Commit 9dd66229 authored by Dirk Eddelbuettel's avatar Dirk Eddelbuettel

Import Upstream version 3.1.3

parent c917ea8b
Revision: 66913
Last Changed Date: 2014-10-31
Revision: 67962
Last Changed Date: 2015-03-09
Pumpkin Helmet
Smooth Sidewalk
......@@ -40,9 +40,9 @@
## The command which runs the C compiler.
## If unspecified, a search is made for gcc and cc (in that order).
## To override this choice, specify the name of the command which runs
## the compiler here, for example 'c99'.
## It is also convenient to set the architecture here, e.g. 'gcc -m32'.
## To override this choice, specify the name or path of the command
## which runs the compiler, for example 'c99'.
## It is also necessary to set the architecture here, e.g. 'gcc -m32'.
## CC=
## Debugging and optimization options for the C compiler.
......@@ -107,7 +107,7 @@
## The flags which are necessary for loading main program which will
## load DLLs at runtime. HP-UX and Linux-elf are examples of platforms
## which use this. These platforms are already taken care of by
## which use this. Those platforms are already taken care of by
## configure, and anything set here will be in addition unless MAIN_LD
## is given.
## For example, one can set flags for profiling here.
......@@ -205,7 +205,7 @@
## Default setting for the R_BROWSER env variable
## If unset configure searches in turn for (currently)
## firefox mozilla galeon opera xdg-open kfmclient gnome-moz-remote open
## and uses the full path.
## and uses the full path of the first it finds.
## R_BROWSER=
## BLAS and LAPACK settings
......@@ -219,12 +219,12 @@
## it is not used if the BLAS already contains LAPACK.
## LAPACK_LIBS=
## Make name.
## Make name or path
## Set this if you want to use a make by another name.
## For example, if your GNU make is called 'gmake', use 'MAKE=gmake'.
## MAKE=
## Tar name
## Tar name or path
## Set this to prefer a tar which has the capability to automagically
## read compressed archives. The default is to choose 'gtar' or
## 'gnutar'(normally GNU tar) then 'tar'.
......
This diff is collapsed.
......@@ -30,7 +30,7 @@ m4_define([R_VERSION],
m4_bpatsubst(m4_esyscmd([cat VERSION]),
[\([0-9.]*\)\(\w\|\W\)*],
[\1]))
AC_INIT([R],[R_VERSION],[http://bugs.r-project.org],[R],[http://www.r-project.org])
AC_INIT([R],[R_VERSION],[https://bugs.r-project.org],[R],[https://www.r-project.org])
AC_CONFIG_SRCDIR([src/include/Defn.h])
AC_CONFIG_AUX_DIR([tools])
......@@ -434,7 +434,7 @@ AC_ARG_WITH([system-xz],
## Valgrind instrumentation
AC_ARG_WITH([valgrind-instrumentation],
[AS_HELP_STRING([--with-valgrind-instrumentation],[Level of additional instrumentation for Valgrind (0/1/2) @<:@0@:>@])],
[AS_HELP_STRING([--with-valgrind-instrumentation],[Level of additional instrumentation for Valgrind (0/1/2/3) @<:@0@:>@])],
[valgrind_level=${withval}],
[valgrind_level=0])
......@@ -2060,13 +2060,6 @@ if test "x${r_cv_have_tm_gmtoff}" = xyes; then
AC_DEFINE(HAVE_TM_GMTOFF, 1, [Define to 1 if your 'struct tm' has tm_gmtoff.])
fi
## check for vecLib framework (potentially to be used for BLAS)
## in theory vecLib is platform-independent, in practice only
## Apple's OS X is known to provide it
## However, as from 10.10 it only provides Accelerate.
R_CHECK_FRAMEWORK(cblas_cdotu_sub, Accelerate)
