Commit 88cb46ae authored by Dirk Eddelbuettel's avatar Dirk Eddelbuettel

Import Upstream version 3.2.3

parent bf46e866

Too many changes to show.

To preserve performance only 1000 of 1000+ files are displayed.

......@@ -19,6 +19,8 @@ CPICFLAGS = @CPICFLAGS@
CPPFLAGS = @CPPFLAGS@
CURL_CPPFLAGS = @CURL_CPPFLAGS@
CURL_LIBS = @CURL_LIBS@
## in case we want to link with this for UBSAN checks
CXX = @CXX@
DEFS = @DEFS@ @R_DEFS@
DISTDIR_TAR_EXCLUDE = --exclude=.svn --exclude=Makefile --exclude="*.o" --exclude="*$(SHLIB_EXT)" --exclude="*~"
DYLIB_EXT = @DYLIB_EXT@
......@@ -66,11 +68,13 @@ MAIN_LINK = $(MAIN_LD) $(MAIN_LDFLAGS) $(LIBR0) $(LDFLAGS)
MKINSTALLDIRS = @R_SHELL@ $(top_srcdir)/src/scripts/mkinstalldirs.in
NOTANGLE = @NOTANGLE@
R_ARCH = @R_ARCH@
R_DYLIB_EXT = @R_DYLIB_EXT@
R_FRAMEWORK_DIR = $(prefix)/R.framework
R_GZIPCMD = @R_GZIPCMD@
## needed for AIX only
@USE_EXPORTFILES_TRUE@ R_HOME = $(top_builddir)
R_OPENMP_CFLAGS = @R_OPENMP_CFLAGS@
## if ever used, need to check that this is compatible with C OpenMP
R_OPENMP_FFLAGS = @R_OPENMP_FFLAGS@
R_OSTYPE = @R_OSTYPE@
R_PKGS = $(R_PKGS_BASE) @USE_RECOMMENDED_PACKAGES_TRUE@ $(R_PKGS_RECOMMENDED)
......@@ -102,6 +106,7 @@ YACC = @YACC@
ALL_CFLAGS = $(R_XTRA_CFLAGS) $(R_OPENMP_CFLAGS) $(MAIN_CFLAGS) $(CFLAGS)
ALL_CPPFLAGS = $(R_XTRA_CPPFLAGS) $(CPPFLAGS) $(DEFS)
## R_OPENMP_FFLAGS should not really be here: see above
ALL_FFLAGS = $(R_XTRA_FFLAGS) $(R_OPENMP_FFLAGS) $(MAIN_FFLAGS) $(FFLAGS)
ALL_CFLAGS_LO = $(R_XTRA_CFLAGS) $(R_OPENMP_CFLAGS) $(CPICFLAGS) $(SHLIB_CFLAGS) $(CFLAGS)
ALL_FFLAGS_LO = $(R_XTRA_FFLAGS) $(R_OPENMP_FFLAGS) $(FPICFLAGS) $(SHLIB_FFLAGS) $(FFLAGS)
......
......@@ -40,6 +40,7 @@ ACINCLUDE_DEPENDENCIES = \
m4/cxx_11.m4 \
m4/gettext.m4 m4/gettext-lib.m4 \
m4/libtool.m4 m4/ltoptions.m4 m4/ltversion.m4 m4/ltsugar.m4 m4/lt~obsolete.m4 \
m4/openmp.m4 \
m4/stat-time.m4
CONFIGURE_DEPENDENCIES = $(srcdir)/VERSION
config.status: $(srcdir)/configure
......@@ -82,8 +83,8 @@ vignettes: stamp-recommended
## This needs packages built, hence 'R' dependence on 'javaconf'
## javareconf gets remade often.
stamp-java : etc/javaconf $(srcdir)/src/scripts/javareconf.in
@$(ECHO) "configuring Java ..."
@-bin/R CMD javareconf
@WANT_JAVA_TRUE@ @$(ECHO) "configuring Java ..."
@WANT_JAVA_TRUE@ @-bin/R CMD javareconf
@touch stamp-java
javaconf: R
......@@ -123,7 +124,7 @@ svnonly:
fi \
fi
@WANT_R_STATIC_FALSE@libR_la = libR$(DYLIB_EXT)
@WANT_R_STATIC_FALSE@libR_la = libR$(R_DYLIB_EXT)
@WANT_R_STATIC_TRUE@libR_la = libR.a
install-libR:
@if test -f lib$(R_ARCH)/$(libR_la); then $(MAKE) install-libR-exists; fi
......@@ -144,7 +145,7 @@ uninstall:
@rm -rf "$(DESTDIR)$(Rexecbindir)" "$(DESTDIR)$(rhome)/lib"
@rmdir "$(DESTDIR)$(rhome)" 2>/dev/null \
|| $(ECHO) " dir $(DESTDIR)$(rhome) not removed"
@rm -f "$(DESTDIR)${libdir}/libR$(DYLIB_EXT)"
@rm -f "$(DESTDIR)${libdir}/libR$(R_DYLIB_EXT)"
mostlyclean: clean
clean:
......
Revision: 69053
Last Changed Date: 2015-08-14
Revision: 69752
Last Changed Date: 2015-12-10
Fire Safety
Wooden Christmas-Tree
......@@ -277,4 +277,15 @@
## CURL_LIBS=`curl-config --static-libs`
## Path to the version of pkg-config to be used for locating cairographics.
## PKGCONF =
## PKGCONF=
## OpenMP settings.
## The configure code is conservative about enabling OpenMP
## so use can be forced here (or non-use if set but empty).
## For packages
## SHLIB_OPENMP_CFLAGS=
## SHLIB_OPENMP_CXXFLAGS=
## SHLIB_OPENMP_FCFLAGS=
## SHLIB_OPENMP_FFLAGS=
## For R itself (src/main/array.c and src/library/stats/src/distance.c)
## R_OPENMP_CFLAGS=
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R FAQ
Frequently Asked Questions on R
Version 3.2.2015-08-09
Version 3.2.2015-12-04
Kurt Hornik
......@@ -199,7 +199,7 @@ script files.
