R-admin.texi

\input texinfo
@c %**start of header
@setfilename R-admin.info
@settitle R Installation and Administration
@defcodeindex en
@c %**end of header

@syncodeindex fn vr

@dircategory Programming
@direntry
* R Administration: (R-admin).      R Installation and Administration.
@end direntry

@finalout

@include R-defs.texi
@include version.texi

@copying
This manual is for R, version @value{VERSION}.

@Rcopyright{2001}

@quotation
@permission{}
@end quotation
@end copying

@titlepage
@title R Installation and Administration
@subtitle Version @value{VERSION}
@author R Core Team
@page
@vskip 0pt plus 1filll
@insertcopying
@end titlepage

@ifplaintext
@insertcopying
@end ifplaintext

@c @ifnothtml
@contents
@c @end ifnothtml

@ifnottex
@node Top
@top R Installation and Administration

This is a guide to installation and administration for R.

@insertcopying

@end ifnottex



@node Obtaining R
@chapter Obtaining R
@cindex Obtaining R

Sources, binaries and documentation for @R{} can be obtained via
@acronym{CRAN}, the ``Comprehensive R Archive Network'' whose current
members are listed at @uref{https://CRAN.R-project.org/mirrors.html}.


@node Getting and unpacking the sources
@section Getting and unpacking the sources
@cindex Sources for R

The simplest way is to download the most recent
@file{R-@var{x}.@var{y}.@var{z}.tar.gz} file, and unpack it with

@example
tar -xf R-@var{x}.@var{y}.@var{z}.tar.gz
@end example

@noindent
on systems that have a suitable@footnote{e.g.@: @acronym{GNU}
@command{tar} version 1.15 or later, or that from the @samp{libarchive}
(as used on macOS) or `@I{Heirloom Toolchest}' distributions.}
@command{tar} installed.  On other systems you need to have the
@command{gzip} program installed, when you can use

@example
gzip -dc R-@var{x}.@var{y}.@var{z}.tar.gz | tar -xf -
@end example

The pathname of the directory into which the sources are unpacked should
not contain spaces, as most @command{make} programs (and specifically
@acronym{GNU} @command{make}) do not expect spaces.

If you want the build to be usable by a group of users, set @code{umask}
before unpacking so that the files will be readable by the target group
(e.g.,@: @code{umask 022} to be usable by all users).  Keep this
setting of @code{umask} whilst building and installing.

If you use a fairly recent @acronym{GNU} version of @command{tar} and do
this as a root account (which on Windows includes accounts with
administrator privileges) you may see many warnings about changing
ownership.  In which case you can use

@example
tar --no-same-owner -xf R-@var{x}.@var{y}.@var{z}.tar.gz
@end example

@noindent
and perhaps also include the option @option{--no-same-permissions}.
@enindex TAR_OPTIONS
(These options can also be set in the @env{TAR_OPTIONS} environment
variable: if more than one option is included they should be separated
by spaces.)


@node Getting patched and development versions
@section Getting patched and development versions

A patched version of the current release, @samp{r-patched}, and the
current development version, @samp{r-devel}, are available as daily
tarballs and via access to the @R{} Subversion repository.  (For the two
weeks prior to the release of a minor (4.x.0) version, @samp{r-patched}
tarballs may refer to beta/release candidates of the upcoming release,
the patched version of the current release being available via
Subversion.)

The tarballs are available from
@uref{https://cran.r-project.org/src/base-prerelease/}.  Download
@file{R-patched.tar.gz} or @file{R-devel.tar.gz} (or the @file{.tar.bz2}
versions) and unpack as described in the previous section.  They are
built in exactly the same way and on the same platform as distributions
of @R{} releases. Notice, that you probably want to use the CRAN master
site for this, due to propagation delays. An
alternative source of daily snapshots is maintained at @uref{https://stat.ethz.ch/R/daily/}.


@c Keep this single-item menu to avoid a spurious warning about
@c an unreferenced node when making info with Texinfo 6.8 and 7.0.
@menu
* Using Subversion and rsync::
@end menu

@node Using Subversion and rsync
@subsection Using Subversion and @I{rsync}
@cindex Subversion

Sources are also available via @uref{https://svn.R-project.org/R/}, the
R Subversion repository.  If you have a Subversion client (see
@uref{https://subversion.apache.org/}), you can check out and update the
current @samp{r-devel} from
@uref{https://svn.r-project.org/R/trunk/} and the current
@samp{r-patched} from
@samp{https://svn.r-project.org/@/R/@/branches/@/R-@var{x}-@var{y}-branch/}
(where @var{x} and @var{y} are the major and minor number of the current
released version of R).  E.g., use

@example
svn checkout https://svn.r-project.org/R/trunk/ @var{path}
@end example

@noindent
to check out @samp{r-devel} into directory @var{path} (which will be
created if necessary).  The alpha, beta and RC versions of an upcoming
@var{x.y.0} release are available from
@samp{https://svn.r-project.org/R/branches/R-@var{x}-@var{y}-branch/} in
the four-week period prior to the release.

Note that @samp{https:} is required@footnote{for some Subversion clients
@samp{http:} may appear to work, but requires continual redirection.},
and that the @abbr{SSL} certificate for the Subversion server of the @R{}
project should be recognized as from a trusted source.

Note that retrieving the sources by e.g.@: @command{wget -r} or
@command{svn export} from that URL will not work (and will give a error
early in the @command{make} process): the Subversion information is
needed to build @R{}.

The Subversion repository does not contain the current sources for the
recommended packages, which can be obtained by @command{rsync} or
downloaded from @acronym{CRAN}.  To use @code{rsync} to install the
appropriate sources for the recommended packages, run
@code{./tools/rsync-recommended} from the top-level directory of the
@R{} sources.

If downloading manually from @acronym{CRAN}, do ensure that you have the
correct versions of the recommended packages: if the number in the file
@file{VERSION} is @samp{@var{x}.@var{y}.@var{z}} you need to download
the contents of @samp{https://CRAN.R-project.org/src/contrib/@var{dir}},
where @var{dir} is @samp{@var{x}.@var{y}.@var{z}/Recommended} for
r-devel or @file{@var{x}.@var{y}-patched/Recommended} for r-patched,
respectively, to directory @file{src/library/Recommended} in the sources
you have unpacked.  After downloading manually you need to execute
@command{tools/link-recommended} from the top level of the sources to
make the requisite links in @file{src/library/Recommended}.  A suitable
incantation from the top level of the @R{} sources using @command{wget}
might be (for the correct value of @file{@var{dir}})

@example
wget -r -l1 --no-parent -A\*.gz -nd -P src/library/Recommended \
  https://CRAN.R-project.org/src/contrib/@var{dir}
./tools/link-recommended
@end example



@node Installing R under Unix-alikes
@chapter Installing R under Unix-alikes
@cindex Installing under Unix-alikes

@R{} will configure and build under most common Unix and Unix-alike
platforms including @samp{@var{cpu}-*-linux-gnu} for the
@cputype{alpha}, @cputype{arm64} (also known as @cputype{aarch64},
@cputype{ix86}, @cputype{mips}, @cputype{mipsel}#, @cputype{ppc64},
@cputype{riscv64}, @cputype{s390x}, @cputype{sparc64}, and
@cputype{x86_64} @acronym{CPU}s,
@c (see e.g.@:  @uref{https://buildd.debian.org/build.php?&pkg=r-base}),
@c Actually, see https://packages.debian.org/unstable/math/r-base-core as
@c the build daemon is not used for all platforms; note also that Debian
@c has x86_64 <=> amd64, ix86 <=> i386.
@samp{aarch64-@/apple-@/darwin}@footnote{aka `Apple Silicon', known to
some as @samp{arm64-@/apple-@/darwin}.} and
@samp{x86_64-@/apple-@/darwin}  as well as perhaps (it is
tested less frequently on these platforms) @samp{x86_64-@/*-@/freebsd},
@samp{x86_64-@/*-@/openbsd} and @samp{powerpc-@/ibm-@/aix6*}

Only 64-bit platforms are tested regularly, and @command{configure}
will warn if it encounters a 32-bit one.

@cindex Linux
@cindex macOS
In addition, binary distributions are available for some common Linux
distributions (see the @acronym{FAQ} for current details) and for
macOS.  These are installed in platform-specific ways, so for the rest
of this chapter we consider only building from the sources.

Cross-building is not possible: installing @R{} builds a minimal version
of @R{} and then runs many @R{} scripts to complete the build.


@node Simple compilation
@section Simple compilation

First review the essential and useful tools and libraries in
@ref{Essential and useful other programs under a Unix-alike}, and install
those you
@enindex TMPDIR
want or need.  Ensure that either the environment variable @env{TMPDIR}
is either unset (and @file{/tmp} exists and can be written in and
scripts can be executed from) or points to the absolute path to a valid
temporary directory (one from which execution of scripts is allowed)
which does not contain spaces.

@findex R_HOME
Choose a directory to install the @R{} tree (@R{} is not just a binary,
but has additional data sets, help files, font metrics etc).  Let us
call this place @var{R_HOME}.  Untar the source code.  This should
create directories @file{src}, @file{doc}, and several more under a
top-level directory: change to that top-level directory (At this point
readers in North American should consult @ref{Setting paper size}.)
Issue the following commands:

@findex configure

@example
./configure
make
@end example

@noindent
(See @ref{Using make} if your make is not called @samp{make}.)  Users of
Debian-based 64-bit systems@footnote{such as Ubuntu. These use
@file{lib} rather than @file{lib64} for their primary 64-bit library
directories: attempts are made to detect such systems.} may need

@example
./configure LIBnn=lib
make
@end example


Then check the built system works correctly by

@example
make check
@end example

@noindent
Failures are not necessarily problems as they might be caused by missing
functionality, but you should look carefully at any reported
discrepancies.  (Some non-fatal errors are expected in locales that do
not support Latin-1, in particular in true @code{C} locales and
non-UTF-8 non-Western-European locales.)  A failure in
@file{tests/ok-errors.R} may indicate inadequate resource limits
(@pxref{Running R}).

More comprehensive testing can be done by

@example
make check-devel
@end example

@noindent
or

@example
make check-all
@end example

@noindent
see @ref{Testing a Unix-alike Installation} for the possibilities of
doing this in parallel.  Note that these checks are only run completely
if the recommended packages are installed (the default) .  If you have a
local CRAN mirror, these checks can be speeded up by either setting
environment variable @env{R_CRAN_WEB} to its URL, or having a file
@file{.R/repositories} specifying it (see @code{?setRepositories}).

@command{make check-devel} checks the included packages' @file{tests}
directories. For @pkg{grDevices} more complete checks will be run if
the environment variable @env{R_GRDEVICES_COMPARE_PS_PDF} is set: those
checks are skipped on platforms using @code{musl} such as Alpine Linux, and
it knows about differences from transliterations in macOS 14 and later.

Parallel make is supported for building @R{} but not for the
@samp{check} targets (as the output is likely to be unreadably
interleaved, although where supported@footnote{not by the version
supplied by macOS.} GNU make's @option{-O} may help).

If the @command{configure} and @command{make} commands execute
successfully, a shell-script front-end called @file{R} will be created
and copied to @file{@var{R_HOME}/bin}.  You can link or copy this script
to a place where users can invoke it, for example to
@file{/usr/local/bin/R}.  You could also copy the man page @file{R.1} to
a place where your @command{man} reader finds it, such as
@file{/usr/local/man/man1}.  If you want to install the complete @R{}
tree to, e.g., @file{/usr/local/lib/R}, see @ref{Installation}.  Note:
you do not @emph{need} to install @R{}: you can run it from where it was
built.

You do not have to build @R{} in the top-level source directory (say,
@file{@var{TOP_SRCDIR}}).  To build in @file{@var{BUILDDIR}}, run

@findex configure

@example
cd @var{BUILDDIR}
@var{TOP_SRCDIR}/configure
make
@end example

@noindent
and so on, as described further below.  This has the advantage of always
keeping your source tree clean and is particularly recommended when you
work with a version of @R{} from Subversion.  (You may need
@acronym{GNU} @command{make} to allow this, and you will need no spaces
in the path to the build directory.  It is unlikely to work if the
source directory has previously been used for a build.)

There are many settings which can be customized when building @R{} and
most are described in the file @file{config.site} in the top-level
source directory.  This can be edited, but for an installation using
@file{@var{BUILDDIR}} it is better to put the changed settings in a
newly-created file @file{config.site} in the build directory.

@c For those obtaining @R{} @emph{via} Subversion, one additional step is
@c necessary:
@c @cindex Vignettes
@c @cindex Subversion

@c @example
@c make vignettes
@c @end example

@c @noindent
@c which makes the @pkg{grid} vignettes (which are contained in the
@c tarballs): it make take several minutes.

Now @code{rehash} if necessary, type @kbd{R}, and read the @R{} manuals
and the @R{} @acronym{FAQ} (files @file{FAQ} or
@file{doc/manual/R-FAQ.html}, or
@uref{https://CRAN.R-project.org/doc/FAQ/R-FAQ.html} which always
has the version for the latest release of @R{}).

Note: if you already have @R{} installed, check that where you installed
@R{} replaces or comes earlier in your path than the previous
installation.  Some systems are set up to have @file{/usr/bin} (the
standard place for a system installation) ahead of @file{/usr/local/bin}
(the default place for a source installation of @R{}) in their default
path, and some do not have @file{/usr/local/bin} on the default path.


@node Help options
@section Help options

@R{} by default provides help pages as plain text displayed in a pager,
with the options (see the help for @code{help}) of displaying help as
HTML or PDF.

By default @HTML{} help pages are created when needed rather than being
built at install time.

If you need to disable its server and want @HTML{} help, there is the
option to build @HTML{} pages when packages are installed
(including those installed with @R{}).  This is enabled by the
@command{configure} option @option{--enable-prebuilt-html}.  Whether
@command{R CMD INSTALL} (and hence @code{install.packages}) pre-builds
@HTML{} pages is determined by looking at the @R{} installation and is
reported by @command{R CMD INSTALL --help}: it can be overridden by
specifying one of the @command{INSTALL} options @option{--html} or
@option{--no-html}.

The server is disabled by setting the environment variable
@enindex R_DISABLE_HTTPD
@env{R_DISABLE_HTTPD} to a non-empty value, either before @R{} is
started or within the @R{} session before @HTML{} help (including
@code{help.start}) is used.  It is also possible that system security
measures will prevent the server from being started, for example if the
loopback interface has been disabled.  See
@code{?tools::startDynamicHelp} for more details.


@node Making the manuals
@section Making the manuals
@cindex Manuals

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

@table @samp
@item fullrefman
Printed versions of all the help pages for base and recommended packages
(around 3900 pages).
@item refman
Printed versions of the help pages for selected base packages (around
2300 pages)
@item R-FAQ
R @acronym{FAQ}
@item R-intro
``An Introduction to R''.
@item R-data
``R Data Import/Export''.
@item R-admin
``R Installation and Administration'', this manual.
@item R-exts
``Writing R Extensions''.
@item R-ints
``R Internals''.
@item R-lang
``The R Language Definition''.
@end table

@noindent
To make these (with @samp{fullrefman} rather than @samp{refman}), use

@c FIXME: mention HTML versions built by default from make docs
@example
make pdf      @r{to create PDF versions}
make info     @r{to create info files (not @samp{refman} nor @samp{fullrefman}).}
@end example

@c texi2any from Feb 2016.
You will not be able to build any of these unless you have
@command{texi2any} version 6.1 or later installed, and for PDF you must
have @command{texi2dvi} and @file{texinfo.tex} installed (which are part
of the @acronym{GNU} @I{Texinfo} distribution but are, especially
@file{texinfo.tex}, often made part of the @TeX{} package @pkg{texinfo} in
re-distributions).  The path to @command{texi2any} can be set by macro
@samp{TEXI2ANY} in @file{config.site}.  NB: @command{texi2any} requires
@command{perl}.

The PDF versions can be viewed using any recent PDF viewer: they have
hyperlinks that can be followed.  The info files are suitable for
reading online with Emacs or the standalone @acronym{GNU} @command{info}
program.  The PDF versions will be created using the paper size selected
at configuration (default ISO a4): this can be overridden by setting
@env{R_PAPERSIZE}
@enindex R_PAPERSIZE
on the @command{make} command line, or setting @env{R_PAPERSIZE} in the
environment and using @command{make -e}.  (If re-making the manuals for
a different paper size, you should first delete the file
@file{doc/manual/version.texi}.  The usual value for North America would
be @samp{letter}.)

There are some issues with making the PDF reference manual,
@file{fullrefman.pdf} or @file{refman.pdf}.  The help files contain both
non-ASCII characters (e.g.@: in @file{text.Rd}) and upright quotes,
neither of which are contained in the standard @LaTeX{} Computer Modern
fonts.  We have provided the following alternatives:

@table @code
@item times
(The default.) Using standard PostScript fonts, Times Roman, Helvetica
and Courier.  This works well both for on-screen viewing and for
printing.  One disadvantage is that the Usage and Examples sections may
come out rather wide: this can be overcome by using @emph{in addition}
either of the options @code{inconsolata} (on a Unix-alike only if found
by @command{configure}) or @code{beramono}, which replace the Courier
monospaced font by @I{Inconsolata} or @I{Bera Sans Mono} respectively.  (You
will need the @LaTeX{} package @pkg{inconsolata}@footnote{Instructions
on how to install the latest version are at
@uref{https://www.ctan.org/tex-archive/fonts/inconsolata/}.
TeX Live bundles @pkg{inconsolata} in @pkg{collection-fontsextra}.} or
@pkg{bera} installed.)

Note that in most @LaTeX{} installations this will not actually use the
standard fonts for PDF, but rather embed the URW clones @I{NimbusRom},
@I{NimbusSans} and (for Courier, if used) @I{NimbusMon}.

This needs @LaTeX{} packages @pkg{times}, @pkg{helvetic} and (if used)
@pkg{courier} installed.

@item lm
Using the @emph{Latin Modern} (@emph{aka} @pkg{lmodern}) fonts,
usually installed even in basic @TeX{} distributions.
@c E.g.: scheme-basic / collection-latex will have it installed.
This uses fonts rather similar to Computer Modern, but is not
so good on-screen as @code{times} and produces larger PDF files.

@c @item cm-super
@c Using type-1 versions of the Computer Modern fonts by Vladimir Volovich.
@c This is a large installation, obtainable from
@c @uref{https://www.ctan.org/tex-archive/fonts/ps-type1/cm-super/}
@c and its mirrors.  These type-1 fonts have poor hinting and so are
@c nowhere near as readable on-screen as the other three options.
@end table

The default can be overridden by setting the environment variable
@enindex R_RD4PDF
@env{R_RD4PDF}.  (On Unix-alikes, this will be picked up at install time
and stored in @file{etc/Renviron}, but can still be overridden when the
manuals are built, using @command{make -e}.)  The usual@footnote{on a
Unix-alike, @samp{inconsolata} is omitted if not found by
@command{configure}.}  default value for @env{R_RD4PDF} is
@samp{times,inconsolata,hyper}: omit @samp{inconsolata} if you do not have
@LaTeX{} package @pkg{inconsolata} installed.
@samp{hyper} is always enabled (with a fallback if @LaTeX{} package
@pkg{hyperref} is not installed).

Further options, e.g@: for @pkg{hyperref}, can be included in a file
@file{Rd.cfg} somewhere on your @LaTeX{} search path.  For example, if
you prefer to hyperlink the text and not the page number in the table of
contents use
@example
\ifthenelse@{\boolean@{Rd@@use@@hyper@}@}@{\hypersetup@{linktoc=section@}@}@{@}
@end example

@noindent
or 
@example
\ifthenelse@{\boolean@{Rd@@use@@hyper@}@}@{\hypersetup@{linktoc=all@}@}@{@}
@end example

@noindent
to hyperlink both text and page number.

Any generated PDF manuals can be compacted by

@example
make compact-pdf
@end example

@noindent
provided @command{qpdf} and @command{gs} are available (see
@code{?tools::compactPDF} for how to specify them if not on the path).

E-book versions of most of the manuals in one or both of @file{.epub} and
@file{.mobi} formats can be made by running in @file{doc/manual} one of
@example
make ebooks
make epub
make mobi
@end example

@noindent
This requires @command{ebook-convert} from
@uref{https://calibre-ebook.com/download, @command{Calibre}}, or from
most Linux distributions.  If necessary the path to
@command{ebook-convert} can be set as make macro @env{EBOOK} by editing
@file{doc/manual/Makefile} (which contains a commented value suitable
for macOS) or using @command{make -e}.


@node Installation
@section Installation
@cindex Installation

To ensure that the installed tree is usable by the right group of users,
set @code{umask} appropriately (perhaps to @samp{022}) before unpacking
the sources and throughout the build process.

After

@findex configure
@example
./configure
make
make check
@end example

@noindent
(or, when building outside the source,
@code{@var{TOP_SRCDIR}/configure}, etc) have been completed
successfully, you can install the complete @R{} tree to your system by
typing

@example
make install
@end example

@noindent
A parallel make can be used (but run @command{make} before @command{make
install}).  Those using GNU @command{make} 4.0 or later may want to use
@command{make -j @var{n} -O} to avoid interleaving of output.

This will install to the following directories:

@table @asis
@item @file{@var{prefix}/bin} or @file{@var{bindir}}
the front-end shell script and other scripts and executables
@item @file{@var{prefix}/man/man1} or @file{@var{mandir}/man1}
the man page
@item @file{@var{prefix}/@var{LIBnn}/R} or @file{@var{libdir}/R}
all the rest (libraries, on-line help system, @dots{}).  Here
@var{LIBnn} is usually @samp{lib}, but may be @samp{lib64} on some
64-bit Linux systems.  This is known as the @R{} home directory.
@end table

@noindent
where @var{prefix} is determined during configuration (typically
@file{/usr/local}) and can be set by running @command{configure} with
the option @option{--prefix}, as in

@findex configure
@example
./configure --prefix=/where/you/want/R/to/go
@end example

@noindent
where the value should be an absolute path.  This causes @command{make
install} to install the @R{} script to
@file{/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 @command{configure}.  The installation may need
to be done by the owner of @file{@var{prefix}}, often a root account.

There is the option of using @command{make install-strip} (@pxref{Debugging
Symbols}).


You can install into another directory tree by using

@example
make prefix=/path/to/here install
@end example

@noindent
at least with @acronym{GNU} @command{make} (but not some other Unix
makes).

More precise control is available at configure time via options: see
@command{configure --help} for details.  (However, most of the `Fine
tuning of the installation directories' options are not used by @R{}.)

Configure options @option{--bindir} and @option{--mandir} are supported
and govern where a copy of the @command{R} script and the @command{man}
page are installed.

The configure option @option{--libdir} controls where the main @R{}
files are installed: the default is @samp{@var{eprefix}/@var{LIBnn}},
where @var{eprefix} is the prefix used for installing
architecture-dependent files, defaults to @var{prefix}, and can be set
via the configure option @option{--exec-prefix}.

Each of @code{bindir}, @code{mandir} and @code{libdir} can also be
specified on the @command{make install} command line (at least for
@acronym{GNU} @command{make}).

The @command{configure} or @command{make} variables @code{rdocdir} and
@code{rsharedir} can be used to install the system-independent
@file{doc} and @file{share} directories to somewhere other than
@code{libdir}.  The C header files can be installed to the value of
@code{rincludedir}: note that as the headers are not installed into a
subdirectory you probably want something like
@code{rincludedir=/usr/local/include/R-@value{VERSIONno}}.

If you want the @R{} home to be something other than
@file{@var{libdir}/R}, use @option{rhome}: for example

@example
make install rhome=/usr/local/lib64/R-@value{VERSIONno}
@end example

@noindent
will use a version-specific @R{} home on a non-Debian Linux 64-bit
system.

If you have made @R{} as a shared/static library you can install it in
your system's library directory by

@example
make prefix=/path/to/here install-libR
@end example

@noindent
where @code{prefix} is optional, and @code{libdir} will give more
precise control.@footnote{This will be needed if more than one
sub-architecture is to be installed.}  However, you should not install
to a directory mentioned in @env{LDPATHS} (e.g.@:
@file{/usr/local/lib64}) if you intend to work with multiple versions of
@R{}, since that directory may be given precedence over the @file{lib}
directory of other @R{} installations.

@example
make install-strip
@end example

@noindent
will install stripped executables, and on platforms where this is
supported, stripped libraries in directories @file{lib} and
@file{modules} and in the standard packages.

Note that installing @R{} into a directory whose path contains spaces is
not supported, and some aspects (such as installing source packages)
will not work.
@c The main problem is the Makefile include in etc/Makeconf

@cindex Manuals, installing

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

@example
make install-info
make install-pdf
@end example

@noindent
Once again, it is optional to specify @code{prefix}, @code{libdir} or
@code{rhome} (the PDF manuals are installed under the @R{} home
directory).  

More precise control is possible.  For info, the setting used is that of
@code{infodir} (default @file{@var{prefix}/info}, set by configure
option @option{--infodir}).  The PDF files are installed into the @R{}
@file{doc} tree, set by the @command{make} variable @code{rdocdir}.

A staged installation is possible, that it is installing @R{} into a
temporary directory in order to move the installed tree to its final
destination.  In this case @code{prefix} (and so on) should reflect the
@enindex DESTDIR
final destination, and @env{DESTDIR} should be used: see
@uref{https://www.gnu.org/prep/standards/html_node/DESTDIR.html}.

You can optionally install the run-time tests that are part of
@command{make check-all} by

@example
make install-tests
@end example

@noindent
which populates a @file{tests} directory in the installation.


@node Uninstallation
@section @I{Uninstallation}

You can uninstall @R{} by

@example
make uninstall
@end example

@noindent
optionally specifying @code{prefix} etc in the same way as specified for
installation.

This will also uninstall any installed manuals.  There are specific
targets to uninstall info and PDF manuals in file
@file{doc/manual/Makefile}.

Target @code{uninstall-tests} will uninstall any installed tests, as
well as removing the directory @file{tests} containing the test results.

An installed shared/static @code{libR} can be uninstalled by

@example
make prefix=/path/to/here uninstall-libR
@end example


@node Sub-architectures
@section Sub-architectures

Now 32-bit builds are unsupported, this section is only of historical
interest, although in future the mechanisms could be used for different
CPU types on the same OS (e.g. @cputype{x86_64} and @cputype{aarch64}).

Some platforms can support closely related builds of @R{} which can
share all but the executables and dynamic objects.  Examples include
builds under Linux for different @acronym{CPU}s or 32- and 64-bit
builds.

@R{} supports the idea of architecture-specific builds, specified by
adding @samp{r_arch=@var{name}} to the @command{configure} line.  Here
@var{name} can be anything non-empty, and is used to name subdirectories
of @file{lib}, @file{etc}, @file{include} and the package @file{libs}
subdirectories.  Example names from other software are the use of
@file{sparcv9} on @I{Sparc} Solaris and @file{32} by @command{gcc} on
@cputype{x86_64} Linux.

If you have two or more such builds you can install them over each other
(and for 32/64-bit builds on one architecture, one build can be done
without @samp{r_arch}).  The space savings can be considerable: on
@cputype{x86_64} Linux a basic install (without debugging symbols) took
74Mb, and adding a 32-bit build added 6Mb.  If you have installed
multiple builds you can select which build to run by

@example
R --arch=@var{name}
@end example

@noindent
and just running @samp{R} will run the last build that was installed.

@code{R CMD INSTALL} will detect if more than one build is installed and
try to install packages with the appropriate library objects for each.
This will not be done if the package has an executable @code{configure}
script or a @file{src/Makefile} file.  In such cases you can install for
extra builds by

@example
R --arch=@var{name} CMD INSTALL --libs-only @var{pkg1} @var{pkg2} @dots{}
@end example

If you want to mix sub-architectures compiled on different platforms
(for example @cputype{x86_64} Linux and @cputype{i686} Linux), it is
wise to use explicit names for each, and you may also need to set
@option{libdir} to ensure that they install into the same place.

When sub-architectures are used the version of @command{Rscript} in
e.g.@: @file{/usr/bin} will be the last installed, but
architecture-specific versions will be available in e.g.@:
@file{/usr/lib64/R/bin/exec$@{@var{R_ARCH}@}}.  Normally all installed
architectures will run on the platform so the architecture of
@command{Rscript} itself does not matter.  The executable
@command{Rscript} will run the @command{R} script, and at that time the
@enindex R_ARCH
setting of the @env{R_ARCH} environment variable determines the
architecture which is run.

When running post-install tests with sub-architectures, use

@example
R --arch=@var{name} CMD make check[-devel|all]
@end example

@noindent
to select a sub-architecture to check.

Sub-architectures were also used on Windows, but by selecting executables
within the appropriate @file{bin} directory such as
@file{@var{R_HOME}/bin/x64}. As from @R{} 4.2.0 only the @samp{x64}
subdirectory is used.


@node Other Options
@section Other Options

There are many other installation options, most of which are listed by
@command{configure --help}.  Almost all of those not listed elsewhere in
this manual are either standard @command{autoconf} options not relevant
to @R{} or intended for specialist uses by the @R{} developers.

@command{configure} will select a C23 compiler if it finds one: to
circumvent this use option @option{--without-C23}.  This will only have
an effect if the compiler in use does not default to C23: GCC 15 does
and might be selected as @command{gcc} if macro @code{CC} is not
specified in @file{config.site}.  (A compiler is considered to be a `C23
compiler' if it supports C23 by default or if such support can be
selected by a flag such as @option{-std=gnu23} or @option{-std=gnu2x}
and it supports the new C23 keywords such as @code{bool}, @code{false}
and @code{true}.)

