This is a guide to installation and administration for R.
The current version of this document is 2.2.1 (2005-12-20).
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 http://cran.r-project.org/mirrors.html.
The simplest way is to download the most recent R-x.y.z.tgz file, and unpack it with
tar xvfz R-x.y.z.tgz
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.tgz | 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.tgz-split.* files and paste them together at the destination with (Unix)
cat R-x.y.z-split.* > R-x.y.z.tgz
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).
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.
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 http://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-patches/' (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.
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 includingcpu-*-linux-gnu for the alpha, amd64, arm, hppa, ix86, ia64, m68k, powerpc, and sparc CPUs (see e.g. http://buildd.debian.org/build.php?&pkg=r-base), powerpc-apple-darwin and sparc-sun-solaris, as well as probably (it is tested less frequently on these) i386-*-freebsd, i386-*-netbsd, i386-*-openbsd, i386-sun-solaris, mips-sgi-irix, alpha-dec-osf*, rs6000-ibm-aix and hppa-hp-hpux.
In addition, binary distributions are available for some common Linux distributions and for Mac OS X (on PowerPC). 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 in 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 correctly, by
make check
Failures are not necessarily problems as they might be caused by missing functionality, but you should look carefully at any reported discrepancies. (Also, the d-p-q-r-tests.R is random and will fail about 1 in 50 runs, so if this fails please re-run make check.) 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 commmands execute successfully, the R binary will be copied to the R_HOME/bin directory. 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”. (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: 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
http://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 the info files unless you have makeinfo version 4.7 or later installed.
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:
timeslmtimes.
cm-superaeBoth Unix and Windows installations default to times. The choice
can be overridden by setting the environment variable R_RD4PDF.
(On Unix, this will be picked up at install time.) The default value is
times,hyper: omit hyper if you do not want hyperlinks,
e.g. for printing.
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
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.
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
libdir=EPREFIX/${LIBnn}
All of bindir and mandir and libdir can also be
specified on the make install command line.
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-2.2.0.
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.
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.
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.
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.
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 and XP (at least) on Intel x86 and clones (but not on other platforms).
You do need one of those Windows versions: Windows 3.11+win32s will not work.
Your file system must allow long file names (as is likely except perhaps for some network-mounted systems).
Installation is via the installer R-2.2.1.exe. Just double-click on the icon and follow the instructions. You can uninstall R from the Control Panel. (Note that you will probably 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 http://www.murdoch-sutherland.com/Rtools/) for details.
Be sure to set your path in the order given in the appendix.
You need to collect the following sets of files:
tar zxvf R-2.2.1.tgz
to create the source tree in R_HOME. Beware: do use
tar to extract the sources rather than broken tools such as
WinZip that don't understand about symbolic links.
It is also possible to obtain the source code using Subversion; see Obtaining R for details.
libpng and jpeg sources (available, e.g., from
http://www.libpng.org, ftp://ftp.uu.net/graphics/[png,jpeg].
You will need files libpng-1.2.8.tar.gz and
jpegsrc.v6b.tar.gz or later.
make
link-recommended. If you have rsync and an Internet connection,
you can do this automatically using
make rsync-recommended
Rblas.dll for various Pentium
and AthlonXP chips are available in the windows/contrib/ATLAS
area on CRAN.
A tuned BLAS which has been available for some CPUs is by
Kazushige Goto. This is currently (October 2005) no longer available
for Windows, and it seems that it will in future only to be offered via
a source-code licence. If you have an earlier version, put the
DLL somewhere in your path or in R_HOME/bin, and
edit R_HOME/src/gnuwin32/MkRules to define
USE_GOTO=YES and the name of the DLL (something like
libgoto_prescott-r0.99.3.dll). Specifying a Goto BLAS takes
preference over ATLAS, and seems a little faster. However, as it is
compiled for MSVC, we have been unable to make it work for complex
arithmetic and so it is only used for real linear algebra.
Another possibility is to use AMD's AMD Core Math Library (ACML)
http://www.amd.com/acml. To use the Cygwin-compiled version
(Cygwin itself is not needed, at least currently), install
acml-2-7-0-win32-g77.exe (or later) and edit
R_HOME/src/gnuwin32/MkRules to define USE_ACML=YES
and set ACML_PATH to the path to libacml.a.
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. Look at the comments in front-ends/Makefile and perhaps uncomment commands to increase the stack size and make the executables large-address-aware. Then run
make
and sit back and wait while the basic compile takes place.
