+# $Header: /var/cvsroot/gentoo-x86/sci-libs/ccp4-libs/ChangeLog,v 1.63 2015/03/16 13:44:11 jlec Exp $

+

+*ccp4-libs-6.1.3-r16 (16 Mar 2015)

+

+ 16 Mar 2015; Justin Lecher <jlec@gentoo.org> +ccp4-libs-6.1.3-r16.ebuild,

+ +files/ccp4-libs-6.1.3-force.patch,

+ +files/ccp4-libs-6.1.3-format-security.patch:

+ Force error on build failure, bug #543028; fix for format-security

+Hash: SHA512

+AUX ccp4-libs-6.1.3-force.patch 448 SHA256 36e31119c685097ed2ba98220e7813dc5d8265cd6fd36d2c202cc87e6a1fc2de SHA512 1045f711ce04f60ae53018c424673eb0b759daef18888b584ff3db106f1fb883f2a902f93a76427ba860e0ded8204db62e36ced23f05f03967e4eefa72a3561c WHIRLPOOL 72b63f206825e7d2cb4aa0a7c1ac783df71b0b695be0eb16a300c88c01080593da61e83f12003cd2c3d10b71b5c12f6a4b3b0d9867ae53a1bc7fe0fa7a88a98c

+AUX ccp4-libs-6.1.3-format-security.patch 626 SHA256 19085719bf567a1f81cbc014773d1185dc3d1698eab463aa5048ad8e78d68eae SHA512 5ae84afa6f3af77abb4bb85ca92a548d61279ec816cef3e1972a268bfe0fd4f3e1d36fa437cb291b45922efd902c87b9a0575bc72e99b437e23d0d5d4c7d44b7 WHIRLPOOL f24b17170bbbde9660881cf348e5f284a38e77c0b7a27eeec9e42c68af5d7f8f5faf8ff590e94959f3c2a7cda93e65d57ebe57449bea1082e975186e41f5aeaf

+EBUILD ccp4-libs-6.1.3-r16.ebuild 11322 SHA256 7cec4339f653ce4b0a1c6ac9fa2d8be4b39b43e0ac9400355c98c3cd4c6eb5cc SHA512 f550ff86a0f30fedeeece8226a997868d767dd4d12a130e7a8ede64ab3589f9443166da4be09fc243dc62c7d1dd10d1b30e1967aa5424d489efb8c8ce210e00e WHIRLPOOL f0b5967c467522b2c509d9ecb6443620ec5c15566424a4c1a25f6a6617446768232647b900284bf0071bc750cf2e16a8655854f88ecfec22c5253a8665bc4f08

+MISC ChangeLog 9684 SHA256 79d330d2931880f969a9973b4916775214ec18cb3334e2cdd5aa7367ab72d86a SHA512 78cfd056536fce839ff2d7e97043edc3e430a6c8fe2a0bf15714c37d7b837b69dfd7b0776515980623d3b25c3d4121d896db8d723e1a5b39e0f16fc572cef4f0 WHIRLPOOL 1a4bfed48f325d442bbb6e47265d33e52dc7eae2039f103e88ed22290f5f29b0545a18dc739542ad34050fe967397004b73e99da5baf88cfb7253cd35c3cd7d8

+Version: GnuPG v2.0

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+iWhiLe/E2L3CT7HXLkjq

+=+YBH

+# Copyright 1999-2015 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-r16.ebuild,v 1.1 2015/03/16 13:44:11 jlec Exp $

+

+EAPI=5

+

+PYTHON_COMPAT=( python2_7 )

+

+inherit autotools eutils fortran-2 gnuconfig multilib python-single-r1 toolchain-funcs

+

+SRC="ftp://ftp.ccp4.ac.uk/ccp4"

+

+#UPDATE="04_03_09"

+#PATCHDATE="090511"

+

+MY_P="${P/-libs}"

+

+PATCH_TOT="0"

+

+DESCRIPTION="Protein X-ray crystallography toolkit - Libraries"

+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.gentoo.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 ~ppc ~x86 ~amd64-linux ~x86-linux"

+IUSE=""

+

+REQUIRED_USE="${PYTHON_REQUIRED_USE}"

+

+RDEPEND="

+ ${PYTHON_DEPS}

+ !<sci-chemistry/ccp4-6.1.3

+ !<sci-chemistry/ccp4-apps-${PV}-r10

+ app-shells/tcsh

+ dev-lang/tcl

+ >=sci-libs/cbflib-0.9.2.2

+ sci-libs/fftw:2.1

+ sci-libs/mmdb:0

+ sci-libs/monomer-db

+ sci-libs/ssm

+ virtual/jpeg:0=

+ virtual/lapack

+ virtual/blas"

+DEPEND="${RDEPEND}

+ virtual/pkgconfig"

