This is a guide to installation and administration for R.
The current version of this document is 2.6.1 (2007-11-26).
ISBN 3-900051-09-7
Sources, binaries and documentation for R can be obtained via
CRAN, the “Comprehensive R Archive Network” whose current
members are listed at cran.r-project.org/mirrors.html.
The simplest way is to download the most recent R-x.y.z.tar.gz file, and unpack it with
tar xvfz R-x.y.z.tar.gz
on systems that have GNU tar installed. On other systems you need at least to have the gzip program installed. Then you can use
gzip -dc R-x.y.z.tar.gz | tar xvf -
The pathname of the directory into which the sources are unpacked should not contain spaces, as make (specifically GNU make 3.80) does not expect spaces.
If you need to transport the sources on floppy disks, you can download the R-x.y.z.tar.gz-split.* files and paste them together at the destination with (Unix)
cat R-x.y.z-split.* > R-x.y.z.tar.gz
and proceed as above. 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.)
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 (2.x.0) version, `r-patched' will refer to beta/release candidates of the upcoming release, the patched version of the current release being available only via Subversion.)
The tarballs are available from
ftp://ftp.stat.math.ethz.ch/pub/Software/R/. Download
either 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.
Sources are also available via https://svn.R-project.org/R/, the R
Subversion repository. If you have a Subversion client (see
subversion.tigris.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. 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 required, and that the SSL certificate for the Subversion server of the R project is
Certificate information:
- Hostname: svn.r-project.org
- Valid: from Jul 16 08:10:01 2004 GMT until Jul 14 08:10:01 2014 GMT
- Issuer: Department of Mathematics, ETH Zurich, Zurich, Switzerland, CH
- Fingerprint: c9:5d:eb:f9:f2:56:d1:04:ba:44:61:f8:64:6b:d9:33:3f:93:6e:ad
(currently, there is no “trusted certificate”). You can accept this certificate permanently and will not be asked about it anymore.
Note that retrieving the sources by e.g. wget -r or svn export from that URL will not work: 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 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 `http://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
wget -r -l1 --no-parent -A\*.gz -nd -P src/library/Recommended \
http://CRAN.R-project.org/src/contrib/dir
./tools/link-recommended
R will configure and build under a number of common Unix and Unix-alike platforms including `cpu-*-linux-gnu' for the `alpha', `arm', `hppa', `ix86', `ia64', `m68k', `mips', `mipsel', `powerpc', `s390', `sparc', and `x86_64' CPUs, `powerpc-apple-darwin', `i386-apple-darwin' and `sparc-sun-solaris', as well as probably (it is tested less frequently on these platforms) `i386-*-freebsd', `x86_64-*-freebsd', `i386-*-netbsd', `i386-*-openbsd', `i386-sun-solaris', `mips-sgi-irix' and `alpha-dec-osf*'.
In addition, binary distributions are available for some common Linux distributions and for Mac OS X. 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.
First review the essential and useful tools and libraries in Essential and useful other programs under Unix, and install those you want or need. Ensure that the environment variable TMPDIR is either unset (and /tmp exists and can be written in and executed from) or points to a valid temporary directory.
Choose a place 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. (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'.)
Then check the built system works correctly1, 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. (Note that the tests may not run successfully in all
locales: we expect them to do so using an 8-bit or UTF-8 character set,
but probably not using other multibyte character sets. If you have
problems try C or an English locale – a UTF-8 locale if you
usually use UTF-8.)
To re-run the tests including those successfully run you would need
make check FORCE=FORCE
More comprehensive testing can be done by
make check-devel
or
make check-all
see tests/README.
If the command configure and make commands execute successfully, the R binary will be copied to R_HOME/bin/exec/R. In addition, a shell-script front-end called R will be created and copied to the same directory. You can 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 the pathname of the build directory should not contain spaces.)
Make will also build plain text help pages as well as HTML and
LaTeX versions of the R object documentation (the three kinds can
also be generated separately using make help, make html
and make latex). Note that you need Perl version 5.8.x: if this
is not available on your system, you can obtain PDF versions of the
documentation files via CRAN.
For those obtaining R via Subversion, one additional step is necessary:
make vignettes
which makes the grid vignettes (which are contained in the tarballs): it takes several minutes.
Now rehash if necessary, type R, and read the R manuals
and the R FAQ (files FAQ or
doc/manual/R-FAQ.html, or
CRAN.R-project.org/doc/FAQ/R-FAQ.html which always has
the latest version).
There is a set of manuals that can be built from the sources,
To make these, use
make dvi to create DVI versions make pdf to create PDF versions make info to create info files (not `refman').
You will not be able to build any of these unless you have makeinfo version 4.7 or later installed, and for DVI or 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 DVI versions can be previewed and printed using standard programs such as xdvi and dvips. The PDF versions can be viewed using Acrobat Reader or (fairly recent versions of) xpdf and ghostscript: they have hyperlinks that can be followed in the first two. The info files are suitable for reading online with Emacs or the standalone GNU Info. The DVI and PDF versions will be created using the papersize 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 papersize, you should first delete the file doc/manual/version.texi.)
There are some issues with making the reference manual, and in particular with the PDF version 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:
timeslmwww.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-superwww.ctan.org/tex-archive/fonts/ps-type1/cm-super
and its mirrors. These type-1 fonts have poor hinting and so are
nowhere near so readable on-screen as the other three options.
aeThe default can be overridden by setting the environment variables
R_RD4PDF and R_RD4DVI. (On Unix, these will be picked up
at install time.) The default value for R_RD4PDF is
times,hyper: omit hyper if you do not want hyperlinks,
e.g. for printing. The default for R_RD4DVI is ae.
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
This will install to the following directories:
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
This causes make install to install the R executable 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. You can install into another directory tree by using
make prefix=/path/to/here install
at least with GNU make (but not e.g. Solaris 8's make).
More precise control is available at configure time via options: see configure --help for details. (However, many of them are currently unused.)
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-2.6.1.
If you want the R home to be something other than libdir/R, use rhome: for example
make install rhome=/usr/local/lib64/R-2.6.0
will use a version-specific R home on a Linux 64-bit system.
If you have made R as a shared/dynamic 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.
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.
To install DVI, info and PDF versions of the manuals, use one or more of
make install-dvi
make install-info
make install-pdf
Once again, it is optional to specify prefix, libdir or
rhome (the DVI and 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 DVI and 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
http://www.gnu.org/prep/standards/html_node/DESTDIR.html
You can uninstall R by
make uninstall
specifying prefix etc in the same way as specified for
installation.
This will also uninstall any installed manuals. There are specific targets to uninstall DVI, info and PDF manuals in doc/manual/Makefile.
Some platforms can support closely related builds of R which can share all but the executables and dynamic objects. Examples include builds under Solaris for different chips (in particular, 32- and 64-bit builds), 64- and 32- bit builds on `x86_64' Linux and different CPUs (`ppc', `ppc64', `i386' and `x86_64') under Mac OS >= 10.4.
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 libs. Example
names from other systems 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 63Mb, 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 that 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 pkg(s)
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.
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 Windows 95, 98, NT4, 2000, ME, XP, 2003 Server and Vista (at least) on Intel x86 and clones (including AMD64/EM64T chips and Windows x64).
Your file system must allow long file names (as is likely except perhaps for some network-mounted systems).
Installation is via the installer R-2.6.1-win32.exe. Just double-click on the icon and follow the instructions. You can uninstall R from the Control Panel. (Note that you will probably (depending on the Windows language settings) be asked to choose a language for installation, and that choice applies to both installation and un-installation but not to running R itself.)
See the R Windows FAQ for more details.
If you want to build R from the sources, you will first need to
collect, install and test an extensive set of tools. See The Windows toolset (and perhaps updates in
www.murdoch-sutherland.com/Rtools) for details.
The Rtools.exe executable installer described in The Windows toolset also includes some additions to the R source as
noted below. You should run it first, to obtain a working tar
and other necessities. Choose a “Full installation”, and install
the extra files into your intended R source directory, e.g.
C:/R. The directory name should not contain spaces. We
will call this directory R_HOME below.
To avoid warnings you may want to set the environment variable CYGWIN to `nodosfilewarning'.
You need to collect the following sets of files:
tar zxvf R-2.6.1.tar.gz
to create the source tree in R_HOME. Beware: do use tar to extract the sources rather than tools such as WinZip that do not understand about symbolic links.
It is also possible to obtain the source code using Subversion; see Obtaining R for details.
make
link-recommended. If you have an Internet
connection, you can do this automatically using
make rsync-recommended
math-atlas.sourceforge.net) tuned to your system for fast linear
algebra routines. Pre-built Rblas.dll for various Pentium and
AthlonXP chips are available in the windows/contrib/ATLAS area on
CRAN. If you are building R from source, there are macros
USE_ATLAS and ATLAS_PATH in the file MkRules. Set
USE_ATLAS = YES and ATLAS_PATH to where the ATLAS
libraries are located. You will need to make the libraries
yourself2: none of the binaries we have seen are compiled for
the correct compiler. Since R has its own `xerbla' it is best
to delete that in ATLAS by
ar d /path/to/libf77blas.a xerbla.o
There used to be support for AMD's AMD Core Math Library (ACML) and Kazushige Goto's BLAS, but neither is currently available for use with the current compilers used.
The following additional items are normally installed by Rtools.exe. If instead you choose to do a completely manual build (or a cross-build), you will also need
libpng and jpeg sources (available, e.g., from
www.libpng.org,
ftp://ftp.uu.net/graphics/[png,jpeg]. You will need files
libpng-1.2.18.tar.gz and jpegsrc.v6b.tar.gz or later.
Working in the directory R_HOME
/src/gnuwin32/bitmap, install the libpng and
jpeg sources in sub-directories. The libpng sub-directory must
be named libpng (as required by the libpng
documentation). The jpeg sub-directory for version 6b is named
jpeg-6b; if you use a different version, edit Makefile
and change the definition of JPEGDIR.
Example:
> tar xzvf libpng-1.2.20.tar.gz
> mv libpng-1.2.20 libpng
> tar xzvf jpegsrc.v6b.tar.gz
You may need to compile under a case-honouring file system: we found that a samba-mounted file system (which maps all file names to lower case) did not work.
