, a shell-script front-end called R will be created
and copied to R_HOME/bin. You can link or copy this script
to a place where users can invoke it, for example to
/usr/local/bin/R. You could also copy the man page R.1 to
a place where your man
reader finds it, such as
/usr/local/man/man1. If you want to install the complete R
tree to, e.g., /usr/local/lib/R, see Installation. Note:
you do not need to install R: you can run it from where it was
built.
You do not necessarily have to build R in the top-level source directory (say, TOP_SRCDIR). To build in BUILDDIR, run
cd BUILDDIR TOP_SRCDIR/configure make
and so on, as described further below. This has the advantage of always
keeping your source tree clean and is particularly recommended when you
work with a version of R from Subversion. (You may need
GNU make
to allow this, and you will need no spaces
in the path to the build directory. It is unlikely to work if the
source directory has previously been used for a build.)
Now rehash
if necessary, type R, and read the R manuals
and the R FAQ (files FAQ or
doc/manual/R-FAQ.html, or
https://CRAN.R-project.org/doc/FAQ/R-FAQ.html which always
has the version for the latest release of R).
Note: if you already have R installed, check that where you installed R replaces or comes earlier in your path than the previous installation. Some systems are set up to have /usr/bin (the standard place for a system installation) ahead of /usr/local/bin (the default place for installation of R) in their default path, and some do not have /usr/local/bin on the default path.
Next: Making the manuals, Previous: Simple compilation, Up: Installing R under Unix-alikes [Contents][Index]
R by default provides help pages as plain text displayed in a pager,
with the options (see the help for help
) of displaying help as
HTML or PDF.
By default HTML help pages are created when needed rather than being built at install time.
If you need to disable the server and want HTML help, there is the
option to build HTML pages when packages are installed
(including those installed with R). This is enabled by the
configure
option --enable-prebuilt-html. Whether
R CMD INSTALL
(and hence install.packages
) pre-builds
HTML pages is determined by looking at the R installation and is
reported by R CMD INSTALL --help
: it can be overridden by
specifying one of the INSTALL
options --html or
--no-html.
The server is disabled by setting the environment variable
R_DISABLE_HTTPD
to a non-empty value, either before R is
started or within the R session before HTML help (including
help.start
) is used. It is also possible that system security
measures will prevent the server from being started, for example if the
loopback interface has been disabled. See
?tools::startDynamicHelp
for more details.
Next: Installation, Previous: Help options, Up: Installing R under Unix-alikes [Contents][Index]
There is a set of manuals that can be built from the sources,
Printed versions of all the help pages for base and recommended packages (around 3750 pages).
Printed versions of the help pages for selected base packages (around 2200 pages)
R FAQ
“An Introduction to R”.
“R Data Import/Export”.
“R Installation and Administration”, this manual.
“Writing R Extensions”.
“The R Language Definition”.
To make these (with ‘fullrefman’ rather than ‘refman’), use
make pdf to create PDF versions make info to create info files (not ‘refman’ nor ‘fullrefman’).
You will not be able to build any of these unless you have
texi2any
version 5.1 or later installed, and for PDF you must
have texi2dvi
and texinfo.tex installed (which are part
of the GNU texinfo distribution but are, especially
texinfo.tex, often made part of the TeX package in
re-distributions). The path to texi2any
can be set by macro
‘TEXI2ANY’ in config.site. NB: texi2any
require
perl
.
The PDF versions can be viewed using any recent PDF viewer: they have
hyperlinks that can be followed. The info files are suitable for
reading online with Emacs or the standalone GNU info
program. The PDF versions will be created using the paper size selected
at configuration (default ISO a4): this can be overridden by setting
R_PAPERSIZE
on the make
command line, or setting R_PAPERSIZE
in the
environment and using make -e
. (If re-making the manuals for
a different paper size, you should first delete the file
doc/manual/version.texi. The usual value for North America would
be ‘letter’.)
There are some issues with making the PDF reference manual, fullrefman.pdf or refman.pdf. The help files contain both ISO Latin1 characters (e.g. in text.Rd) and upright quotes, neither of which are contained in the standard LaTeX Computer Modern fonts. We have provided four alternatives:
times
(The default.) Using standard PostScript fonts, Times Roman, Helvetica
and Courier. This works well both for on-screen viewing and for
printing. One disadvantage is that the Usage and Examples sections may
come out rather wide: this can be overcome by using in addition
either of the options inconsolata
(on a Unix-alike only if found
by configure
) or beramono
, which replace the Courier
monospaced font by Inconsolata or Bera Sans mono respectively. (You
will need a recent version of the appropriate LaTeX package
inconsolata5 or
bera installed.)
Note that in most LaTeX installations this will not actually use the standard fonts for PDF, but rather embed the URW clones NimbusRom, NimbusSans and (for Courier, if used) NimbusMon.
This needs LaTeX packages times, helvetic and (if used) courier installed.
lm
Using the Latin Modern fonts. These are not often installed as
part of a TeX distribution, but can obtained from
https://www.ctan.org/tex-archive/fonts/ps-type1/lm/ and
mirrors. This uses fonts rather similar to Computer Modern, but is not
so good on-screen as times
.
cm-super
Using type-1 versions of the Computer Modern fonts by Vladimir Volovich. This is a large installation, obtainable from https://www.ctan.org/tex-archive/fonts/ps-type1/cm-super/ and its mirrors. These type-1 fonts have poor hinting and so are nowhere near as readable on-screen as the other three options.
ae
A package to use composites of Computer Modern fonts. This works well most of the time, and its PDF is more readable on-screen than the previous two options. There are three fonts for which it will need to use bitmapped fonts, tctt0900.600pk, tctt1000.600pk and tcrm1000.600pk. Unfortunately, if those files are not available, Acrobat Reader will substitute completely incorrect glyphs so you need to examine the logs carefully.
The default can be overridden by setting the environment variable
R_RD4PDF
. (On Unix-alikes, this will be picked up at install time
and stored in etc/Renviron, but can still be overridden when the
manuals are built, using make -e
.) The usual6 default value for R_RD4PDF
is
‘times,inconsolata,hyper’: omit ‘hyper’ if you do not want
hyperlinks (e.g. for printing the manual) or do not have LaTeX
package hyperref, and omit ‘inconsolata’ if you do not have
LaTeX package inconsolata installed.
Further options, e.g for hyperref, can be included in a file Rd.cfg somewhere on your LaTeX search path. For example, if you prefer to hyperlink the text and not the page number in the table of contents use
\ifthenelse{\boolean{Rd@use@hyper}}{\hypersetup{linktoc=section}}{}
or
\ifthenelse{\boolean{Rd@use@hyper}}{\hypersetup{linktoc=all}}{}
to hyperlink both text and page number.
Ebook versions of most of the manuals in one or both of .epub and .mobi formats can be made by running in doc/manual one of
make ebooks make epub make mobi
This requires ebook-convert
from Calibre
(http://calibre-ebook.com/download), or from most Linux
distributions. If necessary the path to ebook-convert
can be
set as make macro EBOOK
to by editing doc/manual/Makefile
(which contains a commented value suitable for macOS) or using
make -e
.
Next: Uninstallation, Previous: Making the manuals, Up: Installing R under Unix-alikes [Contents][Index]
To ensure that the installed tree is usable by the right group of users,
set umask
appropriately (perhaps to ‘022’) before unpacking
the sources and throughout the build process.
After
./configure make make check
(or, when building outside the source,
TOP_SRCDIR/configure
, etc) have been completed
successfully, you can install the complete R tree to your system by
typing
make install
A parallel make can be used (but run make
before make
install
). Those using GNU make
4.0 or later may want to use
make -j n -O
to avoid interleaving of output.
This will install to the following directories:
the front-end shell script and other scripts and executables
the man page
all the rest (libraries, on-line help system, …). Here LIBnn is usually ‘lib’, but may be ‘lib64’ on some 64-bit Linux systems. This is known as the R home directory.
where prefix is determined during configuration (typically
/usr/local) and can be set by running configure
with
the option --prefix, as in
./configure --prefix=/where/you/want/R/to/go
where the value should be an absolute path. This causes make
install
to install the R script to
/where/you/want/R/to/go/bin, and so on. The prefix of the
installation directories can be seen in the status message that is
displayed at the end of configure
. The installation may need
to be done by the owner of prefix, often a root account.
There is the option of using make install-strip
(see Debugging Symbols).
You can install into another directory tree by using
make prefix=/path/to/here install
at least with GNU make
(but not some other Unix
makes).
More precise control is available at configure time via options: see
configure --help
for details. (However, most of the ‘Fine
tuning of the installation directories’ options are not used by R.)
Configure options --bindir and --mandir are supported
and govern where a copy of the R
script and the man
page are installed.
The configure option --libdir controls where the main R files are installed: the default is ‘eprefix/LIBnn’, where eprefix is the prefix used for installing architecture-dependent files, defaults to prefix, and can be set via the configure option --exec-prefix.
Each of bindir
, mandir
and libdir
can also be
specified on the make install
command line (at least for
GNU make
).
The configure
or make
variables rdocdir
and
rsharedir
can be used to install the system-independent
doc and share directories to somewhere other than
libdir
. The C header files can be installed to the value of
rincludedir
: note that as the headers are not installed into a
subdirectory you probably want something like
rincludedir=/usr/local/include/R-4.0.2
.
If you want the R home to be something other than libdir/R, use rhome: for example
make install rhome=/usr/local/lib64/R-4.0.2
will use a version-specific R home on a non-Debian Linux 64-bit system.
If you have made R as a shared/static library you can install it in your system’s library directory by
make prefix=/path/to/here install-libR
where prefix
is optional, and libdir
will give more
precise control.7 However, you should not install
to a directory mentioned in LDPATHS
(e.g.
/usr/local/lib64) if you intend to work with multiple versions of
R, since that directory may be given precedence over the lib
directory of other R installations.
make install-strip
will install stripped executables, and on platforms where this is supported, stripped libraries in directories lib and modules and in the standard packages.
Note that installing R into a directory whose path contains spaces is not supported, and some aspects (such as installing source packages) will not work.
To install info and PDF versions of the manuals, use one or both of
make install-info make install-pdf
Once again, it is optional to specify prefix
, libdir
or
rhome
(the PDF manuals are installed under the R home
directory).
More precise control is possible. For info, the setting used is that of
infodir
(default prefix/info, set by configure
option --infodir). The PDF files are installed into the R
doc tree, set by the make
variable rdocdir
.
A staged installation is possible, that it is installing R into a
temporary directory in order to move the installed tree to its final
destination. In this case prefix
(and so on) should reflect the
final destination, and DESTDIR
should be used: see
https://www.gnu.org/prep/standards/html_node/DESTDIR.html.
You can optionally install the run-time tests that are part of
make check-all
by
make install-tests
which populates a tests directory in the installation.
Next: Sub-architectures, Previous: Installation, Up: Installing R under Unix-alikes [Contents][Index]
You can uninstall R by
make uninstall
optionally specifying prefix
etc in the same way as specified for
installation.
This will also uninstall any installed manuals. There are specific targets to uninstall info and PDF manuals in file doc/manual/Makefile.
Target uninstall-tests
will uninstall any installed tests, as
well as removing the directory tests containing the test results.
An installed shared/static libR
can be uninstalled by
make prefix=/path/to/here uninstall-libR
Next: Other Options, Previous: Uninstallation, Up: Installing R under Unix-alikes [Contents][Index]
Some platforms can support closely related builds of R which can share all but the executables and dynamic objects. Examples include builds under Linux and Solaris for different CPUs or 32- and 64-bit builds.
R supports the idea of architecture-specific builds, specified by
adding ‘r_arch=name’ to the configure
line. Here
name can be anything non-empty, and is used to name subdirectories
of lib, etc, include and the package libs
subdirectories. Example names from other software are the use of
sparcv9 on Sparc Solaris and 32 by gcc
on
‘x86_64’ Linux.
If you have two or more such builds you can install them over each other (and for 32/64-bit builds on one architecture, one build can be done without ‘r_arch’). The space savings can be considerable: on ‘x86_64’ Linux a basic install (without debugging symbols) took 74Mb, and adding a 32-bit build added 6Mb. If you have installed multiple builds you can select which build to run by
R --arch=name
and just running ‘R’ will run the last build that was installed.
R CMD INSTALL
will detect if more than one build is installed and
try to install packages with the appropriate library objects for each.
This will not be done if the package has an executable configure
script or a src/Makefile file. In such cases you can install for
extra builds by
R --arch=name CMD INSTALL --libs-only pkg1 pkg2 …
If you want to mix sub-architectures compiled on different platforms (for example ‘x86_64’ Linux and ‘i686’ Linux), it is wise to use explicit names for each, and you may also need to set libdir to ensure that they install into the same place.
When sub-architectures are used the version of Rscript
in
e.g. /usr/bin will be the last installed, but
architecture-specific versions will be available in e.g.
/usr/lib64/R/bin/exec${R_ARCH}. Normally all installed
architectures will run on the platform so the architecture of
Rscript
itself does not matter. The executable
Rscript
will run the R
script, and at that time the
setting of the R_ARCH
environment variable determines the
architecture which is run.
When running post-install tests with sub-architectures, use
R --arch=name CMD make check[-devel|all]
to select a sub-architecture to check.
Sub-architectures are also used on Windows, but by selecting executables
within the appropriate bin directory,
R_HOME/bin/i386 or R_HOME/bin/x64. For
backwards compatibility there are executables
R_HOME/bin/R.exe and R_HOME/bin/Rscript.exe:
these will run an executable from one of the subdirectories, which one
being taken first from the
R_ARCH
environment variable, then from the
--arch command-line option8 and finally from the
installation default (which is 32-bit for a combined 32/64 bit R
installation).
• Multilib |
Previous: Sub-architectures, Up: Sub-architectures [Contents][Index]
For some Linux distributions9, there is an alternative mechanism for mixing
32-bit and 64-bit libraries known as multilib. If the Linux
distribution supports multilib, then parallel builds of R may be
installed in the sub-directories lib (32-bit) and lib64
(64-bit). The build to be run may then be selected using the
setarch
command. For example, a 32-bit build may be run by
setarch i686 R
The setarch
command is only operational if both 32-bit and
64-bit builds are installed. If there is only one installation of R,
then this will always be run regardless of the architecture specified
by the setarch
command.
There can be problems with installing packages on the non-native
architecture. It is a good idea to run e.g. setarch i686 R
for
sessions in which packages are to be installed, even if that is the only
version of R installed (since this tells the package installation
code the architecture needed).
There is a potential problem with packages using Java, as the post-install for a ‘i686’ RPM on ‘x86_64’ Linux reconfigures Java and will find the ‘x86_64’ Java. If you know where a 32-bit Java is installed you may be able to run (as root)
export JAVA_HOME=<path to jre directory of 32-bit Java> setarch i686 R CMD javareconf
to get a suitable setting.
When this mechanism is used, the version of Rscript
in
e.g. /usr/bin will be the last installed, but an
architecture-specific version will be available in
e.g. /usr/lib64/R/bin. Normally all installed architectures
will run on the platform so the architecture of Rscript
does
not matter.
Next: Testing a Unix-alike Installation, Previous: Sub-architectures, Up: Installing R under Unix-alikes [Contents][Index]
There are many other installation options, most of which are listed by
configure --help
. Almost all of those not listed elsewhere in
this manual are either standard autoconf
options not relevant
to R or intended for specialist uses by the R developers.
One that may be useful when working on R itself is the option
--disable-byte-compiled-packages, which ensures that the base
and recommended packages are not byte-compiled. (Alternatively the
(make or environment) variable R_NO_BASE_COMPILE
can be set to a
non-empty value for the duration of the build.)
Option --with-internal-tzcode makes use of R’s own code and
copy of the IANA database for managing timezones. This will be
preferred where there are issues with the system implementation, usually
involving times after 2037 or before 1916. An alternative time-zone
directory10 can be used, pointed
to by environment variable TZDIR
: this should contain files such
as Europe/London. On all tested OSes the system timezone was
deduced correctly, but if necessary it can be set as the value of
environment variable TZ
.
• Debugging Symbols | ||
• OpenMP Support | ||
• C++ Support | ||
• Link-Time Optimization |
Next: OpenMP Support, Previous: Other Options, Up: Other Options [Contents][Index]
By default, configure
adds a flag (usually -g) to the
compilation flags for C, Fortran and CXX sources. This will slow down
compilation and increase object sizes of both R and packages, so it
may be a good idea to change those flags (set ‘CFLAGS’ etc in
config.site before configuring, or edit files Makeconf
and etc/Makeconf between running configure
and
make
).
Having debugging symbols available is useful both when running R under a
debugger (e.g., R -d gdb
) and when using sanitizers and
valgrind
, all things intended for experts.
Debugging symbols (and some others) can be ‘stripped’ on installation by using
make install-strip
How well this is supported depends on the platform: it works best on
those using GNU binutils
. On ‘x86_64’ Linux a typical
reduction in overall size was from 92MB to 66MB. On macOS debugging
symbols are not by default included in .dylib and .so
files, so there is negligible difference.
Next: C++ Support, Previous: Debugging Symbols, Up: Other Options [Contents][Index]
By default configure
searches for suitable flags11
for OpenMP support for the C, C++ (default standard) and Fortran
compilers.
Only the C result is currently used for R itself, and only if
MAIN_LD
/DYLIB_LD
were not specified. This can be
overridden by specifying
R_OPENMP_CFLAGS
Use for packages has similar restrictions (involving SHLIB_LD
and
similar: note that as Fortran code is by default linked by the C (or
C++) compiler, both need to support OpenMP) and can be overridden by
specifying some of
SHLIB_OPENMP_CFLAGS SHLIB_OPENMP_CXXFLAGS SHLIB_OPENMP_FFLAGS
Setting these to an empty value will disable OpenMP for that compiler
(and configuring with --disable-openmp will disable all
detection12 of OpenMP). The
configure
detection test is to compile and link a standalone
OpenMP program, which is not the same as compiling a shared object and
loading it into the C program of R’s executable. Note that
overridden values are not tested.
Next: Link-Time Optimization, Previous: OpenMP Support, Up: Other Options [Contents][Index]
C++ is not used by R itself, but support is provided for installing
packages with C++ code via make
macros defined in file
etc/Makeconf (and with explanations in file config.site):
CXX CXXFLAGS CXXPICFLAGS CXXSTD CXX11 CXX11STD CXX11FLAGS CXX11PICFLAGS CXX14 CXX14STD CXX14FLAGS CXX14PICFLAGS CXX17 CXX17STD CXX17FLAGS CXX17PICFLAGS CXX20 CXX20STD CXX20FLAGS CXX20PICFLAGS
The macros CXX
etc are those used by default for C++ code.
configure
will attempt to set the rest suitably, choosing for
CXXSTD
and CXX11STD
a suitable flag such as
-std=c++11 for C++11 support (which is required if C++ is to be
supported at all). Similarly, configure
will if possible
choose for CXX14STD
a flag13 such as -std=c++14 for C++14 support,
-std=c++17 or -std=c++1z for support for C++17 and
-std=c++20 or -std=c++2a for support for C++20.. The
inferred values can be overridden in file config.site or on the
configure
command line: user-supplied values will be tested by
compiling some C++11/14/17/20 code.
It may be that there is no suitable flag for C++14/17/20 support with
the default compiler, in which case a different compiler could be
selected for CXX14
or CXX17
or CXX20
with its
corresponding flags.
The -std flag is supported by the GCC, clang++
, Intel
and Solaris compilers (the latter from version 12.4). Currently
accepted values are (plus some synonyms)
g++: c++11 gnu+11 c++14 gnu++14 c++17 gnu++17 c++2a gnu++2a (from 8) c++20 gnu++20 (from 10) Intel: c++11 c++14 (from 16.0) c++17 (from 17.0) Solaris: c++11 c++14 (from 12.5)
(Those for clang++
are documented at
https://clang.llvm.org/cxx_status.html, and follow g++
:
-std=c++20
is supported from Clang 10.)
‘Standards’ for g++
starting with ‘gnu’ enable ‘GNU
extensions’: what those are is hard to track down.
For the use of C++11 and later in R packages see the ‘Writing R Extensions’ manual. Prior to R 3.6.0 the default C++ standard was that of the compiler used: currently it is C++11: this can be overridden by setting ‘CXXSTD’ when R is configured, for example to ‘-std=gnu++14’.
https://en.cppreference.com/w/cpp/compiler_support indicates which versions of common compilers support (parts of) which C++ standards.
Previous: C++ Support, Up: Other Options [Contents][Index]
There is support for using link-time optimization (LTO) if the toolchain supports it: configure with flag --enable-lto.
