From 7d62034735e700ca67e977470d79f5571b15b221 Mon Sep 17 00:00:00 2001 From: Justin Lecher Date: Mon, 26 Oct 2015 08:29:56 +0100 Subject: Drop "CCP4: Software for Macromolecular Crystallography" obsoletes: Gentoo-Bug: https://bugs.gentoo.org/show_bug.cgi?id=160190 Gentoo-Bug: https://bugs.gentoo.org/show_bug.cgi?id=324059 Gentoo-Bug: https://bugs.gentoo.org/show_bug.cgi?id=332485 Gentoo-Bug: https://bugs.gentoo.org/show_bug.cgi?id=367771 Gentoo-Bug: https://bugs.gentoo.org/show_bug.cgi?id=367773 Gentoo-Bug: https://bugs.gentoo.org/show_bug.cgi?id=383227 Gentoo-Bug: https://bugs.gentoo.org/show_bug.cgi?id=448756 Gentoo-Bug: https://bugs.gentoo.org/show_bug.cgi?id=460502 Gentoo-Bug: https://bugs.gentoo.org/show_bug.cgi?id=460504 Gentoo-Bug: https://bugs.gentoo.org/show_bug.cgi?id=466936 Gentoo-Bug: https://bugs.gentoo.org/show_bug.cgi?id=467040 Gentoo-Bug: https://bugs.gentoo.org/show_bug.cgi?id=467048 Gentoo-Bug: https://bugs.gentoo.org/show_bug.cgi?id=476580 Gentoo-Bug: https://bugs.gentoo.org/show_bug.cgi?id=478580 Gentoo-Bug: https://bugs.gentoo.org/show_bug.cgi?id=478586 Gentoo-Bug: https://bugs.gentoo.org/show_bug.cgi?id=478588 Gentoo-Bug: https://bugs.gentoo.org/show_bug.cgi?id=478594 Gentoo-Bug: https://bugs.gentoo.org/show_bug.cgi?id=478604 Gentoo-Bug: https://bugs.gentoo.org/show_bug.cgi?id=521646 Gentoo-Bug: https://bugs.gentoo.org/show_bug.cgi?id=528512 Gentoo-Bug: https://bugs.gentoo.org/show_bug.cgi?id=530878 Gentoo-Bug: https://bugs.gentoo.org/show_bug.cgi?id=540760 Gentoo-Bug: https://bugs.gentoo.org/show_bug.cgi?id=555614 Gentoo-Bug: https://bugs.gentoo.org/show_bug.cgi?id=556498 Gentoo-Bug: https://bugs.gentoo.org/show_bug.cgi?id=557038 Gentoo-Bug: https://bugs.gentoo.org/show_bug.cgi?id=561196 Gentoo-Bug: https://bugs.gentoo.org/show_bug.cgi?id=562780 Signed-off-by: Justin Lecher --- sci-libs/ccp4-libs/Manifest | 1 - sci-libs/ccp4-libs/ccp4-libs-6.1.3-r16.ebuild | 359 ------------- .../files/6.0.2-ppc-double-define-gerror.patch | 11 - sci-libs/ccp4-libs/files/6.1.3-cbf.patch | 16 - sci-libs/ccp4-libs/files/6.1.3-ccif-shared.patch | 33 -- .../ccp4-libs/files/6.1.3-dont-build-mmdb.patch | 24 - .../files/6.1.3-dont-make-dirs-in-configure.patch | 87 --- sci-libs/ccp4-libs/files/6.1.3-glibc2.10.patch | 22 - sci-libs/ccp4-libs/files/6.1.3-impl-dec.patch | 140 ----- sci-libs/ccp4-libs/files/6.1.3-lapack.patch | 597 --------------------- sci-libs/ccp4-libs/files/6.1.3-link-proberly.patch | 230 -------- sci-libs/ccp4-libs/files/6.1.3-no-pypath.patch | 87 --- sci-libs/ccp4-libs/files/6.1.3-noinstall.patch | 142 ----- sci-libs/ccp4-libs/files/6.1.3-overflows.patch | 35 -- .../ccp4-libs/files/6.1.3-unbundle-libs-ng.patch | 367 ------------- .../ccp4-libs/files/6.1.3-unbundle-libs-ng2.patch | 395 -------------- sci-libs/ccp4-libs/files/6.1.3-unbundle-libs.patch | 203 ------- .../ccp4-libs/files/ccp4-libs-6.1.3-force.patch | 16 - .../files/ccp4-libs-6.1.3-format-security.patch | 16 - sci-libs/ccp4-libs/metadata.xml | 9 - 20 files changed, 2790 deletions(-) delete mode 100644 sci-libs/ccp4-libs/Manifest delete mode 100644 sci-libs/ccp4-libs/ccp4-libs-6.1.3-r16.ebuild delete mode 100644 sci-libs/ccp4-libs/files/6.0.2-ppc-double-define-gerror.patch delete mode 100644 sci-libs/ccp4-libs/files/6.1.3-cbf.patch delete mode 100644 sci-libs/ccp4-libs/files/6.1.3-ccif-shared.patch delete mode 100644 sci-libs/ccp4-libs/files/6.1.3-dont-build-mmdb.patch delete mode 100644 sci-libs/ccp4-libs/files/6.1.3-dont-make-dirs-in-configure.patch delete mode 100644 sci-libs/ccp4-libs/files/6.1.3-glibc2.10.patch delete mode 100644 sci-libs/ccp4-libs/files/6.1.3-impl-dec.patch delete mode 100644 sci-libs/ccp4-libs/files/6.1.3-lapack.patch delete mode 100644 sci-libs/ccp4-libs/files/6.1.3-link-proberly.patch delete mode 100644 sci-libs/ccp4-libs/files/6.1.3-no-pypath.patch delete mode 100644 sci-libs/ccp4-libs/files/6.1.3-noinstall.patch delete mode 100644 sci-libs/ccp4-libs/files/6.1.3-overflows.patch delete mode 100644 sci-libs/ccp4-libs/files/6.1.3-unbundle-libs-ng.patch delete mode 100644 sci-libs/ccp4-libs/files/6.1.3-unbundle-libs-ng2.patch delete mode 100644 sci-libs/ccp4-libs/files/6.1.3-unbundle-libs.patch delete mode 100644 sci-libs/ccp4-libs/files/ccp4-libs-6.1.3-force.patch delete mode 100644 sci-libs/ccp4-libs/files/ccp4-libs-6.1.3-format-security.patch delete mode 100644 sci-libs/ccp4-libs/metadata.xml (limited to 'sci-libs/ccp4-libs') diff --git a/sci-libs/ccp4-libs/Manifest b/sci-libs/ccp4-libs/Manifest deleted file mode 100644 index 9d3fe2806365..000000000000 --- a/sci-libs/ccp4-libs/Manifest +++ /dev/null @@ -1 +0,0 @@ -DIST ccp4-6.1.3-core-src.tar.gz 242134076 SHA256 1e529c660e7f390ec0feca9d45caa00a2813d23156c10a2747c427117293c324 SHA512 413eba806107ebcdbd93e9122275463709133d9b2a9ce44ae57a6c2350465a47ba66ad9875237aead74f5d422c0104f58f728ab37a757b10d82cde92af444c20 WHIRLPOOL faebf8ee7920013bc3d0e83565207dca1f31ba0b5c92fe1eae4b740f70ff2031d95787fa0d545b09c853d25657c08973527e43de02fddc086988123ca2a6339c diff --git a/sci-libs/ccp4-libs/ccp4-libs-6.1.3-r16.ebuild b/sci-libs/ccp4-libs/ccp4-libs-6.1.3-r16.ebuild deleted file mode 100644 index dcd741637048..000000000000 --- a/sci-libs/ccp4-libs/ccp4-libs-6.1.3-r16.ebuild +++ /dev/null @@ -1,359 +0,0 @@ -# Copyright 1999-2015 Gentoo Foundation -# Distributed under the terms of the GNU General Public License v2 -# $Id$ - -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} https://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/${!NAME}" -done - -LICENSE="ccp4" -SLOT="0" -KEYWORDS="amd64 ppc x86 ~amd64-linux ~x86-linux" -IUSE="minimal" - -REQUIRED_USE="${PYTHON_REQUIRED_USE}" - -RDEPEND=" - ${PYTHON_DEPS} - !=sci-libs/cbflib-0.9.2.2 - sci-libs/fftw:2.1 - sci-libs/mmdb:0 - sci-libs/monomer-db - sci-libs/ssm - virtual/jpeg:0= - virtual/lapack - virtual/blas" -DEPEND="${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 "${S}"/include/ccp4.setup-sh || die - - if ! use minimal; then - # Setup scripts - insinto /etc/profile.d - newins "${S}"/include/ccp4.setup-csh 40ccp4.setup.csh - newins "${S}"/include/ccp4.setup-sh 40ccp4.setup.sh - - # Data - insinto /usr/share/ccp4/data/ - doins -r "${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 - fi - - rm -f "${S}"/include/ccp4.setup* || die - - dodoc "${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} -} diff --git a/sci-libs/ccp4-libs/files/6.0.2-ppc-double-define-gerror.patch b/sci-libs/ccp4-libs/files/6.0.2-ppc-double-define-gerror.patch deleted file mode 100644 index a77d9494a05c..000000000000 --- a/sci-libs/ccp4-libs/files/6.0.2-ppc-double-define-gerror.patch +++ /dev/null @@ -1,11 +0,0 @@ ---- ccp4-6.0.1.orig/lib/src/library_f.c 2006-06-12 07:06:22.000000000 -0700 -+++ ccp4-6.0.1/lib/src/library_f.c 2006-06-12 07:21:56.000000000 -0700 -@@ -716,7 +716,7 @@ - - #endif /* end of apple xlf support */ - --#if ( defined (__linux__) && defined (_CALL_SYSV) ) -+#if ( defined (__linux__) && defined (_CALL_SYSV) && ! defined(G95) && ! defined (GFORTRAN) ) - /* linuxppc xlf support */ - void gerror_ (str, Lstr) - char *str; diff --git a/sci-libs/ccp4-libs/files/6.1.3-cbf.patch b/sci-libs/ccp4-libs/files/6.1.3-cbf.patch deleted file mode 100644 index 6930fcad766a..000000000000 --- a/sci-libs/ccp4-libs/files/6.1.3-cbf.patch +++ /dev/null @@ -1,16 +0,0 @@ - lib/DiffractionImage/DiffractionImageCBF.cpp | 2 +- - 1 files changed, 1 insertions(+), 