# R Installation and Administration

This is a guide to installation and administration for R.

The current version of this document is 1.3.1 (2001-08-31).

# 1 Obtaining R

Sources, binaries and documentation for R can be obtained via CRAN, the "Comprehensive R Archive Network". See the file `RESOURCES` for information on CRAN.

## 1.1 Getting and unpacking the sources

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 -

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).

Finally, for minor-minor releases (`x.y.z` with z != 0), a patch against the preceding release is made available in `R-x.y.{z-1}-x.y.z.diff.gz` (e.g., `R-1.2.2-1.2.3.diff.gz`), which is generally a much smaller file that the `.tgz` files. Such a file can be applied to the sources of the previous version by changing to the top directory of it and

    gzip -dc /path/to/it/R-x.y.{z-1}-x.y.z.diff.gz | patch -E -p1

Beware that this does not necessarily work if the older sources have been modified (e.g., by building in their directories).

## 1.2 Using rsync

Sources are also available via anonymous rsync. Use

    rsync -rC rsync.r-project.org::module R

to create a copy of the source tree specified by module in the subdirectory `R` of the current directory, where module specifies one of the four existing flavors of the R sources, and can be one of `r-release` (current released version), `r-patched` (patched released version), and `r-devel` (development version, less stable), and `r-ng` (next generation, unstable). The rsync trees are created directly from the master CVS archive and are updated hourly. The `-C` option in the `rsync` command is to cause it to skip the CVS directories. Further information on `rsync` is available at http://rsync.samba.org/rsync/.

# 2 Installing R under Unix

R will configure and build from source under a number of common Unix-like platforms, including `i386-freebsd`, `i386-linux`, `i386-sun-solaris`, `ppc-linux`, `mips-sgi-irix`, `alpha-linux`, `alpha-dec-osf4`, `rs6000-ibm-aix`, `hppa-hp-hpux`, `sparc-linux` and `sparc-sun-solaris`.

In addition, binary distributions are available for most common Linux distributions, Compaq Alpha systems running OSF/Tru64, and for MacOS X (Darwin) with X11. 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.

## 2.1 Simple compilation

First review the essential and useful tools and libraries in Essential and useful other programs, and install those you want or need.

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. 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. To re-run the tests you would need

    make check FORCE=FORCE

If these commands 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.)

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.

Now `rehash` if necessary, type `R`, and read the R manuals and the R FAQ (files `FAQ` or `doc/html/faq.html`, or http://www.ci.tuwien.ac.at/~hornik/R/R-FAQ.html which always has the latest version).

## 2.2 Making the manuals

There is a set of manuals that can be built from the sources,

`refman`
  Printed versions of all the help pages.
`R-FAQ`
  R FAQ (which is already built for you).
`R-intro`
  "An Introduction to R".
`R-data`
  "R Data Import/Export".
`R-admin`
  "R Installation and Administration", this manual.
`R-exts`
  "Writing R Extensions".
`R-lang`
  "The R Language Definition".

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 or later installed (and some Linux distributions have 3.12).

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 (recent versions of) ghostscript: they have hyperlinks that can be followed in Acrobat Reader. The info files are suitable for reading online with Emacs or the standalone GNU Info.

## 2.3 Installation

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:

`${prefix}/bin`
  the front-end shell script
`${prefix}/man/man1`
  the man page
`${prefix}/lib/R`
  all the rest (libraries, on-line help system, ...)

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 by using

    make prefix=/path/to/here install

To install DVI, info and PDF versions of the manuals, use one or more of

    make install-dvi
    make install-info
    make install-pdf

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.

# 3 Installing R under Windows

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 and ME (at least) on Intel 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).

The simplest way is to use `SetupR.exe` or `miniR.exe`. Just double-click on the icon and follow the instructions. If you installed R this way you can uninstall it from the Control Panel or Start Menu (unless you suppressed making a group for R).

See the R Windows FAQ for more details.

## 3.1 Building from source

If you want to build this port from the sources, see the file `src/gnuwin32/INSTALL` in the source distribution. You will need to collect, install and test an extensive set of tools: see http://www.stats.ox.ac.uk/pub/Rtools/ for the current locations.

