* [gentoo-commits] gentoo-x86 commit in sci-libs/ccp4-libs: ChangeLog ccp4-libs-6.1.3-r4.ebuild
@ 2010-10-04 17:02 Kacper Kowalik (xarthisius)
0 siblings, 0 replies; 3+ messages in thread
From: Kacper Kowalik (xarthisius) @ 2010-10-04 17:02 UTC (permalink / raw
To: gentoo-commits
xarthisius 10/10/04 17:02:08
Modified: ChangeLog
Added: ccp4-libs-6.1.3-r4.ebuild
Log:
Fix buffer overflows wrt bug 339706. Thanks to Diego for the report.
(Portage version: 2.1.9.13/cvs/Linux x86_64)
Revision Changes Path
1.13 sci-libs/ccp4-libs/ChangeLog
file : http://sources.gentoo.org/viewvc.cgi/gentoo-x86/sci-libs/ccp4-libs/ChangeLog?rev=1.13&view=markup
plain: http://sources.gentoo.org/viewvc.cgi/gentoo-x86/sci-libs/ccp4-libs/ChangeLog?rev=1.13&content-type=text/plain
diff : http://sources.gentoo.org/viewvc.cgi/gentoo-x86/sci-libs/ccp4-libs/ChangeLog?r1=1.12&r2=1.13
Index: ChangeLog
===================================================================
RCS file: /var/cvsroot/gentoo-x86/sci-libs/ccp4-libs/ChangeLog,v
retrieving revision 1.12
retrieving revision 1.13
diff -u -r1.12 -r1.13
--- ChangeLog 16 Jul 2010 10:14:47 -0000 1.12
+++ ChangeLog 4 Oct 2010 17:02:08 -0000 1.13
@@ -1,6 +1,12 @@
# ChangeLog for sci-libs/ccp4-libs
# Copyright 1999-2010 Gentoo Foundation; Distributed under the GPL v2
-# $Header: /var/cvsroot/gentoo-x86/sci-libs/ccp4-libs/ChangeLog,v 1.12 2010/07/16 10:14:47 jlec Exp $
+# $Header: /var/cvsroot/gentoo-x86/sci-libs/ccp4-libs/ChangeLog,v 1.13 2010/10/04 17:02:08 xarthisius Exp $
+
+*ccp4-libs-6.1.3-r4 (04 Oct 2010)
+
+ 04 Oct 2010; Kacper Kowalik <xarthisius@gentoo.org>
+ +files/6.1.3-overflows.patch, +ccp4-libs-6.1.3-r4.ebuild:
+ Fix buffer overflows wrt bug 339706. Thanks to Diego for the report.
16 Jul 2010; Justin Lecher <jlec@gentoo.org> -ccp4-libs-6.1.3.ebuild,
-ccp4-libs-6.1.3-r1.ebuild, -ccp4-libs-6.1.3-r2.ebuild:
1.1 sci-libs/ccp4-libs/ccp4-libs-6.1.3-r4.ebuild
file : http://sources.gentoo.org/viewvc.cgi/gentoo-x86/sci-libs/ccp4-libs/ccp4-libs-6.1.3-r4.ebuild?rev=1.1&view=markup
plain: http://sources.gentoo.org/viewvc.cgi/gentoo-x86/sci-libs/ccp4-libs/ccp4-libs-6.1.3-r4.ebuild?rev=1.1&content-type=text/plain
Index: ccp4-libs-6.1.3-r4.ebuild
===================================================================
# Copyright 1999-2010 Gentoo Foundation
# Distributed under the terms of the GNU General Public License v2
# $Header: /var/cvsroot/gentoo-x86/sci-libs/ccp4-libs/ccp4-libs-6.1.3-r4.ebuild,v 1.1 2010/10/04 17:02:08 xarthisius Exp $
EAPI="3"
inherit fortran eutils gnuconfig multilib toolchain-funcs
FORTRAN="g77 gfortran ifc"
SRC="ftp://ftp.ccp4.ac.uk/ccp4"
#UPDATE="04_03_09"
#PATCHDATE="090511"
MY_P="${P/-libs}"
PATCH_TOT="0"
# Here's a little scriptlet to generate this list from the provided
# index.patches file
#
# i=1; while read -a line; do [[ ${line//#} != ${line} ]] && continue;
# echo "PATCH${i}=( ${line[1]}"; echo "${line[0]} )"; (( i++ )); done <
# index.patches
#PATCH1=( src/topp_
#topp.f-r1.16.2.5-r1.16.2.6.diff )
#PATCH2=( .