1 deletions(-) - -diff --git a/lib/DiffractionImage/DiffractionImageCBF.cpp b/lib/DiffractionImage/DiffractionImageCBF.cpp -index 69b32b0..3ffee26 100755 ---- a/lib/DiffractionImage/DiffractionImageCBF.cpp -+++ b/lib/DiffractionImage/DiffractionImageCBF.cpp -@@ -62,7 +62,7 @@ namespace DI - int* tmpimg; - tmpimg=new int[height*width]; - test= cbf_decompress_byte_offset ((void *)tmpimg,sizeof(int),sign, -- nelements,&nread,0,32,sign,ccbbff,0, -+ nelements,&nread,0,0,32,sign,ccbbff,0, - byte_ord.c_str(),2,(size_t) width, - (size_t) height,1,(size_t) padding); - for(int i=0;i/dev/null && \ - cat /dev/null > /tmp/$$.cache_file && \ -- ./configure $xopts --libdir=${libdir} --srcdir=${srcdir}/lib/ccif --cache-file=/tmp/$$.cache_file ) || \ -- ./configure $xopts --libdir=${libdir} --srcdir=${srcdir}/lib/ccif -+ ./configure $xopts --libdir=${libdir} --srcdir=${srcdir}/lib/ccif --cache-file=/tmp/$$.cache_file --enable-shared-lib ) || \ -+ ./configure $xopts --libdir=${libdir} --srcdir=${srcdir}/lib/ccif --enable-shared-lib - rm -f /tmp/$$.cache_file - if [ "X$LIBFOPTIM" != "X" ]; then - FOPTIM=$FOPTIM_save ---- lib/ccif/configure 2009-08-04 22:35:37.000000000 +0200 -+++ lib/ccif/configure.new 2009-08-04 23:05:44.000000000 +0200 -@@ -5568,7 +5568,7 @@ - enable_shared_lib=no - ;; - -- i?86-unknown-linux | i?86-pc-linux-gnu ) -+ i?86-unknown-linux | i?86-pc-linux-gnu | x86_64-unknown-linux-gnu) - if test $enable_shared_lib = yes ; then - - SO_LOC_VAR='LD_LIBRARY_PATH' -@@ -5585,7 +5585,7 @@ - else - SHARED_LIB_PATH='LD_LIBRARY_PATH=`pwd`' - fi -- SHARED_LIB_CMD='$(CC) $(SHARED_LIB_FLAGS) -shared -Wl,-soname -Wl,$(SHARED_LIB_NAME) '"$SHARED_LIB_RESTRICT"' ${LOBJS} $(RX_LFLAG) -o $(SHARED_LIB_NAME)' -+ SHARED_LIB_CMD='$(CC) $(SHARED_LIB_FLAGS) -shared -Wl,-soname -Wl,$(SHARED_LIB_NAME) '"$SHARED_LIB_RESTRICT"' ${LOBJS} $(RX_LFLAG) -o $(SHARED_LIB_NAME) -lm' - # SHARED_LIB_EXPORTS_CMD='cp libccif-universal-ld.lis $(SHARED_LIB_EXPORTS)' - SHARED_LIB_EXPORTS_CMD='' - fi 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 deleted file mode 100644 index b3147ad81bbf..000000000000 --- a/sci-libs/ccp4-libs/files/6.1.3-dont-build-mmdb.patch +++ /dev/null @@ -1,24 +0,0 @@ -diff --git a/lib/src/Makefile.in b/lib/src/Makefile.in -index c23f488..b32dd1e 100755 ---- a/lib/src/Makefile.in -+++ b/lib/src/Makefile.in -@@ -176,7 +176,7 @@ $(mmdbsrcdir)/mmdb_sbase0.h $(mmdbsrcdir)/hybrid_36.h - - ##### Makefile targets ###### - --all: fsplit $(LMMDB) $(LC) $(LF) $(SCRIPT_MODULES) -+all: fsplit $(LC) $(LF) $(SCRIPT_MODULES) - # maybe create shared library - $(SHARE_LIB) - -@@ -717,10 +717,8 @@ uninstall-mmdbHEADERS: - 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) - $(SHARE_INST) diff --git a/sci-libs/ccp4-libs/files/6.1.3-dont-make-dirs-in-configure.patch b/sci-libs/ccp4-libs/files/6.1.3-dont-make-dirs-in-configure.patch deleted file mode 100644 index 583697cea0a1..000000000000 --- a/sci-libs/ccp4-libs/files/6.1.3-dont-make-dirs-in-configure.patch +++ /dev/null @@ -1,87 +0,0 @@ ---- ccp4-6.0.99e.orig/configure 2008-07-31 10:37:22.000000000 -0700 -+++ ccp4-6.0.99e/configure 2008-07-31 10:39:18.000000000 -0700 -@@ -643,45 +643,45 @@ - # echo "! Beware -- the $system installation isn't properly tested." ; } - syswarn='echo; echo "! Beware -- the $system installation is not properly tested."' - --if test -z "$onlylibs" ; then -- for i in CCP4_SCR BINSORT_SCR; do -- if ( eval test -d \$$i || eval mkdir -p \$$i ) ; then : -- else -- eval echo "! No directory \$$i and can\'t create it." -- echo " Check the value of $i." -- badvar=1 -- fi -- done -- -- for i in libdir bindir includedir; do -- if ( eval test -d \$$i || eval mkdir -p \$$i ) ; then : -- else -- eval echo "! No directory \$$i and can\'t create it." -- echo " Check the argument of --$i." -- badvar=1 -- fi -- done -- -- for i in $dotsrc $dotunsupp $dotunsuppsrc $dotdeprec $dotdeprecsrc ./lib ./lib/src ./lib/data ./ccp4i/etc/unix $mosflmdir/lib $mosflmdir/bin $mosflmdir/cbf/lib ; do -- if test -d $i || mkdir $i; then : -- else -- eval echo "! No directory $i and can\'t create it." -- badvar=1 -- fi -- done --else -- # Kludge to fool the "Makefile" target in the top-level CCP4 -- # Makefile into not trying to remake src/Makefile.in -- for i in $srcdir/src $srcdir/lib/src ; do -- if test -d $i || mkdir $i; then -- if ! test -f $i/Makefile.in ; then -- echo -- echo "onlylibs: making dummy file $i/Makefile.in" -- touch $i/Makefile.in -- fi -- fi -- done --fi -+#if test -z "$onlylibs" ; then -+# for i in CCP4_SCR BINSORT_SCR; do -+# if ( eval test -d \$$i || eval mkdir -p \$$i ) ; then : -+# else -+# eval echo "! No directory \$$i and can\'t create it." -+# echo " Check the value of $i." -+# badvar=1 -+# fi -+# done -+# -+# for i in libdir bindir includedir; do -+# if ( eval test -d \$$i || eval mkdir -p \$$i ) ; then : -+# else -+# eval echo "! No directory \$$i and can\'t create it." -+# echo " Check the argument of --$i." -+# badvar=1 -+# fi -+# done -+# -+# for i in $dotsrc $dotunsupp $dotunsuppsrc $dotdeprec $dotdeprecsrc ./lib ./lib/src ./lib/data ./ccp4i/etc/unix $mosflmdir/lib $mosflmdir/bin $mosflmdir/cbf/lib ; do -+# if test -d $i || mkdir $i; then : -+# else -+# eval echo "! No directory $i and can\'t create it." -+# badvar=1 -+# fi -+# done -+#else -+# # Kludge to fool the "Makefile" target in the top-level CCP4 -+# # Makefile into not trying to remake src/Makefile.in -+# for i in $srcdir/src $srcdir/lib/src ; do -+# if test -d $i || mkdir $i; then -+# if ! test -f $i/Makefile.in ; then -+# echo -+# echo "onlylibs: making dummy file $i/Makefile.in" -+# touch $i/Makefile.in -+# fi -+# fi -+# done -+#fi - - ### sanity checks - diff --git a/sci-libs/ccp4-libs/files/6.1.3-glibc2.10.patch b/sci-libs/ccp4-libs/files/6.1.3-glibc2.10.patch deleted file mode 100644 index 6e3997647955..000000000000 --- a/sci-libs/ccp4-libs/files/6.1.3-glibc2.10.patch +++ /dev/null @@ -1,22 +0,0 @@ ---- lib/ccif/configure.in 2009-06-10 13:52:59.000000000 +0200 -+++ lib/ccif/configure.in.new 2009-06-10 14:04:31.000000000 +0200 -@@ -363,7 +363,7 @@ - fi - SHARED_LIB_CMD='$(LD) $(SHARED_LIB_FLAGS) -shared -soname $(SHARED_LIB_NAME) \\\ - --whole-archive '"$SHARED_LIB_RESTRICT"' $L \\\ -- $(RX_LFLAG) -o $(SHARED_LIB_NAME)' -+ $(RX_LFLAG) -o $(SHARED_LIB_NAME) -lm' - SHARED_LIB_EXPORTS_CMD='cp libccif-universal-ld.lis $(SHARED_LIB_EXPORTS)' - fi - ;; ---- lib/ccif/configure 2009-06-10 14:26:58.000000000 +0200 -+++ lib/ccif/configure.new 2009-06-10 14:43:31.000000000 +0200 -@@ -1807,7 +1807,7 @@ - SHARED_LIB_CMD='$(LD) $(SHARED_LIB_CFLAGS) -shared -soname \\\ - $(SHARED_LIB_NAME) \\\ - --whole-archive $L \\\ -- -o $(SHARED_LIB_NAME)' -+ -o $(SHARED_LIB_NAME) -lm' - SHARED_LIB_EXPORTS_CMD='' - fi - ;; diff --git a/sci-libs/ccp4-libs/files/6.1.3-impl-dec.patch b/sci-libs/ccp4-libs/files/6.1.3-impl-dec.patch deleted file mode 100644 index 8bfa7db8cbff..000000000000 --- a/sci-libs/ccp4-libs/files/6.1.3-impl-dec.patch +++ /dev/null @@ -1,140 +0,0 @@ -diff --git a/lib/DiffractionImage/Bruker/FRM_LIB.c b/lib/DiffractionImage/Bruker/FRM_LIB.c -index bfda882..f821e04 100755 ---- a/lib/DiffractionImage/Bruker/FRM_LIB.c -+++ b/lib/DiffractionImage/Bruker/FRM_LIB.c -@@ -38,6 +38,8 @@ FRM_LIB: Routines for reading, writing, and handling frame files. - #include "sys/types.h" /* _open, etc. */ - #include "sys/stat.h" /* _open, etc. */ - -+#include -+ - #ifndef _MSC_VER - int min(int a, int b) - { -diff --git a/lib/DiffractionImage/MAR/mar300_header.c b/lib/DiffractionImage/MAR/mar300_header.c -index 1a933de..1c40c32 100755 ---- a/lib/DiffractionImage/MAR/mar300_header.c -+++ b/lib/DiffractionImage/MAR/mar300_header.c -@@ -23,6 +23,9 @@ - */ - #include "mar300_header.h" - -+#include -+#include -+ - /* - * Local functions - */ -diff --git a/lib/DiffractionImage/MAR/mar345_header.c b/lib/DiffractionImage/MAR/mar345_header.c -index a8351ea..16d0f7b 100755 ---- a/lib/DiffractionImage/MAR/mar345_header.c -+++ b/lib/DiffractionImage/MAR/mar345_header.c -@@ -32,6 +32,9 @@ - */ - #include "mar345_header.h" - -+#include -+#include -+ - /* - * Definitions - */ -diff --git a/lib/DiffractionImage/MAR/nb_header.c b/lib/DiffractionImage/MAR/nb_header.c -index 07f2741..6364ca4 100755 ---- a/lib/DiffractionImage/MAR/nb_header.c -+++ b/lib/DiffractionImage/MAR/nb_header.c -@@ -20,6 +20,8 @@ - #include - #endif - -+#include -+#include - /* - * mar software include files - */ -diff --git a/lib/DiffractionImage/MAR/swap.c b/lib/DiffractionImage/MAR/swap.c -index 443bb8c..0d96b3f 100755 ---- a/lib/DiffractionImage/MAR/swap.c -+++ b/lib/DiffractionImage/MAR/swap.c -@@ -10,6 +10,9 @@ - * - **********************************************************************/ - -+#define _XOPEN_SOURCE -+#include -+ - void swaplong(); - void swapshort(); - -diff --git a/lib/ccif/f_interface.c b/lib/ccif/f_interface.c -index 0f6a6b7..a09dc48 100755 ---- a/lib/ccif/f_interface.c -+++ b/lib/ccif/f_interface.c -@@ -25,6 +25,7 @@ - ********************************************************************/ - - #include "stdpccts.h" -+#include - - /* This file is terribly organised, and badly needs re-doing. There is probably - * scope for splitting this into three modules: -diff --git a/lib/src/ccp4_general_f.c b/lib/src/ccp4_general_f.c -index 8b5d04f..74ee3f7 100755 ---- a/lib/src/ccp4_general_f.c -+++ b/lib/src/ccp4_general_f.c -@@ -26,6 +26,7 @@ - #include - #include - #include -+#include - #include "ccp4_errno.h" - #include "ccp4_fortran.h" - #include "ccp4_parser.h" -diff --git a/lib/src/ccp4_program.c b/lib/src/ccp4_program.c -index 3e83d4d..bb3e975 100755 ---- a/lib/src/ccp4_program.c -+++ b/lib/src/ccp4_program.c -@@ -25,6 +25,7 @@ - #include - #include - #include -+#include - #include "ccp4_program.h" - #include "ccp4_parser.h" - #include "ccp4_utils.h" -diff --git a/lib/src/fsplit.c b/lib/src/fsplit.c -index ee8af24..c6fb3cd 100755 ---- a/lib/src/fsplit.c -+++ b/lib/src/fsplit.c -@@ -50,6 +50,7 @@ static char sccsid[] = "@(#)fsplit.c 5.5 (Berkeley) 3/12/91"; - #include - #include - #include -+#include - - /* - * usage: fsplit [-e efile] ... [file] -diff --git a/src/clipper_progs/src/pirate/compress42.c b/src/clipper_progs/src/pirate/compress42.c -index ea52e96..30dbd56 100755 ---- a/src/clipper_progs/src/pirate/compress42.c -+++ b/src/clipper_progs/src/pirate/compress42.c -@@ -142,6 +142,7 @@ - #include - #include - #include -+#include - - #ifdef DIRENT - # include -diff --git a/src/mtz2cif_/mtz2cif.c b/src/mtz2cif_/mtz2cif.c -index e224430..c7b82f4 100755 ---- a/src/mtz2cif_/mtz2cif.c -+++ b/src/mtz2cif_/mtz2cif.c -@@ -28,6 +28,7 @@ - #include "cmtzlib.h" - #include "ccp4_parser.h" - #include "ccp4_general.h" -+#include "ccp4_program.h" - #include "csymlib.h" - #include "mtz2cif_lib.h" - diff --git a/sci-libs/ccp4-libs/files/6.1.3-lapack.patch b/sci-libs/ccp4-libs/files/6.1.3-lapack.patch deleted file mode 100644 index 0463b3719525..000000000000 --- a/sci-libs/ccp4-libs/files/6.1.3-lapack.patch +++ /dev/null @@ -1,597 +0,0 @@ -diff --git a/configure b/configure -index 833f483..bcfa62d 100755 ---- a/configure -+++ b/configure -@@ -3226,574 +3226,14 @@ else - echo - echo "Warning: this option has not been extensively tested!" - echo "Please report problems to ccp4@ccp4.ac.uk" -- # Search for vendor LAPACK/BLAS first -- if test ! "$with_netlib_lapack" ; then -- # Initialise variables to blank -- lapackdir= -- XLAPACK_LIB= -- # Possible directories to check for vendor or pre-existing LAPACK or -- # BLAS - add to these if you want to test others -- trydirs="`echo $LD_LIBRARY_PATH |sed -e s/:/\ /g` /lib /usr/lib /usr/local/lib" -- # Possible library names -- # These are the names like xxxx where the library will be libxxxx.a -- # or libxxxx.so -- echo -- echo "Guessing names for native/vendor LAPACK and/or BLAS libraries" -- echo "on this system" -- case $system in -- linux | linux64 | linux32 ) -- # linux users will usually have them in /usr/lib but don't call it -- trylapack="lapack" -- tryblas="blas" -- # if code is non_shared then this can lead to problems. both blas and lapack -- # need to be resolved even if they are not called! -- if test "$non_shared" = yes; then -- echo "You are compiling linux non_shared. This sometimes causes problems " -- echo " so checking for requirements." -- echo "Checking: try to link library against test program" -- if test -f testlink.f || test -f testlink ; then -- rm -f testlink* -- fi -- cat > testlink.f <& /dev/null ) 2>&1; } && test -s testlink ; then -- # Compilation was okay -- echo "... only -llapack needed" -- XLAPACK_LIB="-llapack" -- # Set the next two variables so that configure -- # doesn't try to build netlib libraries -- LAPACKLIB="lapack" -- noblas=yes -- trylapack= -- tryblas= -- else -- echo "more than just -llapack needed...." -- test_compile="$FC $FOPTIM $XFFLAGS -o testlink testlink.f -llapack -lblas" -- echo $test_compile -- if { (eval $test_compile ) 2>&1; } && test -s testlink ; then -- # Compilation was okay -- echo "...-llapack and -lblas were needed" -- XLAPACK_LIB="-llapack -lblas" -- # Set the next two variables so that configure -- # doesn't try to build netlib libraries -- LAPACKLIB="lapack blas" -- noblas=no -- trylapack= -- tryblas= -- else -- echo "....could not find either lapack or blas." -- fi -- fi -- fi -- # add 64 bit libs -- case $system in -- linux64 ) trydirs="/usr/lib64 ${trydirs}" ;; -- esac -- -- ;; -- osf1) -- # OSF1 has dxml (old version) and cxml -- # which should have both lapack and blas -- trylapack="dxml cxml" -- tryblas= -- trydirs="${trydirs} /usr/shlib" -- ;; -- irix) -- # Additional search paths for IRIX -- trydirs="${trydirs} /usr/lib32" -- # SCSL should have both LAPACK and BLAS -- trylapack="scs" -- tryblas="blas" -- ;; -- irix64) -- # Additional search paths for IRIX64 -- trydirs="${trydirs} /usr/lib64" -- # SCSL should have both LAPACK and BLAS -- trylapack="scs" -- tryblas="blas" -- # Extra compiler flags? -- #XLAPACKFLAGS="-OPT:IEEE_NaN_inf=ON" -- ;; -- aix) -- # Additional search paths for AIX -- trydirs="${trydirs}" -- # AIX might have ESSL library - blas only I think -- trylapack= -- tryblas="essl" -- ;; -- hpux) -- # Additional search paths for HPUX -- trydirs="${trydirs} /opt/fortran/lib /opt/fortran/lib/pa2.0 /opt/mlib/lib/pa2.0" -- # HPUX should have both LAPACK (part of mlib) and BLAS -- trylapack="lapack" -- tryblas="blas" -- # Extra compiler flags? -- # +U77 required for ETIME function - this is already in XFFLAGS -- #XLAPACKFLAGS="+U77" -- ;; -- -- sunos | sunos64) -- # Sun has libraries with BLAS and LAPACK invoked using -- # -xlic_lib=sunperf -- trylapack= -- tryblas= -- echo "SunOs can use the Sun Performance Library (if installed)" -- echo "which has both BLAS and LAPACK 3.0" -- echo -- echo "Looking for