Chapter 16 Environment variable index

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Index Entry

 

Section


B

BINPREF:

 

Windows packages

BINPREF64:

 

Windows packages

BLAS_LIBS:

 

BLAS


C

CC:

 

Using FORTRAN

CONFIG_SITE:

 

Configuration variables

CPP:

 

Using FORTRAN

CYGWIN:

 

The command line tools


D

DESTDIR:

 

Installation

DESTDIR:

 

Unix-alike standalone


F

F2C:

 

Using FORTRAN

F2CLIBS:

 

Using FORTRAN

FPICFLAGS:

 

Using FORTRAN


J

JAVA_HOME:

 

Java support


L

LANG:

 

Localization of messages

LANGUAGE:

 

Localization of messages

LANGUAGE:

 

Localization of messages

LAPACK_LIBS:

 

LAPACK

LC_ALL:

 

Localization of messages

LC_COLLATE:

 

Testing a Unix-alike Installation

LC_MESSAGES:

 

Localization of messages

LD_LIBRARY_PATH:

 

Unix-alike standalone

LD_LIBRARY_PATH:

 

ACML

LD_LIBRARY_PATH:

 

Using FORTRAN

LD_LIBRARY_PATH:

 

Compile and load flags

LD_LIBRARY_PATH:

 

Using gcc

LOCAL_SOFT:

 

Windows packages


O

OBJECT_MODE:

 

AIX


P

PAPERSIZE:

 

Setting paper size

PATH:

 

Essential programs and libraries

PATH:

 

Using FORTRAN

PATH:

 

AIX

PATH:

 

The Windows toolset


R

R_ARCH:

 

Sub-architectures

R_ARCH:

 

Sub-architectures

R_BROWSER:

 

Setting the browsers

R_DEFAULT_PACKAGES:

 

Default packages

R_DISABLE_HTTPD:

 

Help options

R_GSCMD:

 

Useful libraries and programs

R_INSTALL_TAR:

 

Windows packages

R_JAVA_LD_LIBRARY_PATH:

 

Java support

R_JAVA_LD_LIBRARY_PATH:

 

Java support

R_LIBS:

 

Add-on packages

R_LIBS_SITE:

 

Managing libraries

R_LIBS_USER:

 

Managing libraries

R_PAPERSIZE:

 

Making the manuals

R_PAPERSIZE:

 

Running R

R_PAPERSIZE:

 

Setting paper size

R_PAPERSIZE:

 

Making manuals

R_PDFVIEWER:

 

Setting the browsers

R_RD4PDF:

 

Making the manuals

R_RD4PDF:

 

Making manuals

R_RD4PDF:

 

LaTeX

R_SHELL:

 

AIX

R_USER:

 

Running R


T

TAR:

 

Essential programs and libraries

TAR_OPTIONS:

 

Getting and unpacking the sources

TAR_OPTIONS:

 

Getting the source files

TEMP:

 

Running R

TMP:

 

Running R

TMPDIR:

 

Simple compilation

TMPDIR:

 

Building the core files

TMPDIR:

 

Running R

TMPDIR:

 

Running R

TMPDIR:

 

Installing packages


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Footnotes

(1)

e.g. GNU tar version 1.15 or later, or that from the ‘libarchive’ (as used on macOS versions 10.6 and later) or ‘Heirloom Toolchest’ distributions.

(2)

for some Subversion clients ‘http:’ may appear to work, but requires continual redirection.

(3)

Most aspects will work with paths containing spaces, but external software used by R, e.g. texi2dvi version 4.8, may not.

(4)

which use lib rather than lib64 for their primary 64-bit library directories.

(5)

Instructions on how to install the latest version are at https://www.ctan.org/tex-archive/fonts/inconsolata/.

(6)

on a Unix-alike, ‘inconsolata’ is omitted if not found by configure.

(7)

This will be needed if more than one sub-architecture is to be installed.

(8)

with possible values ‘i386’, ‘x64’, ‘32’ and ‘64’.

(9)

mainly on RedHat and Fedora, whose layout is described here.

(10)

How to prepare such a directory is described in file src/extra/tzone/Notes in the R sources.

(11)

for example, -fopenmp, -xopenmp or -qopenmp. This includes for clang 3.7.x and the Intel C compiler.

(12)

Currently this is a valid option for g++ 5 and later and 2016 versions of the Intel and Solaris compilers. For earlier versions of g++ one could try -std=c++1y.

(13)

This is true for earlier versions of g++ such as 4.2.1, and also for commonly-used versions of the Solaris compiler CC.

(14)

Currently only GCC 6 and later, but this has been mooted for others.

(15)

For when features were supported, see https://gcc.gnu.org/projects/cxx-status.html#cxx11.

(16)

Suitable distributions include Strawberry Perl, http://strawberryperl.com/ and ActivePerl, https://www.activestate.com/activeperl.

(17)

The installer as puts links to R and Rscript in /usr/local/bin. If these are missing, you can run directly the copies in /Library/Frameworks/R.framework/Resources/.

(18)

The framework for R 3.3.x was named org.r-project.R.mavericks.fw.pkg: use pkgutil –pkgs | grep org.r-project to check for earlier versions of R.

(19)

More precisely, of the package of the same name: this means that installing a package for 3.3.x does 3.4.x does not remove an installation of the other series.

(20)

unless they were excluded in the build.

(21)

its binding is locked once the startup files have been read, so users cannot easily change it.

(22)

If a proxy needs to be set, see ?download.file.

(23)

for a small number of CRAN packages where this is known to be safe and is needed by the autobuilder this is the default. Look at the source of tools:::.install_packages for the list. It can also be specified in the package’s DESCRIPTION file.

(24)

or by adding it in a file such as etc/i386/Makevars.site, which does not exist by default.