+

+S="${WORKDIR}/${MY_P}"

+

+MAKEOPTS+=" -j1"

+

+pkg_setup() {

+ fortran-2_pkg_setup

+ python-single-r1_pkg_setup

+}

+

+src_prepare() {

+ tc-export PKG_CONFIG RANLIB AR

+

+ sed \

+ -e "/^AR/s:ar:$(tc-getAR):g" \

+ -i lib/src/Makefile.in src/Makefile.in src/ccp4mapwish_/Makefile.in lib/ccif/Makefile.in || die

+

+ 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-ng2.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

+

+ # Fix upstreams code

+ ccp_patch "${FILESDIR}"/${PV}-impl-dec.patch

+

+ # use pkg-config to detect BLAS/LAPACK

+ ccp_patch "${FILESDIR}"/${PV}-lapack.patch

+

+ # proto type changing in version 0.9.2.2

+ ccp_patch "${FILESDIR}"/${PV}-cbf.patch

+

+ # proto type changing in version 0.9.2.2

+ ccp_patch "${FILESDIR}"/${PV}-no-pypath.patch

+

+ ccp_patch "${FILESDIR}"/${P}-force.patch

+

+ ccp_patch "${FILESDIR}"/${P}-format-security.patch

+

+ einfo "Done." # done applying Gentoo patches

+ echo

+

+ # not needed, we have it extra

+ rm -rf src/rapper/{libxml2,gc7.0} || die

+

+ 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' \

+ -e 's:sleep 1:sleep .2:g' \

+ -i configure || die

+

+ gnuconfig_update

+

+ for i in lib/DiffractionImage src/rapper src/pisa; do

+ pushd ${i} > /dev/null

+ sed 's:-g::g' -i configure* || die

+ [[ -f configure.in ]] && mv configure.{in,ac}

+ eautoreconf

+ popd > /dev/null

+ done

+

+ ## unbundle libssm

+ sed -e '/libdir/s:ssm::g' -i Makefile.in || die

+ find ./lib/src/mmdb ./lib/ssm ./lib/clipper ./lib/fftw lib/lapack -delete || die

+}

+

+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 [[ "$(tc-getFC)" = "ifort" ]]; 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 || die

+

+ # We agree to the license by emerging this, set in LICENSE

+ sed -i \

+ -e "s~^\(^agreed=\).*~\1yes~g" \

+ "${S}"/configure || die

+

+ # Fix up variables -- need to reset CCP4_MASTER at install-time

+ sed -i \

+ -e "s~^\(setenv CCP4_MASTER.*\)/.*~\1${WORKDIR}~g" \

+ -e "s~^\(export CCP4_MASTER.*\)/.*~\1${WORKDIR}~g" \

+ -e "s~^\(.*export CBIN=.*\)\$CCP4.*~\1\$CCP4/libexec/ccp4/bin/~g" \

+ -e "s~^\(.*setenv CBIN .*\)\$CCP4.*~\1\$CCP4/libexec/ccp4/bin/~g" \

+ -e "s~^\(setenv CCP4I_TCLTK.*\)/usr/local/bin~\1${EPREFIX}/usr/bin~g" \

+ "${S}"/include/ccp4.setup* || die

+

+ # Set up variables for build

+ source "${S}"/include/ccp4.setup-sh

+

+ export CC=$(tc-getCC)

+ export CXX=$(tc-getCXX)

+ export COPTIM=${CFLAGS}

+ export CXXOPTIM=${CXXFLAGS}

+ # Default to -O2 if FFLAGS is unset

+ export FC=$(tc-getFC)

+ export FOPTIM=${FFLAGS:- -O2}

+

+ 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 && \

+ $(tc-getFC) ${userldflags} -shared -Wl,-soname,libccp4f.so -o libccp4f.so \${FORTRANLOBJS} \${FINTERFACEOBJS} -L../ccif/ -lccif -L. -lccp4c $($(tc-getPKG_CONFIG) --libs mmdb) $(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 \

+ --disable-ssm \

+ --tmpdir="${TMPDIR}" \

+ --bindir="${EPREFIX}/usr/libexec/ccp4/bin/" \

+ --libdir="${EPREFIX}/usr/$(get_libdir)" \

+ ${GENTOO_OSNAME} || die "configure failed"