a valid library to use..." -- echo -- # Loop over the possible library names -- try_libs="sunperf" -- for testlib in $try_libs -- do -- if test ! "$XLAPACK_LIB" ; then -- # Try running a test compile to see if this a valid library -- if test -f testlink.f || test -f testlink ; then -- rm -f testlink* -- fi -- cat > testlink.f <&1; } && test -s testlink ; then -- # Compilation was okay -- echo "... -xlic_lib=$testlib is okay" -- XLAPACK_LIB="-dalign -xlic_lib=$testlib" -- # Set the next two variables so that configure -- # doesn't try to build netlib libraries -- LAPACKLIB="$testlib" -- noblas=yes -- else -- # Compilation failed -- echo "... cannot use -xlic_lib=$testlib" -- fi -- # End of test for testlib -- fi -- # End of loop over possible lib names -- done -- # Report if no suitable library was found -- if test ! "$XLAPACK_LIB" ; then -- echo -- echo "No suitable LAPACK library was found." -- echo "This may be because the Sun Performance Library is not" -- echo "installed on your system" -- echo "Contact your system administrator or Sun vendor" -- fi -- ;; -- Darwin | Darwin32 | Darwin64 ) -- # Darwin has libraries with BLAS and LAPACK invoked using -- # -framework vecLib -- echo "Darwin can use the vecLib Library (if installed)" -- echo "which has both BLAS and LAPACK 3.0" -- echo -- # This is a special case so try running a test compile -- echo "Checking: try to link library against test program" -- if test -f testlink.f || test -f testlink ; then -- rm -f testlink* -- fi -- cat > testlink.f <&1; } && test -s testlink ; then -- # Compilation was okay -- echo "... -framework vecLib is okay" -- XLAPACK_LIB="-framework vecLib" -- # Set the next two variables so that configure -- # doesn't try to build netlib libraries -- LAPACKLIB="vecLib" -- noblas=yes -- else --#alternative linking for vecLib libraries -- case `uname -sr` in -- *Darwin\ 7.* ) test_compile="$FC $FOPTIM $XFFLAGS -o testlink testlink.f -lcc_dynamic -Wl,-framework -Wl,vecLib" ;; -- * ) test_compile="$FC $FOPTIM $XFFLAGS -o testlink testlink.f -Wl,-framework -Wl,vecLib" ;; -- esac -- -- echo $test_compile -- if { (eval $test_compile ) 2>&1; } && test -s testlink ; then -- # Compilation was okay -- echo "... -framework vecLib is okay" -- XLAPACK_LIB="-Wl,-framework -Wl,vecLib" -- # Set the next two variables so that configure -- # doesn't try to build netlib libraries -- LAPACKLIB="-Wl,-framework -Wl,vecLib" -- noblas=yes -- else -- # Compilation failed -- echo "... cannot use -framework vecLib" -- echo -- fi -- fi -- trylapack= -- tryblas= --# try the fink installation -- trydirs="${trydirs} /sw" -- ;; -- Darwin_ibm_compilers ) -- # Darwin has libraries with BLAS and LAPACK invoked using -- # -framework vecLib -- echo "Darwin can use the vecLib Library (if installed)" -- echo "which has both BLAS and LAPACK 3.0" -- echo -- # This is a special case so try running a test compile -- echo "Checking: try to link library against test program" -- if test -f testlink.f || test -f testlink ; then -- rm -f testlink* -- fi -- cat > testlink.f <&1; } && test -s testlink ; then -- # Compilation was okay -- echo "... -framework vecLib is okay" -- # Set the next two variables so that configure -- # doesn't try to build netlib libraries -- LAPACKLIB="vecLib" -- noblas=yes -- else -- # Compilation failed -- XLAPACK_LIB="" -- echo "... cannot use -framework vecLib" -- echo -- fi -- trylapack= -- tryblas= --# try the fink installation -- trydirs="${trydirs} /sw" -- ;; -- -- Darwin_intel_compilers) -- # Darwin has libraries with BLAS and LAPACK invoked using -- # -F vecLib -- echo "Darwin can use the vecLib Library (if installed)" -- echo "which has both BLAS and LAPACK 3.0" -- echo -- # This is a special case so try running a test compile -- echo "Checking: try to link library against test program" -- if test -f testlink.f || test -f testlink ; then -- rm -f testlink* -- fi -- cat > testlink.f <&1; } && test -s testlink ; then -- # Compilation was okay -- # doesn't try to build netlib libraries -- XLAPACK_LIB="-F /System/Library/Frameworks -Qoption,ld,-framework -Qoption,ld,vecLib" -- LAPACKLIB="vecLib" -- noblas=yes -- else -- # Compilation failed -- echo "... cannot use -framework vecLib" -- echo -- fi -- trylapack= -- tryblas= --# try the fink installation -- trydirs="${trydirs} /sw" -- ;; -- --# linux_ia64_sgi_altix) --# SGI Japan -- ia64_linux_intel) -- # Additional search paths for Linux/IA64 -- trydirs="${trydirs} /opt/scsl/lib /usr/lib /usr/local/lib" -- # SCSL and MKL should have both LAPACK and BLAS -- trylapack="mkl_lapack scs lapack" -- tryblas="mkl scs blas" -- ;; -- linux_ibm_compilers ) -- trylapack="lapack" -- tryblas="blas" -- ;; -- linux64_ibm_compilers ) -- trydirs="/usr/lib64 ${trydirs}" -- trylapack="lapack" -- tryblas="blas" -- ;; -- linux_intel_compilers ) -- trydirs="/usr/lib64 ${trydirs}" -- trylapack="mkl_lapack lapack" -- tryblas="mkl blas" -- ;; -- *) -- echo "The guesses for this system may not be correct - please" -- echo "e-mail ccp4@ccp4.ac.uk if you have any extra information" -- echo -- # Default guess is just libblas -- trylapack="lapack" -- tryblas="blas" -- ;; -- esac -- # -- # Search for LAPACK libraries -- # -- # Write out what the guesses are -- if test "$trylapack" ; then -- echo "Possible LAPACK library names for this system:" -- for libname in $trylapack -- do -- echo " lib$libname" -- done -- # Possible library name extensions -- tryexts="a so dylib" -- # Now loop over all the possibilities and see if anything -- # turns up -- echo -- echo "Searching for libraries with LAPACK and BLAS:" -- for testdir in $trydirs -- do -- for testlib in $trylapack -- do -- for ext in $tryexts -- do -- if test ! "$LAPACKLIB"; then -- if test -s "$testdir/lib$testlib.$ext" ; then -- echo "...found LAPACK library: $testdir/lib$testlib.$ext" -- # Now try and link to a test program -- # This is really for IRIX where libraries can be -- # o32 or n32 -- echo " Testing: try to link library against test program" -- if test -f testlink.f || test -f testlink ; then -- rm -f testlink* -- fi -- cat > testlink.f <&1; } && test -s testlink ; then -- have_lapack=yes -- else --# cover clapack option -- echo $test_ccompile -- if { (eval $test_ccompile ) 2>&1; } && test -s testlink ; then -- have_lapack=yes -- fi -- fi -- if test x$have_lapack = xyes ; then -- # This one is okay -- LAPACKLIB="$testlib" -- LAPACKDIR="$testdir" -- echo "Link ok - using lib$LAPACKLIB from $LAPACKDIR" -- # -- XLAPACK_LIB="-L$LAPACKDIR -l$LAPACKLIB" -- # -- # Test to see if we need BLAS too -- # Do this by trying to compile a test program -- # Use the LSAME test for now -- echo -- echo " * Checking whether we need a separate BLAS library *" -- echo " Testing: try linking library against test program" -- cd lib/lapack/test -- if test -f testlsame ; then -- rm -f testsame testlsame.o -- fi -- test_compile="$FC $FOPTIM $XFFLAGS -o testlsame lsametst.f -L$LAPACKDIR -l$LAPACKLIB" -- test_ccompile="$FC $FOPTIM $XFFLAGS -o testlsame lsametst.f -L$LAPACKDIR -l$LAPACKLIB $XLDFLAGS" -- echo $test_compile -- if { ( eval $test_compile) 2>&1;} && test -s testlsame ; then -- have_blas=yes -- else --#cblas route -- echo $test_ccompile -- if { ( eval $test_ccompile) 2>&1;} && test -s testlsame ; then -- have_blas=yes -- fi -- fi -- if test x$have_blas = xyes ; then -- echo "Test program okay - additional separate