One that may be useful when working on @R{} itself is the option
@option{--disable-byte-compiled-packages}, which ensures that the base
and recommended packages are not byte-compiled.  (Alternatively the
(make or environment) variable @env{R_NO_BASE_COMPILE} can be set to a
non-empty value for the duration of the build.)

Option @option{--with-internal-tzcode} makes use of @R{}'s own code and
copy of the @abbr{IANA} database for managing timezones.  This will be
preferred where there are issues with the system implementation, usually
involving times after 2037 or before 1916.  An alternative time-zone
directory@footnote{How to prepare such a directory is described in file
@file{src/extra/tzone/Notes} in the @R{} sources.} can be used, pointed
to by environment variable @env{TZDIR}: this should contain files such
as @file{Europe/London}.  On all recently tested OSes the system
timezone was deduced correctly, but if necessary it can be set as the
value of environment variable @env{TZ}.

Options @option{--with-internal-iswxxxxx},
@option{--with-internal-towlower} and @option{--with-internal-wcwidth}
control the replacement of the system wide-character classification
(such as @code{iswprint}), case-changing (@code{wctrans}) and width
(@code{wcwidth} and @code{wcswidth}) functions by ones contained in the
@R{} sources.  Replacement of the classification functions has been done
for many years on macOS and @abbr{AIX} (and Windows): option
@option{--with-internal-iswxxxxx} allows this to be suppressed on those
platforms or used on others.  Replacing the case-changing functions is
the default on macOS and Windows.  Replacement of the width functions
has also been done for many years and remains the default.  These
options will only matter to those working with non-ASCII character data,
especially in languages written in a non-Western script@footnote{But on
Windows problems have been seen with case-changing functions on accented
Latin-1 characters.} (which includes `symbols' such as emoji).  Note
that one of those @code{iswxxxxx} is @code{iswprint} which is used to
decide whether to output a character as a glyph or as a
@samp{\U@{xxxxxx@}} escape---for example, try @samp{"\U1f600"}, an
emoji.  The width functions are of most importance in East Asian locale:
their values differ between such locales.  (Replacing the system
functions provides a degree of platform-independence (including to OS
updates) but replaces it with a dependence on the @R{} version.)


@node Debugging Symbols
@subsection Debugging Symbols

By default, @command{configure} adds a flag (usually @option{-g}) to the
compilation flags for C, Fortran and C++ sources.  This will slow down
compilation and increase object sizes of both @R{} and packages, so it
may be a good idea to change those flags (set @samp{CFLAGS} etc in
@file{config.site} before configuring, or edit files @file{Makeconf}
and @file{etc/Makeconf} between running @command{configure} and
@command{make}).

Having debugging symbols available is useful both when running @R{} under a
debugger (e.g., @command{R -d gdb}) and when using sanitizers and
@command{valgrind}, all things intended for experts.

Debugging symbols (and some others) can be `stripped' on installation by
using
@example
make install-strip
@end example
@noindent
How well this is supported depends on the platform: it works best on
those using GNU @code{binutils}.  On @cputype{x86_64} Linux a typical
reduction in overall size was from 92MB to 66MB.   On macOS debugging
symbols are not by default included in @file{.dylib} and @file{.so}
files, so there is negligible difference.

@node OpenMP Support
@subsection @abbr{OpenMP} Support

By default @command{configure} searches for suitable flags@footnote{for
example, @option{-fopenmp}, @option{-fiopenmp}, @option{-xopenmp} or
@option{-qopenmp}.  This includes for @command{clang} and the Intel and
Oracle compilers.}  for @abbr{OpenMP} support for the C, C++ (default standard)
and Fortran compilers.

Only the C result is currently used for @R{} itself, and only if
@code{MAIN_LD}/@code{DYLIB_LD} were not specified.  This can be
overridden by specifying
@example
R_OPENMP_CFLAGS
@end example

Use for packages has similar restrictions (involving @code{SHLIB_LD} and
similar: note that as Fortran code is by default linked by the C (or
C++) compiler, both need to support @abbr{OpenMP}) and can be overridden by
specifying some of
@example
SHLIB_OPENMP_CFLAGS
SHLIB_OPENMP_CXXFLAGS
SHLIB_OPENMP_FFLAGS
@end example

@noindent
Setting these to an empty value will disable @abbr{OpenMP} for that compiler
(and configuring with @option{--disable-openmp} will disable all
detection@footnote{This does not necessarily disable @emph{use} of
@abbr{OpenMP} -- the @command{configure} code allows for platforms where @abbr{OpenMP}
is used without a flag. For the @command{flang} compiler in late 2017,
the Fortran runtime always used @abbr{OpenMP}.} of @abbr{OpenMP}).  The
@command{configure} detection test is to compile and link a standalone
@abbr{OpenMP} program, which is not the same as compiling a shared object and
loading it into the C program of @R{}'s executable.  Note that
overridden values are not tested.

@node C++ Support
@subsection C++ Support

C++ is not used by @R{} itself, but support is provided for installing
packages with C++ code via @command{make} macros defined in file
@file{etc/Makeconf} (and with explanations in file @file{config.site}):
@example
CXX
CXXFLAGS
CXXPICFLAGS
CXXSTD

CXX11
CXX11STD
CXX11FLAGS
CXX11PICFLAGS

CXX14
CXX14STD
CXX14FLAGS
CXX14PICFLAGS

CXX17
CXX17STD
CXX17FLAGS
CXX17PICFLAGS

CXX20
CXX20STD
CXX20FLAGS
CXX20PICFLAGS

CXX23
CXX23STD
CXX23FLAGS
CXX23PICFLAGS

CXX26
CXX26STD
CXX26FLAGS
CXX26PICFLAGS
@end example
@noindent
The macros @code{CXX} etc are those used by default for C++ code.
@command{configure} will attempt to set the rest suitably, choosing for
@code{CXXSTD} and @code{CXX11STD} a suitable flag such as
@option{-std=gnu++17} for C++17 support (which is required if C++ is to
be supported by default).  Inferred values can be overridden in file
@file{config.site} or on the @command{configure} command line:
user-supplied values will be tested by compiling some
C++11/14/17/20/23/26 code.

It may be that there is no suitable flag for C++14/17/20/23/26 support
with the default compiler, in which case a different compiler could be
selected for
@code{CXX14}/@code{CXX17}/@code{CXX20}/@code{CXX23}/@code{CXX236} with
its corresponding flags.

If no suitable compiler/flag is found for the default C++ compiler, one
can be set in file @file{config.site} @emph{via} macros @code{CXX}
and @code{CXXSTD}.  A user-specified compiler does not need to pass the
C++17 tests, so do this at your own risk as some packages may not compile.

The @option{-std} flag is supported by the GCC, @command{clang++} and
Intel compilers.  Currently accepted values are (plus some synonyms)
@example
g++:     c++11 gnu+11 c++14 gnu++14 c++17 gnu++17 c++2a gnu++2a (from 8)
         c++20 gnu++20 (from 10) c++23 gnu++23 c++2b gnu++2b (from 11)
         c++2c gnu++2c
Intel:   c++11  gnu+11 c++14 gnu++14 c++17 gnu++17
         c++20 gnu++20 (from 2021.1) c++2b gnu++2b (from 2022.2)
         c++23 gnu++23 (at least from 2024.0)
@end example
@noindent
(Those for @I{LLVM} @command{clang++} are documented at
@uref{https://clang.llvm.org/cxx_status.html}, and follow @code{g++}:
@code{-std=c++20} is supported from Clang 10, @code{-std=c++2b} from
Clang 13 and @code{-std=c++23} and @code{-std=c++2c} from Clang 17.
Apple Clang supports @code{-std=c++2b} from 13.1.6 and @code{-std=c++23}
and @code{-std=c++2c} from 16.0.0.)

@c c++1y does not pass the configure test in gcc 4.9.3
@c , with @option{-std=c++1y} (introduced@footnote{See
@c @uref{https://gcc.gnu.org/projects/cxx-status.html#cxx14} for which
@c C++14 features it supported.} in version 4.9.x) remaining as a deprecated
@c synonym.

`Standards' for @command{g++} starting with @samp{gnu} enable `GNU
extensions': what those are is hard to track down.

For the use of C++ in @R{} packages,
@pxref{, , , R-exts, Writing R Extensions}.
@c Prior to @R{} 3.6.0 the default C++ standard was
@c that of the compiler used: currently it is C++17.

@uref{https://en.cppreference.com/w/cpp/compiler_support} indicates
which versions of common compilers support (parts of) which C++
standards.

@node C standards
@subsection C standards

Compiling @R{} requires some POSIX features (such as
@code{strdup}@footnote{this is part of C23, but part of the C library
not the compiler.} and the @code{ssize_t} type) not in the C
standards. Typically compilers make these available, but @strong{not} if
strict C compliance is specified by for example @option{-std=c17}.  So
if you want to specify a non-default standard use something like
@option{-std=gnu17}.

Compiling @R{} requires C99 or later: C11 and C17 are minor updates, but
the substantial update `C23' (finally published in October 2024) is also
supported for recent versions of GCC@footnote{At least 13--15: 15
defaults to C23},  @command{clang}@footnote{including @I{LLVM} clang 18--20
and Apple clang 15/16.} and Intel @command{icx}.  @R{} 4.5.0 defaults
to C23 if supported by the chosen compiler.

As from @R{} 4.3.0 there is support for packages to indicate their
preferred C version.  Macros @code{CC17}, @code{C17FLAGS}, @code{CC23}
and @code{C23FLAGS} can be set in @file{config.site} (there are examples
there).  Those for C17 should support C17 or earlier and not allow C23
additions so for example @code{bool}, @code{true} and @code{false} can
be used as identifiers.  Those for C23 should support the new keywords
such as @code{bool}.

There is also support for requesting earlier standards @emph{via}
@code{CC99} and @code{CC90}: however these are very rarely needed as
compilers accept legacy (even K&R) code in C17 mode (but not C23 mode).

Some compilers warn enthusiastically about prototypes.  For most,
omitting @option{-Wstrict-prototypes} in @code{C17FLAGS} suffices.
However, versions 15 and later of @I{LLVM} @command{clang} and 14.0.3 and
later of Apple clang warn by default in all modes if @option{-Wall} or
@option{-pedantic} is used, and may need
@option{-Wno-strict-prototypes}.

@node Link-Time Optimization
@subsection Link-Time Optimization

There is support for using link-time optimization (@abbr{LTO}) if the
toolchain supports it: configure with flag @option{--enable-lto}.  When
@abbr{LTO} is enabled it is also used for compiled code in add-on
packages unless the flag @option{--enable-lto=R} is used@footnote{Then
all add-on packages, including recommended packages are not installed
with @abbr{LTO}.}.

The main benefit seen to date from @abbr{LTO} has been detecting long-standing
bugs in the ways packages pass arguments to compiled code and between
compilation units.  @I{Benchmarking} in 2020 with
@command{gcc}/@command{gfortran}@tie{}10 showed gains of a few percent
in increased performance and reduction in installed size for builds
without debug symbols, but large size reductions for some
packages@footnote{A complete @acronym{CRAN} installation reduced from 50
to 35GB.} with debug symbols.  (Performance and size gains are said to be
most often seen in complex C++ builds.)

Whether toolchains support @abbr{LTO} is often unclear: all of the C compiler,
the Fortran compiler@footnote{although there is the possibility to
exclude Fortran but that misses some of the benefits.} and linker have
to support it, and support it by the same mechanism (so mixing compiler
families may not work and a non-default linker may be needed).  It has
been supported by the GCC and @I{LLVM} projects for some years with
diverging implementations.

@abbr{LTO} support was added in 2011 for GCC@tie{}4.5 on Linux but was little
used before 2019: compiler support has steadily improved over those
years and @option{--enable-lto=R} is nowadays used for some routine
@acronym{CRAN} checking.

Unfortunately @option{--enable-lto} may be accepted but silently do
nothing useful if some of the toolchain does not support @abbr{LTO}: this is
less common than it once was.

Various macros can be set in file @file{config.site} to customize how
@abbr{LTO} is used.  If the Fortran compiler is not of the same family as the
C/C++ compilers, set macro @samp{LTO_FC} (probably to empty).  Macro
@samp{LTO_LD} can be used to select an alternative linker should that be
needed.


@node LTO with GCC
@subsubsection @abbr{LTO} with GCC

This has been tested on Linux with
@command{gcc}/@command{gfortran}@tie{}8 and later: that needed setting
(e.g.@: in @file{config.site})
@example
AR=gcc-ar
RANLIB=gcc-ranlib
@end example
@noindent
For non-system compilers or if those wrappers have not been installed
one may need something like
@example
AR="ar --plugin=/path/to/liblto_plugin.so"
RANLIB="ranlib --plugin=/path/to/liblto_plugin.so"
@end example
@noindent
and @code{NM} may be needed to be set analogously. (If using an
@abbr{LTO}-enabled build to check packages, set environment variable
@env{UserNM}@footnote{not @env{NM} as we found @command{make}
overriding that.} to @samp{gcc-nm}.)

@c http://hubicka.blogspot.com/2019/05/gcc-9-link-time-and-inter-procedural.html
It is possible to parallelize parts of the @abbr{LTO}
linking process: set the make macro @samp{LTO} to something like
@samp{LTO=-flto=8} (to use 8 threads), for example in file
@file{config.site}.

Under some circumstances and for a few packages, the PIC flags have
needed overriding on Linux with GCC 9: e.g@: use in
@file{config.site}:
@example
CPICFLAGS=-fPIC
CXXPICFLAGS=-fPIC
CXX11PICFLAGS=-fPIC
CXX14PICFLAGS=-fPIC
CXX17PICFLAGS=-fPIC
CXX20PICFLAGS=-fPIC
FPICFLAGS=-fPIC
@end example
@noindent
We suggest only using these if the problem is encountered (it had not
been seen on @acronym{CRAN} with GCC 10--15 at the time of writing).

Note that @R{} will usually need to be re-compiled after even a minor
update to the compiler (e.g.@: from 13.1 to 13.2).

@node LTO with LLVM
@subsubsection @abbr{LTO} with @I{LLVM}

@I{LLVM} supports another type of @abbr{LTO} called `Thin @abbr{LTO}' as well as a similar
implementation to GCC, sometimes called `Full @abbr{LTO}'.  (See
@uref{https://clang.llvm.org/docs/ThinLTO.html}.)  Currently the @I{LLVM}
compilers relevant to @R{} are @command{clang} and @command{flang}
(formerly @command{Flang-new}) for
which this can be selected by setting macro @samp{LTO=-flto=thin}.  @I{LLVM}
has
@example
AR=llvm-ar
RANLIB=llvm-ranlib
@end example
@noindent
(but macOS does not, and these are not needed there).  Where the linker
supports a parallel backend for Thin @abbr{LTO} this can be specified @emph{via}
the macro @samp{LTO_LD}: see the URL above for per-linker settings and
further linking optimizations.)

For example, on macOS one might use
@example
LTO=-flto=thin
LTO_FC=
LTO_LD=-Wl,-mllvm,-threads=4
@end example
to use Thin @abbr{LTO} with 4 threads for C/C++ code, but skip @abbr{LTO} for Fortran
code compiled with @command{gfortran}.

It is said to be particularly beneficial to use @option{-O3} for
@command{clang} in conjunction with @abbr{LTO}.

It seems that @command{flang} may in future support @abbr{LTO}.

The 2020s versions of Intel's C/C++ compilers are based on @I{LLVM} and as
such support @I{LLVM}-style @abbr{LTO}, both `full' and `thin'.  This might use
something like
@example
LTO=-flto=thin -flto-jobs=8
@end example

@node LTO for package checking
@subsubsection @abbr{LTO} for package checking

@abbr{LTO} effectively compiles all the source code in a package as a single
compilation unit and so allows the compiler (with sufficient diagnostic
flags such as @option{-Wall}) to check consistency between what are
normally separate compilation units.

With @command{gcc}/@command{gfortran} 9.x and later@footnote{probably
also 8.4 and later.} @abbr{LTO} will flag inconsistencies in calls to Fortran
subroutines/functions, both between Fortran source files and between
Fortran and C/C++.  @command{gfortran} 8.4, 9.2 and later can help
understanding these by extracting C prototypes from Fortran source files
with option @option{-fc-prototypes-external}, e.g.@: that (at the time
of writing) Fortran @code{LOGICAL} corresponds to @code{int_least32_t *}
in C.

@c This worked in 2019 but with Fedora 32 did not export dpotrf from dlapack.o
@c On some systems it is possible to build the BLAS, LINPACK and LAPACK
@c support as static libraries containing intermediate-level code that @abbr{LTO}
@c will compile for all objects linked against these libraries, by
@c configuring @R{} with @option{--enable-lto=check}.  This checks the
@c consistency of calls to BLAS/LINPACK/LAPACK in any packages installed
@c using the build. @strong{NB:} as its name suggests, this option is
@c intended only for checking installation of @R{} and packages: it
@c includes these library routines (those called directly and all they
@c depend on) in each package.  This is unlikely to work in conjunction
@c with non-default options for BLAS and LAPACK, and `linking' against
@c these libraries may be very slow.


@node Testing a Unix-alike Installation
@section Testing an Installation

Full post-installation testing is possible only if the test files have
been installed with

@example
make install-tests
@end example

@noindent
which populates a @file{tests} directory in the installation.

If this has been done, two testing routes are available.  The first is
to move to the home directory of the @R{} installation (as given by
@command{R RHOME} or from @R{} as @code{R.home()}) and run

@example
cd tests
## followed by one of
../bin/R CMD make check
../bin/R CMD make check-devel
../bin/R CMD make check-all
@end example

@noindent
and other useful targets are @code{test-BasePackages} and
@code{test-Recommended} to run tests of the standard and recommended
packages (if installed) respectively.

This re-runs all the tests relevant to the installed @R{} (including for
example the code in the package vignettes), but not for example the ones
checking the example code in the manuals nor making the standalone @I{Rmath}
library.  This can occasionally be useful when the operating environment
has been changed, for example by OS updates or by substituting the
@acronym{BLAS} (@pxref{Shared BLAS}).

Parallel checking of packages may be possible: set the environment
variable @env{TEST_MC_CORES} to the maximum number of processes to be
run in parallel.  This affects both checking the package examples (part
of @command{make check}) and package sources (part of @command{make
check-devel} and @command{make check-recommended}).  It does require a
@command{make} command which supports the @command{make -j @var{n}}
option: most do.


Alternatively, the installed @R{} can be run, preferably with
@option{--vanilla}.  Then
@enindex LC_COLLATE

@example
pdf("tests.pdf") ## optional, but prevents flashing graphics windows
Sys.setenv(LC_COLLATE = "C", LC_TIME = "C", LANGUAGE = "en")
tools::testInstalledBasic("both")
tools::testInstalledPackages(scope = "base")
tools::testInstalledPackages(scope = "recommended")
@end example

@noindent
runs the basic tests and then all the tests on the standard and
recommended packages.  These tests can be run from anywhere: the basic
tests write their results in the @file{tests} folder of the @R{} home
directory and run fewer tests than the first approach: in particular
they do not test things which need Internet access---that can be tested
by
@example
tools::testInstalledBasic("internet")
@end example

It is possible to test the installed packages (but not their
package-specific tests) by @code{testInstalledPackages} even if
@command{make install-tests} was not run. The outputs are written under the
current directory unless a different one is specified by @code{outDir}.

Note that the results may depend on the language set for times and
messages: for maximal similarity to reference results you may want to
try setting (before starting the @R{} session)

@example
LANGUAGE=en
@end example

@noindent
and use a UTF-8 or Latin-1 locale.



@node Installing R under Windows
@chapter Installing R under Windows
@cindex Installing under Windows

[The rest of this paragraph is only relevant after release.]
The @file{bin/windows} directory of a @acronym{CRAN} site contains
binaries for a base distribution and a large number of add-on packages
from @acronym{CRAN} to run on 64-bit @cputype{x86_64} Windows.

R is most tested on current versions of Windows 10 and Windows Server 2022
with UTF-8 as the charset encoding.  It works also on Windows 11.  It runs
on older versions of Windows, but normally with other charset encoding and
may require manual installation of the Universal C Runtime (@abbr{UCRT}).

Your file system must allow long file names (as is likely except
perhaps for some network-mounted systems).  If it does not also support
conversion to short name equivalents (a.k.a. DOS 8.3 names), then @R{}
@emph{must} be installed in a path that does not contain spaces.

Installation is @emph{via} the installer
@file{@value{RWVERSION}-win.exe}.  Just double-click on the icon and
follow the instructions. You can uninstall @R{} from the Control Panel.

You will be asked to choose a language for installation: that choice
applies to both installation and @I{un-installation} but not to running @R{}
itself.

See the @uref{https://CRAN.R-project.org/bin/windows/base/rw-FAQ.html, R
Windows @acronym{FAQ}} for more details on the binary installer and for
information on use on older Windows systems.


@node Building from source
@section Building from source

It is possible to use other 64-bit toolchains (including `MSYS2') with
@abbr{UCRT} support to build @R{}, but this manual only documents that
used for recent binary distributions of @R{}.  When using other
toolchains, makefiles of @R{} and packages may need to be adapted.


@node The Windows toolset
@subsection The Windows toolset

The binary distribution of @R{} is currently built with tools
from
@uref{https://CRAN.R-project.org/bin/windows/Rtools/rtools44/rtools.html,Rtools44
for Windows}. See 
@uref{https://CRAN.R-project.org/bin/windows/base/howto-@value{RWTVERSION}.html,
Building @value{RWTVERSION} and packages on Windows} for more details on how to use it.

The toolset includes compilers (currently GCC version 13.2.0 with
selected additional patches) and runtime libraries from
@uref{http://mingw-w64.org/,the `@I{MinGW-w64}' project} and a number of
pre-compiled static libraries and headers used by @R{} and @R{}
packages, compiled by @uref{https://mxe.cc/,'MXE'} (M cross environment,
with updates maintained by @I{Tomas Kalibera}).  The toolset also
includes build tools from the @uref{https://www.msys2.org/, the 'MSYS2'
project}.  Additional build tools packaged by 'MSYS2' may be installed
via a package manager (@samp{pacman}).

There is also an experimental variant of @I{Rtools44} with support for
64-bit ARM CPUs (@I{aarch64}) via @I{LLVM} 17 toolchain using
@command{clang}/@command{flang} compilers, @command{lld} linker, and
@I{libc++}.

The toolsets used for 64-bit Windows from 2008 to 2022 were based on
@I{MinGW-w64}.  The assistance of @I{Yu Gong} at a crucial step in
porting @R{} to @I{MinGW-w64} is gratefully acknowledged, as well as
help from @I{Kai Tietz}, the lead developer of the @I{MinGW-w64} project
and from @I{Martin Storsjo}.

@node LaTeX on Windows
@subsection @LaTeX{}

Both building @R{} and checking packages need a distribution of @LaTeX{}
installed, with the directory containing @command{pdflatex} on the path.

The @samp{MiKTeX} (@uref{https://miktex.org/}) distribution of
@LaTeX{} is that used on @acronym{CRAN}.  This can be set up to install
extra packages `on the fly' (without asking), which is the simplest way
to use it.  The `basic' version of @samp{MiKTeX} will need to add some
packages.@footnote{There are reports of segfaults when @samp{MiKTeX}
installs additional packages when making @file{NEWS.pdf}: re-running
@command{make} seems to solve this.}  In any case ensure that the
@pkg{inconsolata} package is installed---you can check with the
@samp{MiKTeX} Package Manager.

It is also possible to use the TeX Live distribution from
@uref{https://www.tug.org/texlive/}.  (The @acronym{CRAN} package
@CRANpkg{tinytex} can install and manage a subset of TeX Live.)


@node Checking the build
@section Checking the build

You can test a build by running

@example
make check
@end example

@noindent
The recommended packages can be checked by

@example
make check-recommended
@end example

@noindent
Other levels of checking are

@example
make check-devel
@end example

@noindent
for a more thorough check of the @R{} functionality, and

@example
make check-all
@end example

@noindent
for both @code{check-devel} and @code{check-recommended}.

If a test fails, there will almost always be a @file{.Rout.fail} file in
the directory being checked (often @file{tests/Examples} or
@file{tests}): examine the file to help pinpoint the problem.

Parallel checking of package sources (part of @command{make check-devel}
and @command{make check-recommended}) is possible: see the environment
variable @env{TEST_MC_CORES} to the maximum number of processes to be
run in parallel.


@node Testing a Windows Installation
@section Testing an Installation

The Windows installer contains a set of test files used when building
@R{}.

The toolset is not needed to run these tests, but more comprehensive
analysis of errors will be given if @command{diff} is in the path.

Launch either @code{Rgui} or @code{Rterm} (preferred), preferably with
@option{--vanilla}.  Then run

@example
Sys.setenv(LC_COLLATE = "C", LC_TIME="C", LANGUAGE = "en")
tools::testInstalledBasic("both")
tools::testInstalledPackages(scope = "base")
tools::testInstalledPackages(scope = "recommended")
@end example

@noindent
runs the basic tests and then all the tests on the standard and recommended
packages.  These tests can be run from anywhere: @code{testInstalledBasic}
writes results in the @file{tests} folder of the @R{} home directory (as
given by @code{R.home()}) and @code{testInstalledPackages} under the current
directory unless a different one is specified by @code{outDir}.

For the @file{tests} folder to be writeable, one normally needs to install
@R{} to a directory other than the default @file{C:\Program Files}.  The
installer also allows to install @R{} without Administrator privileges, see
the @uref{https://CRAN.R-project.org/bin/windows/base/rw-FAQ.html, R Windows
@acronym{FAQ}} for more details.

The results of @code{example(md5sums)} when testing @pkg{tools} may
differ from the reference output as some files are installed with
Windows' CRLF line endings. Also, expect differences in
@file{reg-plot-latin1.pdf}.

One can also run tests from the toolset shell (e.g.  @command{bash}) similarly
to a Unix-like installation.  Move to the home directory of the @R{}
installation (as given by @command{R RHOME} or from @R{} as @code{R.home()})
and run

@example
cd tests
## followed by one of
../bin/R CMD make check
../bin/R CMD make check-devel
../bin/R CMD make check-all
@end example

Remember that @LaTeX{} needs to be on the path.



@node Installing R under macOS
@chapter Installing R under macOS
@cindex macOS

@macro Rapp{}
@sc{R.app}
@end macro

[The rest of this paragraph is only relevant after release.]
@c
The front page of a @acronym{CRAN} site has a link `Download R for (Mac)
OS X' which takes you to a new page. Two files are offered for download,
@file{R-@value{VERSIONno}-arm64.pkg} and @file{R-@value{VERSIONno}-x86_64.pkg}.
Both are for macOS 11 or later (@I{Big Sur}, @I{Monterey}, @I{Ventura},
@I{Sonoma}, @dots{}).

The first is for `Apple Silicon' (@emph{aka} `M1', `M2', @dots{}) Macs, the
second for older Macs with an @cputype{x86_64} (Intel) CPU.

@c Package @file{R-@value{VERSIONno}.pkg} also be installed on `Apple
@c Silicon' CPUs using `Rosetta' emulation@footnote{You may be asked to
@c install Rosetta at first use --
@c @url{https://support.apple.com/en-us/102527} -- which may need
@c administrator privileges.}, but the native build is preferred.  It is a
@c little faster (and for some tasks, considerably so) but may give
@c different numerical results from the more common @cputype{x86_64}
@c platforms (on Windows, Linux, @dots{} as well as macOS) as ARM hardware
@c lacks extended-precision floating-point operations.

It is important that if you use a binary installer package that your OS
is fully updated: look at `Software Update' in 'System Preferences'
to be sure.

To install, just double-click on the icon of the file you downloaded.
At the `Installation Type' stage, note the option to `Customize'.  This
currently shows four components: everyone will need the `R Framework'
component: the remaining components are optional. (The `Tcl/Tk'
component is needed to use package @pkg{tcltk}. The `@I{Texinfo}' component
is only needed by those installing source packages or @R{} from its
sources.)

Note for @I{Ventura} users: installation from the @file{Downloads} folder
may not be allowed or may require additional authorization, so we
suggest you download somewhere else such as your desktop or home folder.

These are Apple Installer packages.  If you encounter any problem during
the installation, please check the Installer log by clicking on the
``Window'' menu and item ``Installer Log''. The full output (select
``Show All Log'') is useful for tracking down problems.  Note that the
installer is clever enough to try to upgrade the last-installed version
of the application where you installed it (which may not be where you
want this time @dots{}).

Various parts of the build require @I{XQuartz} to be installed: see
@uref{https://www.xquartz.org/releases/}.@footnote{At the time of
writing, version 2.8.5 or later.}  These include the @pkg{tcltk} package
and the @code{X11} graphics device: attempting to use these without
@I{XQuartz} will remind you.  This is also needed for some
@cindex Cairo
builds of the @I{cairographics}-based devices (which are not often used on
macOS) such as @code{png(type = "cairo")} and @code{svg()} and some
third-party packages (e.g.@: @CRANpkg{rgl}).

If you update your macOS version, you should re-install @R{} (and
perhaps @I{XQuartz}): the installer may tailor the installation to the
current version of the OS.

Installers for R-patched and R-devel are usually available from
@uref{https://mac.R-project.org}.  (Some of these packages may be
unsigned/not notarized: to install those Control/right/two-finger click,
select @samp{Open With} and @samp{Installer}.)