Whether toolchains support LTO is often unclear: all of the C compiler,
the Fortran compiler and linker have to support it, and support it by
the same mechanism (so mixing compiler families may not work and a
non-system linker such as gold
14 may be needed). It has been tested
recently on Linux with gcc
/gfortran
8.x and later:
that needed setting
AR=gcc-ar RANLIB=gcc-ranlib
(e.g. in config.site). For non-system compilers or if those wrappers have not been installed one may need something like
AR="ar --plugin=/path/to/liblto_plugin.so" RANLIB="ranlib --plugin=/path/to/liblto_plugin.so"
amd it may be needed to set NM
similarly.
Unfortunately --enable-lto may be accepted but silently do nothing if some of the toolchain does not support LTO: that has happened on macOS.
When LTO is enabled it is used for compiled code in packages (including the recommended packages) unless the flag --enable-lto=R is used. With sufficient diagnostic flags (e.g. -Wall in GCC) this can flag inconsistencies between source files in a package.
Option --enable-lto=check in addition builds the BLAS and LAPACK support as static libraries containing intermediate-level code that LTO will compile for all objects linked against these libraries. This checks the consistency of calls to BLAS/LAPACK both in R itself and in any packages installed using the build. (This is unlikely to work in conjunction with non-default options for BLAS and LAPACK, and ‘linking’ against these libraries may be very slow. Note that the static libraries may need to be re-compiled for even a minor update to the compiler.) It also checks consistency of LINPACK calls from package to R. NB: as its name suggests, this option is intended only for checking installation of R and packages: it includes these library routines (those called directly and all they depend on) in each package.
Under some circumstances and for a few packages, the PIC flags have needed overriding on Linux with GCC 9: e.g in config.site:
CPICFLAGS=-fPIC CXXPICFLAGS=-fPIC CXX11PICFLAGS=-fPIC CXX14PICFLAGS=-fPIC CXX17PICFLAGS=-fPIC FPICFLAGS=-fPIC
LTO support was added in 2011 for gcc
4.5.x on Linux but was
little used before 2019.
With gcc
/gfortran
9.x and later15 this will flag inconsistencies in calls to Fortran
subroutines/functions, both between Fortran source files and between
Fortran and C/C++. gfortran
9.2 and later can help
understanding these by extracting C prototypes from Fortran source files
with its -fc-prototypes-external option, e.g. that (at the
time of writing) Fortran LOGICAL
corresponds to
int_least32_t *
.
Previous: Other Options, Up: Installing R under Unix-alikes [Contents][Index]
Full post-installation testing is possible only if the test files have been installed with
make install-tests
which populates a tests directory in the installation.
If this has been done, two testing routes are available. The first is
to move to the home directory of the R installation (as given by
R RHOME
or from R as R.home()
) and run
cd tests ## followed by one of ../bin/R CMD make check ../bin/R CMD make check-devel ../bin/R CMD make check-all
and other useful targets are test-BasePackages
and
test-Recommended
to run tests of the standard and recommended
packages (if installed) respectively.
This re-runs all the tests relevant to the installed R (including for example the code in the package vignettes), but not for example the ones checking the example code in the manuals nor making the standalone Rmath library. This can occasionally be useful when the operating environment has been changed, for example by OS updates or by substituting the BLAS (see Shared BLAS).
Parallel checking of packages may be possible: set the environment
variable TEST_MC_CORES
to the maximum number of processes to be
run in parallel. This affects both checking the package examples (part
of make check
) and package sources (part of make
check-devel
and make check-recommended
). It does require a
make
command which supports the make -j n
option: most do but on Solaris you need to select GNU make
or
dmake
.
Alternatively, the installed R can be run, preferably with --vanilla. Then
Sys.setenv(LC_COLLATE = "C", LC_TIME = "C", LANGUAGE = "en") tools::testInstalledBasic("both") tools::testInstalledPackages(scope = "base") tools::testInstalledPackages(scope = "recommended")
runs the basic tests and then all the tests on the standard and recommended packages. These tests can be run from anywhere: the basic tests write their results in the tests folder of the R home directory and run fewer tests than the first approach: in particular they do not test things which need Internet access—that can be tested by
tools::testInstalledBasic("internet")
These tests work best if diff
(in Rtools*.exe for
Windows users) is in the path.
It is possible to test the installed packages (but not their
package-specific tests) by testInstalledPackages
even if
make install-tests
was not run.
Note that the results may depend on the language set for times and messages: for maximal similarity to reference results you may want to try setting (before starting the R session)
LANGUAGE=en
and use a UTF-8 or Latin-1 locale.
Next: Installing R under macOS, Previous: Installing R under Unix-alikes, Up: Top [Contents][Index]
The bin/windows directory of a CRAN site contains binaries for a base distribution and a large number of add-on packages from CRAN to run on 32- or 64-bit Windows (Windows 7 and later are tested; XP is known to fail some tests) on ‘ix86’ and ‘x86_64’ CPUs.
Your file system must allow long file names (as is likely except perhaps for some network-mounted systems). If it does not also support conversion to short name equivalents (a.k.a. DOS 8.3 names), then R must be installed in a path that does not contain spaces.
Installation is via the installer R-4.0.2-win.exe. Just double-click on the icon and follow the instructions. When installing on a 64-bit version of Windows the options will include 32- or 64-bit versions of R (and the default is to install both). You can uninstall R from the Control Panel.
You will be asked to choose a language for installation: that choice applies to both installation and un-installation but not to running R itself.
See the R Windows FAQ for more details on the binary installer.
• Building from source | ||
• Checking the build | ||
• Testing a Windows Installation |
Next: Checking the build, Previous: Installing R under Windows, Up: Installing R under Windows [Contents][Index]
It is possible to use other toolchains (including that used for R 3.6.3, ‘MSYS2’ and ‘MXE’ (M cross environment)) to build R, but this manual only documents that used for binary distributions of R 4.0.x.
• The Windows toolset | ||
• LaTeX on Windows |
Next: LaTeX on Windows, Previous: Building from source, Up: Building from source [Contents][Index]
The binary distribution of R is currently built with tools distributed in rtools40-x86_64.exe. The webpage https://cran.r-project.org/bin/windows/Rtools/ describes how to install the toolset and has links to example scripts to build and package R.
This toolset was modified (by Jeroen Ooms) from the ’MSYS2’ project, which uses compilers (GCC version 8.3.0) and runtime libraries from the ‘Mingw-w64’ project16 and provides a package manager (‘pacman’) for components and additional libraries.
The toolsets used for 64-bit Windows from 2008–20 were based on Mingw-w64. The assistance of Yu Gong at a crucial step in porting R to Mingw-w64 is gratefully acknowledged, as well as help from Kai Tietz, the lead developer of the Mingw-w64 project.
Previous: The Windows toolset, Up: Building from source [Contents][Index]
Both building R and checking packages need a distribution of LaTeX
installed, with the directory containing pdflatex
on the path.
The ‘MiKTeX’ (http://www.miktex.org/) distribution of LaTeX is that used on CRAN. This can be set up to install extra packages ‘on the fly’ (without asking), which is the simplest way to use it. The ‘basic’ version of ‘MiKTeX’ will need to add some packages.17 In any case ensure that the inconsolata package is installed—you can check with the ‘MiKTeX’ Package Manager.
It is also possible to use the TeX Live distribution from https://www.tug.org/texlive/. (The CRAN package tinytex can install and manage a subset of TeX Live.)
Next: Testing a Windows Installation, Previous: Building from source, Up: Installing R under Windows [Contents][Index]
You can test a build by running
make check
The recommended packages can be checked by
make check-recommended
Other levels of checking are
make check-devel
for a more thorough check of the R functionality, and
make check-all
for both check-devel
and check-recommended
.
If a test fails, there will almost always be a .Rout.fail file in the directory being checked (often tests/Examples or tests): examine the file to help pinpoint the problem.
Parallel checking of package sources (part of make check-devel
and make check-recommended
) is possible: see the environment
variable TEST_MC_CORES
to the maximum number of processes to be
run in parallel.
Previous: Checking the build, Up: Installing R under Windows [Contents][Index]
The Windows installer contains a set of test files used when building R.
The toolset is not needed to run these tests, but more comprehensive
analysis of errors will be given if diff
is in the path (and
errorsAreFatal = FALSE
is then not needed below).
Launch either Rgui
or Rterm
, preferably with
--vanilla. Then run
Sys.setenv(LC_COLLATE = "C", LANGUAGE = "en") library("tools") testInstalledBasic("both") testInstalledPackages(scope = "base", errorsAreFatal = FALSE) testInstalledPackages(scope = "recommended", errorsAreFatal = FALSE)
runs the basic tests and then all the tests on the standard and
recommended packages. These tests can be run from anywhere: they write
some of their results in the tests folder of the R home
directory (as given by R.home()
), and hence may need to be run
under the account used to install R.
The results of example(md5sums)
when testing tools will
differ from the reference output as some files are installed with
Windows’ CRLF line endings.
Next: Running R, Previous: Installing R under Windows, Up: Top [Contents][Index]
(‘macOS’ was known as ‘OS X’ from 2012–2016 and as ‘Mac OS X’ before that.)
The front page of a CRAN site has a link ‘Download R for (Mac) OS X’. Click on that, then download the file R-4.0.2.pkg and install it. This runs on macOS 10.13 and later (High Sierra, Mojave, Catalina, …).
Installers for R-patched and R-devel are usually available from https://mac.R-project.org. (Some of these packages are unsigned/not notarized: to install those Control/right/two-finger click, select ‘Open With’ and ‘Installer’.)
For some older versions of the OS you can in principle (it is little tested) install R from the sources (see macOS).
It is important that if you use a binary installer package that your OS is fully updated: look at ‘Updates’ from the ‘App Store’ (‘Software Update’ in ’System Preferences’ on Catalina) to be sure. (If using XQuartz, check that is current.)
To install, just double-click on the icon of the file you downloaded. At the ‘Installation Type’ stage, note the option to ‘Customize’. This currently shows four components: everyone will need the ‘R Framework’ component: the remaining components are optional. (The ‘Tcl/Tk’ component is needed to use package tcltk. The ‘Texinfo’ component is only needed by those installing source packages or R from its sources.)
This is an Apple Installer package. If you encounter any problem during the installation, please check the Installer log by clicking on the “Window” menu and item “Installer Log”. The full output (select “Show All Log”) is useful for tracking down problems. Note the the installer is clever enough to try to upgrade the last-installed version of the application where you installed it (which may not be where you want this time …).
Various parts of the build require XQuartz to be installed: see
https://xquartz.macosforge.org/. These include the tcltk
package and the X11
device: attempting to use these without
XQuartz will remind you. Also for the cairographics-based devices
(which are not often used on macOS) such as png(type = "cairo")
.
If you update your macOS version, you should re-install R (and perhaps XQuartz): the installer may tailor the installation to the current version of the OS.
For building R from source, see macOS.
• Running R under macOS | ||
• Uninstalling under macOS | ||
• Multiple versions |
Next: Uninstalling under macOS, Previous: Installing R under macOS, Up: Installing R under macOS [Contents][Index]
There are two ways to run R on macOS from a CRAN binary distribution.
There is a GUI console normally installed with the R icon in /Applications which you can run by double-clicking (e.g. from Launchpad or Finder). (If you cannot find it there it was possibly installed elsewhere so try searching for it in Spotlight.) This is usually referred to as R.APP to distinguish it from command-line R: its user manual is currently part of the macOS FAQ at https://cran.r-project.org/bin/macosx/RMacOSX-FAQ.html and can be viewed from R.APP’s ‘Help’ menu.
You can run command-line R and Rscript
from a
Terminal18 so these can be
typed as commands like any other Unix-alike: see the next chapter of
this manual. There are some small differences which may surprise users
of R on other platforms, notably the default location of the personal
library directory (under ~/Library/R,
e.g. ~/Library/R/4.0/library), and that warnings, messages and
other output to stderr are highlighted in bold.
It has been reported that running R.APP may fail if no preferences are stored, so if it fails when launched for the very first time, try it again (the first attempt will store some preferences).
Users of R.APP need to be aware of the ‘App Nap’ feature (https://developer.apple.com/library/mac/releasenotes/MacOSX/WhatsNewInOSX/Articles/MacOSX10_9.html) which can cause R tasks to appear to run very slowly when not producing output in the console. Here are ways to avoid it:
defaults write org.R-project.R NSAppSleepDisabled -bool YES
(see https://developer.apple.com/library/mac/releasenotes/MacOSX/WhatsNewInOSX/Articles/MacOSX10_9.html).
Using the X11
device or the X11-based versions of View()
and edit()
for data frames and matrices (the latter are the
default for command-line R but not R.APP) requires an X sub-system
to be installed: see macOS. So do the tcltk package and
some third-party packages.
Next: Multiple versions, Previous: Running R under macOS, Up: Installing R under macOS [Contents][Index]
R for macOS consists of two parts: the GUI (R.APP) and the R framework. Un-installation is as simple as removing those folders (e.g. by dragging them onto the Trash aka Bin). The typical installation will install the GUI into the /Applications/R.app folder and the R framework into the /Library/Frameworks/R.framework folder. The links to R and Rscript in /usr/local/bin should also be removed.
If you want to get rid of R more completely using a Terminal, simply run:
sudo rm -Rf /Library/Frameworks/R.framework /Applications/R.app \ /usr/local/bin/R /usr/local/bin/Rscript
The installation consists of up to four Apple packages:19 org.r-project.R.fw.pkg
, org.r-project.R.GUI.pkg
,
org.r-project.x86_64.tcltk.x11
and
org.r-project.x86_64.texinfo
. You can use pkgutil --forget
if you want the Apple Installer to forget about the package without
deleting its files (useful for the R framework when installing
multiple R versions in parallel), or after you have deleted the
files.
Uninstalling the Tcl/Tk or Texinfo components (which are installed under /usr/local) is not as simple. You can list the files they installed in a Terminal by
pkgutil --files org.r-project.x86_64.tcltk.x11 pkgutil --files org.r-project.x86_64.texinfo
These are paths relative to /, the root of the file system.
Previous: Uninstalling under macOS, Up: Installing R under macOS [Contents][Index]
The installer will remove any previous version20 of
the R framework which it finds installed. This can be avoided by
using pkgutil --forget
(see the previous section). However,
note that different versions are installed under
/Library/Frameworks/R.framework/Versions as 4.0,
3.6 and so on, so it is not possible to have different
‘3.x.y’ or ‘4.x.y’ versions installed for the same ‘x’.
A version of R can be run directly from the command-line as e.g.
/Library/Frameworks/R.framework/Versions/4.0/Resources/bin/R
However, R.APP will always run the ‘current’ version, that is the last
installed version. A small utility, Rswitch.app
(available at
https://mac.R-project.org/#other: it is 32-bit so not usable on
Catalina), can be used to change the ‘current’ version. This is of
limited use as R.APP is compiled against a particular version of R
and will likely crash if switched to an earlier version. This may allow
you to install a development version of R (de-selecting R.APP) and
then switch back to the release version.
Next: Add-on packages, Previous: Installing R under macOS, Up: Top [Contents][Index]
How to start R and what command-line options are available is discussed in Invoking R in An Introduction to R.
You should ensure that the shell has set adequate resource limits: R
expects a stack size of at least 8MB and to be able to open at least 256
file descriptors. (Any modern OS should have default limits at least as
large as these, but apparently NetBSD may not. Use the shell command
ulimit
(sh
/bash
) or limit
(csh
/tcsh
) to check.) For some
compilers21 and packages
a larger stack size has been needed: 20-25MB has sufficed to date.
R makes use of a number of environment variables, the default values
of many of which are set in file R_HOME/etc/Renviron (there
are none set by default on Windows and hence no such file). These are
set at configure
time, and you would not normally want to
change them – a possible exception is R_PAPERSIZE
(see Setting paper size). The paper size will be deduced from the ‘LC_PAPER’
locale category if it exists and R_PAPERSIZE
is unset, and this
will normally produce the right choice from ‘a4’ and ‘letter’
on modern Unix-alikes (but can always be overridden by setting
R_PAPERSIZE
).
Various environment variables can be set to determine where R creates
its per-session temporary directory. The environment variables
TMPDIR
, TMP
and TEMP
are searched in turn and the
first one which is set and points to a writable area is used. If none
do, the final default is /tmp on Unix-alikes and the value of
R_USER
on Windows. The path should be an absolute path not
containing spaces (and it is best to avoid non-alphanumeric characters
such as +
).
Some Unix-alike systems are set up to remove files and directories
periodically from /tmp, for example by a cron
job
running tmpwatch
. Set TMPDIR
to another directory
before starting long-running jobs on such a system.
Note that TMPDIR
will be used to execute configure
scripts when installing packages, so if /tmp has been mounted as
‘noexec’, TMPDIR
needs to be set to a directory from which
execution is allowed.
Next: Internationalization, Previous: Running R, Up: Top [Contents][Index]
• Default packages | ||
• Managing libraries | ||
• Installing packages | ||
• Updating packages | ||
• Removing packages | ||
• Setting up a package repository | ||
• Checking installed source packages |
It is helpful to use the correct terminology. A package is
loaded from a library by the function library()
. Thus a
library is a directory containing installed packages; the main library
is R_HOME/library, but others can be used, for example by
setting the environment variable R_LIBS
or using the R function
.libPaths()
. To avoid any confusion you will often see a library
directory referred to as a ‘library tree’.
Next: Managing libraries, Previous: Add-on packages, Up: Add-on packages [Contents][Index]
The set of packages loaded on startup is by default
> getOption("defaultPackages") [1] "datasets" "utils" "grDevices" "graphics" "stats" "methods"
(plus, of course, base) and this can be changed by setting the
option in startup code (e.g. in ~/.Rprofile). It is initially
set to the value of the environment variable R_DEFAULT_PACKAGES
if
set (as a comma-separated list). Setting R_DEFAULT_PACKAGES=NULL
ensures that only package base is loaded.
Changing the set of default packages is normally used to reduce the set
for speed when scripting: in particular not using methods will
reduce the start-up time by a factor of up to two. But it can also be
used to customize R, e.g. for class use. Rscript
also checks the environment variable R_SCRIPT_DEFAULT_PACKAGES
;
if set, this takes precedence over R_DEFAULT_PACKAGES
.
Next: Installing packages, Previous: Default packages, Up: Add-on packages [Contents][Index]
R packages are installed into libraries, which are directories in the file system containing a subdirectory for each package installed there.
R comes with a single library, R_HOME/library which is the value of the R object ‘.Library’ containing the standard and recommended22 packages. Both sites and users can create others and make use of them (or not) in an R session. At the lowest level ‘.libPaths()’ can be used to add paths to the collection of libraries or to report the current collection.
R will automatically make use of a site-specific library
R_HOME/site-library if this exists (it does not in a
vanilla R installation). This location can be overridden by
setting23 ‘.Library.site’ in
R_HOME/etc/Rprofile.site, or (not recommended) by setting
the
environment variable R_LIBS_SITE
. Like ‘.Library’, the
site libraries are always included by ‘.libPaths()’.
Users can have one or more libraries, normally specified by the
environment variable R_LIBS_USER
. This has a default value (to
see it, use ‘Sys.getenv("R_LIBS_USER")’ within an R session),
but that is only used if the corresponding directory actually exists
(which by default it will not).
Both R_LIBS_USER
and R_LIBS_SITE
can specify multiple
library paths, separated by colons (semicolons on Windows).
Next: Updating packages, Previous: Managing libraries, Up: Add-on packages [Contents][Index]
• Windows packages | ||
• macOS packages | ||
• Customizing package compilation | ||
• Multiple sub-architectures | ||
• Byte-compilation | ||
• External software |
Packages may be distributed in source form or compiled binary form. Installing source packages which contain C/C++/Fortran code requires that compilers and related tools be installed. Binary packages are platform-specific and generally need no special tools to install, but see the documentation for your platform for details.
Note that you may need to specify implicitly or explicitly the library to which the package is to be installed. This is only an issue if you have more than one library, of course.
Ensure that the environment variable TMPDIR
is either unset (and
/tmp exists and can be written in and executed from) or is the
absolute path to a valid temporary directory, not containing spaces.
For most users it suffices to call ‘install.packages(pkgname)’ or its GUI equivalent if the intention is to install a CRAN package and internet access is available.24 On most systems ‘install.packages()’ will allow packages to be selected from a list box (typically with thousands of items).
To install packages from source on a Unix-alike use in a terminal
R CMD INSTALL -l /path/to/library pkg1 pkg2 …
The part ‘-l /path/to/library’ can be omitted, in which case the
first library of a normal R session is used (that shown by
.libPaths()[1]
).
There are a number of options available: use R CMD INSTALL --help
to see the current list.
Alternatively, packages can be downloaded and installed from within
R. First choose your nearest CRAN mirror using
chooseCRANmirror()
. Then download and install packages
pkg1 and pkg2 by
> install.packages(c("pkg1", "pkg2"))
The essential dependencies of the specified packages will also be fetched.