#configure-r1.372.2.18-r1.372.2.19.diff )
DESCRIPTION="Protein X-ray crystallography toolkit"
HOMEPAGE="http://www.ccp4.ac.uk/"
SRC_URI="${SRC}/${PV}/${MY_P}-core-src.tar.gz"
# patch tarball from upstream
[[ -n ${UPDATE} ]] && SRC_URI="${SRC_URI} ${SRC}/${PV}/updates/${P}-src-patch-${UPDATE}.tar.gz"
# patches created by us
[[ -n ${PATCHDATE} ]] && SRC_URI="${SRC_URI} http://dev.gentooexperimental.org/~jlec/science-dist/${PV}-${PATCHDATE}-updates.patch.bz2"
for i in $(seq $PATCH_TOT); do
NAME="PATCH${i}[1]"
SRC_URI="${SRC_URI}
${SRC}/${PV}/patches/${!NAME}"
done
LICENSE="ccp4"
SLOT="0"
KEYWORDS="~amd64 ~x86 ~amd64-linux ~x86-linux"
IUSE=""
RDEPEND="
media-libs/jpeg:0
app-shells/tcsh
!<sci-chemistry/ccp4-6.1.3
sci-libs/cbflib
=sci-libs/fftw-2*
sci-libs/mmdb
sci-libs/monomer-db
virtual/lapack
virtual/blas"
DEPEND="${RDEPEND}"
S="${WORKDIR}/${MY_P}"
src_prepare() {
einfo "Applying upstream patches ..."
for patch in $(seq $PATCH_TOT); do
base="PATCH${patch}"
dir=$(eval echo \${${base}[0]})
p=$(eval echo \${${base}[1]})
pushd "${dir}" >& /dev/null
ccp_patch "${DISTDIR}/${p}"
popd >& /dev/null
done
einfo "Done."
echo
[[ -n ${PATCHDATE} ]] && epatch "${WORKDIR}"/${PV}-${PATCHDATE}-updates.patch
einfo "Applying Gentoo patches ..."
# fix buffer overflows wrt bug 339706
ccp_patch "${FILESDIR}"/${PV}-overflows.patch
# it tries to create libdir, bindir etc on live system in configure
ccp_patch "${FILESDIR}"/${PV}-dont-make-dirs-in-configure.patch
# gerror_ gets defined twice on ppc if you're using gfortran/g95
ccp_patch "${FILESDIR}"/6.0.2-ppc-double-define-gerror.patch
# make creation of libccif.so smooth
ccp_patch "${FILESDIR}"/${PV}-ccif-shared.patch
# lets try to build libmmdb seperatly
ccp_patch "${FILESDIR}"/${PV}-dont-build-mmdb.patch
# unbundle libjpeg and cbflib
ccp_patch "${FILESDIR}"/${PV}-unbundle-libs.patch
# Fix missing DESTIDR
# not installing during build
ccp_patch "${FILESDIR}"/${PV}-noinstall.patch
sed \
-e '/SHARE_INST/s:$(libdir):$(DESTDIR)/$(libdir):g' \
-i configure || die
einfo "Done." # done applying Gentoo patches
echo
sed \
-e "s:/usr:${EPREFIX}/usr:g" \
-e 's:-Wl,-rpath,$CLIB::g' \
-e 's: -rpath $CLIB::g' \
-e 's: -I${srcdir}/include/cpp_c_headers::g' \
-i configure || die
gnuconfig_update
}
src_configure() {
rm -rf lib/DiffractionImage/{jpg,CBFlib} || die
# Build system is broken if we set LDFLAGS
userldflags="${LDFLAGS}"
export SHARED_LIB_FLAGS="${LDFLAGS}"
unset LDFLAGS
# GENTOO_OSNAME can be one of:
# irix irix64 sunos sunos64 aix hpux osf1 linux freebsd
# linux_compaq_compilers linux_intel_compilers generic Darwin
# ia64_linux_intel Darwin_ibm_compilers linux_ibm_compilers
if [[ "${FORTRANC}" = "ifc" ]]; then
if use ia64; then
GENTOO_OSNAME="ia64_linux_intel"
else
# Should be valid for x86, maybe amd64
GENTOO_OSNAME="linux_intel_compilers"
fi
else
# Should be valid for x86 and amd64, at least
GENTOO_OSNAME="linux"
fi
# Sets up env
ln -s \
ccp4.setup-bash \
"${S}"/include/ccp4.setup
# We agree to the license by emerging this, set in LICENSE
sed -i \
-e "s~^\(^agreed=\).*~\1yes~g" \
