From c31214c33b7faafaedd8affad558dace6a8089c4 Mon Sep 17 00:00:00 2001 From: Justin Lecher Date: Tue, 29 Jun 2010 19:55:41 +0000 Subject: [PATCH] Change way of installation, fixed insecure runpaths Package-Manager: portage-2.2_rc67/cvs/Linux x86_64 --- sci-libs/ccp4-libs/ChangeLog | 9 +- sci-libs/ccp4-libs/Manifest | 15 +- sci-libs/ccp4-libs/ccp4-libs-6.1.3-r3.ebuild | 231 ++++++++++++++++++ sci-libs/ccp4-libs/files/6.1.3-destdir.patch | 0 .../files/6.1.3-dont-build-mmdb.patch | 15 -- .../ccp4-libs/files/6.1.3-noinstall.patch | 143 +++++++++++ 6 files changed, 391 insertions(+), 22 deletions(-) create mode 100644 sci-libs/ccp4-libs/ccp4-libs-6.1.3-r3.ebuild create mode 100644 sci-libs/ccp4-libs/files/6.1.3-destdir.patch create mode 100644 sci-libs/ccp4-libs/files/6.1.3-noinstall.patch diff --git a/sci-libs/ccp4-libs/ChangeLog b/sci-libs/ccp4-libs/ChangeLog index 05ee496e8104..68ded4b4b867 100644 --- a/sci-libs/ccp4-libs/ChangeLog +++ b/sci-libs/ccp4-libs/ChangeLog @@ -1,6 +1,13 @@ # 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 1.6 2010/05/22 10:04:27 jlec Exp $ +# $Header: /var/cvsroot/gentoo-x86/sci-libs/ccp4-libs/ChangeLog,v 1.7 2010/06/29 19:55:41 jlec Exp $ + +*ccp4-libs-6.1.3-r3 (29 Jun 2010) + + 29 Jun 2010; Justin Lecher +files/6.1.3-destdir.patch, + files/6.1.3-dont-build-mmdb.patch, +files/6.1.3-noinstall.patch, + +ccp4-libs-6.1.3-r3.ebuild: + Change way of installation, fixed insecure runpaths *ccp4-libs-6.1.3-r2 (22 May 2010) diff --git a/sci-libs/ccp4-libs/Manifest b/sci-libs/ccp4-libs/Manifest index 746bc7557575..82e8456834d2 100644 --- a/sci-libs/ccp4-libs/Manifest +++ b/sci-libs/ccp4-libs/Manifest @@ -3,21 +3,24 @@ Hash: SHA1 AUX 6.0.2-ppc-double-define-gerror.patch 424 RMD160 4f012233446fffa61e8d775a19a0dacea4ae2234 SHA1 209fa1bdf1e59b4055177e343b69e487d9183fb3 SHA256 09c2c1e0176bee94673b21609b2b00118b2bb4f5942f3feb35c64c61c99ebc61 AUX 6.1.3-ccif-shared.patch 1668 RMD160 803687b13dbe93aaeed8264a73dfe7303b5fcdfb SHA1 3d833aefea874c08e61140613b0a5c75a90e0382 SHA256 57c201ee81e3fd95f174fecfd810ddf12509f0c2bfb1b2f317f893561eb60e3f -AUX 6.1.3-dont-build-mmdb.patch 861 RMD160 f2cfce178bb421c36e1b1114435f8e0ee97102d8 SHA1 d39439dfd9c23781a232551ef9690df6f9ea7681 SHA256 fb4711188e41e6be0a86464425fd9b04ae5dba58fb00202c7234182d002dc795 +AUX 6.1.3-destdir.patch 0 RMD160 9c1185a5c5e9fc54612808977ee8f548b2258d31 SHA1 da39a3ee5e6b4b0d3255bfef95601890afd80709 SHA256 e3b0c44298fc1c149afbf4c8996fb92427ae41e4649b934ca495991b7852b855 +AUX 6.1.3-dont-build-mmdb.patch 324 RMD160 b9ad1f72415d7a95fba58d07440c19c78062ddb6 SHA1 4d53ff4106b4ff216def790177801f1c50da8cce