Unless the library is specified (argument lib
) the first library
in the library search path is used: if this is not writable, R will
ask the user (in an interactive session) if the default personal library
should be created, and if allowed to will install the packages there.
If you want to fetch a package and all those it depends on (in any way) that are not already installed, use e.g.
> install.packages("Rcmdr", dependencies = TRUE)
install.packages
can install a source package from a local
.tar.gz file (or a URL to such a file) by setting argument
repos
to NULL
: this will be selected automatically if the
name given is a single .tar.gz file.
install.packages
can look in several repositories, specified as a
character vector by the argument repos
: these can include a
CRAN mirror, Bioconductor, R-forge, rforge.net,
local archives, local files, …). Function
setRepositories()
can select amongst those repositories that the
R installation is aware of.
Naive users sometimes forget that as well as installing a package, they
have to use library
to make its functionality available.
Next: macOS packages, Previous: Installing packages, Up: Installing packages [Contents][Index]
What install.packages
does by default is different on Unix-alikes
(except macOS) and Windows. On Unix-alikes it consults the list of
available source packages on CRAN (or other
repository/ies), downloads the latest version of the package sources,
and installs them (via R CMD INSTALL
). On Windows it looks (by
default) first at the list of binary versions of packages
available for your version of R and downloads the latest versions (if
any). If no binary version is available or the source version is newer,
it will install the source versions of packages without compiled
C/C++/Fortran code, and offer to do so for those with, if make
is available (and this can be tuned by option
"install.packages.compile.from.source"
).
On Windows install.packages
can also install a binary package
from a local zip file (or the URL of such a file) by setting
argument repos
to NULL
. Rgui.exe
has a menu
Packages
with a GUI interface to install.packages
,
update.packages
and library
.
Windows binary packages for R are distributed as a single binary containing either or both architectures (32- and 64-bit).
R CMD INSTALL
works in Windows to install source packages. No
additional tools are needed if the package does not contain compiled
code, and install.packages(type="source")
will work for such
packages. Those with compiled code need the tools (see The Windows toolset) to be on the path: this can be set from within an R session
by something like
Sys.setenv(PATH=paste("C:\\rtools40\\usr\\bin", Sys.getenv("PATH"), sep=";"))
Occasional permission problems after unpacking source packages have been
seen on some systems: these have been circumvented by setting the
environment variable R_INSTALL_TAR
to ‘tar.exe’.
If you have only a source package that is known to work with current R and just want a binary Windows build of it, you could make use of the building service offered at https://win-builder.r-project.org/.
For almost all packages R CMD INSTALL
will attempt to install
both 32- and 64-bit builds of a package if run from a 32/64-bit install
of R. It will report success if the installation of the architecture
of the running R
succeeded, whether or not the other
architecture was successfully installed. The exceptions are packages
with a non-empty configure.win script or which make use of
src/Makefile.win. If configure.win does something
appropriate to both architectures use25 option
--force-biarch: otherwise R CMD INSTALL
--merge-multiarch
can be applied to a source tarball to merge separate
32- and 64-bit installs. (This can only be applied to a tarball, and
will only succeed if both installs succeed.)
If you have a package without compiled code and no Windows-specific help, you can zip up an installation on another OS and install from that zip file on Windows. However, such a package can be installed from the sources on Windows without any additional tools.
Next: Customizing package compilation, Previous: Windows packages, Up: Installing packages [Contents][Index]
On macOS install.packages
works as it does on
other Unix-alike systems, but there is an additional type
mac.binary
(available for the CRAN distribution but not
when compiling R from source) which can be passed to
install.packages
in order to download and install binary packages
from a suitable repository. These binary package files for macOS have
the extension ‘.tgz’. The R.APP GUI provides menus for
installation of either binary or source packages, from CRAN or
local files.
On R builds using binary packages, the default is type both
:
this looks first at the list of binary packages available for your
version of R and installs the latest versions (if any). If no binary
version is available or the source version is newer, it will install the
source versions of packages without compiled C/C++/Fortran code and offer
to do so for those with, if make
is available.
Note that most binary packages which include compiled code are tied to a particular series (e.g. R 4.0.x or 3.6.x) of R.
Installing source packages which do not contain compiled code should
work with no additional tools. For others you will need the
‘Command Line Tools’ for Xcode
and compilers which match those
used to build R: see macOS.
Package rJava and those which depend on it need a Java runtime installed and several packages need X11 installed, including those using Tk. See macOS and Java (macOS).
Tcl/Tk extensions BWidget
and Tktable
used to be
distributed with R but no longer are.
A few of the binary packages need other software to be installed on your system. In particular packages using Gtk+ (RGtk2, cairoDevice and those that depend on them) need the GTK framework installed from https://mac.R-project.org/libs/: the appropriate version at the time of writing was https://mac.R-project.org/libs/GTK_2.24.17-X11.pkg
The default compilers specified are shown in file
/Library/Frameworks/R.framework/Resources/etc/Makeconf. At
the time of writing those settings assumed that the C, Fortran and C++
compilers were on the path, using gfortran
8.2.0 (see
macOS). The settings can be changed, either by editing that file
or in a file such as ~/.R/Makevars (see the next section).
Entries which may need to be changed include ‘CC’, ‘CXX’,
‘FC’, ‘FLIBS’ and the corresponding flags, and perhaps
‘CXXCPP’, ‘DYLIB_LD’, ‘MAIN_LD’, ‘SHLIB_CXXLD’ and
‘SHLIB_LD’, as well as the ‘CXX11’, ‘CXX14’,
‘CXX17’ and ‘CXX20’ variants
So for example on Mojave or Catalina you could select a specific
non-Apple build of clang
for both C and C++ with extensive
checking by having in ~/.R/Makevars
CC=/usr/local/clang/bin/clang -isysroot /Library/Developer/CommandLineTools/SDKs/MacOSX.sdk CXX=/usr/local/clang/bin/clang++ -isysroot /Library/Developer/CommandLineTools/SDKs/MacOSX.sdk CXX11 = $CXX CXX14 = $CXX CXX17 = $CXX CXX20 = $CXX CFLAGS = -g -O2 -Wall -pedantic -Wconversion -Wno-sign-conversion CXXFLAGS = -g -O2 -Wall -pedantic -Wconversion -Wno-sign-conversion CXX11FLAGS = $CXXFLAGS CXX14FLAGS = $CXXFLAGS CXX17FLAGS = $CXXFLAGS CXX20FLAGS = $CXXFLAGS
(long lines split for the manual only) and gfortran
by
FC = /usr/local/gfortran/bin/gfortran FLIBS = -L/usr/local/gfortran/lib/gcc/x86_64-apple-darwin18/8.2.0 -L/usr/local/gfortran/lib -lgfortran -lquadmath -lm
(with lines broken here for legibility). If that clang
build
supports OpenMP, you can add
SHLIB_OPENMP_CFLAGS = -fopenmp SHLIB_OPENMP_CXXFLAGS = -fopenmp
to compile OpenMP-using packages. It will also be necessary to arrange
for the libomp.dylib
library to be found at both install time and run
time, for example by copying/linking it somewhere that is searched such
as /usr/local/lib.
Apple includes many Open Source libraries in macOS but increasingly
without the corresponding headers (not even in Xcode nor the Command
Line Tools): they are often rather old versions. If installing packages
from source using them it is usually easiest to install a
statically-linked up-to-date copy of the Open Source package from its
sources or from https://mac.R-project.org/libs-4. But sometimes
it is desirable/necessary to use Apple’s dynamically linked library, in
which case appropriate headers could be extracted from the
sources26 available via
https://opensource.apple.com – this has been used for
OpenSSL
and iodbc
.
Next: Multiple sub-architectures, Previous: macOS packages, Up: Installing packages [Contents][Index]
The R system and package-specific compilation flags can be overridden
or added to by setting the appropriate Make variables in the personal
file HOME/.R/Makevars-R_PLATFORM (but
HOME/.R/Makevars.win or HOME/.R/Makevars.win64
on Windows), or if that does not exist, HOME/.R/Makevars,
where ‘R_PLATFORM’ is the platform for which R was built, as
available in the platform
component of the R variable
R.version
. The path to an alternative personal
file27 can be specified via the environment variable
R_MAKEVARS_USER
.
Package developers are encouraged to use this mechanism 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 or for clang
.
Note that this mechanism can also be used when it necessary to change the optimization level whilst installing a particular package. For example
## for C code CFLAGS = -g -O -mtune=native ## for C++ code CXXFLAGS = -g -O -mtune=native ## for fixed-form Fortran code FFLAGS = -g -O -mtune=native
Another use is to override the settings in a binary installation of R. For example, to use a different Fortran compiler on macOS
FC = /usr/local/gfortran/bin/gfortran FLIBS = -L/usr/local/gfortran/lib/gcc/x86_64-apple-darwin16/6.3.0 -L/usr/local/gfortran/lib -lgfortran -lquadmath -lm
(line split for legibility here).
There is also provision for a site-wide Makevars.site file under
R_HOME/etc (in a sub-architecture-specific directory if
appropriate). This is read immediately after Makeconf, and the
path to an alternative file can be specified by environment variable
R_MAKEVARS_SITE
.
Note that these mechanisms do not work with packages which fail to pass settings down to sub-makes, perhaps reading etc/Makeconf in makefiles in subdirectories. Fortunately such packages are unusual.
Next: Byte-compilation, Previous: Customizing package compilation, Up: Installing packages [Contents][Index]
When installing packages from their sources, there are some extra considerations on installations which use sub-architectures. These are commonly used on Windows but can in principle be used on other platforms.
When a source package is installed by a build of R which supports multiple sub-architectures, the normal installation process installs the packages for all sub-architectures. The exceptions are
where there is an configure script, or a file src/Makefile.
where there is a non-empty configure.win script, or a file src/Makefile.win (with some exceptions where the package is known to have an architecture-independent configure.win, or if --force-biarch or field ‘Biarch’ in the DESCRIPTION file is used to assert so).
In those cases only the current architecture is installed. Further sub-architectures can be installed by
R CMD INSTALL --libs-only pkg
using the path to R
or R --arch
to select the
additional sub-architecture. There is also R CMD INSTALL
--merge-multiarch
to build and merge the two architectures, starting
with a source tarball.
Next: External software, Previous: Multiple sub-architectures, Up: Installing packages [Contents][Index]
As from R 3.6.0, all packages are by default byte-compiled.
Byte-compilation can be controlled on a per-package basis by the ‘ByteCompile’ field in the DESCRIPTION file.
Previous: Byte-compilation, Up: Installing packages [Contents][Index]
Some R packages contain compiled code which links to external software libraries. Unless the external library is statically linked (which is done as much as possible for binary packages on Windows and macOS), the libraries have to be found when the package is loaded and not just when it is installed. How this should be done depends on the OS (and in some cases the version).
For Unix-alikes except macOS the primary mechanism is the ld.so
cache controlled by ldconfig
: external dynamic libraries
recorded in that cache will be found. Standard library locations will
be covered by the cache, and well-designed software will add its
locations (as for example openmpi does on Fedora). The secondary
mechanism is to consult the environment variable LD_LIBRARY_PATH
.
The R script controls that variable, and sets it to the concatenation
of R_LD_LIBRARY_PATH
, R_JAVA_LD_LIBRARY_PATH
and the
environment value of LD_LIBRARY_PATH
. The first two have defaults
which are normally set when R is installed (but can be overridden in
the environment) so LD_LIBRARY_PATH
is the best choice for a user
to set.
On macOS the primary mechanism is to embed the absolute path to
dependent dynamic libraries into an object when it is compiled. Few
R packages arrange to do so, but it can be edited28 via
install_name_tool
— that only deals with direct dependencies
and those would also need to be compiled to include the absolute paths
of their dependencies. If the choice of absolute path is to be deferred
to load time, how they are resolved is described in man dyld
:
the role of LD_LIBRARY_PATH
is replaced on macOS by
DYLD_LIBRARY_PATH
and DYLD_FALLBACK_LIBRARY_PATH
. Running
R CMD otool -L
on the package shared object will show where
(if anywhere) its dependencies are
resolved. DYLD_FALLBACK_LIBRARY_PATH
is preferred (and it is that
which is manipulated by the R script), but as from 10.11 (‘El
Capitan’) the default behaviour had been changed for security reasons to
discard these environment variables when invoking a shell script (and
R is a shell script). That makes the only portable option to set
R_LD_LIBRARY_PATH
in the environment, something like
export R_LD_LIBRARY_PATH="`R RHOME`/lib:/opt/local/lib"
The precise rules for where Windows looks for DLLs are complex and
depend on the version of Windows. But for present purposes the main
solution is to put the directories containing the DLLs the package
links to (and any those DLLs link to) on the PATH
. 64-bit
versions of Windows will ignore 32-bit DLLs from 64-bit R and
vice versa.
The danger with any of the methods which involve setting environment
variables is of inadvertently masking a system library. This is less
for DYLD_FALLBACK_LIBRARY_PATH
and for appending to
PATH
on Windows (as it should already contain the system library
paths).
Next: Removing packages, Previous: Installing packages, Up: Add-on packages [Contents][Index]
The command update.packages()
is the simplest way to ensure that
all the packages on your system are up to date. It downloads the list
of available packages and their current versions, compares it with those
installed and offers to fetch and install any that have later versions
on the repositories.
An alternative interface to keeping packages up-to-date is provided by
the command packageStatus()
, which returns an object with
information on all installed packages and packages available at multiple
repositories. The print
and summary
methods give an
overview of installed and available packages, the upgrade
method
offers to fetch and install the latest versions of outdated packages.
One sometimes-useful additional piece of information that
packageStatus()
returns is the status of a package, as
"ok"
, "upgrade"
or "unavailable"
(in the currently
selected repositories). For example
> inst <- packageStatus()$inst > inst[inst$Status != "ok", c("Package", "Version", "Status")] Package Version Status Biobase Biobase 2.8.0 unavailable RCurl RCurl 1.4-2 upgrade Rgraphviz Rgraphviz 1.26.0 unavailable rgdal rgdal 0.6-27 upgrade
Next: Setting up a package repository, Previous: Updating packages, Up: Add-on packages [Contents][Index]
Packages can be removed in a number of ways. From a command prompt they can be removed by
R CMD REMOVE -l /path/to/library pkg1 pkg2 …
From a running R process they can be removed by
> remove.packages(c("pkg1", "pkg2"), lib = file.path("path", "to", "library"))
Finally, one can just remove the package directory from the library.
Next: Checking installed source packages, Previous: Removing packages, Up: Add-on packages [Contents][Index]
Utilities such as install.packages
can be pointed at any
CRAN-style repository, and R users may want to set up their
own. The ‘base’ of a repository is a URL such as
http://www.stats.ox.ac.uk/pub/RWin: this must be an URL scheme
that download.packages
supports (which also includes
‘https://’, ‘ftp://’ and ‘file://’). Under that base URL
there should be directory trees for one or more of the following types
of package distributions:
"source"
: located at src/contrib and containing
.tar.gz files. Other forms of compression can be used, e.g.
.tar.bz2 or .tar.xz files. Complete repositories contain
the sources corresponding to any binary packages, and in any case it is
wise to have a src/contrib area with a possibly empty
PACKAGES file.
"win.binary"
: located at bin/windows/contrib/x.y for
R versions x.y.z and containing .zip files for Windows.
"mac.binary"
: located at
bin/macosx/contrib/4.y for the CRAN builds for
macOS for R versions 4.y.z, containing
.tgz files.
"mac.binary.el-capitan"
: located at
bin/macosx/el-capitan/contrib/3.y for the CRAN
builds for R versions 3.y.z, containing .tgz files.
Each terminal directory must also contain a PACKAGES file. This
can be a concatenation of the DESCRIPTION files of the packages
separated by blank lines, but only a few of the fields are needed. The
simplest way to set up such a file is to use function
write_PACKAGES
in the tools package, and its help explains
which fields are needed. Optionally there can also be
PACKAGES.rds and PACKAGES.gz files, downloaded in
preference to PACKAGES. (If you have a mis-configured server
that does not report correctly non-existent files you may need these
files.)
To add your repository to the list offered by setRepositories()
,
see the help file for that function.
Incomplete repositories are better specified via a
contriburl
argument than via being set as a repository.
A repository can contain subdirectories, when the descriptions in the PACKAGES file of packages in subdirectories must include a line of the form
Path: path/to/subdirectory
—once again write_PACKAGES
is the simplest way to set this up.
Previous: Setting up a package repository, Up: Add-on packages [Contents][Index]
It can be convenient to run R CMD check
on an installed
package, particularly on a platform which uses sub-architectures. The
outline of how to do this is, with the source package in directory
pkg (or a tarball filename):
R CMD INSTALL -l libdir pkg > pkg.log 2>&1 R CMD check -l libdir --install=check:pkg.log pkg
Where sub-architectures are in use the R CMD check
line can be
repeated with additional architectures by
R --arch arch CMD check -l libdir --extra-arch --install=check:pkg.log pkg
where --extra-arch selects only those checks which depend on
the installed code and not those which analyse the sources. (If
multiple sub-architectures fail only because they need different
settings, e.g. environment variables, --no-multiarch may need
to be added to the INSTALL
lines.) On Unix-alikes the
architecture to run is selected by --arch: this can also be
used on Windows with R_HOME/bin/R.exe, but it is more usual
to select the path to the Rcmd.exe
of the desired
architecture.
So on Windows to install, check and package for distribution a source package from a tarball which has been tested on another platform one might use
.../bin/i386/Rcmd INSTALL -l libdir tarball --build > pkg.log 2>&1 .../bin/i386/Rcmd check -l libdir --extra-arch --install=check:pkg.log pkg .../bin/x64/Rcmd check -l libdir --extra-arch --install=check:pkg.log pkg
where one might want to run the second and third lines in a different shell with different settings for environment variables and the path (to find external software, notably for Gtk+).
R CMD INSTALL
can do a i386
install and then add the
x64
DLL from a single command by
R CMD INSTALL --merge-multiarch -l libdir tarball
and --build can be added to zip up the installation.
Next: Choosing between 32- and 64-bit builds, Previous: Add-on packages, Up: Top [Contents][Index]
Internationalization refers to the process of enabling support for many human languages, and localization to adapting to a specific country and language.
Current builds of R support all the character sets that the
underlying OS can handle. These are interpreted according to the
current locale
, a sufficiently complicated topic to merit a
separate section. Note though that R has no built-in support for
right-to-left languages and bidirectional output, relying on the OS
services. For example, how character vectors in UTF-8 containing both
English digits and Hebrew characters are printed is OS-dependent (and
perhaps locale-dependent).
The other aspect of the internationalization is support for the translation of messages. This is enabled in almost all builds of R.
• Locales | ||
• Localization of messages |
Next: Localization of messages, Previous: Internationalization, Up: Internationalization [Contents][Index]
A locale is a description of the local environment of the user,
including the preferred language, the encoding of characters, the
currency used and its conventions, and so on. Aspects of the locale are
accessed by the R functions Sys.getlocale
and
Sys.localeconv
.
The system of naming locales is OS-specific. There is quite wide agreement on schemes, but not on the details of their implementation. A locale needs to specify
@latin
, @cyrillic
for Serbian, @iqtelif
)
or language dialect (e.g. @saaho
, a dialect of Afar, and
@bokmal
and @nynorsk
, dialects of Norwegian regarded by
some OSes as separate languages, no
and nn
).
R is principally concerned with the first (for translations) and third. Note that the charset may be deducible from the language, as some OSes offer only one charset per language.
• Locales under Unix-alikes | ||
• Locales under Windows | ||
• Locales under macOS |
Next: Locales under Windows, Previous: Locales, Up: Locales [Contents][Index]
Modern Linux uses the XPG29 locale specifications which have the form
‘en_GB’, ‘en_GB.UTF-8’, ‘aa_ER.UTF-8@saaho’,
‘de_AT.iso885915@euro’, the components being in the order listed
above. (See man locale
and locale -a
for more
details.) Similar schemes are used by most Unix-alikes: some (including
some distributions of Linux) use ‘.utf8’ rather than ‘.UTF-8’.
Note that whereas UTF-8 locales are nowadays almost universally used, locales such as ‘en_GB’ use 8-bit encodings for backwards compatibility.
Next: Locales under macOS, Previous: Locales under Unix-alikes, Up: Locales [Contents][Index]
Windows also uses locales, but specified in a rather less concise way. Most users will encounter locales only via drop-down menus, but more information and lists can be found by searching for ‘Windows language country strings’).
It offers only one encoding per language.
Some care is needed with Windows’ locale names. For example,
chinese
is Traditional Chinese and not Simplified Chinese as used
in most of the Chinese-speaking world.
