| 1 |
jlec 10/06/29 19:55:41 |
| 2 |
|
| 3 |
Modified: ChangeLog |
| 4 |
Added: ccp4-libs-6.1.3-r3.ebuild |
| 5 |
Log: |
| 6 |
Change way of installation, fixed insecure runpaths |
| 7 |
(Portage version: 2.2_rc67/cvs/Linux x86_64) |
| 8 |
|
| 9 |
Revision Changes Path |
| 10 |
1.7 sci-libs/ccp4-libs/ChangeLog |
| 11 |
|
| 12 |
file : http://sources.gentoo.org/viewvc.cgi/gentoo-x86/sci-libs/ccp4-libs/ChangeLog?rev=1.7&view=markup |
| 13 |
plain: http://sources.gentoo.org/viewvc.cgi/gentoo-x86/sci-libs/ccp4-libs/ChangeLog?rev=1.7&content-type=text/plain |
| 14 |
diff : http://sources.gentoo.org/viewvc.cgi/gentoo-x86/sci-libs/ccp4-libs/ChangeLog?r1=1.6&r2=1.7 |
| 15 |
|
| 16 |
Index: ChangeLog |
| 17 |
=================================================================== |
| 18 |
RCS file: /var/cvsroot/gentoo-x86/sci-libs/ccp4-libs/ChangeLog,v |
| 19 |
retrieving revision 1.6 |
| 20 |
retrieving revision 1.7 |
| 21 |
diff -u -r1.6 -r1.7 |
| 22 |
--- ChangeLog 22 May 2010 10:04:27 -0000 1.6 |
| 23 |
+++ ChangeLog 29 Jun 2010 19:55:41 -0000 1.7 |
| 24 |
@@ -1,6 +1,13 @@ |
| 25 |
# ChangeLog for sci-libs/ccp4-libs |
| 26 |
# Copyright 1999-2010 Gentoo Foundation; Distributed under the GPL v2 |
| 27 |
-# $Header: /var/cvsroot/gentoo-x86/sci-libs/ccp4-libs/ChangeLog,v 1.6 2010/05/22 10:04:27 jlec Exp $ |
| 28 |
+# $Header: /var/cvsroot/gentoo-x86/sci-libs/ccp4-libs/ChangeLog,v 1.7 2010/06/29 19:55:41 jlec Exp $ |
| 29 |
+ |
| 30 |
+*ccp4-libs-6.1.3-r3 (29 Jun 2010) |
| 31 |
+ |
| 32 |
+ 29 Jun 2010; Justin Lecher <jlec@g.o> +files/6.1.3-destdir.patch, |
| 33 |
+ files/6.1.3-dont-build-mmdb.patch, +files/6.1.3-noinstall.patch, |
| 34 |
+ +ccp4-libs-6.1.3-r3.ebuild: |
| 35 |
+ Change way of installation, fixed insecure runpaths |
| 36 |
|
| 37 |
*ccp4-libs-6.1.3-r2 (22 May 2010) |
| 38 |
|
| 39 |
|
| 40 |
|
| 41 |
|
| 42 |
1.1 sci-libs/ccp4-libs/ccp4-libs-6.1.3-r3.ebuild |
| 43 |
|
| 44 |
file : http://sources.gentoo.org/viewvc.cgi/gentoo-x86/sci-libs/ccp4-libs/ccp4-libs-6.1.3-r3.ebuild?rev=1.1&view=markup |
| 45 |
plain: http://sources.gentoo.org/viewvc.cgi/gentoo-x86/sci-libs/ccp4-libs/ccp4-libs-6.1.3-r3.ebuild?rev=1.1&content-type=text/plain |
| 46 |
|
| 47 |
Index: ccp4-libs-6.1.3-r3.ebuild |
| 48 |
=================================================================== |
| 49 |
# Copyright 1999-2010 Gentoo Foundation |
| 50 |
# Distributed under the terms of the GNU General Public License v2 |
| 51 |
# $Header: /var/cvsroot/gentoo-x86/sci-libs/ccp4-libs/ccp4-libs-6.1.3-r3.ebuild,v 1.1 2010/06/29 19:55:41 jlec Exp $ |
| 52 |
|
| 53 |
EAPI="3" |
| 54 |
|
| 55 |
inherit fortran eutils gnuconfig multilib toolchain-funcs |
| 56 |
|
| 57 |