Open a command window at R_HOME/src/gnuwin32. Edit MkRules to set the appropriate paths as needed and to set the type(s) of help that you want built. Beware: MkRules contains tabs and some editors (e.g., WinEdt) silently remove them. Then run
make all recommended
and sit back and wait while the basic compile takes place.
Notes:
malloc in the file
R_HOME/src/gnuwin32/malloc.c is used for R's internal memory
allocations. You can opt out of this by commenting the line
LEA_MALLOC=YES in MkRules, in which case the
malloc in msvcrt.dll is used. This does work but
imposes a considerable performance penalty.
make -j2 all
make recommended
but this is only likely to be worthwhile on a dual-processor/dual-core machine with ample (at least 384Mb) of memory. (On a dual AthlonMP it reduced the build time by about 30%.) Note that this may sometimes stop and have to be restarted.
The file R_HOME/bin/Rbitmap.dll is not built automatically.
Running make in R_HOME/src/gnuwin32/bitmap
or make bitmapdll in R_HOME/src/gnuwin32
should build Rbitmap.dll and install it in R_HOME/bin.
You can test a build by running make check. You may need to set
TMPDIR to the absolute path to a suitable temporary directory: the
default is `c:/TEMP'. (Use forward slashes and do not use a path
including spaces.)
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 check-devel and check-recommended.
The PDF manuals can be made by
make manuals
If you want to make the info versions (not the Reference Manual), use
cd ../../doc/manual
make -f Makefile.win info
To make DVI versions of the manuals use
cd ../../doc/manual
make -f Makefile.win dvi
(all assuming you have tex and latex installed and in your path).
See the Making the manuals section in the Unix section for setting options such as the paper size.
You need to have the files for a complete R build, including bitmap and Tcl/Tk support and the manuals, as well as the recommended packages and Inno Setup (see The Inno Setup installer).
Once everything is set up
make distribution
make check-all
will make all the pieces and the installers and put them in the gnuwin32/cran subdirectory, then check the build. This works by building all the parts in the sequence:
Rpwd.exe (a utility needed in the build) rbuild (the executables, the FAQ docs etc.) rpackage (the base packages) htmldocs (the HTML documentation) bitmapdll (the bitmap support files) recommended (the recommended packages) vignettes (the vignettes in package grid: only needed if building from svn checkout) manuals (the PDF manuals) rinstaller (the install program) crandir (the CRAN distribution directory)
The parts can be made individually if a full build is not needed, but earlier parts must be built before later ones. (The Makefile doesn't enforce this dependency—some build targets force a lot of computation even if all files are up to date.) The first four targets are the default build if just `make' is run.
If you want to customize the installation by adding extra packages,
replace make rinstaller by something like
make rinstaller EXTRA_PKGS='pkg1 pkg2 pkg3'
An alternative way to customize the installer starting with a binary distribution is to first make a full installation of R from the standard installer (that is, select `Full Installation' from the `Select Components' screen), then add packages and make other customizations to that installation. Then in src/gnuwin32/installer run
make myR IMAGEDIR=rootdir
where rootdir is the path to the root of the customized installation (forward slashes and no spaces, please). This creates an executable with the standard name, R-2.6.1-win32.exe, so please rename it to indicate that it is customized.
The defaults for the startup parameters may also be customized. For example
make myR IMAGEDIR=rootdir MDISDI=1
will create an installer that defaults to installing R to run in SDI mode. See src/gnuwin32/installer/Makefile for the names and values that can be set.
It is also possible to build an installer for use with Microsoft Installer. This is intended for use by sysadmins doing automated installs, and is not recommended for casual use.
It makes use of the Windows Installer XML (WiX) toolkit available from http://wix.sourceforge.net/: we tested version 2.0. (This needs the .NET 1.1 framework installed: it ran on a vanilla Windows XP SP2 machine. Probably Windows 2000 or later is required by some of the features used.) Once WiX is installed, set the path to its home directory in MkRules.
You need to have the files for a complete R build, including bitmap and Tcl/Tk support and the manuals, as well as the recommended packages. Then
cd installer
make msi
which will results in a file of about 40Mb with a name like R-2.6.0-win32.msi. This can be double-clicked to be installed, but those who need it will know what to do with it.
Thanks to David del Campo (Dept of Statistics, University of Oxford) for suggesting WiX and building a prototype installer.
It is possible to cross-build R or packages on (at least) `ix86' and `x86_64' Linux, and the `ix86' cross-compilers have also been used successfully on `x86_64' Linux.
The preferred build environment is to use gcc 4.2.1: this can easily be built from the sources as a cross-compiler, but the MinGW-specific patches are not yet stable (and not needed to build R).
You will need suitable cross-compilers installed and in your path.
There is currently a complete set of tools based on gcc 3.4.5
at www.stats.ox.ac.uk/pub/Rtools/mingw-cross5.tar.bz2 (Just unpack
this into a directory somewhere and put its bin directory in your
path.) It is also straightforward to build a set of cross-compilers via
the scripts available at
http://sourceforge.net/forum/forum.php?forum_id=632611.
Cross-compilers based on both gcc 3 and gcc 4 are
supported: the flavour is selected by the macro CROSS-GCC.
You will need Perl, zip and unzip installed and (to
make the manuals) makeinfo version 4.7 or later (part of GNU
texinfo) as well as texinfo.tex.
You also need the R source (R-2.6.1.tar.gz), R_Tcl.zip and iconv.dll (see above).
Then: untar R-2.6.1.tar.gz somewhere, unpack R_Tcl.zip at the top level and put iconv.dll in src/gnuwin32/unicode, then
cd /somewhere/R-2.6.1/src/gnuwin32
Edit MkRules to set BUILD=CROSS, CROSS-GCC as
appropriate and the appropriate paths (including HEADER if
needed).
Edit MkRules to set the type(s) of help that you want built. (You
will not be able to cross-build .chm files, so WINHELP is
automatically set to NO.)
You also need a working copy of this version of R on Linux:
uncomment and set R_EXE in MkRules to point to it.
Then run make (and parallel make works reliably, unlike on Windows).
Packages can be made in the same way as natively: see Customizing package compilation under Windows, via the Makefiles but not via `R CMD INSTALL'. So care is needed where packages have dependencies: Linux versions of the dependencies must be installed in a library in the search path. So for example to cross-build the MCMCpack package we used
# MCMCpack depends on coda, so point to the library containing it
export R_LIBS=/R/library
make PKGDIR=/mysources pkg-MCMCpack
make PKGDIR=/mysources lazyload-MCMCpack
cd ../../library
zip -r9X /dest/MCMCpack_0.7-4.zip MCMCpack
Even so, packages which depend on others that need to run compiled code to load may not work (methods is a special exception).
To distribute a cross-build (or just to transfer it to a Windows machine for testing) use
make all recommended manuals
cd installer
make imagedir
zip -r9X R-2.6.1.zip R-2.6.1 # or something similar
Note that .chm help files (the default for a vanilla binary installation) will not be made when cross-building.
Also based on this facility is Makefile-rcb by J. Yan and A. J. Rossini. For details, see the Makefile-rcb file itself, or http://cran.r-project.org/doc/contrib/cross-build.pdf.
The bin/macosx directory of a CRAN site contains binaries for Mac OS X for a base distribution and a large number of add-on packages from CRAN to run on Mac OS X version 10.4.4 or higher.
The simplest way is to use R-2.6.1.dmg. Just double-click on the icon and the disk image file will be mounted. Read the ReadMe.txt inside the disk image and follow the instructions.
See the R for Mac OS X FAQ for more details.
If you want to build this port from the sources, you can read the above mentioned R for Mac OS X FAQ for full details. You will need to collect and install some tools as explained in the document. Then you have to expand the R sources and configure R appropriately, for example
tar zxvf R-2.6.1.tar.gz
cd R-2.6.1
./configure --with-blas='-framework vecLib' --with-lapack \
--with-aqua --enable-R-framework
make
and then sit back and wait. The first two options are the default (and
strongly recommended), and with some toolsets have been essential. The
second line of options is also default on Mac OS X, but needed only if
you want to build R for use with R.app Console, and imply
--enable-R-shlib to build R as a shared/dynamic library.
These options configure R to be built and installed as a framework called R.framework. The default path for R.framework is /Library/Frameworks but this can be changed at configure time specifying the flag --enable-R-framework[=DIR] or at install time as
make prefix=/where/you/want/R.framework/to/go install
the R.framework has not to be specified in the path.
Note that building the R.app GUI console is a separate project: see the FAQ for details.
How to start R and what command-line options are available is discussed in Invoking R.
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). As from R 2.4.0 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.
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 running 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.
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().
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 three or more. But it can also be used to customize R, e.g. for class use.
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 recommended3 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.
As from R 2.5.0 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 setting4 `.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()'.
As from R 2.5.0 users can have one or more libraries, normally specified by the environment variable R_LIBS_USER. This has a default value (use `Sys.getenv("R_LIBS_USER")' within an R session to see what it is), but only is 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).
Packages may be distributed in source form or compiled binary form. Installing source packages requires that compilers and tools (including Perl 5.8.0 or later) 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 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.
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.5 On most systems `install.packages()' will allow packages to be selected from a list box.
To install packages from source in Unix use
R CMD INSTALL -l /path/to/library pkg1 pkg2 ...
The part `-l /path/to/library' can be omitted, in which case the first library in R_LIBS is used if set, otherwise the main library R_HOME/library is used. (R_LIBS is looked for in the environment: note that .Renviron is not read by R CMD.) Ensure that the environment variable TMPDIR is either unset (and /tmp exists and can be written in and executed from) or points to a valid temporary directory.
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 set the option CRAN to 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 user 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 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 by setting argument repos to NULL.
install.packages can look in several repositories, specified as a
character vector by the argument repos: these can include a
CRAN mirror, Bioconductor, Omegahat, local archives, local
files, ...).
What install.packages does by default is different on Unix 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) at the list of
binary versions of packages available for your version of R
and downloads the latest versions (if any), although optionally it will
also download and install a source package by setting the type
argument.
On Windows install.packages can also install a binary package
from a local zip file by setting argument repos to
NULL. Rgui.exe has a menu Packages with a GUI
interface to install.packages, update.packages and
library.
R CMD INSTALL works in Windows to install source packages if
you have the source-code package files (option “Source Package
Installation Files” in the installer) and toolset (see The Windows toolset) installed. Installation of binary packages must be done by
install.packages. R CMD INSTALL --help will tell you
the current options under Windows (which differ from those on a
Unix-alike): in particular there is a choice of the types of
documentation to be installed.