Previous: Locales under Windows, Up: Locales [Contents][Index]
macOS supports locales in its own particular way, but the R GUI tries to
make this easier for users. See
https://developer.apple.com/library/content/documentation/MacOSX/Conceptual/BPInternational/
for how users can set their locales. As with Windows, end users will
generally only see lists of languages/territories. Users of R in a
terminal may need to set the locale to something like ‘en_GB.UTF-8’
if it defaults to ‘C’ (as it sometimes does when logging in
remotely and for batch jobs: note whether Terminal
sets the
LANG
environment variable is an (advanced) preference, but does so
by default).
Internally macOS uses a form similar to Linux: the main difference from
other Unix-alikes is that where a character set is not specified it is
assumed to be UTF-8
.
Previous: Locales, Up: Internationalization [Contents][Index]
The preferred language for messages is by default taken from the locale.
This can be overridden first by the setting of the environment variable
LANGUAGE
and then30
by the environment variables LC_ALL
, LC_MESSAGES
and
LANG
. (The last three are normally used to set the locale and so
should not be needed, but the first is only used to select the language
for messages.) The code tries hard to map locales to languages, but on
some systems (notably Windows) the locale names needed for the
environment variable LC_ALL
do not all correspond to XPG language
names and so LANGUAGE
may need to be set. (One example is
‘LC_ALL=es’ on Windows which sets the locale to Estonian and the
language to Spanish.)
It is usually possible to change the language once R is running
via (not Windows) Sys.setlocale("LC_MESSAGES",
"new_locale")
, or by setting an environment variable such as
LANGUAGE
, provided31 the language you are changing to can be output in
the current character set. But this is OS-specific, and has been known
to stop working on an OS upgrade.
Messages are divided into domains, and translations may be available for some or all messages in a domain. R makes use of the following domains.
R
for the C-level error and warning messages from the R
interpreter.
R-pkg
for the R stop
, warning
and
message
messages in each package, including R-base
for the
base package.
pkg
for the C-level messages in each package.
RGui
for the menus etc of the R for Windows GUI front-end.
Dividing up the messages in this way allows R to be extensible: as packages are loaded, their message translation catalogues can be loaded too.
R can be built without support for translations, but it is enabled by default.
R-level and C-level domains are subtly different, for example in the way strings are canonicalized before being passed for translation.
Translations are looked for by domain according to the currently specified language, as specifically as possible, so for example an Austrian (‘de_AT’) translation catalogue will be used in preference to a generic German one (‘de’) for an Austrian user. However, if a specific translation catalogue exists but does not contain a translation, the less specific catalogues are consulted. For example, R has catalogues for ‘en_GB’ that translate the Americanisms (e.g., ‘gray’) in the standard messages into English.32 Two other examples: there are catalogues for ‘es’, which is Spanish as written in Spain and these will by default also be used in Spanish-speaking Latin American countries, and also for ‘pt_BR’, which are used for Brazilian locales but not for locales specifying Portugal.
Translations in the right language but the wrong charset are made use of
by on-the-fly re-encoding. The LANGUAGE
variable (only) can be a
colon-separated list, for example ‘se:de’, giving a set of
languages in decreasing order of preference. One special value is
‘en@quot’, which can be used in a UTF-8 locale to have American
error messages with pairs of single quotes translated to Unicode directional
quotes.
If no suitable translation catalogue is found or a particular message is not translated in any suitable catalogue, ‘English’33 is used.
See https://developer.r-project.org/Translations30.html for how to prepare and install translation catalogues.
Next: The standalone Rmath library, Previous: Internationalization, Up: Top [Contents][Index]
Almost all current CPUs have both 32- and 64-bit sets of instructions. Most OSes running on such CPUs offer the choice of building a 32-bit or a 64-bit version of R (and details are given below under specific OSes). For most a 32-bit version is the default, but for some (e.g., ‘x86_64’ Linux and macOS ≥ 10.6) 64-bit is.
All current versions of R use 32-bit integers (this is enforced in the build) and ISO/IEC 6055934 double-precision reals, and so compute to the same precision35 and with the same limits on the sizes of numerical quantities. The principal difference is in the size of the pointers.
64-bit builds have both advantages and disadvantages:
R allocates memory for large objects as needed, and removes any unused ones at garbage collection. When the sizes of objects become an appreciable fraction of the address limit, fragmentation of the address space becomes an issue and there may be no hole available that is the size requested. This can cause more frequent garbage collection or the inability to allocate large objects. As a guide, this will become an issue for 32-bit builds with objects more than 10% of the size of the address space (around 300Mb) or when the total size of objects in use is around one third (around 1Gb).
configure
selects suitable defines if this is
possible. (We have also largely worked around that limit on 32-bit
Windows.) 64-bit builds have much larger limits.
So, for speed you may want to use a 32-bit build (especially on a laptop), but to handle large datasets (and perhaps large files) a 64-bit build. You can often build both and install them in the same place: See Sub-architectures. (This is done for the Windows binary distributions.)
Even on 64-bit builds of R there are limits on the size of R
objects (see help("Memory-limits")
), some of which stem from the
use of 32-bit integers (especially in Fortran code). For example, each
dimension of an array is limited to 2^{31} - 1.
Next: Essential and useful other programs under a Unix-alike, Previous: Choosing between 32- and 64-bit builds, Up: Top [Contents][Index]
The routines supporting the distribution and special36 functions in R and a few others are declared in C header file Rmath.h. These can be compiled into a standalone library for linking to other applications. (Note that they are not a separate library when R is built, and the standalone version differs in several ways.)
The makefiles and other sources needed are in directory src/nmath/standalone, so the following instructions assume that is the current working directory (in the build directory tree on a Unix-alike if that is separate from the sources).
Rmath.h contains ‘R_VERSION_STRING’, which is a character
string containing the current R version, for example "4.0.0"
.
There is full access to R’s handling of NaN
, Inf
and
-Inf
via special versions of the macros and functions
ISNAN, R_FINITE, R_log, R_pow and R_pow_di
and (extern) constants R_PosInf
, R_NegInf
and NA_REAL
.
There is no support for R’s notion of missing values, in particular
not for NA_INTEGER
nor the distinction between NA
and
NaN
for doubles.
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 shared library or DLL you may have to use the one supplied, which is the Marsaglia-multicarry with an entry point
set_seed(unsigned int, unsigned int)
to set its seeds).
The facilities to change the normal random number generator are
available through the constant N01_kind
. This takes values
from the enumeration type
typedef enum { BUGGY_KINDERMAN_RAMAGE, AHRENS_DIETER, BOX_MULLER, USER_NORM, INVERSION, KINDERMAN_RAMAGE } N01type;
(and ‘USER_NORM’ is not available).
• Unix-alike standalone | ||
• Windows standalone |
Next: Windows standalone, Previous: The standalone Rmath library, Up: The standalone Rmath library [Contents][Index]
If R has not already been made in the directory tree,
configure
must be run as described in the main build
instructions.
Then (in src/nmath/standalone)
make
will make standalone libraries libRmath.a and libRmath.so (libRmath.dylib on macOS): ‘make static’ and ‘make shared’ will create just one of them.
To use the routines in your own C or C++ programs, include
#define MATHLIB_STANDALONE #include <Rmath.h>
and link against ‘-lRmath’ (and ‘-lm’ if needed on your OS).
The example file test.c does nothing useful, but is provided to
test the process (via make test
). Note that you will probably
not be able to run it unless you add the directory containing
libRmath.so to the LD_LIBRARY_PATH
environment variable
(libRmath.dylib, DYLD_FALLBACK_LIBRARY_PATH
on macOS).
The targets
make install make uninstall
will (un)install the header Rmath.h and shared and static
libraries (if built). Both prefix=
and DESTDIR
are
supported, together with more precise control as described for the main
build.
‘make install’ installs a file for pkg-config
to use by
e.g.
$(CC) `pkg-config --cflags libRmath` -c test.c $(CC) `pkg-config --libs libRmath` test.o -o test
On some systems ‘make install-strip’ will install a stripped shared library.
Previous: Unix-alike standalone, Up: The standalone Rmath library [Contents][Index]
You need to set up37 almost all the tools to make R and then run (in a Unix-like shell)
(cd ../../gnuwin32; make MkRules) (cd ../../include; make -f Makefile.win config.h Rconfig.h Rmath.h) make -f Makefile.win
Alternatively, in a cmd.exe shell use
cd ../../include make -f Makefile.win config.h Rconfig.h Rmath.h cd ../nmath/standalone make -f Makefile.win
This creates a static library libRmath.a and a DLL Rmath.dll. If you want an import library libRmath.dll.a (you don’t need one), use
make -f Makefile.win shared implib
To use the routines in your own C or C++ programs using MinGW-w64, include
#define MATHLIB_STANDALONE #include <Rmath.h>
and link against ‘-lRmath’. This will use the first found of libRmath.dll.a, libRmath.a and Rmath.dll in that order, so the result depends on which files are present. You should be able to force static or dynamic linking via
-Wl,-Bstatic -lRmath -Wl,Bdynamic -Wl,-Bdynamic -lRmath
or by linking to explicit files (as in the ‘test’ target in Makefile.win: this makes two executables, test.exe which is dynamically linked, and test-static.exe, which is statically linked).
It is possible to link to Rmath.dll using other compilers, either directly or via an import library: if you make a MinGW-w64 import library as above, you will create a file Rmath.def which can be used (possibly after editing) to create an import library for other systems such as Visual C++.
If you make use of dynamic linking you should use
#define MATHLIB_STANDALONE #define RMATH_DLL #include <Rmath.h>
to ensure that the constants like NA_REAL
are linked correctly.
(Auto-import will probably work with MinGW-w64, but it is better to be
sure. This is likely to also work with VC++, Borland and similar
compilers.)
Next: Configuration on a Unix-alike, Previous: The standalone Rmath library, Up: Top [Contents][Index]
This appendix gives details of programs you will need to build R on
Unix-like platforms, or which will be used by R if found by
configure
.
Remember that some package management systems (such as RPM and Debian/Ubuntu’s) make a distinction between the user version of a package and the development version. The latter usually has the same name but with the extension ‘-devel’ or ‘-dev’: you need both versions installed.
• Essential programs and libraries | ||
• Useful libraries and programs | ||
• Linear algebra |
Next: Useful libraries and programs, Previous: Essential and useful other programs under a Unix-alike, Up: Essential and useful other programs under a Unix-alike [Contents][Index]
You need a means of compiling C and Fortran 90 (see Using Fortran). Your C compiler should be
ISO/IEC 6005938, POSIX 1003.1 and C99-compliant.39 R tries to choose suitable
flags40 for the C compilers it knows about, but you may have to
set CC
or CFLAGS
suitably. For versions of gcc
prior to 5.1 with glibc
-based Linux this means including
-std=gnu9941. (Note that options essential to run the compiler
even for linking, such as those to set the architecture, should be
specified as part of CC
rather than in CFLAGS
.)
Unless you do not want to view graphs on-screen (or use macOS) you need ‘X11’ installed, including its headers and client libraries. For recent Fedora/RedHat distributions it means (at least) RPMs ‘libX11’, ‘libX11-devel’, ‘libXt’ and ‘libXt-devel’. On Debian/Ubuntu we recommend the meta-package ‘xorg-dev’. If you really do not want these you will need to explicitly configure R without X11, using --with-x=no.
The command-line editing (and command completion) depends on the
GNU readline
library (including its headers): version
4.2 or later is needed for all the features to be enabled. Otherwise
you will need to configure with --with-readline=no (or
equivalent).
A suitably comprehensive iconv
function is essential. The R
usage requires iconv
to be able to translate between
"latin1"
and "UTF-8"
, to recognize ""
(as the
current encoding) and "ASCII"
, and to translate to and from the
Unicode wide-character formats "UCS-[24][BL]E"
— this is true
by default for glibc
42 but not of most commercial Unixes. However, you
can make use of GNU libiconv
(as used on macOS: see
https://www.gnu.org/software/libiconv/).
The OS needs to have enough support43 for wide-character types: this is checked at configuration. Some C99 functions44 are required and checked for at configuration. A small number of POSIX functions45 are essential, and others46 will be used if available.
Installations of zlib
(version 1.2.5 or later), libbz2
(version 1.0.6 or later: called bzip2-libs/bzip2-devel or
libbz2-1.0/libbz2-dev by some Linux distributions) and
liblzma
47 version 5.0.3 or
later are required.
Either PCRE1 (version 8.32 or later, formerly known as just PCRE) or
PCRE2 is required: PCRE2 is preferred and using PCRE1 requires
configure
option --with-pcre1. Only the 8-bit
library and headers are needed if these are packaged separately. JIT
support (optional) is desirable for the best performance. For PCRE2 >=
10.30 (which is desirable as matching has been re-written not to use
recursion and the Unicode tables were updated to version 10)
./configure --enable-jit
suffices. If building PCRE1 for use with R a suitable
configure
command might be
./configure --enable-utf --enable-unicode-properties --enable-jit --disable-cpp
The --enable-jit flag is supported for most common CPUs. (See also the comments for Solaris.)
Some packages require the ‘Unicode properties’ which are
optional for PCRE1: support for this and JIT can be checked at run-time
by calling pcre_config()
.
Library libcurl
(version 7.28.0 or later48) is required. Information on libcurl
is
found from the curl-config
script: if that is missing or needs
to be overridden49 there are macros to
do so described in file config.site.
A tar
program is needed to unpack the sources and packages
(including the recommended packages). A version50 that can
automagically detect compressed archives is preferred for use with
untar()
: the configure script looks for gtar
and
gnutar
before
tar
– use environment variable TAR
to override this.
(On NetBSD/OpenBSD systems set this to bsdtar
if that is
installed.)
There need to be suitable versions of the tools grep
and
sed
: the problems are usually with old AT&T and BSD variants.
configure
will try to find suitable versions (including
looking in /usr/xpg4/bin which is used on some commercial
Unixes).
You will not be able to build most of the manuals unless you have
texi2any
version 5.1 or later installed, and if not most of
the HTML manuals will be linked to a version on CRAN. To
make PDF versions of the manuals you will also need file
texinfo.tex installed (which is part of the GNU
texinfo distribution but is often made part of the TeX package
in re-distributions) as well as
texi2dvi
.51
Further, the versions of texi2dvi
and texinfo.tex need
to be compatible: we have seen problems with older TeX distributions.
If you want to build from the R Subversion repository then
texi2any
is highly recommended as it is used to create files
which are in the tarball but not stored in the Subversion repository.
The PDF documentation (including doc/NEWS.pdf) and building
vignettes needs pdftex
and pdflatex
. We require
LaTeX version 2005/12/01
or later (for UTF-8 support).
Building PDF package manuals (including the R reference manual) and
vignettes is sensitive to the version of the LaTeX package
hyperref and we recommend that the TeX distribution used is
kept up-to-date. A number of standard LaTeX packages are required
(including url and some of the font packages such as times,
helvetic, ec and cm-super) and others such as
hyperref and inconsolata are desirable (and without them you
may need to change R’s defaults: see Making the manuals). Note
that package hyperref (currently) requires packages
kvoptions, ltxcmds and refcount. For distributions
based on TeX Live the simplest approach may be to install collections
collection-latex, collection-fontsrecommended,
collection-latexrecommended, collection-fontsextra and
collection-latexextra (assuming they are not installed by
default): Fedora uses names like texlive-collection-fontsextra and
Debian/Ubuntu like texlive-fonts-extra.
The essential programs should be in your PATH
at the time
configure
is run: this will capture the full paths.
Those distributing binary versions of R may need to be aware of the
licences of the external libraries it is linked to (including ‘useful’
libraries from the next section). The liblzma
library is in the
public domain and X11, libbzip2
, libcurl
and zlib
have MIT-style licences. PCRE and PCRE2 have a BSD-style licence which
requires distribution of the licence (included in R’s
COPYRIGHTS file) in binary distributions. GNU readline
is
licensed under GPL (which version(s) of GPL depends on the
readline
version).
Next: Linear algebra, Previous: Essential programs and libraries, Up: Essential and useful other programs under a Unix-alike [Contents][Index]
The ability to use translated messages makes use of gettext
and
most likely needs GNU gettext
: you do need this to work
with new translations, but otherwise the version contained in the R
sources will be used if no suitable external gettext
is found.
The ‘modern’ version of the X11()
, jpeg()
, png()
and tiff()
graphics devices uses the cairo
and
(optionally) Pango
libraries. Cairo version 1.2.0 or later is
required. Pango needs to be at least version 1.10, and 1.12 is the
earliest version we have tested. (For Fedora users we believe the
pango-devel
RPM and its dependencies suffice.) R checks for
pkg-config
, and uses that to check first that the
‘pangocairo’ package is installed (and if not, ‘cairo’) and if
additional flags are needed for the ‘cairo-xlib’ package, then if
suitable code can be compiled. These tests will fail if
pkg-config
is not installed52, and are likely to fail if cairo
was built
statically (unusual). Most systems with Gtk+
2.8 or later
installed will have suitable libraries.
For the best font experience with these devices you need suitable fonts
installed: Linux users will want the urw-fonts
package. On
platforms which have it available, the msttcorefonts
package53 provides
TrueType versions of Monotype fonts such as Arial and Times New Roman.
Another useful set of fonts is the ‘liberation’ TrueType fonts available
at
https://fedorahosted.org/liberation-fonts/,54 which cover the Latin, Greek and Cyrillic alphabets
plus a fair range of signs. These share metrics with Arial, Times New
Roman and Courier New, and contain fonts rather similar to the first two
(https://en.wikipedia.org/wiki/Liberation_fonts). Then there
is the ‘Free UCS Outline Fonts’ project
(https://www.gnu.org/software/freefont/) which are
OpenType/TrueType fonts based on the URW fonts but with extended Unicode
coverage. See the R help on X11
on selecting such fonts.
The bitmapped graphics devices jpeg()
, png()
and
tiff()
need the appropriate headers and libraries installed:
jpeg
(version 6b or later, or libjpeg-turbo
) or
libpng
(version 1.2.7 or later) and zlib
or libtiff
(versions 4.0.[5-10] and 4.1.0 have been tested) respectively.
pkg-config
is used if available and so needs the appropriate
.pc file (which requires libtiff
version 4.x and is not
available on all platforms for jpeg
before version 9c). They
also need support for either X11
or cairo
(see above).
Should support for these devices not be required or broken
system libraries need to be avoided there are configure
options --without-libpng, --without-jpeglib and
--without-libtiff. The TIFF library has many optional features
such as jpeg
, libz
, lzma
, jbig
and
jpeg12
, none of which is required for the tiff()
devices
but may need to be present to link the library (usually only an issue
for static linking).
Option --with-system-tre is also available: it needs a recent
version of TRE. (The latest (2016) sources are in the git
repository at https://github.com/laurikari/tre/, but at the time
of writing the resulting build will not pass its checks.).
An implementation of XDR is required, and the R sources
contain one which is likely to suffice (although a system version may
have higher performance). XDR is part of RPC and
historically has been part of libc on a Unix-alike. (In
principle man xdr_string
should tell you which library is
needed, but it often does not: on Solaris and others it is provided by
libnsl
.) However some builds55 of glibc
omit or
hide it with the intention that the TI-RPC library be used, in
which case libtirpc
(and its development version) should be
installed, and its headers56 need
to be on the C include path or under /usr/include/tirpc.
Use of the X11 clipboard selection requires the Xmu
headers and
libraries. These are normally part of an X11 installation (e.g. the
Debian meta-package ‘xorg-dev’), but some distributions have split
this into smaller parts, so for example recent versions of Fedora
require the ‘libXmu’ and ‘libXmu-devel’ RPMs.
Some systems (notably macOS and at least some FreeBSD systems) have
inadequate support for collation in multibyte locales. It is possible
to replace the OS’s collation support by that from ICU (International
Components for Unicode, http://site.icu-project.org/), and this
provides much more precise control over collation on all systems. ICU
is available as sources and as binary distributions for (at least) most
Linux distributions, Solaris, FreeBSD and AIX, usually as libicu
or icu4c
. It will be used by default where available: should a
very old or broken version of ICU be found this can be suppressed by
--without-ICU.
The bitmap
and dev2bitmap
devices and function
embedFonts()
use ghostscript
(http://www.ghostscript.com/). This should either be in your
path when the command is run, or its full path specified by the
environment variable R_GSCMD
at that time.
