* [gentoo-commits] gentoo-x86 commit in dev-lang/R: ChangeLog metadata.xml R-2.2.1-r1.ebuild R-2.6.0-r1.ebuild R-2.5.1.ebuild
@ 2007-11-15 12:06 Sebastien Fabbro (bicatali)
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From: Sebastien Fabbro (bicatali) @ 2007-11-15 12:06 UTC (permalink / raw
To: gentoo-commits
bicatali 07/11/15 12:06:24
Modified: ChangeLog metadata.xml
Added: R-2.2.1-r1.ebuild R-2.6.0-r1.ebuild
Removed: R-2.5.1.ebuild
Log:
Security fix with pcre (bug #198385), now use system libs.
(Portage version: 2.1.3.19, RepoMan options: --force)
Revision Changes Path
1.91 dev-lang/R/ChangeLog
file : http://sources.gentoo.org/viewcvs.py/gentoo-x86/dev-lang/R/ChangeLog?rev=1.91&view=markup
plain: http://sources.gentoo.org/viewcvs.py/gentoo-x86/dev-lang/R/ChangeLog?rev=1.91&content-type=text/plain
diff : http://sources.gentoo.org/viewcvs.py/gentoo-x86/dev-lang/R/ChangeLog?r1=1.90&r2=1.91
Index: ChangeLog
===================================================================
RCS file: /var/cvsroot/gentoo-x86/dev-lang/R/ChangeLog,v
retrieving revision 1.90
retrieving revision 1.91
diff -u -r1.90 -r1.91
--- ChangeLog 6 Oct 2007 14:21:27 -0000 1.90
+++ ChangeLog 15 Nov 2007 12:06:24 -0000 1.91
@@ -1,6 +1,15 @@
# ChangeLog for dev-lang/R
# Copyright 1999-2007 Gentoo Foundation; Distributed under the GPL v2
-# $Header: /var/cvsroot/gentoo-x86/dev-lang/R/ChangeLog,v 1.90 2007/10/06 14:21:27 markusle Exp $
+# $Header: /var/cvsroot/gentoo-x86/dev-lang/R/ChangeLog,v 1.91 2007/11/15 12:06:24 bicatali Exp $
+
+*R-2.6.0-r1 (15 Nov 2007)
+*R-2.2.1-r1 (15 Nov 2007)
+
+ 15 Nov 2007; Sébastien Fabbro <bicatali@gentoo.org> -files/R.desktop,
+ -files/R-logo.png, metadata.xml, +R-2.2.1-r1.ebuild, -R-2.5.1.ebuild,
+ +R-2.6.0-r1.ebuild:
+ Security fix with pcre (bug #198385), now use system libs. New ebuild on
+ soon to be commited.
*R-2.6.0 (06 Oct 2007)
1.2 dev-lang/R/metadata.xml
file : http://sources.gentoo.org/viewcvs.py/gentoo-x86/dev-lang/R/metadata.xml?rev=1.2&view=markup
plain: http://sources.gentoo.org/viewcvs.py/gentoo-x86/dev-lang/R/metadata.xml?rev=1.2&content-type=text/plain
diff : http://sources.gentoo.org/viewcvs.py/gentoo-x86/dev-lang/R/metadata.xml?r1=1.1&r2=1.2
Index: metadata.xml
===================================================================
RCS file: /var/cvsroot/gentoo-x86/dev-lang/R/metadata.xml,v
retrieving revision 1.1
retrieving revision 1.2
diff -u -r1.1 -r1.2
--- metadata.xml 16 Oct 2003 19:55:34 -0000 1.1
+++ metadata.xml 15 Nov 2007 12:06:24 -0000 1.2
@@ -2,4 +2,23 @@
<!DOCTYPE pkgmetadata SYSTEM "http://www.gentoo.org/dtd/metadata.dtd">
<pkgmetadata>
<herd>sci</herd>
+<longdescription lang="en">
+R is a system for statistical computation and graphics. It consists of
+a language plus a run-time environment with graphics, a debugger,
+access to certain system functions, and the ability to run programs
+stored in script files.