Notes:
windres is run, so you may need to disable
it. (Norton Anti-Virus 2002 causes no problems.)
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
but this is only likely to be worthwhile on a dual-processor (or perhaps a hyperthreaded P4) machine with ample (at least 384Mb) of memory. On a dual AthlonMP it reduced the build time by about 30% whereas on a single P4HT it reduced it by 10%. Note that this may sometimes stop and have to be restarted.
The file R_HOME/bin/Rbitmap.dll is not built automatically.
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-1.2.8.tar.gz
> mv libpng-1.2.8 libpng
> tar xzvf jpegsrc.v6b.tar.gz
Once everything is set up in directory bitmap, make
in that directory or make bitmapdll in the parent directory
should build Rbitmap.dll and install it in R_HOME/bin.
This version of R can be built with support for some multibyte character sets such those used in Chinese, Japanese and Korean.
Define SUPPORT_MBCS in config.h to enable support in the
R engine for multi-byte character sets. This is only useful if you
have an `East Asian' version of Windows, as only those versions have
multi-byte locales. (This is the default in the sources, but the
distribution builds two versions of R.dll, the default choice
being that without SUPPORT_MBCS.)
This also enables support for multi-byte locales in the RGui
console, pager, data and script editors (this is based loosely on the
Japanization patches by Nakama and Okada). The Rterm
command-line editor is not supported in such locales.
Define both SUPPORT_MBCS and SUPPORT_UTF8 in
config.h to enable support in the R engine and in the Windows
graphics device for UTF-8 character sets. Since there are no UTF-8
locales on Windows, this sets the locale to be UTF-8 and expects
input/output in UTF-8. It would only be useful with a customized
front-end to R.dll.
If any of these is defined you need the DLL msvcp60.dll to be installed. It is on recent versions of Windows, and can be obtained by an Internet search.
You can test a build by (optionally) building the recommended packages
(see below) and 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 built by
make recommended
and checked by
make 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-no-mbcs (the non-East Asian version of R.dll) 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, third, fourth and fifth targets are the default build if just `make' is run, but the second (which builds the default version of R.dll) needs to be run first.
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-2.2.1.exe, so please rename it to indicate that it is customized.
You will need i386-mingw32 cross-compilers installed and in your path. There is currently a complete set of tools at http://www.stats.ox.ac.uk/pub/Rtools/mingw-cross5.tar.bz2 (Just unpack this somewhere and put its bin directory in your path.)
You will need Perl, zip and unzip installed
and makeinfo version 4.7 or later (part of GNU texinfo).
You also need the R source (R-2.x.y.tgz).
Then: untar R-2.x.y.tgz somewhere, and
cd /somewhere/R-2.x.y/src/gnuwin32
Edit MkRules to set BUILD=CROSS and the appropriate
paths (including HEADER) as 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 Add-on packages.
(It is possible to cross-build the installers using WINE, which we leave as an exercise for the reader.)
To distribute a cross-build (or just to transfer it to a Windows machine for testing) use
cd installer
make imagedir
zip -r9X R-2.2.1.zip R-2.2.1 # or something similar
We have not found a reliable way to convert base to lazy-loading when cross-building, so it is left in the old format.
The bin/macosx directory of a CRAN site contains binaries for MacOS X (at the time of writing only for PowerPC) for a base distribution and a large number of add-on packages from CRAN to run on Mac OS X version 10.3.0 or higher.
The simplest way is to use R.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. Than you have to expand the R sources and configure R appropriately, for example
tar zxvf R-2.2.1.tgz
cd R-2.2.1
./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 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.
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).
Various environment variables can be set to determine where R creates its per-session temporary directory. For Unix-alike versions launched from the (usual) shell-script front-end, this is set by TMPDIR and defaults to /tmp: this is also used by a number of utilities such as R CMD INSTALL. There is no check made that this points to an actual directory that is user-writable. For Windows and embedded Unix-alike versions of R (including the MacOS X console) the environment variables TMPDIR (not Windows), TMP and TEMP are searched in turn and the first one which is set (and on Windows 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 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.
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().
Packages may be distributed in source form or compiled binary form. Installing source packages requires that compilers and tools (including Perl 5.004 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.
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.
The same command works in Windows if you have the source-code package files (option “Source Package Installation Files” in the installer) and toolset (see The Windows toolset) installed.