For building @R{} from source, see @ref{macOS}.


@node Running R under macOS
@section Running R under macOS

There are two ways to run @R{} on macOS from a @acronym{CRAN} binary
distribution.

There is a GUI console normally installed with the @R{} icon in
@file{/Applications} which you can run by double-clicking (e.g.@: from
Launchpad or Finder).  (If you cannot find it there it was possibly
installed elsewhere so try searching for it in Spotlight.) This is
usually referred to as @Rapp{} to distinguish it from command-line @R{}:
its user manual is currently part of the macOS FAQ at
@uref{https://cran.r-project.org/bin/macosx/RMacOSX-FAQ.html} and
can be viewed from @Rapp{}'s `Help' menu.


You can run command-line @R{} and @command{Rscript} from a
Terminal@footnote{The installer puts links to @command{R} and
@command{Rscript} in @file{/usr/local/bin}.  If these are missing or
that is not on your path, you can run directly the copies in
@file{/Library/Frameworks/R.framework/Resources/bin} or link those
yourself to somewhere on your path.} so these can be typed as commands
as on any other Unix-alike: see the next chapter of this manual.  There
are some small differences which may surprise users of @R{} on other
platforms, notably the default location of the personal library
directory (under @file{~/Library/R}, e.g.@:
@file{~/Library/R/arm64/4.4/library}), and that warnings, messages and
other output to @file{stderr} are highlighted in bold.

@c https://ryanhomer.github.io/posts/build-openmp-macos-catalina-complete
Those using the @command{zsh} shell (the default for new user accounts)
might find the command @command{R} being masked by the @command{zsh}
builtin @command{r} (which recalls commands).  One can use a full path
to @R{} in an alias, or add @code{disable r} to @file{~/.zshrc}.

@c If you have installed both installer packages on an @code{arm64} Mac,
@c the last installed will be used.

@c https://stat.ethz.ch/pipermail/r-sig-mac/2014-October/011131.html
It has been reported that running @Rapp{} may fail if no preferences are
stored, so if it fails when launched for the very first time, try it
again (the first attempt will store some preferences).

Users of @Rapp{} need to be aware of the `App Nap' feature
(@uref{https://developer.apple.com/library/archive/releasenotes/MacOSX/WhatsNewInOSX/Articles/MacOSX10_9.html})
which can cause @R{} tasks to appear to run very slowly when not
producing output in the console.  Here are ways to avoid it:

@itemize
@item
Ensure that the console is completely visible (or at least the activity
indicator at the top right corner is visible).

@item
In a Terminal, run
@example
defaults write org.R-project.R NSAppSleepDisabled -bool YES
@end example

@noindent
(see @uref{https://developer.apple.com/library/archive/releasenotes/MacOSX/WhatsNewInOSX/Articles/MacOSX10_9.html}).
@end itemize

Using the @code{X11} graphics device or the X11-based versions of @code{View()}
and @code{edit()} for data frames and matrices (the latter are the
default for command-line @R{} but not @Rapp{}) requires
@uref{https://www.xquartz.org/, XQuartz} to be installed.

Under some rather nebulous circumstances messages have been seen from
@code{fontconfig} about missing/unreadable configuration files when
using @I{cairo}-based devices, especially @code{X11(type = "cairo")}.  With
@I{XQuartz} installed there are two @code{fontconfig} areas from different
versions and it can help to set
@example
setenv FONTCONFIG_PATH /opt/X11/lib/X11/fontconfig
@end example
@noindent
Another symptom has been that italic/oblique fonts are replaced by
upright ones.


@node Uninstalling under macOS
@section Uninstalling under macOS

@R{} for macOS consists of two parts: the GUI (@Rapp{}) and the R
framework. @I{Un-installation} is as simple as removing those folders
(e.g.@: by dragging them onto the Bin@footnote{Formerly known as the
Trash.}). The typical installation will install the GUI into the
@file{/Applications/R.app} folder and the R framework into the
@file{/Library/Frameworks/R.framework} folder.  The links to @file{R}
and @file{Rscript} in @file{/usr/local/bin} should also be removed.

If you want to get rid of @R{} more completely using a Terminal, simply
run:

@example
sudo rm -Rf /Library/Frameworks/R.framework /Applications/R.app \
   /usr/local/bin/R /usr/local/bin/Rscript
@end example

The installation consists of up to four Apple packages:@footnote{At the
time of writing: use @command{pkgutil --pkgs | grep -i org.r-project} to
check.} for the `Apple Silicon' build, @code{org.R-project.arm64.R.fw.pkg},
@code{org.R-project.arm64.R.GUI.pkg}, @code{org.r-project.arm64.tcltk}
and @code{org.r-project.arm64.texinfo}. You can use @code{sudo pkgutil
--forget} if you want the Apple Installer to forget about the package
without deleting its files (useful for the @R{} framework when
installing multiple @R{} versions in parallel), or after you have
deleted the files. @strong{NB:} the package names are case-sensitive and
the @R{} domain is named inconsistently.

Uninstalling the Tcl/Tk and @I{Texinfo} components (which are installed under
@file{/opt/R/arm64} on a @cputype{arm64} build and @file{/opt/R/x86_64}
for an @cputype{x86_64} one) is not as simple.  You can list the files
they installed in a Terminal by e.g.@:

@example
pkgutil --files org.r-project.arm64.tcltk
pkgutil --files org.r-project.arm64.texinfo
@end example

@noindent
(For the `Intel build, replace @code{arm64} by @code{x86_64}.)
These are paths relative to @file{/}, the root of the file system.
@c Maybe too dangerous for naive users.
@c file.remove removes empty directories on Unix.
@c The second could be uninstalled by an @R{} script like

@c @example
@c lis <- system2("pkgutil", "--files org.r-project.x86_64.texinfo", stdout = TRUE)
@c setwd("/")
@c file.remove(rev(lis))
@c @end example

@c @noindent
@c run as the owner of @file{/usr/local}.

If you are not compiling @R{} nor installing packages from source you
could remove all of @file{/opt/R/arm64} or @file{/opt/R/x86_64}.


@node Multiple versions
@section Multiple versions

The installer will remove any previous version@footnote{More precisely,
of the Apple package of the same name: this means that ARM and Intel
versions can be installed together.} of the @R{} framework which it
finds installed.  This can be avoided by using @command{pkgutil
--forget} (see the previous section).  However, note that different
versions are installed under
@file{/Library/Frameworks/R.framework/Versions} as @file{4.4-arm64} (or
@file{4.4-x86_64}), @file{4.3} and so on, so it is not possible to have
different @samp{4.x.y} versions installed for the same @samp{x} and CPU
type.

@Rapp{} will always run the `current' version of @R{}, that is the last
installed version.



@node Running R
@chapter Running R

How to start @R{} and what command-line options are available is discussed
in 
@ref{Invoking R, , , R-intro, An Introduction to R}.

You should ensure that the shell has set adequate resource limits: @R{}
expects a stack size of at least 8MB and to be able to open at least 256
file descriptors.  (Any modern OS should have default limits at least as
large as these, but apparently @I{NetBSD} may not.  Use the shell command
@command{ulimit} (@command{sh}/@command{bash}) or @command{limit}
(@command{csh}/@command{tcsh}) to check.)  For some
compilers@footnote{Including GCC 9 on Linux.} and packages a larger
stack size has been needed: 20-25MB has sufficed to date.

@R{} makes use of a number of environment variables, the default values
of many of which are set in file @file{@var{R_HOME}/etc/Renviron} (there
are none set by default on Windows and hence no such file).  These are
set at @command{configure} time, and you would not normally want to
@enindex R_PAPERSIZE
change them -- a possible exception is @env{R_PAPERSIZE} (@pxref{Setting
paper size}).  The paper size will be deduced from the @samp{LC_PAPER}
locale category if it exists and @env{R_PAPERSIZE} is unset, and this
will normally produce the right choice from @samp{a4} and @samp{letter}
on modern Unix-alikes (but can always be overridden by setting
@env{R_PAPERSIZE}).

Various environment variables can be set to determine where @R{} creates
its per-session temporary directory.  The environment variables
@enindex TMPDIR
@enindex TMP
@enindex TEMP
@env{TMPDIR}, @env{TMP} and @env{TEMP} are searched in turn and the
first one which is set and points to a writable area is used.  If none
do, the final default is @file{/tmp} on Unix-alikes and the value of
@enindex R_USER
@env{R_USER} on Windows.  The path should be an absolute path not
containing spaces@footnote{On Windows a path containing spaces will be
replaced by the `short path' version if available and that does not
contain spaces.}  (and it is best to avoid non-alphanumeric characters
such as @code{+} or quotes).

Some Unix-alike systems are set up to remove files and directories
periodically from @file{/tmp}, for example by a @command{cron} job
@enindex TMPDIR
running @command{tmpwatch}.  Set @env{TMPDIR} to another directory
before starting long-running jobs on such a system.

Note that @env{TMPDIR} will be used to execute @command{configure}
scripts when installing packages, so if @file{/tmp} has been mounted as
@samp{noexec}, @env{TMPDIR} needs to be set to a directory from which
execution is allowed.



@node Add-on packages
@chapter Add-on packages
@cindex Packages
@cindex Libraries


It is helpful to use the correct terminology.  A @emph{package} is
loaded from a @emph{library} by the function @code{library()}.  Thus a
library is a directory containing installed packages; the main library
is @file{@var{R_HOME}/library}, but others can be used, for example by
@enindex R_LIBS
setting the environment variable @env{R_LIBS} or using the @R{} function
@code{.libPaths()}.  To avoid any confusion you will often see a library
directory referred to as a `library tree'.


@node Default packages
@section Default packages
@cindex Packages, default

The set of packages loaded on startup is by default

@example
> getOption("defaultPackages")
[1] "datasets"  "utils"     "grDevices" "graphics"  "stats"     "methods"
@end example

@noindent
(plus, of course, @pkg{base}) and this can be changed by setting the
option in startup code (e.g.@: in @file{~/.Rprofile}).  It is initially
@enindex R_DEFAULT_PACKAGES
set to the value of the environment variable @env{R_DEFAULT_PACKAGES} if
set (as a comma-separated list).  Setting @env{R_DEFAULT_PACKAGES=NULL}
ensures that only package @pkg{base} is loaded.

Changing the set of default packages is normally used to reduce the set
for speed when scripting: in particular not using @pkg{methods} will
reduce the start-up time by a factor of up to two.  But it can also be
used to customize @R{}, e.g.@: for class use. @command{Rscript}
also checks the environment variable @env{R_SCRIPT_DEFAULT_PACKAGES};
@enindex R_SCRIPT_DEFAULT_PACKAGES
if set, this takes precedence over @env{R_DEFAULT_PACKAGES}.


@node Managing libraries
@section Managing libraries
@cindex Libraries, managing

@R{} packages are installed into @emph{libraries}, which are
directories in the file system containing a subdirectory for each
package installed there.

@R{} comes with a single library, @file{@var{R_HOME}/library} which is
the value of the @R{} object @samp{.Library} containing the standard and
recommended@footnote{unless they were excluded in the build.}  packages.
Both sites and users can create others and make use of them (or not) in
an @R{} session.  At the lowest level @samp{.libPaths()} can be used to
add paths to the collection of libraries or to report the current
collection.

@cindex Libraries, site
@cindex Site libraries
@R{} will automatically make use of a site-specific library
@file{@var{R_HOME}/site-library} if this exists (it does not in a
vanilla @R{} installation).  This location can be overridden by
setting@footnote{its binding is locked once the startup files have been
read, so users cannot easily change it. See @code{?.libPaths} for how
to make use of the new value.} @samp{.Library.site} in
@file{@var{R_HOME}/etc/Rprofile.site}, or (not recommended) by setting
the
@enindex R_LIBS_SITE
environment variable @env{R_LIBS_SITE}.

@cindex Libraries, user
@cindex User libraries
@enindex R_LIBS_USER
Users can have one or more libraries, normally specified by the
environment variable @env{R_LIBS_USER}.  This has a default value (to
see it, use @samp{Sys.getenv("R_LIBS_USER")} within an @R{} session),
but that is only used if the corresponding directory actually exists
(which by default it will not).

Both @env{R_LIBS_USER} and @env{R_LIBS_SITE} can specify multiple
library paths, separated by colons (semicolons on Windows).


@node Installing packages
@section Installing packages
@cindex Packages, installing


Packages may be distributed in source form or compiled binary form.
Installing source packages which contain C/C++/Fortran code requires
that compilers and related tools be installed.  Binary packages are
platform-specific and generally need no special tools to install, but
see the documentation for your platform for details.

Note that you may need to specify implicitly or explicitly the library to
which the package is to be installed.  This is only an issue if you have
more than one library, of course.

@c If installing packages on a Unix-alike to be used by other users, ensure
@c that the system @code{umask} is set to give sufficient permissions (see
@c also @code{Sys.umask} in @R{}).  (To a large extent this is unnecessary
@c in recent versions of @R{}, which install packages as if @code{umask = 022}.)

@enindex TMPDIR
Ensure that the environment variable @env{TMPDIR} is either unset (and
@file{/tmp} exists and can be written in and executed from) or is the
absolute path to a valid temporary directory, not containing spaces.

For most users it suffices to call
@samp{install.packages(@var{pkgname})} or its GUI equivalent if the
intention is to install a @acronym{CRAN} package and Internet access is
available.@footnote{If a proxy needs to be set, see
@command{?download.file}.}  On most systems @samp{install.packages()}
will allow packages to be selected from a list box (typically with
tens of thousands of items).

To install packages from source on a Unix-alike use in a terminal

@example
R CMD INSTALL -l /path/to/library @var{pkg1} @var{pkg2} @dots{}
@end example

@noindent
The part @samp{-l /path/to/library} can be omitted, in which case the
first library of a normal @R{} session is used (that shown by
@code{.libPaths()[1]}).

There are a number of options available: use @code{R CMD INSTALL --help}
to see the current list.

@findex install.packages
Alternatively, packages can be downloaded and installed from within
@R{}.  First choose your nearest @acronym{CRAN} mirror using
@command{chooseCRANmirror()}.  Then download and install packages
@pkg{pkg1} and @pkg{pkg2} by

@example
> install.packages(c("pkg1", "pkg2"))
@end example

@noindent
The essential dependencies of the specified packages will also be fetched.
Unless the library is specified (argument @code{lib}) the first library
in the library search path is used: if this is not writable, @R{} will
ask the user (in an interactive session) if the default personal library
should be created, and if allowed to will install the packages there.


If you want to fetch a package and all those it depends on (in any way)
that are not already installed, use e.g.

@example
> install.packages("Rcmdr", dependencies = TRUE)
@end example

@code{install.packages} can install a source package from a local
@file{.tar.gz} file (or a URL to such a file) by setting argument
@code{repos} to @code{NULL}: this will be selected automatically if the
name given is a single @file{.tar.gz} file.

@code{install.packages} can look in several repositories, specified as a
character vector by the argument @code{repos}: these can include a
@acronym{CRAN} mirror, Bioconductor, R-forge, @I{rforge.net},
local archives, local files, @dots{}).  Function
@code{setRepositories()} can select amongst those repositories that the
@R{} installation is aware of.

Something which sometimes puzzles users is that @code{install.packages()}
may report that a package which they believe should be available is not
found.  Some possible reasons:
@itemize
@item
The package, such as @pkg{grid} or @pkg{tcltk}, is part of @R{}
itself and not otherwise available.

@item
The package is not in the available repositories, so check which have been
selected by
@example
getOption("repos")
@end example

@item
The package is available, but not for the current version of @R{} or for
the type of OS (Unix/Windows).  To retrieve the information on available
versions of package @code{@var{pkg}}, use

@example
av <- available.packages(filters=list())
av[av[, "Package"] == @var{pkg}, ]
@end example

@noindent
in your @R{} session, and look at the @samp{Depends} and @samp{OS_type}
fields (there may be more than one matching entry).  If the package
depends on a version of @R{} later than the one in use, it is possible
that an earlier version is available which will work with your version
of @R{}: for @acronym{CRAN} look for `Old sources' on the package's
@acronym{CRAN} landing page and manually retrieve an appropriate version (of
comparable age to your version of @R{}).
@end itemize

Naive users sometimes forget that as well as installing a package, they
have to use @code{library} to make its functionality available.


@node Windows packages
@subsection Windows

What @code{install.packages} does by default is different on Unix-alikes
(except macOS) and Windows.  On Unix-alikes it consults the list of
available @emph{source} packages on @acronym{CRAN} (or other
repositories), downloads the latest version of the package sources, and
installs them (via @code{R CMD INSTALL}).  On @cputype{x86_64} Windows
it looks (by default) first at the list of @emph{binary} versions of
packages available for your version of @R{} and downloads the latest
versions (if any).  If no binary version is available or the source
version is newer, it will install the source versions of packages
without compiled C/C++/Fortran code, and offer to do so for those with,
if @command{make} is available (and this can be tuned by option
@code{"install.packages.compile.from.source"}).

[At present binary packages are not distributed for @cputype{aarch64}
Windows, so most of this subsection only applies to @cputype{x86_64}.]

On Windows @code{install.packages} can also install a binary package
from a local @file{zip} file (or the URL of such a file) by setting
argument @code{repos} to @code{NULL}.  @code{Rgui.exe} has a menu
@code{Packages} with a GUI interface to @code{install.packages},
@code{update.packages} and @code{library}.

Windows binary packages for @R{} were distributed as a single binary
containing either or both architectures (32- and 64-bit).  Prior to @R{}
4.2.0, they might contain only the 32-bit architecture.

@c A few of the binary packages need other software to be installed on your
@c system.
@c Packages using Gtk+ (@CRANpkg{Cairo}, @CRANpkg{RGtk2},
@c @CRANpkg{cairoDevice} and those that depend on them) need the @file{bin}
@c directory of a bundled distribution of Gtk2 from
@c @uref{http://ftp.gnome.org/pub/gnome/binaries/win32/gtk+} or
@c @uref{http://ftp.gnome.org/pub/gnome/binaries/win64/gtk+} in
@c the path: it should work to have both 32- and 64-bit Gtk+ @file{bin}
@c directories in the path on a 64-bit version of @R{}.

@command{R CMD INSTALL} works in Windows to install source packages.  No
additional tools are needed if the package does not contain compiled
code, and @code{install.packages(type="source")} will work for such
packages. Those with compiled code need the tools (see @ref{The Windows
toolset}). The tools are found automatically by @R{} when installed by
the toolset installer. See
@uref{https://cran.r-project.org/bin/windows/base/howto-@value{RWTVERSION}.html,
Building @value{RWTVERSION} and packages on Windows} for more details.

Occasional permission problems after unpacking source packages have been
seen on some systems: these have been circumvented by setting the
environment variable @env{R_INSTALL_TAR} to @samp{tar.exe}.
@enindex R_INSTALL_TAR

If you have only a source package that is known to work with current
@R{} and just want a binary Windows build of it, you could make use of
the building service offered at
@uref{https://win-builder.r-project.org/}.

For almost all packages @command{R CMD INSTALL} will attempt to install
both 32- and 64-bit builds of a package if run from a 32/64-bit install
of @R{} (only 64-bit builds and installs are supported since @R{} 4.2.0).
It will report success if the installation of the architecture
of the running @command{R} succeeded, whether or not the other
architecture was successfully installed.  The exceptions are packages
with a non-empty @file{configure.win} script or which make use of
@file{src/Makefile.win}.  If @file{configure.win} does something
appropriate to both architectures use@footnote{for a small number of
@acronym{CRAN} packages where this is known to be safe and is needed by
the @I{autobuilder} this is the default.  Look at the source of
@file{tools:::.install_packages} for the list.  It can also be specified
in the package's @file{DESCRIPTION} file.} option
@option{--force-biarch}: otherwise @command{R CMD INSTALL
--merge-multiarch} can be applied to a source tarball to merge separate
32- and 64-bit installs.  (This can only be applied to a tarball, and
will only succeed if both installs succeed.)

If you have a package without compiled code and no Windows-specific
help, you can zip up an installation on another OS and install from that
zip file on Windows.  However, such a package can be installed from the
sources on Windows without any additional tools.

@node macOS packages
@subsection macOS

On macOS @code{install.packages} works as it does on other Unix-alike
systems, but there is an additional type @code{binary} (available
for the @acronym{CRAN} distribution but not when compiling @R{} from
source) which can be passed to @code{install.packages} in order to
download and install binary packages from a suitable repository.  These
binary package files for macOS have the extension @samp{.tgz}.  The
@Rapp{} GUI provides menus for installation of either binary or source
packages, from @acronym{CRAN}, other repositories or local files.

On @R{} builds using binary packages, the default is type @code{both}:
this looks first at the list of binary packages available for your
version of @R{} and installs the latest versions (if any).  If no binary
version is available or the source version is newer, it will install the
source versions of packages without compiled C/C++/Fortran code and offer
to do so for those with, if @command{make} is available.

Note that most binary packages which include compiled code are tied to a
particular series (e.g.@: @R{} 4.5.x or 4.4.x) of @R{}.

Installing source packages which do not contain compiled code should
work with no additional tools. For others you will need the `Command
Line Tools' for @command{Xcode} and compilers which match those used to
build @R{}, plus a Fortran compiler for packages which contain Fortran
code: see @ref{macOS}.  Packages with C/C++ source code which link to
Fortran libraries (which include the @acronym{BLAS} and @acronym{LAPACK}
libraries) will need either the Fortran compiler or, for @acronym{CRAN}
binary distributions of @R{}, to specify
@example
FLIBS = -L/Library/Frameworks/R.framework/Resources/lib -lgfortran -lquadmath
@end example
@noindent
in a @file{Makevars} file (see the next section) to point to the Fortran
libraries in the binary distribution.

Package @CRANpkg{rJava} and those which depend on it need a Java runtime
installed and several packages need X11 installed, including those using
Tk.  See @ref{macOS} and @ref{Java (macOS)}.  Package @CRANpkg{rjags}
needs a build of JAGS installed under @file{/usr/local}, such as those
at
@uref{https://sourceforge.net/projects/mcmc-jags/files/JAGS/4.x/Mac%20OS%20X/}.

Tcl/Tk extension @code{BWidget} used to be
distributed with @R{} but no longer is; @code{Tktable} has been
distributed with recent versions of @R{}.
@c (but not 4.0.0 and not @cputype{arm64} builds of 4.1.0 or 4.1.1).

@c A few of the binary packages need other software to be installed on your
@c system.  In particular packages using Gtk+ (@CRANpkg{RGtk2},
@c @CRANpkg{cairoDevice} and those that depend on them) need the GTK
@c framework installed from @uref{https://mac.R-project.org/libs/}: the
@c appropriate version at the time of writing was
@c @uref{https://mac.R-project.org/libs/GTK_2.24.17-X11.pkg}.

@c The same instructions apply when installing binary packages into the
@c @acronym{CRAN} distribution of @R{} running on an @cputype{arm64} (aka
@c `Apple Silicon' aka `M1') Mac.

The default compilers specified are shown in file
@file{/Library/Frameworks/@/R.framework/@/Resources/etc/Makeconf}.  At
the time of writing those settings assumed that the C, Fortran and C++
compilers were on the path (see @ref{macOS}).  The settings can be
changed, either by editing that file or in a file such as
@file{~/.R/Makevars} (see the next section).  Entries which may need to
be changed include @samp{CC}, @samp{CXX}, @samp{FC}, @samp{FLIBS} and
the corresponding flags, and perhaps @samp{CXXCPP}, @samp{DYLIB_LD},
@samp{MAIN_LD}, @samp{SHLIB_CXXLD} and @samp{SHLIB_LD}, as well as their
@samp{CXX11}, @samp{CXX14}, @samp{CXX17} and @samp{CXX20} variants.

So for example you could select a specific @I{LLVM}
@command{clang} for both C and C++ with extensive checking by having in
@file{~/.R/Makevars}
@example
SDK=/Library/Developer/CommandLineTools/SDKs/MacOSX.sdk
CC = /usr/local/clang/bin/clang -isysroot $(SDK)
CXX = /usr/local/clang/bin/clang++ -isysroot $(SDK)
CXX11 = $CXX
CXX14 = $CXX
CXX17 = $CXX
CXX20 = $CXX
CXX23 = $CXX
CFLAGS = -g -O2 -Wall -pedantic -Wconversion -Wno-sign-conversion
CXXFLAGS = -g -O2 -Wall -pedantic -Wconversion -Wno-sign-conversion
CXX11FLAGS = $CXXFLAGS
CXX14FLAGS = $CXXFLAGS
CXX17FLAGS = $CXXFLAGS
CXX20FLAGS = $CXXFLAGS
CXX23FLAGS = $CXXFLAGS
@end example
@noindent
(the current @I{SDK} can be found by running @command{xcrun -show-sdk-path})
and for the current macOS distribution of @command{gfortran} at
@uref{https://mac.r-project.org/tools/}
@example
FC = /opt/gfortran/bin/gfortran
(arm64)
FLIBS =  -L/opt/gfortran/lib/gcc/aarch64-apple-darwin20.0/14.2.0
  -L/opt/gfortran/lib -lgfortran -lemutls_w -lheapt_w -lquadmath
(Intel)
FLIBS =  -L/opt/gfortran/lib/gcc/x86_64-apple-darwin20.0/14.2.0
  -L/opt/gfortran/lib -lgfortran -lquadmath
@end example
@noindent
(line broken here for the manual only).

If that @command{clang} build
supports @abbr{OpenMP}, you can add
@example
SHLIB_OPENMP_CFLAGS = -fopenmp
SHLIB_OPENMP_CXXFLAGS = -fopenmp
@end example
@noindent
to compile @abbr{OpenMP}-using packages.  It will also be necessary to arrange
for the @code{libomp.dylib} library to be found at both install time and run
time, for example by copying/linking it somewhere that is searched such
as @file{/usr/local/lib}.

Apple includes many Open Source libraries in macOS but increasingly
without the corresponding headers (not even in @I{Xcode} nor the Command
Line Tools): they are often rather old versions.  If installing packages
from source using them it is usually easiest to install a
statically-linked up-to-date copy of the Open Source package from its
sources or from @uref{https://mac.r-project.org/bin/}.
But sometimes it is desirable/necessary to use Apple's dynamically
linked library, in which case appropriate headers could be extracted
from the sources@footnote{Note that capitalization and versioning may
differ from the Open Source project.} available @emph{via}
@uref{https://opensource.apple.com/releases} -- this has been used for
@code{iodbc}.

Some care may be needed with selecting compilers when installing external
software for use with packages.  The `system' compilers as used when
building @R{} are @command{clang} and @command{clang++}, but the Apple
toolchain also provides compilers called @command{gcc} and @command{g++}
which despite their names are based on @I{LLVM} and @code{libc++} like the
system ones and which behave in almost the same way as the system ones.
Most Open Source software has a @command{configure} script developed
using GNU @command{autoconf} and hence will select @command{gcc} and
@command{g++} as the default compilers: this usually works fine.  For
consistency one can use

@example
./configure CC=clang CFLAGS=-O2 CXX=clang++ CXXFLAGS=-O2
@end example

@noindent
(avoiding @command{autoconf}'s default @option{-g}).
@command{R CMD INSTALL} and @code{install.packages()} try to invoke
@command{configure} with the same compilers and flags used to build
@R{}.

@c For @cputype{arm64}, not all configure scripts have been updated to
@c recognize the platform and so might need the flag
@c @option{--build=aarch64-apple-darwin20.1.0}.
@c Also, be aware that
@c running the compilers from a @cputype{x86_64} application switches them
@c to generating code for that CPU: this applies to a Terminal, a shell,
@c older @command{cmake} or (non-system) @command{make}, and from
@c @command{R CMD INSTALL} or @code{install.packages()}.  One can use

@c @example
@c ./configure CC="clang -arch arm64" CFLAGS=-O2 CXX="clang++ -arch arm64" CXXFLAGS=-O2
@c @end example

@c @noindent
@c to force @cputype{arm64} code.

@node Customizing package compilation
@subsection Customizing package compilation

The @R{} system and package-specific compilation flags can be overridden
or added to by setting the appropriate Make variables in the personal
file @file{@var{HOME}/.R/Makevars-@var{R_PLATFORM}} (but
@file{@var{HOME}/.R/Makevars.win} or @file{@var{HOME}/.R/Makevars.win64}
on Windows), or if that does not exist, @file{@var{HOME}/.R/Makevars},
where @samp{R_PLATFORM} is the platform for which @R{} was built, as
available in the @code{platform} component of the @R{} variable
@code{R.version}.  The full path to an alternative personal
file@footnote{using a path containing spaces is likely to cause
problems} can be specified @emph{via} the environment variable
@env{R_MAKEVARS_USER}.

Package developers are encouraged to use this mechanism to enable a
reasonable amount of diagnostic messaging (``warnings'') when compiling,
such as e.g.@: @option{-Wall -pedantic} for tools from GCC, the GNU
Compiler Collection, and for @I{LLVM} (@command{clang} and @command{flang}).

Note that this mechanism can also be used when it is necessary to change
the optimization level whilst installing a particular package.  For
example

@example
## @r{for C code}
CFLAGS = -g -O -mtune=native
## @r{for C++ code}
CXXFLAGS = -g -O -mtune=native
## @r{for C++11 code}
CXX11FLAGS = -g -O -mtune=native
## @r{for fixed-form Fortran code}
FFLAGS = -g -O -mtune=native
## @r{for C17 code}
C17FLAGS = -g -O -mtune=native -Wno-strict-prototypes
@end example

@noindent
Note that if you have specified a non-default C++ or C standard, you need to
set the flag(s) appropriate to that standard.