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 win-builder.r-project.org.
On Mac OS X install.packages works as it does on other Unix-like
systems, but there is an additional type mac.binary that can be
passed to install.packages in order to download and install
binary packages from a suitable repository, and is the default if
running from the GUI console. These Macintosh binary package files have
the extension `tgz'. The R GUI provides for installation of
either binary or source packages, from CRAN or local files.
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, 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.
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.
This section describes ways to customize package compilation using the standard C, C++ and FORTRAN compilers and tools. For instructions on using non-standard tools, see the README.packages file.
The Makefiles can be customized: in particular the name of the DLL can
be set (for example we once needed integrate-DLLNM=adapt), the
compile flags can be set (see the examples in MakeDll) and the
types of help (if any) to be generated can be chosen (variables
HELP, HELPTYPES and WINHELP). The simplest way to
customize the compilation steps is to set variables in a file
src/Makevars.win, which will automatically be included by
MakeDLL. For example, for RODBC src/Makevars.win could
include the line
DLLLIBS+=-lodbc32
or, equivalently,
RODBC-DLLLIBS=-lodbc32
but in fact contains the single line
PKG_LIBS=-lodbc32
If you have a file src/Makefile.win, that will be used as the makefile for source compilation in place of our makefile and MakeDll and src/Makevars.win will be ignored.
Package-specific compilation flags can be overridden or added to using
the personal file $HOME/.R/Makevars.win, or if that does not
exist, $HOME/.R/Makevars. (See the rw-FAQ for the meaning
of $HOME.) For the record, the order of precedence is (last wins)
Beware: references to variables in R.dll are converted to the right form by using the header files. You must include them.
For additional control, R_HOME/src/gnuwin32/Makefile
contains additional make targets corresponding to various options to
R CMD INSTALL. These assume that package foo's source
code has been installed in directory
R_HOME/src/library/foo. Then make pkg-foo is similar
to R CMD INSTALL foo (but the latter would require
R_HOME/src/library to be the current directory). Other
targets are
ziponly-foo, to use zip to compress the help files after building
the package.
ziphelp-foo to both compress the help files and to keep the
originals.
zipdata-foo to compress the data files. This is recommended if
you have either many small data files (as in package Devore5) or a
few large data files.
pkgcheck-foo to check the package (like R CMD check foo).
Using this approach allows variables to be set during the build, e.g.
make PKGDIR=/mysources RLIB=/R/library pkg-foo
Some variables that may be used include:
DEBUG=T to compile with debugging information for gdb.
PKG_CFLAGS= to specify options to the C compiler.
PKG_CPPFLAGS= to specify options to the preprocessor.
PKG_CXXFLAGS= to specify options to the C++ compiler.
PKG_FFLAGS= to specify options to the FORTRAN 77 compiler.
PKG_FCFLAGS= to specify options to the Fortran 95 compiler (if
specified).
PKG_LIBS= to specify options to the linking step making the DLL.
PKGDIR=/path/to/source to specify the path to the package source files.
RLIB=/path/to/library to specify the path to the library
where the package should be installed.
PKG_* flags are those
typically included in Makevars files.
The command update.packages() is the simplest way to ensure that
all the packages on your system are up to date. Set the repos
argument as in the previous section. The update.packages()
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.
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, in most installations one can just remove the package directory from the library.
Note: only remove.packages can remove package
bundles.
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.omegahat.org/R: this must be an URL scheme that
download.packages supports (which also includes `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.
"win.binary": located at bin/windows/contrib/x.y for
R versions x.y.z and containing .zip files.
"mac.binary": located at
bin/macosx/universal/contrib/x.y for R versions x.y.z
and containing .tgz files. If the repository contains only
packages for a specific architecture, the package distribution type
can be set to "mac.binary.xxx" where xxx specifies the
architecture, replacing universal by xxx in the path
above.
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 (provided there are no bundles), 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
a PACKAGES.gz file, a gzip-compressed version of
PACKAGES.
To add your repository to the list offered by setRepositories(),
see the help file for that function.
Internationalization refers to the process of enabling support for non-English languages, and localization to adapting to a specific country and language.
R long worked in the ISO Latin-1 8-bit character set and so covered English and most Western European languages (if not necessarily their currency symbols). Since R 2.1.0 it has supported (where possible) multi-byte character sets such as UTF-8 and others used in Chinese, Japanese and Korean.
Full internationalization of the character sets is enabled unless R is built under Unix-alikes using configure option --disable-mbcs provided the OS can support it: see Configuration on Unix. Under Windows, support for Windows' own MBCS is always included.
All builds of R support all single-byte 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. Fully internationalized builds can also handle most
multi-byte locales, in which a single character is represented by one,
two or more consecutive bytes: examples of such locales are those using
UTF-8 (becoming standard under Linux but non-existent under Windows) and
those for Chinese, Japanese and Korean.
The other aspect of the internationalization is support of the translation of messages. This is enabled in almost all builds of R.
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
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, and most OSes have only one charset each for many languages. Note too the remark above about Chinese.
Modern Linux uses the XPG locale specifications which have the form `en_GB', `en_GB.utf8', `aa_ER.utf8@saaho', `de_AT.iso885915@euro', the components being in the order listed above. (See man locale and locale -a for more details.) Similar schemes (but often in different cases) are used by most Unix-alikes.
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 at
msdn.microsoft.com/library/default.asp?url=/library/en-us/vccore98/html/_crt_language_and_country_strings.asp.
Mac OS X supports locales in its own particular way, but the R GUI tries
to make this easier for users. See
developer.apple.com/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'.
Internally Mac OS X uses a form similar to Linux but without
specifying the encoding (which is UTF-8). It is based on ICU
locales (http://icu.sourceforge.net/userguide/locale.html) and
not POSIX ones.
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 then 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 environment variables such as
LANGUAGE.
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 basic C-level error messages.
R-pkg for the R stop, warning and
message messages in each package, including R-base for the
base 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.
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. 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 be made use of by on-the-fly re-encoding (on almost all systems). 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 English/American error messages with pairs of 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 is used.
See developer.r-project.org/Translations.html for how to prepare
and install translation catalogues.
Many current CPUs have both 32- and 64-bit sets of instructions: this has long been true for UltraSparc and more recently for MIPS, PPC and `x86_64' (AMD Opteron and Athlon64, Intel Xeon and Pentium/'Core' supporting EM64T). Many 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) 64-bit is.
All current versions of R use 32-bit integers and IEC 605596 double-precision reals, and so compute to the same precision7 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 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).
So, for speed you may want to use a 32-bit build, but to handle large datasets (and perhaps large files) a 64-bit build. You can build both and install them in the same place: See Sub-architectures.
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). On all versions of
R, the maximum length (number of elements) of a vector is
2^31-1, about 2 billion, and on 64-bit systems the size of a
block of memory allocated is limited to 2^34-1 bytes (8GB). It
is anticipated these will be raised eventually but routine use of 8GB
objects is (in 2005) several years off.
Currently the Windows build of R is a 32-bit executable. This runs happily on Windows 64 on AMD64 and EM64T, but is limited to (we are told) a 2GB address space. It will not be possible to provide a native version for Windows 64 until suitable compilers are available, and currently (mid-2007) that is not imminent.9
The routines supporting the distribution and special10 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 Unix 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 "2.6.0".
There is full access to R's handling of NaNs, 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 will 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 facilties 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).
If R has not already be made in the directory tree, configure must tbe run as described in the main build instructions.
Then
make
will make standalone libraries libRmath.a and libRmath.so.
`make static' and make shared will create just one of them.
NB: certain compilers are unable to do compile-time IEEE-754
arithmetic and so cannot compile mlutils.c and several other
files. The known example is earlier versions of Sun's cc
(e.g. Forte 6 and 7): the Sun Studio 11 suite does work.
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.
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.
You need to set up almost all the tools to make R and then run
(cd ../../include; make -f Makefile.win config.h Rconfig.h Rmath.h)
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, 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,dynamic
-Wl,-Bdynamic -lRmath
or by linking to explicit files (as in the `test' target in
Makefile.win: this makes two executable test.exe which is
dynamically linked, and test-static, which is statically
linked).
If you make use of dynamic linking you should use
#define MATHLIB_STANDALONE
#define RMATH_DLL
#include <Rmath.h>
to ensure that the constant like NA_REAL are linked correctly.
(Auto-import will probably work, but it is better to be sure.)
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 deb) 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.
You need a means of compiling C and FORTRAN 77 (see Using FORTRAN). Some add-on packages also need a C++ compiler. Your C
compiler should be IEC 6005911, POSIX 1003.1 and C99-compliant if at all
possible. R tries to choose suitable flags for the C compilers it
knows about, but you may have to set CC or CFLAGS
suitably. For recent versions of gcc with glibc this
means including -std=gnu9912. If the compiler is
detected as gcc, -std=gnu99 will be appended to
CC unless it conflicts with a setting of CFLAGS.
Unless you do not want to view graphs on-screen you need `X11' installed, including its headers and client libraries. (On Fedora Core 3 and SuSE 9.x Linux this meant the `xorg-x11-devel' and `xorg-x11-libs' RPMs. For Fedora Core 5 and 6 it means (at least) `libX11', `libX11-devel', `libXt' and `libXt-devel'. On Debian 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 depends on the readline library
available from any GNU mirror: 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).
The use of multi-byte characters, conversion between encodings
(including for translated messages) and the R iconv function
depend on having the system iconv function: this is part of
recent versions of glibc and many Unixes. You can also install
GNU libiconv (which is not the same as that in
glibc), possibly as a plug-in replacement: see
www.gnu.org/software/libiconv. Note that the R usage
requires iconv to be able to translate between "latin1"
and "UTF-8", to recognize "" as the current encoding and
to translate to and from the Unicode wide-character formats
"UCS-[24][BL]E" – this is not true of most commercial Unixes.
This is regarded as essential from R 2.5.0: if you do not have it
will need to configure with --without-iconv (or equivalent),
and make check (and other checks) are likely to fail.
You will need Perl version 5.8.0 or later, available via
www.perl.com/CPAN, to build any
of the on-line documentation, which includes the examples needed for
regression testing.