## BLAS.
## <NOTE>
## This has to come *after* checking for Fortran 77 compiler/converter
......@@ -2331,7 +2324,8 @@ AC_FUNC_FSEEKO
if test ${valgrind_level} -eq 0; then
AC_DEFINE(NVALGRIND, 1, [Define to disable Valgrind instrumentation])
fi
AC_DEFINE_UNQUOTED(VALGRIND_LEVEL, ${valgrind_level}, [Define as 1 or 2 to specify levels of Valgrind instrumentation])
AC_DEFINE_UNQUOTED(VALGRIND_LEVEL, ${valgrind_level}, [Define as 1, 2 or 3 to specify levels of Valgrind instrumentation])
if test x${use_internal_tzcode} = xdefault; then
case "${host_os}" in
......@@ -2826,9 +2820,21 @@ if test "${acx_lapack_ok}" = "yes"; then
esac
R_SH_VAR_ADD(r_external_libs, [LAPACK(${r_lapack})], [, ])
fi
if test "${have_zlib}" = yes; then
R_SH_VAR_ADD(r_external_libs, [zlib], [, ])
fi
if test "${have_bzlib}" = yes; then
R_SH_VAR_ADD(r_external_libs, [bzlib], [, ])
fi
if test "${have_lzma}" = yes; then
R_SH_VAR_ADD(r_external_libs, [lzma], [, ])
fi
if test "${have_pcre}" = yes; then
R_SH_VAR_ADD(r_external_libs, [PCRE], [, ])
fi
if test "${have_tre}" = yes; then
R_SH_VAR_ADD(r_external_libs, [tre], [, ])
fi
r_capabilities=
r_no_capabilities=
......
......@@ -33,3 +33,6 @@ Stefano Iacus up to July 2014.
Current R-core members can be contacted via email to R-project.org
with name made up by replacing spaces by dots in the name listed above.
(The authors of code from other projects included in the R distribution
are listed in the COPYRIGHTS file.)
R FAQ
Frequently Asked Questions on R
Version 3.1.2014-10-26
Version 3.1.2015-03-04
Kurt Hornik
......@@ -121,7 +121,7 @@ questions about R.
1.1 Legalese
============
This document is copyright © 1998-2014 by Kurt Hornik.
This document is copyright © 1998-2015 by Kurt Hornik.
This document is free software; you can redistribute it and/or modify
it under the terms of the GNU General Public License as published by the
......@@ -154,7 +154,7 @@ CRAN site (*note What is CRAN?::).
1.3 Citing this document
========================
In publications, please refer to this FAQ as Hornik (2014), "The R FAQ",
In publications, please refer to this FAQ as Hornik (2015), "The R FAQ",
and give the above, _official_ URL:
@Misc{,
......@@ -255,7 +255,7 @@ mips-sgi-irix, i386-freebsd, rs6000-ibm-aix, and sparc-sun-solaris.
2.3 What is the current version of R?
=====================================
The current released version is 3.1.2. Based on this
The current released version is 3.1.3. Based on this
'major.minor.patchlevel' numbering scheme, there are two development
versions of R, a patched version of the current release ('r-patched')
and one working towards the next minor or eventually major ('r-devel')
......@@ -273,7 +273,7 @@ Subversion repository, but currently not via anonymous rsync (nor CVS).
Tarballs with daily snapshots of the r-devel and r-patched
development versions of R can be found at
<ftp://ftp.stat.math.ethz.ch/Software/R>.
<ftp://ftp.stat.math.ethz.ch/Software/R/>.
2.5 How can R be installed?
===========================
......@@ -477,7 +477,7 @@ can be found at
John M. Chambers (2008), "Software for Data Analysis: Programming
with R". Springer, New York, ISBN 978-0-387-75935-7,
<http://stat.stanford.edu/~jmc4/Rbook/>.
<http://statweb.stanford.edu/~jmc4/Rbook/>.
Peter Dalgaard (2008), "Introductory Statistics with R", 2nd
edition. Springer, ISBN 978-0-387-79053-4,
......@@ -614,20 +614,21 @@ can be found at the URL
Daily mirrors are available at URLs including
<http://cran.at.R-project.org/> (WU Wien, Austria)
<http://cran.au.R-project.org/> (PlanetMirror, Australia)
<http://cran.at.R-project.org/> (Wirtschaftsuniversität
Wien, Austria)
<http://cran.au.R-project.org/> (University of Melbourne,
Australia)
<http://cran.br.R-project.org/> (Universidade Federal do
Paraná, Brazil)
<http://cran.ch.R-project.org/> (ETH Zürich, Switzerland)
<http://cran.dk.R-project.org/> (SunSITE, Denmark)
<http://cran.dk.R-project.org/> (dotsrc.org, Aalborg,
Denmark)
<http://cran.es.R-project.org/> (Spanish National Research
Network, Madrid, Spain)
<http://cran.fr.R-project.org/> (INRA, Toulouse, France)
<http://cran.pt.R-project.org/> (Universidade do Porto,
Portugal)
<http://cran.uk.R-project.org/> (U of Bristol, United
Kingdom)
<http://cran.za.R-project.org/> (Rhodes U, South Africa)
See <http://CRAN.R-project.org/mirrors.html> for a complete list of
mirrors. Please use the CRAN site closest to you to reduce network
......@@ -769,11 +770,9 @@ the S Repository (http://lib.stat.cmu.edu/S/) at CMU.