The design of R has been heavily influenced by two existing
languages: Becker, Chambers & Wilks' S (*note What is S?::) and
Sussman's Scheme
(http://www.cs.indiana.edu/scheme-repository/home.html). Whereas the
(https://www.cs.indiana.edu/scheme-repository/home.html). Whereas the
resulting language is very similar in appearance to S, the underlying
implementation and semantics are derived from Scheme. *Note What are
the differences between R and S?::, for further details.
......@@ -256,7 +256,7 @@ 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 3.2.2. Based on this
The current released version is 3.2.3. 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')
......@@ -378,7 +378,7 @@ Iacus). The "R for Mac OS X FAQ
details.
Snapshots of the r-patched and r-devel versions of R are available as
Apple installer packages at <http://r.research.att.com>.
Apple installer packages at <https://r.research.att.com>.
2.6 Are there Unix-like binaries for R?
=======================================
......@@ -401,7 +401,7 @@ install r-base-dev' to obtain the additional tools required for this.
So-called "backports" of the current R packages for at least the
"stable" distribution of Debian are provided by Johannes Ranke, and
available from CRAN. See
<https://CRAN.R-project.org/bin/linux/debian/README.html> for details on
<https://CRAN.R-project.org/bin/linux/debian/index.html> for details on
R Debian packages and installing the backports, which should also be
suitable for other Debian derivatives. Native backports for Ubuntu are
provided by Michael Rutter.
......@@ -478,7 +478,7 @@ can be found at
John M. Chambers (2008), "Software for Data Analysis: Programming
with R". Springer, New York, ISBN 978-0-387-75935-7,
<https://statweb.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,
......@@ -537,7 +537,7 @@ obtained by 'citation()'.
===================================
Thanks to Martin Maechler <Martin.Maechler@R-project.org>, there are
four mailing lists devoted to R.
several mailing lists devoted to R, including the following:
'R-announce'
A moderated list for major announcements about the development of R
......@@ -553,6 +553,9 @@ four mailing lists devoted to R.
'R-devel'
This list is for questions and discussion about code development in
R.
'R-package-devel'
A list which which provides a forum for learning about the R
package development process.
Please read the posting guide
(https://www.R-project.org/posting-guide.html) _before_ sending anything
......@@ -613,25 +616,8 @@ can be found at the URL
<https://CRAN.R-project.org/>
Daily mirrors are available at URLs including
<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/> (dotsrc.org, Aalborg,
Denmark)
<http://cran.es.R-project.org/> (Spanish National Research
Network, Madrid, Spain)
<http://cran.pt.R-project.org/> (Universidade do Porto,
Portugal)
<http://cran.uk.R-project.org/> (U of Bristol, United
Kingdom)
See <https://CRAN.R-project.org/mirrors.html> for a complete list of
and is mirrored daily to many sites around the world. See
<https://CRAN.R-project.org/mirrors.html> for a complete list of
mirrors. Please use the CRAN site closest to you to reduce network
load.
......@@ -658,7 +644,7 @@ all Open Source licenses, permits all and any use of the package. It
only restricts distribution of R or of other programs containing code
from R. This is made clear in clause 6 ("No Discrimination Against
Fields of Endeavor") of the Open Source Definition
(http://www.opensource.org/docs/definition.html):
(https://opensource.org/docs/definition.html):
The license must not restrict anyone from making use of the program
in a specific field of endeavor. For example, it may not restrict
......@@ -756,13 +742,13 @@ S.
* John M. Chambers (1998), "Programming with Data," New York:
