[gentoo-commits] gentoo-x86 commit in dev-lang/R: ChangeLog R-2.7.1.ebuild R-2.6.1-r1.ebuild R-2.7.2.ebuild R-2.6.2.ebuild R-2.7.0.ebuild

[Markus Dittrich (markusle)]

markusle    08/08/27 23:01:41

  Modified:             ChangeLog R-2.7.1.ebuild R-2.6.1-r1.ebuild
  Added:                R-2.7.2.ebuild
  Removed:              R-2.6.2.ebuild R-2.7.0.ebuild
  Log:
  Added patch from Debian to fix insecure tempfile handling in javareconf (fixes bug #235822). NOTE: R-2.2.1-r1.ebuild is not vulnerable since it does not include the javereconf script. Also removed old ebuilds and removed two tests from the test suite since they fail with portage.
  (Portage version: 2.2_rc8/cvs/Linux 2.6.26-SENTINEL-2 i686)

Revision  Changes    Path
1.126                dev-lang/R/ChangeLog

file : http://sources.gentoo.org/viewcvs.py/gentoo-x86/dev-lang/R/ChangeLog?rev=1.126&view=markup
plain: http://sources.gentoo.org/viewcvs.py/gentoo-x86/dev-lang/R/ChangeLog?rev=1.126&content-type=text/plain
diff : http://sources.gentoo.org/viewcvs.py/gentoo-x86/dev-lang/R/ChangeLog?r1=1.125&r2=1.126

Index: ChangeLog
===================================================================
RCS file: /var/cvsroot/gentoo-x86/dev-lang/R/ChangeLog,v
retrieving revision 1.125
retrieving revision 1.126
diff -u -r1.125 -r1.126
--- ChangeLog	18 Jul 2008 12:45:45 -0000	1.125
+++ ChangeLog	27 Aug 2008 23:01:40 -0000	1.126
@@ -1,6 +1,18 @@
 # ChangeLog for dev-lang/R
 # Copyright 1999-2008 Gentoo Foundation; Distributed under the GPL v2
-# $Header: /var/cvsroot/gentoo-x86/dev-lang/R/ChangeLog,v 1.125 2008/07/18 12:45:45 markusle Exp $
+# $Header: /var/cvsroot/gentoo-x86/dev-lang/R/ChangeLog,v 1.126 2008/08/27 23:01:40 markusle Exp $
+
+*R-2.7.2 (27 Aug 2008)
+
+  27 Aug 2008; Markus Dittrich <markusle@g.o>
+  +files/R-javareconf.patch, +files/R-2.7.1-test-fix.patch,
+  -2.6.1-r1.ebuild, -R-2.6.2.ebuild, -R-2.7.0.ebuild, 
+  R-2.7.1.ebuild, +R-2.7.2.ebuild:
+  Added patch from Debian to fix insecure tempfile handling in 
+  javareconf (fixes bug #235822). NOTE: R-2.2.1-r1.ebuild is not 
+  vulnerable since it does not include the javereconf script. 
+  Also removed old ebuilds and removed two tests from the test
+  suite since they fail with portage.
 
   18 Jul 2008; Markus Dittrich <markusle@g.o> R-2.7.1.ebuild:
   Added missing cairo use flag (see bug #231970).



1.3                  dev-lang/R/R-2.7.1.ebuild

file : http://sources.gentoo.org/viewcvs.py/gentoo-x86/dev-lang/R/R-2.7.1.ebuild?rev=1.3&view=markup
plain: http://sources.gentoo.org/viewcvs.py/gentoo-x86/dev-lang/R/R-2.7.1.ebuild?rev=1.3&content-type=text/plain
diff : http://sources.gentoo.org/viewcvs.py/gentoo-x86/dev-lang/R/R-2.7.1.ebuild?r1=1.2&r2=1.3

Index: R-2.7.1.ebuild
===================================================================
RCS file: /var/cvsroot/gentoo-x86/dev-lang/R/R-2.7.1.ebuild,v
retrieving revision 1.2
retrieving revision 1.3
diff -u -r1.2 -r1.3
--- R-2.7.1.ebuild	18 Jul 2008 12:45:45 -0000	1.2
+++ R-2.7.1.ebuild	27 Aug 2008 23:01:40 -0000	1.3
@@ -1,6 +1,6 @@
 # Copyright 1999-2008 Gentoo Foundation
 # Distributed under the terms of the GNU General Public License v2
-# $Header: /var/cvsroot/gentoo-x86/dev-lang/R/R-2.7.1.ebuild,v 1.2 2008/07/18 12:45:45 markusle Exp $
+# $Header: /var/cvsroot/gentoo-x86/dev-lang/R/R-2.7.1.ebuild,v 1.3 2008/08/27 23:01:40 markusle Exp $
 