Another use is to override the settings in a binary installation of R.
For example, for the current distribution of @command{gfortran} at
@uref{https://mac.r-project.org/tools/}

@example
FC = /opt/gfortran/bin/gfortran
FLIBS =  -L/opt/gfortran/lib/gcc/x86_64-apple-darwin20.0/14.2.0
  -L/opt/gfortran/lib -lgfortran -lquadmath
@end example

@noindent
(line broken here for the manual only).

There is also provision for a site-wide @file{Makevars.site} file under
@file{@var{R_HOME}/etc} (in a sub-architecture-specific directory if
appropriate).  This is read immediately after @file{Makeconf}, and the
path to an alternative file can be specified by environment variable
@env{R_MAKEVARS_SITE}.

Note that these mechanisms do not work with packages which fail to pass
settings down to sub-makes, perhaps reading @file{etc/Makeconf} in
makefiles in subdirectories.  Fortunately such packages are unusual.

@node Multiple sub-architectures
@subsection Multiple sub-architectures

When installing packages from their sources, there are some extra
considerations on installations which use sub-architectures.  These were
commonly used on Windows prior to @R{} 4.2.0 but can in principle be
used on other platforms.

When a source package is installed by a build of @R{} which supports
multiple sub-architectures, the normal installation process installs the
packages for all sub-architectures.  The exceptions are

@table @emph
@item Unix-alikes

where there is an @file{configure} script, or a file @file{src/Makefile}.

@item Windows

where there is a non-empty @file{configure.win} script, or a file
@file{src/Makefile.win} (with some exceptions where the package is known
to have an architecture-independent @file{configure.win}, or if
@option{--force-biarch} or field @samp{Biarch} in the @file{DESCRIPTION}
file is used to assert so).

@end table

@noindent
In those cases only the current architecture is installed.  Further
sub-architectures can be installed by

@example
R CMD INSTALL --libs-only @var{pkg}
@end example

@noindent
using the path to @command{R} or @command{R --arch} to select the
additional sub-architecture.  There is also @command{R CMD INSTALL
--merge-multiarch} to build and merge the two architectures, starting
with a source tarball.

@node Byte-compilation
@subsection Byte-compilation

Packages are by default byte-compiled on installation.
Byte-compilation can be controlled on a per-package basis by the
@samp{ByteCompile} field in the @file{DESCRIPTION} file.

@node External software
@subsection External software

Some @R{} packages contain compiled code which links to external
software libraries.  Unless the external library is statically linked
(which is done as much as possible for binary packages on Windows and
macOS), the libraries have to be found when the package is loaded and
not just when it is installed.  How this should be done depends on the
OS (and in some cases the version).

For Unix-alikes except macOS the primary mechanism is the @code{ld.so}
cache controlled by @command{ldconfig}: external dynamic libraries
recorded in that cache will be found.  Standard library locations will
be covered by the cache, and well-designed software will add its
locations (as for example @pkg{openmpi} does on Fedora).  The secondary
mechanism is to consult the environment variable @env{LD_LIBRARY_PATH}.
The @R{} script controls that variable, and sets it to the concatenation
of @env{R_LD_LIBRARY_PATH}, @env{R_JAVA_LD_LIBRARY_PATH} and the
environment value of @env{LD_LIBRARY_PATH}.  The first two have defaults
which are normally set when @R{} is installed (but can be overridden in
the environment) so @env{LD_LIBRARY_PATH} is the best choice for a user
to set.

On macOS the primary mechanism is to embed the absolute path to
dependent dynamic libraries into an object when it is compiled.  Few
@R{} packages arrange to do so, but it can be edited@footnote{They need
to have been created using @option{-headerpad_max_install_names}, which
is the default for an @R{} package.} @emph{via}
@command{install_name_tool} --- that only deals with direct dependencies
and those would also need to be compiled to include the absolute paths
of their dependencies.  If the choice of absolute path is to be deferred
to load time, how they are resolved is described in @command{man dyld}:
the role of @env{LD_LIBRARY_PATH} is replaced on macOS by
@env{DYLD_LIBRARY_PATH} and @env{DYLD_FALLBACK_LIBRARY_PATH}.  Running
@command{R CMD otool -L} on the package shared object will show where
(if anywhere) its dependencies are
resolved.  @env{DYLD_FALLBACK_LIBRARY_PATH} is preferred (and it is that
which is manipulated by the @R{} script), but as from 10.11 (`@I{El
Capitan}') the default behaviour had been changed for security reasons
to discard these environment variables when invoking a shell script (and
@file{R} is a shell script).  That makes the only portable option to set
@env{R_LD_LIBRARY_PATH} in the environment, something like

@example
export R_LD_LIBRARY_PATH="`R RHOME`/lib:/opt/local/lib"
@end example

The precise rules for where Windows looks for DLLs are complex and
depend on the version of Windows.  But for present purposes the main
solution is to put the directories containing the DLLs the package
links to (and any those DLLs link to) on the @env{PATH}.

@c 64-bit versions of Windows will ignore 32-bit DLLs from 64-bit @R{} and
@c @emph{vice versa}.

The danger with any of the methods which involve setting environment
variables is of inadvertently masking a system library.  This is less
for @env{DYLD_FALLBACK_LIBRARY_PATH} and for @emph{appending} to
@env{PATH} on Windows (as it should already contain the system library
paths).


@node Updating packages
@section Updating packages
@findex update.packages
@cindex Packages, updating

The command @code{update.packages()} is the simplest way to ensure that
all the packages on your system are up to date.  It downloads the list
of available packages and their current versions, compares it with those
installed and offers to fetch and install any that have later versions
on the repositories.

An alternative interface to keeping packages up-to-date is provided by
the command @code{packageStatus()}, which returns an object with
information on all installed packages and packages available at multiple
repositories.  The @code{print} and @code{summary} methods give an
overview of installed and available packages, the @code{upgrade} method
offers to fetch and install the latest versions of outdated packages.

One sometimes-useful additional piece of information that
@code{packageStatus()} returns is the status of a package, as
@code{"ok"}, @code{"upgrade"} or @code{"unavailable"} (in the currently
selected repositories).  For example

@example
> inst <- packageStatus()$inst
> inst[inst$Status != "ok", c("Package", "Version", "Status")]
                  Package Version      Status
Biobase           Biobase   2.8.0 unavailable
RCurl               RCurl   1.4-2     upgrade
Rgraphviz       Rgraphviz  1.26.0 unavailable
rgdal               rgdal  0.6-27     upgrade
@end example


@node Removing packages
@section Removing packages
@findex remove.packages
@cindex Packages, removing

Packages can be removed in a number of ways.  From a command prompt they
can be removed by

@example
R CMD REMOVE -l /path/to/library @var{pkg1} @var{pkg2} @dots{}
@end example

From a running @R{} process they can be removed by

@example
> remove.packages(c("pkg1", "pkg2"),
                  lib = file.path("path", "to", "library"))
@end example

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


@node Setting up a package repository
@section Setting up a package repository
@cindex Repositories

Utilities such as @code{install.packages} can be pointed at any
@acronym{CRAN}-style repository, and @R{} users may want to set up their
own.  The `base' of a repository is a URL such as
@uref{https://www.stats.ox.ac.uk/pub/RWin/}: this must be an URL scheme
that @code{download.packages} supports (which also includes
@samp{https://}, @samp{ftp://} and @samp{file://}).  Under that base URL
there should be directory trees for one or more of the following types
of package distributions:

@itemize
@item 
@code{"source"}: located at @file{src/contrib} and containing
@file{.tar.gz} files.  Other forms of compression can be used, e.g.@:
@file{.tar.bz2} or @file{.tar.xz} files.  Complete repositories contain
the sources corresponding to any binary packages, and in any case it is
wise to have a @file{src/contrib} area with a possibly empty
@file{PACKAGES} file.

@item 
@code{"binary"}: binary packages are located under
@file{bin/@var{os}/@var{build}/contrib/@var{x.y}} for @R{} versions
@var{x.y.z}, where @var{os} is either @file{windows} for Windows or
@file{macosx} for macOS and OS X. The @var{build} variable is defined
by the third part of the @code{type} value after @code{binary} and
may be empty. For example, in @R{} 4.4.1
@code{"mac.binary.big-sur-arm64"} specifies the
@file{bin/macosx/big-sur-arm64/4.4} location, while
@code{"win.binary"} specifies @file{bin/windows/contrib/4.4}. The
platform and build specification in @acronym{CRAN} @R{} binaries can
be obtained from @code{.Platform$pkgType}. Windows binary package
files use @file{.zip} extension while Mac files use @file{.tgz}.
@end itemize

Each terminal directory must also contain a @file{PACKAGES} file.  This
can be a concatenation of the @file{DESCRIPTION} files of the packages
separated by blank lines, but only a few of the fields are needed.  The
simplest way to set up such a file is to use function
@code{write_PACKAGES} in the @pkg{tools} package, and its help explains
which fields are needed.  Optionally there can also be
@file{PACKAGES.rds} and @file{PACKAGES.gz} files, downloaded in
preference to @file{PACKAGES}.  (If you have a @I{mis-configured} server
that does not report correctly non-existent files you may need these
files.)

To add your repository to the list offered by @code{setRepositories()},
see the help file for that function.

Incomplete repositories are better specified @emph{via} a
@code{contriburl} argument than @emph{via} being set as a repository.

A repository can contain subdirectories, when the descriptions in the
@file{PACKAGES} file of packages in subdirectories must include a line
of the form

@example
Path: @var{path/to/subdirectory}
@end example

@noindent
---once again @code{write_PACKAGES} is the simplest way to set this up.


@node Checking installed source packages
@section Checking installed source packages

It can be convenient to run @command{R CMD check} on an installed
package, particularly on a platform which uses sub-architectures.  The
outline of how to do this is, with the source package in directory
@file{@var{pkg}} (or a tarball filename):

@example
R CMD INSTALL -l @var{libdir} @var{pkg} > @var{pkg}.log 2>&1
R CMD check -l @var{libdir} --install=check:@var{pkg}.log @var{pkg}
@end example

@noindent
Where sub-architectures are in use the @command{R CMD check} line can be
repeated with additional architectures by

@example
R --arch @var{arch} CMD check -l @var{libdir} --extra-arch --install=check:@var{pkg}.log @var{pkg}
@end example

@noindent
where @option{--extra-arch} selects only those checks which depend on
the installed code and not those which analyse the sources.  (If
multiple sub-architectures fail only because they need different
settings, e.g.@: environment variables, @option{--no-multiarch} may need
to be added to the @code{INSTALL} lines.)  On Unix-alikes the
architecture to run is selected by @option{--arch}: this can also be
used on Windows with @file{@var{R_HOME}/bin/R.exe}, but it is more usual
to select the path to the @command{Rcmd.exe} of the desired
architecture.

So on Windows to install, check and package for distribution a source
package from a tarball which has been tested on another platform one
might use

@example
.../bin/x64/Rcmd INSTALL -l @var{libdir} @var{tarball} --build > @var{pkg}.log 2>&1
@end example



@node Internationalization
@chapter Internationalization and Localization
@cindex Internationalization
@cindex Localization

@emph{Internationalization} refers to the process of enabling support
for many human languages, and @emph{localization} to adapting to a
specific country and language.

Current builds of @R{} support all the character sets that the
underlying OS can handle.  These are interpreted according to the
@cindex Locale
current @code{locale}, a sufficiently complicated topic to merit a
separate section.  Note though that @R{} has no built-in support for
right-to-left languages and bidirectional output, relying on the OS
services.  For example, how character vectors in UTF-8 containing both
English digits and Hebrew characters are printed is OS-dependent (and
perhaps locale-dependent).

The other aspect of the internationalization is support for the
translation of messages.  This is enabled in almost all builds of @R{}.


@node Locales
@section Locales
@cindex Locale

A @emph{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 @code{Sys.getlocale} and
@code{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
@itemize
@item
A human language.  These are generally specified by a lower-case
two-character abbreviation following ISO 639 (see e.g.@:
@uref{https://en.wikipedia.org/wiki/ISO_639-1}).

@item
A `territory', used mainly to specify the currency. These are generally
specified by an upper-case two-character abbreviation following ISO 3166
(see e.g.@: @uref{https://en.wikipedia.org/wiki/ISO_3166}).

@item
A charset encoding, which determines both how a byte stream should be
divided into characters, and which characters the subsequences of bytes
represent.  Sometimes the combination of language and territory is used
to specify the encoding, for example to distinguish between traditional
and simplified Chinese.

@item
Optionally, a modifier, for example to indicate that Austria is to be
considered pre- or post-Euro.  The modifier is also used to indicate the
script (@code{@@latin}, @code{@@cyrillic} for Serbian, @code{@@iqtelif})
or language dialect (e.g.@: @code{@@saaho}, a dialect of Afar, and
@code{@@bokmal} and @code{@@nynorsk}, dialects of Norwegian regarded by
some OSes as separate languages, @code{no} and @code{nn}).
@end itemize

@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.


@node Locales under Unix-alikes
@subsection Locales under Unix-alikes

Modern Linux uses the @abbr{XPG}@footnote{`X/Open Portability Guide', which has
had several versions.} locale specifications which have the form
@samp{en_GB}, @samp{en_GB.UTF-8}, @samp{aa_ER.UTF-8@@saaho},
@samp{de_AT.iso885915@@euro}, the components being in the order listed
above.  (See @command{man locale} and @command{locale -a} for more
details.)  Similar schemes are used by most Unix-alikes: some (including
some distributions of Linux) use @samp{.utf8} rather than @samp{.UTF-8}.

Note that whereas UTF-8 locales are nowadays almost universally used,
locales such as @samp{en_GB} use 8-bit encodings for backwards
compatibility.

@node Locales under Windows
@subsection Locales under Windows

Windows also uses locales, but specified in a rather less concise way.
Most users will encounter locales only via drop-down menus, but more
information and lists can be found by searching for @samp{Windows
language country strings}).

It offers only one encoding per language.

Some care is needed with Windows' locale names.  For example,
@code{chinese} is Traditional Chinese and not Simplified Chinese as used
in most of the Chinese-speaking world.

@node Locales under macOS
@subsection Locales under macOS

macOS supports locales in its own particular way, but the @R{} GUI tries to
make this easier for users. See
@uref{https://developer.apple.com/library/archive/documentation/MacOSX/Conceptual/BPInternational/}
for how users can set their locales.  End users will
generally only see lists of languages/territories.  Users of @R{} in a
terminal may need to set the locale to something like @samp{en_GB.UTF-8}
if it defaults to @samp{C} (as it sometimes does when logging in
remotely and for batch jobs: note whether @command{Terminal} sets the
@env{LANG} environment variable is an (advanced) preference, but does so
by default).

Internally macOS uses a form similar to Linux: the main difference from
other Unix-alikes is that where a character set is not specified it is
assumed to be @code{UTF-8}.


@node Localization of messages
@section Localization of messages

The preferred language for messages is by default taken from the locale.
This can be overridden first by the setting of the environment variable
@enindex LANGUAGE
@enindex LC_ALL
@enindex LC_MESSAGES
@enindex LANG
@env{LANGUAGE} and then@footnote{On some systems setting
@env{LC_ALL} or @env{LC_MESSAGES} to @samp{C} disables @env{LANGUAGE}.}
by the environment variables @env{LC_ALL}, @env{LC_MESSAGES} and
@env{LANG}. (The last three are normally used to set the locale and so
should not be needed, but the first is only used to select the language
for messages.)  The code tries hard to map locales to languages, but on
some systems (notably Windows) the locale names needed for the
environment variable @env{LC_ALL} do not all correspond to @abbr{XPG} language
names and so @env{LANGUAGE} may need to be set.  (One example is
@samp{LC_ALL=es} on Windows which sets the locale to Estonian and the
language to Spanish.)

It is usually possible to change the language once @R{} is running
@emph{via} (not Windows) @code{Sys.setlocale("LC_MESSAGES",
"new_locale")}, or by setting an environment variable such as
@env{LANGUAGE}, @emph{provided}@footnote{If you try changing from French
to Russian except in a UTF-8 locale, you may find messages change to
English.} the language you are changing to can be output in the current
character set.  But this is OS-specific, and has been known to stop
working on an OS upgrade.  Note that translated messages may be cached,
so attempting to change the language of an error that has already been
output in another language may not work.

Messages are divided into @emph{domains}, and translations may be
available for some or all messages in a domain.  @R{} makes use of the
following domains.

@itemize
@item
Domain @code{R} for the C-level error and warning messages from the @R{}
interpreter.

@item
Domain @code{R-@var{pkg}} for the @R{} @code{stop}, @code{warning} and
@code{message} messages in each package, including @code{R-base} for the
@pkg{base} package.

@item
Domain @code{@var{pkg}} for the C-level messages in each package.

@item
Domain @code{RGui} for the menus etc of the @R{} for Windows GUI front-end.

@end itemize

Dividing up the messages in this way allows @R{} to be extensible: as
packages are loaded, their message translation catalogues can be loaded
too.

@R{} can be built without support for translations, but it is enabled by
default.

R-level and C-level domains are subtly different, for example in the way
strings are canonicalized before being passed for translation. 

Translations are looked for by domain according to the currently
specified language, as specifically as possible, so for example an
Austrian (@samp{de_AT}) translation catalogue will be used in preference
to a generic German one (@samp{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 @samp{en_GB} that translate the Americanisms
(e.g., @samp{gray}) in the standard messages into English.@footnote{the
language written in England: some people living in the USA appropriate
this name for their language.}  Two other examples: there are catalogues
for @samp{es}, which is Spanish as written in Spain and these will by
default also be used in Spanish-speaking Latin American countries, and
also for @samp{pt_BR}, which are used for Brazilian locales but not for
locales specifying Portugal.

Translations in the right language but the wrong charset are made use of
@enindex LANGUAGE
by on-the-fly re-encoding.  The @env{LANGUAGE} variable (only) can be a
colon-separated list, for example @samp{se:de}, giving a set of
languages in decreasing order of preference.  One special value is
@samp{en@@quot}, which can be used in a UTF-8 locale to have American
error messages with pairs of single quotes translated to Unicode directional
quotes.

If no suitable translation catalogue is found or a particular message is
not translated in any suitable catalogue, `English'@footnote{with
Americanisms.} is used.

See @uref{https://developer.r-project.org/Translations30.html} for how to
prepare and install translation catalogues.



@node Choosing between 32- and 64-bit builds
@chapter Choosing between 32- and 64-bit builds

As from @R{} 4.4.0 32-bit builds are unsupported.



@node The standalone Rmath library
@chapter The standalone @I{Rmath} library

The routines supporting the distribution and
special@footnote{e.g.@: Bessel, beta and gamma functions} functions in @R{}
and a few others are declared in C header file @file{Rmath.h}.  These
can be compiled into a standalone library for linking to other
applications.  (Note that they are not a separate library when @R{} is
built, and the standalone version differs in several ways.)

The makefiles and other sources needed are in directory
@file{src/nmath/standalone}, so the following instructions assume that
is the current working directory (in the build directory tree on a
Unix-alike if that is separate from the sources).

@file{Rmath.h} contains @samp{R_VERSION_STRING}, which is a character
string containing the current @R{} version, for example @code{"4.4.0"}.

There is full access to @R{}'s handling of @code{NaN}, @code{Inf} and
@code{-Inf} via special versions of the macros and functions

@example
    ISNAN, R_FINITE, R_log, R_pow and R_pow_di
@end example

@noindent
and (extern) constants @code{R_PosInf}, @code{R_NegInf} and @code{NA_REAL}.

There is no support for @R{}'s notion of missing values, in particular
not for @code{NA_INTEGER} nor the distinction between @code{NA} and
@code{NaN} for doubles.

A little care is needed to use the random-number routines. You will
need to supply the uniform random number generator 

@example
    double unif_rand(void)
@end example

@noindent
or use the one supplied (and with a shared library or DLL you may
have to use the one supplied, which is the @I{Marsaglia}-@I{multicarry} with
an entry point

@example
    set_seed(unsigned int, unsigned int)
@end example

@noindent
to set its seeds).

The facilities to change the normal random number generator are
available through the constant @code{N01_kind}. This takes values
from the enumeration type

@example
typedef enum @{
    BUGGY_KINDERMAN_RAMAGE,
    AHRENS_DIETER,
    BOX_MULLER,
    USER_NORM,
    INVERSION,
    KINDERMAN_RAMAGE
@} N01type;
@end example

@noindent
(and @samp{USER_NORM} is not available).


@node Unix-alike standalone
@section Unix-alikes

If @R{} has not already been made in the directory tree,
@command{configure} must be run as described in the main build
instructions.

Then (in @file{src/nmath/standalone})

@example
make
@end example

@noindent
will make standalone libraries @file{libRmath.a} and @file{libRmath.so}
(@file{libRmath.dylib} on macOS): @samp{make static} and @samp{make
shared} will create just one of them.

To use the routines in your own C or C++ programs, include

@example
#define MATHLIB_STANDALONE
#include <Rmath.h>
@end example

@noindent
and link against @samp{-lRmath} (and @samp{-lm} if needed on your OS).
The example file @file{test.c} does nothing useful, but is provided to
test the process (via @command{make test}).  Note that you will probably
not be able to run it unless you add the directory containing
@enindex LD_LIBRARY_PATH
@file{libRmath.so} to the @env{LD_LIBRARY_PATH} environment variable
(@file{libRmath.dylib}, @env{DYLD_FALLBACK_LIBRARY_PATH} on macOS).

The targets

@example
make install
make uninstall
@end example

@noindent
will @I{(un)install} the header @file{Rmath.h} and shared and static
@enindex DESTDIR
libraries (if built).  Both @code{prefix=} and @env{DESTDIR} are
supported, together with more precise control as described for the main
build.

@samp{make install} installs a file for @command{pkg-config} to use by
e.g.

@example
$(CC) `pkg-config --cflags libRmath` -c test.c
$(CC) `pkg-config --libs libRmath` test.o -o test
@end example

On some systems @samp{make install-strip} will install a stripped shared
library.


@node Windows standalone
@section Windows

You need to set up@footnote{including copying @file{MkRules.dist} to
@file{MkRule.local} and selecting the architecture.} almost all the
tools to make @R{} and then run (in a Unix-like shell)

@example
(cd ../../gnuwin32; make MkRules)
(cd ../../include; make -f Makefile.win config.h Rconfig.h Rmath.h)
make -f Makefile.win
@end example

@noindent
Alternatively, in a @file{cmd.exe} shell use

@example
cd ../../include
make -f Makefile.win config.h Rconfig.h Rmath.h
cd ../nmath/standalone
make -f Makefile.win
@end example


This creates a static library @file{libRmath.a} and a DLL
@file{Rmath.dll}.  If you want an import library @file{libRmath.dll.a}
(you don't need one), use

@example
make -f Makefile.win shared implib
@end example

To use the routines in your own C or C++ programs using @I{MinGW-w64}, include

@example
#define MATHLIB_STANDALONE
#include <Rmath.h>
@end example

@noindent
and link against @samp{-lRmath}.  This will use the first found of
@file{libRmath.dll.a}, @file{libRmath.a} and @file{Rmath.dll} in that
order, so the result depends on which files are present.  You should be
able to force static or dynamic linking  @emph{via}

@example
-Wl,-Bstatic -lRmath -Wl,Bdynamic
-Wl,-Bdynamic -lRmath
@end example

@noindent
or by linking to explicit files (as in the @samp{test} target in
@file{Makefile.win}: this makes two executables, @file{test.exe} which
is dynamically linked, and @file{test-static.exe}, which is statically
linked).

It is possible to link to @file{Rmath.dll} using other compilers, either
directly or via an import library: if you make a @I{MinGW-w64} import library as
above, you will create a file @file{Rmath.def} which can be used
(possibly after editing) to create an import library for other systems
such as Visual C++.

If you make use of dynamic linking you should use

@example
#define MATHLIB_STANDALONE
#define RMATH_DLL
#include <Rmath.h>
@end example

@noindent
to ensure that the constants like @code{NA_REAL} are linked correctly.
(Auto-import will probably work with @I{MinGW-w64}, but it is better to be
sure. This is likely to also work with @I{VC++}, @I{Borland} and similar
compilers.)



@node Essential and useful other programs under a Unix-alike
@appendix Essential and useful other programs under a Unix-alike

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
@command{configure}.

Remember that some package management systems (such as @abbr{RPM} and
Debian/Ubuntu's) make a distinction between the user version of a
package and the development version.  The latter usually has the same
name but with the extension @samp{-devel} or @samp{-dev}: you need both
versions installed.


@node Essential programs and libraries
@section Essential programs and libraries

You need a means of compiling C and Fortran 90 (see @ref{Using
Fortran}).  Your C compiler should be
@acronym{ISO}/@acronym{IEC}@tie{}60059@footnote{also known as
@acronym{IEEE}@tie{}754}, POSIX 1003.1 and C99-compliant.@footnote{Note
that C11 compilers need not be C99-compliant: @R{} requires support for
@code{double complex} and variable-length arrays which are optional in
C11 but are mandatory in C99.  C17 (also known as C18 as it was
published in 2018) is a `bugfix release' of C11, clarifying the
standard. However, all known recent compilers in C11 or C17 mode are
C99-compliant, and most default to C17.} @R{} tries to choose suitable
flags@footnote{Examples are @option{-std=gnu99}, @option{-std=c99} and
@option{-c99}.} for the C compilers it knows about, but you may have to
set @code{CC} or @code{CFLAGS} suitably. (Note that options essential
to run the compiler even for linking, such as those to set the
architecture, should be specified as part of @code{CC} rather than in
@code{CFLAGS}.)

Unless you do not want to view graphs on-screen (or use macOS) you need
@samp{X11} installed, including its headers and client libraries. For
recent Fedora/@I{RedHat} distributions it means (at least) @abbr{RPM}s
@samp{libX11}, @samp{libX11-devel}, @samp{libXt} and @samp{libXt-devel}.
On Debian/Ubuntu we recommend the meta-package @samp{xorg-dev}.  If you
really do not want these you will need to explicitly configure @R{}
without X11, using @option{--with-x=no}.

The command-line editing (and command completion) depends on the
@acronym{GNU} @code{readline} library (including its headers): version
6.0 or later is needed for all the features to be enabled.  Otherwise
you will need to configure with @option{--with-readline=no} (or
equivalent).

A suitably comprehensive @code{iconv} function is essential.  The @R{}
usage requires @code{iconv} to be able to translate between
@code{"latin1"} and @code{"UTF-8"}, to recognize @code{""} (as the
current encoding) and @code{"ASCII"}, and to translate to and from the
Unicode wide-character formats @code{"UCS-[24][BL]E"} --- this is true
by default for @code{glibc}@footnote{However, it is possible to break
the default behaviour of @code{glibc} by re-specifying the @code{gconv}
modules to be loaded.} but not of most commercial Unixes.  However, you
can make use of @acronym{GNU} @code{libiconv} (as used on macOS: see
@uref{https://www.gnu.org/software/libiconv/}).

The OS needs to have enough support@footnote{specifically, the C99
functionality of headers @file{wchar.h} and @file{wctype.h}, types
@code{wctans_t} and @code{mbstate_t} and functions @code{mbrtowc},
@code{mbstowcs}, @code{wcrtomb}, @code{wcscoll}, @code{wcstombs},
@code{wctrans}, @code{wctype}, and @code{iswctype}.} for wide-character
types: this is checked at configuration.  Some C99
functions@footnote{including @code{expm1}, @code{hypot}, @code{log1p},
@code{nearbyint} and @code{va_copy}.} are required and checked for at
configuration.  A small number of POSIX functions@footnote{including
@code{opendir}, @code{readdir}, @code{closedir}, @code{popen},
@code{stat}, @code{glob}, @code{access}, @code{getcwd} and @code{chdir}
system calls, @code{select} on a Unix-alike, and either @code{putenv} or
@code{setenv}.} are essential, and others@footnote{such as
@code{realpath}, @code{symlink}.} will be used if available.

@c zlib 1.2.5 is from July 2010, bzip2 1.0.6 from Sept 2010
@c xz 5.0.3 is from May 2011
Installations of @code{zlib} (version 1.2.5 or later), @code{libbz2}
(version 1.0.6 or later: called @pkg{bzip2-libs}/@pkg{bzip2-devel} or
@pkg{libbz2-1.0}/@pkg{libbz2-dev} by some Linux distributions) and
@code{liblzma}@footnote{most often distributed as part of @code{xz}:
possible names in Linux distributions include
@code{xz-devel}/@code{xz-libs} and @code{liblzma-dev}.} version 5.0.3 or
later are required.  Some software distributions@footnote{for example,
Fedora 40} replace @code{zlib} by
@code{zlib-ng}@footnote{@uref{https://github.com/zlib-ng/zlib-ng}} which
has an optional compatibility interface.

@c PCRE[1] 8.32 is from Nov 2012.
@c Debian Wheezy had 8.30, Ubuntu 14.04LTS had 8.31 but both are EOL.
@c PCRE2: Ubuntu 16.04LTS (EOL Apr 2021) and RHEL/Centos 6 have 10.21,
@c OpenCSW has 10.20.
@c PCRE2 10.30 is from Aug 2017.  Ubuntu 18.04LTS has 10.31.
Either PCRE1 (version 8.32 or later, formerly known as just PCRE) or
PCRE2 is required: PCRE2 is preferred and using PCRE1 requires
@command{configure} option @option{--with-pcre1}.  Only the 8-bit
library and headers are needed if these are packaged separately. @abbr{JIT}
support (optional) is desirable for the best performance.  For PCRE2 >=
10.30 (which is desirable as matching has been re-written not to use
recursion and the Unicode tables were updated to version 10)
@example
./configure --enable-jit
@end example
@noindent
suffices.  If building PCRE1 for use with @R{} a suitable
@command{configure} command might be
@example
./configure --enable-utf --enable-unicode-properties --enable-jit --disable-cpp
@end example
@noindent  
The @option{--enable-jit} flag is supported for most common CPUs but
does not work (well or at all) for @cputype{arm64} macOS.