At the time of writing a full installation on Fedora Linux used the following packages and their development versions, and this may provide a useful checklist for other systems:
bzip2 cairo fontconfig freetype fribidi glib2 harfbuzz libX11 libXext libXt libcurl libicu libjpeg libpng libtiff libtirpc libxcrypt ncurses pango pcre2 readline tcl tk xz zlib
• Tcl/Tk | ||
• Java support | ||
• Other compiled languages |
Next: Java support, Previous: Useful libraries and programs, Up: Useful libraries and programs [Contents][Index]
The tcltk package needs Tcl/Tk ≥ 8.4 installed: the sources are available at https://www.tcl.tk/. To specify the locations of the Tcl/Tk files you may need the configuration options
use Tcl/Tk, or specify its library directory
specify location of tclConfig.sh
specify location of tkConfig.sh
or use the configure variables TCLTK_LIBS
and
TCLTK_CPPFLAGS
to specify the flags needed for linking against
the Tcl and Tk libraries and for finding the tcl.h and
tk.h headers, respectively. If you have both 32- and 64-bit
versions of Tcl/Tk installed, specifying the paths to the correct config
files may be necessary to avoid confusion between them.
Versions of Tcl/Tk up to 8.5.19 and 8.6.9 have been tested (including most versions of 8.4.x, but not recently).
Note that the tk.h header includes57 X11 headers, so you will need X11 and its development files installed.
Next: Other compiled languages, Previous: Tcl/Tk, Up: Useful libraries and programs [Contents][Index]
The build process looks for Java support on the host system, and if it
finds it sets some settings which are useful for Java-using packages
(such as rJava and JavaGD: these require a full
JDK). This check can be suppressed by configure option
--disable-java.
Configure variable JAVA_HOME
can be set to point to a specific
JRE/JDK, on the configure
command line or in the environment.
Principal amongst these settings are some paths to the Java
libraries and JVM, which are stored in environment variable
R_JAVA_LD_LIBRARY_PATH
in file R_HOME/etc/ldpaths (or
a sub-architecture-specific version). A typical setting for
‘x86_64’ Linux is
JAVA_HOME=/usr/lib/jvm/java-1.8.0-openjdk-1.8.0.252.b09-0.fc32.x86_64/jre R_JAVA_LD_LIBRARY_PATH=${JAVA_HOME}/lib/that/server
Unfortunately this depends on the exact version of the JRE/JDK
installed, and so may need updating if the Java installation is updated.
This can be done by running R CMD javareconf
which updates
settings in both R_HOME/etc/Makeconf and
R_HOME/etc/ldpaths. See R CMD javareconf --help
for
details: note that this needs to be done by the account owning the R
installation.
Another way of overriding those settings is to set the environment variable
R_JAVA_LD_LIBRARY_PATH
(before R is started, hence not in
~/.Renviron), which suffices to run already-installed
Java-using packages. For example
R_JAVA_LD_LIBRARY_PATH=/usr/lib/jvm/java-1.8.0/jre/lib/amd64/server
It may be possible to avoid this by specifying an invariant link as the path when configuring. For example, on that system any of
JAVA_HOME=/usr/lib/jvm/java JAVA_HOME=/usr/lib/jvm/java-1.8.0 JAVA_HOME=/usr/lib/jvm/java-1.8.0/jre JAVA_HOME=/usr/lib/jvm/jre-1.8.0
worked (since the ‘auto’ setting of /etc/alternatives
chose
Java 8 aka 1.8.0).
‘Non-server’ Oracle distributions of Java as from version 11 are of a full JDK. However, Linux distributions can be confusing: for example Fedora 32 had
java-1.8.0-openjdk java-1.8.0-openjdk-devel java-openjdk java-openjdk-devel java-11-openjdk java-11-openjdk-devel java-latest-openjdk java-latest-openjdk-devel
where the -devel
RPMs are needed to complete the JDK. (At the
time of writing java-openjdk
was Java 14.) Debian/Ubuntu use
‘-jre’ and ‘-jdk’, e.g.
sudo apt install default-jdk
Previous: Java support, Up: Useful libraries and programs [Contents][Index]
Some add-on packages need a C++ compiler. This is specified by the
configure variables CXX
, CXXFLAGS
and similar.
configure
will normally find a suitable compiler. However, in
many cases this will be a C++98 compiler, and it is
possible to specify an alternative compiler for use with C++11 by the
configure variables CXX11
, CXX11STD
, CXX11FLAGS
and
similar (see C++ Support). Again, configure
will normally
find a suitable value for CXX11STD
if the compiler given by
CXX
is capable of compiling C++11 code, but it is possible that a
completely different compiler will be needed.
For source files with extension .f90 or .f95 containing
free-form Fortran, the compiler defined by the macro FC
is used
by R CMD INSTALL
. Note that it is detected by the name of the
command without a test that it can actually compile Fortran 90 code.
Set the configure variable FC
to override this if necessary:
variables FCFLAGS
and FCLIBS_XTRA
might also need to be
set.
See file config.site in the R source for more details about these variables.
Previous: Useful libraries and programs, Up: Essential and useful other programs under a Unix-alike [Contents][Index]
• BLAS | ||
• LAPACK | ||
• Caveats |
Next: LAPACK, Previous: Linear algebra, Up: Linear algebra [Contents][Index]
The linear algebra routines in R can make use of enhanced BLAS (Basic Linear Algebra Subprograms, http://www.netlib.org/blas/faq.html) routines. However, these have to be explicitly requested at configure time: R provides an internal BLAS which is well-tested and will be adequate for most uses of R.
You can specify a particular BLAS library via a value
for the configuration option --with-blas and not to use an
external BLAS library by --without-blas (the
default). If --with-blas is given with no =
, its value
is taken from the
environment variable BLAS_LIBS
, set for example in
config.site. If neither the option nor the environment variable
supply a value, a search is made for a suitable58 BLAS. If the value is
not obviously a linker command (starting with a dash or giving the path
to a library), it is prefixed by ‘-l’, so
--with-blas="foo"
is an instruction to link against ‘-lfoo’ to find an external BLAS (which needs to be found both at link time and run time).
The configure code checks that the external BLAS is complete
(it must include all double precision and double complex routines, as
well as LSAME
), and appears to be usable. However, an external
BLAS has to be usable from a shared object (so must contain
position-independent code), and that is not checked.
Some enhanced BLASes are compiler-system-specific
(sunperf
on Solaris59, libessl
on IBM,
Accelerate
on macOS). The correct incantation for these is often
found via --with-blas with no value on the appropriate
platforms.
Some of the external BLASes are multi-threaded. One issue is
that R profiling (which uses the SIGPROF
signal) may cause
problems, and you may want to disable profiling if you use a
multi-threaded BLAS. Note that using a multi-threaded
BLAS can result in taking more CPU time and even
more elapsed time (occasionally dramatically so) than using a similar
single-threaded BLAS. On a machine running other tasks, there
can be contention for CPU caches that reduces the effectiveness of the
optimization of cache use by a BLAS implementation: some
people warn that this is especially problematic for hyperthreaded CPUs.
Note that under Unix (but not under Windows) if R is compiled against a non-default BLAS and --enable-BLAS-shlib is not used (it is the default on all platforms except AIX), then all BLAS-using packages must also be. So if R is re-built to use an enhanced BLAS then packages such as quantreg will need to be re-installed; they may be under other circumstances.
R relies on ISO/IEC 60559 compliance of an
external BLAS. This can be broken if for example the code
assumes that terms with a zero factor are always zero and do not need to
be computed—whereas x*0
can be NaN
. This is checked in
the test suite.
External BLAS implementations often make less use of extended-precision floating-point registers (where available) and will almost certainly re-order computations. This can result in less accuracy than using a reference BLAS, and may result in different solutions, e.g. different signs in SVD and eigendecompositions.
Debian/Ubuntu systems provide a system-specific way to switch the BLAS
in use. Build R with -with-blas to select the OS version
of the reference BLAS, and then use update-alternatives
to
switch between the available BLAS libraries. See
https://wiki.debian.org/DebianScience/LinearAlgebraLibraries.
The URIs for several of these BLAS have been subject to frequent gratuitous changes, so you will need to search for their current locations.
BLAS (and LAPACK) routines may be used inside threaded code, for example in OpenMP sections in packages such as mgcv. The reference implementations are thread-safe but external ones may not be (even single-threaded ones): this can lead to hard-to-track-down incorrect results or segfaults.
NOTE: BLAS libraries built with gfortran
9 (and
later and versions 8.4, 7.5 and later in those series) require calls
from C/C++ to handle ‘hidden’ character lengths — R itself does so
but many packages do not and some segfault. (This applies also to
external LAPACK libraries.)
• ATLAS | ||
• OpenBLAS | ||
• MKL | ||
• Shared BLAS |
ATLAS (http://math-atlas.sourceforge.net/) is a “tuned” BLAS that runs on a wide range of Unix-alike platforms. Unfortunately it is built by default as a static library that on some platforms may not be able to be used with shared objects such as are used in R packages. Be careful when using pre-built versions of ATLAS static libraries (they seem to work on ‘ix86’ platforms, but not always on ‘x86_64’ ones).
ATLAS contains replacements for a small number of LAPACK routines, but can be built to merge these with LAPACK sources to include a full LAPACK library.
Recent versions of ATLAS can be built as a single shared library, either
libsatlas
or libtatlas
(serial or threaded respectively):
these may even contain a full LAPACK. Such builds can be used by one of
--with-blas=satlas --with-blas=tatlas
or, as on ‘x86_64’ Fedora where a path needs to be specified,
--with-blas="-L/usr/lib64/atlas -lsatlas" --with-blas="-L/usr/lib64/atlas -ltatlas"
Distributed ATLAS libraries cannot be tuned to your machine and so are a compromise: for example Fedora tunes ‘x86_64’ for CPUs with SSE3 extensions, and separate ‘atlas-sse2’ and ‘atlas-sse3’ ‘i686’ RPMs are available.60
Note that building R on Linux against distributed shared libraries may need ‘-devel’ or ‘-dev’ packages installed.
Linking against multiple static libraries requires one of
--with-blas="-lf77blas -latlas" --with-blas="-lptf77blas -lpthread -latlas" --with-blas="-L/path/to/ATLAS/libs -lf77blas -latlas" --with-blas="-L/path/to/ATLAS/libs -lptf77blas -lpthread -latlas"
Consult its installation guide61 for how to build ATLAS as a shared library or as a static library with position-independent code (on platforms where that matters).
According to the ATLAS FAQ62 the maximum number of threads used by multi-threaded ATLAS is set at compile time. Also, the author advises against using multi-threaded ATLAS on hyperthreaded CPUs without restricting affinities at compile-time to one virtual core per physical CPU. (For the Fedora libraries the compile-time flag specifies 4 threads.)
Dr Kazushige Goto wrote a tuned BLAS for several processors and OSes, which was frozen in mid-2010. OpenBLAS (http://www.openblas.net/) is a descendant project with support for some later CPUs.
This can be used by configuring R with something like
--with-blas="-lopenblas"
See see Shared BLAS for an alternative (and in many ways preferable) way to use them.
Some platforms provide multiple builds of OpenBLAS: for example Fedora 32 has RPMs63
openblas openblas-threads openblas-openmp
providing shared libraries
libopenblas.so libopenblasp.so libopenblaso.so
respectively, each of which can be used as a shared BLAS. For the
second and third the number of threads is controlled by
OPENBLAS_NUM_THREADS
and OMP_NUM_THREADS
(as usual for
OpenMP) respectively. There is also a Fedora RPM ‘openblas-Rblas’
to replace libRblas.so in their distribution of R.
Note that building R on Linux against distributed libraries may need ‘-devel’ or ‘-dev’ packages installed.
For ‘ix86’ and ‘x86_64’ most distributed libraries contain several alternatives for different CPU microarchitectures with the choice being made at run time.
Next: Shared BLAS, Previous: OpenBLAS, Up: BLAS [Contents][Index]
For Intel processors (and perhaps others) and some distributions of Linux, there is Intel’s Math Kernel Library. You are strongly encouraged to read the MKL User’s Guide, which is installed with the library, before attempting to link to MKL. This includes a ‘link line advisor’ which will suggest appropriate incantations: its use is recommended. Or see https://software.intel.com/en-us/articles/intel-mkl-link-line-advisor.
There are also versions of MKL for macOS64 and Windows, but when these have been tried they did not work with the default compilers used for R on those platforms.
The MKL interface has changed several times but has been stable in recent years: the following examples have been used with versions 10.3 to 2020.1, for GCC compilers on ‘x86_64’.
To use a sequential version of MKL we used
MKL_LIB_PATH=/path/to/intel_mkl/mkl/lib/intel64 export LD_LIBRARY_PATH=$MKL_LIB_PATH MKL="-L${MKL_LIB_PATH} -lmkl_gf_lp64 -lmkl_core -lmkl_sequential" ./configure --with-blas="$MKL" --with-lapack
The option --with-lapack is used since MKL contains a tuned copy of LAPACK (often older than the current version) as well as BLAS (see LAPACK), although this can be omitted.
Threaded MKL may be used by replacing the line defining the variable
MKL
by
MKL="-L${MKL_LIB_PATH} -lmkl_gf_lp64 -lmkl_core \ -lmkl_gnu_thread -dl -fopenmp"
R can also be linked against a single shared library,
libmkl_rt.so
, for both BLAS and LAPACK, but the correct OpenMP and
MKL interface layer then has to be selected via environment variables. With
64-bit builds and the GCC compilers, we used
export MKL_INTERFACE_LAYER=GNU,LP64 export MKL_THREADING_LAYER=GNU
On Debian/Ubuntu, MKL is provided by package intel-mkl-full
and one
can set libmkl_rt.so
as the system-wide implementation of both BLAS
and LAPACK during installation of the package, so that also R installed
from Debian/Ubuntu package r-base
would use it. It is, however,
still essential to set MKL_INTERFACE_LAYER
and
MKL_THREADING_LAYER
before running R, otherwise MKL computations
will produce incorrect results. R does not have to be rebuilt to use MKL,
but configure
include tests which may discover some errors such as a
failure to set the correct OpenMP and MKL interface layer.
The default number of threads will be chosen by the OpenMP software, but
can be controlled by setting OMP_NUM_THREADS
or
MKL_NUM_THREADS
, and in recent versions seems to default to a
sensible value for sole use of the machine. (Parallel MKL has not
always passed make check-all
, but did with MKL 2019.4.)
MKL includes a partial implementation of FFTW3, which causes trouble for applications that require some of the FFTW3 functionality unsupported in MKL. Please see the MKL manuals for description of these limitations and for instructions on how to create a custom version of MKL which excludes the FFTW3 wrappers.
It was reported in 2015 that
--with-blas='-mkl=parallel' --with-lapack
worked with the Intel 2015.3 compilers on Centos 6.
The BLAS library will be used for many of the add-on packages as well as for R itself. This means that it is better to use a shared/dynamic BLAS library, as most of a static library will be compiled into the R executable and each BLAS-using package.
R offers the option of compiling the BLAS into a dynamic
library libRblas
stored in R_HOME/lib and linking
both R itself and all the add-on packages against that library.
This is the default on all platforms except AIX unless an external BLAS is specified and found: for the latter it can be used by specifying the option --enable-BLAS-shlib, and it can always be disabled via --disable-BLAS-shlib.
This has both advantages and disadvantages.
libRblas
, and that can be replaced.
Note though that any dynamic libraries the replacement links to will
need to be found by the linker: this may need the library path to be
changed in R_HOME/etc/ldpaths.
Another option to change the BLAS in use is to symlink a single dynamic BLAS library to R_HOME/lib/libRblas.so. For example, just
mv R_HOME/lib/libRblas.so R_HOME/lib/libRblas.so.keep ln -s /usr/lib64/libopenblasp.so.0 R_HOME/lib/libRblas.so
on ‘x86_64’ Fedora will change the BLAS used to
multithreaded OpenBLAS. A similar link works for most versions of the
OpenBLAS (provided the appropriate lib directory is in the
run-time library path or ld.so
cache). It can also be used
for a single-library ATLAS, so on ‘x86_64’ Fedora
ln -s /usr/lib64/atlas/libsatlas.so.3 R_HOME/lib/libRblas.so ln -s /usr/lib64/atlas/libtatlas.so.3 R_HOME/lib/libRblas.so
can be used with its distributed ATLAS libraries. (If you have the
‘-devel’ RPMS installed you can omit the .0
/.3
.)
Note that rebuilding or symlinking libRblas.so may not suffice if the intention is to use a modified LAPACK contained in an external BLAS: the latter could even cause conflicts. However, on Fedora where the OpenBLAS distribution contains a copy of LAPACK, it is the latter which is used.
Next: Caveats, Previous: BLAS, Up: Linear algebra [Contents][Index]
Provision is made for using an external LAPACK library, principally to
cope with BLAS libraries which contain a copy of LAPACK (such
as sunperf
on Solaris, Accelerate
on macOS and ATLAS and MKL
on ‘ix86’/‘x86_64’ Linux). At least LAPACK version 3.2
is required. This can only be done if --with-blas has been used.
However, the likely performance gains are thought to be small (and may be negative). The default is not to search for a suitable LAPACK library, and this is definitely not recommended. You can specify a specific LAPACK library or a search for a generic library by the configuration option --with-lapack. The default for --with-lapack is to check the BLAS library and then look for an external library ‘-llapack’. Sites searching for the fastest possible linear algebra may want to build a LAPACK library using the ATLAS-optimized subset of LAPACK: this is simplest with a dynamic ATLAS library which contains a full LAPACK, when --with-lapack suffices.
A value for --with-lapack can be set via the environment
variable
LAPACK_LIBS
, but this will only be used if --with-lapack
is specified (as the default value is no
) and the BLAS library
does not contain LAPACK.
If you do use --with-lapack, be aware of potential problems
with bugs in the LAPACK sources (or in the posted corrections to those
sources). In particular, bugs in DGEEV
and DGESDD
have
resulted in error messages such as
DGEBRD gave error code -10
. Other potential problems are incomplete versions of the libraries, seen several times in Linux distributions over the years.
Please do bear in mind that using --with-lapack is ‘definitely not recommended’: it is provided only because it is necessary on some platforms and because some users want to experiment with claimed performance improvements. Reporting problems where it is used unnecessarily will simply irritate the R helpers.
Note too the comments about ISO/IEC 60559 compliance in the section of external BLAS: these apply equally to an external LAPACK, and for example the Intel MKL documentation has said
LAPACK routines assume that input matrices do not contain IEEE 754 special values such as INF or NaN values. Using these special values may cause LAPACK to return unexpected results or become unstable.
We rely on limited support in LAPACK for matrices with 2^{31} or more elements: it is possible that an external LAPACK will not have that support.
Previous: LAPACK, Up: Linear algebra [Contents][Index]
As with all libraries, you need to ensure that they and R were
compiled with compatible compilers and flags. For example, this has
meant that on Sun Sparc using the Oracle compilers the flag
-dalign is needed if sunperf
is to be used.
On some systems it has been necessary that an external BLAS/LAPACK was built with the same Fortran compiler used to build R.
LAPACK 3.9.0 has a bug in which the DCOMBSSQ subroutine has a bug that may cause NA to be interpreted as zero. This is fixed in the R 3.6.3 and later sources, but if you use an external LAPACK, you may need to fix it there.
The code (in dlapack.f
) should read
* .. * .. Executable Statements .. * IF( V1( 1 ).GE.V2( 1 ) ) THEN IF( V1( 1 ).NE.ZERO ) THEN V1( 2 ) = V1( 2 ) + ( V2( 1 ) / V1( 1 ) )**2 * V2( 2 ) ELSE V1( 2 ) = V1( 2 ) + V2( 2 ) END IF ELSE V1( 2 ) = V2( 2 ) + ( V1( 1 ) / V2( 1 ) )**2 * V1( 2 ) V1( 1 ) = V2( 1 ) END IF RETURN
(The inner ELSE clause was missing in LAPACK 3.9.0.)
Next: Platform notes, Previous: Essential and useful other programs under a Unix-alike, Up: Top [Contents][Index]
• Configuration options | ||
• Internationalization support | ||
• Configuration variables | ||
• Setting the shell | ||
• Using make | ||
• Using Fortran | ||
• Compile and load flags | ||
• Maintainer mode |
Next: Internationalization support, Previous: Configuration on a Unix-alike, Up: Configuration on a Unix-alike [Contents][Index]
configure
has many options: running
./configure --help
will give a list. Probably the most important ones not covered elsewhere are (defaults in brackets)
use the X Window System [yes]
X include files are in DIR
X library files are in DIR
use readline library (if available) [yes]
attempt to compile support for Rprof()
[yes]
attempt to compile support for Rprofmem()
and tracemem()
[no]
build R as a shared/dynamic library [no]
build the BLAS as a shared/dynamic library [yes, except on AIX]
You can use --without-foo or --disable-foo for the negatives.
You will want to use --disable-R-profiling if you are building a profiled executable of R (e.g. with ‘-pg)’. Support for R profiling requires OS support for POSIX threads (aka ‘pthreads’), which are available on all mainstream Unix-alike platforms.