BLAS not required" -- noblas=yes -- else -- echo "Test program failed - need a separate BLAS library" -- fi -- cd ../../.. -- else -- # Keep looking -- echo " link failed - cannot use lib$testlib" -- fi -- fi -- fi -- done -- done -- if test ! "$LAPACKLIB"; then -- echo "...nothing in $testdir" -- fi -- done -- fi -- -- # If LAPACKLIB hasn't been set at this point then no LAPACK library -- # was found -- if test ! "$LAPACKLIB" ; then -- echo -- echo "No pre-existing LAPACK library found - NetLib LAPACK will be built instead" -- make_lapack=lapacklib -- fi -- # Look for possible BLAS -- if test ! "$noblas" ; then -- if test "$tryblas" ; then -- echo -- echo "Possible BLAS library names for this system:" -- for libname in $tryblas -- do -- echo " lib$libname" -- done -- # Possible library name extensions -- tryexts="a so" -- # Now loop over all the possibilities and see if anything -- # turns up -- echo -- echo "Searching for libraries with BLAS:" -- for testdir in $trydirs -- do -- for testlib in $tryblas -- do -- for ext in $tryexts -- do -- if test ! "$BLASLIB"; then -- if test -s "$testdir/lib$testlib.$ext" ; then -- echo "...found BLAS library: $testdir/lib$testlib.$ext" -- # Now try and link to a test program -- # This is really for IRIX where libraries can be -- # o32 or n32 -- echo " Testing: try to link library against test program" -- if test -f testlink.f || test -f testlink ; then -- rm -f testlink* -- fi -- cat > testlink.f <&1;} && test -s testlink ; then -- have_blas=yes -- else -- echo $test_ccompile -- if { ( eval $test_compile) 2>&1;} && test -s testlink ; then -- have_blas=yes -- fi -- fi -- if test x$have_blas = xyes ; then -- # This one is okay -- BLASLIB="$testlib" -- BLASDIR="$testdir" -- BLASEXT="$ext" -- echo "Link ok - using lib$BLASLIB from $BLASDIR" -- XLAPACK_LIB="$XLAPACK_LIB -L$BLASDIR -l$BLASLIB" -- else -- # Keep looking -- echo " link failed - cannot use lib$testlib" -- fi -- fi -- fi -- done -- done -- if test ! "$BLASLIB"; then -- echo "...nothing in $testdir" -- fi -- done -- fi -- # Do we need to build BLAS too? -- if test ! "$BLASLIB" ; then -- echo -- echo "No pre-existing BLAS library was found - NetLib BLAS will be built instead" -- echo "This may result in poorer performance of the LAPACK routines" -- make_blas=blaslib -- BLASLIB=blas -- BLASDIR="$srcdir/lib/lapack" -- BLASEXT="a" -- fi -- fi -+ # gentoo is clever -+ make_blas= -+ make_lapack= -+ BLASLIB=$(${PKG_CONFIG} --libs lapack) -+ LAPACKLIB=$(${PKG_CONFIG} --libs lapack) -+ XLAPACK_LIB="${BLASLIB} ${LAPACKLIB}" -+ XFFLAGS_LAPACK="$(${PKG_CONFIG} --cflags lapack blas)" - # Otherwise force building of NetLib BLAS and LAPACK libs -- else -- echo -- echo "! Force building of NetLib BLAS and LAPACK..." -- make_blas=blaslib -- make_lapack=lapacklib -- BLASLIB=blas -- BLASDIR="$srcdir/lib/lapack" -- BLASEXT="a" -- fi - # need to know if we the lapack library was linked using the C or - # fortran linker - if test -f testlink.f || test -f testlink || test -f testlink.c ; then -@@ -3916,8 +3356,8 @@ RANLIB = ${RANLIB} - INSTALL_DATA = ${INSTALL_DATA} - libdir = $libdir - # --BLASLIB = lib${BLASLIB}.${BLASEXT} --LAPACKLIB = liblapack.a -+BLASLIB = ${BLASLIB} -+LAPACKLIB = ${LAPACKLIB} - # - # These variables define targets in the main Makefile - blaslib = ${make_blas} diff --git a/sci-libs/ccp4-libs/files/6.1.3-link-proberly.patch b/sci-libs/ccp4-libs/files/6.1.3-link-proberly.patch deleted file mode 100644 index 24a0a2d8e4a2..000000000000 --- a/sci-libs/ccp4-libs/files/6.1.3-link-proberly.patch +++ /dev/null @@ -1,230 +0,0 @@ ---- lib/src/Makefile.in 2009-03-02 17:53:15.000000000 +0100 -+++ lib/src/Makefile.in.new 2009-03-02 17:52:09.000000000 +0100 -@@ -172,9 +172,8 @@ - - ##### Makefile targets ###### - --all: fsplit $(LMMDB) $(LC) $(LF) $(SCRIPT_MODULES) -+all: fsplit $(LMMDB) LMMDB_SO $(LC) LC_SO $(LF) LF_SO $(SCRIPT_MODULES) - # maybe create shared library -- $(SHARE_LIB) - - $(LC) : $(CORELIBOBJS) $(CGENERALOBJS) $(CUCOBJS) $(CMTZOBJS) $(CMAPOBJS) $(CSYMOBJS) - $(AR) $(LC) $? -@@ -186,6 +185,27 @@ - $(AR) $(LF) $(FINTERFACEOBJS) - $(RANLIB) $@ - -+LMMDB_SO : -+ $(CC) $(COPTIM) -shared -Wl,-soname,libmmdb.so.0 -o libmmdb.so.0.0.0 \ -+ $(MMDBOBJS) && \ -+ ln -sf libmmdb.so.0.0.0 libmmdb.so.0 && \ -+ ln -sf libmmdb.so.0.0.0 libmmdb.so -+ -+LC_SO : -+ $(CC) $(COPTIM) -shared -Wl,-soname,libccp4c.so.0 -o libccp4c.so.0.0.0 \ -+ $(CORELIBOBJS) $(CGENERALOBJS) $(CUCOBJS) $(CMTZOBJS) $(CMAPOBJS) $(CSYMOBJS) && \ -+ ln -sf libccp4c.so.0.0.0 libccp4c.so.0 && \ -+ ln -sf libccp4c.so.0.0.0 libccp4c.so -+ -+LF_SO : -+ $(FC) $(FOPTIM) -shared -Wl,-soname,libccp4f.so.0 -o libccp4f.so.0.0.0 \ -+ parser.dir/*.o ccplib.dir/*.o lgglib.dir/*.o plot84lib.dir/*.o \ -+ libhtml.dir/*.o pxxml.dir/*.o rwbrook.dir/*.o cciflib.dir/*.o \ -+ harvlib.dir/*.o keyparse.dir/*.o dna_output.dir/*.o plotsubs.dir/*.o \ -+ modlib.dir/*.o fftlib.dir/*.o unix.dir/*.o pack_f.o pack_c.o $(FINTERFACEOBJS) && \ -+ ln -sf libccp4f.so.0.0.0 libccp4f.so.0 && \ -+ ln -sf libccp4f.so.0.0.0 libccp4f.so -+ - # cmtz library only - - cmtz: $(LCMTZ) -@@ -339,9 +356,7 @@ - fi - cd parser.dir && \ - for i in `pwd`/*.$F; do \ -- $(FC) -c $(FFLAGS) $(SHARED_LIB_FFLAGS) $$i; done\ -- && $(AR) ../$(LF) *.o -- rm -f parser.dir/*.o -+ $(FC) -c $(FFLAGS) $(SHARED_LIB_FFLAGS) $$i; done - parser : parser.o - $(RANLIB) $(LF) - -@@ -351,9 +366,7 @@ - echo ' END' >> ccplib.dir/ccplib.$F - cd ccplib.dir && $(fsplit_dir)/fsplit $(srcdir)/ccplib.f >/dev/null && $(RMEMPTY) && \ - for i in `pwd`/*.$F; do \ -- $(FC) -c $(FFLAGS) $(SHARED_LIB_FFLAGS) $$i; done\ -- && $(AR) ../$(LF) *.o -- rm -f ccplib.dir/*.o -+ $(FC) -c $(FFLAGS) $(SHARED_LIB_FFLAGS) $$i; done - ccplib : ccplib.o - $(RANLIB) $(LF) - -@@ -364,9 +377,7 @@ - @$(SETFLAGS) ; \ - cd lgglib.dir && $(fsplit_dir)/fsplit $(srcdir)/lgglib.f >/dev/null && $(RMEMPTY) && \ - for i in `pwd`/*.$F; do \ -- eval $(FC) -c $${lgglib_FLAGS-"$(FFLAGS)"} $(SHARED_LIB_FFLAGS) $$i; done\ -- && $(AR) ../$(LF) *.o -- rm -f lgglib.dir/*.o -+ eval $(FC) -c $${lgglib_FLAGS-"$(FFLAGS)"} $(SHARED_LIB_FFLAGS) $$i; done - lgglib : lgglib.o - $(RANLIB) $(LF) - -@@ -376,9 +387,7 @@ - echo ' END' >> plot84lib.dir/plot84lib.$F - cd plot84lib.dir && $(fsplit_dir)/fsplit $(srcdir)/plot84lib.f >/dev/null && $(RMEMPTY) && \ - for i in `pwd`/*.$F; do \ -- $(FC) -c $(FFLAGS) $(SHARED_LIB_FFLAGS) $$i; done\ -- && $(AR) ../$(LF) *.o -- rm -f plot84lib.dir/*.o -+ $(FC) -c $(FFLAGS) $(SHARED_LIB_FFLAGS) $$i; done - plot84lib : plot84lib.o - $(RANLIB) $(LF) - -@@ -388,9 +397,7 @@ - echo ' END' >> libhtml.dir/libhtml.$F - cd libhtml.dir && $(fsplit_dir)/fsplit $(srcdir)/libhtml.f >/dev/null && $(RMEMPTY) && \ - for i in `pwd`/*.$F; do \ -- $(FC) -c $(FFLAGS) $(SHARED_LIB_FFLAGS) $$i; done\ -- && $(AR) ../$(LF) *.o -- rm -f libhtml.dir/*.o -+ $(FC) -c $(FFLAGS) $(SHARED_LIB_FFLAGS) $$i; done - libhtml : libhtml.o - $(RANLIB) $(LF) - -@@ -400,9 +407,7 @@ - echo ' END' >> pxxml.dir/pxxml.$F - cd pxxml.dir && $(fsplit_dir)/fsplit $(srcdir)/pxxml.f >/dev/null && $(RMEMPTY) && \ - for i in `pwd`/*.$F; do \ -- $(FC) -c $(FFLAGS) $(SHARED_LIB_FFLAGS) $$i; done\ -- && $(AR) ../$(LF) *.o -- rm -f pxxml.dir/*.o -+ $(FC) -c $(FFLAGS) $(SHARED_LIB_FFLAGS) $$i; done - pxxml : pxxml.o - $(RANLIB) $(LF) - -@@ -412,9 +417,7 @@ - echo ' END' >> rwbrook.dir/rwbrook.