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 commands window at a directory whose path does not contain spaces, and run something like

    tar zxvf R-1.3.0.tgz
    cd R-1.3.0\src\gnuwin32
    make

sit back and wait (for about 5 minutes on 1GHz PIII with a fast local disc).

For further details, including how to make the documentation and how to cross-compile, see `src/gnuwin32/INSTALL`.

# 4 Installing R on Classic MacOS

The `bin/macos` directory of a CRAN site contains `bin-hex`ed (`hqx`) and `stuffit` (`sit`) archives for a base distribution and a large number of add-on packages to run under MacOS 8.6 to MacOS 9.1 or MacOS X natively. Just extract one of these archives in a suitable folder using standard utilities like Aladdin Stuffit Expander (tm).

There is also a port to MacOS X which is considered to be a Unix variant in this document. You can find it in the `bin/macosx` directory at of a CRAN site.

# 5 Add-on packages

This chapter applies to Unix-like and Windows versions of R, but not to the Classic MacOS port.

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 the R object `.lib.loc`.

## 5.1 Installing packages

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 on Unix use

    R CMD INSTALL -l /path/to/library pkg1 pkg2 ...

The part `-l /path/to/library` can be omitted, when the first library in `R_LIBS` is used if set, otherwise the main library `R_HOME/library`.

The Windows equivalent is1

    Rcmd INSTALL -l /path/to/library pkg1 pkg2 ...

Alternatively, packages can be downloaded and installed from within R. First set the option `CRAN` to your nearest CRAN mirror, for example

    > options(CRAN = "http://cran.us.r-project.org/")

Then download and install package foo by

    > install.packages("foo")

Unless the library is specified (argument `lib`) the first library in `.lib.loc` is used.

What this does is different on Unix and Windows. On Unix it consults the list of available source packages on CRAN, downloads the latest version of the foo sources, and installs it (via `R CMD INSTALL`). On Windows it looks at the list of binary versions of packages and downloads the latest version (if any).

On Windows `install.packages` can also install a binary package from a local `zip` file by setting argument `CRAN` to `NULL`. `RGui.exe` has a menu `Packages` with a GUI interface to `install.packages`, `update.packages` and `library`.

## 5.2 Updating packages

The command `update.packages()` is the simplest way to ensure that all the packages on your system are up to date. Set the `CRAN` option 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 CRAN.

## 5.3 Removing 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 ...

(Unix) or

    Rcmd REMOVE -l /path/to/library pkg1 pkg2 ...

(Windows).

From a running R process they can be removed by

    > remove.packages(c("pkg1", "pkg2"), lib="/path/to/library")

Finally, in most installations one can just remove the package directory from the library.

# Appendix A Essential and useful other programs

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`.

## A.1 Essential programs

You need a means of compiling C and FORTRAN (see Using FORTRAN). Some add-on packages also need a C++ compiler.

You will need Perl version 5, 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 or later installed (and some Linux distributions have 3.12).

The typeset documentation needs `tex` and `latex`, or `pdftex` and `pdflatex`.

### A.1.1 Building on MacOS X

You can build R as a Unix application on MacOS X. You will need the DevTools, `f2c` (ftp://netlib.bell-labs.com/netlib/f2c.tar 2) and the `dlcompat` libraries3.

You will also need to install a X sub-system or configure with `--without-x`.

## A.2 Useful libraries and programs

The command-line editing depends on the `readline` library available from any GNU mirror: you will need a fairly recent version.

Use of `gzfile` connections needs `zlib` (version 1.1.3 or later).

The bitmapped graphics devices `jpeg()` and `png()` need the appropriate libraries installed: `jpeg` (version 6b or later) or `libpng` (version 1.0.5 or later) and `zlib` (version 1.1.3 or later) respectively.

The `bitmap` and `dev2bitmap` devices make use of ghostscript (http://www.cs.wisc.edu/~ghost).