You will not be able to build most of the manuals unless you have makeinfo version 4.7 or later installed, and if not some of the HTML manuals will be linked to CRAN. (Version 4.6 is known to create incorrect HTML files.) To make DVI or PDF versions of the manuals you will also need 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 (part of the GNU texinfo distribution).
The DVI and PDF documentation and building vignettes needs tex and latex, or pdftex and pdflatex.
If you want to build from the R Subversion repository you need Perl, makeinfo and pdflatex.
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 bitmapped graphics devices jpeg() and png() need the
appropriate headers and libraries installed: jpeg (version 6b or
later) or libpng (version 1.2.3 or later) and zlib
(version 1.1.3 or later) respectively.
The bitmap and dev2bitmap devices and also
embedFonts() use ghostscript (www.cs.wisc.edu/~ghost).
If you have them installed (including the appropriate headers and of
recent enough versions), zlib, libbz2 and PCRE will be
used if specified by --with-system-zlib,
--with-system-bzlib or --with-system-pcre: otherwise
versions in the R sources will be compiled in. As the latter suffice
and are tested with R you should not need to change this. In
particular, the version of zlib 1.2.3 in the R sources has
enhancements to work with large file systems on 32-bit platforms.
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 Fedora Core 5/6 require
the `libXmu' and `libXmu-devel' RPMs.
The tcltk package needs Tcl/Tk installed: the sources are
available at www.tcl.tk. To specify
the locations of the Tcl/Tk files you may need the configuration options
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, setting the paths to the correct config
files may be necessary to avoid confusion between them.
Versions of Tcl/Tk from 8.3 to 8.4.16 have been used successfully: 8.0 is no longer supported.
configure looks for Java support on the host system, and if it finds it sets some settings which are useful for Java-using packages. JAVA_HOME can be set during the configure run to point to a specific JRE/JDK.
Principal amongst these are some library 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 Sun Java is
/usr/java/jdk1.5.0_06/jre/lib/amd64/server:/usr/java/jdk1.5.0_06/jre/lib/amd64
Note that this unfortunately depends on the exact version of the JRE/JDK
installed, and so will need updating if the Java installation is
updated. This can be done by running R CMD javareconf. The
script re-runs Java detection in a manner similar to that of the
configure script and updates settings in both Makeconf
and R_HOME/etc/ldpaths. See R CMD javareconf --help for
details.
Another alternative of overriding those setting is to set R_JAVA_LD_LIBRARY_PATH (e.g. in ~/.Renviron), or use /etc/ld.so.conf to specify the Java runtime library paths to the system. Other settings are recorded in etc/Makeconf (or a sub-architecture-specific version), e.g.
JAVA = /usr/bin/java
JAVAC = /usr/bin/javac
JAVA_HOME = /usr/java/jdk1.5.0_06/jre
JAVA_LD_LIBRARY_PATH = $(JAVA_HOME)/lib/amd64/server:$(JAVA_HOME)/lib/amd64:\
$(JAVA_HOME)/../lib/amd64:/usr/local/lib64
JAVA_LIBS = -L$(JAVA_HOME)/lib/amd64/server -L$(JAVA_HOME)/lib/amd64
-L$(JAVA_HOME)/../lib/amd64 -L/usr/local/lib64 -ljvm
where `JAVA_LIBS' contains flags necessary to link JNI programs.
Some of the above variables can be queried using R CMD config.
The linear algebra routines in R can make use of enhanced BLAS (Basic
Linear Algebra Subprograms, www.netlib.org/blas/faq.html) routines. However, as from R
2.4.013 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 suitable 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 14 double
precision and double complex routines15, 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 (libsunperf on
Sun Sparc16, libessl on IBM, vecLib on Mac OS X). The
correct incantation for these is usually 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.
Note that under Unix (but not under Windows) if R is compiled against a non-default BLAS and --enable-BLAS-shlib is not used, 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.
ATLAS (math-atlas.sourceforge.net) is a “tuned” BLAS that runs on a
wide range of Unix-alike platforms. If no more specific library is
found, a libblas library in the library path will be used. (The
later may not be an enhanced BLAS and so may be less desirable than the
internal BLAS.)
The usual way to specify ATLAS will be via
--with-blas="-lf77blas -latlas"
if the libraries are in the library path, otherwise by
--with-blas="-L/path/to/ATLAS/libs -lf77blas -latlas"
For systems with multiple processors it is possible to use a multi-threaded version of ATLAS, by specifying
--with-blas="-lptf77blas -lpthread -latlas"
Users of Fedora Core 4 Extras may want to use
--with-blas="-lf77blas -latlas -llapack_atlas" --with-lapack
since the basic BLAS on that system is incomplete.
The BLAS library must be usable with dynamically-loadable code: this can be a problem with ATLAS on some platforms (including Linux on `x86_64') as it is not by default built with position-independent code.
An ATLAS `tuned' BLAS can also be used on Windows: see see Getting the source files when building from source, and R Windows FAQ for adding pre-compiled support to binary versions.
For `x86_64' and `ix86' processors under Linux and
Solaris 10 there is the AMD Core Math Library (ACML)
www.amd.com/acml. For the
gcc version we could use
--with-blas="-lacml"
if the appropriate library directory (such as /opt/acml4.0.0/gfortran64/lib) is in the LD_LIBRRARY_PATH. For other compilers, see the ACML documentation. There is a multithreaded Linux version of ACML available for gfortran which needs gcc >= 4.2.0 (or some RedHat versions of 4.1.1). To make use of this you will need something like
--with-blas="-L/opt/acml4.0.0/gfortran64_mp/lib -lacml_mp"
See see Shared BLAS for an alternative (and in many ways preferable) way to use ACML.
ACML can be used on Windows when building from source.
Kazushige Goto has written another tuned BLAS which is available for several processors and OSes.
This has been made available in several formats, but is currently
available only as source code. For academic use only (after
registering) it can be obtained via
www.tacc.utexas.edu/resources/software/software.php. Once this
is built and installed, it can be used by configuring with
--with-blas="-lgoto"
It has been reported that on some RedHat-based Linux systems it is
necessary to set GOTO_NUM_THREADS=1 or OMP_NUM_THREADS=1
(to disable multiple threads) in the environment when using a
multi-threaded Goto BLAS, but others run happily with multiple threads.
Note that currently (Nov 2007) a multi-threaded Goto BLAS will be built by default if and only if the building is on a multi-processor system (counting multiple cores and hyperthreading), and at run time the default number of threads is the number of CPUs detected.
See see Shared BLAS for an alternative (and in many ways preferable) way to use recent versions of the Goto BLAS.
For Intel processors under Linux, Intel's Math Kernel Library
(www.intel.com/software/products/mkl) can be used
by
--with-blas="-lmkl -lguide -lpthread"
This is multi-threaded, but the number of threads defaults to 1 (and can
be increased by setting OMP_NUM_THREADS).
(Thanks to Andy Liaw for the information.)
See see Shared BLAS for an alternative (and in many ways preferable) way to use MKL.
Note that 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 most platforms 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 etc/ldpaths.
Another option to change the BLAS in use is to symlink a dynamic BLAS library (such as ACML or Goto's) to R_HOME/lib/libRblas.so. For example, just
mv R_HOME/lib/libRblas.so R_HOME/lib/libRblas.so.keep
ln -s /opt/acml4.0.0/gfortran64_mp/lib/libacml_mp.so R_HOME/lib/libRblas.so
will change the BLAS in use to multithreaded ACML. A similar link works for recent versions of the Goto BLAS and for MKL (provided the appropriate lib directory is in the run-time library path or ld.so cache).
Provision is made for using an external LAPACK library, principally to
cope with BLAS libraries which contain a copy of LAPACK (such as
libsunperf on Solaris, vecLib on Mac OS X and ACML on
`ix86'/`x86_64' Linux and Solaris). However, the likely
performance gains are thought to be small (and may be negative), and 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. To do so specify something like
--with-lapack="-L/path/to/libs -llapack -lcblas"
since the ATLAS subset of LAPACK depends on libcblas. 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.
Since ACML contains a full LAPACK, if selected as the BLAS it can be used as the LAPACK via --with-lapack.
Intel's Math Kernel Library suppies a full LAPACK which can be used via
--with-lapack="-L/path/to/libs -lmkl_lapack64"
or `-lmkl_lapack32': library mkl_lapack is static and not
PIC. However, the version 8.0.1.006 we tested failed a regression test
in the complex LAPACK.
If you do use --with-lapack, be aware of potential problems
with bugs in the LAPACK 3.0 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
(seen with the Debian -llapack which was current in late 2002,
Fedora Core 4 Extras -llapack in September 2005 and 64-bit
libsunperf in Forte 7). Other potential problems are incomplete
versions of the libraries: for example libsunperf from Sun Forte
6.x was missing the entry point for DLANGE and vecLib has
omitted the BLAS routine LSAME. For problems compiling LAPACK
using recent versions of gcc on `ix86' Linux, see
New platforms: these problems have surfaced in Fedora Core 3's
distribution, for example.
Please do bear in mind that using --with-lapack is `definitely not recommended': it is provided only because it is necessary on some platforms.
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 native compilers the flag
-dalign is needed so libsunperf can be used.
On some systems it is necessary that an external BLAS/LAPACK was built with the same FORTRAN compiler used to build R: known problems are with R built with gfortran, see Using gfortran.
configure has many options: running
./configure --help
will give a list. Probably the most important ones not covered elsewhere are (defaults in brackets)
Rprof() [yes]
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)'.
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 performance17 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.
If you need to re-configure R with different options you may need to run
make clean or even make distclean before doing so.
R can be compiled with support for multi-byte character sets (MBCS), in particular for UTF-8 locales (which are usually identified by suffix `.utf8', something like `en_GB.utf8'18. UTF-8 is an encoding of Unicode and in principle covers all human languages simultaneously: however, a given system may not have fonts capable of displaying more than a few of these languages.
Support for MBCS is selected if possible at configure time
(unless disabled with --disable-mbcs). This will check for a
large number of features, notably support for the C99/UNIX98 wide
character functions, for UTF-8 or MBCS support in X11 and for
iconv with a rich enough functionality. If enough of these
are found, MBCS will be listed as one of the “Additional
capabilities”. Then if R is started in a UTF-8 locale it assumes
that the terminal will supply and display UTF-8-encoded
characters19.
If run in a single-byte locale, R behaves almost exactly as if it was
configured with --disable-mbcs.