$F - cd rwbrook.dir && $(fsplit_dir)/fsplit $(srcdir)/rwbrook.f >/dev/null && $(RMEMPTY) && \ - for i in `pwd`/*.$F; do \ -- $(FC) -c $(FFLAGS) $(SHARED_LIB_FFLAGS) $$i; done\ -- && $(AR) ../$(LF) *.o -- rm -f rwbrook.dir/*.o -+ $(FC) -c $(FFLAGS) $(SHARED_LIB_FFLAGS) $$i; done - rwbrook : rwbrook.o - $(RANLIB) $(LF) - -@@ -424,9 +427,7 @@ - echo ' END' >> cciflib.dir/cciflib.$F - cd cciflib.dir && $(fsplit_dir)/fsplit $(srcdir)/cciflib.f >/dev/null && $(RMEMPTY) && \ - for i in `pwd`/*.$F; do \ -- $(FC) -c $(FFLAGS) $(SHARED_LIB_FFLAGS) -I$(srcdir) $$i; done\ -- && $(AR) ../$(LF) *.o -- rm -f cciflib.dir/*.o -+ $(FC) -c $(FFLAGS) $(SHARED_LIB_FFLAGS) -I$(srcdir) $$i; done - cciflib : cciflib.o - $(RANLIB) $(LF) - -@@ -440,9 +441,7 @@ - && $(AR) ../$(LF) *.o ; else \ - cd harvlib.dir && $(fsplit_dir)/fsplit $(srcdir)/harv_dummy.f >/dev/null && $(RMEMPTY) && \ - for i in `pwd`/*.$F; do \ -- $(FC) -c $(FFLAGS) $(SHARED_LIB_FFLAGS) -I$(srcdir) $$i; done\ -- && $(AR) ../$(LF) *.o ; fi -- rm -f harvlib.dir/*.o -+ $(FC) -c $(FFLAGS) $(SHARED_LIB_FFLAGS) -I$(srcdir) $$i; done; fi - harvlib : harvlib.o - $(RANLIB) $(LF) - -@@ -452,9 +451,7 @@ - echo ' END' >> keyparse.dir/keyparse.$F - cd keyparse.dir && $(fsplit_dir)/fsplit $(srcdir)/keyparse.f >/dev/null && $(RMEMPTY) && \ - for i in `pwd`/*.$F; do \ -- $(FC) -c $(FFLAGS) $(SHARED_LIB_FFLAGS) $$i; done\ -- && $(AR) ../$(LF) *.o -- rm -f keyparse.dir/*.o -+ $(FC) -c $(FFLAGS) $(SHARED_LIB_FFLAGS) $$i; done - keyparse : keyparse.o - $(RANLIB) $(LF) - -@@ -464,9 +461,7 @@ - echo ' END' >> dna_output.dir/dna_output.$F - cd dna_output.dir && $(fsplit_dir)/fsplit $(srcdir)/dna_output.f >/dev/null && $(RMEMPTY) && \ - for i in `pwd`/*.$F; do \ -- $(FC) -I$(srcdir) -c $(FFLAGS) $(SHARED_LIB_FFLAGS) $$i; done\ -- && $(AR) ../$(LF) *.o -- rm -f dna_output.dir/*.o -+ $(FC) -I$(srcdir) -c $(FFLAGS) $(SHARED_LIB_FFLAGS) $$i; done - dna_output : dna_output.o - $(RANLIB) $(LF) - -@@ -474,10 +469,9 @@ - # for ipdisp. May be useful but could be moved. - $(LF)(pack_c.o): $(srcdir)/pack_c.c $(srcdir)/pack_c.h - $(CC) $(CFLAGS) $(SHARED_LIB_CFLAGS) -I$(srcdir) -c $(srcdir)/pack_c.c -- $(AR) $(LF) pack_c.o && rm pack_c.o -+ $(AR) $(LF) pack_c.o - $(LF)(pack_f.o): $(srcdir)/pack_f.f -- $(FC) -c $(FFLAGS) $(SHARED_LIB_FFLAGS) $(srcdir)/pack_f.$(F) && $(AR) $(LF) pack_f.o \ -- && rm pack_f.o -+ $(FC) -c $(FFLAGS) $(SHARED_LIB_FFLAGS) $(srcdir)/pack_f.$(F) && $(AR) $(LF) pack_f.o - pack: $(LF)(pack_c.o) $(LF)(pack_f.o) - $(RANLIB) $(LF) - -@@ -488,9 +482,7 @@ - echo ' END' >> sorting_main.dir/sorting_main.$F - cd sorting_main.dir && $(fsplit_dir)/fsplit $(srcdir)/sorting_main.f >/dev/null && $(RMEMPTY) && \ - for i in `pwd`/*.$F; do \ -- $(FC) -c $(FFLAGS) $(SHARED_LIB_FFLAGS) $$i; done\ -- && $(AR) ../$(LF) *.o -- rm -f sorting_main.dir/*.o -+ $(FC) -c $(FFLAGS) $(SHARED_LIB_FFLAGS) $$i; done - sorting_main : sorting_main.o - $(RANLIB) $(LF) - -@@ -500,9 +492,7 @@ - echo ' END' >> plotsubs.dir/plotsubs.$F - cd plotsubs.dir && $(fsplit_dir)/fsplit $(srcdir)/plotsubs.f >/dev/null && $(RMEMPTY) && \ - for i in `pwd`/*.$F; do \ -- $(FC) -c $(FFLAGS) $(SHARED_LIB_FFLAGS) $$i; done\ -- && $(AR) ../$(LF) *.o -- rm -f plotsubs.dir/*.o -+ $(FC) -c $(FFLAGS) $(SHARED_LIB_FFLAGS) $$i; done - plotsubs : plotsubs.o - $(RANLIB) $(LF) - -@@ -512,9 +502,7 @@ - echo ' END' >> modlib.dir/modlib.$F - cd modlib.dir && $(fsplit_dir)/fsplit $(srcdir)/modlib.f >/dev/null && $(RMEMPTY) && \ - for i in `pwd`/*.$F; do \ -- $(FC) -c $(FFLAGS) $(SHARED_LIB_FFLAGS) $$i; done\ -- && $(AR) ../$(LF) *.o -- rm -f modlib.dir/*.o -+ $(FC) -c $(FFLAGS) $(SHARED_LIB_FFLAGS) $$i; done - modlib : modlib.o - $(RANLIB) $(LF) - -@@ -524,9 +512,7 @@ - echo ' END' >> fftlib.dir/fftlib.$F - cd fftlib.dir && $(fsplit_dir)/fsplit $(srcdir)/fftlib.f >/dev/null && $(RMEMPTY) && \ - for i in `pwd`/*.$F; do \ -- $(FC) -c $(FFLAGS) $(SHARED_LIB_FFLAGS) $$i; done \ -- && $(AR) ../$(LF) *.o -- rm -f fftlib.dir/*.o -+ $(FC) -c $(FFLAGS) $(SHARED_LIB_FFLAGS) $$i; done - fftlib : fftlib.o - $(RANLIB) $(LF) - -@@ -541,9 +527,7 @@ - echo ' END' >> unix.dir/unix.f - cd unix.dir && $(fsplit_dir)/fsplit ../unix.f >/dev/null && $(RMEMPTY) && \ - for i in `pwd`/*.$F; do \ -- $(FC) -c $(FFLAGS) $(SHARED_LIB_FFLAGS) $$i; done\ -- && $(AR) ../$(LF) *.o -- rm -f unix.dir/*.o -+ $(FC) -c $(FFLAGS) $(SHARED_LIB_FFLAGS) $$i; done - unix : unix.o - $(RANLIB) $(LF) - diff --git a/sci-libs/ccp4-libs/files/6.1.3-no-pypath.patch b/sci-libs/ccp4-libs/files/6.1.3-no-pypath.patch deleted file mode 100644 index 6a0cb5be7c3d..000000000000 --- a/sci-libs/ccp4-libs/files/6.1.3-no-pypath.patch +++ /dev/null @@ -1,87 +0,0 @@ - include/ccp4.setup-bash | 8 -------- - include/ccp4.setup-csh | 11 ----------- - include/ccp4.setup-sh | 8 -------- - include/ccp4.setup-zsh | 10 ---------- - 4 files changed, 37 deletions(-) - -diff --git a/include/ccp4.setup-bash b/include/ccp4.setup-bash -index 3a67791..80aef23 100755 ---- a/include/ccp4.setup-bash -+++ b/include/ccp4.setup-bash -@@ -185,14 +185,6 @@ else - fi - fi - --#Python path for the subprocess fixed module -- --if [ $ccp4_first_in_path -eq 1 ]; then -- setenv PYTHONPATH ${CCP4}/share/python:${PYTHONPATH} --else -- setenv PYTHONPATH ${PYTHONPATH}:${CCP4}/share/python --fi -- - ### PLOT_COMMAND PRINT_COMMAND for the XCCPJIFFY programs to compile ### - setenv PLOT_COMMAND 'lp -s -dmicrolaser' - setenv PRINT_COMMAND 'lp -s -denscript' -diff --git a/include/ccp4.setup-csh b/include/ccp4.setup-csh -index 10d3ab8..72cc479 100755 ---- a/include/ccp4.setup-csh -+++ b/include/ccp4.setup-csh -@@ -177,17 +177,6 @@ else - endif - endif - --#Python path for the subprocess fixed module --if (${?PYTHONPATH}) then -- if ($ccp4_first_in_path) then -- setenv PYTHONPATH ${CCP4}/share/python:${PYTHONPATH} -- else -- setenv PYTHONPATH ${PYTHONPATH}:${CCP4}/share/python -- endif --else -- setenv PYTHONPATH ${CCP4}/share/python --endif -- - ### PLOT_COMMAND PRINT_COMMAND for the XCCPJIFFY programs to compile ### - setenv PLOT_COMMAND 'lp -s -dmicrolaser' - setenv PRINT_COMMAND 'lp -s -denscript' -diff --git a/include/ccp4.setup-sh b/include/ccp4.setup-sh -index 2298bba..44643ab 100755 ---- a/include/ccp4.setup-sh -+++ b/include/ccp4.setup-sh -@@ -225,14 +225,6 @@ test -r $CCP4/include/ccp4.msg && cat $CCP4/include/ccp4.msg - - ################### EXPERIENCED USERS STOP HERE ##################### - --#Python path for the subprocess fixed module -- --if test $ccp4_first_in_path -eq 1; then -- export PYTHONPATH=${CCP4}/share/python:${PYTHONPATH} --else -- export PYTHONPATH=${PYTHONPATH}:${CCP4}/share/python --fi -- - ################### THE REST SHOULDN'T NEED EDITING ##################### - - ### dbCCP4i database handler setup ### -diff --git a/include/ccp4.setup-zsh b/include/ccp4.setup-zsh -index 660b35b..e453db9 100755 ---- a/include/ccp4.setup-zsh -+++ b/include/ccp4.setup-zsh -@@ -154,16 +154,6 @@ export CCP4_BIN=$CBIN - CLASSPATH=$CBIN:$CLASSPATH # edit this if necessary - export CLASSPATH - --#Python path for the subprocess fixed module -- --if ($ccp4_first_in_path) then -- PYTHONPATH=${CCP4}/share/python:${PYTHONPATH} -- export PYTHONPATH --else -- PYTHONPATH=${PYTHONPATH}:${CCP4}/share/python -- export PYTHONPATH --fi -- - ### PLOT_COMMAND PRINT_COMMAND for the XCCPJIFFY programs to compile ### - export PLOT_COMMAND='lpr' - export PRINT_COMMAND='lpr' diff --git a/sci-libs/ccp4-libs/files/6.1.3-noinstall.patch b/sci-libs/ccp4-libs/files/6.1.3-noinstall.patch deleted file mode 100644 index c1479f2b1155..000000000000 --- a/sci-libs/ccp4-libs/files/6.1.3-noinstall.patch +++ /dev/null @@ -1,142 +0,0 @@ -diff --git a/Makefile.in b/Makefile.in -index ac552fe..fab1a87 100755 ---- a/Makefile.in -+++ b/Makefile.in -@@ -30,8 +30,7 @@ lapacklib : FORCE - - cciflib : FORCE - if test -n "$(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..017502d 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 . -- ./fontpack -- $(INSTALL) `pwd`/font84.dat $(libdir)/font84.dat -+ test -f font84.ascii || $(LNS) $(DESTDIR)/$(srcdir)/font84.ascii . -+ LD_LIBRARY_PATH="../src:../ccif" ./fontpack -+ $(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 b32dd1e..6aa107d 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 $$p | sed -e 's|^.