Springer, ISBN 0-387-98503-4
(<https://statweb.stanford.edu/~jmc4/Sbook/>).
(<http://statweb.stanford.edu/~jmc4/Sbook/>).
This "_Green Book_" describes version 4 of S, a major revision of S
designed by John Chambers to improve its usefulness at every stage
of the programming process.
See <https://statweb.stanford.edu/~jmc4/papers/96.7.ps> for further
See <http://statweb.stanford.edu/~jmc4/papers/96.7.ps> for further
information on the "Evolution of the S Language".
There is a huge amount of user-contributed code for S, available at
......@@ -1192,7 +1178,7 @@ enterprise-class statistical analysis system based on R, suitable for
deployment in professional, commercial and regulated environments.
See also
<http://en.wikipedia.org/wiki/R_programming_language#Commercialized_versions_of_R>
<https://en.wikipedia.org/wiki/R_programming_language#Commercialized_versions_of_R>
for pointers to commercialized versions of R.
4 R Web Interfaces
......@@ -1437,13 +1423,14 @@ Bioconductor (https://www.bioconductor.org/) is an open source and open
development software project for the analysis and comprehension of
genomic data. Most Bioconductor components are distributed as R add-on
packages. Initially most of the Bioconductor software packages
(https://www.bioconductor.org/packages/bioc/) focused primarily on DNA
microarray data analysis. As the project has matured, the functional
scope of the software packages broadened to include the analysis of all
types of genomic data, such as SAGE, sequence, or SNP data. In
addition, there are metadata (annotation, CDF and probe) and experiment
data packages. See <https://www.bioconductor.org/download/> for
available packages and a complete taxonomy via BioC Views.
(https://bioconductor.org/packages/release/BiocViews.html#___Software)
focused primarily on DNA microarray data analysis. As the project has
matured, the functional scope of the software packages broadened to
include the analysis of all types of genomic data, such as SAGE,
sequence, or SNP data. In addition, there are metadata (annotation, CDF
and probe) and experiment data packages. See
<https://www.bioconductor.org/download/> for available packages and a
complete taxonomy via BioC Views.
5.1.5 Other add-on packages
---------------------------
......@@ -1634,7 +1621,7 @@ from transcript files).
The latest stable version of ESS is available via CRAN or the ESS web
page (http://ESS.R-project.org/). The HTML version of the documentation
can be found at <http://stat.ethz.ch/ESS/>.
can be found at <https://stat.ethz.ch/ESS/>.
ESS comes with detailed installation instructions.
......@@ -2836,8 +2823,8 @@ maintainers, mentioning the package in the subject line.
A bug report can be generated using the function 'bug.report()'. For
reports on R this will open the Web page at
<http://bugs.R-project.org/>: for a contributed package it will open the
package's bug tracker Web page or help you compose an email to the
<https://bugs.R-project.org/>: for a contributed package it will open
the package's bug tracker Web page or help you compose an email to the
maintainer.
There is a section of the bug repository for suggestions for
......
R News
CHANGES IN R 3.2.3:
NEW FEATURES:
* Some recently-added Windows time zone names have been added to
the conversion table used to convert these to Olson names.
(Including those relating to changes for Russia in Oct 2014, as
in PR#16503.)
* (Windows) Compatibility information has been added to the
manifests for Rgui.exe, Rterm.exe and Rscript.exe. This should
allow win.version() and Sys.info() to report the actual Windows
version up to Windows 10.
* Windows "wininet" FTP first tries EPSV / PASV mode rather than
only using active mode (reported by Dan Tenenbaum).