Some packages require the `Unicode properties' which are
optional for PCRE1: support for this and @abbr{JIT} can be checked at run-time
by calling @code{pcre_config()}.

@c libcurl 7.22.0 was released in Sep 2011, in Ubuntu 12.04 LTS,
@c   end-of-life Apr 2017
@c libcurl 7.26.0 was released in May 2012, still in Debian 7 Wheezy LTS,
@c   end-of-life May 2018. 
@c libcurl 7.28.0 was released in Oct 2012
@c libcurl 7.32.0 was released in Aug 2013
@c Ubuntu 14.04LTS has 7.35.0  RHEL/Centos 7 has 7.29.0 (we are told)
Library @code{libcurl} (version 7.28.0 or later) is required.
Information on @code{libcurl} is found from the @command{curl-config}
script: if that is missing or needs to be overridden@footnote{for
example to specify static linking with a build which has both shared and
static libraries.} there are macros to do so described in file
@file{config.site}.

A @command{tar} program is needed to unpack the sources and packages
(including the recommended packages).  A version@footnote{Such as
@acronym{GNU} @command{tar} 1.15 or later, @command{bsdtar} (from
@uref{https://github.com/libarchive/libarchive/}, used as
@command{tar} by FreeBSD and macOS 10.6 and later) or @command{tar} from
the @I{Heirloom Toolchest}
(@uref{https://heirloom.sourceforge.net/tools.html}), although the
latter does not support @command{xz} compression.} that can
automagically detect compressed archives is preferred for use with
@code{untar()}: the configure script looks for @command{gtar} and
@command{gnutar} before
@enindex TAR
@command{tar} -- use environment variable @env{TAR} to override this.
(On @I{NetBSD}/@I{OpenBSD} systems set this to @command{bsdtar} if that is
installed.)

There need to be suitable versions of the tools @command{grep} and
@command{sed}: the problems are usually with old AT&T and BSD variants.
@command{configure} will try to find suitable versions (including
looking in @file{/usr/xpg4/bin} which is used on some commercial
Unixes).

You will not be able to build most of the manuals unless you have
@command{texi2any} version 6.1 or later installed (which requires
@command{perl}), and if not most of the @HTML{} manuals will be linked
to a version on @acronym{CRAN}. To make PDF versions of the manuals you
will also need file @file{texinfo.tex} installed (which is part of the
@acronym{GNU} @I{Texinfo} distribution but is often made part of the
@TeX{} package @pkg{texinfo} in re-distributions) as well as
@command{texi2dvi}.@footnote{@command{texi2dvi} is normally a shell
script.  Some of the issues which have been observed with broken
versions of @command{texi2dvi} can be circumvented by setting the
environment variable @env{R_TEXI2DVICMD} to the value @code{emulation}.}
Further, the versions of @command{texi2dvi} and @file{texinfo.tex} need
to be compatible: we have seen problems with older @TeX{} distributions.

@cindex Subversion
If you want to build from the @R{} Subversion repository then
@command{texi2any} is highly recommended as it is used to create files
which are in the tarball but not stored in the Subversion repository.

@cindex Vignettes
The PDF documentation (including @file{doc/NEWS.pdf}) and building
vignettes needs @command{pdftex} and @command{pdflatex}.  We require
@LaTeX{} version @code{2005/12/01} or later (for UTF-8 support).
Building PDF package manuals (including the @R{} reference manual) and
vignettes is sensitive to the version of the @LaTeX{} package
@pkg{hyperref} and we recommend that the @TeX{} distribution used is
kept up-to-date.  A number of standard @LaTeX{} packages are required
for the PDF manuals
(including @pkg{url} and some of the font packages such as @pkg{times}
and @pkg{helvetic} and also @pkg{amsfonts}) and others such
as @pkg{hyperref} and @pkg{inconsolata} are desirable (and without them
you may need to change @R{}'s defaults: @pxref{Making the manuals}).
Note that package @pkg{hyperref} (currently) requires packages
@pkg{etoolbox}, @pkg{kvoptions}, @pkg{ltxcmds} and @pkg{refcount},
and @pkg{inconsolata} requires @pkg{xkeyval}.
Building the base vignettes requires @pkg{hyperref}, @pkg{fancyvrb},
@pkg{natbib}, @pkg{parskip} and @pkg{listings}.
For distributions
based on TeX Live the simplest approach may be to install collections
@pkg{collection-latex}, @pkg{collection-fontsrecommended},
@pkg{collection-latexrecommended}, @pkg{collection-fontsextra} and
@pkg{collection-latexextra} (assuming they are not installed by
default): Fedora uses names like @pkg{texlive-collection-fontsextra} and
Debian/Ubuntu like @pkg{texlive-fonts-extra}.

Programs @command{qpdf} and @I{Ghostscript} (@command{gs}) are desirable as
these will be used to compact the installed PDF vignettes and any PDF
manuals.

@enindex PATH
The essential programs should be in your @env{PATH} at the time
@command{configure} is run: this will capture the full paths.

For date-times to work correctly it is essential that the tables
defining time zones are installed: these are usually in an OS component
named something like @code{tzdata}. On most OSes they are required
@c with glibc by glibc-common
but installations of Alpine Linux have been seen without them.  There is
a @command{configure} check that recent date-times to work correctly in
different time zones which catches this when installing from source (but
not for binary distributions).

Those distributing binary versions of @R{} may need to be aware of the
licences of the external libraries it is linked to (including `useful'
libraries from the next section).  The @code{liblzma} library is in the
public domain and X11, @code{libbzip2}, @code{libcurl} and @code{zlib}
have MIT-style licences. PCRE and PCRE2 have a BSD-style licence which
requires distribution of the licence (included in @R{}'s
@file{COPYRIGHTS} file) in binary distributions.  GNU @code{readline} is
licensed under GPL (which version(s) of GPL depends on the
@code{readline} version).


@node Useful libraries and programs
@section Useful libraries and programs

The ability to use translated messages makes use of @code{gettext} and
most likely needs @acronym{GNU} @code{gettext}: you do need this to work
with new translations, but otherwise the version of the @code{gettext}
runtime contained in the R sources will be used if no suitable external
@code{gettext} is found.

@cindex Cairo
@cindex @I{Pango}
The `modern' version of the @code{X11()}, @code{jpeg()}, @code{png()}
and @code{tiff()} graphics devices uses the Cairo and @I{Pango} libraries.
Cairo version 1.2.0 or later and @I{Pango} version 1.10 or later are
required (but much later versions are current).  @R{} checks for
@command{pkg-config}, and uses that to check first that the
@samp{pangocairo} package is installed (and if not, @samp{cairo}) then
if suitable code can be compiled.  These tests will fail if
@command{pkg-config} is not installed@footnote{If necessary the path to
@command{pkg-config} can be specified by setting @env{PKG_CONFIG} in
@file{config.site}, on the @command{configure} command line or in the
environment. There is a compatible re-implementation of
@command{pkg-config} called @command{pkgconf} which can be used in the
unlikely event that is installed but not linked to
@command{pkg-config}.}, and might fail if @code{cairo} was built
statically unless @command{configure} option
@option{--with-static-cairo} is used.  Most systems with @code{Gtk+} 2.8
or later installed will have suitable libraries: for Fedora users the
@code{pango-devel} @abbr{RPM} and its dependencies suffice.
@c arm64 Homebrew did in early 2021.
It is possible (but very unusual on a platform with X11) to build Cairo
without its @code{cairo-xlib} module in which case @code{X11(type =
"cairo")} will not be available.  @I{Pango} is optional but highly desirable
as it is likely to give much better text rendering, including kerning.

For the best font experience with these devices you need suitable fonts
installed: Linux users will want the @code{urw-fonts} package.  On
platforms which have it available, the @code{msttcorefonts}
package@footnote{also known as @code{ttf-mscorefonts-installer} in the
Debian/Ubuntu world: see also
@uref{https://en.wikipedia.org/wiki/Core_fonts_for_the_Web}.} provides
@I{TrueType} versions of @I{Monotype} fonts such as @I{Arial} and Times New Roman.
Another useful set of fonts is the `liberation' @I{TrueType} fonts available
at
@uref{https://pagure.io/liberation-fonts},@footnote{@code{ttf-liberation}
in Debian/Ubuntu.} which cover the Latin, Greek and Cyrillic alphabets
plus a fair range of signs.  These share metrics with @I{Arial}, Times New
Roman and Courier New, and contain fonts rather similar to the first two
(@uref{https://en.wikipedia.org/wiki/Liberation_fonts}).  Then there
is the `Free @I{UCS} Outline Fonts' project
(@uref{https://www.gnu.org/software/freefont/}) which are
@I{OpenType}/@I{TrueType} fonts based on the URW fonts but with extended Unicode
coverage.  See the @R{} help on @code{X11} on selecting such fonts.

The bitmapped graphics devices @code{jpeg()}, @code{png()} and
@code{tiff()} need the appropriate headers and libraries installed:
@code{jpeg} (version 6b or later, or @code{libjpeg-turbo}) or
@code{libpng} (version 1.2.7 or later) and @code{zlib} or @code{libtiff}
respectively.
@command{pkg-config} is used if available and so needs the appropriate
@file{.pc} file (which requires @code{libtiff} version 4.x and is not
available on all platforms for @code{jpeg} before version 9c).  They
also need support for either @code{X11} or @code{cairo} (see above).
Should support for these devices @strong{not} be required or broken
system libraries need to be avoided there are @command{configure}
options @option{--without-libpng}, @option{--without-jpeglib} and
@option{--without-libtiff}.  The TIFF library has many optional features
such as @code{jpeg}, @code{libz}, @code{zstd}, @code{lzma}, @code{webp},
@code{jbig} and @code{jpeg12}, none of which is required for the
@code{tiff()} devices but may need to be present to link the library
(usually only an issue for static linking).  @command{pkg-config} can
tell you what other libraries are required for linking, for example by
@code{pkg-config libtiff-4 --static --libs}.
@c --print-requires and --print-requires-private are not recursive.

Option @option{--with-system-tre} is also available: it needs a recent
version of @I{TRE}. (The latest sources are in the @command{git} repository
at @url{https://github.com/laurikari/tre/}, but at the time of writing
the resulting build did not complete its checks, nor did @R{} built
against the version supplied by Fedora.)

An implementation of @acronym{XDR} is required, and the @R{} sources
contain one which is likely to suffice (although a system version may
have higher performance).  @acronym{XDR} is part of @acronym{RPC} and
historically has been part of @file{libc} on a Unix-alike.  (In
principle @command{man xdr_string} should tell you which library is
needed, but it often does not: on some OSes it is provided by
@code{libnsl}.)  However some builds@footnote{Including that used by
Fedora 28 and later} of @code{glibc} omit or hide it with the intention
that the @acronym{TI-RPC} library be used, in which case @code{libtirpc}
(and its development version) should be installed, and its
headers@footnote{@R{} uses @file{rpc/xdr.h} but that includes
@file{netconfig.h} from the top @file{tirpc} directory.} need to be on
the C include path or under @file{/usr/include/tirpc}.

Library @code{libdeflate} (@url{https://github.com/ebiggers/libdeflate})
is used by @code{memCompress()} and @code{memDecompress()} if available.

Use of the X11 clipboard selection requires the @code{Xmu} headers and
libraries.  These are normally part of an X11 installation (e.g.@: the
Debian meta-package @samp{xorg-dev}), but some distributions have split
this into smaller parts, so for example recent versions of Fedora
require the @samp{libXmu} and @samp{libXmu-devel} @abbr{RPM}s.

Some systems (notably macOS and at least some FreeBSD systems) have
inadequate support for collation in multibyte locales.  It is possible
to replace the OS's collation support by that from ICU (International
Components for Unicode, @uref{https://icu.unicode.org/}), and this
provides much more precise control over collation on all systems.  ICU
is available as sources and as binary distributions for (at least) most
Linux distributions, FreeBSD, macOS and @abbr{AIX}, usually as @code{libicu} or
@code{icu4c}.  It will be used by default where available: should a very
old or broken version of ICU be found this can be suppressed by
@option{--without-ICU}.

The @code{bitmap} and @code{dev2bitmap} devices and function
@code{embedFonts()} use @I{Ghostscript}
(@uref{https://www.ghostscript.com/}).  This should either be in your
path when the command is run, or its full path specified by the
environment variable @env{R_GSCMD} at that time.
@enindex R_GSCMD

At the time of writing a full installation on Fedora Linux used the
following packages and their development versions, and this may provide
a useful checklist for other systems:
@example
bzip2 cairo fontconfig freetype fribidi gcc gcc-gfortran gcc-c++ glib2
glibc harfbuzz lapack libX11 libXext libXt libcurl libdeflate libicu
libjpeg libpng libtiff libtirpc libxcrypt ncurses pango
pkgconf-pkg-config pcre2 readline tcl tk xz zlib
@end example
@noindent
plus, preferably a TeX installation and Java.


@node Tcl/Tk
@subsection Tcl/Tk

The @pkg{tcltk} package needs Tcl/Tk @geq{} 8.4 installed: the sources are
available at @uref{https://www.tcl-lang.org/}.  To specify the locations of the
Tcl/Tk files you may need the configuration options

@table @option
@item --with-tcltk
use Tcl/Tk, or specify its library directory
@item --with-tcl-config=@var{TCL_CONFIG}
specify location of @file{tclConfig.sh}
@item --with-tk-config=@var{TK_CONFIG}
specify location of @file{tkConfig.sh}
@end table

@noindent
or use the configure variables @code{TCLTK_LIBS} and
@code{TCLTK_CPPFLAGS} to specify the flags needed for linking against
the Tcl and Tk libraries and for finding the @file{tcl.h} and
@file{tk.h} headers, respectively.  If you have both 32- and 64-bit
versions of Tcl/Tk installed, specifying the paths to the correct config
files may be necessary to avoid confusion between them.

Versions of Tcl/Tk up to 8.5.19 and 8.6.12 have been tested (including
most versions of 8.4.x, but not recently).

Note that the @file{tk.h} header includes@footnote{This is true even for
the `Aqua' version of Tk on macOS, but distributions of that include a
copy of the X11 files needed.} X11 headers, so you will need X11 and its
development files installed.

@node Java support
@subsection Java support

The build process looks for Java support on the host system, and if it
finds it sets some settings which are useful for Java-using packages
(such as @CRANpkg{rJava} and @CRANpkg{JavaGD}: installing these from
source requires a full @abbr{JDK}).  This check can be suppressed by
configure option @option{--disable-java}.
@enindex JAVA_HOME
Configure variable @env{JAVA_HOME} can be set to point to a specific
@abbr{JRE}/@abbr{JDK}, on the @command{configure} command line or in the environment.

Principal amongst these settings are some paths to the Java
libraries and JVM, which are stored in environment variable
@enindex R_JAVA_LD_LIBRARY_PATH
@env{R_JAVA_LD_LIBRARY_PATH} in file @file{@var{R_HOME}/etc/ldpaths} (or
a sub-architecture-specific version).  A typical setting for
@cputype{x86_64} Linux is

@example
JAVA_HOME=/usr/lib/jvm/java-1.8.0-openjdk-1.8.0.322.b06-6.fc34.x86_64/jre
R_JAVA_LD_LIBRARY_PATH=$@{JAVA_HOME@}/lib/amd64/server
@end example

Unfortunately this depends on the exact version of the @abbr{JRE}/@abbr{JDK}
installed, and so may need updating if the Java installation is updated.
This can be done by running @code{R CMD javareconf} which updates
settings in both @file{@var{R_HOME}/etc/Makeconf} and
@file{@var{R_HOME}/etc/ldpaths}. See @code{R CMD javareconf --help} for
details: note that this needs to be done by the account owning the @R{}
installation.

Another way of overriding those settings is to set the environment variable
@enindex R_JAVA_LD_LIBRARY_PATH
@env{R_JAVA_LD_LIBRARY_PATH} (before @R{} is started, hence not in
@file{~/.Renviron}), which suffices to run already-installed
Java-using packages.  For example

@example
R_JAVA_LD_LIBRARY_PATH=/usr/lib/jvm/java-1.8.0/jre/lib/amd64/server
@end example

It may be possible to avoid this by specifying an invariant link as the
path when configuring. For example, on that system any of

@example
JAVA_HOME=/usr/lib/jvm/java
JAVA_HOME=/usr/lib/jvm/java-1.8.0
JAVA_HOME=/usr/lib/jvm/java-1.8.0/jre
JAVA_HOME=/usr/lib/jvm/jre-1.8.0
@end example

@noindent
worked (since the `auto' setting of @command{/etc/alternatives} chose
Java 8 aka 1.8.0).

`Non-server' Oracle distributions of Java as from version 11 are of a
full @abbr{JDK}.  However, Linux distributions can be confusing: for example
Fedora 38 had
@example
java-1.8.0-openjdk
java-1.8.0-openjdk-devel
java-11-openjdk
java-11-openjdk-devel
java-17-openjdk
java-17-openjdk-devel
java-latest-openjdk
java-latest-openjdk-devel
@end example
@noindent
where the @code{-devel} @abbr{RPM}s are needed to complete the @abbr{JDK}. Debian/Ubuntu use
@samp{-jre} and @samp{-jdk}, e.g.
@example
sudo apt install default-jdk
@end example
@c https://www.digitalocean.com/community/tutorials/how-to-install-java-with-apt-on-ubuntu-22-04

@node Other compiled languages
@subsection Other compiled languages

Some add-on packages need a C++ compiler.  This is specified by the
configure variables @code{CXX}, @code{CXXFLAGS} and similar.
@command{configure} will normally find a suitable compiler.  It is
possible to specify an alternative C++17 compiler by the configure
variables @code{CXX17}, @code{CXX17STD}, @code{CXX17FLAGS} and similar
(@pxref{C++ Support}).  Again, @command{configure} will normally find a
suitable value for @code{CXX17STD} if the compiler given by @code{CXX}
is capable of compiling C++17 code, but it is possible that a completely
different compiler will be needed.  (Similar macros are provided for
C++20.)

For source files with extension @file{.f90} or @file{.f95} containing
free-form Fortran, the compiler defined by the macro @code{FC} is used
by @command{R CMD INSTALL}.  Note that it is detected by the name of the
command without a test that it can actually compile Fortran 90 code.
Set the configure variable @code{FC} to override this if necessary:
variables @code{FCFLAGS} and @code{FCLIBS_XTRA} might also need to be
set.

See file @file{config.site} in the @R{} source for more details about
these variables.


@node Linear algebra
@section Linear algebra
@cindex BLAS library


The linear algebra routines in @R{} make use of @acronym{BLAS} (Basic
Linear Algebra Subprograms, @uref{https://netlib.org/blas/faq.html})
routines, and most make use of routines from @acronym{LAPACK} (@I{Linear
Algebra PACKage}, @uref{https://netlib.org/lapack/}).  The @R{}
sources contain reference (Fortran) implementations of these, but they
can be replaced by external libraries, usually those tuned for speed on
specific CPUs.  These libraries normally contain all of the BLAS
routines and some tuned LAPACK routines and perhaps the rest of LAPACK
from the reference implementation.  Because of the way linking works,
using an external BLAS library may necessitate using the version of
LAPACK it contains.

Note that the alternative implementations will not give identical
numeric results.  Some differences may be benign (such the signs of @abbr{SVD}s
and eigenvectors), but the optimized routines can be less accurate and
(particularly for LAPACK) can be from older versions with fewer
corrections.  However, @R{} relies on
@acronym{ISO}/@acronym{IEC}@tie{}60559 compliance.  This can be broken
if for example the code assumes that terms with a zero factor are always
zero and do not need to be computed---whereas @code{x*0} can be
@code{NaN}.  The internal BLAS has been extensively patched to avoid
this whereas @I{MKL}'s documentation has warned
@quotation
LAPACK routines assume that input matrices do not contain IEEE 754
special values such as INF or NaN values. Using these special values may
cause LAPACK to return unexpected results or become unstable.
@end quotation

Some of the external libraries are multi-threaded.  One issue is
that @R{} profiling (which uses the @code{SIGPROF} signal) may cause
problems, and you may want to disable profiling if you use a
multi-threaded @acronym{BLAS}.  Note that using a multi-threaded
@acronym{BLAS} can result in taking more @acronym{CPU} time and even
more elapsed time (occasionally dramatically so) than using a similar
single-threaded @acronym{BLAS}.  On a machine running other tasks, there
can be contention for CPU caches that reduces the effectiveness of the
optimization of cache use by a @acronym{BLAS} implementation: some
people warn that this is especially problematic for hyper-threaded CPUs.

BLAS and LAPACK routines may be used inside threaded code, for example
in @abbr{OpenMP} sections in packages such as @CRANpkg{mgcv}.  The reference
implementations are thread-safe but external ones may not be (even
single-threaded ones): this can lead to hard-to-track-down incorrect
results or segfaults.
@c Seen for OpenBLAS 0.3.2 in 2018.

There is a tendency for re-distributors of @R{} to use `enhanced' linear
algebra libraries without explaining their downsides.


@node BLAS
@subsection BLAS

An external BLAS library has to be explicitly requested at configure
time.

You can specify a particular @acronym{BLAS} library @emph{via} a value
for the configuration option @option{--with-blas}.  If this is given
with no @code{=}, its value is taken from the
@enindex BLAS_LIBS
environment variable @env{BLAS_LIBS}, set for example in
@file{config.site}.  If neither the option nor the environment variable
supply a value, a search is made for a suitable@footnote{The search
order is currently @I{OpenBLAS}, @I{BLIS}, ATLAS, platform-specific choices (see
below) and finally a generic @file{libblas}.} @acronym{BLAS}.  If the
value is not obviously a linker command (starting with a dash or giving
the path to a library), it is prefixed by @samp{-l}, so

@example
--with-blas="foo"
@end example

@noindent
is an instruction to link against @samp{-lfoo} to find an external
@acronym{BLAS} (which needs to be found both at link time and run time).

The configure code checks that the external @acronym{BLAS} is complete
(as of LAPACK 3.9.1: it must include all double precision and double
complex routines, as well as @code{LSAME}), and appears to be usable.
However, an external @acronym{BLAS} has to be usable from a shared
object (so must contain position-independent code), and that is not
checked.  Also, the BLAS can be switched after configure is run, either
as a symbolic link or by the mechanisms mentioned below, and this can
defeat the completeness check.

Some enhanced @acronym{BLAS}es are compiler-system-specific
(@code{Accelerate} on macOS, @code{sunperf} on Solaris@footnote{Using
the Oracle Developer Studio @command{cc} and @command{f95} compilers},
@code{libessl} on IBM).  The correct incantation for these is often
found @emph{via} @option{--with-blas} with no value on the appropriate
platforms.

Note that under Unix (but not under Windows) if @R{} is compiled against
a non-default @acronym{BLAS} and @option{--enable-BLAS-shlib} is
@strong{not} used (it is the default on all platforms except @abbr{AIX}), then
all @acronym{BLAS}-using packages must also be.  So if @R{} is re-built
to use an enhanced @acronym{BLAS} then packages such as
@CRANpkg{quantreg} will need to be re-installed.

Debian/Ubuntu systems provide a system-specific way to switch the BLAS
in use: Build @R{} with @option{--with-blas} to select the OS version of
the reference BLAS, and then use @command{update-alternatives} to switch
between the available BLAS libraries.  See
@uref{https://wiki.debian.org/DebianScience/LinearAlgebraLibraries}.

Fedora 33 and later offer `@I{FlexiBLAS}', a similar mechanism for switching
the BLAS in use
(@uref{https://www.mpi-magdeburg.mpg.de/projects/flexiblas}).  However,
rather than overriding @code{libblas}, this requires configuring @R{}
with option @option{--with-blas=flexiblas}.  `Backend' wrappers are
available for the reference BLAS, ATLAS and serial, threaded and @abbr{OpenMP}
builds of @I{OpenBLAS} and @I{BLIS}, and perhaps others@footnote{for example,
Intel @I{MKL} not packaged by Fedora.}.  This can be controlled from a
running @R{} session by package @CRANpkg{flexiblas}.

BLAS implementations which use parallel computations can be
non-deterministic: this is known for ATLAS.


@node ATLAS
@subsubsection ATLAS

ATLAS (@uref{https://math-atlas.sourceforge.net/}) is a ``tuned''
@acronym{BLAS} that runs on a wide range of Unix-alike platforms.
Unfortunately it is built by default as a static library that on some
platforms may not be able to be used with shared objects such as are
used in @R{} packages.  Be careful when using pre-built versions of
ATLAS static libraries (they seem to work on @cputype{ix86} platforms,
but not always on @cputype{x86_64} ones).

ATLAS contains replacements for a small number of LAPACK routines, but
can be built to merge these with the reference LAPACK sources to include
a full LAPACK library.

Recent versions of ATLAS can be built as a single shared library, either
@code{libsatlas} or @code{libtatlas} (serial or threaded respectively):
these may even contain a full LAPACK.  Such builds can be used by one of
@example
--with-blas=satlas
--with-blas=tatlas
@end example
@noindent
or, as on @cputype{x86_64} Fedora where a path needs to be specified,
@example
--with-blas="-L/usr/lib64/atlas -lsatlas"
--with-blas="-L/usr/lib64/atlas -ltatlas"
@end example
@noindent
Distributed ATLAS libraries cannot be tuned to your machine and so are a
compromise: for example Fedora tunes@footnote{The only way to see
exactly which CPUs the distributed libraries have been tuned for is to
read the @file{atlas.spec} file.} @cputype{x86_64} @abbr{RPM}s for CPUs with
SSE3 extensions, and separate @abbr{RPM}s may be available for specific CPU
families.

Note that building @R{} on Linux against distributed shared libraries
may need @samp{-devel} or @samp{-dev} packages installed.

Linking against multiple static libraries requires one of
@example
--with-blas="-lf77blas -latlas"
--with-blas="-lptf77blas -lpthread -latlas"
--with-blas="-L/path/to/ATLAS/libs -lf77blas -latlas"
--with-blas="-L/path/to/ATLAS/libs -lptf77blas -lpthread -latlas"
@end example

Consult its installation
guide@footnote{@uref{https://math-atlas.sourceforge.net/atlas_install/}}
for how to build ATLAS as a shared library or as a static library with
position-independent code (on platforms where that matters).

According to the ATLAS
FAQ@footnote{@uref{https://math-atlas.sourceforge.net/faq.html#tnum}} the
maximum number of threads used by multi-threaded ATLAS is set at compile
time.  Also, the author advises against using multi-threaded ATLAS on
hyper-threaded CPUs without restricting affinities at compile-time to one
virtual core per physical CPU.  (For the Fedora libraries the
compile-time flag specifies 4 threads.)
@c https://math-atlas.sourceforge.net/atlas_install/node21.html

@node OpenBLAS and BLIS
@subsubsection @I{OpenBLAS} and @I{BLIS}

@I{Dr Kazushige Goto} wrote a tuned @acronym{BLAS} for several processors
and OSes, which was frozen in 2010.  @I{OpenBLAS}
(@uref{https://www.openblas.net/}) is a descendant project with support
for some later CPUs.

This can be used by configuring @R{} with something like

@example
--with-blas="openblas"
@end example

@noindent
See @pxref{Shared BLAS} for an alternative (and in many ways preferable)
way to use them.

Some platforms provide multiple builds of @I{OpenBLAS}: for example Fedora
has @abbr{RPM}s@footnote{(and more, e.g.@: for 64-bit ints and static versions).}
@example
openblas
openblas-threads
openblas-openmp
@end example
@noindent
providing shared libraries
@example
libopenblas.so
libopenblasp.so
libopenblaso.so
@end example
@noindent
respectively, each of which can be used as a shared BLAS.  For the
second and third the number of threads is controlled by
@env{OPENBLAS_NUM_THREADS} and @env{OMP_NUM_THREADS} (as usual for
@abbr{OpenMP}) respectively.

These and their Debian equivalents contain a complete LAPACK
implementation.

Note that building @R{} on Linux against distributed libraries may need
@samp{-devel} or @samp{-dev} packages installed.

@c https://wiki.debian.org/DebianScience/LinearAlgebraLibraries
For @cputype{ix86} and @cputype{x86_64} CPUs most distributed libraries
contain several alternatives for different CPU microarchitectures with
the choice being made at run time.

Another descendant project is @I{BLIS}
(@uref{https://github.com/flame/blis}).  This has (in Fedora) shared
libraries
@example
libblis.so
libblisp.so
libbliso.so
@end example
@noindent
(@code{p} for `threads', @code{o} for @abbr{OpenMP} as for @I{OpenBLAS}) which can
also be used as a shared BLAS.  The Fedora builds do not include LAPACK
in the @I{BLIS} libraries.