A version of R built with MBCS support can also be run in other multi-byte locales, for example those using the EUC-JP, EUC-KR and EUC-TW encodings on Unix-alikes and the code pages for Chinese, Japanese and Korean on Windows.
Translation of messages is supported via GNU gettext unless
disabled by the configure option --disable-nls or the
underlying OS has insufficiently standard C functions to support it.
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.
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 all the variables you might want to set) 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). To force a single file to be read, set the environment variable CONFIG_SITE to the location of the file.
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 and 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.
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 papersize when making DVI and 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.)
Another precious variable is R_BROWSER, the default browser, which should take a value of an executable in the user's path or specify a full path.
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) 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 (this has been reported to be a problem on HP-UX with
the native cc). 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.
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 on recent systems20
`'-Bdirect,--hash-style=both,-Wl,-O1'' is recommended at
http://lwn.net/Articles/192624/
The default settings for making the manuals are controlled by R_RD4PDF, R_RD4DVI and R_PAPERSIZE.
To compile R, you will most likely find it easiest to use GNU make. On Solaris 2.6/7/8 in particular, you need a version of GNU make different from 3.77; 3.79.1 and later work fine, as does the Sun make. The native make is reported to fail on SGI Irix 6.5 and Alpha/OSF1 (aka Tru64).
To build in a separate directory you need a make that uses the
VPATH variable, for example GNU make, or Sun
make on Solaris 2.7 or later.
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
To compile R, you need a FORTRAN compiler. The default
is to search for
f95, fort, xlf95,
ifort, ifc, efc, pgf95
lf95, gfortran, ftn, g95,
f90, xlf90, pghpf, pgf90,
epcf90,
g77, f77, xlf, frt,
pgf77, cf77, fort77, fl32,
af77 (in that order)21, and use whichever is found first; if none is found,
R cannot be compiled.
However, if CC is gcc, the matching FORTRAN compiler
(g77 for gcc 3 and gfortran for
gcc 4) is used if available.
The search mechanism can be changed using the configure variable
F77 which specifies the command that runs the FORTRAN 77
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 F77 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 COMPLEX*16 variables, which
is a Fortran 90 extension. This is checked for at configure
time22, but you may need to avoid
compiler flags23 asserting
FORTRAN 77 compliance.
For performance reasons24 you may want to choose a FORTRAN 90/95 compiler.
It is possible to use f2c, the FORTRAN-to-C converter
(www.netlib.org/f2c), via a
script. (An example script is given in scripts/f77_f2c: this can
be customized by setting the environment variables F2C,
F2CLIBS, CC and CPP.) You may need to ensure that the
FORTRAN type integer is translated to the C type int.
Normally f2c.h contains `typedef long int integer;', which
will work on a 32-bit platform but not on a 64-bit platform. If your
compiler is not gcc you will need to set FPICFLAGS
appropriately.
gfortran is the F95 compiler that is part of gcc 4.x.y. There were problems compiling R with the first release (gcc 4.0.0) and more with pre-releases, but these are resolved in later versions.
On Linux `x86_64' systems there is an incompatibility in the
return conventions for double-complex functions between
gfortran and g77 which results in the final example
in example(eigen) hanging or segfaulting under external BLASs
built under g77. This should be detected by a
configure test.
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
CPPFLAGSLDFLAGSand others include
CFLAGSMAIN_CFLAGSSHLIB_CFLAGSFFLAGSSAFE_FFLAGSMAIN_FFLAGSSHLIB_FFLAGSMAIN_LDFLAGSSHLIB_LDFLAGSLIBnnCPICFLAGSFPICFLAGSCXXPICFLAGSFPICFLAGSDEFSLibrary 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 library. Since R as a shared library has about 6200 symbols, if in doubt use the larger version.
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, FFLAGS, CXXFLAGS and
LIBS in R_XTRA_CFLAGS (and so on). These are for options
which are always required, for example to force IEC 60559
compliance.
This section provides some notes on building R on different Unix-like 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.
The `X11()' graphics device is the one started automatically on Unix-alikes when plotting. As its name implies, it displays on a (local or remote) X server, and relies on the services and in particular the fonts provided by the X server. So if you sometimes use R at a console and sometimes remotely from an X11 session running on a Windows machine, you may have to setup the fonts differently for the two usages.
When X11 was designed, most displays were around 75dpi, whereas today they are of the order of 100dpi or even higher. If you find that X11() is reporting25 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 Core 5's
xorg-x11-fonts-75dpi
xorg-x11-fonts-100dpi
xorg-x11-fonts-truetype
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-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/X11R6/lib/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.utf8' but not when running in `en_GB.utf8' on the same machine (although on some systems many UTF-8 X11 locales are aliased to `en_US.utf8' 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 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
Linux is the main development platform for R, so compilation from the sources is normally straightforward with the standard compilers.
Remember 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).)
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 for 64-bit CPUs such as that for AMD Opteron. 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.
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 Core 5 we used
CC="gcc -m32"
CXXFLAGS="-m32 -O2 -g"
FFLAGS="-m32 -O2 -g"
FCFLAGS="-m32 -O2 -g"
LDFLAGS="-L/usr/local/lib"
LIBnn=lib
Fedora Core 3 also needed
--x-libraries=/usr/X11R6/lib
and in both cases various `i386' `-devel' RPMs had to be added.
64-bit versions of Linux are built with support for files > 2Gb, and 32-bit versions will be if possible unless --disable-largefile is specified.
R used to include the compiler flag -mieee-fp, but it seems
this was really an alias for the linker flag -lieee. Neither
are needed for a modern Linux (e.g. using glibc 2.2/3/4) but
could conceivably be needed on an older version. glibc 2.1
required -D__NO_MATH_INLINES to achieve
IEC 60059-compliance for exp, and this is included
in R_XTRA_CFLAGS if required.
Several Linux distributions have shipped unreleased versions of gcc 4.0.0 and its FORTRAN compiler gfortran (see the separate comments). Some versions of gcc 4 (such as that in Fedora Core 3) produce incorrect code. In our experiments gcc 3.4.x always produced faster and more reliable code. It seems that gcc 4.0.x cannot compile src/main/plot.c when building R as a shared library on `ix86' unless the optimization level is changed from the default -O2 (-O3 works, as does gcc 4.1.0 with the default settings).
It has been reported that using gcc 4.0.3 on `ppc64' needed the compiler flag -mminimal-toc to avoid errors when linking R as a shared library.
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"
F77="gfortran -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 problems linking against libnmath.a and when linking R as a shared library.
Intel compilers have been used under `ix86' and `x86_64' Linux and R contains code to set the FPU options suitably. Brian Ripley tried version 9.0 of the compilers for `ix86' on Fedora Core 3 via
CC=icc
F77=ifort
CXX=icpc
ICC_LIBS=/opt/compilers/intel/cc/9.0/lib
IFC_LIBS=/opt/compilers/intel/fc/9.0/lib
LDFLAGS="-L$ICC_LIBS -L$IFC_LIBS -L/usr/local/lib"
SHLIB_CXXLD=icpc
and adding optimization flags failed: at least src/main/regex.c and src/modules/lapack/dlamc.f needed to be compiled without optimization. For `x86_64' on Fedora Core 5 he used
CC=icc
CFLAGS="-g -O3 -wd188 -ip"
F77=ifort
FLAGS="-g -O3"
CXX=icpc
CXXFLAGS="-g -O3"
FC=ifort
FCFLAGS="-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
configure will add `-c99' to CC for C99-compliance.
R will add `-mp' in R_XTRA_{C,F,CXX}FLAGS to maintain
correct IEC 60559 arithmetic. 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.
For some comments on building on an Itanium (`ia64') Linux
system with gcc or the Intel compilers see
www.nakama.ne.jp/memo/ia64_linux.
Jennifer Lai used the Portland Group compilers on `x86_64' to build pre-2.2.0. Updated versions of the settings she used are
PG_HOME=/usr/pgi/linux86-64/6.0
CC=pgcc
CFLAGS="-g -O2 -Kieee"
CPPFLAGS="-I$PG_HOME/include -I$PG_HOME/include/CC"
F77=pgf77
FFLAGS="-g -O2 -Kieee"
CXX=pgCC
CXXFLAGS="-g -O2 -Kieee"
FC=pgf95
FCFLAGS="-g -O2 -Kieee"
SHLIB_CXXLDFLAGS=-shared
SHLIB_LDFLAGS=-shared
LDFLAGS="-L$PG_HOME/libso -L/usr/lib64"
Note particularly the last, which is needed to ensure that a shared
version of libc is found. The flag -Kieee ensures strict
compliance to IEC60659. Also,
http://www.amd.com/us-en/assets/content_type/DownloadableAssets/dwamd_PGI_nov603.pdf
suggests that -pc64 may be desirable.
Brian Ripley tested the SunPro Studio 12 compilers (http://developers.sun.com/sunstudio/index.jsp) on `x86_64' Linux with
CC=cc
CFLAGS="-xO5 -xc99 -xlibmil -nofstore"
CPICFLAGS=-Kpic
F77=f95
FFLAGS="-O5 -libmil -nofstore"
FPICFLAGS=-Kpic
CXX=CC
CXXFLAGS="-xO5 -xlibmil -nofstore"
CXXPICFLAGS=-Kpic
FC=f95
FCFLAGS=$FFLAGS
FCPICFLAGS=-Kpic
LDFLAGS=-L/opt/sunstudio12/lib/amd64
SHLIB_LDFLAGS=-shared
SHLIB_CXXLDFLAGS="-G -lCstd"
SHLIB_FCLDFLAGS=-G
SAFE_FFLAGS="-O5 -libmil"
-m64 could be added, but was the default. Do not use
-fast: see the warnings under Solaris.
The resulting build of R was not quite as fast as that built with
gcc 4.2.1 at -O3.
You can build R as a Unix application on Mac OS X using the Apple Developer Tools (`Xcode') and g77 or gfortran. You will also need to install an X sub-system or configure with --without-x. The X window manager is part of the standard Mac OS X distribution since Mac OS X version 10.3 (Panther), but it is typically not pre-installed prior to 10.5 (Leopard).
For more information on how to find these tools please read the R for Mac OS X FAQ.
If you use the X window manager and prefer Terminal.app to
xterm, you should be aware that R, like many Unix tools, uses
the existence of a DISPLAY environment variable to determine
whether an X system is running. This affects the default graphics
device for the commmand-line version of R and the behaviour of the
png and jpeg devices.