+
+The core of R is an interpreted computer language which allows
+branching and looping as well as modular programming using functions.
+Most of the user-visible functions in R are written in R. It is
+possible for the user to interface to procedures written in the C,
+C++, or FORTRAN languages for efficiency. The R distribution contains
+functionality for a large number of statistical procedures. Among
+these are: linear and generalized linear models, nonlinear regression
+models, time series analysis, classical parametric and nonparametric
+tests, clustering and smoothing. There is also a large set of
+functions which provide a flexible graphical environment for creating
+various kinds of data presentations. Additional modules ("add-on
+packages") are available for a variety of specific purposes.
+</longdescription>
</pkgmetadata>
1.1 dev-lang/R/R-2.2.1-r1.ebuild
file : http://sources.gentoo.org/viewcvs.py/gentoo-x86/dev-lang/R/R-2.2.1-r1.ebuild?rev=1.1&view=markup
plain: http://sources.gentoo.org/viewcvs.py/gentoo-x86/dev-lang/R/R-2.2.1-r1.ebuild?rev=1.1&content-type=text/plain
Index: R-2.2.1-r1.ebuild
===================================================================
# Copyright 1999-2007 Gentoo Foundation
# Distributed under the terms of the GNU General Public License v2
# $Header: /var/cvsroot/gentoo-x86/dev-lang/R/R-2.2.1-r1.ebuild,v 1.1 2007/11/15 12:06:24 bicatali Exp $
inherit fortran toolchain-funcs flag-o-matic
DESCRIPTION="R is GNU S - A language and environment for statistical computing and graphics."
HOMEPAGE="http://www.r-project.org/"
SRC_URI="mirror://cran/src/base/R-2/${P}.tar.gz"
LICENSE="GPL-2 LGPL-2.1"
SLOT="0"
KEYWORDS="amd64 ia64 ppc ppc64 sparc x86"
IUSE="blas jpeg nls png readline tk X lapack"
RDEPEND=">=dev-lang/perl-5.6.1-r3
>=dev-libs/libpcre-7.3
app-arch/bzip2
readline? ( >=sys-libs/readline-4.1-r3 )
jpeg? ( >=media-libs/jpeg-6b-r2 )
png? ( >=media-libs/libpng-1.2.1 )
blas? ( virtual/blas )
lapack? ( virtual/lapack )
tk? ( dev-lang/tk
dev-lang/tcl )
X? ( x11-libs/libX11 )"
DEPEND="${RDEPEND}
X? ( x11-proto/xproto
x11-libs/libXt
x11-libs/libX11 )"
AT_M4DIR="${S}/m4"
pkg_setup() {
# Test for a 64 bit architecture - f2c won't work on 64 bit archs with R.
# Thanks to vapier for providing the test.
cd "${T}"
echo 'int main(){}' > test.c
$(tc-getCC) -c test.c -o test.o
if file test.o | grep -qs 64-bit ; then
einfo "64 bit architecture detected, using g77 or gfortran."
FORTRAN="gfortran g77 ifc"
else
FORTRAN="gfortran g77 f2c"
fi
rm -f test.{c,o}
fortran_pkg_setup
filter-ldflags -Wl,-Bdirect -Bdirect
}
src_compile() {
local myconf="--enable-R-profiling --enable-R-shlib --enable-linux-lfs"
if use tk; then
#configure needs to find the files tclConfig.sh and tkConfig.sh
myconf="${myconf} --with-tcltk --with-tcl-config=/usr/lib/tclConfig.sh
--with-tk-config=/usr/lib/tkConfig.sh"
else
myconf="${myconf} --without-tcltk"
fi
econf \
--with-system-zlib \
--with-system-bzlib \
--with-system-pcre \
$(use_enable nls) \
$(use_with blas) \
$(use_with lapack) \
$(use_with jpeg jpeglib) \
$(use_with png libpng) \
$(use_with readline) \
$(use_with X x) \
${myconf} || die "econf failed"
emake || die "emake failed"
}
src_install() {
make \
prefix="${D}"/usr \
mandir="${D}"/usr/share/man \
infodir="${D}"/usr/share/info \
rhome="${D}"/usr/$(get_libdir)/R \
install || die "Installation Failed"
# fix the R wrapper script to have the correct R_HOME_DIR
# sed regexp borrowed from included debian rules
sed \
-e "/^R_HOME_DIR=.*/s::R_HOME_DIR=/usr/$(get_libdir)/R:" \
-i "${D}"/usr/$(get_libdir)/R/bin/R \
|| die "sed failed."