FORTRAN="g77 gfortran ifc" |
| 58 |
|
| 59 |
SRC="ftp://ftp.ccp4.ac.uk/ccp4" |
| 60 |
|
| 61 |
#UPDATE="04_03_09" |
| 62 |
#PATCHDATE="090511" |
| 63 |
|
| 64 |
MY_P="${P/-libs}" |
| 65 |
|
| 66 |
PATCH_TOT="0" |
| 67 |
# Here's a little scriptlet to generate this list from the provided |
| 68 |
# index.patches file |
| 69 |
# |
| 70 |
# i=1; while read -a line; do [[ ${line//#} != ${line} ]] && continue; |
| 71 |
# echo "PATCH${i}=( ${line[1]}"; echo "${line[0]} )"; (( i++ )); done < |
| 72 |
# index.patches |
| 73 |
#PATCH1=( src/topp_ |
| 74 |
#topp.f-r1.16.2.5-r1.16.2.6.diff ) |
| 75 |
#PATCH2=( . |
| 76 |
#configure-r1.372.2.18-r1.372.2.19.diff ) |
| 77 |
|
| 78 |
DESCRIPTION="Protein X-ray crystallography toolkit" |
| 79 |
HOMEPAGE="http://www.ccp4.ac.uk/" |
| 80 |
SRC_URI="${SRC}/${PV}/${MY_P}-core-src.tar.gz" |
| 81 |
# patch tarball from upstream |
| 82 |
[[ -n ${UPDATE} ]] && SRC_URI="${SRC_URI} ${SRC}/${PV}/updates/${P}-src-patch-${UPDATE}.tar.gz" |
| 83 |
# patches created by us |
| 84 |
[[ -n ${PATCHDATE} ]] && SRC_URI="${SRC_URI} http://dev.gentooexperimental.org/~jlec/science-dist/${PV}-${PATCHDATE}-updates.patch.bz2" |
| 85 |
|
| 86 |
for i in $(seq $PATCH_TOT); do |
| 87 |
NAME="PATCH${i}[1]" |
| 88 |
SRC_URI="${SRC_URI} |
| 89 |
${SRC}/${PV}/patches/${!NAME}" |
| 90 |
done |
| 91 |
|
| 92 |
LICENSE="ccp4" |
| 93 |
SLOT="0" |
| 94 |
KEYWORDS="~amd64 ~x86 ~amd64-linux ~x86-linux" |
| 95 |
IUSE="" |
| 96 |
|
| 97 |
RDEPEND=" |
| 98 |
media-libs/jpeg:0 |
| 99 |
app-shells/tcsh |
| 100 |
!<sci-chemistry/ccp4-6.1.3 |
| 101 |
sci-libs/cbflib |
| 102 |
=sci-libs/fftw-2* |
| 103 |
sci-libs/mmdb |
| 104 |
sci-libs/monomer-db |
| 105 |
virtual/lapack |
| 106 |
virtual/blas" |
| 107 |
DEPEND="${RDEPEND}" |
| 108 |
|
| 109 |
S="${WORKDIR}/${MY_P}" |
| 110 |
|
| 111 |
src_prepare() { |
| 112 |
einfo "Applying upstream patches ..." |
| 113 |
for patch in $(seq $PATCH_TOT); do |
| 114 |
base="PATCH${patch}" |
| 115 |
dir=$(eval echo \${${base}[0]}) |
| 116 |
p=$(eval echo \${${base}[1]}) |
| 117 |
pushd "${dir}" >& /dev/null |
| 118 |
ccp_patch "${DISTDIR}/${p}" |
| 119 |
popd >& /dev/null |
| 120 |
done |
| 121 |
einfo "Done." |
| 122 |
echo |
| 123 |
|
| 124 |
[[ -n ${PATCHDATE} ]] && epatch "${WORKDIR}"/${PV}-${PATCHDATE}-updates.patch |
| 125 |
|
| 126 |
einfo "Applying Gentoo patches ..." |
| 127 |
# it tries to create libdir, bindir etc on live system in configure |
| 128 |
ccp_patch "${FILESDIR}"/${PV}-dont-make-dirs-in-configure.patch |
| 129 |
|
| 130 |
# gerror_ gets defined twice on ppc if you're using gfortran/g95 |
| 131 |
ccp_patch "${FILESDIR}"/6.0.2-ppc-double-define-gerror.patch |
| 132 |
|
| 133 |
# make creation of libccif.so smooth |
| 134 |