Alternatively, packages can be downloaded and installed from within
R. First set the option CRAN to your nearest CRAN
mirror using choooseCRANmirror(). Then download
and install packages pkg1 and pkg2 by
> install.packages(c("pkg1", "pkg2"))
Unless the library is specified (argument lib) the first library
in the library search path is used. 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)
What install.packages does by default is different on Unix and
Windows. On Unix-alikes (include MacOS X unless running from the GUI
console) 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.
install.packages can install a source package from a local
.tar.gz file by setting argument repos to NULL.
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.
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, ...).
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.package in order to download and install binary
packages from CRAN. 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++/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 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: files src/Makefile or src/Makevars will be used if they exist and the .win equivalents do not. Such files included in package sources are usually designed for use under Unix and are best removed.
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 compiler.
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/powerpc/contrib/x.y
for R versions x.y.z and containing .tgz files.
Each terminal directory must also contain a PACKAGES file. This
can be a concatenation of the DESCRIPTION files of the packages
separated by blank lines (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 has 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). What characters are valid in names was taken
from the current locale. In general other locales with single-byte
encodings worked, but e.g. postscript() and pdf() needed
to be told about the encoding in use.
Full internationalization can be enabled when R is built under Unix-alikes by the (default) configure option --enable-mbcs: see Configuration on Unix. Under Windows, it is enabled by default in source builds, but support for `East Asian' (Chinese/Japanese/Korean) languages is only enabled in the binary install if it is selected in the installer.
All versions 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 versions 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) and those for Chinese, Japanese
and Korean. Note that only some of the graphics devices can handle
multi-byte or even non-Latin-1 character sets: in particular
postscript and pdf are in practice restricted to ISO
Latin-1, -2, -7, -9 and Cyrillic.
The other aspect of the internationalization is support of the translation of messages. This is enabled in almost all builds of R as from version 2.1.0.
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 http://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
http://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.
Internally Mac OS X uses a form similar to Linux but without specifying
the encoding (which is .UTF-8).
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 locale
names to languages, even on Windows.
Note that you should not expect to be able to change the language once R
is running, and so LC_MESSAGES is not supported by
Sys.setlocale.
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.
Translations in the right language but the wrong charset can generally
be made use of by on-the-fly re-encoding. The LANGUAGE variable
(only) can be a colon-separated list, for example se:de, giving a
set of languages in decreasing order of preference. One special value
is en@quot, which can be used in a UTF-8 locale to have
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 http://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. 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) 64-bit is.
All current versions of R use 32-bit integers and IEC 605591 double-precision reals, and so compute to the same accuracy 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.
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 a 3GB address space. It will not be possible to build a native version for Windows 64 until suitable compilers are available, and currently (mid-2005) that is not in prospect.
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 IEC600593,
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 CFLAGS suitably. For recent versions of gcc with
glibc this means including -std=gnu99 in CFLAGS
(-std=c99 excludes POSIX functionality).
Unless you do not want to view graphs on-screen you need `X11' installed, including its headers and client libraries. (On Fedora Core Linux this means the `xorg-x11-devel' and `xorg-x11-libs' RPMs, for example. Older Linuxen used `XFree86-'. Sone Debian derivatives apparently also require `libxt-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: you will need a fairly recent
version. Otherwise you will need to configure with
--with-readline=no (or equivalent).
You will need Perl version 5.004 or later, available via http://www.perl.com/CPAN/, to build any of the on-line documentation.
You will not be able to build the info files unless you have makeinfo version 4.7 or later installed, and if not some of the HTML manuals will be linked to CRAN. (makeinfo version 4.7 is fairly recent, but version 4.6 is known to create incorrect HTML files.)
The typeset 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 use of encodings 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
http://www.gnu.org/software/libiconv/. Note that the R usage
requires iconv to be able to translate between "latin1"
and "UTF-8" and to recognize "" as the current encoding –
this is not true of most commercial Unixes.
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 that 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 use ghostscript
(http://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.
The tcltk package needs Tcl/Tk installed: the sources are available at http://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.
Versions of Tcl/Tk from 8.3 to 8.4.11 have been used successfully: 8.0 is no longer supported.
The linear algebra routines in R can make use of enhanced BLAS (Basic
Linear Algebra Subprograms, http://www.netlib.org/blas/faq.html)
routines. Some are compiler-system-specific (libsunperf on Sun
Sparc4, libessl on IBM, vecLib on Mac OS
X) but ATLAS (http://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. 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. (Alternatively,
the environment variable BLAS_LIBS can be set, for example in
config.site.)