The vecLib library can be used via the (default)
configuration options
--with-blas="-framework vecLib" --with-lapack
to provide higher-performance versions of the BLAS and LAPACK routines. Building R without these options via
--without-blas --without-lapack
used not to work with earlier versions of gcc, but can be done with gcc 3.3 and later.
64-bit builds are supported as from R 2.7.0 on 10.5 (Leopard) only.
For R 2.6.1 (and patched) on 10.5 (Leopard) only, use
CONFIG_SHELL=/bin/bash ./configure
since R is built with `SHELL=/bin/bash' to avoid some settings used for /bin/sh (in particular `xpg_echo' is set).
R has been built successfully on Solaris 10 (both Sparc and `x86') using gcc 3/g77, gcc 4/gfortran and the (free) Sun Studio 11/12 compilers. Sun packages for R are available from http://www.sunfreeware.com/ for both architectures. (Recent Sun machines are Opterons (`x86-64') rather than `x86', but 32-bit `x86' executables are the default.)
There are also reports of success on OpenSolaris (aka Solaris Express Community Edition, and sometimes as Solaris 11) on `x86'.
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.
Modern Solaris systems allow a large selection of Open Source software
to be installed via pkg-get: a Sparc Solaris 10 system came
with libreadline and libiconv and a choice of gcc3
and gcc4 compilers, installed under /opt/csw. (You will
need GNU libiconv: the Solaris version of iconv is not
sufficiently powerful.)
If using gcc, do 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. A version of gcc optimized for Sparc (using technology from Sun's compilers) is available from Sun.26
When using the Sun compilers27 do not specify -fast, as this disables IEEE arithmetic and make check will fail.
To compile for a 64-bit Sparc target with gcc 4 we used
CC="gcc -m64"
F77="gfortran -m64"
CXX="g++ -m64"
FC="gfortran -m64"
LDFLAGS="-L/opt/csw/gcc4/lib/sparcv9 -L/opt/csw/lib/sparcv9"
replacing `gfortran' with `g77' for gcc 3.x.y. Note that paths such as /opt/csw/gcc4/lib/sparcv9 may need to be in the LD_LIBRARY_PATH during configuration.
For the Sun Studio compilers a little juggling of paths is needed to
ensure GNU libiconv is used rather than the Solaris iconv:
we used
CC="cc -xc99"
CPPFLAGS=-I/opt/csw/include
CFLAGS="-O -xlibmieee"
F77=f95
FFLAGS=-O4
CXX=CC
CXXFLAGS=-O
FC=f95
FCFLAGS=$FFLAGS
LDFLAGS=-L/opt/csw/lib
SHLIB_CXXLDFLAGS=-G -lCstd
to ensure that the libiconv version of iconv.h was found.
For a 64-bit target add -xarch=v9 (or v9b, or
amd64) to each of the compiler commands, or for Sun Studio 12 add
-m64. You can target specific Sparc architectures for (slightly)
higher performance: Sun recommend
32-bit: -xtarget=ultra3 -xarch=v8plusa
64-bit: -xtarget=ultra3 -xarch=v9a
(in CFLAGS etc.) as a good compromise for recent Sparc chipsets.
By default the Sun Studio compilers do not conform to the C99 standard
(appendix F 8.9) on the return values of functions such as log:
use -xlibmieee to ensure this.
On `x86' you will get marginally higher performance via
CFLAGS="-xO5 -xc99 -xlibmieee -xlibmil -nofstore"
FFLAGS="-O5 -libmil -nofstore"
CXXFLAGS="-xO5 -xlibmil -nofstore"
SAFE_FFLAGS="-O5 -libmil -fstore"
Building on `x86' with gcc 4 failed make check in the complex LAPACK tests: using Sun Studio 11 worked correctly.
There is limited support for `x86-64' builds in the pre-built
GNU software repositories, with 64-bit libraries (which are in
/opt/csw/lib/amd64 and so on) being scarce (and not including the
gcc support libraries). The Sun Studio compilers do support
64-bit builds via -xarch=amd64.
The Sun performance library libsunperf is available with the Sun
Studio compilers. If selected as a BLAS, it must also be selected as
LAPACK via
./configure --with-blas=sunperf --with-lapack
However, our tests were none too successful: Sparc 64-bit builds crashed.
These are now obsolete operating systems, so this subsection refers to equally old compiler versions.
Sun packages for R are available from http://www.sunfreeware.com/ for both Sparc and `x86'.
R 2.5.1 was built successfully on Sparc Solaris 8 (aka Solaris 2.8 aka SunOS 5.8) using gcc 3/g77, gcc 4/gfortran and the `Sun ONE Studio 7 Compiler Suite' (aka Forte 7).
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.
gcc 3.2.1 and 3.2.2 generate incorrect code on 32-bit Solaris
builds with optimization, but versions 3.2.3 and later work correctly.
(The symptom was that make check failed at the first attempt to
plot.)
If using gcc, do 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
so (for example) gcc compiled under Solaris 2.6 will not
compile R under Solaris 2.7. Also, do ensure that it was compiled
for the assembler/loader in use: if you download gcc from
www.sunfreeware.com then you
need to download binutils too. To avoid all these pitfalls we
recommended you compile gcc from the sources yourself.
It was reported by Mike Pacey that Sun Forte 9 requires
`-xopenmp=stubs' added to LDFLAGS.
When using the Sun compilers do not specify -fast, as this disables IEEE arithmetic and make check will fail. The maximal set of optimization options known to work on Sparc Solaris 8 is
-xlibmil -xO5 -dalign
(`x86' versions do not need `-dalign', and some do not
support it.) To get correct results for log requires
-xlibmieee, but R works around that.
We have found little performance difference between gcc and
cc but considerable benefit from using a SunPro Fortran
compiler: the gcc/f77 combination worked well. For
many C++ applications Forte 7 requires `-lCstd', which the
configure script will add to SHLIB_CXXLDFLAGS if it identifies
the compiler correctly.
To compile for a 64-bit target on Sparc Solaris (which needs an UltraSparc chip and for support to be enabled in the OS) with the Forte 7 compilers we used
CC="cc -xarch=v9 -xc99"
CFLAGS="-xO5 -xlibmil -dalign"
F77="f95 -xarch=v9"
FFLAGS="-xO5 -xlibmil -dalign"
CXX="CC -xarch=v9"
CXXFLAGS="-xO5 -xlibmil -dalign"
FC="f95 -xarch=v9"
FCFLAGS="-xO5 -xlibmil -dalign"
in config.site.
For 64-bit compilation with gcc 3.4.x we used
CC="gcc -m64"
F77="g77 -m64"
CXX="g++ -m64"
FC="gfortran -m64"
LDFLAGS="-L/usr/local/lib/sparcv9 -L/usr/local/lib"
replacing `g77' with `gfortran' for gcc 4.x.y. Note
that /usr/local/lib/sparcv9 may need to be in the
LD_LIBRARY_PATH during configuration. (configure will
append -std=gnu99 to CC.)
Solaris on Sparc CPUs need `PIC' and not `pic' versions of CPICFLAGS and FPICFLAGS since the `pic' version only allows 1024 symbols on a 64-bit build (and 2048 on a 32-bit build).
Note that using f95 allows the Sun performance library
libsunperf to be selected: it may not work28 with f77, and will not with g77.
libsunperf contains both BLAS and LAPACK code, and
--with-lapack may be required if you use it. On our test
system using libsunperf failed for 64-bit builds with both Forte
7 and Sun Studio 11, albeit in different ways. Our experience has been
that ATLAS's BLAS is faster than libsunperf, especially for
complex numbers.
For a 64-bit build, 64-bit libraries must be used. As the configuration
process by default sets LDFLAGS to `-L/usr/local/lib', you
may need to set it to avoid finding 32-bit addons (as in the
gcc -m64 example above). It is possible to build Tcl/Tk as
64-bit libraries with the configure option --enable-64bit, but
only with the Sun compilers (and not with gcc) as of
Tcl/Tk 8.4.5.
There have been alignment issues, with Sun libraries requiring 8-byte alignment of doubles (which gcc generated by default, but cc did not).
% R-help 2007 Nov 1/2, and follow up to BDR Nov 6. Fan Long built R 2.6.0 on HP-UX 11.23 on `ia64' using the native compilers via
CC=cc
CFLAGS="+z +DD64"
CXX=aCC
CXXFLAGS="-b -lxnet +z +DD64"
FC=f90
FCFLAGS=+DD64
F77=f90
FFLAGS=+DD64
LDFLAGS="-L/usr/lib/hpux64 -L/opt/fortran90/lib"
Here `+z' selects PIC code and +DD64 a 64-bit build.
He found that stdbool.h was detected but was non-standard, so `HAVE_STDBOOL_H' had to be undefined in src/include/config.h. In addition, the compiler objected to
static const pthread_once_t fresh_once = {PTHREAD_ONCE_INIT};
(line 362 of src/extra/intl/lock.c) and needed the braces removed.
The remaining reports on HP-UX here predate R 2.0.0.
R has been built successfully on HP-UX 11.0 using both native compilers and gcc. By default, R is configured to use gcc and g77 on HP-UX (if available). Some installations of g77 only install a static version of the g2c library that cannot be linked into a shared library since its files have not been compiled with the appropriate flag for producing position independent code (PIC). This will result in make failing with a linker error similar to
ld: CODE_ONE_SYM fixup to non-code subspace in file foo.o -
shared library must be position independent. Use +z or +Z to recompile.
(+z and +Z are the PIC flags for the native compiler cc.) If this is the case you either need to modify your g77 installation or configure with
F77=fort77
to specify use of the native POSIX-compliant FORTRAN 77 compiler.
You may find that configure detects other libraries that R needs to use as shared libraries but are only available as static libraries. If you cannot install shared versions you will need to tell configure not to use these libraries, or make sure they are not in the library path. The symptom will be the linker error shown in the last paragraph. Static libraries that might be found and would cause problems are
BLAS use --without-blas Tcl/Tk use --without-tcltk libpng use --without-libpng jpeg use --without-jpeglib zlib use --without-system-zlib
and bzip2 and pcre are problematic when building
libR.so, only. These can be avoided by
--without-system-bzlib and --without-system-pcre
respectively, but these are the defaults.