ccp_patch "${FILESDIR}"/${PV}-ccif-shared.patch |
| 135 |
|
| 136 |
# lets try to build libmmdb seperatly |
| 137 |
ccp_patch "${FILESDIR}"/${PV}-dont-build-mmdb.patch |
| 138 |
|
| 139 |
# unbundle libjpeg and cbflib |
| 140 |
ccp_patch "${FILESDIR}"/${PV}-unbundle-libs.patch |
| 141 |
|
| 142 |
# Fix missing DESTIDR |
| 143 |
ccp_patch "${FILESDIR}"/${PV}-destdir.patch |
| 144 |
|
| 145 |
# not installing during build |
| 146 |
ccp_patch "${FILESDIR}"/${PV}-noinstall.patch |
| 147 |
sed \ |
| 148 |
-e '/SHARE_INST/s:$(libdir):$(DESTDIR)/$(libdir):g' \ |
| 149 |
-i configure || die |
| 150 |
|
| 151 |
einfo "Done." # done applying Gentoo patches |
| 152 |
echo |
| 153 |
|
| 154 |
sed \ |
| 155 |
-e "s:/usr:${EPREFIX}/usr:g" \ |
| 156 |
-e 's:-Wl,-rpath,$CLIB::g' \ |
| 157 |
-e 's: -rpath $CLIB::g' \ |
| 158 |
-e 's: -I${srcdir}/include/cpp_c_headers::g' \ |
| 159 |
-i configure || die |
| 160 |
|
| 161 |
gnuconfig_update |
| 162 |
} |
| 163 |
|
| 164 |
src_configure() { |
| 165 |
|
| 166 |
rm -rf lib/DiffractionImage/{jpg,CBFlib} || die |
| 167 |
|
| 168 |
# Build system is broken if we set LDFLAGS |
| 169 |
userldflags="${LDFLAGS}" |
| 170 |
export SHARED_LIB_FLAGS="${LDFLAGS}" |
| 171 |
unset LDFLAGS |
| 172 |
|
| 173 |
# GENTOO_OSNAME can be one of: |
| 174 |
# irix irix64 sunos sunos64 aix hpux osf1 linux freebsd |
| 175 |
# linux_compaq_compilers linux_intel_compilers generic Darwin |
| 176 |
# ia64_linux_intel Darwin_ibm_compilers linux_ibm_compilers |
| 177 |
if [[ "${FORTRANC}" = "ifc" ]]; then |
| 178 |
if use ia64; then |
| 179 |
GENTOO_OSNAME="ia64_linux_intel" |
| 180 |
else |
| 181 |
# Should be valid for x86, maybe amd64 |
| 182 |
GENTOO_OSNAME="linux_intel_compilers" |
| 183 |
fi |
| 184 |
else |
| 185 |
# Should be valid for x86 and amd64, at least |
| 186 |
GENTOO_OSNAME="linux" |
| 187 |
fi |
| 188 |
|
| 189 |
# Sets up env |
| 190 |
ln -s \ |
| 191 |
ccp4.setup-bash \ |
| 192 |
"${S}"/include/ccp4.setup |
| 193 |
|
| 194 |
# We agree to the license by emerging this, set in LICENSE |
| 195 |
sed -i \ |
| 196 |
-e "s~^\(^agreed=\).*~\1yes~g" \ |
| 197 |
"${S}"/configure |
| 198 |
|
| 199 |
# Fix up variables -- need to reset CCP4_MASTER at install-time |
| 200 |
sed -i \ |
| 201 |
-e "s~^\(setenv CCP4_MASTER.*\)/.*~\1"${WORKDIR}"~g" \ |
| 202 |
-e "s~^\(setenv CCP4I_TCLTK.*\)/usr/local/bin~\1${EPREFIX}/usr/bin~g" \ |
| 203 |
"${S}"/include/ccp4.setup* |
| 204 |
|
| 205 |
# Set up variables for build |
| 206 |
source "${S}"/include/ccp4.setup |
| 207 |
|
| 208 |
export CC=$(tc-getCC) |
| 209 |
export CXX=$(tc-getCXX) |
| 210 |
export COPTIM=${CFLAGS} |
| 211 |
export CXXOPTIM=${CXXFLAGS} |
| 212 |