For systems with multiple processors it is possible to use a
multi-threaded version of ATLAS. An 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 version of ATLAS. You can
use a multi-threaded ATLAS by specifying
--with-blas="-lptf77blas -lpthread -latlas"
Another tuned BLAS which is available for some processors under Linux is by Kazushige Goto, currently available for academic use only (after registering) via http://www.tacc.utexas.edu/resources/software/software.php. (Recent versions are multi-threaded only.) Once this is installed, it can be used by configuring with
--with-blas="-lgoto -lpthread"
It has been reported that on some RedHat-based Linux systems it is
necessary to set 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. That environment variable should be set
when using R profiling.
For Intel processors under Linux, Intel's Math Kernel Library http://www.intel.com/software/products/mkl/ can be used by
--with-blas="-lmkl -lguide -lpthread"
with the same caveat on multi-threading (but the number of threads defaults to 1). (Thanks to Andy Liaw for the information.)
For x86_64 and ix86 processors under Linux there is the AMD Core Math
Library (ACML) http://www.amd.com/acml. For the gcc
version5 (which is single-threaded only) we
could use
--with-blas="-lacml"
if the appropriate library directory such as
/opt/acml2.7.0/gnu64/lib is in the LD_LIBRRARY_PATH.
For other compilers, see the ACML documentation. Although the
documentation is unclear, 32-bit versions of ACML do run on other
ia32 chips such as AthlonMP and P4.
Note that the BLAS library will be used for several add-on packages as well as for R itself. This means that it is better to use a shared BLAS library, as most of a static library will be compiled into the R executable and each BLAS-using package. In any case, the BLAS library must be usable with dynamically-loadable code: this can be a problem with ATLAS on some platforms (including x86_64) as it is not by default built with position-independent code.
You will need double-precision and double-complex versions of the BLAS, but not single-precision nor complex routines.
On some systems it is necessary that an external BLAS was built with the same FORTRAN compiler used to build R: known problems are with R built with gfortran see Using gfortran.
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). 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, 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: -lmkl_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 means
that on Sun Sparc using the native compilers the flag -dalign
is needed so libsunperf can be used.
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. Other BLASs can also be used when building from source.
Note that under Unix (but not under Windows) if R is compiled against a non-default BLAS, then all BLAS-using packages must also be. So if R is re-built after ATLAS is installed, then packages such as quantreg will need to be re-installed.
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 performance6 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 a R system linked with --enable-R-shlib are linked against the dynamic library and so such packages cannot be used from a R system built in the default way.
R supports multi-byte character sets (MBCS), in particular
for UTF-8 locales (which are usually identified by suffix .utf8,
something like en_GB.utf87. 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 UTF-8 is selected 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 and for UTF-8 or MBCS support in X11. 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
characters8.
If run in a single-byte locale, R behaves almost exactly as if it was
configured with --disable-mbcs.
A version of R 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'.)
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 LDFLAGS=-L/usr/local/lib
(/usr/local/lib64 on most 64-bit Linux OSes) and
CPPFLAGS=-I/usr/local/include 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).
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 works 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 2.7/8/9 (but not earlier).
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 or f2c, the
FORTRAN-to-C converter (http://www.netlib.org/f2c). 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)9, and then for f2c, 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 variables
F77 and F2C which specify the commands that run the
FORTRAN 77 compiler and FORTRAN-to-C converter, respectively. If
F77 is given, it is used to compile FORTRAN; otherwise, if
F2C is given, f2c is used even if a FORTRAN compiler would be be
available. 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. Because of
this, f2c will not be accepted on a 64-bit platform as it
produces 64-bit integers, incompatible with C's int on such
platforms.
Some of the FORTRAN code makes use of COMPLEX*16 variables, which
is a FORTRAN 90 extension. This is checked for at configure
time10, but you may need to avoid
compiler flags11 asserting
FORTRAN 77 compliance.
For performance reasons12 you may want to choose a FORTRAN 90/95 compiler.
If you use f2c 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, where f2c
is not allowed.
gfortran is the F95 compiler that is part of gcc 4.x.y.
There was a problem with the version in the gcc 4.0.0 release and
most pre-releases. At least on ix86 and x86_64 Linux and
MacOS X the dynamic version of the FORTRAN runtime libgfortran
could not be used: if this is loaded redirection of C stdin
(which R uses in many of its scripts) becomes non-functional. A
workaround is to set the environment variable GFORTRAN_STDIN_UNIT
to -1, but versions before 10 April 2005 had another bug causing
the setting to be ignored. Both problems have been fixed for gcc
4.0.1. The version of gfortran shipping with Fedora Core 4
seems to have the fixes in place.