"${S}"/configure
# Fix up variables -- need to reset CCP4_MASTER at install-time
sed -i \
-e "s~^\(setenv CCP4_MASTER.*\)/.*~\1"${WORKDIR}"~g" \
-e "s~^\(setenv CCP4I_TCLTK.*\)/usr/local/bin~\1${EPREFIX}/usr/bin~g" \
"${S}"/include/ccp4.setup*
# Set up variables for build
source "${S}"/include/ccp4.setup
export CC=$(tc-getCC)
export CXX=$(tc-getCXX)
export COPTIM=${CFLAGS}
export CXXOPTIM=${CXXFLAGS}
# Default to -O2 if FFLAGS is unset
export FC=${FORTRANC}
export FOPTIM=${FFLAGS:- -O2}
# export CCP4_SCR="${T}"
# Fix linking
# $(tc-getCC) ${userldflags} -shared -Wl,-soname,libmmdb.so -o libmmdb.so \${MMDBOBJS} $(gcc-config -L | awk -F: '{for(i=1; i<=NF; i++) printf " -L%s", $i}') -lm -lstdc++ && \
export SHARE_LIB="\
$(tc-getCC) ${userldflags} -shared -Wl,-soname,libccp4c.so -o libccp4c.so \${CORELIBOBJS} \${CGENERALOBJS} \${CUCOBJS} \${CMTZOBJS} \${CMAPOBJS} \${CSYMOBJS} -L../ccif/ -lccif $(gcc-config -L | awk -F: '{for(i=1; i<=NF; i++) printf " -L%s", $i}') -lm && \
${FORTRANC} ${userldflags} -shared -Wl,-soname,libccp4f.so -o libccp4f.so \${FORTRANLOBJS} \${FINTERFACEOBJS} -L../ccif/ -lccif -L. -lccp4c -lmmdb $(gcc-config -L | awk -F: '{for(i=1; i<=NF; i++) printf " -L%s", $i}') -lstdc++ -lgfortran -lm"
# Can't use econf, configure rejects unknown options like --prefix
./configure \
--onlylibs \
--with-shared-libs \
--with-fftw="${EPREFIX}"/usr \
--with-warnings \
--disable-cctbx \
--disable-clipper \
--tmpdir="${TMPDIR}" \
--bindir="${EPREFIX}"/usr/libexec/ccp4/bin/ \
--libdir="${EPREFIX}"/usr/$(get_libdir) \
${GENTOO_OSNAME} || die "econf failed"
}
src_compile() {
emake -j1 \
DESTDIR="${ED}" onlylib || die "emake failed"
}
src_install() {
# Set up variables for build
source "${S}"/include/ccp4.setup
emake -j1 \
DESTDIR="${ED}" \
includedir="${EPREFIX}"/usr/include \
library_includedir="${EPREFIX}"/usr/include \
install || die
# Libs
for file in "${S}"/lib/*; do
if [[ -d ${file} ]]; then
continue
elif [[ -x ${file} ]]; then
dolib.so ${file} || die
else
insinto /usr/$(get_libdir)
doins ${file} || die
fi
done
# Fix libdir in all *.la files
sed -i \
-e "s:^\(libdir=\).*:\1\'${EPREFIX}/usr/$(get_libdir)\':g" \
"${ED}"/usr/$(get_libdir)/*.la || die
# Data
insinto /usr/share/ccp4/data/
doins -r "${S}"/lib/data/{*.PARM,*.prt,*.lib,*.dic,*.idl,*.cif,*.resource,*.york,*.hist,fraglib,reference_structures} || die
dodoc "${S}"/lib/data/*.doc || die
newdoc "${S}"/lib/data/README DATA-README || die
}
# Epatch wrapper for bulk patching
ccp_patch() {
EPATCH_SINGLE_MSG=" ${1##*/} ..." epatch ${1}
}
^ permalink raw reply [flat|nested] 3+ messages in thread
* [gentoo-commits] gentoo-x86 commit in sci-libs/ccp4-libs: ChangeLog ccp4-libs-6.1.3-r4.ebuild
@ 2010-10-20 13:33 Jeremy Olexa (darkside)
0 siblings, 0 replies; 3+ messages in thread
From: Jeremy Olexa (darkside) @ 2010-10-20 13:33 UTC (permalink / raw
To: gentoo-commits
darkside 10/10/20 13:33:10
Modified: ChangeLog ccp4-libs-6.1.3-r4.ebuild
Log:
Fix for Gentoo Prefix, bug 341811 by Johan Hattne
(Portage version: 2.1.9.12/cvs/Linux x86_64)
Revision Changes Path