Some versions of gcc may contain what appears to be a bug at the -O2 optimization level that causes
> 2 %/% 2
[1] 1
> 1:2 %/% 2
[1] 0 0 # wrong!!
which will cause make check to fail. If this is the case, you
should use CFLAGS to specify -O as the optimization
level to use.
You can configure R to use both the native cc and fort77 with
./configure CC=cc F77=fort77
f90 insists on linking against a static libF90.a which
typically resides in a non-standard directory (e.g.,
/opt/fortran90/lib). Hence, to use f90 one needs to
add this directory to the linker path via the configure variable
LDFLAGS (e.g.,
./configure F77=f90 LDFLAGS=/opt/fortran90/lib).
R 2.1.0 has been successfully built on IRIX64 6.5 using both gcc and the native (MipsPro 7.4) compiler. However, neither version has passed make check due to a problem with time zones (see below). A 64-bit executable has not been successfully built.
It appears that some (but not all) versions of IRIX have broken wide-character header files and so may need --disable-mbcs.
To build R with gcc use something like the following configuration flags
CPPFLAGS="-I/usr/freeware/include"
LDFLAGS="-L/usr/freeware/lib32"
To build the Tcl/Tk package you will most likely need to add
--with-tclconfig=/usr/freeware/lib/tclConfig.sh
--with-tkconfig=/usr/freeware/lib/tkConfig.sh
since these configuration scripts are not on your path.
To build R with the native compilers, use something like the following configuration flags
CC=cc F77=f77 CXX=CC
CPPFLAGS="-I/usr/freeware/include" LDFLAGS="-L/usr/freeware/lib32"
CFLAGS="-O2" FFLAGS="-O2" CXXFLAGS="-O2"
--with-system-bzlib=yes
The MipsPro compiler will not build the bzlib library, so you must use
the external one provided by SGI as a freeware package.
After configuration, it is necessary to use gmake instead of the native make to build R.
There is a problem with the time zones on IRIX (originally reported by
George N. White III for 1.9.0) which will cause the strptime
tests to fail unless Arthur Olson's timezone data
ftp://elsie.nci.nih.gov/pub/ has been installed (see also
cspry.co.uk/computing/Indy_admin/TIMEZONE.html) and
-ltz is added to the list of libraries (for example, in
environment variable LIBS).
The flag -OPT:IEEE_NaN_inf=ON is added for the native compilers.
R has been built successfully on an Alpha running OSF1 V4.0 / V5.1
using gcc/g77 and cc/f77.
Mixing cc and g77 fails to configure. The
configure option --without-blas was used since the
native blas seems not to have been built with the flags needed to
suppress SIGFPE's. Currently R does not set a signal handler
for SIGFPE on platforms that support IEEE arithmetic,
so these are fatal.
At some point in the past using cc required -std1 to
be set so `__STDC__' was defined. As far as we know this is no
longer needed, and configure no longer sets it, but it does
set -ieee_with_inexact for the C compiler and -fpe3
for the FORTRAN compiler (and -mieee-with-inexact and
-mieee for gcc/g77) (in the appropriate
R_XTRA_* flags).
Attempts to build R on an Alpha with FreeBSD 4.3 have been only
partly successful. Configuring with -mieee added to both
CFLAGS and FFLAGS builds successfully, but tests fail with
SIGFPE's. It would appear that -mieee only defers these
rather than suppressing them entirely. Advice on how to complete this
port would be greatly appreciated.
We no longer support AIX prior to 4.2, and configure will throw an error on such systems. The recent testing has been under AIX 5.2 on `powerpc', where Ei-ji Nakama was able to build pre-2.5.0 with gcc 4.0.3 in several configurations.
Mr Nakama found 32-bit versions of R could be built with configure --without-iconv as well as --enable-R-shlib. For 64-bit versions he used
OBJECT_MODE=64
CC="gcc -maix64"
CXX="g++ -maix64"
F77="gfortran -maix64"
FC="gfortran -maix64"
and was also able to build with the IBM xlc and Hitachi
f90 compilers by
OBJECT_MODE=64
CC="xlc -q64"
CXX="g++ -maix64"
F77="f90 -cpu=pwr4 -hf77 -parallel=0 -i,L -O3 -64"
FC="f90 -cpu=pwr4 -hf77 -parallel=0 -i,L -O3 -64"
FLIBS="-L/opt/ofort90/lib -lhf90vecmath -lhf90math -lf90"
The AIX native iconv does not support encodings `latin1' nor
`""' and so cannot be used. (As far as we know GNU libiconv
could be installed.)
The Cygwin emulation layer on Windows can be treated as a Unix-alike OS. This is unsupported, but experiments have been conducted and a few workarounds added for R 2.6.0.
Only building as a shared library works,29 so use
./configure --disable-nls --disable-mbcs --enable-R-shlib
make
MBCS does not work—wcstod is missing—but would only be of any
use in a CJK locale. NLS does work, although
--with-included-gettext is preferable. You will see many
warnings about the use of auto-import.
It almost passes make check: FIFOs are supposedly supported but hung in `example(fifo)'.
Note that this gives you a command-line application using readline for command editing. The `X11' graphics device will work if a suitable X server is running, and the standard Unix-alike ways of installing source packages work. There was a bug in the /usr/lib/tkConfig.sh script in the version we looked at, which needs to have
TK_LIB_SPEC='-ltk84'
The overhead of using shell scripts makes this noticeably slower than a native build of R on Windows.
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 know 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 requires 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 Solaris
SunPro compilers causes R's NaN to be set incorrectly.
Shared Libraries: There seems to be very little agreement across platforms on what needs to be done to build shared libraries. 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. Set the configure variable SAFE_FFLAGS to the flags to be used for this file. If configure detects GNU FORTRAN it adds flag -ffloat-store to FFLAGS. (Other settings are needed when using icc on `ix86' Linux, for example.)
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 ....
There is a search engine available from the front page of the HTML
help system, the page that is displayed by help.start(). The
search engine is written in Java and invoked by Javascript code, so the
first thing to do is to ensure that both are enabled in your favourite
browser. Then try it and see: with most browsers you should see
Applet SearchEngine started
displayed in the status bar. (Internet Explorer shows Applet
started.) Then click on one of the keywords and after a short delay
(several seconds) you should see a page of search results.
If this fails you should double-check that Java is enabled in your
browser by visiting a page such as
www.java.com/en/download/help/testvm.jsp (although that will
fail for earlier versions of Java such as the Microsoft JVM which do
work with R). Java 1.1 is sufficent.
On Mozilla-based browsers the links on the results page will become inactive if you return to it: to work around this you can open a link in a new tab or window.
Many thanks to Marc Schwartz in tracking down many of these issues with enabling the Java search engine.
We are aware of problems with certain Java installations. In
particular, Sun's Java Run-time Environment j2re 1.4.2_02 to
_05 do not work under `ix86' Linux. Version
jre 1.5.0 is strongly recommended for Mozilla-based
browsers.
This and j2re 1.4.2_01 do work: the latter can be found in
Sun's archive at java.sun.com/products/archive/.
Other Java installations, for example those from Blackdown and IBM, have been used.
Other useful links are for Mozilla,
plugindoc.mozdev.org/faqs/java.html
and
www.mozilla.org/releases/mozilla1.7/installation-extras.html,
for Konqueror www.konqueror.org/javahowto/,
for Opera
www.opera.com/support/search/supsearch.dml?index=459
and for Debian GNU/Linux
www.debian.org/doc/manuals/debian-java-faq/.
Note that there appears not to be a Sun Java plugin for 64-bit browsers
on `x86_64' Linux:
(forum.java.sun.com/thread.jspa?threadID=568127&tstart=75) but
32-bit browsers have been used on that platform, and a Blackdown Java
plugin is available (but failed when tried on FC3).
We have much less experience than under Linux, but we do know that Sun's
Run-time Environment j2re 1.4.2_03 does not work under
Solaris, whereas jre 1.5.0 and j2re 1.4.2_01
(available from java.sun.com/products/archive) do.
We have not seen any problems on Windows provided a Java Virtual Machine
has been installed and is operational: Sun's current
j2re 1.5.0 works in Internet Explorer, Netscape 7.x,
Mozilla 1.6/7 and Mozilla Firefox on Windows XP. Note that a
recent Windows system may not have a JVM installed at all. For
Netscape/Mozilla/Firefox visit
java.sun.com/getjava/manual.html to install a Sun JVM. Which
(if any) JVM is enabled can be set in `Set Program Access and Defaults'
in Windows XP (SP1 or later), and which JVM is used by browser plugins
may also be controlled by the Sun Java applet in the Control Panel.
Recent versions of Internet Explorer may block the use of Java applets and need the block removed via the information bar.
The HTML search engine does not work with Safari under Mac OS X, but
j2re 1.4.x may work with Mozilla, Firefox and Camino if the
Java Embedding Plugin (javaplugin.sourceforge.net) is used.
The Aqua GUI provides an interface to help.search that may
substitute for the Java search.
If you want to build R or add-on packages from source in Windows, you
will need to collect, install and test an extensive set of tools. See
www.murdoch-sutherland.com/Rtools for the current locations and
other updates to these instructions. (Most Windows users will not need
to build add-on packages from source; see Add-on packages for
details.)
There are known problems with one of the compilers sets in this toolset on Windows Vista: see the workaround below. (With that workaround it has been used on both 32- and 64-bit versions of Vista: the recommended gcc 4.2.1 does not need the workaround, and it may indeed be harmful.)
We have found that the build process for R is quite sensitive to the choice of tools: please follow our instructions exactly, even to the choice of particular versions of the tools.30 The build process for add-on packages is somewhat more forgiving, but we recommend using the exact toolset at first, and only substituting other tools once you are familiar with the process.
This section contains a lot of prescriptive comments. They are here as a result of bitter experience. Please do not report problems to R-help unless you have followed all the prescriptions.
We have collected most of the necessary tools (unfortunately not all, due to license or size limitations) into an executable installer named Rtools.exe, available from http://www.murdoch-sutherland.com/Rtools. You should download and run it, choosing the default “Package authoring installation” to build add-on packages, or the “full installation” if you intend to build R.
You will need the following items to build R and packages. See the subsections below for detailed descriptions.
A complete build of R including compiled HTML help files and PDF manuals, and producing the standalone installer R-2.6.1-win32.exe will also need the following:
It is important to set your PATH properly. The Rtools.exe optionally sets the path to components that it installs.