3.2 What is S-PLUS?
===================
S-PLUS is a value-added version of S sold by Insightful Corporation
(http://www.insightful.com), which in 2008 was acquired by TIBCO
Software Inc (http://www.tibco.com/). See the Insightful S-PLUS page
(http://www.insightful.com/products/splus/) and the TIBCO Spotfire S+
Products page for further information.
S-PLUS is a value-added version of S currently sold by TIBCO Software
Inc (http://www.tibco.com/) as 'TIBCO Spotfire S+'. See
<http://en.wikipedia.org/wiki/S-PLUS> for more information.
3.3 What are the differences between R and S?
=============================================
......@@ -1191,12 +1190,6 @@ released REvolution R
enterprise-class statistical analysis system based on R, suitable for
deployment in professional, commercial and regulated environments.
Random Technologies (http://www.random-technologies-llc.com/) offers
RStat (http://random-technologies-llc.com/products/RStat/rstat), an
enterprise-strength statistical computing environment which combines R
with enterprise-level validation, documentation, software support, and
consulting services, as well as related R-based products.
See also
<http://en.wikipedia.org/wiki/R_programming_language#Commercialized_versions_of_R>
for pointers to commercialized versions of R.
......@@ -1224,7 +1217,7 @@ on-line programming environment for R which intends to make the first
steps in statistical programming with R (especially with time series) as
easy as possible. There is no need for a local installation since the
only requirement for the user is a JavaScript capable browser. See
<http://osvisions.com/r-online/> for more information.
<http://www.osvisions.com/r_online/> for more information.
*Rcgi* is a CGI WWW interface to R by MJ Ray <mjr@dsl.pipex.com>. It
had the ability to use "embedded code": you could mix user input and
......@@ -1237,10 +1230,9 @@ of *Rcgi* by Mai Zhou <mai@ms.uky.edu> (actually, two versions: one with
(bitmap) graphics and one without) as well as the original code are
available from <http://www.ms.uky.edu/~statweb/>.
CGI-based web access to R is also provided at
<http://hermes.sdu.dk/cgi-bin/go/>. There are many additional examples
of web interfaces to R which basically allow to submit R code to a
remote server, see for example the collection of links available from
There are many additional examples of web interfaces to R which
basically allow to submit R code to a remote server, see for example the
collection of links available from
<http://biostat.mc.vanderbilt.edu/twiki/bin/view/Main/StatCompCourse>.
David Firth (http://www.warwick.ac.uk/go/dfirth) has written
......@@ -1257,12 +1249,6 @@ the Journal of Statistical Software
Duncan Temple Lang <duncan@wald.ucdavis.edu> and has a web page at
<http://www.omegahat.org/CGIwithR/>.
Rpad (http://www.rpad.org/Rpad), developed and actively maintained by
Tom Short, provides a sophisticated environment which combines some of
the features of the previous approaches with quite a bit of JavaScript,
allowing for a GUI-like behavior (with sortable tables, clickable
graphics, editable output), etc.
Jeff Horner is working on the R/Apache Integration Project which
embeds the R interpreter inside Apache 2 (and beyond). A tutorial and
presentation are available from the project web page at
......@@ -1274,12 +1260,6 @@ which allows other programs to use facilities of R. Clients are
available from the web site for Java and C++ (and could be written for
other languages that support TCP/IP sockets).
OpenStatServer (http://openstatserver.org/index.html) is being
developed by a team lead by Greg Warnes; it aims "to provide clean
access to computational modules defined in a variety of computational
environments (R, SAS, Matlab, etc) via a single well-defined client
interface" and to turn computational services into web services.