@node MKL
@subsubsection Intel @I{MKL}
For Intel processors (and perhaps others) and some distributions of
Linux, there is Intel's Math Kernel Library@footnote{Nowadays known as
`@I{Intel oneAPI Math Kernel Library}' or even `@I{oneMKL}'.}.  You are
encouraged to read the documentation which is installed with the library
before attempting to link to @I{MKL}.  This includes a `link line advisor'
which will suggest appropriate incantations: its use is recommended.  Or
see
@uref{https://www.intel.com/content/www/us/en/developer/tools/oneapi/onemkl-link-line-advisor.html#gs.vpt6qp}
(which at the time of writing selected the Intel library for linking with
GCC).

There are also versions of @I{MKL} for macOS@footnote{The issue for macOS
has been the use of double-complex routines.} and Windows, but when
these have been tried they did not work with the default compilers used
for @R{} on those platforms.

The following examples have been used with @I{MKL} versions 10.3 to
2023.2.0, for GCC compilers on @cputype{x86_64} CPUs.  (See also
@ref{Intel compilers}.)

To use a sequential version of @I{MKL} we used

@example
MKL_LIB_PATH=/path/to/intel_mkl/mkl/lib/intel64
export LD_LIBRARY_PATH=$MKL_LIB_PATH
MKL="-L$@{MKL_LIB_PATH@} -lmkl_gf_lp64 -lmkl_core -lmkl_sequential"
./configure --with-blas="$MKL" --with-lapack
@end example

@noindent
The option @option{--with-lapack} is used since @I{MKL} contains a tuned
copy of LAPACK (often older than the current version) as well as the
@acronym{BLAS} (@pxref{LAPACK}), although this can be omitted.

Threaded @I{MKL} may be used by replacing the line defining the variable
@code{MKL} by

@example
MKL="-L$@{MKL_LIB_PATH@} -lmkl_gf_lp64 -lmkl_core \
     -lmkl_gnu_thread -dl -fopenmp"
@end example

@R{} can also be linked against a single shared library,
@code{libmkl_rt.so}, for both BLAS and LAPACK, but the correct @abbr{OpenMP} and
@I{MKL} interface layer then has to be selected via environment variables.  With
64-bit builds and the GCC compilers, we used

@example
export MKL_INTERFACE_LAYER=GNU,LP64 
export MKL_THREADING_LAYER=GNU
@end example

On Debian/Ubuntu, @I{MKL} is provided by package @code{intel-mkl-full} and one
can set @code{libmkl_rt.so} as the system-wide implementation of both BLAS
and LAPACK during installation of the package, so that also @R{} installed
from Debian/Ubuntu package @code{r-base} would use it.  It is, however,
still essential to set @code{MKL_INTERFACE_LAYER} and
@code{MKL_THREADING_LAYER} before running @R{}, otherwise @I{MKL} computations
will produce incorrect results. @R{} does not have to be rebuilt to use @I{MKL},
but @code{configure} includes tests which may discover some errors such as a
failure to set the correct @abbr{OpenMP} and @I{MKL} interface layer.

Note that the Debian/Ubuntu distribution can be quite old (for example
@code{2020.4} in mid-2023 when @code{2023.1} was current): this can be
important for the LAPACK version included.

@noindent
The default number of threads will be chosen by the @abbr{OpenMP} software, but
can be controlled by setting @code{OMP_NUM_THREADS} or
@code{MKL_NUM_THREADS}, and in recent versions seems to default to a
sensible value for sole use of the machine.  (Parallel @I{MKL} has not
always passed @command{make check-all}, but did with @I{MKL} 2019.4 and later.)

@I{MKL} includes a partial implementation of @I{FFTW3}, which causes trouble
for applications that require some of the @I{FFTW3} functionality
unsupported in @I{MKL}.  Please see the @I{MKL} manuals for description of these
limitations and for instructions on how to create a custom version of
@I{MKL} which excludes the @I{FFTW3} wrappers.

There is Intel documentation for building @R{} with @I{MKL} at
@uref{https://www.intel.com/content/www/us/en/developer/articles/technical/using-onemkl-with-r.html}:
that includes
@example
-Wl,--no-as-needed
@end example
@noindent
which we have not found necessary.

@c https://stat.ethz.ch/pipermail/r-devel/2015-September/071717.html
@c It was reported in 2015 that

@c @example
@c --with-blas='-mkl=parallel' --with-lapack
@c @end example

@c @noindent
@c worked with the Intel 2015.3 compilers on Centos 6.

@node Shared BLAS
@subsubsection Shared BLAS

The @acronym{BLAS} library will be used for many of the add-on packages
as well as for @R{} itself.  This means that it is better to use a
shared/dynamic @acronym{BLAS} library, as most of a static library will
be compiled into the @R{} executable and each @acronym{BLAS}-using
package.

@R{} offers the option of compiling the @acronym{BLAS} into a dynamic
library @code{libRblas} stored in @file{@var{R_HOME}/lib} and linking
both @R{} itself and all the add-on packages against that library.

This is the default on all platforms except @abbr{AIX} unless an external
@acronym{BLAS} is specified and found: for the latter it can be used by
specifying the option @option{--enable-BLAS-shlib}, and it can always be
disabled via @option{--disable-BLAS-shlib}.

This has both advantages and disadvantages.

@itemize
@item
It saves space by having only a single copy of the @acronym{BLAS}
routines, which is helpful if there is an external static @acronym{BLAS}
(as used to be standard for ATLAS).

@item
There may be performance disadvantages in using a shared @acronym{BLAS}.
Probably the most likely is when @R{}'s internal @acronym{BLAS} is used
and @R{} is @emph{not} built as a shared library, when it is possible to
build the @acronym{BLAS} into @file{R.bin} (and @file{libR.a}) without
using position-independent code.  However, experiments showed that in
many cases using a shared @acronym{BLAS} was as fast, provided high
levels of compiler optimization are used.

@item
It is easy to change the @acronym{BLAS} without needing to re-install
@R{} and all the add-on packages, since all references to the
@acronym{BLAS} go through @code{libRblas}, and that can be replaced.
Note though that any dynamic libraries the replacement links to will
need to be found by the linker: this may need the library path to be
changed in @file{@var{R_HOME}/etc/ldpaths}.
@end itemize

Another option to change the @acronym{BLAS} in use is to symlink a
single dynamic @acronym{BLAS} library to
@file{@var{R_HOME}/lib/libRblas.so}.  For example, just

@example
mv @var{R_HOME}/lib/libRblas.so @var{R_HOME}/lib/libRblas.so.keep
ln -s /usr/lib64/libopenblasp.so.0 @var{R_HOME}/lib/libRblas.so
@end example

@noindent
on @cputype{x86_64} Fedora will change the @acronym{BLAS} used to
multithreaded @I{OpenBLAS}.  A similar link works for most versions of the
@I{OpenBLAS} (provided the appropriate @file{lib} directory is in the
run-time library path or @command{ld.so} cache).  It can also be used
for a single-library ATLAS, so on @cputype{x86_64} Fedora either of

@example
ln -s /usr/lib64/atlas/libsatlas.so.3 @var{R_HOME}/lib/libRblas.so
ln -s /usr/lib64/atlas/libtatlas.so.3 @var{R_HOME}/lib/libRblas.so
@end example

@noindent
can be used with its distributed ATLAS libraries.  (If you have the
@samp{-devel} @abbr{RPM}s installed you can omit the @code{.0}/@code{.3}.)

Note that rebuilding or symlinking @file{libRblas.so} may not suffice
if the intention is to use a modified LAPACK contained in an external
BLAS: the latter could even cause conflicts.  However, on Fedora where
the @I{OpenBLAS} distribution contains a copy of LAPACK, it is the latter
which is used.


@node LAPACK
@subsection LAPACK

@cindex LAPACK library

If when configuring @R{} a system LAPACK library is found of version
3.9.0 or later (and does not contain BLAS routines) it will be used
instead of compiling the LAPACK code in the package sources.  This can
be prevented by configuring @R{} with @option{--without-lapack}.
Using a static @file{liblapack.a} is not supported.

It is assumed that @code{-llapack} is the reference LAPACK library but
on Debian/Ubuntu it can be switched, including after @R{} is installed.
On such a platform it is better to use @option{--without-lapack} or
@option{--with-blas --with-lapack} (see below) explicitly.  The known
examples@footnote{ATLAS, @I{OpenBLAS} and @I{Accelerate}.} of a
non-reference LAPACK library found at installation all contain BLAS
routines so are not used by a default @command{configure} run.

Provision is made for specifying an external LAPACK library with option
@option{--with-lapack}, principally to cope with @acronym{BLAS}
libraries which contain a copy of LAPACK (such as @code{Accelerate} on
macOS and some builds of ATLAS, @I{FlexiBLAS}, @I{MKL} and @I{OpenBLAS} on
@cputype{ix86}/@cputype{x86_64} Linux).  At least LAPACK version 3.2 is
required.  This can only be done if @option{--with-blas} has been used.

However, the likely performance gains are thought to be small (and may
be negative).  The default is not to search for a suitable LAPACK
library, and this is definitely @strong{not} recommended.  You can
specify a specific LAPACK library or a search for a generic library by
the configuration option @option{--with-lapack} without a value.  The
default for @option{--with-lapack} is to check the @acronym{BLAS}
library (for function @code{DPSTRF}) and then look for an external
library @samp{-llapack}.  Sites searching for the fastest possible
linear algebra may want to build a LAPACK library using the
ATLAS-optimized subset of LAPACK.  Similarly, @I{OpenBLAS} can be built to
contain an optimized subset of LAPACK or a full LAPACK (the latter
seeming to be the default).

A value for @option{--with-lapack} can be set @emph{via} the environment
variable
@enindex LAPACK_LIBS
@env{LAPACK_LIBS}, but this will only be used if @option{--with-lapack}
is specified and the @acronym{BLAS} library does not contain LAPACK.

Please bear in mind that using @option{--with-lapack} is provided
@strong{only} because it is necessary on some platforms and because some
users want to experiment with claimed performance improvements.  In
practice its main uses are without a value,

@itemize
@item
with an `enhanced' BLAS such as ATLAS, @I{FlexiBLAS}, @I{MKL} or @I{OpenBLAS} which
contains a full LAPACK (to avoid possible conflicts), or

@item
on Debian/Ubuntu systems to select the system @code{liblapack} which can
be switched by the `alternatives' mechanism.
@end itemize

If building LAPACK from its @I{Netlib} sources, be aware that @command{make}
with its supplied @file{Makefile} will make a @emph{static} library and
@R{} requires a shared/dynamic one.  To get one, use @command{cmake} as
documented briefly in @file{README.md}.  Something like (to build only
the double and double complex subroutines with 32-bit array indices),

@example
mkdir build
cd build
cmake \
-DCMAKE_INSTALL_PREFIX=/where/you/want/to/install \
-DCMAKE_BUILD_TYPE:STRING=Release \
-DBUILD_DEPRECATED=ON -DBUILD_SHARED_LIBS=ON \
-DBUILD_INDEX64_EXT_API:BOOL=OFF \
-DBUILD_SINGLE:BOOL=OFF -DBUILD_COMPLEX:BOOL=OFF \
-DLAPACKE=OFF -DCBLAS=OFF \
-S ..
make -j10
@end example
@noindent
This builds the reference BLAS and the reference LAPACK linked to it.

Note that @command{cmake} files do not provide an @code{uninstall}
target, but @file{build/install_manifest.txt} is a list of the files
installed, so you can remove them @emph{via} shell commands or from
@R{}.

If using @option{--with-lapack} to get a generic LAPACK (or allowing the
default to select one), consider also using @option{--with-blas} (with a
path if an enhanced BLAS is installed).


@node Caveats
@subsection Caveats

As with all libraries, you need to ensure that they and @R{} were
compiled with compatible compilers and flags.  For example, this has
meant that on Sun @I{Sparc} using the Oracle compilers the flag
@option{-dalign} is needed if @code{sunperf} is to be used.

On some systems it has been necessary that an external
@acronym{BLAS}/LAPACK was built with the same Fortran compiler used to
build @R{}.

BLAS and LAPACK libraries built with recent versions of
@command{gfortran} require calls from C/C++ to handle `hidden' character
lengths --- @R{} itself does so but many packages used not to and some
have segfaulted.  This was largely circumvented by using the Fortran
flag @option{-fno-optimize-sibling-calls} (formerly set by
@command{configure} if it detected @command{gfortran}@tie{}7 or later):
however use of the @R{} headers which include those character-length
arguments is no longer optional in packages.

LAPACK 3.9.0 (and probably earlier) had a bug in which the @code{DCOMBSSQ}
subroutine may cause NA to be interpreted as zero. This is fixed in the
@R{} 3.6.3 and later sources, but if you use an external LAPACK, you may
need to fix it there. (The bug was corrected in 3.9.1 and the routine
removed in 3.10.1.)

The code (in @code{dlapack.f}) should read
@example
*     ..
*     .. Executable Statements ..
*
      IF( V1( 1 ).GE.V2( 1 ) ) THEN
         IF( V1( 1 ).NE.ZERO ) THEN
            V1( 2 ) = V1( 2 ) + ( V2( 1 ) / V1( 1 ) )**2 * V2( 2 )
         ELSE
            V1( 2 ) = V1( 2 ) + V2( 2 )
         END IF
      ELSE
         V1( 2 ) = V2( 2 ) + ( V1( 1 ) / V2( 1 ) )**2 * V1( 2 )
         V1( 1 ) = V2( 1 )
      END IF
      RETURN
@end example
(The inner ELSE clause was missing in LAPACK 3.9.0.)

If you do use an external LAPACK, be aware of potential problems with
other bugs in the LAPACK sources (or in the posted corrections to those
sources), seen several times in Linux distributions over the years.  We
have even seen distributions with missing LAPACK routines from their
@code{liblapack}.

We rely on limited support in LAPACK for matrices with @math{2^{31}} or
more elements: it is possible that an external LAPACK will not have that
support.



@node Configuration on a Unix-alike
@appendix Configuration on a Unix-alike


@node Configuration options
@section Configuration options

@command{configure} has many options: running

@example
./configure --help
@end example

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

@table @option
@item --with-x
use the X Window System [yes]
@item --x-includes=@var{DIR}
X include files are in @var{DIR}
@item --x-libraries=@var{DIR}
X library files are in @var{DIR}
@item --with-readline
use @I{readline} library (if available) [yes]
@item --enable-R-profiling
attempt to compile support for @code{Rprof()} [yes]
@item --enable-memory-profiling
attempt to compile support for @code{Rprofmem()} and @code{tracemem()} [no]
@item --enable-R-shlib
build @R{} as a shared/dynamic library [no]
@item --enable-BLAS-shlib
build the @acronym{BLAS} as a shared/dynamic library [yes, except on @abbr{AIX}]
@end table

@noindent
You can use @option{--without-foo} or @option{--disable-foo} for the
negatives.

You will want to use @option{--disable-R-profiling} if you are building
a profiled executable of @R{} (e.g.@: with @samp{-pg)}.  Support for @R{}
profiling requires OS support for POSIX threads (@emph{aka}
@samp{pthreads}), which are available on all mainstream Unix-alike
platforms.

Flag @option{--enable-R-shlib} causes the make process to build @R{} as
a dynamic (shared) library, typically called @file{libR.so}, and link
the main @R{} executable @file{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
performance@footnote{We have measured 15--20% on @cputype{i686} Linux
and around 10% on @cputype{x86_64} Linux.} penalty.  So you probably
only want this if you will be using an application which embeds @R{}.
Note that C code in packages installed on an @R{} system linked with
@option{--enable-R-shlib} is linked against the dynamic library and so
such packages cannot be used from an @R{} system built in the default
way.  Also, because packages are linked against @R{} they are on some
OSes also linked against the dynamic libraries @R{} itself is linked
against, and this can lead to symbol conflicts.

For maximally effective use of @command{valgrind}, @R{} should be
compiled with @I{Valgrind} instrumentation. The @command{configure} option
is @option{--with-valgrind-instrumentation=@var{level}}, where
@var{level} is 0, 1 or 2.  (Level 0 is the default and does not add
anything.)  The system headers for @command{valgrind} are required: on
Linux they may be in a separate package such as @pkg{valgrind-devel}.

If you need to re-configure @R{} with different options you may need to run
@code{make clean} or even @code{make distclean} before doing so.

The @file{configure} script has other generic options added by
@command{autoconf} and which are not supported for @R{}: in particular
building for one architecture on a different host is not possible.


@node Internationalization support
@section Internationalization support

Translation of messages is supported via @acronym{GNU} @code{gettext}
unless disabled by the configure option @option{--disable-nls}.
The @code{configure} report will show @code{NLS} as one of the
`Additional capabilities' if support has been compiled in, and running
in an English locale (but not the @code{C} locale) will include

@example
  Natural language support but running in an English locale
@end example

@noindent
in the greeting on starting R.


@node Configuration variables
@section Configuration variables

@findex configure
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
@file{config.site} (which documents many of the variables you might want
to set: others can be seen in file @file{etc/Renviron.in}) or on the
command line as

@example
./configure @var{VAR}=@var{value}
@end example

@noindent
If you are building in a directory different from the sources, there can
be copies of @file{config.site} in the source and the build directories,
and both will be read (in that order).  In addition, if there is a file
@file{~/.R/config}, it is read between the @file{config.site} files in
the source and the build directories.

There is also a general @command{autoconf} mechanism for
@file{config.site} files, which are read before any of those mentioned
in the previous paragraph.  This looks first at a file specified by the
@enindex CONFIG_SITE
environment variable @env{CONFIG_SITE}, and if not is set at files such
as @file{/usr/local/share/config.site} and
@file{/usr/local/etc/config.site} in the area (exemplified by
@file{/usr/local}) where @R{} would be installed.

These variables are @emph{precious}, implying that they do not have to
be exported to the environment, are kept in the cache even if not
specified on the command line, checked for consistency between two
configure runs (provided that caching is used), and are kept during
automatic reconfiguration as if having been passed as command line
arguments, even if no cache is used.

See the variable output section of @code{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 @file{config.cache}, and it
is a good idea to remove that file (if it exists) before re-configuring.
Note that caching is turned @emph{off} by default: use the command line
option @option{--config-cache} (or @option{-C}) to enable caching.


@node Setting paper size
@subsection Setting paper size
@enindex R_PAPERSIZE
One common variable to change is @env{R_PAPERSIZE}, which defaults to
@samp{a4}, not @samp{letter}.  (Valid values are @samp{a4},
@samp{letter}, @samp{legal} and @samp{executive}.)

This is used both when configuring @R{} to set the default, and when
running @R{} to override the default.  It is also used to set the
paper size when making PDF manuals.

The configure default will most often be @samp{a4} if @env{R_PAPERSIZE}
is unset.  (If the program @command{paperconf} is found, present in many
Linux distributions,
@enindex PAPERSIZE
or the environment variable @env{PAPERSIZE} is set, these are used to
produce the default.)

@node Setting the browsers
@subsection Setting the browsers

@enindex R_BROWSER
Another precious variable is @env{R_BROWSER}, the default @HTML{}
browser, which should take a value of an executable in the user's path
or specify a full path.

@enindex R_PDFVIEWER
Its counterpart for PDF files is  @env{R_PDFVIEWER}.

@node Compilation flags
@subsection Compilation flags

If you have libraries and header files, e.g., for @acronym{GNU}
@I{readline}, in non-system directories, use the variables @code{LDFLAGS}
(for libraries, using @samp{-L} flags to be passed to the linker) and
@code{CPPFLAGS} (for header files, using @samp{-I} flags to be passed to
the C/C++ preprocessors), respectively, to specify these locations.
These default to @samp{-L/usr/local/lib} (@code{LDFLAGS},
@samp{-L/usr/local/lib64} on most 64-bit Linux OSes) and
@samp{-I/usr/local/include} (@code{CPPFLAGS}, but note that on most
systems @file{/usr/local/include} is regarded as a system include
directory and so instances in that macro will be skipped) to catch the
most common cases.  If libraries are still not found, then maybe your
compiler/linker does not support re-ordering of @option{-L} and
@option{-l} flags.
@c (years ago this was reported to be a problem on HP-UX with the native
@c @command{cc}).  
In this case, use a different compiler (or a front-end shell script
which does the re-ordering).

These flags can also be used to build a faster-running version of @R{}.
On most platforms using @command{gcc}, having @samp{-O3} in
@code{CFLAGS} and @code{FFLAGS} produces worthwhile
performance gains with @command{gcc} and @command{gfortran}, but may
result in a less reliable build (both segfaults and incorrect numeric
computations have been seen).  On systems using the @acronym{GNU} linker
(especially those using @R{} as a shared library), it is likely that
including @samp{-Wl,-O1} in @code{LDFLAGS} is worthwhile, and
@samp{'-Bdirect,--hash-style=both,-Wl,-O1'} is recommended at
@uref{https://lwn.net/Articles/192624/}.  Tuning compilation to a
specific @acronym{CPU} family (e.g.@: @samp{-mtune=native} for
@command{gcc}) can give worthwhile performance gains, especially on
older architectures such as @cputype{ix86}.

@node Making manuals
@subsection Making manuals

@enindex R_RD4PDF
@enindex R_PAPERSIZE
The default settings for making the manuals are controlled by
@env{R_RD4PDF} and @env{R_PAPERSIZE}.


@node Setting the shell
@section Setting the shell

By default the shell scripts such as @file{R} will be @samp{#!/bin/sh}
scripts (or using the @env{SHELL} chosen by @file{configure}).  This is
almost always satisfactory, but on a few systems @file{/bin/sh} is not a
@I{Bourne} shell or clone, and the shell to be used can be changed by
setting the configure variable @env{R_SHELL} to a suitable value (a full
path to a shell, e.g.@: @file{/usr/local/bin/bash}).


@node Using make
@section Using make
@findex make

To build in a separate directory you need a @command{make} that supports
the @code{VPATH} variable, for example @acronym{GNU} @command{make} and
@command{dmake}.

If you want to use a @command{make} by another name, for example if your
@acronym{GNU} @command{make} is called @samp{gmake}, you need to set the
variable @code{MAKE} at configure time, for example

@findex configure
@example
./configure MAKE=gmake
@end example


@node Using Fortran
@section Using Fortran
@cindex Fortran

To compile @R{}, you need a Fortran 90 compiler.  The current default
is to search for
@c From AC_PROG_FC
@command{gfortran}, @command{g95}, @command{xlf95} @command{f95},
@command{fort}, @command{ifort}, @command{ifc}, @command{efc},
@command{pgfortran}, @command{pgf95} @command{lf95}, @command{ftn},
@command{nagfor}, @command{xlf90}, @command{f90}, @command{pgf90},
@command{pghpf}, @command{epcf90}.  (Note that these are searched for by
name, without checking the standard of Fortran they support.)  The
command and flags used should support fixed-form Fortran with extension
@file{.f}: in the unusual case that a specific flag is needed for
free-form Fortran with extension @file{.f90} or @file{.f95}, this can be
specified as part of @code{FCFLAGS}.

The search mechanism can be changed using the configure variable
@code{FC} which specifies the command that runs the Fortran compiler.
If your Fortran compiler is in a non-standard location, you
@enindex PATH
should set the environment variable @env{PATH} accordingly before
running @command{configure}, or use the configure variable @code{FC} to
specify its full path.

If your Fortran libraries are in slightly peculiar places, you should
@enindex LD_LIBRARY_PATH
also look at @env{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 @code{integer} is equivalent to a C @code{int} pointer and
Fortran @code{double precision} is equivalent to a C @code{double}
pointer.  This is checked during the configuration process.

Some of the Fortran code makes use of @code{DOUBLE COMPLEX} and
@code{COMPLEX*16} variables.  This is checked for at configure time, as
well as its equivalence to the @code{Rcomplex} C structure defined in
@file{R_ext/Complex.h}.

@command{gfortran}@tie{}10 by default gives a compilation error for the
previously widespread practice of passing a Fortran array element where
an array is expected, or a scalar instead of a length-one array.  See
@uref{https://gcc.gnu.org/gcc-10/porting_to.html}. @command{gfortran}@tie{}12
errors in more cases of this.


@node Compile and load flags
@section Compile and load flags

A wide range of flags can be set in the file @file{config.site} or as
configure variables on the command line.  We have already mentioned

@table @code
@item CPPFLAGS
header file search directory (@option{-I}) and any other miscellaneous
options for the C and C++ preprocessors and compilers
@item LDFLAGS
path (@option{-L}), stripping (@option{-s}) and any other miscellaneous
options for the linker
@end table

@noindent
and others include

@table @code
@item CFLAGS
debugging and optimization flags, C
@item MAIN_CFLAGS
ditto, for compiling the main program (e.g.@: when profiling)
@item SHLIB_CFLAGS
for shared objects (no known examples)
@item FFLAGS
debugging and optimization flags, fixed-form Fortran
@item FCFLAGS
debugging and optimization flags, free-form Fortran
@item SAFE_FFLAGS
ditto for source files which need exact floating point behaviour
@item MAIN_FFLAGS
ditto, for compiling the main program (e.g.@: when profiling)
@item SHLIB_FFLAGS
for shared objects (no known examples)
@item MAIN_LDFLAGS
additional flags for the main link
@item SHLIB_LDFLAGS
additional flags for linking the shared objects
@item LIBnn
the primary library directory, @file{lib} or @file{lib64}
@item CPICFLAGS
special flags for compiling C code to be turned into a shared object
@item FPICFLAGS
special flags for compiling Fortran code to be turned into a shared object
@item CXXPICFLAGS
special flags for compiling C++ code to be turned into a shared object
@item DEFS
defines to be used when compiling C code in @R{} itself
@end table

@noindent
Library paths specified as @option{-L/lib/path} in @code{LDFLAGS} are
@enindex LD_LIBRARY_PATH
collected together and prepended to @env{LD_LIBRARY_PATH} (or your
system's equivalent), so there should be no need for @option{-R} or
@option{-rpath} flags.

Variables such as @env{CPICFLAGS} are determined where possible by
@command{configure}.  Some systems allows two types of PIC flags, for
example @samp{-fpic} and @samp{-fPIC}, and if they differ the first
allows only a limited number of symbols in a shared object.  Since @R{}
as a shared library has about 6200 symbols, if in doubt use the larger
version.

Other variables often set by @command{configure} include
@samp{MAIN_LDFLAGS}, @samp{SAFE_FFLAGS}, @samp{SHLIB_LDFLAGS} and
@samp{SHLIB_CXXLDFLAGS}: see file @file{config.site} in the sources for
more documentation on these and others.

To compile a profiling version of @R{}, one might for example want to
use @samp{MAIN_CFLAGS=-pg}, @samp{MAIN_FFLAGS=-pg},
@samp{MAIN_LDFLAGS=-pg} on platforms where @samp{-pg} cannot be used
with position-independent code.

@strong{Beware}: it may be necessary to set @code{CFLAGS} and
@code{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 @command{configure} will select additional flags for
@code{CFLAGS}, @code{CPPFLAGS} and @code{LIBS} in @code{R_XTRA_CFLAGS}
(and so on).  These are for options which are always required, for
example to force @acronym{IEC}@tie{}60559 compliance.


@node Maintainer mode
@section Maintainer mode

There are several files that are part of the @R{} sources but can be
re-generated from their own sources by configuring with option
@option{--enable-maintainer-mode} and then running @command{make} in the
build directory.  This requires other tools to be installed, discussed
in the rest of this section.

File @file{configure} is created from @file{configure.ac} and the files
under @file{m4} by @command{autoconf} and @command{aclocal} (part of the
@pkg{automake} package).  There is a formal version requirement on
@command{autoconf} of 2.72 or later, but it is unlikely that anything
other than the most recent versions@footnote{at the time of revision of
this para in early 2024, @pkg{autoconf-2.72} and
@pkg{automake-1.16.5}. Previously @pkg{autoconf-2.71} was used.}
have been thoroughly tested.

File @file{src/include/config.h} is created by @command{autoheader}
(part of @pkg{autoconf}).

Grammar files @file{*.y} are converted to C sources by an implementation
of @command{yacc}, usually @command{bison -y}: these are found in
@file{src/main} and @file{src/library/tools/src}.  It is known that
earlier versions of @command{bison} generate code which reads (and in
some cases writes) outside array bounds: @command{bison} 3.8.2 is
currently used.

The ultimate sources for package @pkg{compiler} are in its @file{noweb}
directory.  To re-create the sources from
@file{src/library/compiler/noweb/compiler.nw}, the command
@command{notangle} is required.  Some Linux distributions include this
command in package @pkg{noweb}.  It can also be installed from the
sources at @url{https://www.cs.tufts.edu/~nr/noweb/}@footnote{The links
there have proved difficult to access, in which case grab the copy
made available at
@uref{https://developer.r-project.org/noweb-2.11b.tgz}.}.  The package
sources are only re-created even in maintainer mode if
@file{src/library/compiler/noweb/compiler.nw} has been updated.

@c It is likely that in future creating @code{configure} will need the GNU
@c `autoconf archive' installed.  This can be found at
@c @c and it has moved to github!
@c @url{https://www.gnu.org/software/autoconf-archive/} and as a package
@c (usually called @pkg{autoconf-archive}) in most packaged distributions,
@c for example Debian, Fedora, OpenCSW, Homebrew and MacPorts.



@node Platform notes
@appendix Platform notes

This section provides some notes on building @R{} on different Unix-alike
platforms.  These notes are based on tests run on one or two systems in
each case with particular sets of compilers and support libraries.
Success in building @R{} depends on the proper installation and functioning
of support software; your results may differ if you have other versions
of compilers and support libraries.

Older versions of this manual contain notes on platforms such as
@I{HP-UX}, @abbr{IRIX}, Alpha/@I{OSF1} (for @R{} < 2.10.0, and support
has since been removed for all of these) and @abbr{AIX} (for @R{} < =
3.5.x) for which we have had no recent reports.