1.14 sci-libs/ccp4-libs/ChangeLog
file : http://sources.gentoo.org/viewvc.cgi/gentoo-x86/sci-libs/ccp4-libs/ChangeLog?rev=1.14&view=markup
plain: http://sources.gentoo.org/viewvc.cgi/gentoo-x86/sci-libs/ccp4-libs/ChangeLog?rev=1.14&content-type=text/plain
diff : http://sources.gentoo.org/viewvc.cgi/gentoo-x86/sci-libs/ccp4-libs/ChangeLog?r1=1.13&r2=1.14
Index: ChangeLog
===================================================================
RCS file: /var/cvsroot/gentoo-x86/sci-libs/ccp4-libs/ChangeLog,v
retrieving revision 1.13
retrieving revision 1.14
diff -u -r1.13 -r1.14
--- ChangeLog 4 Oct 2010 17:02:08 -0000 1.13
+++ ChangeLog 20 Oct 2010 13:33:10 -0000 1.14
@@ -1,6 +1,9 @@
# ChangeLog for sci-libs/ccp4-libs
# Copyright 1999-2010 Gentoo Foundation; Distributed under the GPL v2
-# $Header: /var/cvsroot/gentoo-x86/sci-libs/ccp4-libs/ChangeLog,v 1.13 2010/10/04 17:02:08 xarthisius Exp $
+# $Header: /var/cvsroot/gentoo-x86/sci-libs/ccp4-libs/ChangeLog,v 1.14 2010/10/20 13:33:10 darkside Exp $
+
+ 20 Oct 2010; Jeremy Olexa <darkside@gentoo.org> ccp4-libs-6.1.3-r4.ebuild:
+ Fix for Gentoo Prefix, bug 341811 by Johan Hattne
*ccp4-libs-6.1.3-r4 (04 Oct 2010)
1.2 sci-libs/ccp4-libs/ccp4-libs-6.1.3-r4.ebuild
file : http://sources.gentoo.org/viewvc.cgi/gentoo-x86/sci-libs/ccp4-libs/ccp4-libs-6.1.3-r4.ebuild?rev=1.2&view=markup
plain: http://sources.gentoo.org/viewvc.cgi/gentoo-x86/sci-libs/ccp4-libs/ccp4-libs-6.1.3-r4.ebuild?rev=1.2&content-type=text/plain
diff : http://sources.gentoo.org/viewvc.cgi/gentoo-x86/sci-libs/ccp4-libs/ccp4-libs-6.1.3-r4.ebuild?r1=1.1&r2=1.2
Index: ccp4-libs-6.1.3-r4.ebuild
===================================================================
RCS file: /var/cvsroot/gentoo-x86/sci-libs/ccp4-libs/ccp4-libs-6.1.3-r4.ebuild,v
retrieving revision 1.1
retrieving revision 1.2
diff -u -r1.1 -r1.2
--- ccp4-libs-6.1.3-r4.ebuild 4 Oct 2010 17:02:08 -0000 1.1
+++ ccp4-libs-6.1.3-r4.ebuild 20 Oct 2010 13:33:10 -0000 1.2
@@ -1,6 +1,6 @@
# Copyright 1999-2010 Gentoo Foundation
# Distributed under the terms of the GNU General Public License v2
-# $Header: /var/cvsroot/gentoo-x86/sci-libs/ccp4-libs/ccp4-libs-6.1.3-r4.ebuild,v 1.1 2010/10/04 17:02:08 xarthisius Exp $
+# $Header: /var/cvsroot/gentoo-x86/sci-libs/ccp4-libs/ccp4-libs-6.1.3-r4.ebuild,v 1.2 2010/10/20 13:33:10 darkside Exp $
EAPI="3"
@@ -189,7 +189,7 @@
src_compile() {
emake -j1 \
- DESTDIR="${ED}" onlylib || die "emake failed"
+ DESTDIR="${D}" onlylib || die "emake failed"
}
src_install() {
@@ -197,7 +197,7 @@
source "${S}"/include/ccp4.setup
emake -j1 \
- DESTDIR="${ED}" \
+ DESTDIR="${D}" \
includedir="${EPREFIX}"/usr/include \
library_includedir="${EPREFIX}"/usr/include \
install || die
^ permalink raw reply [flat|nested] 3+ messages in thread
* [gentoo-commits] gentoo-x86 commit in sci-libs/ccp4-libs: ChangeLog ccp4-libs-6.1.3-r4.ebuild
@ 2010-12-20 12:28 Markos Chandras (hwoarang)
0 siblings, 0 replies; 3+ messages in thread
From: Markos Chandras (hwoarang) @ 2010-12-20 12:28 UTC (permalink / raw
To: gentoo-commits
hwoarang 10/12/20 12:28:01