Some versions of g95 (from http://www.g95.org) have the same problem.
On x86_64 systems there is an incompatibility in the return
conventions for double-complex functions between gfortran and
g77 which result in the final example in example(eigen)
hanging or segfaulting under external BLASs built under g77,
as well as with Dr Goto's BLAS. As from R 2.2.0 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_CFLAGSFFLAGSMAIN_FFLAGSSHLIB_FFLAGSMAIN_LDFLAGSSHLIB_LDFLAGSLIBnnLibrary 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.
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 IEC60559 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.
Many 32-bit systems have a means of using files > 2Gb, and most are based on that in the Single Unix specification: see http://ftp.sas.com/standards/large.file/x_open.20Mar96.html. However, this is only covered under Linux and Solaris.
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 the `gcc' compilers normally produce PIC code on
`ix86' Linux but do not necessarily do so on 64-bit versions 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 we used
CFLAGS="-m32 -O2 -g -Wall -pedantic -std=gnu99"
CXXFLAGS="-m32 -O2 -g"
FFLAGS="-m32 -O2 -g"
LDFLAGS=-m32
LIBnn=lib
--x-libraries=/usr/X11R6/lib
and had to build readline ourselves as Fedora Core 3 only shipped
a 64-bit version.
64-bit versions of Linux are built with support for files > 2Gb, but 32-bit versions usually are not. This can be enabled for Linux kernels 2.4.x or later by the configure option --enable-linux-lfs: it tests for Linux, a suitable kernel and a 32-bit `long' type. A discussion of which Linux systems support large files can be found at http://www.suse.de/~aj/linux_lfs.html: it has been available since about 2001.
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 or 2.3) but
could conceivably be needed on an older version. glibc 2.1
required -D__NO_MATH_INLINES to achieve IEC60059-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 gcc4 (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 4.0.1 and gcc 4.0.2 cannot compile
src/main/plot.c when building R as a shared library on
`ix86' unless the optimization level is reduced from the default
-O2.
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 via
CC=icc
F77=ifort
CXX=icc
ICC_LIBS=/opt/compilers/intel/cc/9.0/lib
IFC_LIBS=/opt/compilers/intel/fc/9.0/lib
LDFLAGS="-L$ICC_LIBS -L$IFC_LIBS -L/usr/local/lib"
and adding optimization flags failed: at least src/main/regex.c
and src/modules/lapack/dlamc.f need to be compiled without
optimization. For x86_64 he used
CC=icc
CFLAGS="-mp -g -O2"
F77=ifort
FFLAGS="-mp -g -O2"
CXX=icc
CXXFLAGS="-mp -g -O2"
ICC_LIBS=/opt/compilers/intel/cce/9.0/lib
IFC_LIBS=/opt/compilers/intel/fce/9.0/lib
LDFLAGS="-L$ICC_LIBS -L$IFC_LIBS -L/usr/local/lib"
Note the use of -mp to maintain correct IEC60559 arithmetic:
these are the default flags selected by configure if none are
supplied. (-mieee-fp is an alternative name for -mp.)
For some comments on building on an Itanium (`ia64') Linux system with gcc or the Intel compilers see http://www.nakama.ne.jp/memo/ia64_linux/.
Jennifer Lai used the Portland Group compilers on `x86_64' to build pre-2.2.0 with settings
PG_HOME=/usr/pgi/linux86-64/6.0
CC=pgcc
CFLAGS="-g -O2 -mieee-fp"
CPPFLAGS="-I$PG_HOME/include -I$PG_HOME/include/CC"
CPICFLAGS=-fpic
F77=pgf77
FFLAGS=-O2
FPICFLAGS=-fpic
CXX=pgCC
CXXPICFLAGS=-fpic
SHLIB_CXXLDFLAGS=-shared
SHLIB_LDFLAGS=-shared
LDFLAGS="-L$PG_HOME/libso -L/usr/lib64"
Note particularly the last, which is needed to ensure that a shared
version of libc is found. As from R 2.2.1, we include
-mieee-fp in R_XTRA_CFLAGS so it should not be included in
CFLAGS.
You can build R as a Unix application on Mac OS X using the Apple Developer Tools and f2c or 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).
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 of Mac OS X >= 10.2.2 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.