(25)

Note that capitalization and version may differ from the Open Source project.

(26)

using a path containing spaces is likely to cause problems

(27)

They need to have been created using -headerpad_max_install_names, which is the default for an R package.

(28)

‘X/Open Portability Guide’, which has had several versions.

(29)

On some systems setting LC_ALL or LC_MESSAGES to ‘C’ disables LANGUAGE.

(30)

If you try changing from French to Russian except in a UTF-8 locale, you will most likely find messages change to English.

(31)

the language written in England: some people living in the USA appropriate this name for their language.

(32)

with Americanisms.

(33)

also known as IEEE 754

(34)

at least when storing quantities: the on-FPU precision is allowed to vary

(35)

e.g. Bessel, beta and gamma functions

(36)

including copying MkRules.dist to MkRule.local and selecting the architecture.

(37)

also known as IEEE 754

(38)

Note that C11 compilers need not be C99-compliant: R requires support for double complex and variable-length arrays which are optional in C11 but is mandatory in C99.

(39)

Examples are -std=gnu99, -std=c99 and -c99.

(40)

-std=c99 excludes POSIX functionality, but config.h will turn on all GNU extensions to include the POSIX functionality for R itself: this does not apply to badly-written packages. The default mode for GCC 5.1 and later is -std=gnu11, which currently includes the optional features R needs.

(41)

However, it is possible to break the default behaviour of glibc by re-specifying the gconv modules to be loaded.

(42)

specifically, the C99 functionality of headers wchar.h and wctype.h, types wctans_t and mbstate_t and functions mbrtowc, mbstowcs, wcrtomb, wcscoll, wcstombs, wctrans, wctype, and iswctype.

(43)

including opendir, readdir, closedir, popen, stat, glob, access, getcwd and chdir system calls, select on a Unix-alike, and either putenv or setenv.

(44)

such as realpath, symlink.

(45)

most often distributed as part of xz: possible names in Linux distributions include xz-devel/xz-libs and liblzma-dev.

(46)

sometimes known as PCRE1, and not PCRE2 which started at version 10.0.

(47)

but not a major version greater than 7 should there ever be one: the major version has been 7 since 2000.

(48)

for example to specify static linking with a build which has both shared and static libraries.

(49)

Such as GNU tar 1.15 or later, bsdtar (from https://github.com/libarchive/libarchive/, as used by FreeBSD and OS X 10.6 and later) or tar from the Heirloom Toolchest (http://heirloom.sourceforge.net/tools.html).

(50)

texi2dvi is normally a shell script. Some versions (including that from texinfo 5.2 and 6.0) need to be run under bash rather than a Bourne shell, especially on Solaris. Some of the issues which have been observed with broken versions of texi2dvi can be circumvented by setting the environment variable R_TEXI2DVICMD to the value emulation.

(51)

If necessary the path to pkg-config can be specified by setting PKGCONF in config.site, on the configure command line or in the environment.

(52)

also known as ttf-mscorefonts-installer in the Debian/Ubuntu world: see also https://en.wikipedia.org/wiki/Core_fonts_for_the_Web.

(53)

ttf-liberation in Debian/Ubuntu.

(54)

This is true even for the ‘Aqua’ version of Tk on macOS, but distributions of that include a copy of the X11 files needed.

(55)

Using the Oracle Developer Studio cc and f95 compilers

(56)

and ‘i686’ for earlier versions.

(57)

We have measured 15–20% on ‘i686’ Linux and around 10% on ‘x86_64’ Linux.

(58)

We believe that versions 3.4.0 to 3.10.1 are compatible.

(59)

On HP-UX fort77 is the POSIX compliant FORTRAN compiler, and comes after g77.

(60)

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

(61)

at the time of revsion of this para in 2017, autoconf-2.69 from 2012 and automake-1.15 from 2015.

(62)

The links there have proved difficult to access, in which case either point an FTP client at ftp://www.eecs.harvard.edu/pub/nr/ or grab the copy made available at http://developer.r-project.org/noweb-2.11b.tgz.

(63)

for example, X11 font at size 14 could not be loaded.

(64)

For example, glibc: other C libraries such as musl have been used but are not routinely tested.

(65)

or -mtune=corei7 for Intel Core i3/15/17 with gcc ≥ 4.6.0.

(66)

This also needs the OpenMP runtime which has sometimes been distributed separately.

(67)

It will be necessary to install later versions of software such as libcurl.

(68)

Apple provides a partial emulation of GNU readline 4.2 based on the NetBSD editline library. That is not recommended but for the time being R’s installation scripts will make use of it if GNU readline is not found.

(69)

These days that is defined by Apple’s implementation of clang, so it is strongly recommended to use that.

(70)

Some of these are unsigned packages: to install them you may need to right-click and select Open with -> Installer.

(71)

It was reported that for some non-Apple toolchains CPPFLAGS needed to contain -D__ACCELERATE__: not needed for clang 4.0.0, though.

(72)

E.g. via tlmgr install cm-super helvetic inconsolata texinfo .

(73)

This is not the case if the non-default configure option –without-internal-tzcode was used – but R then does not pass its checks.

(74)

For more details see http://www.macstrategy.com/article.php?3.

(75)

In the unlikely event that the version reported does not start with 1.8.0 you need to update your Java.

(76)

Oracle Solaris Studio prior to 2016, and previously Sun Studio.

(77)

using the -V flag.

(78)

When last checked it failed in tests/reg-BLAS.R, and on some builds, including for ‘amd64’, it failed in example(eigen).

(79)

In particular, header cmath in C++11 mode includes math.h and iso/math_c99.h and gcc had ‘fixed’ an earlier version of the latter.

(80)

For example, the Cygwin version of make 3.81 fails to work correctly.

(81)

such as sort, find and perhaps make.