Two projects use PHP to provide a web interface to R. R_PHP_Online
(http://steve-chen.net/R_PHP/) by Steve Chen (though it is unclear if
this project is still active) is somewhat similar to the above Rcgi and
......@@ -2165,9 +2145,9 @@ Ghostscript you can use 'bitmap()', which produces a PostScript or PDF
file then converts it to any bitmap format supported by Ghostscript. On
some installations this produces ugly output, on others it is perfectly
satisfactory. Many systems now come with Xvfb from X.Org
(http://www.x.org/Downloads.html) (possibly as an optional install),
which is an X11 server that does not require a screen; and there is the
*GDD* (http://CRAN.R-project.org/package=GDD) package from CRAN, which
(http://www.x.org/) (possibly as an optional install), which is an X11
server that does not require a screen; and there is the *GDD*
(http://CRAN.R-project.org/package=GDD) package from CRAN, which
produces PNG, JPEG and GIF bitmaps without X11.
7.20 How can I get command line editing to work?
......
R News
CHANGES IN R 3.1.3:
NEW FEATURES:
* The internal method of download.file() can now handle files
larger than 2GB on 32-bit builds which support such files (tested
on 32-bit R running on 64-bit Windows).
* kruskal.test() warns on more types of suspicious input.
* The as.dendrogram() method for "hclust" objects gains a check
argument protecting against memory explosion for invalid inputs.
* capabilities() has a new item long.double which indicates if the
build uses a long double type which is longer than double.
* nlm() no longer modifies the callback argument in place (a new
vector is allocated for each invocation, which mimics the
implicit duplication that occurred in R < 3.1.0); note that this
is a change from the previously documented behavior. (PR#15958)
* icuSetCollate() now accepts locale = "ASCII" which uses the basic
C function strcmp and so collates strings byte-by-byte in
numerical order.
* sessionInfo() tries to report the OS version in use (not just
that compiled under, and including details of Linux
distributions).
* model.frame() (used by lm() and many other modelling functions)
now warns when it drops contrasts from factors. (Wish of
PR#16119)
* install.packages() and friends now accept the value type =
"binary" as a synonym for the native binary type on the platform
(if it has one).
* Single source or binary files can be supplied for
install.packages(type = "both") and the appropriate type and
repos = NULL will be inferred.
* New function pcre_config() to report on some of the configuration
options of the version of PCRE in use. In particular, this
reports if regular expressions using \p{xx} are supported.
* (Windows.) download.file(cacheOK = FALSE) is now supported when
internet2.dll is used.
* browseURL() has been updated to work with Firefox 36.0 which has
dropped support for the -remote interface.
INSTALLATION and INCLUDED SOFTWARE:
* The included version of PCRE has been updated to 8.36.
* configure accepts MAKEINFO=texi2any as another way to ensure
texinfo 5.x is used when both 5.x and 4.x are installed.
UTILITIES:
* R CMD check now checks the packages used in \donttest sections of
the examples are specified in the DESCRIPTION file. (These are
needed to run the examples interactively.)
* R CMD check checks for the undeclared use of GNU extensions in
Makefiles, and for Makefiles with a missing final linefeed.
R CMD build will correct line endings in all Makefiles, not just
those in the src directory.
* R CMD check notes uses of library() and require() in package
code: see the section 'Suggested packages' of 'Writing R
Extensions' for good practice.
DEPRECATED AND DEFUNCT:
* The configure option --with-valgrind-instrumentation=3 is
deprecated and will be removed in R 3.2.0.
BUG FIXES:
* (Windows.) Rscript.exe was missing a manifest specifying the
modern style for common controls (e.g., the download progress
bar).
* If a package had extra documentation files but no vignette, the
HTML help system produced an empty index page.
* The parser now gives an error if a null character is included in
a string using Unicode escapes. (PR#16046)
* qr.Q() failed on complex arguments due to pre-3.0(!) typo.
(PR#16054)
* abs() failed with named arguments when the argument was complex.
(PR#16047)
* "noquote" objects may now be used as columns in dataframes.
(PR#15997)
* Some values with extremely long names were printed incorrectly.
(PR#15999)
* Extremely large exponents on zero expressed in scientific
notation (e.g. 0.0e50000) could give NaN. (PR#15976)
* download.file() reported downloaded sizes as 0KB if less than