R has been built successfully on Solaris 8 aka Solaris 2.8 aka SunOS 5.8 using gcc/g77, gcc4/gfortran and the `Sun ONE Studio 7 Compiler Suite' (aka Forte 7), and less regularly on Solaris 9 and 10. GNU make was needed prior to Solaris 2.7 for building other than in the source tree, and is sometimes needed to establish the correct dependencies when rebuilding.
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 3.1, 3.2, 3.2.3 and later work
correctly. (make check fails 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
http://www.sunfreeware.com then you need to download
binutils too. To avoid all these pitfalls we strongly
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 SunPro compilers do not specify -fast, as this disables IEEE arithmetic and make check will fail. The maximal set of optimization options known to work is
-xlibmil -xO5 -dalign
We have found little performance difference between gcc and
cc but considerable benefit from using a SunPro FORTRAN
compiler: the gcc/f77 combination works well. For
many C++ applications Forte 7 requires -lCstd, which the
configure script will add to SHLIB_CXXLDFLAGS if it identifies
the compiler correctly.
A 32-bit version of R is built without large file support and so can only handle files up to 2Gb (unlike 64-bit versions). According to `man lfcompile' this restriction can be removed if -D_FILE_OFFSET_BITS=64 -D_LARGEFILE_SOURCE=1 is added to `CFLAGS'.
To compile for a 64-bit target on 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"
CFLAGS="-xO5 -xlibmil -dalign"
F77="f95 -xarch=v9"
FFLAGS="-xO5 -xlibmil -dalign"
CXX="CC -xarch=v9"
CXXFLAGS="-xO5 -xlibmil -dalign"
in config.site.
For 64-bit compilation with gcc 3.2.x and later we used
CC="gcc -m64"
F77="g77 -m64"
CXX="g++ -m64"
LDFLAGS="-L/usr/local/lib/sparcv9 -L/usr/local/lib"
replacing `g77' with `gfortran' for gcc 4.0.x. Note that `/usr/local/lib/sparcv9' will need to be in the `LD_LIBRARY_PATH' during configuration.
Note that using f95 allows the Sun performance library
libsunperf to be selected: it may not work13 with f77, and will not with g77.
libsunperf contains both BLAS and LAPACK code, and
--with-lapack is recommended for 32-bit builds using
f95, but not for 64-bit builds where on our test system it
failed in both Forte 6U1 and 7, albeit in different ways. Our
experience has been that ATLAS's BLAS is faster than libsunperf,
especially for complex numbers.
Some care is needed to ensure that libraries found by
configure are compatible with the R executable and modules, as
the testing process will not detect many of the possible problems. For
32-bit builds under cc the flag -dalign is needed for
some of the Sun libraries: fortunately the equivalent flag for
gcc, -mno-unaligned-doubles, is the default. In
theory, libraries such as libpng, libjpeg, zlib and
the ATLAS libraries need to be built with a pic or PIC
flag, which could be a problem if static libraries are used. In
practice this seems to give little problem for 32-bit builds.
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 Forte compiler (and not with gcc) as of Tcl/Tk 8.4.5.
The reports on HP-UX here predate R 2.0.0.
R has been built successfully on HP-UX 10.2 and HP-UX 11.0 using both native compilers and gcc. However, 10.2 has not been tested since R 1.4.0. 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.
Some systems running HP-UX 11.0 may have a gcc that was
installed under HP-UX 10.2. Between versions 10.2 and 11.0 HP-UX
changed its support functions for IEEE arithmetic from the
recommended functions of the IEEE standard to the ones
specified in the C9x draft standard. In particular, this means that
finite has been replaced by isfinite. A gcc
configured for HP-UX 10.2 run on 11.0 will not find isfinite, and
as a result configure does not recognize the machine as fully
supporting IEEE arithmetic and so will not complete. The best
solution is to install a properly configured gcc. An
alternative work-around is to add -DIEEE_754 to the
CFLAGS variable.
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
http://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.
On AIX 4.3.3 and AIX 5.1/2, it was found that the use of “run time
linking” (as opposed to normal AIX style linking) was required. For
this, the R main program must be linked to the runtime linker with
the -brtl linker option, and shareable objects must be enabled
for runtime linking with the -G linker option. Without these
options, the AIX linker would not automatically link to any shared
object with a .so extension. Also, the R main program would
be unable to dynamically load modules (such as X11) with the
dlopen call.
When setting MAIN_LDFLAGS and SHLIB_LDFLAGS accordingly,
note that linker flags must be escaped using `-Wl,' if
gcc is used for linking: use `MAIN_LDFLAGS="-Wl,brtl"'
and `SHLIB_LDFLAGS="-Wl,-G"' in this case.