C macros to select particular platforms can be tricky to track down
(there is a fair amount of misinformation on the Web).  The Wiki
(currently) at @uref{https://sourceforge.net/p/predef/wiki/Home/}
can be helpful.  The @R{} sources have used (often in included software
under @file{src/extra})
@example
AIX: _AIX
Cygwin: __CYGWIN__
FreeBSD: __FreeBSD__
HP-UX: __hpux__, __hpux
IRIX: sgi, __sgi
Linux: __linux__
macOS: __APPLE__
NetBSD: __NetBSD__
OpenBSD: __OpenBSD__
Windows: _WIN32, _WIN64
Windows on 64-but ARM: _M_ARM64 or _WIN32 plus __aarch64__
@end example

Identifying compilers can be very tricky.  GCC defines @code{__GNUC__},
but so do other compilers claiming conformance with it, notably (@I{LLVM}
and Apple) @command{clang} and Intel compilers.  Further, some use the
value of @code{__GNUC__} for their version, not the version of GCC they
claim to be compatible with.@footnote{Most @command{clang}-based
compilers give @code{4}, but not those distributed by FreeBSD.  Intel's
@command{icx} reported @code{12} in 2023.}  @command{clang}-based
compilers define @code{__clang__}.  Both @I{LLVM} and Apple @command{clang}
define @code{__clang_major__} as a string giving their major version,
but for example Apple's 13.x.y is very different from @I{LLVM}'s 13.x.y.
And compilers based on @I{LLVM} @command{clang}, for example from Intel and
IBM, will define these.  Some of the included software uses
@code{__APPLE_CC__} to identify an Apple compiler (which used to include
Apple builds of GCC), but Apple @command{clang} is better identified by
the @code{__apple_build_version__} macro.


@node X11 issues
@section X11 issues

The @samp{X11()} graphics device is the one started automatically on
Unix-alikes (except most macOS builds) when plotting.  As its name
implies, it displays on a (local or remote) X server, and relies on the
services provided by the X server.

@cindex Cairo
The `modern' version of the @samp{X11()} device is based on @samp{cairo}
graphics and (in most implementations) uses @samp{fontconfig} to pick and
render fonts.  This is done on the server, and although there can be
selection issues, they are more amenable than the issues with
@samp{X11()} discussed in the rest of this section.

When X11 was designed, most displays were around 75dpi, whereas today
they are of the order of 100dpi or more.  If you find that X11()
is reporting@footnote{for example, @code{X11 font at size 14 could not
be loaded}.} missing font sizes, especially larger ones, it is likely
that you are not using scalable fonts and have not installed the 100dpi
versions of the X11 fonts.  The names and details differ by system, but
will likely have something like Fedora's
@example
xorg-x11-fonts-75dpi
xorg-x11-fonts-100dpi
xorg-x11-fonts-ISO8859-2-75dpi
xorg-x11-fonts-Type1
xorg-x11-fonts-cyrillic
@end example

@noindent
and you need to ensure that the @samp{-100dpi} versions are installed
and on the X11 font path (check via @command{xset -q}).  The
@samp{X11()} device does try to set a pointsize and not a pixel size:
laptop users may find the default setting of 12 too large (although very
frequently laptop screens are set to a fictitious dpi to appear like a
scaled-down desktop screen).

More complicated problems can occur in non-Western-European locales, so
if you are using one, the first thing to check is that things work in
the @code{C} locale.  The likely issues are a failure to find any fonts
or glyphs being rendered incorrectly (often as a pair of @acronym{ASCII}
characters).  X11 works by being asked for a font specification and
coming up with its idea of a close match.  For text (as distinct from
the symbols used by @I{plotmath}), the specification is the first element of
the option @code{"X11fonts"} which defaults to

@example
"-adobe-helvetica-%s-%s-*-*-%d-*-*-*-*-*-*-*"
@end example

If you are using a single-byte encoding, for example ISO 8859-2 in
Eastern Europe or @I{KOI8-R} in Russian, use @command{xlsfonts} to find an
appropriate family of fonts in your encoding (the last field in the
listing).  If you find none, it is likely that you need to install
further font packages, such as @samp{xorg-x11-fonts-ISO8859-2-75dpi} and
@samp{xorg-x11-fonts-cyrillic} shown in the listing above.

Multi-byte encodings (most commonly UTF-8) are even more complicated.
There are few fonts in @samp{iso10646-1}, the Unicode encoding, and they
only contain a subset of the available glyphs (and are often fixed-width
designed for use in terminals).  In such locales @emph{@I{fontset}s} are
used, made up of fonts encoded in other encodings.  If the locale you
are using has an entry in the @samp{XLC_LOCALE} directory (typically
@file{/usr/share/X11/locale}), it is likely that all you need to do is to
pick a suitable font specification that has fonts in the encodings
specified there.  If not, you may have to get hold of a suitable locale
entry for X11.  This may mean that, for example, Japanese text can be
displayed when running in @samp{ja_JP.UTF-8} but not when running in
@samp{en_GB.UTF-8} on the same machine (although on some systems many
UTF-8 X11 locales are aliased to @samp{en_US.UTF-8} which covers several
character sets, e.g.@: ISO 8859-1 (Western European), @I{JISX0208} (Kanji),
@I{KSC5601} (Korean), @I{GB2312} (Chinese Han) and @I{JISX0201} (Kana)).

On some systems scalable fonts are available covering a wide range of
glyphs.  One source is @I{TrueType}/@I{OpenType} fonts, and these can provide
high coverage.  Another is Type 1 fonts: the URW set of Type 1 fonts
provides standard typefaces such as Helvetica with a larger coverage of
Unicode glyphs than the standard X11 bitmaps, including Cyrillic.  These
are generally not part of the default install, and the X server may need
to be configured to use them.  They might be under the X11 @file{fonts}
directory or elsewhere, for example,

@example
/usr/share/fonts/default/Type1
/usr/share/fonts/ja/TrueType
@end example


@node Linux
@section Linux
@cindex Linux

Linux is the main development platform for @R{}, so compilation from the
sources is normally straightforward with the most common compilers and
libraries.@footnote{For example, @code{glibc}: other C libraries such as
@code{musl} (as used by Alpine Linux) have been used but are not
routinely tested.}

This section is about the GCC compilers:
@command{gcc}/@command{gfortran}/@command{g++}.

Recall that some package management systems (such as @acronym{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 @samp{-devel} or @samp{-dev}: you need both versions
installed.  So please check the @code{configure} output to see if the
expected features are detected: if for example @samp{readline} is
missing add the developer package.  (On most systems you will also need
@samp{ncurses} and its developer package, although these should be
dependencies of the @samp{readline} package(s).)  You should expect to
see in the @command{configure} summary

@example
  Interfaces supported:      X11, tcltk
  External libraries:        pcre2, readline, curl
  Additional capabilities:   PNG, JPEG, TIFF, NLS, cairo, ICU
@end example

When @R{} has been installed from a binary distribution there are
sometimes problems with missing components such as the Fortran
compiler.  Searching the @samp{R-help} archives will normally reveal
what is needed.

It seems that @cputype{ix86} Linux accepts non-PIC code in shared
libraries, but this is not necessarily so on other platforms, in
particular on 64-bit @acronym{CPU}s such as @cputype{x86_64}.  So care
can be needed with @acronym{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, @code{libpng},
@code{libjpeg} and @code{zlib}) which might be linked against.
Fortunately these are normally built as shared libraries with the
exception of the ATLAS @acronym{BLAS} libraries.

The default optimization settings chosen for @code{CFLAGS} etc are
conservative.  It is likely that using @option{-mtune} will result in
significant performance improvements on recent CPUs: one possibility is
to add @option{-mtune=native} for the best possible performance on the
machine on which @R{} is being installed.  It is also possible to
increase the optimization levels to @option{-O3}: however for many
versions of the compilers this has caused problems in at least one
@acronym{CRAN} package.

Do not use @option{-O3} with @command{gcc} 11.0 or 11.1: it @I{mis-compiles}
code resulting in plausible but
incorrect results.  (This was seen in package @CRANpkg{MASS} but has
been worked around there as from version 3.1-57.)

For comments on @cputype{ix86} builds (including 32-bit builds on
@cputype{x86_64}) see the version of this manual for @R{} 4.3.x.

To build a 64-bit version of @R{} on @cputype{ppc64} (also known as
@cputype{powerpc64}) with @command{gcc}@tie{}4.1.1, @I{Ei-ji Nakama} used

@example
CC="gcc -m64"
CXX="gxx -m64"
FC="gfortran -m64"
CFLAGS="-mminimal-toc -fno-optimize-sibling-calls -g -O2"
FFLAGS="-mminimal-toc -fno-optimize-sibling-calls -g -O2"
@end example

@noindent
the additional flags being needed to resolve problems linking against
@file{libnmath.a} and when linking @R{} as a shared library.

@c suggestion of https://gcc.gnu.org/wiki/FloatingPointMath
The setting of the macro @samp{SAFE_FFLAGS} may need some help.  It
should not need additional flags on platforms other than @cputype{68000}
(not likely to be encountered) and @cputype{ix86}.  For the latter, if
the Fortran compiler is GNU (@command{gfortran} or possibly
@command{g77}) the flags
@example
-msse2 -mfpmath=sse
@end example
@noindent
are added: earlier versions of @R{} added @option{-ffloat-store} and
this might still be needed if a @cputype{ix86} CPU is encountered
without SSE2 support.  Note that it is a @emph{replacement} for
@samp{FFLAGS}, so should include all the flags in that macro (except
perhaps the optimization level).

Additional compilation flags can be specified for added safety/security
checks.  For example Fedora adds

@example
-Werror=format-security -Wp,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS
-Fexceptions -fstack-protector-strong -fasynchronous-unwind-tables
-fstack-clash-protection -fcf-protection
@end example

@noindent
to all the C, C++ and Fortran compiler flags (even though
@code{_GLIBCXX_ASSERTIONS} is only for C++ in current GCC and
@code{glibc} and none of these are documented for @code{gfortran}).
Use of @code{_GLIBCXX_ASSERTIONS} will link @code{abort} and
@code{printf} into almost all C++ code, and @command{R CMD check
--as-cran} will warn.


@node Clang
@subsection Clang

@R{} has been built with Linux @cputype{ix86} and @cputype{x86_64} C and
C++ compilers (@uref{https://clang.llvm.org}) based on the Clang
front-ends, invoked by @code{CC=clang CXX=clang++}, together with
@command{gfortran}.  These take very similar options to the
corresponding GCC compilers.

This has to be used in conjunction with a Fortran compiler: the
@command{configure} code will remove @option{-lgcc} from @env{FLIBS},
which is needed for some versions of @command{gfortran}.

The current out-of-the-box default for @command{clang++} is to use the
C++ runtime from the installed @command{g++}.  Using the runtime from
the @url{https://libcxx.llvm.org/, @code{libc++}} project (Fedora @acronym{RPM}
@code{libcxx-devel}) @emph{via} @option{-stdlib=libc++} has also been
tested.

Recent versions have (optional when built) @abbr{OpenMP} support.@footnote{This
also needs the @abbr{OpenMP} runtime which has sometimes been distributed
separately.}

There are problems mixing @command{clang} 15.0.0 and later built as
default on Linux to produce PIE code and @command{gfortran} 11 or later,
which does not.  One symptom is that @command{configure} does not detect
@code{FC_LEN_T}, which can be overcome by setting
@example
FPIEFLAGS=-fPIE
@end example
@noindent
in @file{config.site}. (@command{configure} tries that value if it is
unset.)

@node flang
@subsection @I{flang}

The name @command{flang} has been used for two projects: this is about
the sub-project of @I{LLVM} which builds a Fortran compiler and runtime
libraries.  The compiler command was @command{flang-new} prior to
version 20.

The version in @I{LLVM} 16 and later was able to build @R{} on @cputype{x86_64} Linux
with
@example
FC=/path/to/flang
@end example
@noindent
with the matching @command{clang} used as the C compiler, and the build
passed @command{make check-all}.  There is also support for
@cputype{aarch64} and @cputype{ppc64le} Linux, but these have not been
tested with @R{}.


@c It is recommended to use C flag @option{-Wno-strict-prototypes}
@c (disabling a C23 feature) if using @code{-pedantic} in @command{clang}
@c 15.0.0 and later, as @R{} is not yet optimized for C23.  For more detail
@c see the release notes at
@c @uref{https://releases.llvm.org/15.0.0/tools/clang/docs/ReleaseNotes.html#id9},
@c under `improvements to diagnostics'..

@c This was about 'Classic Flang'.  The newer version is not
@c yet able to compile Fortran.
@c There is a project called @command{flang}
@c (@uref{https://github.com/flang-compiler/flang})) to develop a
@c Fortran compiler similar to clang but based on the Portland Group's front
@c end.  This needs something like
@c @example
@c FC=/usr/local/flang/bin/flang
@c LDFLAGS="-L/usr/local/flang/lib -L/usr/local/lib64"
@c @end example

@c Note that @command{flang} accepts all the flags which @command{clang}
@c does (the driver is a modified version of @command{clang}, and
@c @command{flang} is a symbolic link to @command{clang}), but does not
@c implement all of them for Fortran compilation: it also accepts most
@c PGI-style flags such as @option{-mp} for @abbr{OpenMP}.  It currently produces
@c few diagnostics even with @option{-Wall -pedantic}.

@c @command{flang}'s Fortran runtime is compiled against @abbr{OpenMP} and it
@c seems this conflicts with using @abbr{OpenMP} in @R{}.  So it may be necessary
@c to disable the latter by configuring @R{} using @option{--disable-openmp}.

@c It is not clear what architectures @command{flang} intends to support:
@c our experiments were done on @cputype{x86_64}.  At the time of writing
@c binary `releases' were available for that platform (called by them
@c @cputype{x86}) and @cputype{ppc64le}.

@node Intel compilers
@subsection Intel compilers

In late 2020 Intel revamped their C/C++ compilers (and later their
Fortran compiler) to use an @I{LLVM} back-end (and for the C/C++ compilers,
a modified version of @command{clang} as the front-end).  Those
compilers are only for @cputype{x86_64}: the earlier (now called
`Classic') C/C++ compilers were discontinued in late 2023 (and are covered in
the version of this manual for @R{} 4.3.x: the Fortran compiler
@command{ifort} remains part of the Fortran distribution)..

The compilers are now all under Intel's `@I{oneAPI}' brand. The revamped
ones are @command{icx}, @command{icpx} and @command{ifx}; they are
identified by the C/C++ macro @code{__INTEL_LLVM_COMPILER} (and do not
define @code{__INTEL_COMPILER}: they also define @code{__clang__} and
@code{__clang_major__}).

The C++ compiler uses the system's @code{libstdc++} as its runtime
library rather than @I{LLVM}'s @code{libc++}.

Standalone installers (which are free-of-charge) are available from
@uref{https://www.intel.com/content/www/us/en/developer/articles/tool/oneapi-standalone-components.html}:
they are also part of the @I{oneAPI} Base and HPC (for Fortran) toolkits.

We tried the compilers in @I{oneAPI} 2024.2.1 and 2023.x.y using (the paths
do differ by compiler version)
@example
IP=/path/to/compilers/bin/
CC=$IP/icx
CXX=$IP/icpx
FC=$IP/ifx
CFLAGS="-O3 -fp-model precise -Wall -Wstrict-prototypes"
C17FLAGS="-O3 -fp-model precise -Wall -Wno-strict-prototypes"
FFLAGS="-O3 -fp-model precise -warn all,noexternals"
FCFLAGS="-free -O3 -fp-model precise -warn all,noexternals"
CXXFLAGS="-O3 -fp-model precise -Wall"
LDFLAGS="-L/path/to/compilers/compiler/lib -L/usr/local/lib64"
@end example
@noindent
but the build segfaulted in the checks (in complex arithmetic in
@file{tests/lapack.R}).

Intel document building @R with @I{MKL}: for the Intel compilers this needed
something like
@example
MKL_LIB_PATH=/path/to/intel_mkl/mkl/lib/intel64
export LD_LIBRARY_PATH="$MKL_LIB_PATH"
MKL="-L$@{MKL_LIB_PATH@} -lmkl_intel_lp64 -lmkl_core -lmkl_sequential"
./configure --with-blas="$MKL" --with-lapack
@end example
@noindent
and the build passed its checks with @I{MKL} 2023.2.0 (but not 2024.x on the
hardware tested).  It may also be possible to use a compiler option like
@option{-qmkl=sequential}.

One quirk is that the Intel Fortran compilers do not accept @file{.f95}
files, only @file{.f90}, for free-format Fortran.  @command{configure}
adds @option{-Tf} which tells the compiler this is indeed a Fortran file
(and needs to immediately precede the file name), but @option{-free} is
needed to say it is free-format.  Hence setting the @code{FCFLAGS}
macro.
@c https://www.intel.com/content/www/us/en/docs/fortran-compiler/developer-guide-reference/2023-2/file-extensions.html

The compilers have many options: as the C/C++ and Fortran compilers have
different origins for their front-ends, there is little consistency in
their options.
@c https://www.intel.com/content/www/us/en/docs/dpcpp-cpp-compiler/developer-guide-reference/2023-2/compiler-options.html
@c https://www.intel.com/content/www/us/en/docs/fortran-compiler/developer-guide-reference/2023-2/compiler-options-001.html
(The C/C++ compilers support `all' @command{clang} options even if
undocumented for @command{icx}/@command{icpc}, such as
@option{-Wno-strict-prototypes} above, However it is unclear for which
version of @command{clang}: the Intel manual suggests checking
@command{icx -help}.)  The C/C++ compilers support clang-style
@abbr{LTO}: it is not clear if the Fortran one does.

@c https://community.intel.com/t5/Intel-C-Compiler/Troubles-with-getrusage-when-using-icx/m-p/1509374#M41116
For some earlier versions (including 2023.2.0) all CPU times in e.g.@:
@code{proc.time()} are reported as zero.  If you see this, uncomment the
@samp{INTEL_ICX_FIX} setting in @file{config.site} and re-build.

@c https://www.intel.com/content/www/us/en/docs/fortran-compiler/developer-guide-reference/2023-2/stand.html
The preferred Fortran standard for @command{ifx} can be set by one of
@option{-std90}, @option{-std95}, @option{-std03}, @option{-std08} or
@option{-std18} (and variants).  However, this is documented to only
affect warnings on non-standard features: the default is no such
warnings.

Warning to package maintainers: the Intel Fortran compiler interprets
comments intended for Visual Fortran@footnote{as the `Classic' compiler
has been known on Windows.} like
@c from package tseriesentropy 0.6-0
@example
!DEC$ ATTRIBUTES DLLEXPORT,C,REFERENCE,ALIAS:'kdenestmlcvb' :: kdenestmlcvb
@end example
@noindent
The @code{DLLEXPORT} gives a warning but the remainder silently
generates incorrectly named entry points.  Such comment lines need to be
removed from code for use with @R{} (even if using Intel Fortran on
Windows).


@c What this architecture is known as varies. The kernel is called
@c 'Darwin' and so autoconf uses 'apple-darwin<kernel version>' with
@c current architectures x86_64 and aarch64.
@c OTOH, 'file' reports architectures x86_64, arm64 and arm64e and
@c Apple's clang has a -target flag with values like
@c x86_64-apple-macos10.12 and arm64-apple-macos11
@c 'Activity monitor' reports the architectures as 'Intel' and 'Apple'


@node macOS
@section macOS
@cindex macOS

The instructions here are for `Apple Silicon' (@cputype{arm64}) or Intel
64-bit (@cputype{x86_64}) builds on macOS 11 (@I{Big Sur}), 12
(@I{Monterey)}, 13 (@I{Ventura}), 14 (@I{Sonoma}) and likely later.
(They may well work on Intel macOS 10.14 or 10.15, but are untested
there.)


@node Prerequisites
@subsection Prerequisites

The Apple silicon components install into @file{/opt/R/arm64}, the
Intel ones into @file{/opt/R/x86_64}.  That may not exist@footnote{it
will if @R{} has been installed from @acronym{CRAN} since @R{} 4.3.0.}
so it is simplest to first create the directory and adjust its ownership
if desired: for example by

@example
sudo mkdir -p /opt/R/arm64
sudo chown -R $USER /opt/R
@end example
@noindent
Also, add @file{/opt/R/arm64/bin} or @file{/opt/R/x86_64/bin} to your path.

Define an appropriate variable in your Terminal:
@example
set LOCAL=/opt/R/arm64  # Apple Silicon
set LOCAL=/opt/R/x86_64 # Intel
@end example
@noindent
to use the code snippets here.

The following are essential to build @R{}:

@itemize
@item 
Apple's `Command Line Tools': these can be (re-)installed by running
@command{xcode-select --install} in a terminal.

If you have a fresh OS installation, running e.g.@: @command{make} in a
terminal will offer the installation of the command-line tools.  If you
have installed @I{Xcode}, this provides the command-line tools.  The tools
may need to be reinstalled when macOS is upgraded, as upgrading may
partially or completely remove them.

The Command Line Tools provide C and C++ compilers derived from @I{LLVM}'s
@command{clang} but nowadays known as `Apple clang' with different
versioning (so Apple clang 15 is unrelated to @I{LLVM} clang 15).

@item
A Fortran compiler. @xref{Fortran compilers}.

@item
Binary components @code{pcre2}@footnote{If compiling it from source on
@cputype{arm64}, @code{pcre2} (at least up to version 10.39) needs to
be built without JIT support (the default) as the @R{} build segfaults
if that is enabled, so do run @code{make check} on your build.} and
@code{xz} (for @code{liblzma}) from
@uref{https://mac.r-project.org/bin/}.  There is an @R{} script there to
help with installing all the needed components.  (At the time of writing
@code{install.libs("r-base-dev")} installed neither @code{readline5} nor
those needed to support @I{Pango}.)

Intel users want the @code{darwin20} components: the @code{darwin17}
ones are for macOS 10.13--10.15.

Or this can be done manually, by for example
@example
curl -OL https://mac.r-project.org/bin/darwin20/arm64/pcre2-10.44-darwin.20-arm64.tar.xz
sudo tar -xvzf pcre2-10.44-darwin.20-arm64.tar.gz -C /
curl -OL https://mac.r-project.org/bin/darwin20/arm64/xz-5.6.3-darwin.20-arm64.tar.xz
sudo tar -xvzf xz-5.6.3-darwin.20-arm64.tar.xz -C /
@end example
@noindent
(@command{sudo} is not needed if your account owns @file{/opt/R/arm64} or
@file{/opt/R/x86_64} as appropriate.)

Messages like @samp{opt/R/: Can't restore time} should be ignored.
@end itemize
@noindent
and desirable
@itemize
@item
Component @code{readline5}.@footnote{For licence reasons this is version
5.2 of @code{readline}: for those who want a more recent version it is
straightforward to compile it from its sources.}  If @code{readline} is
not present, the emulation in Apple's version of @code{libedit} (aka
@code{editline}) will be used: if you wish to avoid that, configure with
@option{--without-readline}.

@item
Components @code{jpeg}, @code{libpng}, @code{pkgconfig}, @code{tiff} and
@code{zlib-system-stub} from @uref{https://mac.r-project.org/bin//} for
the full range of bitmapped graphics devices.  (Some builds of
@code{tiff} may require @code{libwebp} and/or @code{openjpeg}.)

@item
An X sub-system unless configuring using @option{--without-x}: see
@uref{https://www.xquartz.org/}. @R{}'s @command{configure}
script can be told to look for @code{X11} in @I{XQuartz}'s main
location of @file{/opt/X11}, e.g.@: by
@example
--x-includes=/opt/X11/include --x-libraries=/opt/X11/lib
@end example

Be wary of pre-release versions of @I{XQuartz}, which may be offered as an
update.

@item
An Objective-C compiler, as provided by @command{clang} in the Command
Line Tools: this is needed for the @code{quartz()} graphics device.

Use @option{--without-aqua} if you want a standard Unix-alike build:
apart from disabling @code{quartz()} and the ability to use the build
with @Rapp{}, it also changes the default location of the personal
library (see @code{?.libPaths}).

@item A Tcl/Tk installation,  @xref{ Tcl/Tk headers and libraries}.

@item
Support for Cairo-based graphics devices. @xref{Cairo graphics}.

@item
A TeX installation. @xref{Other libraries}.

@item
@command{texi2any} from a @I{Texinfo} distribution, which requires
@command{perl} (currently a default part of macOS but it has been
announced that it may not be in future).
@c macOS 10.15 release notes, but is in 11
@c https://developer.apple.com/documentation/macos-release-notes/macos-catalina-10_15-release-notes
A version of @command{texi2any} has been included in the binary
distribution of @R{} and there is a @samp{texinfo} component at
@uref{https://mac.r-project.org/bin/}.
@end itemize

To build @R{} itself from the sources with the C/C++ compilers in the
Command Line Tools (or @I{Xcode}) and @command{gfortran} from the installer
mentioned below, use a file @file{config.site} containing
@example
CC=clang
OBJC=$CC
FC="/opt/gfortran/bin/gfortran -mtune=native"
CPPFLAGS='-isystem $LOCAL/include'
CXX=clang++
@end example
@noindent
and configure by something like
@example
./configure -C \
--enable-R-shlib --enable-memory-profiling \
--x-includes=/opt/X11/include --x-libraries=/opt/X11/lib \
--with-tcl-config=$LOCAL/lib/tclConfig.sh \
--with-tk-config=$LOCAL/lib/tkConfig.sh \
PKG_CONFIG_PATH=$LOCAL/lib/pkgconfig:/usr/lib/pkgconfig
@end example
@noindent
(See below for other options for Tcl/Tk.)  For an @cputype{arm64} build
further flags are desirable in @file{config.site}:
@example
CFLAGS="-falign-functions=8 -g -O2"
@end example
@noindent
is needed to inter-work with @command{gfortran} without segfaulting in
some packages.  Some builds of @command{gfortran} have targetted the
current version of macOS (unlike @command{clang}), causing linker
warnings: to avoid these use
@example
FFLAGS="-g -O2 -mmacosx-version-min=11.0"
FCFLAGS="-g -O2 -mmacosx-version-min=11.0"
@end example
@noindent
or perhaps
@example
FFLAGS="-g -O2 -mmacos-version-min=11.0"
FCFLAGS="-g -O2 -mmacos-version-min=11.0"
@end example
@noindent
where @code{11.0} can be replaced by @code{12.0}, @code{13.0},
@code{14.0} or @code{15.0}

To install packages using compiled code one needs the Command Line Tools
(or @I{Xcode}) and appropriate compilers, e.g.@: the C/C++ compilers from
those tools and/or @command{gfortran}. Some packages have further
requirements such as component @command{pkgconfig} (and to set
@env{PKG_CONFIG_PATH=} as above).

@c svn was in CLT 11.3.1, even in the opensource.apple.com repository
A subversion client can be obtained from
@uref{https://mac.r-project.org/tools/}, for example by (Apple Silicon)
@example
curl -OL https://mac.r-project.org/tools/subversion-1.14.3-darwin.20-arm64.tar.gz
tar xf subversion-1.14.3-darwin.20-arm64.tar.gz 
sudo cp subversion-1.14.3-darwin-20-arm64/svn $LOCAL/bin
@end example
@noindent
or (Intel)
@example
curl -OL https://mac.r-project.org/tools/subversion-1.14.3-darwin15.6.tar.gz
tar xf subversion-1.14.3-darwin15.6.tar.gz
sudo cp subversion-1.14.3-darwin15.6/svn $LOCAL/bin
@end example

If building software or installing source packages with @command{cmake}
(or a non-Apple @command{make}) for `Apple Silicon' ensure it contains
the @cputype{arm64} architecture (use @command{file} to be sure).
Running Apple compilers from an @cputype{x86_64} executable will
generate @cputype{x86_64} code @dots{}.

@c If you have a build@footnote{For example, some Homebrew
@c distributions.} of @code{cairo} with dynamic libraries, you can add
@c option @option{--without-static-cairo} to the @command{configure} call
@c (it probably would work anyway).

Updating an @cputype{arm64} build may fail because of the bug described
at @uref{https://openradar.appspot.com/FB8914243} but @emph{ab initio}
builds work.  This has been far rarer since macOS 13.

If you are using the macOS 13 @abbr{SDK}@footnote{@command{ls -l `xcrun
-show-sdk-path`} in a terminal will show you which @abbr{SDK} is selected.},
you may need to add something like @code{-mmacos-version-min=12.0} to
@samp{CFLAGS}.

Linker warnings like
@example
ld: warning: could not create compact unwind for _sort_:
   register 26 saved somewhere other than in frame
ld: warning: ld: warning:
   could not create compact unwind for _arcoef_: registers 23 and 24 not saved contiguously in frame
ld: warning: could not create compact unwind for ___emutls_get_address:
   registers 23 and 24 not saved contiguously in frame
@end example
@noindent
can be ignored.  These stem from compiled Fortran code, including its
run-time libraries.

The default security settings can make it difficult to install Apple
packages which have not been `notarized'@footnote{See
@uref{https://developer.apple.com/documentation/xcode/notarizing_macos_software_before_distribution}.}
by Apple.  And not just packages, as this has been seen for executables
contained in tarballs/@I{zipfiles} (for example, for @command{pandoc}).
Usually one can use @samp{Open With} (Control/right/two-finger-click in
Finder), then select @samp{Installer} and @samp{Open} if you get a
further warning message.