Your PATH may include . first, then the bin
directories of the tools, Perl, MinGW and LaTeX, as well as the Help
Workshop directory. Do not use filepaths containing spaces: you can
always use the short forms (found by dir /x at the Windows
command line). Network shares (with paths starting \\) are not
supported. For example, all on one line,
PATH=c:\Rtools\bin;c:\Rtools\perl\bin;c:\Rtools\MinGW\bin;c:\texmf\miktex\bin;
c:\progra~1\htmhe~1;c:\R\bin;c:\windows;c:\windows\system32
It is essential that the directory containing the command line tools comes first or second in the path: there are typically like-named tools in other directories, and they will not work. The ordering of the other directories is less important, but if in doubt, use the order above.
On Vista systems when using the gcc 3.4.5 compilers you will need to add
c:\Rtools\MinGW\libexec\gcc\mingw\3.4.5
to the path. (Do not do this when using the recommended gcc 4.2.1 compilers.)
Edit R_HOME/src/gnuwin32/MkRules to set the appropriate paths as needed and to set the type(s) of help that you want built. Beware: MkRules contains tabs and some editors (e.g., WinEdt) silently remove them.
Set the appropriate environment variables.
Our toolset contains copies of Cygwin DLLs that may conflict with other ones on your system if both are in the path at once. The normal recommendation is to delete the older ones; however, at one time we found our tools did not work with a newer version of the Cygwin DLLs, so it may be safest not to have any other version of the Cygwin DLLs in your path.
You will need a Windows port of perl5 (but only the basic
functionality, not any of the third-party Win32 extensions). The
Vanilla Perl package is included in Rtools.exe. A more full-
featured distribution is available from
www.activestate.com/Products/ActivePerl, and this was used
in releases of R up to R 2.5.1. Alternatives are listed at
win32.perl.org.
Beware: you do need a Windows port and not the Cygwin one. Users of 64-bit Windows can use a Win64 Perl (such as that from ActiveState) if they prefer.
To make compiled html (.chm) files you will need the Microsoft
HTML Help Workshop, currently available for download at
msdn.microsoft.com/library/en-us/htmlhelp/html/hwmicrosofthtmlhelpdownloads.asp
and www.microsoft.com/office/ork/xp/appndx/appa06.htm.
This is not included in Rtools.exe.
You may need this on the same drive as the other tools. (Although we regularly use it on a different drive, problems have been reported in the past.)
To skip building compiled html help when building R, set
WINHELP=NO in MkRules. In this case the Help Workshop
will not be needed (but it will be needed for installing packages by
R CMD INSTALL with the default settings).
The `MiKTeX' (www.miktex.org)
distribution of LaTeX includes a suitable port of pdftex. The
`basic' version of `MiKTeX' almost suffices (the grid
vignettes need fancyvrb.sty), but it will install the 15Mb
`lm' package if allowed to (although that is not actually used).
The Rtools.exe installer does not include any version of
LaTeX.
Please read Making the manuals about how to make refman.pdf and set the environment variables R_RD4DVI and R_RD4PDF suitably; ensure you have the required fonts installed.
To make the installer package (R-2.6.1-win32.exe) we require
Inno Setup 5.1.7 or later (including 5.2.x) from jrsoftware.org. This is not included in Rtools.exe.
Edit file src/gnuwin32/MkRules and change ISDIR to the
location where Inno Setup was installed.
This item and the next are installed by the Rtools.exe installer.
If you choose to install these yourself, you will need suitable
versions of at least basename, cat, cmp,
comm, cp, cut, diff, echo,
egrep, expr, find, gawk, grep,
gzip, head, ls, make, makeinfo,
mkdir, mv, rm, rsync, sed,
sh, sort, texindex and touch; we use those
from the Cygwin distribution (www.cygwin.com) or compiled from the sources. You will also
need zip and unzip from the Info-ZIP project
(www.info-zip.org). All of
these tools are in Rtools.exe.
Beware: `Native' ports of make are not suitable
(including that at the mingw site). There were also problems with
several earlier versions of the cygwin tools and DLLs. To avoid
frustration, please use our tool set, and make sure it is at the front
of your path (including before the Windows system directories). If you
are using a Windows shell, type PATH at the prompt to find out.
This version of R is set up to use gcc 4.2.1 for
which MinGW compilers were released in August 2007. For those
compilers, use the default setting of BUILD=GCC4 in file
src/gnuwin32/MkRules. For earlier MinGW compilers set
BUILD=GCC3 in file src/gnuwin32/MkRules.
The Rtools.exe installer currently includes both versions 3.4.5 and
4.2.1 of the MinGW port of gcc from
http://sourceforge.net/project/showfiles.php?group_id=2435.
If you would like to install your own copy, we recommed downloading from
the URL above, as the download links from www.mingw.org have
led to obsolete versions. See the notes on
www.murdoch-sutherland.com/Rtools for updates.
To download the components individually, currently you need
mingw-runtime-3.13.tar.gz
w32api-3.10.tar.gz
binutils-2.17.50-20060824-1.tar.gz
gcc-core-4.2.1-sjlj-2.tar.gz
gcc-g++-4.2.1-sjlj-2.tar.gz
gcc-gfortran-4.2.1-sjlj-2.tar.gz
(and gcc-objc-4.2.1-sjlj-2.tar.gz if you want Objective C
support). Unpack these into the same directory (using tar zxf
tarball_name). (You may need to copy bin/gcc-sjlj.exe to
bin/gcc.exe and a few badly-written packages need
bin/g++-sjlj.exe copied to bin/g++.exe.) This compiler
should work on Windows Vista without any workarounds.
Note that mingw-runtime-3.13.tar.gz or later and gcc-3.4.5
or later are needed to get a correct build of R itself. (The
`Snapshot' binutils-2.17.50-20070129-1.tar.gz has also be
tested.) There are known problems with using other compiler sets on
Windows Vista
(http://www.nabble.com/environment-hosed-during-upgrade-tf3305745.html#a9195667
and that a suitable PATH needs to be set to include the path to
cc1.
Other builds of gcc 4 are available from
http://gcc.gnu.org/wiki/GFortranBinaries and
http://www.tdragon.net/recentgcc/: these need the PATH
workaround on Vista.
configure: Using makeconfigure: Configuration variablesconfigure: Installationconfigure: Simple compilationHELP: Customizing package compilation under WindowsHELPTYPES: Customizing package compilation under Windowsinstall.packages: Installing packagesmake: Using makeMakeDll: Customizing package compilation under WindowsMakevars.win: Customizing package compilation under WindowsR_HOME: Simple compilationremove.packages: Removing packagesupdate.packages: Updating packagesWINHELP: Customizing package compilation under WindowsBLAS_LIBS: BLASCONFIG_SITE: Configuration variablesDISPLAY: Mac OS XJAVA_HOME: Java supportLANG: Localization of messagesLANGUAGE: Localization of messagesLAPACK_LIBS: LAPACKLC_ALL: Localization of messagesLC_MESSAGES: Localization of messagesLD_LIBRARY_PATH: Sparc Solaris 9 and earlierLD_LIBRARY_PATH: Solaris 10 and Open SolarisLD_LIBRARY_PATH: Compile and load flagsLD_LIBRARY_PATH: Using FORTRANLD_LIBRRARY_PATH: ACMLLIBS: IRIXPAPERSIZE: Setting paper sizeR_BROWSER: Setting the browserR_DEFAULT_PACKAGES: Default packagesR_JAVA_LD_LIBRARY_PATH: Java supportR_LIBS: Installing packagesR_LIBS: Add-on packagesR_LIBS_SITE: Managing librariesR_LIBS_USER: Managing librariesR_PAPERSIZE: Making manualsR_PAPERSIZE: Setting paper sizeR_PAPERSIZE: Making the manualsR_RD4DVI: LaTeXR_RD4DVI: Making manualsR_RD4DVI: Making the manualsR_RD4PDF: LaTeXR_RD4PDF: Making manualsR_RD4PDF: Making the manualsTMPDIR: Installing packagesTMPDIR: Running RTMPDIR: Checking the buildTMPDIR: Simple compilation[1] This needs Perl to be available.
[2] We do this using the Cygwin compilers, often with some difficulty.
[3] unless they were excluded in the build.
[4] its binding is looked once that files has been read, so users cannot easily change it.
[5] If a proxy needs to be set, see ?download.file.
[6] also known as IEC 559 and IEEE 754
[7] at least when storing quantities: the on-FPU precision is allowed to vary
[8] until recently this limit applied to all processes, not just to one process
[9] It is likely that commercial 64-bit compilers could be used, but those we have looked at do not work in the same way as the MinGW compilers so extensive changes to the build system would be needed. Also, end users would need to have the same compilers to install extension packages. There is an experimental version of MinGW for 64-bit Windows, but it is not yet good enough to build a working R.
[10] e.g. Bessel, beta and gamma function
[11] also known as IEEE 754
[12] -std=c99 excludes POSIX functionality, but config.h will turn on all GNU extensions include the POSIX functuonality.
[13] Earlier versions of R searched for external BLASes, but this caused frequent difficulties.
[14] he generic BLAS supplied with Fedora Core 3 and 4
Extras is missing drotm, drotmg and zdrot
[15] unless FORTRAN double complex is not supported on the platform
[16] Using the Sun Studio cc and f95 compilers
[17] We have measured 15–20% on i686 Linux and around 10% on `x86_64' Linux.
[18] AIX has to be different: it has `EN_US.UTF-8'!
[19] You may have to set this with luit, but it
should be the default in a window manager session started in UTF-8.
[20] e.g. Fedora Core 6
[21] On HP-UX fort77 is the POSIX compliant FORTRAN compiler, and comes after g77.
[22] as well as its equivalence to the Rcomplex
structure defined in R_ext/Complex.h.
[23] In particular, avoid g77's -pedantic, which gives confusing error messages.
[24] e.g., to use an optimized BLAS on Sun/Sparc
[25] for example, X11 font at size 14 could not
be loaded.
[26] http://www.sun.com/download/index.jsp?cat=Application%20Development&tab=3&subcat=Development%20Tools
[27] including gcc for Sparc from Sun.
[28] recent versions have f77 as a wrapper for f95, and these do work.
[29] DLLs need to have all links resolved at build time and so cannot resolve against R.bin.
[30] For
example, the Cygwin version of make 3.81 fails to work
correctly.