Modified: ChangeLog ccp4-libs-6.1.3-r4.ebuild
Log:
Stable on amd64 wrt bug #348872
(Portage version: 2.1.9.25/cvs/Linux x86_64)
Revision Changes Path
1.17 sci-libs/ccp4-libs/ChangeLog
file : http://sources.gentoo.org/viewvc.cgi/gentoo-x86/sci-libs/ccp4-libs/ChangeLog?rev=1.17&view=markup
plain: http://sources.gentoo.org/viewvc.cgi/gentoo-x86/sci-libs/ccp4-libs/ChangeLog?rev=1.17&content-type=text/plain
diff : http://sources.gentoo.org/viewvc.cgi/gentoo-x86/sci-libs/ccp4-libs/ChangeLog?r1=1.16&r2=1.17
Index: ChangeLog
===================================================================
RCS file: /var/cvsroot/gentoo-x86/sci-libs/ccp4-libs/ChangeLog,v
retrieving revision 1.16
retrieving revision 1.17
diff -u -r1.16 -r1.17
--- ChangeLog 16 Dec 2010 14:28:58 -0000 1.16
+++ ChangeLog 20 Dec 2010 12:28:01 -0000 1.17
@@ -1,6 +1,9 @@
# ChangeLog for sci-libs/ccp4-libs
# Copyright 1999-2010 Gentoo Foundation; Distributed under the GPL v2
-# $Header: /var/cvsroot/gentoo-x86/sci-libs/ccp4-libs/ChangeLog,v 1.16 2010/12/16 14:28:58 jlec Exp $
+# $Header: /var/cvsroot/gentoo-x86/sci-libs/ccp4-libs/ChangeLog,v 1.17 2010/12/20 12:28:01 hwoarang Exp $
+
+ 20 Dec 2010; Markos Chandras <hwoarang@gentoo.org> ccp4-libs-6.1.3-r4.ebuild:
+ Stable on amd64 wrt bug #348872
16 Dec 2010; Justin Lecher <jlec@gentoo.org> ccp4-libs-6.1.3-r3.ebuild,
ccp4-libs-6.1.3-r4.ebuild:
1.5 sci-libs/ccp4-libs/ccp4-libs-6.1.3-r4.ebuild
file : http://sources.gentoo.org/viewvc.cgi/gentoo-x86/sci-libs/ccp4-libs/ccp4-libs-6.1.3-r4.ebuild?rev=1.5&view=markup
plain: http://sources.gentoo.org/viewvc.cgi/gentoo-x86/sci-libs/ccp4-libs/ccp4-libs-6.1.3-r4.ebuild?rev=1.5&content-type=text/plain
diff : http://sources.gentoo.org/viewvc.cgi/gentoo-x86/sci-libs/ccp4-libs/ccp4-libs-6.1.3-r4.ebuild?r1=1.4&r2=1.5
Index: ccp4-libs-6.1.3-r4.ebuild
===================================================================
RCS file: /var/cvsroot/gentoo-x86/sci-libs/ccp4-libs/ccp4-libs-6.1.3-r4.ebuild,v
retrieving revision 1.4
retrieving revision 1.5
diff -u -r1.4 -r1.5
--- ccp4-libs-6.1.3-r4.ebuild 16 Dec 2010 14:28:58 -0000 1.4
+++ ccp4-libs-6.1.3-r4.ebuild 20 Dec 2010 12:28:01 -0000 1.5
@@ -1,6 +1,6 @@
# Copyright 1999-2010 Gentoo Foundation
# Distributed under the terms of the GNU General Public License v2
-# $Header: /var/cvsroot/gentoo-x86/sci-libs/ccp4-libs/ccp4-libs-6.1.3-r4.ebuild,v 1.4 2010/12/16 14:28:58 jlec Exp $
+# $Header: /var/cvsroot/gentoo-x86/sci-libs/ccp4-libs/ccp4-libs-6.1.3-r4.ebuild,v 1.5 2010/12/20 12:28:01 hwoarang Exp $
EAPI="3"
@@ -41,7 +41,7 @@
LICENSE="ccp4"
SLOT="0"
-KEYWORDS="~amd64 ~x86 ~amd64-linux ~x86-linux"
+KEYWORDS="amd64 ~x86 ~amd64-linux ~x86-linux"
IUSE=""
RDEPEND="
^ permalink raw reply [flat|nested] 3+ messages in thread
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2010-10-20 13:33 [gentoo-commits] gentoo-x86 commit in sci-libs/ccp4-libs: ChangeLog ccp4-libs-6.1.3-r4.ebuild Jeremy Olexa (darkside)
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2010-10-04 17:02 Kacper Kowalik (xarthisius)
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