# The same kinds of seds are needed for these variables too, see bug 115140
sed \
-e "/^R_SHARE_DIR=.*/s::R_SHARE_DIR=/usr/$(get_libdir)/R/share:" \
-e "/^R_INCLUDE_DIR=.*/s::R_INCLUDE_DIR=/usr/$(get_libdir)/R/include:" \
-e "/^R_DOC_DIR=.*/s::R_DOC_DIR=/usr/$(get_libdir)/R/doc:" \
-i "${D}"/usr/$(get_libdir)/R/bin/R \
|| die "sed failed."
# R installs two identical wrappers under /usr/bin and /usr/lib/R/bin/
# the 2nd one is corrected by above sed, the first is replaced by a symlink
cd "${D}"/usr/bin/
rm R
dosym ../$(get_libdir)/R/bin/R /usr/bin/R
dodir /etc/env.d
echo -n \
"LDPATH=\"/usr/$(get_libdir)/R/lib\"" \
> "${D}"/etc/env.d/99R
cd "${S}"
dodoc AUTHORS BUGS COPYING* ChangeLog FAQ *NEWS README \
RESOURCES THANKS VERSION Y2K
}
1.1 dev-lang/R/R-2.6.0-r1.ebuild
file : http://sources.gentoo.org/viewcvs.py/gentoo-x86/dev-lang/R/R-2.6.0-r1.ebuild?rev=1.1&view=markup
plain: http://sources.gentoo.org/viewcvs.py/gentoo-x86/dev-lang/R/R-2.6.0-r1.ebuild?rev=1.1&content-type=text/plain
Index: R-2.6.0-r1.ebuild
===================================================================
# Copyright 1999-2007 Gentoo Foundation
# Distributed under the terms of the GNU General Public License v2
# $Header: /var/cvsroot/gentoo-x86/dev-lang/R/R-2.6.0-r1.ebuild,v 1.1 2007/11/15 12:06:24 bicatali Exp $
inherit fortran toolchain-funcs flag-o-matic
DESCRIPTION="R is GNU S - A language and environment for statistical computing and graphics."
HOMEPAGE="http://www.r-project.org/"
SRC_URI="mirror://cran/src/base/R-2/${P}.tar.gz"
LICENSE="GPL-2 LGPL-2.1"
SLOT="0"
KEYWORDS="~amd64 ~ia64 ~ppc ~ppc64 ~sparc ~x86"
IUSE="blas jpeg nls png readline tk X lapack gd"
RDEPEND=">=dev-lang/perl-5.6.1-r3
>=dev-libs/libpcre-7.3
app-arch/bzip2
readline? ( >=sys-libs/readline-4.1-r3 )
jpeg? ( >=media-libs/jpeg-6b-r2 )
png? ( >=media-libs/libpng-1.2.1 )
blas? ( virtual/blas )
lapack? ( virtual/lapack )
gd? ( >=media-libs/gd-2 )
tk? ( dev-lang/tk
dev-lang/tcl )
X? ( x11-libs/libX11 )"
DEPEND="${RDEPEND}
X? ( x11-proto/xproto
x11-libs/libXt
x11-libs/libX11 )"
pkg_setup() {
# Test for a 64 bit architecture - f2c won't work on 64 bit archs with R.
# Thanks to vapier for providing the test.
cd "${T}"
echo 'int main(){}' > test.c
$(tc-getCC) -c test.c -o test.o
if file test.o | grep -qs 64-bit ; then
einfo "64 bit architecture detected, using g77 or gfortran."