Tim Hoar <thoar at cgd dot ucar dot edu> reported success building R 1.9.0 under AIX 5.1 in 64-bit mode with
OBJECT_MODE=64
CC=/usr/bin/xlc_r
F77=/usr/bin/xlf_r
CXX=/usr/bin/xlC_r
LDFLAGS='-brtl'
CFLAGS='-O -qstrict'
FFLAGS='-O -qstrict'
CXXFLAGS='-O -qstrict'
and the X11() device worked. [His system required the
Makeconf file to be edited to replace /lib/crt0.o by
/lib/crt0_64.o in R_XTRA_LIBS, but configure now
tries to detect this.]
Paul Boutros reported success building R 2.0.1 under AIX 5.2 with
gcc 3.3.2 using
OBJECT_MODE=64
MAIN_LDFLAGS=-Wl,-brtl
SHLIB_LDFLAGS=-Wl,-G
(note it is Wl (W ell) not W1 (W one)).
We understand that --enable-R-shlib does not work under AIX.
Ei-ji Nakama has reported that src/main/regex.c in R 2.2.0 has
to be compiled with -D_LINUX_SOURCE_COMPAT in CFLAGS in
AIX 5.x (and does not work correctly with AIX 4.x). We believe that the
patch applied since obviates the need for this. He tested R 2.2.1
beta on AIX 5.2.
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 IEC60559, 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. Althugh 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 (and will most likely never support f2c: 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. If configure detects GNU FORTRAN or the use of f2c it adds flag -ffloat-store which suffices, but it is possible that src/modules/lapack/Makefile will need to be edited to remove optimization on other platforms. (This is true 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 ....
This interface is experimental and incomplete. The console offers a basic command line editing and history mechanism, along with tool and button bars that give a point-and-click console to some R commands. Many of the features of the console are currently stubs, and the console is no longer under development: it has been kept available as an example of adding a front-end to R.
A gtk() graphics device (a port of the x11() device to
GDK (the GIMP Drawing Kit)) is available from CRAN
as package gtkDevice: this cooperates rather better with the
console than the x11() device.
The sources for the GNOME console for R are now available as package gnomeGUI on CRAN and via Subversion by
svn co https://svn.r-project.org/R-packages/trunk/gnomeGUI
You need to have built R first with the --enable-R-shlib option, and installed R to where you are going to use it from.
Please check you have all the requirements. You need at least the following packages or later installed:
audiofile-0.2.1
esound-0.2.23
glib-1.2.10
gtk+-1.2.10
imlib-1.9.10
ORBit-0.5.12
gnome-libs-1.4.1.2
libxml-1.8.16
libglade-0.17
It is preferable to have a complete installation of the GNOME desktop environment. If you use Linux, then this should be provided with your distribution. (Note: `libglade2' is not a suitable version of `libglade'.)
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'. If you use a pre-packaged version of GNOME then you must have the developer versions of the above packages in order to compile the R-GNOME console.
It is possible to install the front-end in the same way as an R
package, via R CMD INSTALL or install.packages.
For greater control, it can be configured and built independently of R. Create a build directory, and from there run
/path/to/gnomeGUI/configure R_HOME=/path/to/R/installation
make
make install
This installs the two files bin/exec/Rgnome and share/glade/gnome-interface.glade in R_HOME.
The full list of options to this configure is
How to invoke the GNOME console is described under Invoking R: in brief, use command-line option --gui=gnome.
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 http://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 http://java.sun.com/products/archive/.
Other Java installations, for example those from Blackdown and IBM, have been used.
Other useful links are for Mozilla, http://plugindoc.mozdev.org/faqs/java.html and http://www.mozilla.org/releases/mozilla1.6/installation-extras.html, for Konqueror http://www.konqueror.org/javahowto/, for Opera http://www.opera.com/support/search/supsearch.dml?index=459 and for Debian GNU/Linux http://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: http://forum.java.sun.com/thread.jspa?threadID=568127&tstart=75, but 32-bit browsers have been used on that platform.
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
http://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
http://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 http://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 from the sources in Windows, you will need to collect, install and test an extensive set of tools. See http://www.murdoch-sutherland.com/Rtools/ for the current locations and other updates to these instructions.
Some of these tools are also necessary for building add-on packages from source. (Most Windows users will not need to do that; see Add-on packages for details.) 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. 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.
You will certainly need the following items to produce a working copy of R. 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-2.2.1.exe will also need the following:
Your path should 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).
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.