 inherit fortran flag-o-matic bash-completion
 
@@ -65,6 +65,15 @@
 	filter-ldflags -Wl,-Bdirect -Bdirect
 }
 
+
+src_unpack() {
+	unpack ${A}
+	cd "${S}"
+	epatch "${FILESDIR}"/${PN}-javareconf.patch
+	epatch "${FILESDIR}"/${P}-test-fix.patch
+}
+
+
 src_compile() {
 	# fix packages.html for doc (bug #205103)
 	# check in later versions if fixed
@@ -116,6 +125,12 @@
 	emake -j1 -C src/nmath/standalone || die "emake math library failed"
 }
 
+src_test() {
+	# we need to unset R_HOME otherwise some of the diff based
+	# tests fail due to warnings in the output
+	R_HOME="" make check || die "Some of the tests failed"
+}
+
 src_install() {
 	# -j1 because creates various dirs sequentially (hit should be small)
 	emake -j1 DESTDIR="${D}" install || die "emake install failed"



1.13                 dev-lang/R/R-2.6.1-r1.ebuild

file : http://sources.gentoo.org/viewcvs.py/gentoo-x86/dev-lang/R/R-2.6.1-r1.ebuild?rev=1.13&view=markup
plain: http://sources.gentoo.org/viewcvs.py/gentoo-x86/dev-lang/R/R-2.6.1-r1.ebuild?rev=1.13&content-type=text/plain
diff : http://sources.gentoo.org/viewcvs.py/gentoo-x86/dev-lang/R/R-2.6.1-r1.ebuild?r1=1.12&r2=1.13

Index: R-2.6.1-r1.ebuild
===================================================================
RCS file: /var/cvsroot/gentoo-x86/dev-lang/R/R-2.6.1-r1.ebuild,v
retrieving revision 1.12
retrieving revision 1.13
diff -u -r1.12 -r1.13
--- R-2.6.1-r1.ebuild	15 Apr 2008 15:27:19 -0000	1.12
+++ R-2.6.1-r1.ebuild	27 Aug 2008 23:01:40 -0000	1.13
@@ -1,6 +1,6 @@
 # Copyright 1999-2008 Gentoo Foundation
 # Distributed under the terms of the GNU General Public License v2
-# $Header: /var/cvsroot/gentoo-x86/dev-lang/R/R-2.6.1-r1.ebuild,v 1.12 2008/04/15 15:27:19 armin76 Exp $
+# $Header: /var/cvsroot/gentoo-x86/dev-lang/R/R-2.6.1-r1.ebuild,v 1.13 2008/08/27 23:01:40 markusle Exp $
 
 inherit fortran flag-o-matic bash-completion
 
@@ -57,6 +57,13 @@
 	use ppc64 && append-flags -mminimal-toc
 }
 
+src_unpack() {
+	unpack ${A}
+	cd "${S}"
+	epatch "${FILESDIR}"/${PN}-javareconf.patch
+}
+
+
 src_compile() {
 	# fix packages.html for doc (bug #205103)
 	# check in later versions if fixed



1.1                  dev-lang/R/R-2.7.2.ebuild

file : http://sources.gentoo.org/viewcvs.py/gentoo-x86/dev-lang/R/R-2.7.2.ebuild?rev=1.1&view=markup
plain: http://sources.gentoo.org/viewcvs.py/gentoo-x86/dev-lang/R/R-2.7.2.ebuild?rev=1.1&content-type=text/plain

Index: R-2.7.2.ebuild
===================================================================
# Copyright 1999-2008 Gentoo Foundation
# Distributed under the terms of the GNU General Public License v2
# $Header: /var/cvsroot/gentoo-x86/dev-lang/R/R-2.7.2.ebuild,v 1.1 2008/08/27 23:01:40 markusle Exp $

inherit fortran flag-o-matic bash-completion

DESCRIPTION="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
	bash-completion? ( mirror://gentoo/R.bash_completion.bz2 )"

LICENSE="GPL-2 LGPL-2.1"
SLOT="0"
KEYWORDS="~alpha ~amd64 ~hppa ~ia64 ~ppc ~ppc64 ~sparc ~x86 ~x86-fbsd"

IUSE="doc java jpeg lapack minimal nls png readline tk X cairo"