### A.2.1 Tcl/Tk

The tcltk package needs Tcl/Tk installed: the sources are available at http://dev.scriptics.com/. To specify the locations of the Tcl/Tk files you may need the configuration options

`--with-tcltk`
  use Tcl/Tk, or specify its library directory
`--with-tcl-config=TCL_CONFIG`
  specify location of `tclConfig.sh`
`--with-tk-config=TK_CONFIG`
  specify location of `tkConfig.sh`

### A.2.2 Linear algebra

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) but ATLAS (http://www.netlib.org/atlas/) 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 specific BLAS library by the configuration option `--with-blas` and not to use an external BLAS library by `--without-blas`.

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.

You will need double-precision and double-complex versions of the BLAS, but not single-precision nor complex routines.

Optimized versions of LAPACK are available, but no provision is made for using them with R as the likely performance gains are thought to be small.

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 `src/gnuwin32/INSTALL` for how to enable this.

# Appendix B Configuration on Unix

## B.1 Configuration options

`configure` has many options: running

    ./configure --help

will give a list. Probably the most important ones not covered elsewhere are (defaults in brackets)

`--with-x`
  use the X Window System
`--x-includes=DIR`
  X include files are in DIR
`--x-libraries=DIR`
  X library files are in DIR
`--with-readline`
  use readline library (if available) [yes]
`--enable-R-profiling`
  attempt to compile support for `Rprof()` [yes]
`--enable-R-shlib`
  build R as a shared library [no]

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 shared library, typically called `libR.so`, and to take considerably longer, so you probably only want this if you will be using an application which embeds R.

## B.2 Configuration variables

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

    VAR="..." ./configure              # Bourne shell compatibles
    (setenv VAR "..."; ./configure)	   # C shell

One common variable to change is `R_PAPERSIZE`, which defaults to `a4`, not `letter`.

If you have libraries and header files, e.g., for GNU readline, in non-system directories, use the variables `LIBS` (for libraries) and `CPPFLAGS` (for header files), respectively, to specify these locations. These default to `/usr/local/lib` and `/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).

If you find you need to alter configure variables, it is worth noting that some settings are cached in the file `config.cache`, and it is a good idea to remove that file before re-configuring.

## B.3 Using make

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 works fine, as does the Sun `make`.

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 (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 environment variable `MAKE` at configure time, for example

    MAKE=gmake ./configure        (sh, bash)
    env MAKE=gmake ./configure    (csh)

## B.4 Using FORTRAN

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 `g77`, `f77`, `xlf`, `cf77`, `cft77`, `pgf77`, `fl32`, `af77`, `fort77`, `f90`, `xlf90`, `pgf90`, `epcf90`, `f95`, `xlf95`, `lf9`5, `g95`, and `fc` (in that order), and then for `f2c`, and use whichever is found first; if none is found, R cannot be compiled. The search mechanism can be changed using the `--with-g77`, `--with-f77`, and `--with-f2c` command line options to `configure`. If your FORTRAN compiler is in a non-standard location, you should set the environment variable `PATH` accordingly before running `configure`.

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.

You must set whatever compilation flags (if any) are needed to ensure that FORTRAN `integer` is equivalent to a C `int` pointer and FORTRAN `double precision` is equivalent to a C `double` pointer. This is checked during the configuration process.

Some of the FORTRAN code makes use of `COMPLEX*16` variables, which is a FORTRAN 90 extension. This is checked for at configure time5, but you may need to avoid compiler flags6 asserting FORTRAN 77 compliance.

For performance reasons7 you may want to choose a FORTRAN 90/95 compiler.

## B.5 Compile and load flags

A wide range of flags can be set in the file `config.site` or via environment variables. We have already mentioned

`CPPFLAGS`
  extra include flags
`LIBS`
  libraries and `-L/lib/path` flags

and others include

`CFLAGS`
  debugging and optimization flags, C
`MAIN_CFLAGS`
  ditto, for compiling the main program
`SHLIB_CFLAGS`
  for shared libraries
`FFLAGS`
  debugging and optimization flags, FORTRAN
`MAIN_FFLAGS`
  ditto, for compiling the main program
`SHLIB_FFLAGS`
  for shared libraries
`MAIN_LDFLAGS`
  additional flags for the main link
`SHLIB_LDFLAGS`
  additional flags for linking the shared libraries

Library paths specified as `-L/lib/path` in `LIBS` 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.