Flag --enable-R-shlib causes the make process to build R as a dynamic (shared) library, typically called libR.so, and link the main R executable R.bin against that library. This can only be done if all the code (including system libraries) can be compiled into a dynamic library, and there may be a performance65 penalty. So you probably only want this if you will be using an application which embeds R. Note that C code in packages installed on an R system linked with --enable-R-shlib is linked against the dynamic library and so such packages cannot be used from an R system built in the default way. Also, because packages are linked against R they are on some OSes also linked against the dynamic libraries R itself is linked against, and this can lead to symbol conflicts.
For maximally effective use of valgrind
, R should be
compiled with valgrind instrumentation. The configure
option
is --with-valgrind-instrumentation=level, where
level is 0, 1 or 2. (Level 0 is the default and does not add
anything.) The system headers for valgrind
can be requested
by option --with-system-valgrind-headers: they will be used if
present (on Linux they may be in a separate package such as
valgrind-devel). Note though that there is no guarantee that the
code in R will be compatible with very old66 or future valgrind
headers.
If you need to re-configure R with different options you may need to run
make clean
or even make distclean
before doing so.
The configure script has other generic options added by
autoconf
and which are not supported for R: in particular
building for one architecture on a different host is not possible.
Next: Configuration variables, Previous: Configuration options, Up: Configuration on a Unix-alike [Contents][Index]
Translation of messages is supported via GNU gettext
unless disabled by the configure option --disable-nls.
The configure
report will show NLS
as one of the
‘Additional capabilities’ if support has been compiled in, and running
in an English locale (but not the C
locale) will include
Natural language support but running in an English locale
in the greeting on starting R.
Next: Setting the shell, Previous: Internationalization support, Up: Configuration on a Unix-alike [Contents][Index]
If you need or want to set certain configure variables to something other than their default, you can do that by either editing the file config.site (which documents many of the variables you might want to set: others can be seen in file etc/Renviron.in) or on the command line as
./configure VAR=value
If you are building in a directory different from the sources, there can be copies of config.site in the source and the build directories, and both will be read (in that order). In addition, if there is a file ~/.R/config, it is read between the config.site files in the source and the build directories.
There is also a general autoconf
mechanism for
config.site files, which are read before any of those mentioned
in the previous paragraph. This looks first at a file specified by the
environment variable CONFIG_SITE
, and if not is set at files such
as /usr/local/share/config.site and
/usr/local/etc/config.site in the area (exemplified by
/usr/local) where R would be installed.
These variables are precious, implying that they do not have to be exported to the environment, are kept in the cache even if not specified on the command line, checked for consistency between two configure runs (provided that caching is used), and are kept during automatic reconfiguration as if having been passed as command line arguments, even if no cache is used.
See the variable output section of configure --help
for a list of
all these variables.
If you find you need to alter configure variables, it is worth noting that some settings may be cached in the file config.cache, and it is a good idea to remove that file (if it exists) before re-configuring. Note that caching is turned off by default: use the command line option --config-cache (or -C) to enable caching.
• Setting paper size | ||
• Setting the browsers | ||
• Compilation flags | ||
• Making manuals |
Next: Setting the browsers, Previous: Configuration variables, Up: Configuration variables [Contents][Index]
One common variable to change is R_PAPERSIZE
, which defaults to
‘a4’, not ‘letter’. (Valid values are ‘a4’,
‘letter’, ‘legal’ and ‘executive’.)
This is used both when configuring R to set the default, and when running R to override the default. It is also used to set the paper size when making PDF manuals.
The configure default will most often be ‘a4’ if R_PAPERSIZE
is unset. (If the (Debian Linux) program paperconf
is found
or the environment variable PAPERSIZE
is set, these are used to
produce the default.)
Next: Compilation flags, Previous: Setting paper size, Up: Configuration variables [Contents][Index]
Another precious variable is R_BROWSER
, the default HTML
browser, which should take a value of an executable in the user’s path
or specify a full path.
Its counterpart for PDF files is R_PDFVIEWER
.
Next: Making manuals, Previous: Setting the browsers, Up: Configuration variables [Contents][Index]
If you have libraries and header files, e.g., for GNU
readline, in non-system directories, use the variables LDFLAGS
(for libraries, using ‘-L’ flags to be passed to the linker) and
CPPFLAGS
(for header files, using ‘-I’ flags to be passed to
the C/C++ preprocessors), respectively, to specify these locations.
These default to ‘-L/usr/local/lib’ (LDFLAGS
,
‘-L/usr/local/lib64’ on most 64-bit Linux OSes) and
‘-I/usr/local/include’ (CPPFLAGS
, but note that on most
systems /usr/local/include is regarded as a system include
directory and so instances in that macro will be skipped) to catch the
most common cases. If libraries are still not found, then maybe your
compiler/linker does not support re-ordering of -L and
-l flags.
In this case, use a different compiler (or a front-end shell script
which does the re-ordering).
These flags can also be used to build a faster-running version of R.
On most platforms using gcc
, having ‘-O3’ in
CFLAGS
and FFLAGS
produces worthwhile
performance gains with gcc
and gfortran
, but may
result in a less reliable build (both segfaults and incorrect numeric
computations have been seen). On systems using the GNU linker
(especially those using R as a shared library), it is likely that
including ‘-Wl,-O1’ in LDFLAGS
is worthwhile, and
‘'-Bdirect,--hash-style=both,-Wl,-O1'’ is recommended at
https://lwn.net/Articles/192624/. Tuning compilation to a
specific CPU family (e.g. ‘-mtune=native’ for
gcc
) can give worthwhile performance gains, especially on
older architectures such as ‘ix86’.
Previous: Compilation flags, Up: Configuration variables [Contents][Index]
The default settings for making the manuals are controlled by
R_RD4PDF
and R_PAPERSIZE
.
Next: Using make, Previous: Configuration variables, Up: Configuration on a Unix-alike [Contents][Index]
By default the shell scripts such as R will be ‘#!/bin/sh’
scripts (or using the SHELL
chosen by configure). This is
almost always satisfactory, but on a few systems /bin/sh is not a
Bourne shell or clone, and the shell to be used can be changed by
setting the configure variable R_SHELL
to a suitable value (a full
path to a shell, e.g. /usr/local/bin/bash).
Next: Using Fortran, Previous: Setting the shell, Up: Configuration on a Unix-alike [Contents][Index]
To compile R, you will most likely find it easiest to use
GNU make
, although the Sun make
works on
Solaris.
To build in a separate directory you need a make
that supports
the VPATH
variable, for example GNU make
and
Sun make
.
dmake
has also been used. e.g, on Solaris 10.
If you want to use a make
by another name, for example if your
GNU make
is called ‘gmake’, you need to set the
variable MAKE
at configure time, for example
./configure MAKE=gmake
Next: Compile and load flags, Previous: Using make, Up: Configuration on a Unix-alike [Contents][Index]
To compile R, you need a Fortran 90 compiler. The current default
is to search for
gfortran
, g95
, xlf95
f95
,
fort
, ifort
, ifc
, efc
,
pgfortran
, pgf95
lf95
, ftn
,
nagfor
, xlf90
, f90
, pgf90
,
pghpf
, epcf90
. (Note that these are searched for by
name, without checking the standard of Fortran they support.) The
command and flags used should support fixed-form Fortran with extension
.f: in the unusual case that a specific flag is needed for
free-form Fortran with extension .f90 or .f95, this can be
specified as part of FCFLAGS
.
The search mechanism can be changed using the configure variable
FC
which specifies the command that runs the Fortran compiler.
If your Fortran compiler is in a non-standard location, you
should set the environment variable PATH
accordingly before
running configure
, or use the configure variable FC
to
specify its full path.
If your Fortran libraries are in slightly peculiar places, you should
also look at LD_LIBRARY_PATH
(or your system’s equivalent) to make
sure that all libraries are on this path.
Note that only Fortran compilers which convert identifiers to lower case are supported.
You must set whatever compilation flags (if any) are needed to ensure
that Fortran integer
is equivalent to a C int
pointer and
Fortran double precision
is equivalent to a C double
pointer. This is checked during the configuration process.
Some of the Fortran code makes use of DOUBLE COMPLEX
and
COMPLEX*16
variables. This is checked for at configure time, as
well as its equivalence to the Rcomplex
C structure defined in
R_ext/Complex.h.
gfortran
10 by default gives a compilation error for the
previously widespread practice of passing a Fortran array element where
an array is expected, or a scalar instead of a length-one array. See
https://gcc.gnu.org/gcc-10/porting_to.html.
Next: Maintainer mode, Previous: Using Fortran, Up: Configuration on a Unix-alike [Contents][Index]
A wide range of flags can be set in the file config.site or as configure variables on the command line. We have already mentioned
CPPFLAGS
header file search directory (-I) and any other miscellaneous options for the C and C++ preprocessors and compilers
LDFLAGS
path (-L), stripping (-s) and any other miscellaneous options for the linker
and others include
CFLAGS
debugging and optimization flags, C
MAIN_CFLAGS
ditto, for compiling the main program (e.g. when profiling)
SHLIB_CFLAGS
for shared objects (no known examples)
FFLAGS
debugging and optimization flags, fixed-form Fortran
FCFLAGS
debugging and optimization flags, free-form Fortran
SAFE_FFLAGS
ditto for source files which need exact floating point behaviour
MAIN_FFLAGS
ditto, for compiling the main program (e.g. when profiling)
SHLIB_FFLAGS
for shared objects (no known examples)
MAIN_LDFLAGS
additional flags for the main link
SHLIB_LDFLAGS
additional flags for linking the shared objects
LIBnn
the primary library directory, lib or lib64
CPICFLAGS
special flags for compiling C code to be turned into a shared object
FPICFLAGS
special flags for compiling Fortran code to be turned into a shared object
CXXPICFLAGS
special flags for compiling C++ code to be turned into a shared object
DEFS
defines to be used when compiling C code in R itself
Library paths specified as -L/lib/path in LDFLAGS
are
collected together and prepended to LD_LIBRARY_PATH
(or your
system’s equivalent), so there should be no need for -R or
-rpath flags.
Variables such as CPICFLAGS
are determined where possible by
configure
. Some systems allows two types of PIC flags, for
example ‘-fpic’ and ‘-fPIC’, and if they differ the first
allows only a limited number of symbols in a shared object. Since R
as a shared library has about 6200 symbols, if in doubt use the larger
version.
Other variables often set by configure
include
‘MAIN_LDFLAGS’, ‘SAFE_FFLAGS’, ‘SHLIB_LDFLAGS’ and
‘SHLIB_CXXLDFLAGS’: see file config.site in the sources for
more documentation on these and others.
To compile a profiling version of R, one might for example want to use ‘MAIN_CFLAGS=-pg’, ‘MAIN_FFLAGS=-pg’, ‘MAIN_LDFLAGS=-pg’ on platforms where ‘-pg’ cannot be used with position-independent code.
Beware: it may be necessary to set CFLAGS
and
FFLAGS
in ways compatible with the libraries to be used: one
possible issue is the alignment of doubles, another is the way
structures are passed.
On some platforms configure
will select additional flags for
CFLAGS
, CPPFLAGS
and LIBS
in R_XTRA_CFLAGS
(and so on). These are for options which are always required, for
example to force IEC 60559 compliance.
Previous: Compile and load flags, Up: Configuration on a Unix-alike [Contents][Index]
There are several files that are part of the R sources but can be
re-generated from their own sources by configuring with option
--enable-maintainer-mode and then running make
in the
build directory. This requires other tools to be installed, discussed
in the rest of this section.
File configure is created from configure.ac and the files
under m4 by autoconf
and aclocal
(part of the
automake package). There is a formal version requirement on
autoconf
of 2.69 or later, but it is unlikely that anything
other than the most recent versions67 have been thoroughly tested.
File src/include/config.h is created by autoheader
(part of autoconf).
Grammar files *.y are converted to C sources by an implementation
of yacc
, usually bison -y
: these are found in
src/main and src/library/tools/src. It is known that
earlier versions of bison
generate code which reads (and in
some cases writes) outside array bounds: bison
2.6.1 was found
to be satisfactory.
The ultimate sources for package compiler are in its noweb
directory. To re-create the sources from
src/library/compiler/noweb/compiler.nw, the command
notangle
is required. Some Linux distributions include this
command in package noweb. It can also be installed from the
sources at https://www.cs.tufts.edu/~nr/noweb/68. The package
sources are only re-created even in maintainer mode if
src/library/compiler/noweb/compiler.nw has been updated.
Next: Function and variable index, Previous: Configuration on a Unix-alike, Up: Top [Contents][Index]
This section provides some notes on building R on different Unix-alike platforms. These notes are based on tests run on one or two systems in each case with particular sets of compilers and support libraries. Success in building R depends on the proper installation and functioning of support software; your results may differ if you have other versions of compilers and support libraries.
Older versions of this manual contain notes on platforms such as HP-UX, IRIX, Alpha/OSF1 (for R < 2.10.0, and support has since been removed for all of these) and AIX (for R < = 3.5.x) for which we have had no recent reports.
C macros to select particular platforms can be tricky to track down (there is a fair amount of misinformation on the Web). The Wiki (currently) at http://sourceforge.net/p/predef/wiki/Home/ can be helpful. The R sources have used (often in included software under src/extra)
AIX: _AIX Cygwin: __CYGWIN__ FreeBSD: __FreeBSD__ HP-UX: __hpux__, __hpux IRIX: sgi, __sgi Linux: __linux__ macOS: __APPLE__ NetBSD: __NetBSD__ OpenBSD: __OpenBSD__ Solaris: __sun, sun Windows: _WIN32, _WIN64
• X11 issues | ||
• Linux | ||
• macOS | ||
• Solaris | ||
• FreeBSD | ||
• OpenBSD | ||
• Cygwin | ||
• New platforms |
Next: Linux, Previous: Platform notes, Up: Platform notes [Contents][Index]
The ‘X11()’ graphics device is the one started automatically on Unix-alikes (except most macOS builds) when plotting. As its name implies, it displays on a (local or remote) X server, and relies on the services provided by the X server.
The ‘modern’ version of the ‘X11()’ device is based on ‘cairo’ graphics and (in most implementations) uses ‘fontconfig’ to pick and render fonts. This is done on the server, and although there can be selection issues, they are more amenable than the issues with ‘X11()’ discussed in the rest of this section.
When X11 was designed, most displays were around 75dpi, whereas today they are of the order of 100dpi or more. If you find that X11() is reporting69 missing font sizes, especially larger ones, it is likely that you are not using scalable fonts and have not installed the 100dpi versions of the X11 fonts. The names and details differ by system, but will likely have something like Fedora’s
xorg-x11-fonts-75dpi xorg-x11-fonts-100dpi xorg-x11-fonts-ISO8859-2-75dpi xorg-x11-fonts-Type1 xorg-x11-fonts-cyrillic
and you need to ensure that the ‘-100dpi’ versions are installed
and on the X11 font path (check via xset -q
). The
‘X11()’ device does try to set a pointsize and not a pixel size:
laptop users may find the default setting of 12 too large (although very
frequently laptop screens are set to a fictitious dpi to appear like a
scaled-down desktop screen).
More complicated problems can occur in non-Western-European locales, so
if you are using one, the first thing to check is that things work in
the C
locale. The likely issues are a failure to find any fonts
or glyphs being rendered incorrectly (often as a pair of ASCII
characters). X11 works by being asked for a font specification and
coming up with its idea of a close match. For text (as distinct from
the symbols used by plotmath), the specification is the first element of
the option "X11fonts"
which defaults to
"-adobe-helvetica-%s-%s-*-*-%d-*-*-*-*-*-*-*"
If you are using a single-byte encoding, for example ISO 8859-2 in
Eastern Europe or KOI8-R in Russian, use xlsfonts
to find an
appropriate family of fonts in your encoding (the last field in the
listing). If you find none, it is likely that you need to install
further font packages, such as ‘xorg-x11-fonts-ISO8859-2-75dpi’ and
‘xorg-x11-fonts-cyrillic’ shown in the listing above.
Multi-byte encodings (most commonly UTF-8) are even more complicated. There are few fonts in ‘iso10646-1’, the Unicode encoding, and they only contain a subset of the available glyphs (and are often fixed-width designed for use in terminals). In such locales fontsets are used, made up of fonts encoded in other encodings. If the locale you are using has an entry in the ‘XLC_LOCALE’ directory (typically /usr/share/X11/locale), it is likely that all you need to do is to pick a suitable font specification that has fonts in the encodings specified there. If not, you may have to get hold of a suitable locale entry for X11. This may mean that, for example, Japanese text can be displayed when running in ‘ja_JP.UTF-8’ but not when running in ‘en_GB.UTF-8’ on the same machine (although on some systems many UTF-8 X11 locales are aliased to ‘en_US.UTF-8’ which covers several character sets, e.g. ISO 8859-1 (Western European), JISX0208 (Kanji), KSC5601 (Korean), GB2312 (Chinese Han) and JISX0201 (Kana)).
On some systems scalable fonts are available covering a wide range of glyphs. One source is TrueType/OpenType fonts, and these can provide high coverage. Another is Type 1 fonts: the URW set of Type 1 fonts provides standard typefaces such as Helvetica with a larger coverage of Unicode glyphs than the standard X11 bitmaps, including Cyrillic. These are generally not part of the default install, and the X server may need to be configured to use them. They might be under the X11 fonts directory or elsewhere, for example,
/usr/share/fonts/default/Type1 /usr/share/fonts/ja/TrueType
Next: macOS, Previous: X11 issues, Up: Platform notes [Contents][Index]
Linux is the main development platform for R, so compilation from the sources is normally straightforward with the most common compilers and libraries.70
Recall that some package management systems (such as RPM and
deb) make a distinction between the user version of a package and the
developer version. The latter usually has the same name but with the
extension ‘-devel’ or ‘-dev’: you need both versions
installed. So please check the configure
output to see if the
expected features are detected: if for example ‘readline’ is
missing add the developer package. (On most systems you will also need
‘ncurses’ and its developer package, although these should be
dependencies of the ‘readline’ package(s).) You should expect to
see in the configure
summary
Interfaces supported: X11, tcltk External libraries: pcre2, readline, curl Additional capabilities: PNG, JPEG, TIFF, NLS, cairo, ICU
When R has been installed from a binary distribution there are sometimes problems with missing components such as the Fortran compiler. Searching the ‘R-help’ archives will normally reveal what is needed.
It seems that ‘ix86’ Linux accepts non-PIC code in shared
libraries, but this is not necessarily so on other platforms, in
particular on 64-bit CPUs such as ‘x86_64’. So care
can be needed with BLAS libraries and when building R as a
shared library to ensure that position-independent code is used in any
static libraries (such as the Tcl/Tk libraries, libpng
,
libjpeg
and zlib
) which might be linked against.
Fortunately these are normally built as shared libraries with the
exception of the ATLAS BLAS libraries.
The default optimization settings chosen for CFLAGS
etc are
conservative. It is likely that using -mtune will result in
significant performance improvements on recent CPUs: one possibility is
to add -mtune=native for the best possible performance on the
machine on which R is being installed. It is also possible to
increase the optimization levels to -O3: however for many
versions of the compilers this has caused problems in at least one
CRAN package.
For platforms with both 64- and 32-bit support, it is likely that
LDFLAGS="-L/usr/local/lib64 -L/usr/local/lib"
is appropriate since most (but not all) software installs its 64-bit libraries in /usr/local/lib64. To build a 32-bit version of R on ‘x86_64’ with Fedora 32 we used
CC="gcc -m32" CXX="g++ -m32" FC="gfortran -m32" OBJC=${CC} LDFLAGS="-L/usr/local/lib" LIBnn=lib
Note the use of ‘LIBnn’: ‘x86_64’ Fedora installs its
64-bit software in /usr/lib64 and 32-bit software in
/usr/lib. Linking will skip over inappropriate binaries, but for
example the 32-bit Tcl/Tk configure scripts are in /usr/lib. It
may also be necessary to set the pkg-config
path, e.g. by
export PKG_CONFIG_PATH=/usr/local/lib/pkgconfig:/usr/lib/pkgconfig
The 32-bit system libcurl
did not work with the system CA
certificates: this is worked around in R’s test suite.
64-bit versions on Linux are built with support for files > 2Gb, and 32-bit versions will be if possible unless --disable-largefile is specified.
Note that 32-bit glibc
before version 2.29 uses a 32-bit
time_t
type, so to pass all the date-time checks needs R built
with flag --with-internal-tzcode.
Users of ‘ix86’ CPUs with SSE2 support71 may prefer to use the C/C++/Fortran flags
-mfpmath=sse -msse2
to force floating-point to use the same instructions as ‘x86_64’
builds and hence not make use of 80-bit ‘extended precision’
intermediate results. (NB: this affects more than floating-point
operations. For some OSes and versions of gcc
it might be
necessary to add -mstackrealign.)