+}

+

+src_compile() {

+ emake DESTDIR="${D}" onlylib

+}

+

+src_install() {

+ # Set up variables for build

+ source "${S}"/include/ccp4.setup-sh

+

+ emake \

+ DESTDIR="${D}" \

+ includedir="${EPREFIX}/usr/include" \

+ library_includedir="${EPREFIX}/usr/include" \

+ install

+

+ sed \

+ -e "330,1000d" \

+ -i "${S}"/include/ccp4.setup-sh || die

+

+ sed \

+ -e "378,1000d" \

+ -i "${S}"/include/ccp4.setup-csh || die

+

+ sed \

+ -e "s:-${PV/-r*/}::g" \

+ -e "s:^\(.*export CCP4_MASTER=\).*:\1${EPREFIX}/usr:g" \

+ -e "s:^\(.*setenv CCP4_MASTER\).*:\1 ${EPREFIX}/usr:g" \

+ -e "s:^\(.*export CCP4=\).*CCP4_MASTER.*:\1${EPREFIX}/usr:g" \

+ -e "s:^\(.*setenv CCP4\).*CCP4_MASTER.*:\1 ${EPREFIX}/usr:g" \

+ -e "s:^\(.*export CCP4_SCR=\).*:\1${EPREFIX}/tmp:g" \

+ -e "s:^\(.*setenv CCP4_SCR \).*:\1${EPREFIX}/tmp:g" \

+ -e "s:^\(.*export BINSORT_SCR=\).*:\1${EPREFIX}/tmp:g" \

+ -e "s:^\(.*setenv BINSORT_SCR \).*:\1${EPREFIX}/tmp:g" \

+ -e "s:^\(.*export CCP4I_TOP=\).*:\1${EPREFIX}/usr/$(get_libdir)/ccp4/ccp4i:g" \

+ -e "s:^\(.*setenv CCP4I_TOP \).*:\1${EPREFIX}/usr/$(get_libdir)/ccp4/ccp4i:g" \

+ -e "s:^\(.*export CCP4I_TCLTK=\).*:\1${EPREFIX}/usr/bin:g" \

+ -e "s:^\(.*setenv CCP4I_TCLTK \).*:\1${EPREFIX}/usr/bin:g" \

+ -e "s:^\(.*export CCP4I_HELP=\).*:\1${EPREFIX}/usr/$(get_libdir)/ccp4/ccp4i/help:g" \

+ -e "s:^\(.*setenv CCP4I_HELP \).*:\1${EPREFIX}/usr/$(get_libdir)/ccp4/ccp4i/help:g" \

+ -e "s:^\(.*export CBIN=\).*:\1${EPREFIX}/usr/libexec/ccp4/bin:g" \

+ -e "s:^\(.*setenv CBIN \).*:\1${EPREFIX}/usr/libexec/ccp4/bin:g" \

+ -e "s:^\(.*export CCP4_BIN=\).*:\1${EPREFIX}/usr/libexec/ccp4/bin:g" \

+ -e "s:^\(.*setenv CCP4_BIN \).*:\1${EPREFIX}/usr/libexec/ccp4/bin:g" \

+ -e "s:^\(.*export CLIBD_MON=\).*:\1${EPREFIX}/usr/share/ccp4/data/monomers/:g" \

+ -e "s:^\(.*setenv CLIBD_MON \).*:\1${EPREFIX}/usr/share/ccp4/data/monomers/:g" \

+ -e "s:^\(.*export CLIBD=\).*:\1${EPREFIX}/usr/share/ccp4/data:g" \

+ -e "s:^\(.*setenv CLIBD \).*:\1${EPREFIX}/usr/share/ccp4/data:g" \

+ -e "s:^\(.*export CCP4_LIB=\).*:\1${EPREFIX}/usr/$(get_libdir):g" \

+ -e "s:^\(.*setenv CCP4_LIB \).*:\1${EPREFIX}/usr/$(get_libdir):g" \

+ -e "s:^\(.*export CCP4_BROWSER=\).*:\1firefox:g" \

+ -e "s:^\(.*setenv CCP4_BROWSER \).*:\1firefox:g" \

+ -e "s:^\(.*export MANPATH=\).*:\1\${MANPATH}:g" \

+ -e "s:^\(.*setenv MANPATH \).*:\1\${MANPATH}:g" \

+ -e "s:^\(.*export DBCCP4I_TOP=\).*:\1${EPREFIX}/usr/share/ccp4/dbccp4i:g" \

+ -e "s:^\(.*setenv DBCCP4I_TOP \).*:\1${EPREFIX}/usr/share/ccp4/dbccp4i:g" \

+ -e "s:^\(.*export MOLREPLIB=\).*:\1${EPREFIX}/usr/share/ccp4/data/monomers/:g" \

+ -e "s:^\(.*setenv MOLREPLIB \).*:\1${EPREFIX}/usr/share/ccp4/data/monomers/:g" \