## B.6 Building the GNOME interface

This interface is experimental, incomplete and not currently being developed. It provides a console and a graphics device `(gtk()`; the `x11()` device can also be used). Many of the `features' of the console are currently stubs.

The GNOME interface for R will only be built if you specify it by running configure with the `--with-gnome` option. For example, you might run

    ./configure --with-gnome

but please check you have all the requirements first. It is advisable to have reasonably-up-to-date versions of the `gnome` and `gtk+` libraries. You can find the versions you have by

    gnome-config --version
    gtk-config --version

We know 1.0.10 and 1.2.3 suffice. On Red Hat systems, you need the following RPMs and their dependencies installed:

    gnome-libs
    gnome-libs-devel
    gtk+
    gtk+-devel
    glib
    glib-devel

You will need also `libglade` 0.5 or later for correct behaviour. For more information on `libglade` and to download the source, see http://www.daa.com.au/~james/gnome/. The sources are also available from the GNOME ftp site (ftp://ftp.gnome.org/ and mirrors). RPMs are in RedHat 6.1 and later.

Library `libglade` needs `libxml` 1.4 or later, the source for which is available from the GNOME ftp site (ftp://ftp.gnome.org/ and mirrors).

The locations of some of these libraries can be set as configuration options, by (defaults in brackets)

`--with-gnome`
  use GNOME, or specify its prefix [no]
`--with-gnome-includes=DIR`
  specify location of GNOME headers
`--with-gnome-libs=DIR`
  specify location of GNOME libs
`--with-libglade-config=LIBGLADE_CONFIG`
  specify location of `libglade-config`

# Appendix C New platforms

There are a number of sources of problems when installing R on a new hardware/OS platform. These include

Floating Point Arithmetic: R supports the POSIX, SVID and IEEE models for floating point arithmetic. The POSIX and SVID models provide no problems. The IEEE model however 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. The technique we use is to first interrogate the X window system about what it does (using `xmkmf`), and maybe override this in situations where we know better. This often works, but you may have to manually override the results. Scanning the `cc(1)` and `ld(1)` manual entries 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.

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 get in touch to ask questions. We've had a fair amount of practice at porting R to new platforms ....

# Function and variable index

- `configure`: Using make, Configuration variables, Installation, Simple compilation
- `install.packages`: Installing packages
- `make`: Using make
- `R_HOME`: Simple compilation
- `remove.packages`: Removing packages
- `rsync`: Using rsync
- `update.packages`: Updating packages

# Concept index

- FORTRAN: Using FORTRAN
- Help pages: Simple compilation
- Installation: Installation
- Installing under MacOS: Installing R on Classic MacOS
- Installing under Unix: Installing R under Unix
- Installing under Windows: Installing R under Windows
- Linux: Installing R under Unix
- MacOS X: Installing R on Classic MacOS, Installing R under Unix
- Manuals: Making the manuals
- Manuals, installing: Installation
- Obtaining R: Obtaining R
- Packages: Add-on packages
- Packages, installing: Installing packages
- Packages, removing: Removing packages
- Packages, updating: Updating packages
- Patch files: Getting and unpacking the sources
- Sources for R: Getting and unpacking the sources

#### Footnotes

1. if you have Perl and the source-code package files installed

2. compile with `c++` or comment out `sigcatch(0)` in line 520 of `main.c`

3. e.g. http://fink.sourceforge.net/files/dlcompat-20010123.tar.gz

4. Using the SunPro `cc` and `f95` compilers

5. as well as its equivalence to the `Rcomplex` structure defined in `R_ext/Complex.h`.

6. In particular, avoid `g77`'s `-pedantic`, which gives confusing error messages.

7. e.g., to use an optimized BLAS on Sun/Sparc