To build a 64-bit version of R on ‘ppc64’ (also known as
‘powerpc64’) with gcc
4.1.1, Ei-ji Nakama used
CC="gcc -m64" CXX="gxx -m64" FC="gfortran -m64" CFLAGS="-mminimal-toc -fno-optimize-sibling-calls -g -O2" FFLAGS="-mminimal-toc -fno-optimize-sibling-calls -g -O2"
the additional flags being needed to resolve problems linking against libnmath.a and when linking R as a shared library.
The setting of the macro ‘SAFE_FFLAGS’ may need some help. It
should not need additional flags on platforms other than ‘68000’
(not likely to be encountered) and ‘ix86’. For the latter, if
the Fortran compiler is GNU (gfortran
or possibly
g77
) the flags
-msse2 -mfpmath=sse
are added: earlier versions of R added -ffloat-store and this might still be needed if a ‘ix86’ CPU is encountered without SSE2 support. Note that it is a replacement for ‘FFLAGS’, so should include all the flags in that macro (except perhaps the optimization level).
Additional compilation flags can be specified for added safety/security checks. For example Fedora adds
-Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -Fexceptions -fstack-protector-strong -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection
to all the C, C++ and Fortran compiler flags (even though
_GLIBCXX_ASSERTIONS
is only for C++ in current GCC and
glibc
and none of these are documented for gfortran
).
Use of _GLIBCXX_ASSERTIONS
will link abort
and
printf
into almost all C++ code, and R CMD check
--as-cran
will warn.
• Clang | ||
• Intel compilers |
Next: Intel compilers, Previous: Linux, Up: Linux [Contents][Index]
R has been built with Linux ‘ix86’ and ‘x86_64’ C and
C++ compilers (http://clang.llvm.org) based on the Clang
front-ends, invoked by CC=clang CXX=clang++
, together with
gfortran
. These take very similar options to the
corresponding GCC compilers.
This has to be used in conjunction with a Fortran compiler: the
configure
code will remove -lgcc from FLIBS
,
which is needed for some versions of gfortran
.
The current out-of-the-box default for clang++
is to use the
C++ runtime from the installed g++
. Using the runtime from
the libc++
project (http://libcxx.llvm.org/, Fedora RPM
libcxx-devel
) via -stdlib=libc++ has also been
tested.
Recent versions have (optional when built) OpenMP support.72
There is a project called flang
(https://github.com/flang-compiler/flang)) to develop a
Fortran compiler similar to clang but based on the Portland Group’s front
end. This needs something like
FC=/usr/local/flang/bin/flang LDFLAGS="-L/usr/local/flang/lib -L/usr/local/lib64"
Note that flang
accepts all the flags which clang
does (the driver is a modified version of clang
, and
flang
is a symbolic link to clang
), but does not
implement all of them for Fortran compilation: it also accepts most
PGI-style flags such as -mp for OpenMP. It currently produces
few diagnostics even with -Wall -pedantic.
flang
’s Fortran runtime is compiled against OpenMP and it
seems this conflicts with using OpenMP in R. So it may be necessary
to disable the latter by configuring R using --disable-openmp.
It is not clear what architectures flang
intends to support:
our experiments were done on ‘x86_64’. At the time of writing
binary ‘releases’ were available for that platform (called by them
‘x86’) and ‘ppc64le’.
Intel compilers have been used under ‘ix86’ and ‘x86_64’ Linux. Brian Ripley used version 9.0 of the compilers for ‘x86_64’ on Fedora Core 5 with
CC=icc CFLAGS="-g -O3 -wd188 -ip -mp" FC=ifort FLAGS="-g -O3 -mp" CXX=icpc CXXFLAGS="-g -O3 -mp" ICC_LIBS=/opt/compilers/intel/cce/9.1.039/lib IFC_LIBS=/opt/compilers/intel/fce/9.1.033/lib LDFLAGS="-L$ICC_LIBS -L$IFC_LIBS -L/usr/local/lib64" SHLIB_CXXLD=icpc
It may be necessary to use CC="icc -std=c99"
or CC="icc
-c99"
for C99-compliance. The flag -wd188 suppresses a large
number of warnings about the enumeration type ‘Rboolean’. Because
the Intel C compiler sets ‘__GNUC__’ without complete emulation of
gcc
, we suggest adding CPPFLAGS=-no-gcc
.
To maintain correct IEC 60559 arithmetic you most likely
need add flags to CFLAGS
, FFLAGS
and
CXXFLAGS
such as -mp (shown above) or -fp-model
precise -fp-model source, depending on the compiler version.
Others have reported success with versions 10.x and 11.x. Bjørn-Helge Mevik reported success with version 2015.3 of the compilers, using (for a SandyBridge CPU on Centos 6.x)
fast="-fp-model precise -ip -O3 -opt-mem-layout-trans=3 -xHost -mavx" CC=icc CFLAGS="$fast -wd188" FC=ifort FFLAGS="$fast" CXX=icpc CXXFLAGS="$fast"
It is possible that 32-builds need to force the use of SSE2 instructions
in SAFE_FFLAGS
, e.g. by
SAFE_FFLAGS=-axsse2
Next: Solaris, Previous: Linux, Up: Platform notes [Contents][Index]
(‘macOS’ was known as ‘OS X’ from 2012–2016.)
The instructions here are for 64-bit (‘x86_64’) builds on 10.13
(High Sierra) or later. R can in principle be built for 10.6 and
later, although this is little tested and it may be necessary to install
later versions of software such as libcurl
.
• Prerequisites | ||
• Other C/C++ compilers | ||
• Other libraries | ||
• Tcl/Tk headers and libraries | ||
• Java (macOS) | ||
• Frameworks | ||
• Building R.app | ||
• Building binary packages |
Next: Other C/C++ compilers, Previous: macOS, Up: macOS [Contents][Index]
The following are essential to build R
xcode-select --install
in a terminal. (If you have a fresh OS
installation, running e.g. make
in a terminal will offer the
installation of the command-line tools. If you have installed Xcode,
this provides the command-line tools. The tools may need to be
reinstalled when macOS is upgraded, as upgrading partially removes
them.)
The Command Line Tools provide C and C++ compilers derived from LLVM’s
clang
.
These install into /usr/local/gfortran: its bin directory
does not need to be on the path as a full path can be used for
FC
: see below.
pcre2
and xz
(for
liblzma
) from https://mac.R-project.org/libs-4. For example
curl -OL https://mac.r-project.org/libs-4/pcre2-10.34-darwin.17-x86_64.tar.gz sudo tar -xvzf pcre2-10.34-darwin.17-x86_64.tar.gz -C / curl -OL https://mac.r-project.org/libs-4/xz-5.2.4-darwin.17-x86_64.tar.gz sudo tar -xvzf xz-5.2.4-darwin.17-x86_64.tar.gz -C /
and desirable
readline
from https://mac.R-project.org/libs-4, or
configure with --without-readline.
jpeg
, libpng
, pkgconfig
and tiff
from https://mac.R-project.org/libs-4, for the full range of
bitmapped graphics devices.
configure
script can be told to look for X11
in XQuartz
’s main
location of /opt/X11, e.g. by
--x-includes=/opt/X11/include --x-libraries=/opt/X11/lib
although linked versions under /usr/X11 will be found. (It seems that for recent versions of macOS/XQuartz /usr/X11 may exist but be a link to a non-existent directory: reinstalling XQuartz might help.)
clang
in the Command
Line Tools: this is needed for the quartz()
graphics device.
Use --without-aqua if you want a standard Unix-alike build:
apart from disabling quartz()
and the ability to use the build
with R.APP, it also changes the default location of the personal
library (see ?.libPaths
).
cairo
(without Pango
) can be enabled if
pkg-config
and XQuartz are available. Make sure the XQuartz’s
pkg-config
files are found first on the configuration path: for
example by setting
export PKG_CONFIG_PATH=/opt/X11/lib/pkgconfig:/usr/local/lib/pkgconfig:/usr/lib/pkgconfig
or appending that variable to the configure
command (as below).
texi2any
from a ‘texinfo’ distribution, which requires
perl
(currently part of macOS but it has been announced that
it will not be from macOS 10.16). An old version of texi2any
has been included in the binary distribution of R and there is a
texinfo
component at https://mac.R-project.org/libs-4.
For C/C++ compilers supporting OpenMP, see the subsection below.
To build R itself from the sources with the compilers in the Command
Line Tools (or Xcode) and one of the gfortran
installers, use
a file config.site containing
CC=clang OBJC=$CC FC=/usr/local/gfortran/bin/gfortran CXX=clang++
and configure by something like
./configure -C \ --enable-R-shlib --enable-memory-profiling \ --x-includes=/opt/X11/include --x-libraries=/opt/X11/lib \ PKG_CONFIG_PATH=/opt/X11/lib/pkgconfig:/usr/local/lib/pkgconfig:/usr/lib/pkgconfig
To install packages using compiled code one needs the Command Line Tools
and appropriate compilers, e.g. Fortran and the C/C++ compilers from
those tools. Some packages have further requirements such as
pkg-config
.
• Note for Catalina users |
Previous: Prerequisites, Up: Prerequisites [Contents][Index]
The default security settings for Catalina can make it difficult to
install Apple packages built after 2019-06-01 which have not been
‘notarized’74
by Apple. And not just packages, as this has been seen for executables
contained in tarballs/zipfiles (for example, for pandoc
).
There are workarounds, including in some cases not installing the latest version. Usually one can use ‘Open With’ (Control/right/two-finger-click in Finder), then select ‘Installer’ and ‘Open’ if you get a further warning message.
This applies also to some ‘nightly builds’ from https://mac.r-project.org/.
Next: Other libraries, Previous: Prerequisites, Up: macOS [Contents][Index]
Other distributions of clang
are available from
http://releases.llvm.org/. In particular, these include support
for OpenMP which Apple builds of clang
do not, and may contain
more bugfixes and new features (such as better diagnostics) than that in
Command Line Tools/Xcode.
Suppose one of these distributions is installed under /usr/local/clang. Use a file config.site containing
CC=/usr/local/clang/bin/clang OBJC=$CC FC=/usr/local/gfortran/bin/gfortran CXX=/usr/local/clang/bin/clang++ LDFLAGS="-L/usr/local/clang/lib -L/usr/local/lib" R_LD_LIBRARY_PATH=/usr/local/clang/lib:/usr/local/lib
The care to specify library paths is to ensure that the OpenMP runtime library, here /usr/local/clang/lib/libomp.dylib, is found when needed. If this works, you should see the line
checking whether OpenMP SIMD reduction is supported... yes
in the configure
output. Also, ‘R_LD_LIBRARY_PATH’ needs
to be set to find the latest version of the C++ run-time libraries
rather than the system ones.
For Catalina, the system paths need to be specified via
CC="/usr/local/clang/bin/clang -isysroot /Library/Developer/CommandLineTools/SDKs/MacOSX.sdk" CXX="/usr/local/clang/bin/clang++ -isysroot /Library/Developer/CommandLineTools/SDKs/MacOSX.sdk"
(Long lines split for the manual, only.) Should the location of the SDK
change, it can be found by running xcrun -show-sdk-path
.
The approach in the previous paragraph also works for Mojave, but for versions 10.x of the Command Line Tools an alternative as to install the headers to /usr/include: from a Terminal run
sudo installer -pkg \ /Library/Developer/CommandLineTools/Packages/macOS_SDK_headers_for_macOS_10.14.pkg \ -target /
(This will need to be re-run if the OS decides to update the Command Line Tools.)
Next: Tcl/Tk headers and libraries, Previous: Other C/C++ compilers, Up: macOS [Contents][Index]
Pre-compiled versions of many of the Useful libraries and programs are available from https://mac.R-project.org/libs-4/ or https://mac.R-project.org/libs/.
The Accelerate
library75
can be used via the configuration options
--with-blas="-framework Accelerate"
to provide potentially higher-performance versions of the BLAS and LAPACK routines.76 This also includes a full LAPACK which can be used via --with-lapack: however, the version of LAPACK it contains is often seriously old.
Threading in Accelerate is controlled by ‘Grand Central Dispatch’ and is said not to need user control.
Looking at the top of /Library/Frameworks/R.framework/Resources/etc/Makeconf will show the compilers and configuration options used for the CRAN binary package for R: at the time of writing the non-default options
--enable-memory-profiling --enable-R-framework --x-libraries=/opt/X11/lib --x-includes=/opt/X11/include
were used. (--enable-R-framework implies --enable-R-shlib.)
Configure option --with-internal-tzcode is the default on macOS,
as the system implementation of time zones does not work correctly for
times before 1902 or after 2037 (despite using a 64-bit time_t
).
The TeX implementation used by the developers is MacTeX77 (https://www.tug.org/mactex/): the full installation is about 7GB, but a smaller version (‘Basic TeX’) is available at https://www.tug.org/mactex/morepackages.html to which you will need to add some packages to build R, e.g. for the 2020 version we needed to add78 cm-super, helvetic, inconsolata and texinfo which brought this to about 380MB. ‘TeX Live Utility’ (available via the MacTeX front page) provides a graphical means to manage TeX packages. This is documented to require Sierra or later: for earlier versions see the instructions on the MacTeX front page.
Checking packages thoroughly requires ghostscript
(part of the
full MacTeX distribution or separately from
https://www.tug.org/mactex/morepackages.html) and qpdf
(from https://mac.r-project.org/libs-4, a version of which is in
the bin directory of a binary installation of R, usually
/Library/Frameworks/R.framework/Resources/bin/qpdf).
One macOS quirk is that the default path has /usr/local/bin after /usr/bin, contrary to common practice on Unix-alikes. This means that if you install tools from the sources they will by default be installed under /usr/local and not supersede the system versions.
Next: Java (macOS), Previous: Other libraries, Up: macOS [Contents][Index]
If you plan to use the tcltk
package for R, you need to
install a distribution of Tcl/Tk. There are two alternatives. If you
use R.APP you will want to use X11-based Tcl/Tk (as used on other
Unix-alikes), which is installed as part of the CRAN binary
for R and available as separate tcl
and tk
components
from https://mac.R-project.org/libs-4/. This may need
configure
options
-with-tcltk=/usr/local/lib
or
--with-tcl-config=/usr/local/lib/tclConfig.sh --with-tk-config=/usr/local/lib/tkConfig.sh
Note that this requires a matching XQuartz installation.
There is also a native (‘Aqua’) version of Tcl/Tk which produces widgets in the native macOS style: this will not work with R.APP because of conflicts over the macOS menu, but for those only using command-line R this provides a much more intuitive interface to Tk for experienced Mac users. Most versions of macOS come with Aqua Tcl/Tk libraries, but these are often not at all recent versions of Tcl/Tk (8.5.9 in High Sierra, which is not even the latest patched version in that series). It is better to install Tcl/Tk 8.6.x from the sources or a binary distribution from https://www.activestate.com/activetcl/downloads. Configure R with
--with-tcl-config=/Library/Frameworks/Tcl.framework/tclConfig.sh --with-tk-config=/Library/Frameworks/Tk.framework/tkConfig.sh
If you need to find out which distribution of Tk is in use at run time, use
library(tcltk) tclvalue(.Tcl("tk windowingsystem")) # "x11" or "aqua"
Next: Frameworks, Previous: Tcl/Tk headers and libraries, Up: macOS [Contents][Index]
The situation with Java support on macOS is messy,79 and distribution of Java for all platforms changed in 2018.
macOS no longer comes with an installed Java runtime (JRE), and a macOS
upgrade may remove one if already installed: it is intended to be
installed at first use. Check if a JRE is installed by running
java -version
in a Terminal
window: if Java is not
installed80 this should prompt you to install it. You can also install
directly a recent Java from Oracle (currently from
http://www.oracle.com/technetwork/java/javase/downloads/index.html).
Builds of OpenJDK may also be available, e.g. from
https://adoptopenjdk.net or http://jdk.java.net/. We
recommend you install a version with long-term support, e.g. 8 or 11
(but not 9, 10, 12–16 which have/had a 6-month lifetime).
Binary distributions of R are built against a specific version
(e.g. 11.0.6) of Java so sudo R CMD javareconf
will likely be
needed before using Java-using packages.
To see what compatible versions of Java are currently installed, run
/usr/libexec/java_home -V -a x86_64
. If needed, set the
environment variable JAVA_HOME
to choose between these, both when
R is built from the sources and when R CMD javareconf
is
run.
Configuring and building R both looks for a JRE and for support for compiling JNI programs (used by packages rJava and JavaGD); the latter requires a JDK (Java SDK) and not just a JRE81.
The build process tries to fathom out what JRE/JDK to use, but it may
need some help, e.g. by setting JAVA_HOME
. A Oracle JDK can be
specified explicitly by something like
JAVA_HOME=/Library/Java/JavaVirtualMachines/jdk-11.jdk/Contents/Home JAVA_CPPFLAGS="-I/${JAVA_HOME}/include -I/${JAVA_HOME}/include/darwin" JAVA_LD_LIBRARY_PATH="${JAVA_HOME}/lib/server" JAVA_LIBS="-L/${JAVA_HOME}/lib/server -ljvm"
or
JAVA_HOME=/Library/Java/JavaVirtualMachines/jdk1.8.0_191.jdk/Contents/Home JAVA_CPPFLAGS="-I/${JAVA_HOME}/include -I/${JAVA_HOME}/include/darwin" JAVA_LD_LIBRARY_PATH="${JAVA_HOME}/jre/lib/server" JAVA_LIBS="-L/${JAVA_HOME}/jre/lib/server -ljvm"
in config.site.
To use the builds of OpenJDK from https://adoptopenjdk.net (Apple
package) or http://jdk.java.net/ (tarball) set JAVA_HOME
to
e.g. one of
JAVA_HOME=/Library/Java/JavaVirtualMachines/adoptopenjdk-11.jdk/Contents/Home JAVA_HOME=/path/to/JDK/jdk-11.jdk/Contents/Home
where /path/to/JDK is wherever the tarball was unpacked.
Note that it is necessary to set the environment variable NOAWT
to
1
to install many of the Java-using packages.
Next: Building R.app, Previous: Java (macOS), Up: macOS [Contents][Index]
The CRAN build of R is installed as a framework, which is selected by the option
./configure --enable-R-framework
(This is intended to be used with an Apple toolchain: others may not
support frameworks correctly but those from releases.llvm.org
do.)
It is only needed if you want to build R for use with the R.APP console, and implies --enable-R-shlib to build R as a dynamic library. This option configures R to be built and installed as a framework called R.framework. The default installation path for R.framework is /Library/Frameworks but this can be changed at configure time by specifying the flag --enable-R-framework[=DIR] (or --prefix) or at install time via
make prefix=/where/you/want/R.framework/to/go install
Note that installation as a framework is non-standard (especially to a
non-standard location) and Unix utilities may not support it (e.g. the
pkg-config
file libR.pc will be put somewhere unknown
to pkg-config
).
Next: Building binary packages, Previous: Frameworks, Up: macOS [Contents][Index]
Note that building the R.APP GUI console is a separate project, using Xcode. Before compiling R.APP make sure the current version of R is installed in /Library/Frameworks/R.framework and working at the command-line (this can be a binary install).
The current sources can be checked out by
svn co https://svn.r-project.org/R-packages/trunk/Mac-GUI
and built by loading the R.xcodeproj
project (select the
R
target and a suitable configuration), or from the command-line
by e.g.
xcodebuild -target R -configuration Release
See also the INSTALL file in the checkout or directly at https://svn.r-project.org/R-packages/trunk/Mac-GUI/INSTALL.
R.APP does not need to be installed in any specific way. Building R.APP results in the R.APP bundle which appears as one R icon. This application bundle can be run anywhere and it is customary to place it in the /Applications folder.
Previous: Building R.app, Up: macOS [Contents][Index]
CRAN macOS binary packages are distributed as tarballs with
suffix .tgz to distinguish them from source tarballs. One can
tar
an existing installed package, or use R CMD
INSTALL --build
.
However, there are some important details.
CC="clang -mmacosx-version-min=10.13" CXX="clang++ -mmacosx-version-min=10.13" FC="gfortran -mmacosx-version-min=10.13"
otool -L
or
objdump -macho -dylibs-used
. This can include C++ and Fortran
run-time libraries under /usr/local: one can use
install_name_tool
to point these at system versions or those
shipped with R, for example
install_name_tool -change /usr/local/clang/lib/libc++.1.dylib \ /usr/lib/libc++.1.dylib \ pkg.so install_name_tool -change /usr/local/gfortran/lib/libgfortran.5.dylib \ /Library/Frameworks/R.framework/Versions/4.0/Resources/lib/libgfortran.5.dylib \ pkg.so
(where the details depend on the compilers and CRAN macOS R release).