# Default to -O2 if FFLAGS is unset |
| 213 |
export FC=${FORTRANC} |
| 214 |
export FOPTIM=${FFLAGS:- -O2} |
| 215 |
# export CCP4_SCR="${T}" |
| 216 |
|
| 217 |
# Fix linking |
| 218 |
# $(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++ && \ |
| 219 |
export SHARE_LIB="\ |
| 220 |
$(tc-getCC) ${userldflags} -shared -Wl,-soname,libccp4c.so -o libccp4c.so \${CORELIBOBJS} \${CGENERALOBJS} \${CUCOBJS} \${CMTZOBJS} \${CMAPOBJS} \${CSYMOBJS} -L.. -lccif $(gcc-config -L | awk -F: '{for(i=1; i<=NF; i++) printf " -L%s", $i}') -lm && \ |
| 221 |
${FORTRANC} ${userldflags} -shared -Wl,-soname,libccp4f.so -o libccp4f.so \${FORTRANLOBJS} \${FINTERFACEOBJS} -L.. -lccif -L. -lccp4c -lmmdb $(gcc-config -L | awk -F: '{for(i=1; i<=NF; i++) printf " -L%s", $i}') -lstdc++ -lgfortran -lm" |
| 222 |
|
| 223 |
# Can't use econf, configure rejects unknown options like --prefix |
| 224 |
./configure \ |
| 225 |
--onlylibs \ |
| 226 |
--with-shared-libs \ |
| 227 |
--with-fftw="${EPREFIX}"/usr \ |
| 228 |
--with-warnings \ |
| 229 |
--disable-cctbx \ |
| 230 |
--disable-clipper \ |
| 231 |
--tmpdir="${TMPDIR}" \ |
| 232 |
--bindir="${EPREFIX}"/usr/libexec/ccp4/bin/ \ |
| 233 |
--libdir="${EPREFIX}"/usr/$(get_libdir) \ |
| 234 |
${GENTOO_OSNAME} || die "econf failed" |
| 235 |
} |
| 236 |
|
| 237 |
src_compile() { |
| 238 |
emake -j1 \ |
| 239 |
DESTDIR="${ED}" onlylib || die "emake failed" |
| 240 |
} |
| 241 |
|
| 242 |
src_install() { |
| 243 |
# Set up variables for build |
| 244 |
source "${S}"/include/ccp4.setup |
| 245 |
|
| 246 |
emake -j1 \ |
| 247 |
DESTDIR="${ED}" \ |
| 248 |
includedir="${EPREFIX}"/usr/include \ |
| 249 |
library_includedir="${EPREFIX}"/usr/include \ |
| 250 |
install || die |
| 251 |
|
| 252 |
# Libs |
| 253 |
for file in "${S}"/lib/*; do |
| 254 |
if [[ -d ${file} ]]; then |
| 255 |
continue |
| 256 |
elif [[ -x ${file} ]]; then |
| 257 |
dolib.so ${file} || die |
| 258 |
else |
| 259 |
insinto /usr/$(get_libdir) |
| 260 |
doins ${file} || die |
| 261 |
fi |
| 262 |
done |
| 263 |
|
| 264 |
# Fix libdir in all *.la files |
| 265 |
sed -i \ |
| 266 |
-e "s:^\(libdir=\).*:\1\'${EPREFIX}/usr/$(get_libdir)\':g" \ |
| 267 |
"${ED}"/usr/$(get_libdir)/*.la || die |
| 268 |
|
| 269 |
# Data |
| 270 |
insinto /usr/share/ccp4/data/ |
| 271 |
doins -r "${S}"/lib/data/{*.PARM,*.prt,*.lib,*.dic,*.idl,*.cif,*.resource,*.york,*.hist,fraglib,reference_structures} || die |
| 272 |
dodoc "${S}"/lib/data/*.doc || die |
| 273 |
newdoc "${S}"/lib/data/README DATA-README || die |
| 274 |
} |
| 275 |
|
| 276 |
# Epatch wrapper for bulk patching |
| 277 |
ccp_patch() { |
| 278 |
EPATCH_SINGLE_MSG=" ${1##*/} ..." epatch ${1} |
| 279 |
} |
Archives