FORTRAN="gfortran g77 ifc"
else
FORTRAN="gfortran g77 f2c"
fi
rm -f test.{c,o}
fortran_pkg_setup
filter-ldflags -Wl,-Bdirect -Bdirect
# this is needed to properly compile additional R packages
# (see bug #152379)
append-flags -std=gnu99
}
src_unpack() {
unpack ${A}
sed -e "s:\$(rhome):/usr/$(get_libdir)/R:g" \
-i "${S}"/src/unix/Makefile.in ||
die "Failed to fix Rscript makefile"
}
src_compile() {
local myconf="--enable-R-profiling --enable-R-shlib --enable-linux-lfs"
if use tk; then
#configure needs to find the files tclConfig.sh and tkConfig.sh
myconf="${myconf} --with-tcltk --with-tcl-config=/usr/lib/tclConfig.sh
--with-tk-config=/usr/lib/tkConfig.sh"
else
myconf="${myconf} --without-tcltk"
fi
econf \
--with-system-zlib \
--with-system-bzlib \
--with-system-pcre \
$(use_enable nls) \
$(use_with blas) \
$(use_with lapack) \
$(use_with jpeg jpeglib) \
$(use_with png libpng) \
$(use_with readline) \
$(use_with X x) \
${myconf} || die "econf failed"
# R-2.5.0 started to have issues with parallel make
emake -j1 || die "emake failed"
}
src_install() {
make \
prefix="${D}"/usr \
mandir="${D}"/usr/share/man \
infodir="${D}"/usr/share/info \
libdir="${D}"/usr/$(get_libdir) \
rhome="${D}"/usr/$(get_libdir)/R \
install || die "Installation Failed"
# fix the R wrapper script to have the correct R_HOME_DIR
# sed regexp borrowed from included debian rules
sed \
-e "/^R_HOME_DIR=.*/s::R_HOME_DIR=/usr/$(get_libdir)/R:" \
-i "${D}"/usr/$(get_libdir)/R/bin/R \
|| die "sed failed."
# The same kinds of seds are needed for these variables too, see bug 115140
sed \
-e "/^R_SHARE_DIR=.*/s::R_SHARE_DIR=/usr/$(get_libdir)/R/share:" \
-e "/^R_INCLUDE_DIR=.*/s::R_INCLUDE_DIR=/usr/$(get_libdir)/R/include:" \
-e "/^R_DOC_DIR=.*/s::R_DOC_DIR=/usr/$(get_libdir)/R/doc:" \
-i "${D}"/usr/$(get_libdir)/R/bin/R \
|| die "sed failed."
# fix paths in libR.pc pkgconfig file
sed -e "s:${D}::" -i "${D}"/usr/$(get_libdir)/pkgconfig/libR.pc \
|| die "Failed to fix libR.pc file"
# R installs two identical wrappers under /usr/bin and /usr/lib/R/bin/
# the 2nd one is corrected by above sed, the first is replaced by a symlink
cd "${D}"/usr/bin/
rm R
dosym ../$(get_libdir)/R/bin/R /usr/bin/R
dodir /etc/env.d
echo -n \
"LDPATH=\"/usr/$(get_libdir)/R/lib\"" \
> "${D}"/etc/env.d/99R
cd "${S}"
dodoc ChangeLog *NEWS README VERSION
}
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2007-11-15 12:06 [gentoo-commits] gentoo-x86 commit in dev-lang/R: ChangeLog metadata.xml R-2.2.1-r1.ebuild R-2.6.0-r1.ebuild R-2.5.1.ebuild Sebastien Fabbro (bicatali)
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