+ -e "s:^\(.*export CDOC=\).*:\1${EPREFIX}/usr/share/doc:g" \

+ -e "s:^\(.*setenv CDOC \).*:\1${EPREFIX}/usr/share/doc:g" \

+ -e "s:^\(.*export CEXAM=\).*:\1${EPREFIX}/usr/share/doc/examples:g" \

+ -e "s:^\(.*setenv CEXAM \).*:\1${EPREFIX}/usr/share/doc/examples:g" \

+ -e "s:^\(.*export CINCL=\).*:\1${EPREFIX}/usr/share/ccp4/include:g" \

+ -e "s:^\(.*setenv CINCL \).*:\1${EPREFIX}/usr/share/ccp4/include:g" \

+ -e "s:\$CLIB/font84.dat:\"${EPREFIX}/usr/$(get_libdir)/font84.dat\":g" \

+ -e "s:\$CLIB/cif_mmdic.lib:\"${EPREFIX}/usr/$(get_libdir)/cif_mmdic.lib\":g" \

+ -e '/# .*LD_LIBRARY_PATH specifies/,/^$/d' \

+ -e '/CLIB=/d' \

+ -e '/CLIB /d' \

+ -e '/CLIBS=/d' \

+ -e '/CLIBS /d' \

+ -e "/alias/d" \

+ -e "/CCP4_HELPDIR/d" \

+ -e "/IMOSFLM_VERSION/d" \

+ -i "${S}"/include/ccp4.setup* || die

+

+ # Don't check for updates on every sourcing of /etc/profile

+ sed -i \

+ -e "s:\(eval python.*\):#\1:g" \

+ "${S}"/include/ccp4.setup* || die

+

+ # Libs

+ for file in "${S}"/lib/*; do

+ if [[ -d ${file} ]]; then

+ continue

+ elif [[ -x ${file} ]]; then

+ dolib.so ${file}

+ else

+ insinto /usr/$(get_libdir)

+ doins ${file}

+ fi

+ done

+

+ prune_libtool_files

+

+ sed \

+ -e 's:test "LD_LIBRARY_PATH":test "$LD_LIBRARY_PATH":g' \

+ -i "${S}"/include/ccp4.setup-sh || die

+

+ # Setup scripts

+ insinto /etc/profile.d

+ newins "${S}"/include/ccp4.setup-csh 40ccp4.setup.csh

+ newins "${S}"/include/ccp4.setup-sh 40ccp4.setup.sh

+ rm -f "${S}"/include/ccp4.setup*

+

+ # Data

+ insinto /usr/share/ccp4/data/

+ doins -r "${S}"/lib/data/{*.PARM,*.prt,*.lib,*.dic,*.idl,*.cif,*.resource,*.york,*.hist,fraglib,reference_structures}

+

+ # Environment files, setup scripts, etc.

+ rm -rf "${S}"/include/{ccp4.setup*,COPYING,cpp_c_headers} || die

+ insinto /usr/share/ccp4/

+ doins -r "${S}"/include

+

+ dodoc "${S}"/lib/data/*.doc

+ newdoc "${S}"/lib/data/README DATA-README

+}

+

+pkg_postinst() {

+ einfo "The Web browser defaults to firefox. Change CCP4_BROWSER"

+ einfo "in ${EPREFIX}/etc/profile.d/40ccp4.setup* to modify this."

+}

+

+# Epatch wrapper for bulk patching

+ccp_patch() {

+ EPATCH_SINGLE_MSG=" ${1##*/} ..." epatch ${1}

+}

+ Makefile.in | 2 +-

+ 1 file changed, 1 insertion(+), 1 deletion(-)

+

+diff --git a/Makefile.in b/Makefile.in

+index 60033eb..13ddbd0 100755

+--- a/Makefile.in

++++ b/Makefile.in

+@@ -53,7 +53,7 @@ clipper: FORCE fftw

+

+ diffractionImg:

+ if test -n "$(diffimdir)"; then cd $(top_srcdir)/$(diffimdir); \

+- $(MAKE) -i $(MFLAGS) $(MVARS); else true; fi

++ $(MAKE) $(MFLAGS) $(MVARS); fi

+

+ ssm:

+ if test -n "$(ssmdir)"; then cd $(top_srcdir)/$(ssmdir); \

+ lib/DiffractionImage/DiffractionImagePythonInterface.cpp | 2 +-

+ 1 file changed, 1 insertion(+), 1 deletion(-)

+

+diff --git a/lib/DiffractionImage/DiffractionImagePythonInterface.cpp b/lib/DiffractionImage/DiffractionImagePythonInterface.cpp

+index f729fc5..4c24e82 100755

+--- a/lib/DiffractionImage/DiffractionImagePythonInterface.cpp

++++ b/lib/DiffractionImage/DiffractionImagePythonInterface.cpp

+@@ -867,7 +867,7 @@ SWIG_Python_AddErrorMsg(const char* mesg)

+ Py_DECREF(old_str);

+ Py_DECREF(value);

+ } else {

+- PyErr_Format(PyExc_RuntimeError, mesg);

++ PyErr_Format(PyExc_RuntimeError, "%s", mesg);

+ }

+ }

+