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 is safest not to have any other version of the Cygwin dlls in your path.
You will need suitable versions of at least basename, cat,
comm, cp, cut, diff, echo,
egrep, expr, find, gawk, grep,
gzip, head, ls, make, makeinfo, mkdir,
mv, rm, sed, sh, sort,
texindex and touch; we use those from the Cygwin
distribution (http://www.cygwin.com) or compiled from the sources.
You will also need zip and unzip from the Info-ZIP project
(http://www.info-zip.org). We have packaged a set of all of these
tools at http://www.murdoch-sutherland.com/Rtools/tools.zip.
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 dll. 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.
You will need the Windows port of perl5. A package containing
this is available from
http://www.activestate.com/Products/ActivePerl/.
Beware: you do need the Windows port and not the Cygwin one.
You need a recent version of the MinGW port of gcc from
http://sourceforge.net/projects/mingw/. See the notes on
http://www.murdoch-sutherland.com/Rtools for updates.
In late 2005 there was an installer MinGW-5.0.0.exe in the
`Proposed' section. Using this, select the `Candidate' package and
add the `g++' and `g77' compilers to the `MinGW base
tools': components will be downloaded from Sourceforge and unpacked.
Note that you do need the `Candidate' compilers (gcc-3.4.4)
to compile some contributed packages correctly, although
gcc-3.4.2 suffices to build R itself.
An alternative is to download the components individually, currently
gcc-core-3.4.4-20050522-1.tar.gz
gcc-g++-3.4.4-20050522-1.tar.gz
gcc-g77-3.4.4-20050522-1.tar.gz
binutils-2.16.91-20050827-1.tar.gz
mingw-runtime-3.9.tar.gz
w32api-3.5.tar.gz
and unpack these into the same directory (using tar zxf
tarball_name). Note that mingw-runtime-3.8.tar.gz or later is
required to build R.
To make compiled html (.chm) files you will need the Microsoft HTML Help Workshop, currently available for download at http://msdn.microsoft.com/library/en-us/htmlhelp/html/hwmicrosofthtmlhelpdownloads.asp and http://www.microsoft.com/office/ork/xp/appndx/appa06.htm.
You may need this on the same drive as the other tools. (Although we regularly use it on a different, problems have been reported in the past.)
To skip building compiled html help, set WINHELP=NO in MkRules.
In this case the Help Workshop will not be needed.
The `MiKTeX' (http://www.miktex.org) distribution of LaTeX
includes a suitable port of pdftex, as does the `ProText'
(http://www.tug.org/protext/) enhanced version. We have also
used the `fptex' distribution (available from any CTAN node such as
http://www.ctan.org/tex-archive/systems/windows/fptex/ and as part
of TexLive 2005 (http://www.tug.org/texlive/)). Another
actively-maintained version is available from
http://www.fsci.fuk.kindai.ac.jp/kakuto/win32-ptex/.
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-2.2.1.exe) we require Inno Setup 5.1.5 or later from http://jrsoftware.org.
Edit file src/gnuwin32/MkRules and change ISDIR to the
location where Inno Setup was installed.
configure: Using makeconfigure: Configuration variablesconfigure: Installationconfigure: Simple compilationHELP: Customizing compilation in Windowsinstall.packages: Installing packagesmake: Using makeMakeDll: Customizing compilation in WindowsMakevars.win: Customizing compilation in WindowsR_HOME: Simple compilationremove.packages: Removing packagesupdate.packages: Updating packagesWINHELP: Customizing compilation in Windows[1] also known as IEC 559 and IEEE 754
[2] until recently this limit applied to all processes, not just to one process
[3] also known as IEEE 754
[4] Using the SunPro aka Forte aka Sun ONE cc and f95 compilers
[5] At the time of writing version 2.7.0 was for gcc3/g77 and version 3.0.0 for gcc4/gfortran.
[6] We have measured 15–20% on i686 Linux and around 10% on x86_64 Linux.
[7] AIX has to be different: it
has EN_US.UTF-8!
[8] You may have to set this with luit, but it
should be the default in a window manager session started in UTF-8.
[9] On HP-UX fort77 is the POSIX compliant FORTRAN compiler, and comes after g77.
[10] as well as its equivalence to the Rcomplex
structure defined in R_ext/Complex.h.
[11] In particular, avoid g77's -pedantic, which gives confusing error messages.
[12] e.g., to use an optimized BLAS on Sun/Sparc
[13] recent versions have f77 as a wrapper for f95, and these do work.