SHA256 06d4bf3ee012e123f141e8dcaf1abffd9b0fbee9720f8c490d78dabe9e944f66 AUX 6.1.3-dont-make-dirs-in-configure.patch 2866 RMD160 ba49e45ab609a42a2d93b96f55af913bf9625610 SHA1 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/dev/null +++ b/sci-libs/ccp4-libs/ccp4-libs-6.1.3-r3.ebuild @@ -0,0 +1,231 @@ +# 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-r3.ebuild,v 1.1 2010/06/29 19:55:41 jlec 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/${!NAME}" +done + +LICENSE="ccp4" +SLOT="0" +KEYWORDS="~amd64 ~x86 ~amd64-linux ~x86-linux" +IUSE="" + +RDEPEND=" + media-libs/jpeg:0 + app-shells/tcsh + !& /dev/null + ccp_patch "${DISTDIR}/${p}" + popd >& /dev/null + done + einfo "Done." + echo + + [[ -n ${PATCHDATE} ]] && epatch "${WORKDIR}"/${PV}-${PATCHDATE}-updates.patch + + einfo "Applying Gentoo patches ..." + # 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}"/${PV}-unbundle-libs.patch + + # Fix missing DESTIDR + ccp_patch "${FILESDIR}"/${PV}-destdir.patch + + # not installing during build + ccp_patch "${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.. -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.. -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} +} diff --git a/sci-libs/ccp4-libs/files/6.1.3-destdir.patch b/sci-libs/ccp4-libs/files/6.1.3-destdir.patch new file mode 100644 index 000000000000..e69de29bb2d1 diff --git a/sci-libs/ccp4-libs/files/6.1.3-dont-build-mmdb.patch b/sci-libs/ccp4-libs/files/6.1.3-dont-build-mmdb.patch index b3fefacdac54..ac52001245e6 100644 --- a/sci-libs/ccp4-libs/files/6.1.3-dont-build-mmdb.patch +++ b/sci-libs/ccp4-libs/files/6.1.3-dont-build-mmdb.patch @@ -9,18 +9,3 @@ # maybe create shared library $(SHARE_LIB) ---- lib/src/Makefile.in 2009-06-18 15:44:08.000000000 +0200 -+++ lib/src/Makefile.in.new 2009-08-11 12:17:53.000000000 +0200 -@@ -716,11 +716,9 @@ - rm -f $(DESTDIR)$(includedir)/mmdb/$$f; \ - done - --install : all install-ccp4HEADERS install-mmdbHEADERS -- $(INSTALL_DATA) `pwd`/$(LMMDB) $(libdir)/$(LMMDB) -+install : all install-ccp4HEADERS - $(INSTALL_DATA) `pwd`/$(LC) $(libdir)/$(LC) - $(INSTALL_DATA) `pwd`/$(LF) $(libdir)/$(LF) -- $(RANLIB) $(libdir)/$(LMMDB) - $(RANLIB) $(libdir)/$(LC) - $(RANLIB) $(libdir)/$(LF) - $(SHARE_INST) diff --git a/sci-libs/ccp4-libs/files/6.1.3-noinstall.patch b/sci-libs/ccp4-libs/files/6.1.3-noinstall.patch new file mode 100644 index 000000000000..bfb526c35661 --- /dev/null +++ b/sci-libs/ccp4-libs/files/6.1.3-noinstall.patch @@ -0,0 +1,143 @@ +diff --git a/Makefile.in b/Makefile.in +index ac552fe..fab1a87 100755 +--- a/Makefile.in ++++ b/Makefile.in +@@ -30,8 +30,7 @@ lapacklib : FORCE + + cciflib : FORCE + if test -n "$(ccifdir)"; then cd $(ccifdir); \ +- $(MAKE) $(MFLAGS) $(MVARS); else true; fi; \ +- $(MAKE) install ++ $(MAKE) $(MFLAGS) $(MVARS); else true; fi + + cctbx: FORCE + if test -n "$(cctbxdir)"; then cd $(top_srcdir)/$(cctbxdir); \ +@@ -40,8 +39,7 @@ cctbx: FORCE + libdir : FORCE lapacklib cciflib libccp4 clipper ssm diffractionImg + + libccp4: FORCE +- cd lib/src; $(MAKE) $(MFLAGS) $(MVARS) ; \ +- $(MAKE) install ++ cd lib/src; $(MAKE) $(MFLAGS) $(MVARS) + + share : FORCE + cd share; $(MAKE) $(MFLAGS) $(MVARS) +@@ -51,18 +49,15 @@ ccp4i : FORCE + + clipper: FORCE fftw + if test -n "$(clipperdir)"; then cd $(top_srcdir)/lib/clipper/clipper; \ +- $(MAKE) -i $(MFLAGS) $(MVARS); else true; fi ; \ +- $(MAKE) install ++ $(MAKE) -i $(MFLAGS) $(MVARS); else true; fi + + diffractionImg: + if test -n "$(diffimdir)"; then cd $(top_srcdir)/$(diffimdir); \ +- $(MAKE) -i $(MFLAGS) $(MVARS); else true; fi ; \ +- $(MAKE) install ++ $(MAKE) -i $(MFLAGS) $(MVARS); else true; fi + + ssm: + if test -n "$(ssmdir)"; then cd $(top_srcdir)/$(ssmdir); \ +- $(MAKE) -i $(MFLAGS) $(MVARS); else true; fi ; \ +- $(MAKE) install ++ $(MAKE) -i $(MFLAGS) $(MVARS); else true; fi + + fftw: FORCE + if test -n "$(fftwdir)"; then cd $(top_srcdir)/lib/fftw; \ +@@ -79,7 +74,7 @@ unsupported : FORCE libdir + $(MAKE) $(MFLAGS) $(MVARS); else true; fi + + datadir : FORCE libdir +- cd lib/data; $(MAKE) $(MFLAGS) $(MVARS) ++ cd lib/data; $(MAKE) $(MFLAGS) $(MVARS) font84.dat + + xwindir : FORCE libdir + if test -f x-windows/Makefile; then cd x-windows; \ +diff --git a/lib/ccif/Makefile.in b/lib/ccif/Makefile.in +index 975f1d9..75eda9f 100755 +--- a/lib/ccif/Makefile.in ++++ b/lib/ccif/Makefile.in +@@ -371,11 +371,11 @@ condition.h condition_list.h: $(srcdir)/condition.list $(srcdir)/condition.awk + # + + install : all +- $(INSTALL_DATA) `pwd`/$L $(libdir)/$L +- $(INSTALL_DATA) `pwd`/$(CIFMMLIB) $(libdir)/$(CIFMMLIB) +- $(RANLIB) $(libdir)/$L ++ $(RANLIB) $L ++ $(INSTALL_DATA) `pwd`/$L $(DESTDIR)/$(libdir)/$L ++ $(INSTALL_DATA) `pwd`/$(CIFMMLIB) $(DESTDIR)$(libdir)/$(CIFMMLIB) + if (test -f $(SHARED_LIB_NAME)); then \ +- $(INSTALL_DATA) `pwd`/$(SHARED_LIB_NAME) $(libdir)/$(SHARED_LIB_NAME); \ ++ $(INSTALL_DATA) `pwd`/$(SHARED_LIB_NAME) $(DESTDIR)/$(libdir)/$(SHARED_LIB_NAME); \ + fi + + uninstall : +diff --git a/lib/data/Makefile.in b/lib/data/Makefile.in +index cc25c5c..7445ca5 100755 +--- a/lib/data/Makefile.in ++++ b/lib/data/Makefile.in +@@ -30,9 +30,9 @@ font84.dat : fontpack $(srcdir)/font84.ascii + + install : all + -rm -f font84.dat +- test -f font84.ascii || $(LNS) $(srcdir)/font84.ascii . ++ test -f font84.ascii || $(LNS) $(DESTIDIR)/$(srcdir)/font84.ascii . + ./fontpack +- $(INSTALL) `pwd`/font84.dat $(libdir)/font84.dat ++ $(INSTALL) `pwd`/font84.dat $(DESTDIR)/$(libdir)/font84.dat + + uninstall : + -rm -f $(libdir)/font84.dat +diff --git a/lib/src/Makefile.in b/lib/src/Makefile.in +index c23f488..3a611f1 100755 +--- a/lib/src/Makefile.in ++++ b/lib/src/Makefile.in +@@ -685,7 +685,7 @@ testlib : $(srcdir)/testlib.f $(LF) + # + + install-ccp4HEADERS: $(ccp4_HEADERS) +- if test ! -d $(DESTDIR)$(includedir)/ccp4; then mkdir $(DESTDIR)$(includedir)/ccp4; fi ++ if test ! -d $(DESTDIR)$(includedir)/ccp4; then mkdir -p $(DESTDIR)$(includedir)/ccp4; fi + @list='$(ccp4_HEADERS)'; for p in $$list; do \ + if test -f "$$p"; then d=; else d="$(srcdir)/"; fi; \ + f="`echo $$p | sed -e 's|^.*/||'`"; \ +@@ -716,13 +716,11 @@ uninstall-mmdbHEADERS: + rm -f $(DESTDIR)$(includedir)/mmdb/$$f; \ + done + +-install : all install-ccp4HEADERS install-mmdbHEADERS +- $(INSTALL_DATA) `pwd`/$(LMMDB) $(libdir)/$(LMMDB) +- $(INSTALL_DATA) `pwd`/$(LC) $(libdir)/$(LC) +- $(INSTALL_DATA) `pwd`/$(LF) $(libdir)/$(LF) +- $(RANLIB) $(libdir)/$(LMMDB) +- $(RANLIB) $(libdir)/$(LC) +- $(RANLIB) $(libdir)/$(LF) ++install : all install-ccp4HEADERS ++ $(RANLIB) $(LC) ++ $(RANLIB) $(LF) ++ $(INSTALL_DATA) `pwd`/$(LC) $(DESTDIR)/$(libdir)/$(LC) ++ $(INSTALL_DATA) `pwd`/$(LF) $(DESTDIR)/$(libdir)/$(LF) + $(SHARE_INST) + + uninstall : uninstall-ccp4HEADERS uninstall-mmdbHEADERS +diff --git a/lib/ssm/Makefile.in b/lib/ssm/Makefile.in +index 27d3aa2..0a14fe5 100755 +--- a/lib/ssm/Makefile.in ++++ b/lib/ssm/Makefile.in +@@ -375,12 +375,12 @@ distclean-libtool: + uninstall-info-am: + install-library_includeHEADERS: $(library_include_HEADERS) + @$(NORMAL_INSTALL) +- test -z "$(library_includedir)" || $(mkdir_p) "$(DESTDIR)$(library_includedir)" ++ test -z "$(library_includedir)" || $(mkdir_p) "$(DESTDIR)$(library_includedir)/ssm" + @list='$(library_include_HEADERS)'; for p in $$list; do \ + if test -f "$$p"; then d=; else d="$(srcdir)/"; fi; \ + f=$(am__strip_dir) \ +- echo " $(library_includeHEADERS_INSTALL) '$$d$$p' '$(DESTDIR)$(library_includedir)/$$f'"; \ +- $(library_includeHEADERS_INSTALL) "$$d$$p" "$(DESTDIR)$(library_includedir)/$$f"; \ ++ echo " $(library_includeHEADERS_INSTALL) '$$d$$p' '$(DESTDIR)$(library_includedir)/ssm/$$f'"; \ ++ $(library_includeHEADERS_INSTALL) "$$d$$p" "$(DESTDIR)$(library_includedir)/ssm/$$f"; \ + done + + uninstall-library_includeHEADERS: -- 2.26.2