# common depends
CDEPEND="dev-lang/perl
	>=dev-libs/libpcre-7.3
	app-arch/bzip2
	virtual/blas
	virtual/ghostscript
	cairo? ( x11-libs/cairo x11-libs/pango )
	readline? ( sys-libs/readline )
	jpeg? ( media-libs/jpeg )
	png? ( media-libs/libpng )
	lapack? ( virtual/lapack )
	tk? ( dev-lang/tk )
	X? ( x11-libs/libXmu x11-misc/xdg-utils )"

DEPEND="${CDEPEND}
	dev-util/pkgconfig
	doc? ( virtual/latex-base
	  || ( dev-texlive/texlive-fontsrecommended virtual/tetex ) )"

RDEPEND="${CDEPEND}
	app-arch/unzip
	app-arch/zip
	java? ( >=virtual/jre-1.5 )"

R_HOME=/usr/$(get_libdir)/${PN}

pkg_setup() {
	FORTRAN="gfortran ifc g77"
	fortran_pkg_setup
	export FFLAGS="${FFLAGS:--O2}"
	[[ ${FORTRANC} = gfortran || ${FORTRANC} = if* ]] && \
		export FCFLAGS="${FCFLAGS:-${FFLAGS}}"

	# make sure cairo and pango are both compiled with "X"
	# use flag (see bug #231970)
	if use cairo; then
		if ( ! built_with_use x11-libs/cairo X ); then
			eerror "x11-libs/cairo needs to be built with USE=\"X\""
			die "Please rebuild x11-libs/cairo with USE=\"X\""
		fi

		if ( ! built_with_use x11-libs/pango X ); then
			eerror "x11-libs/pango needs to be built with USE=\"X\""
			die "Please rebuild x11-libs/pango with USE=\"X\""
		fi
	fi

	filter-ldflags -Wl,-Bdirect -Bdirect
}

src_unpack() {
	unpack ${A}
	cd "${S}"
	epatch "${FILESDIR}"/${PN}-javareconf.patch
	epatch "${FILESDIR}"/${PN}-2.7.1-test-fix.patch
}

src_test() {
	# we need to unset R_HOME otherwise some of the diff based
	# tests fail due to warnings in the output
	R_HOME="" make check || die "Some of the tests failed"
}

src_compile() {
	# fix packages.html for doc (bug #205103)
	# check in later versions if fixed
	sed -i \
		-e "s:../../library:../../../../$(get_libdir)/R/library:g" \
		src/library/tools/R/packageshtml.R \
		|| die "sed failed"

	# fix Rscript
	sed -i \
		-e "s:-DR_HOME='\"\$(rhome)\"':-DR_HOME='\"${R_HOME}\"':" \
		src/unix/Makefile.in || die "sed unix Makefile failed"

	use lapack && \
		export LAPACK_LIBS="$(pkg-config --libs lapack)"

	if use X; then
		export R_BROWSER="$(type -p xdg-open)"
		export R_PDFVIEWER="$(type -p xdg-open)"
	fi

	econf \
		--enable-R-profiling \
		--enable-memory-profiling \
		--enable-R-shlib \
		--enable-linux-lfs \
		--with-system-zlib \
		--with-system-bzlib \
		--with-system-pcre \
		--with-blas="$(pkg-config --libs blas)" \
		--docdir=/usr/share/doc/${PF} \
		rdocdir=/usr/share/doc/${PF} \
		$(use_enable nls) \
		$(use_with lapack) \
		$(use_with tk tcltk) \
		$(use_with jpeg jpeglib) \
		$(use_with !minimal recommended-packages) \
		$(use_with png libpng) \
		$(use_with readline) \
		$(use_with cairo) \
		$(use_with X x) \
		|| die "econf failed"
	emake || die "emake failed"
	if use doc; then
		export VARTEXFONTS="${T}/fonts"
		emake info pdf || die "emake docs failed"
	fi

	emake -j1 -C src/nmath/standalone || die "emake math library failed"
}

src_install() {
	# -j1 because creates various dirs sequentially (hit should be small)
	emake -j1 DESTDIR="${D}" install || die "emake install failed"

	if use doc; then
		emake DESTDIR="${D}" \
			install-info install-pdf || die "emake install docs failed"
	fi

	emake -j1 \
		-C src/nmath/standalone \
		DESTDIR="${D}" install \
		|| die "emake install math library failed"

	# env file
	cat > 99R <<-EOF
		LDPATH=${R_HOME}/lib
		R_HOME=${R_HOME}
	EOF
	doenvd 99R || die "doenvd failed"

	dobashcompletion "${WORKDIR}"/R.bash_completion
}

pkg_config() {
	if use java; then
		einfo "Re-initializing java paths for ${P}"
		R CMD javareconf
	fi
}