SHLIB_CXXLD = /usr/local/clang/bin/clang PKG_LIBS = /usr/local/clang/lib/libc++.a /usr/local/clang/lib/libc++abi.a
in src/Makevars. It would also be possible to static link the
Fortran runtime libraries /usr/local/gfortran/lib/libgfortran.a
and /usr/local/gfortran/lib/libquadmath.a should the Fortran
compiler have later versions (but gfortran
8, 9 and 10 all
have version 5.0.0
).
The CRAN binary packages are built with the Apple compiler on High Sierra, which avoids the first two and any issues with C++ libraries.
Next: FreeBSD, Previous: macOS, Up: Platform notes [Contents][Index]
• 64-bit builds | ||
• Using gcc |
R has been built successfully on Solaris 10 using the (zero cost)
Oracle Developer Studio82 compilers: there has also been success with
gcc
/gfortran
. (Recent Sun machines are AMD Opterons
or Intel Xeons (‘amd64’) rather than ‘x86’, but 32-bit
‘x86’ executables are the default.) How these compilers
identify themselves is slightly confusing: commands CC -V
with
Developer Studio 12.5 and 12.6 report as versions 5.14 and 5.15. We
will only consider Developer Studio versions 12.5 (May 2016) and 12.6
(July 2017).
There have been few reports on Solaris 11, with no known extra issues.
Solaris was last tested on Sparc machines in June 2017.
The Solaris versions of several of the tools needed to build R
(e.g. make
, ar
and ld
) are in
/usr/ccs/bin, so if using those tools ensure this is in your
path. A version of the preferred GNU tar
is (if
installed) in /usr/sfw/bin. It may be necessary to avoid the
tools in /usr/ucb: POSIX-compliant versions of some tools can be
found in /usr/xpg4/bin and /usr/xpg6/bin.
A large selection of Open Source software can be installed from
https://www.opencsw.org, by default installed under
/opt/csw. Solaris 10 ships with bzlib
version 1.0.6
(sufficient) but zlib
version 1.2.3 (too old): OpenCSW has 1.2.8.
(Note from 2019: updating of OpenCSW has slowed or stopped.)
At least when compiling with Oracle compilers, Solaris uses far more stack space than other platforms. This makes it desirable to build PCRE1 (and PCRE2 < 10.30) with the option --disable-stack-for-recursion: the OpenCSW distribution was at the time of writing.
The Oracle compilers are unusual in not including
/usr/local/include in the default include search path: R’s
default CPPFLAGS=-I/usr/local/include
remedies this. If you rely
on OpenCSW software you may need CPPFLAGS=-I/opt/csw/include
(or
both).
You will need GNU libiconv
and readline
: the
Solaris version of iconv
is not sufficiently powerful.
The native make
suffices to build R but a number of
packages require GNU make
(some without declaring it
as ‘SystemRequirements’ in the DESCRIPTION file).
The support for the C99 long double
type on Sparc hardware uses
quad-precision arithmetic, and this is usually slow because it is done
by software emulation. On such systems the configure
option
--disable-long-double can be used for faster but less accurate
computations.
The Solaris time-zone conversion services seem to be unreliable pre-1916
in Europe (when daylight-savings time was first introduced): most often
reporting in the non-existent DST variant. Using configure
option --with-internal-tzcode is recommended, and required if
you find time-zone abbreviations being given odd values (as has been
seen on 64-bit builds without it).
When using the Oracle compilers do not specify -fast, as
this disables IEEE arithmetic and make check
will
fail.
A little juggling of paths was needed to ensure GNU
libiconv
(in /usr/local) was used rather than the Solaris
iconv
:
CC="cc -xc99" CFLAGS="-O -xlibmieee" FC=f95 FFLAGS=-O CXX=CC CXXSTD="-std=c++11 -library=stdcpp,CrunG3" CXX11STD="-std=c++11 -library=stdcpp,CrunG3" CXX14STD="-std=c++14 -library=stdcpp,CrunG3" CXXFLAGS=-O R_LD_LIBRARY_PATH="/opt/developerstudio12.6/lib:/usr/local/lib:/opt/csw/lib"
The Oracle compilers do not by default conform to the C99 standard
(appendix F 8.9) on the return values of functions such as log
:
use -xlibmieee to ensure this.
A peculiarity of some versions of the Fortran compiler has been that when asked to link a shared object they did not link against all the Fortran 9x runtime libraries, hence
FCLIBS_XTRA="-lfsu /opt/developerstudio12.6/lib/libfui.so.2"
has been needed.
Using -xlibmil
in CFLAGS
or FFLAGS
allows more
system mathematical functions to be inlined.
On ‘x86’ you will get marginally higher performance via
CFLAGS="-xO5 -xlibmieee -xlibmil -nofstore -xtarget=native" FFLAGS="-xO5 -xlibmil -nofstore -xtarget=native" CXXFLAGS="-xO5 -xlibmil -nofstore -xtarget=native" SAFE_FFLAGS="-O -xlibmil -fstore -xtarget=native"
but the use of -nofstore
can be less numerically stable, and some
packages have in the past failed to compile at optimization
level 5.
The Oracle compilers provide several implementations of the C++
standards which select both the set of headers and a C++ runtime
library. One of those is selected by the -library flag, which
as it is needed for both compiling and linking is best specified as part
of the compiler or standard. Current R expects a C++11 compiler, for
which the choice given above is the only possibility. Although version
12.5 accepted the flag -std=c++14, it did not pass
configure
’s conformance tests: version 12.6 does.
The performance library sunperf
is available for use with the
Oracle compilers. If selected as a BLAS, it must also be
selected as LAPACK via
./configure --with-blas='-library=sunperf' --with-lapack
This has often given test failures in the past, in several different places.83
Parsing very complex R expressions needs a lot of stack space when the Oracle compilers are used: several packages require the stack increased to at least 20MB.
Some people have reported that the Solaris libintl
needs to be
avoided, for example by using --disable-nls or
--with-included-gettext or using libintl
from OpenCSW.
(On the other hand, there have been many successful installs which
automatically detected libintl
from OpenCSW or selected the
included gettext
.)
It has been reported that some Solaris installations need
INTERNET_LIBS="-lsocket -lnsl"
on the configure
command line or in file config.site;
however, there have been many successful installs without this.
On both ‘x86’ and ‘Sparc’ platforms the compilers default to 32-bit code.
For a 64-bit target add -m64 to the compiler macros
and use something like LDFLAGS=-L/usr/local/lib/amd64
or
LDFLAGS=-L/usr/local/lib/sparcv9
as appropriate (and other 64-bit
library directories if used, e.g. -L/opt/csw/lib/amd64
).
It will also be necessary to point pkg-config
at the 64-bit
directories, e.g. by something like
PKG_CONFIG_PATH= /usr/local/lib/amd64/pkgconfig:/opt/csw/lib/64/pkgconfig:/usr/lib/64/pkgconfig
and to specify a 64-bit Java VM by e.g.
JAVA_CPPFLAGS="-I${JAVA_HOME}/../include -I${JAVA_HOME}/../include/solaris" JAVA_LD_LIBRARY_PATH=${JAVA_HOME}/lib/amd64/server JAVA_LIBS="-L${JAVA_HOME}/lib/amd64/server \ -R${JAVA_HOME}/lib/amd64/server -ljvm"
Previous: 64-bit builds, Up: Solaris [Contents][Index]
If using gcc
, ensure that the compiler was compiled for the
version of Solaris in use. (This can be ascertained from gcc
-v
.) gcc
makes modified versions of some header files, and
several reports of problems were due to using gcc
compiled on
one version of Solaris on a later version. Note that this can even
apply to OS patches: some 2016 patches to Solaris 10 changed its C
header files in way incompatible84 with the modified versions included with OpenCSW’s
binary distribution.
The notes here are for gcc
set up to use the Solaris linker:
it can also be set up to use GNU ld
, but that has not been
tested. The tests were for compilers from the OpenCSW repository:
Solaris systems often come with much older compilers installed under
/usr/sfw/bin. One of -m32 or -m64 will be the
default and could be omitted, but it is not easy to find out which.
(For OpenCSW it is -m32.)
Compilation for an ‘x86’ target with gcc
5.2.0
needed
CC="gcc -m32" CPPFLAGS="-I/opt/csw/include -I/usr/local/include" FC="gfortran -m32" CXX="g++ -m32" LDFLAGS="-L/opt/csw/lib -L/usr/local/lib"
For an ‘amd64’ target we used
CC="gcc -m64" CPPFLAGS="-I/opt/csw/include -I/usr/local/include" FC="gfortran -m64" CXX="g++ -m64" LDFLAGS="-L/opt/csw/lib/amd64 -L/usr/local/lib/amd64"
Note that paths such as /opt/csw/lib, /usr/local/lib/amd64
and /opt/csw/lib/amd64 may need to be in the
LD_LIBRARY_PATH
during configuration.
Next: OpenBSD, Previous: Solaris, Up: Platform notes [Contents][Index]
There have been few recent reports on FreeBSD: there is a ‘port’ at
https://www.freebsd.org/ports/math.html. Recent versions of
FreeBSD use Clang and the libc++
C++ headers and runtime, but the
‘port’ is configured to use GCC.
Use of ICU for collation and the configure
option
--with-internal-tzcode are desirable workarounds.
Next: Cygwin, Previous: FreeBSD, Up: Platform notes [Contents][Index]
Ingo Feinerer installed R version 3.2.2 on OpenBSD 5.8 arch
‘amd64’ (their name for ‘x86_64’). Details of the build
(and patches applied) are at
http://cvsweb.openbsd.org/cgi-bin/cvsweb/ports/math/R/. (Downgrading
the zlib
requirement to 1.2.3 is against the advice of the R
developers.)
Next: New platforms, Previous: OpenBSD, Up: Platform notes [Contents][Index]
The 32-bit version never worked well enough to pass R’s make
check
, and residual support from earlier experiments was removed in
R 3.3.0.
The 64-bit version was never supported.
Previous: Cygwin, Up: Platform notes [Contents][Index]
There are a number of sources of problems when installing R on a new hardware/OS platform. These include
Floating Point Arithmetic: R requires arithmetic compliant
with IEC 60559, also known as IEEE 754.
This mandates the use of plus and minus infinity and NaN
(not a
number) as well as specific details of rounding. Although almost all
current FPUs can support this, selecting such support can be a pain.
The problem is that there is no agreement on how to set the signalling
behaviour; Sun/Sparc, SGI/IRIX and ‘ix86’ Linux require no
special action, FreeBSD requires a call to (the macro)
fpsetmask(0)
and OSF1 required that computation be done with a
-ieee_with_inexact flag etc. On a new platform you must find
out the magic recipe and add some code to make it work. This can often
be done via the file config.site which resides in the top level
directory.
Beware of using high levels of optimization, at least initially. On
many compilers these reduce the degree of compliance to the
IEEE model. For example, using -fast on the Oracle
compilers has caused R’s NaN
to be set incorrectly, and
gcc
’s -ffast-math and clang
’s
-Ofast have given incorrect results.
Shared Objects: There seems to be very little agreement
across platforms on what needs to be done to build shared objects.
there are many different combinations of flags for the compilers and
loaders. GNU libtool cannot be used (yet), as it currently
does not fully support Fortran: one would need a shell wrapper for
this). The technique we use is to first interrogate the X window system
about what it does (using xmkmf
), and then override this in
situations where we know better (for tools from the GNU
Compiler Collection and/or platforms we know about). This typically
works, but you may have to manually override the results. Scanning the
manual entries for cc
and ld
usually reveals the
correct incantation. Once you know the recipe you can modify the file
config.site (following the instructions therein) so that the
build will use these options.
It seems that gcc
3.4.x and later on ‘ix86’ Linux
defeat attempts by the LAPACK code to avoid computations entirely in
extended-precision registers, so file src/modules/lapack/dlamc.f
may need to be compiled without optimization or with additional flags.
Set the configure variable SAFE_FFLAGS
to the flags to be used for
this file.
If you do manage to get R running on a new platform please let us know about it so we can modify the configuration procedures to include that platform.
If you are having trouble getting R to work on your platform please feel free to use the ‘R-devel’ mailing list to ask questions. We have had a fair amount of practice at porting R to new platforms ...
Next: Concept index, Previous: Platform notes, Up: Top [Contents][Index]
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Next: Environment variable index, Previous: Function and variable index, Up: Top [Contents][Index]
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e.g. GNU
tar
version 1.15 or later, or that from the ‘libarchive’
(as used on macOS versions 10.6 and later) or ‘Heirloom Toolchest’
distributions.
for some Subversion clients ‘http:’ may appear to work, but requires continual redirection.
Most aspects will work with paths containing spaces, but external software used by R may not.
which use lib rather than lib64 for their primary 64-bit library directories: attempts are made to detect such systems.
Instructions on how to install the latest version are at https://www.ctan.org/tex-archive/fonts/inconsolata/.
on a
Unix-alike, ‘inconsolata’ is omitted if not found by
configure
.
This will be needed if more than one sub-architecture is to be installed.
with possible values ‘i386’, ‘x64’, ‘32’ and ‘64’.
mainly on RedHat and Fedora, whose layout is described here.
How to prepare such a directory is described in file src/extra/tzone/Notes in the R sources.
for
example, -fopenmp, -xopenmp or -qopenmp.
This includes for clang
and the Intel and Oracle compilers.
This does not necessarily disable use of
OpenMP – the configure
code allows for platforms where OpenMP
is used without a flag. For the flang
compiler in late 2017,
the Fortran runtime always used OpenMP.
This was a valid option for
g++
5 and later and 2016 versions of the Intel and Solaris
compilers. For earlier versions of g++
one could try
-std=c++1y.
Nowadays part of GNU
binutils
and used by LLVM to support LTO. It is sometimes
installed as ld.gold
.
probably also 8.4 and later.
Capitalization of this project’s name is inconsistent even on its own webpages.
There are reports of segfaults when ‘MiKTeX’
installs additional packages when making NEWS.pdf: re-running
make
seems to solve this.
The installer puts links to R
and
Rscript
in /usr/local/bin. If these are missing, you
can run directly the copies in
/Library/Frameworks/R.framework/Resources/.
At the
time of writing: use pkgutil --pkgs | grep org.r-project
to
check..
More precisely, of the Apple package of the same name: this means that installing a package for 3.6.x does not remove an installation for 4.0 or later.
The Oracle compilers on Solaris (where the issue is parsing very complex R expressions) and GCC 9 on Linux.
unless they were excluded in the build.
its binding is locked once the startup files have been read, so users cannot easily change it.
If a proxy needs to be set, see
?download.file
.
for a small number of CRAN packages where this is known to be safe and is needed by the autobuilder this is the default. Look at the source of tools:::.install_packages for the list. It can also be specified in the package’s DESCRIPTION file.
Note that capitalization and versioning may differ from the Open Source project.
using a path containing spaces is likely to cause problems
They need to have been created using -headerpad_max_install_names, which is the default for an R package.
‘X/Open Portability Guide’, which has had several versions.
On some systems setting
LC_ALL
or LC_MESSAGES
to ‘C’ disables LANGUAGE
.
If you try changing from French to Russian except in a UTF-8 locale, you will most likely find messages change to English.
the language written in England: some people living in the USA appropriate this name for their language.
with Americanisms.
also known as IEEE 754
at least when storing quantities: the on-FPU precision is allowed to vary
e.g. Bessel, beta and gamma functions
including copying MkRules.dist to MkRule.local and selecting the architecture.
also known as IEEE 754
Note
that C11 compilers need not be C99-compliant: R requires support for
double complex
and variable-length arrays which are optional in
C11 but are mandatory in C99. C18 (also known as C17) is a ‘bugfix
release’ of C11, clarifying the standard.
Examples are -std=gnu99, -std=c99 and -c99.
-std=c99 excludes POSIX functionality, but config.h will turn on all GNU extensions to include the POSIX functionality for R itself: this does not apply to badly-written packages. The default mode for GCC 5.1 and later is -std=gnu11, which currently includes the optional features R needs.
However, it is possible to break
the default behaviour of glibc
by re-specifying the gconv
modules to be loaded.
specifically, the C99
functionality of headers wchar.h and wctype.h, types
wctans_t
and mbstate_t
and functions mbrtowc
,
mbstowcs
, wcrtomb
, wcscoll
, wcstombs
,
wctrans
, wctype
, and iswctype
.
including expm1
, hypot
, log1p
,
nearbyint
and va_copy
.
including
opendir
, readdir
, closedir
, popen
,
stat
, glob
, access
, getcwd
and chdir
system calls, select
on a Unix-alike, and either putenv
or
setenv
.
such as
realpath
, symlink
.
most often distributed as part of xz
:
possible names in Linux distributions include
xz-devel
/xz-libs
and liblzma-dev
.
but not a major version greater than 7 should there ever be one: the major version has been 7 since 2000.
for example to specify static linking with a build which has both shared and static libraries.
Such as
GNU tar
1.15 or later, bsdtar
(from
https://github.com/libarchive/libarchive/, as used as
tar
by FreeBSD and macOS 10.6 and later) or tar
from
the Heirloom Toolchest
(http://heirloom.sourceforge.net/tools.html), although the
latter does not support xz
compression.
texi2dvi
is normally a shell
script. Some versions (including those from texinfo 5.2 and
6.0-6.6) need to be run under bash
rather than a Bourne shell,
especially on Solaris. Some of the issues which have been observed with
broken versions of texi2dvi
can be circumvented by setting the
environment variable R_TEXI2DVICMD
to the value emulation
.
If necessary the path to
pkg-config
can be specified by setting PKG_CONFIG
in
config.site, on the configure
command line or in the
environment.
also known as ttf-mscorefonts-installer
in the
Debian/Ubuntu world: see also
https://en.wikipedia.org/wiki/Core_fonts_for_the_Web.
ttf-liberation
in Debian/Ubuntu.
This is the default as
from glibc
2.26 and has been confirmed for Fedora >= 28, which does
not mention this on its man
pages.
R uses rpc/xdr.h but that includes netconfig.h from the top tirpc directory.
This is true even for the ‘Aqua’ version of Tk on macOS, but distributions of that include a copy of the X11 files needed.
The search includes OpenBLAS, ATLAS and a generic libblas, plus some platform-specific choices (see below).
Using the Oracle Developer Studio
cc
and f95
compilers
There were others for earlier versions of ATLAS, and are for non-Intel architectures. The only way to see exactly which CPUs the distributed libraries have been tuned for is to read the atlas.spec file: at the time of writing ‘HAMMER64SSE3’ and ‘Corei264AVX’ for ‘x86_64’ Fedora.
http://math-atlas.sourceforge.net/atlas_install/
http://math-atlas.sourceforge.net/faq.html#tnum
(and more, e.g. for 64-bit ints and static versions).
The issue for macOS has been the use of double-complex routines.
We have measured 15–20% on ‘i686’ Linux and around 10% on ‘x86_64’ Linux.
We believe that versions 3.4.0 to 3.15.0 are compatible.
at the time of revision of this para in late 2018, autoconf-2.69 from 2012 and automake-1.16.1 from 2018.
The links there have proved difficult to access, in which case either point an FTP client at ftp://www.eecs.harvard.edu/pub/nr/ or grab the copy made available at http://developer.r-project.org/noweb-2.11b.tgz.
for example, X11 font at size 14 could not
be loaded
.
For example, glibc
: other C libraries such as
musl
have been used but are not routinely tested.
Likely all since 2005, including Pentium 4 and all ‘x86_64’ CPUs with 32-bit compilers.
This also needs the OpenMP runtime which has sometimes been distributed separately.
Some of these are
unsigned packages: to install them you may need to right-click and
select Open with -> Installer
.
See https://developer.apple.com/documentation/xcode/notarizing_macos_software_before_distribution.
https://developer.apple.com/documentation/accelerate.
It was reported that for some non-Apple
toolchains CPPFLAGS
needed to contain -D__ACCELERATE__
:
not needed for clang
from releases.llvm.org though.
An essentially equivalent TeX installation can be obtained by the Unix TeX Live installation scripts: MacTeX also contains GhostScript.
E.g. via tlmgr install cm-super
helvetic inconsolata texinfo
.
For more details see http://www.macstrategy.com/article.php?3.
In the unlikely event that the version reported does
not start with 1.8.0
, 11
or higher you need to update your
Java.
As from Java 11, there is no separate client JRE distribution from Oracle, but there may be from OpenJDK.
Oracle Solaris Studio prior to 2016, and previously Sun Studio.
When last checked it failed in tests/reg-BLAS.R,
and on some builds, including for ‘amd64’, it failed in
example(eigen)
.
In particular, header
cmath in C++11 mode includes math.h and
iso/math_c99.h and gcc
had ‘fixed’ an earlier version
of the latter.