If you run into problems with `quarantine' for tarballs downloaded in a
browser, consider using @command{curl -OL} to download (as illustrated
above) or @command{xattr -c} to remove extended attributes.

@command{configure} defaults to @option{--with-internal-tzcode} on
macOS.  The native implementation used to be unusable on earlier
versions (with a 32-bit @code{time_t} and/or timezone tables missing
information beyond the 32-bit range).  As from macOS 12.6, option
@option{--without-internal-tzcode} can be used to override this and @R{}
contains sufficient workarounds (for example, the native code fails to
recognize dates with a negative @code{tm_year}, that is dates before
1900) for @R{} to pass its checks.  However, there are discrepancies,
notably in Europe in the 1900s and 1940s, even though the Olson database
contains the correct information.

@node Fortran compilers
@subsection Fortran compiler

There is a `universal' (@code{arm64} and Intel) build of
@command{gfortran} 14.2 at
@uref{https://mac.r-project.org/tools/gfortran-14.2-universal.pkg}/
This installs into @file{/opt/gfortran}.

The @file{/opt/gfortran/SDK} symlink should point to the desired path to
the @abbr{SDK} (defaults to the command line tools @abbr{SDK}). This can be updated by
running @file{/opt/gfortran/bin/gfortran-update-sdk} or manually. If the
symlink is broken, the driver will issue a warning and use @code{xcrun
-show-sdk-path} to try to find an @abbr{SDK} and use its path.  (The @abbr{SDK} path
is used when using @command{gfortran} to link, so not when building @R{}
but when installing a few packages.)

Other builds of @command{gfortran} for @code{arm64} macOS 14 are
available at
@uref{https://github.com/fxcoudert/gfortran-for-macOS/releases}. To use
one of the pre-built compilers with Apple @command{clang} needs
something like
@example
LDFLAGS="-L/opt/R/arm64/lib -rpath /usr/local/gfortran/lib"
@end example
@noindent
in @file{config.site} to ensure the matching Fortran run-time libraries are
found.

@node Cairo graphics
@subsection Cairo graphics

@cindex Cairo
Cairo-based graphics devices such as @code{cairo_ps}, @code{cairo_pdf},
@code{X11(type = "cairo")} and the Cairo-based types of devices
@code{bmp} @code{jpeg}, @code{png} and @code{tiff} are not the default
on macOS, and much less used than the Quartz-based devices.  However,
the only SVG device in the @R{} distribution, @code{svg}, is based on
Cairo.

Support for Cairo is optional and can be added in several ways, all of
which need @code{pkg-config}. @command{configure} will add Cairo support
if @code{pkg-config} finds package @code{cairo} unless
@code{--without-cairo} is used.

A way to statically link Cairo is by downloading and unpacking
components @code{cairo}, @code{fontconfig}, @code{freetype},
@code{pixman} and @code{zlib-system-stub} (and do not have
@file{/opt/X11/lib/pkgconfig} in @env{PKG_CONFIG_PATH}).  Some static
builds of @code{fontconfig} need @code{libxml2} (from component
@code{xml2}) and others @code{expat}, supplied by macOS but needing a
file @file{$LOCAL/lib/pkgconfig/expat.pc} along the lines of
@example
Name: expat
Version: 2.2.8
Description: expat XML parser
URL: http://www.libexpat.org
Libs: -lexpat
Cflags: 
@end example
@noindent
Note that the list of components is liable to change: running
@command{pkg-config cairo --exists --print-errors} should tell you if
any others are required.

@c If you have XQuartz 2.7.x installed (not 2.8.x) and ensure XQuartz's
@c @code{pkg-config} files are found first on its configuration path, Cairo
@c will be linked dynamically.  This can be done by setting something like
@c @example
@c export PKG_CONFIG_PATH=/opt/X11/lib/pkgconfig:$LOCAL/lib/pkgconfig:/usr/lib/pkgconfig
@c @end example
@c @noindent
@c or by appending that variable to the @command{configure} command.  (Note
@c that this uses rather old versions of the graphics software.)

@c @c Homebrew is another with dynamic libraries
@c If you use XQuartz or another build of @code{cairo} with dynamic
@c libraries, you can add option @option{--without-static-cairo} to the
@c @command{configure} call (it may work without).
@c @c A possible issue is that --static will require the private
@c @c dependencies of fontconfig, usually either xml2 or expat, and a
@c @c dynamic installation might not have the pkg-config files for those.
@c @c Another issue seen in XQuartz 2.8.0 is that pkg-config requires
@c @c the private dependencies of cairo of which xproto is not included.

@cindex @I{Pango}
The best font experience of Cairo graphics will be to use it in
combination with @I{Pango} which will match that supported on most other
Unix-alikes.  @command{configure} uses @command{pkg-config} to determine
if all the external software required by both @I{Pango} and Cairo is
available: running @command{pkg-config pangocairo --exists
--print-errors} should show if the installation suffices and if not,
what is missing.  At the time of writing using pre-built components
@code{cairo}, @code{fontconfig}, @code{freetype}, @code{ffi},
@code{fribidi}, @code{gettext}, @code{icu}, @code{glib},
@code{harfbuzz}, @code{pango}, @code{pcre}, @code{pixman} and
@code{xml2} sufficed.

@node Other C/C++ compilers
@subsection Other C/C++ compilers

@c Un May 2024, 18.1.6 was the final release of that series, but the
@c latest binary build was 17.0.6.
Other pre-compiled distributions of @command{clang} may be available
from @uref{https://github.com/llvm/llvm-project/releases/} (recently
only for @code{arm64} and usually unsigned/not notarized which makes
them hard to use).  In particular, these include support for
@abbr{OpenMP} which Apple @command{clang} does not.

Suppose one of these distributions is installed under
@file{$LOCAL/llvm}. Use a file @file{config.site} containing
@example
SDK=`xcrun -show-sdk-path`
CC="$LOCAL/llvm/bin/clang -isysroot $SDK"
CXX="$LOCAL/llvm/bin/clang++ -isysroot $SDK"
OBJC=$CC
FC=/opt/gfortran/bin/gfortran
LDFLAGS="-L$LOCAL/llvm/lib -L$LOCAL/lib"
R_LD_LIBRARY_PATH=$LOCAL/llvm/lib:$LOCAL/lib
@end example

The care to specify library paths is to ensure that the @abbr{OpenMP} runtime
library, here @file{$LOCAL/llvm/lib/libomp.dylib}, is found when needed.
If this works, you should see the line
@example
checking whether OpenMP SIMD reduction is supported... yes
@end example
@noindent
in the @command{configure} output.  Also, @samp{R_LD_LIBRARY_PATH} needs
to be set to find the latest version of the C++ run-time libraries
rather than the system ones.

It is normally possible to build @R{} with GCC (built from the sources,
from a @command{gfortran} distribution, from @I{Homebrew}, @dots{}).
@c re-trested with GCC 14.1
When last tested it was not possible to use @command{gcc} to build the
@code{quartz()} device, so @command{configure --without-aqua} may be
required.  @R{} was built and tested with the GCC 14.2 compilers in the
@code{arm64} @command{gfortran} distribution mentioned above using a
@file{config.site} containing
@example
CC=/opt/gfortran/bin/gcc
CXX=/opt/gfortran/bin/g++
FC=/opt/gfortran/bin/gfortran
CFLAGS="-g -O2 -Wall -pedantic -Wstrict-prototypes"
C17FLAGS="-g -O2 -Wall -pedantic -Wno-strict-prototypes"
C90FLAGS=$C17FLAGS
C99FLAGS=$C17FLAGS
CXXFLAGS="-g -O2 -Wall -pedantic"
CPPFLAGS='-isystem /opt/R/arm64/include'
LDFLAGS=-L/opt/R/arm64/lib
@end example

It is usually possible to add some @abbr{OpenMP} support to the Apple
@command{clang} compilers: see @uref{https://mac.r-project.org/openmp/}.
Note that that approach is somewhat fragile as it needs a
@file{libomp.dylib} library matching the version of the compiler
used.

@node Other libraries
@subsection Other libraries


Pre-compiled versions of many of the @ref{Useful libraries and programs}
are available from @uref{https://mac.r-project.org/bin//}.


Looking at the top of
@file{/Library/Frameworks/R.framework/Resources/etc/Makeconf}
will show the compilers and configuration options used for the
@acronym{CRAN} binary package for @R{}: at the time of writing the
non-default options
@example
--enable-memory-profiling --enable-R-framework
--x-libraries=/opt/X11/lib --x-includes=/opt/X11/include
@end example
@noindent
were used. (@option{--enable-R-framework} implies @option{--enable-R-shlib}.)

The main @TeX{} implementation used by the developers is
@I{MacTeX}@footnote{An essentially equivalent @TeX{} installation can be
obtained by the Unix TeX Live installation scripts.}
(@uref{https://www.tug.org/mactex/}): the full installation is about
8.5GB, but a much smaller version (`Basic TeX') is available at
@uref{https://www.tug.org/mactex/morepackages.html} to which you will
need to add some packages to build @R{}, e.g.@: for the 2022 version we
needed to add@footnote{E.g.@: @emph{via} @command{tlmgr install helvetic
inconsolata texinfo} .} @pkg{helvetic}, @pkg{inconsolata} and
@pkg{texinfo} which brought this to about 310MB.@footnote{Adding all the
packages needed to check @acronym{CRAN} increased this to about 600MB.}
@samp{TeX Live Utility} (available @emph{via} the @I{MacTeX} front page)
provides a graphical means to manage @TeX{} packages.  These contain
executables which run natively on both @cputype{arm64} and
@cputype{x86_64}.

Checking packages thoroughly requires @I{Ghostscript} (part of the full
@I{MacTeX} distribution or separately from
@uref{https://www.tug.org/mactex/morepackages.html}) and @command{qpdf}
(from @uref{https://mac.r-project.org/bin//}, a version of which is in
the @file{bin} directory of a binary installation of @R{}, usually
@file{/Library/@/Frameworks/@/R.framework/@/Resources/@/bin/@/qpdf}).

@command{R CMD check --as-cran} makes use of `HTML Tidy'.  macOS at the
time of writing has a version in @file{/usr/bin/tidy} dating from 2006
which is far too old.  Up-to-date versions can be
installed from @uref{http://binaries.html-tidy.org/}.

One macOS quirk is that the default path has @file{/usr/local/bin} after
@file{/usr/bin}, contrary to common practice on Unix-alikes.  This means
that if you install tools from the sources they will by default be
installed under @file{/usr/local} and not supersede the system
versions.

Parallel installation of packages will make use of the utility
@command{timeout} if available.  A `universal'  build can be
downloaded from @uref{https://www.stats.ox.ac.uk/pub/bdr/timeout}: make
it executable (@code{chmod 755 timeout}) and put it somewhere on your
path.


@node Accelerate
@subsubsection @I{Accelerate}

@cindex BLAS library
@cindex LAPACK library
The @code{Accelerate}
library@footnote{@uref{https://developer.apple.com/documentation/accelerate}.}
can be used @emph{via} the configuration option

@example
--with-blas="-framework Accelerate"
@end example

@noindent
@c LAPACK in Accelerate was still 3.2.1 in macOS 13.6 and 14
to provide potentially higher-performance versions of the @acronym{BLAS}
and LAPACK routines.@footnote{It has been reported that for some
non-Apple toolchains @code{CPPFLAGS} needed to contain
@code{-D__ACCELERATE__}: not needed for @command{clang} from @I{LLVM}.}
This includes a full LAPACK which can be used @emph{via}
@option{--with-lapack}: however, the version of LAPACK it contains has
often been seriously old (and is not used unless @option{--with-lapack}
is specified).  Some @acronym{CRAN} builds of @R{} can be
switched@footnote{@url{https://cran.r-project.org/bin/macosx/RMacOSX-FAQ.html#Which-BLAS-is-used-and-how-can-it-be-changed_003f}}
to use @I{Accelerate}'s BLAS.

@c https://developer.apple.com/documentation/macos-release-notes/macos-13_3-release-notes
@c https://developer.apple.com/documentation/xcode-release-notes/xcode-14_3-release-notes
As from macOS 13.3, the BLAS and LAPACK libraries under the @I{Accelerate}
framework are `now inline with reference version
3.9.1'.@footnote{Released 2021-04-01.} However, this has been done by
naming new entry points and so only accessible @emph{via} their C
headers.  That version can be used for BLAS calls @emph{via}
@command{configure} option @option{--with-newAccelerate}: it requires at
least macOS 13.3 and @abbr{SDK} 13.3 (from @I{Xcode CLT} 14.3).  To use it for both
BLAS and LAPACK calls, configure with
@option{--with-newAccelerate=lapack}.  These options cannot be used with
others such as @option{--with-blas} and @option{--with-lapack}.

@c https://developer.apple.com/documentation/accelerate/veclib
Threading in @I{Accelerate} is controlled by `Grand Central
Dispatch'@footnote{E.g.,
@url{https://en.wikipedia.org/wiki/Grand_Central_Dispatch} .} and is
said not to need user control.  Test @file{nls.R} in package @pkg{stats}
has often failed with the @I{Accelerate} BLAS on Intel macOS.  All versions
of @I{Accelerate} show differences from the reference BLAS (and most others)
in the use of @code{NA} @emph{vs} @code{NaN} and a substantial number of
@R{} packages fail their checks.

@node OpenBLAS (macOS)
@subsubsection @I{OpenBLAS}

@R{} has been built on @cputype{arm64} using @I{OpenBLAS} 0.3.24 (sources
from @uref{https://github.com/OpenMathLib/OpenBLAS/releases}) by
symlinking @file{/opt/OpenBLAS/lib/libopenblas.dylib} to
@file{lib/libRblas.dylib} (see @ref{Shared BLAS}).

On macOS, a default build of @I{OpenBLAS} uses @code{pthreads} (as macOS
does not have @abbr{OpenMP}) with the number of threads controlled by
environment variable @env{OPENBLAS_NUM_THREADS}.  On an M1 Pro this
defaulted to 10 threads (there are 8 `performance' cores and 2
`efficiency cores`) and we saw a 9x speedup over the reference BLAS on a
large SVD (which was slightly faster than @I{Accelerate}).


@node Tcl/Tk headers and libraries
@subsection Tcl/Tk headers and libraries

If you plan to use the @code{tcltk} package for @R{}, you will need to
install a distribution of Tcl/Tk.  There are two alternatives.  If you
use @Rapp{} you will want to use X11-based Tcl/Tk (as used on other
Unix-alikes), which is installed under @file{$LOCAL/lib} as part of the @acronym{CRAN} binary for
@R{}.@footnote{Just that component can be selected from the installer
for @R{}: at the `Installation Type' screen select `Customise' and then
just the `Tcl/Tk 8.6.11' component.}  This may need @command{configure}
options
@example
--with-tcltk=$LOCAL/lib
@end example
or
@example
--with-tcl-config=$LOCAL/lib/tclConfig.sh
--with-tk-config=$LOCAL/lib/tkConfig.sh
@end example
Note that this requires a matching @I{XQuartz} installation.

There is also a native (`Aqua') version of Tcl/Tk which produces widgets
in the native macOS style: this will not work with @Rapp{} because of
conflicts over the macOS menu, but for those only using command-line
@R{} this provides a much more intuitive interface to Tk for experienced
Mac users.  Earlier versions of macOS came with an Aqua Tcl/Tk
distribution but these were often not at all recent versions of Tcl/Tk.
It is better to install Tcl/Tk 8.6.x from the sources@footnote{Configure
Tk with @option{--enable-aqua}.} or a binary distribution from
@uref{https://www.activestate.com/platform/supported-languages/tcl/}.
For the latter,
configure @R{} with
@example
--with-tcl-config=/Library/Frameworks/Tcl.framework/tclConfig.sh 
--with-tk-config=/Library/Frameworks/Tk.framework/tkConfig.sh
@end example

If you need to find out which distribution of Tk is in use at run time,
use
@example
library(tcltk)
tclvalue(.Tcl("tk windowingsystem"))  # "x11" or "aqua"
@end example

Note that some Tcl/Tk extensions only support the X11 interface: this
includes @code{Tktable} and the @acronym{CRAN} package
@CRANpkg{tkrplot}.

@node Java (macOS)
@subsection Java

@c The situation with Java support on macOS is messy,@footnote{For more
@c details see @uref{https://www.macstrategy.com/article.php?3}.} and
@c distribution of Java for all platforms changed in 2018.

macOS does not comes with an installed Java runtime (@abbr{JRE}) and a
macOS upgrade may remove one if already installed: it is intended to be
installed at first use.  Check if a @abbr{JRE} is installed by running
@command{java -version} in a @command{Terminal} window: if Java is not
installed this may prompt you to install it from Oracle@footnote{Oracle
Java has a restrictive licence, unlike distributions based on @I{OpenJDK}.}
(but see the next paragraph).  We recommend you install a version with
long-term support, e.g.@: 17 or 21@footnote{The planned next @I{LTS}
release is 25 in September 2025.  Java 8 @emph{aka} 1.8.0 is still
@I{LTS} but some packages require 11 or later.}  but not 18--20, 22--24
with a 6-month lifetime. 

The currently simplest way to install Java is from
@uref{https://adoptium.net, Adoptium}@footnote{which website works with
Safari but not some other browsers.}: this installs into an
Apple-standard location and so works with @command{/usr/bin/java}. Other
builds of @I{OpenJDK} are available from
@uref{https://www.azul.com/downloads/zulu-community/?os=macos&architecture=arm-64-bit&package=jdk}
and from @I{OpenJDK} at @uref{https://jdk.java.net/}, for which
@env{JAVA_HOME} may need to be set both when configuring @R{} and at
runtime.  Note that Java distribution sites may use unusual designations
for macOS CPUs such as @code{AArch64}, @code{x64} or @code{x86
64-bit}.


Binary distributions of @R{} are built against a specific version
(e.g.@: 11.0.18 or 17.0.1) of Java so
@example
sudo R CMD javareconf
@end example
@noindent
will likely be needed to be run before using Java-using packages.

To see what compatible versions of Java are currently installed, run the
appropriate one of
@example
/usr/libexec/java_home -V -a arm64
/usr/libexec/java_home -V -a x86_64
@end example
@noindent
If needed, set the environment variable @env{JAVA_HOME} to choose
between these, both when @R{} is built from the sources and when
@command{R CMD javareconf} is run.

Configuring and building @R{} both looks for a @abbr{JRE} and for support for
compiling @abbr{JNI} programs (used to install packages @CRANpkg{rJava} and
@CRANpkg{JavaGD}); the latter requires a @abbr{JDK} (Java @abbr{SDK}).  Most
distributions of Java 11 or later are of a full @abbr{JDK}.

The build process tries to fathom out what @abbr{JRE}/@abbr{JDK} to use,
but it may need some help, e.g.@: by setting environment variable
@env{JAVA_HOME}.  To select a build from @uref{https://adoptium.net,
Adoptium} set e.g.@:
@example
JAVA_HOME=/Library/Java/JavaVirtualMachines/temurin-21.jdk/Contents/Home
@end example
@noindent
in @file{config.site}.  For Java 21 from @uref{https://jdk.java.net/}
(which might no longer be available), use
@example
JAVA_HOME=/path/to/jdk-21.jdk/Contents/Home
@end example

@c For an @cputype{arm64} build, the earliest Java version which is
@c officially supported is 17.

@c jdk.java.net no longer has Java 11 nor 17 LTS builds.

Note that it is necessary to set the environment variable @env{NOAWT} to
@code{1} to install many of the Java-using packages.

@node Frameworks
@subsection Frameworks

The @acronym{CRAN} build of @R{} is installed as a framework, which is
selected by the option

@example
./configure --enable-R-framework
@end example
@noindent
(This is intended to be used with an Apple toolchain: others may not
support frameworks correctly but those from @I{LLVM} have done so.)

It is only needed if you want to build @R{} for use with the @Rapp{}
console, and implies @option{--enable-R-shlib} to build @R{} as a
dynamic library.  This option configures @R{} to be built and installed
as a framework called @file{R.framework}.  The default installation path
for @file{R.framework} is @file{/Library/Frameworks} but this can be
changed at configure time by specifying the flag
@option{--enable-R-framework[=@var{DIR}]} (or @option{--prefix}) or at
install time @emph{via}

@example
make prefix=/where/you/want/R.framework/to/go install
@end example

Note that installation as a framework is non-standard (especially to a
non-standard location) and Unix utilities may not support it (e.g.@: the
@command{pkg-config} file @file{libR.pc} will be put somewhere unknown
to @command{pkg-config}).

@node Building R.app
@subsection Building R.app

Building the @Rapp{} GUI console is a separate project, using @I{Xcode}.
Before compiling @Rapp{} make sure the current version of @R{} is
installed in @file{/Library/Frameworks/R.framework} and is working at the
command-line (this can be a binary install).

The current sources can be checked out by
@example
svn co https://svn.r-project.org/R-packages/trunk/Mac-GUI
@end example
@noindent
and built by loading the @code{R.xcodeproj} project (select the
@code{R} target and a suitable configuration), or from the command-line
by e.g.@:
@example
xcodebuild -target R -configuration Release
@end example
See also the @file{INSTALL} file in the checkout or directly at
@uref{https://svn.r-project.org/R-packages/trunk/Mac-GUI/INSTALL}.

@Rapp{} does not need to be installed in any specific way. Building
@Rapp{} results in the @Rapp{} bundle which appears as one @R{}
icon. This application bundle can be run from anywhere and it is
customary to place it in the @file{/Applications} folder.

@node Building binary packages
@subsection Building binary packages

@acronym{CRAN} macOS binary packages are distributed as tarballs with
suffix @file{.tgz} to distinguish them from source tarballs.  One can
@command{tar} an existing installed package, or use @command{R CMD
INSTALL --build}.

However, there are some important details.
@itemize

@item
Current @acronym{CRAN} macOS distributions are targeted at @I{Big Sur}
so it is wise to ensure that the compilers generate code that will run
on @I{Big Sur} or later.  With the recommended compilers we can use
@example
CC="clang -mmacos-version-min=11.0"
CXX="clang++ -mmacos-version-min=11.0"
FC="/opt//gfortran/bin/gfortran -mmacosx-version-min=11.0"
@end example
@noindent
or set the environment variable
@example
export MACOSX_DEPLOYMENT_TARGET=11.0
@end example

@item
Using the flag @option{-Werror=partial-availability} can help trigger
compilation errors on functionality not in @I{Big Sur}.

@item
Check that any compiled code is not dynamically linked to libraries only
on your machine, for example by using @command{otool -L} or
@command{objdump -macho -dylibs-used}.  This can include C++ and Fortran
run-time libraries under @file{/opt/R/x86_64/lib} or
@file{/opt/R/arm64/lib}: one can use @command{install_name_tool} to
point these at system versions or those shipped with @R{}, for example
@example
install_name_tool -change /usr/local/llvm/lib/libc++.1.dylib \
/usr/lib/libc++.1.dylib \
@var{pkg}.so

install_name_tool -change
/opt/gfortran/lib/gcc/aarch64-apple-darwin20.0/14.2.0/libgfortran.5.dylib \
/Library/Frameworks/R.framework/Resources/lib/libgfortran.5.dylib \
@var{pkg}.so

install_name_tool -change
/opt/gfortran/lib/gcc/aarch64-apple-darwin20.0/14.2.0/libquadmath.0.dylib \
/Library/Frameworks/R.framework/Resources/lib/libquadmath.0.dylib \
@var{pkg}.so
@end example

@noindent
(where the details depend on the compilers and @acronym{CRAN} macOS @R{}
release).

@item
For C++ code there is the possibility that calls will be generated to
entry points not in the system @file{/usr/lib/libc++.1.dylib}.  The
previous step allows this to be tested against the system library on the
build OS, but not against earlier ones.  It may be possible to
circumvent that by static linking to @file{libc++.a} and
@file{libc++abi.a} by something like
@example
SHLIB_CXXLD = /usr/local/llvm/bin/clang
PKG_LIBS = /usr/local/llvm/lib/libc++.a /usr/local/llvm/lib/libc++abi.a
@end example
@noindent
in @file{src/Makevars}.  It would also be possible to static link the
Fortran runtime libraries @file{libgfortran.a} and @file{libquadmath.a}
should the Fortran compiler have later versions (but @command{gfortran}
8--14 all have version @code{5}).
@end itemize
@noindent
The @acronym{CRAN} binary packages are built with the Apple compiler on
the oldest supported version of macOS, which avoids the first two and
any issues with C++ libraries.

@node Building for Intel on arm64
@subsection Building for Intel on @samp{arm64}

Should one want to build @R{} for Intel on an @cputype{arm64} @I{Big Sur}
Mac, add the target for the compilers:

@example
CC="clang -arch x86_64
OBJC=$CC
CXX="clang++ -arch x86_64"
FC="/opt//gfortran/bin/gfortran -arch x86_64 -mtune=native -mmacosx-version-min=11"
@end example

@noindent
and install the Fortran compiler and external software described above
for Intel builds (and have @file{/opt/R/x86_64/bin} before
@file{/opt/R/arm64/bin} in your path).

To set the correct architecture (which will be auto-detected as
@code{aarch64}), use something like

@example
/path/to/configure --build=x86_64-apple-darwin20
@end example

@node Installer
@subsection Installer

The scripts for the @acronym{CRAN} packaging of @R{} can be found under
@uref{https://svn.r-project.org/R-dev-web/trunk/QA/Simon/R4/}: start
with the @file{README} file in that directory.


@node FreeBSD
@section FreeBSD
@cindex FreeBSD

There have been few recent reports on FreeBSD: there is a `port' at
@uref{https://svnweb.freebsd.org/ports/head/math/R}, currently last
updated for @R{} 4.0.4.  Recent versions of FreeBSD use Clang and the
@code{libc++} C++ headers and runtime, but the `port' has been
configured to use GCC.

Use of ICU for collation and the @command{configure} option
@option{--with-internal-tzcode} are desirable workarounds.


@node OpenBSD
@section @I{OpenBSD}
@cindex @I{OpenBSD}

@I{Ingo Feinerer} installed @R{} version 3.2.2 on OpenBSD 5.8 arch
@cputype{amd64} (their name for @cputype{x86_64}).  Details of the build
(and patches applied) are at
@uref{https://cvsweb.openbsd.org/cgi-bin/cvsweb/ports/math/R/},
currently updated for @R{} 4.2.3.


@node Cygwin
@section @I{Cygwin}

The 32-bit version never worked well enough to pass @R{}'s @command{make
check}, and residual support from earlier experiments was removed in
@R{} 3.3.0.

The 64-bit version was never supported.


@node New platforms
@section New platforms

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

@strong{Floating Point Arithmetic}: @R{} requires arithmetic compliant
with @acronym{IEC}@tie{}60559, also known as @acronym{IEEE}@tie{}754.
This mandates the use of plus and minus infinity and @code{NaN} (not a
number) as well as specific details of rounding.  Although almost all
current @abbr{FPU}s 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; @I{Sun/Sparc}, @I{SGI/IRIX} and @cputype{ix86} Linux require no
special action, FreeBSD requires a call to (the macro)
@code{fpsetmask(0)} and @I{OSF1} required that computation be done with a
@option{-ieee_with_inexact} flag etc. With Intel compilers on 32-bit and
64-bit Intel machines, one has to explicitly disable flush-to-zero and
@I{denormals-are-zero} modes.  Some ARM processors including A12Z and M1
(Apple Silicon) by default use @I{runfast} mode, which includes
flush-to-zero and @I{default-nan} and hence has to be disabled.  With
@I{default-nan} mode, the NaN payload used for representation of numeric NA
values is lost even on simple operations with finite values. 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 @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
@acronym{IEEE} model.  For example, using @option{-fast} on the Oracle
compilers has caused @R{}'s @code{NaN} to be set incorrectly, and
@command{gcc}'s @option{-ffast-math} and @command{clang}'s
@option{-Ofast} have given incorrect results.

@strong{Shared Objects}: There seems to be very little agreement
across platforms on what needs to be done to build shared objects.
there are many different combinations of flags for the compilers and
loaders.  @acronym{GNU} @I{libtool} cannot be used (yet), as it currently
does not fully support Fortran: one would need a shell wrapper for
this).  The technique we use is to first interrogate the X window system
about what it does (using @command{xmkmf}), and then override this in
situations where we know better (for tools from the @acronym{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 @command{cc} and @command{ld} usually reveals the
correct incantation.  Once you know the recipe you can modify the file
@file{config.site} (following the instructions therein) so that the
build will use these options.

It seems that @command{gcc}@tie{}3.4.x and later on @cputype{ix86} Linux
defeat attempts by the LAPACK code to avoid computations entirely in
extended-precision registers, so file @file{src/modules/lapack/dlamc.f}
may need to be compiled without optimization or with additional flags.
Set the configure variable @env{SAFE_FFLAGS} to the flags to be used for
this file.

If you do manage to get @R{} running on a new platform please let us
know about it so we can modify the configuration procedures to include
that platform.

If you are having trouble getting @R{} to work on your platform please
feel free to use the @samp{R-devel} mailing list to ask questions.  We
have had a fair amount of practice at porting @R{} to new platforms
@enddots{}

One thing you might want to add for a new platform is the mapping of
C/C++/Fortran calls to entry point names used for @command{R CMD check}.
See @uref{https://svn.r-project.org/R-dev-web/trunk/sotools.txt} for how
to do so.


@node Function and variable index
@unnumbered Function and variable index

@printindex vr


@node Concept index
@unnumbered Concept index

@printindex cp


@node Environment variable index
@unnumbered Environment variable index

@printindex en


@bye

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