*/||'`"; \ -@@ -716,11 +716,11 @@ uninstall-mmdbHEADERS: - rm -f $(DESTDIR)$(includedir)/mmdb/$$f; \ - done - --install : all install-ccp4HEADERS install-mmdbHEADERS -- $(INSTALL_DATA) `pwd`/$(LC) $(libdir)/$(LC) -- $(INSTALL_DATA) `pwd`/$(LF) $(libdir)/$(LF) -- $(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: diff --git a/sci-libs/ccp4-libs/files/6.1.3-overflows.patch b/sci-libs/ccp4-libs/files/6.1.3-overflows.patch deleted file mode 100644 index 0e3c941d1cc2..000000000000 --- a/sci-libs/ccp4-libs/files/6.1.3-overflows.patch +++ /dev/null @@ -1,35 +0,0 @@ -Fix overflows and array subscript above array bounds - -http://bugs.gentoo.org/show_bug.cgi?id=339706 - ---- ccp4-6.1.3/lib/ccif/f_interface.c -+++ ccp4-6.1.3/lib/ccif/f_interface.c -@@ -926,7 +926,7 @@ - #endif - - { -- char logname_c[81]; -+ char logname_c[MAXFLEN]; - size_t Length; - int unit; - CIF_FILE_LIST file_list_entry; -@@ -4064,7 +4064,7 @@ - #endif - - { -- char lognam_c[81], *blknam_c; -+ char lognam_c[MAXFLEN], *blknam_c; - size_t loglen, blklen; - int i, j, new; - ---- ccp4-6.1.3/lib/src/ccp4_diskio_f.c -+++ ccp4-6.1.3/lib/src/ccp4_diskio_f.c -@@ -705,7 +705,7 @@ - log_name = strdup("diskio.dft"); - if (!(file_name = getenv(log_name))) - file_name = log_name; -- for ( *istrm = 1; *istrm == MAXFILES; *istrm++) -+ for ( *istrm = 1; *istrm < MAXFILES; *istrm++) - if (!strcmp(file_name,_ioChannels[*istrm]->iobj->name)) break; - } - if (*istrm != MAXFILES) { diff --git a/sci-libs/ccp4-libs/files/6.1.3-unbundle-libs-ng.patch b/sci-libs/ccp4-libs/files/6.1.3-unbundle-libs-ng.patch deleted file mode 100644 index 4271d5b76aec..000000000000 --- a/sci-libs/ccp4-libs/files/6.1.3-unbundle-libs-ng.patch +++ /dev/null @@ -1,367 +0,0 @@ -diff --git a/lib/DiffractionImage/DiffractionImageCBF.cpp b/lib/DiffractionImage/DiffractionImageCBF.cpp -index 69b32b0..602e35f 100755 ---- a/lib/DiffractionImage/DiffractionImageCBF.cpp -+++ b/lib/DiffractionImage/DiffractionImageCBF.cpp -@@ -6,10 +6,10 @@ - // images. - - #include "DiffractionImage.h" --#include "cbf.h" --#include "cbf_simple.h" --#include "cbf_string.h" --#include "cbf_byte_offset.h" -+#include -+#include -+#include -+#include - - - using namespace std; -diff --git a/lib/DiffractionImage/MAR/Makefile.am b/lib/DiffractionImage/MAR/Makefile.am -index fedb7ac..89a048e 100755 ---- a/lib/DiffractionImage/MAR/Makefile.am -+++ b/lib/DiffractionImage/MAR/Makefile.am -@@ -2,7 +2,7 @@ AUTOMAKE_OPTIONS = gnu - - noinst_LTLIBRARIES = libmar.la - --AM_CPPFLAGS =-I../CBFlib/src -I../CBFlib/include -+AM_CPPFLAGS = - - libmar_la_SOURCES = mar300_header.c \ - mar345_header.c \ -@@ -12,4 +12,3 @@ libmar_la_SOURCES = mar300_header.c \ - utils.c \ - pck.c - --libmar_la_LDFLAGS = -static -diff --git a/lib/DiffractionImage/MAR/marcif.c b/lib/DiffractionImage/MAR/marcif.c -index d3f4212..2c37108 100755 ---- a/lib/DiffractionImage/MAR/marcif.c -+++ b/lib/DiffractionImage/MAR/marcif.c -@@ -31,8 +31,7 @@ - #include "marcif_header.h" - #include "mar345_header.h" - --#include --#include -+#include - - #define printe(x) printf("%s: %s: %s\n",prg,f,x) - #undef cbf_failnez -diff --git a/lib/DiffractionImage/Makefile.am b/lib/DiffractionImage/Makefile.am -index 189a1d7..6652576 100755 ---- a/lib/DiffractionImage/Makefile.am -+++ b/lib/DiffractionImage/Makefile.am -@@ -1,7 +1,9 @@ - AUTOMAKE_OPTIONS = gnu --SUBDIRS = CBFlib Bruker MAR Rigaku jpg -+SUBDIRS = Bruker MAR Rigaku - --AM_CPPFLAGS =-I./MAR -I./CBFlib/src -I./CBFlib/include -I./jpg -+SYSLIBS = -ljpeg -lcbf -+ -+AM_CPPFLAGS =-I./MAR - lib_LTLIBRARIES = libDiffImage.la - - if WANT_PYTHONMOD -@@ -35,48 +37,56 @@ libDiffImage_la_SOURCES = DiffractionImageJpeg.cpp \ - Profile.cpp \ - Peak.cpp \ - dps_peaksearch_cn.c --libDiffImage_la_LDFLAGS = -static -+libDiffImage_la_LDFLAGS = -shared $(SHARED_LIB_FLAGS) -+libDiffImage_la_LIBADD = $(SYSLIBS) \ -+ ./MAR/libmar.la ./Bruker/libbruker.la \ -+ ./Rigaku/librigaku.la - --libDiffractionImage_la_DEPENDENCIES= libDiffImage.la ./CBFlib/src/libcbf.la \ -+libDiffractionImage_la_DEPENDENCIES= libDiffImage.la \ - ./Bruker/libbruker.la ./MAR/libmar.la \ -- ./Rigaku/librigaku.la ./jpg/libjpeg.la -+ ./Rigaku/librigaku.la - libDiffractionImage_la_SOURCES = DiffractionImageTclInterface.cpp --libDiffractionImage_la_LDFLAGS = -shared --whole-archive libDiffImage.la \ -- ./CBFlib/src/libcbf.la ./Bruker/libbruker.la \ -- ./MAR/libmar.la ./Rigaku/librigaku.la ./jpg/libjpeg.la \ -- --no-whole-archive -rpath '$(libdir)' -+libDiffractionImage_la_LDFLAGS = -shared --whole-archive $(SHARED_LIB_FLAGS) -+libDiffractionImage_la_LIBADD = $(SYSLIBS) -ltcl \ -+ libDiffImage.la \ -+ ./Bruker/libbruker.la \ -+ ./MAR/libmar.la ./Rigaku/librigaku.la - --lib_DiffractionImage_la_DEPENDENCIES = libDiffImage.la ./CBFlib/src/libcbf.la \ -+lib_DiffractionImage_la_DEPENDENCIES = libDiffImage.la \ - ./Bruker/libbruker.la ./MAR/libmar.la \ -- ./Rigaku/librigaku.la ./jpg/libjpeg.la -+ ./Rigaku/librigaku.la - lib_DiffractionImage_la_SOURCES = DiffractionImagePythonInterface.cpp --lib_DiffractionImage_la_LDFLAGS = -shared --whole-archive libDiffImage.la \ -- ./CBFlib/src/libcbf.la ./Bruker/libbruker.la \ -- ./MAR/libmar.la ./Rigaku/librigaku.la ./jpg/libjpeg.la \ -- --no-whole-archive -rpath '$(libdir)' -+lib_DiffractionImage_la_LDFLAGS = -shared --whole-archive $(SHARED_LIB_FLAGS) -+lib_DiffractionImage_la_LIBADD = libDiffImage.la @PYLIB@ $(SYSLIBS) \ -+ ./Bruker/libbruker.la \ -+ ./MAR/libmar.la ./Rigaku/librigaku.la - --libDiffractionImaJ_la_DEPENDENCIES = libDiffImage.la ./CBFlib/src/libcbf.la \ -+libDiffractionImaJ_la_DEPENDENCIES = libDiffImage.la \ - ./Bruker/libbruker.la ./MAR/libmar.la \ -- ./Rigaku/librigaku.la ./jpg/libjpeg.la -+ ./Rigaku/librigaku.la - libDiffractionImaJ_la_SOURCES = DiffractionImageJavaInterface.cpp --libDiffractionImaJ_la_LDFLAGS = -shared --whole-archive libDiffImage.la \ -- ./CBFlib/src/libcbf.la ./Bruker/libbruker.la \ -- ./MAR/libmar.la ./Rigaku/librigaku.la ./jpg/libjpeg.la \ -- --no-whole-archive -rpath '$(libdir)' -+libDiffractionImaJ_la_LDFLAGS = -shared --whole-archive $(SHARED_LIB_FLAGS) -+libDiffractionImaJ_la_LIBADD = libDiffImage.la \ -+ ./Bruker/libbruker.la $(SYSLIBS) \ -+ ./MAR/libmar.la ./Rigaku/librigaku.la - - bin_PROGRAMS = automask diffdump printpeaks diff2jpeg --automask_LDADD = libDiffImage.la ./Bruker/libbruker.la ./CBFlib/src/libcbf.la \ -- ./MAR/libmar.la ./Rigaku/librigaku.la ./jpg/libjpeg.la -+automask_LDADD = libDiffImage.la ./Bruker/libbruker.la \ -+ ./MAR/libmar.la ./Rigaku/librigaku.la $(SYSLIBS) - automask_SOURCES = automask.cpp --diffdump_LDADD = libDiffImage.la ./Bruker/libbruker.la ./CBFlib/src/libcbf.la \ -- ./MAR/libmar.la ./Rigaku/librigaku.la ./jpg/libjpeg.la -+automask_LDFLAGS = $(SHARED_LIB_FLAGS) -+diffdump_LDADD = libDiffImage.la ./Bruker/libbruker.la $(SYSLIBS) \ -+ ./MAR/libmar.la ./Rigaku/librigaku.la - diffdump_SOURCES = diffdump.cpp --printpeaks_LDADD = libDiffImage.la ./Bruker/libbruker.la ./CBFlib/src/libcbf.la \ -- ./MAR/libmar.la ./Rigaku/librigaku.la ./jpg/libjpeg.la -+diffdump_LDFLAGS = $(SHARED_LIB_FLAGS) -+printpeaks_LDADD = libDiffImage.la ./Bruker/libbruker.la \ -+ ./MAR/libmar.la ./Rigaku/librigaku.la $(SYSLIBS) - printpeaks_SOURCES = printpeaks.cpp --diff2jpeg_LDADD = libDiffImage.la ./Bruker/libbruker.la ./CBFlib/src/libcbf.la \ -- ./MAR/libmar.la ./Rigaku/librigaku.la ./jpg/libjpeg.la -+printpeaks_LDFLAGS = $(SHARED_LIB_FLAGS) -+diff2jpeg_LDADD = libDiffImage.la ./Bruker/libbruker.la \ -+ ./MAR/libmar.la ./Rigaku/librigaku.la $(SYSLIBS) - diff2jpeg_SOURCES = diff2jpeg.cpp -+diff2jpeg_LDFLAGS = $(SHARED_LIB_FLAGS) - - install-data-local: - @INSTALL_DATA@ doc/DiffractionImage.doc ${CDOC} -diff --git a/lib/DiffractionImage/configure b/lib/DiffractionImage/configure -index 3fb5784..fdf9683 100755 ---- a/lib/DiffractionImage/configure -+++ b/lib/DiffractionImage/configure -@@ -21768,7 +21768,7 @@ _ACEOF - fi - - --ac_config_files="$ac_config_files Makefile CBFlib/Makefile CBFlib/src/Makefile MAR/Makefile Rigaku/Makefile Bruker/Makefile jpg/Makefile" -+ac_config_files="$ac_config_files Makefile MAR/Makefile Rigaku/Makefile Bruker/Makefile " - - - cat >confcache <<\_ACEOF -@@ -22407,12 +22407,9 @@ do - case $ac_config_target in - "depfiles") CONFIG_COMMANDS="$CONFIG_COMMANDS depfiles" ;; - "Makefile") CONFIG_FILES="$CONFIG_FILES Makefile" ;; -- "CBFlib/Makefile") CONFIG_FILES="$CONFIG_FILES CBFlib/Makefile" ;; -- "CBFlib/src/Makefile") CONFIG_FILES="$CONFIG_FILES CBFlib/src/Makefile" ;; - "MAR/Makefile") CONFIG_FILES="$CONFIG_FILES MAR/Makefile" ;; - "Rigaku/Makefile") CONFIG_FILES="$CONFIG_FILES Rigaku/Makefile" ;; - "Bruker/Makefile") CONFIG_FILES="$CONFIG_FILES Bruker/Makefile" ;; -- "jpg/Makefile") CONFIG_FILES="$CONFIG_FILES jpg/Makefile" ;; - - *) { { echo "$as_me:$LINENO: error: invalid argument: $ac_config_target" >&5 - echo "$as_me: error: invalid argument: $ac_config_target" >&2;} -diff --git a/lib/DiffractionImage/configure.in b/lib/DiffractionImage/configure.in -index 7f54b4b..16efc64 100755 ---- a/lib/DiffractionImage/configure.in -+++ b/lib/DiffractionImage/configure.in -@@ -21,6 +21,8 @@ if test -n "${PYTHON}" ; then - HAVE_PYTHON=1 - CPPFLAGS="${CPPFLAGS} -I${PYTHON_PREFIX}/include/python${PYTHON_VER}" - ]) -+ PYLIB="-lpython${PYTHON_VER}" -+ AC_SUBST(PYLIB) - fi - AC_CHECK_HEADER([tcl.h], [HAVE_TCL=1]) - -@@ -65,11 +67,8 @@ AM_CONDITIONAL([WANT_JAVA], test z${HAVE_JAVA} != z) - AC_CHECK_LIB([m], [sqrt]) - - AC_CONFIG_FILES([Makefile -- CBFlib/Makefile -- CBFlib/src/Makefile - MAR/Makefile - Rigaku/Makefile -- Bruker/Makefile -- jpg/Makefile]) -+ Bruker/Makefile]) - - AC_OUTPUT -diff --git a/lib/ssm/Makefile.am b/lib/ssm/Makefile.am -index e9554e1..a3ba33d 100755 ---- a/lib/ssm/Makefile.am -+++ b/lib/ssm/Makefile.am -@@ -1,7 +1,11 @@ -+ACLOCAL_AMFLAGS = -I macros - #libtool - lib_LTLIBRARIES = libssm.la -+libssm_la_LDFLAGS = -shared $(SHARED_LIB_FLAGS) -+libssm_la_CFLAGS = @MMDB_CFLAGS@ - libssm_la_SOURCES = ssm_superpose.cpp ss_csia.cpp ss_vxedge.cpp \ - ssm_align.cpp ss_graph.cpp -+libssm_la_LIBADD = @MMDB_LIBS@ - - #non libtool - #lib_LIBRARIES = libssm.a -@@ -16,12 +20,10 @@ superpose_SOURCES = superpose.cpp - - bin_PROGRAMS = superpose - --INCLUDES = $(MMDB_CXXFLAGS) -- --AM_LDFLAGS = $(MMDB_LIBS) -+INCLUDES = @MMDB_CFLAGS@ - - EXTRA_DIST = macros/mmdb.m4 - --superpose_LDADD = libssm.la -+superpose_LDADD = libssm.la @MMDB_LIBS@ - - libssm_a_AR = $(AR) $(AR_FLAGS) -diff --git a/lib/ssm/configure.ac b/lib/ssm/configure.ac -index 783cb46..d637d11 100755 ---- a/lib/ssm/configure.ac -+++ b/lib/ssm/configure.ac -@@ -28,31 +28,10 @@ AC_ARG_ENABLE(debug, - [ac_cv_enable_debug=no ] ) - - dnl Optional: Check for MMDB. --AM_PATH_MMDB(, -- [ if test "x$mmdb_prefix" != x ; then -- if test "x$ac_MMDB_CXXFLAGS" != x ; then -- case "$ac_MMDB_CXXFLAGS" in -- *src/mmdb ) -- ac_MMDB_LDOPTS=`echo "$ac_MMDB_CXXFLAGS" | sed s#src/mmdb#src#g` -- ;; -- *include/mmdb ) -- ac_MMDB_LDOPTS=`echo "$ac_MMDB_CXXFLAGS" | sed s#include/mmdb#lib#g` -- ;; -- *) -- esac -- MMDB_CXXFLAGS="$ac_MMDB_CXXFLAGS" -- MMDB_LIBS=`echo "$ac_MMDB_LDOPTS -lmmdb" | sed s#-I#-L#` -- AC_MSG_WARN([assuming library $MMDB_LIBS headers $MMDB_CXXFLAGS]) -- else -- MMDB_CXXFLAGS="-I$mmdb_prefix/lib/src/mmdb -I$mmdb_prefix/include/mmdb" -- MMDB_LIBS="-L$mmdb_prefix/lib/src -L$mmdb_prefix/lib -lmmdb" -- AC_MSG_WARN([assuming library $MMDB_LIBS headers $MMDB_CXXFLAGS]) -- fi -- else -- AC_MSG_WARN([mmdb not found]) -- fi -- ] --) -+ -+PKG_CHECK_MODULES([MMDB],[mmdb]) -+AC_SUBST([MMDB_CFLAGS]) -+AC_SUBST([MMDB_LIBS]) - - # Checks for typedefs, structures, and compiler characteristics. - # -@@ -67,6 +46,7 @@ AC_CHECK_FUNCS([floor pow rint sqrt]) - # test for function in m - AC_CHECK_LIB([m], [sqrt]) - -+ - AC_SUBST(AR_FLAGS) - AC_SUBST(superpose_LDFLAGS) - AM_CONDITIONAL(DEBUG, test "$ac_cv_enable_debug" = yes) -diff --git a/src/pisa/Makefile.am b/src/pisa/Makefile.am -index 094fd6b..922a131 100755 ---- a/src/pisa/Makefile.am -+++ b/src/pisa/Makefile.am -@@ -1,3 +1,4 @@ -+ACLOCAL_AMFLAGS = -I macros - SUBDIRS = molref pisastore sbase - - pkgdatadir = $(datadir)/pisa -@@ -20,8 +21,8 @@ pisa.cpp pisa_lists.cpp seq_superpose.cpp - - bin_PROGRAMS = pisa - --INCLUDES = $(MMDB_CXXFLAGS) $(SSM_CXXFLAGS) -+INCLUDES = @MMDB_CFLAGS@ $(SSM_CXXFLAGS) - --pisa_LDADD = $(SSM_LIBS) $(MMDB_LIBS) -+pisa_LDADD = $(SSM_LIBS) @MMDB_LIBS@ - - EXTRA_DIST = macros/mmdb.m4 macros/ssm.m4 pisa.cfg.in -diff --git a/src/pisa/configure.ac b/src/pisa/configure.ac -index 81afdda..4f99df6 100755 ---- a/src/pisa/configure.ac -+++ b/src/pisa/configure.ac -@@ -32,35 +32,13 @@ AC_CHECK_FUNCS([floor pow rint sqrt]) - AC_CHECK_LIB([m], [sqrt]) - - dnl Optional: Check for MMDB. --AM_PATH_MMDB(, -- [ if test "x$mmdb_prefix" != x ; then -- if test "x$ac_MMDB_CXXFLAGS" != x && test "x$ac_MMDB_LDOPTS" = x ; then -- case "$ac_MMDB_CXXFLAGS" in -- *src/mmdb ) -- ac_MMDB_LDOPTS=`echo "$ac_MMDB_CXXFLAGS" | sed s#src/mmdb#src#g` -- ;; -- *include/mmdb ) -- ac_MMDB_LDOPTS=`echo "$ac_MMDB_CXXFLAGS" | sed s#include/mmdb#lib#g` -- ;; -- *) -- esac -- MMDB_CXXFLAGS="$ac_MMDB_CXXFLAGS" -- MMDB_LIBS=`echo "$ac_MMDB_LDOPTS -lmmdb" | sed s#-I#-L#` -- AC_MSG_WARN([assuming library $MMDB_LIBS headers $MMDB_CXXFLAGS]) -- else -- MMDB_CXXFLAGS="-I$mmdb_prefix/src -I$mmdb_prefix/src/mmdb -I$mmdb_prefix/include -I$mmdb_prefix/include/mmdb" -- MMDB_LIBS="-L$mmdb_prefix/src -L$mmdb_prefix/lib -lmmdb" -- AC_MSG_WARN([assuming library $MMDB_LIBS headers $MMDB_CXXFLAGS]) -- fi -- else -- AC_MSG_ERROR([mmdb not found]) -- fi -- ] --) -+PKG_CHECK_MODULES([MMDB],[mmdb]) -+AC_SUBST([MMDB_CFLAGS]) -+AC_SUBST([MMDB_LIBS]) - - ac_saved_CXXFLAGS=$CXXFLAGS - ac_saved_LIBS=$LIBS --CXXFLAGS="$CXXFLAGS $MMDB_CXXFLAGS" -+CXXFLAGS="$CXXFLAGS $MMDB_CFLAGS" - LIBS="$MMDB_LIBS $LIBS" - AM_PATH_SSM(, - [ if test "x$ssm_prefix" != x ; then -diff --git a/src/rapper/Makefile.am b/src/rapper/Makefile.am -index e78b10d..486b931 100755 ---- a/src/rapper/Makefile.am -+++ b/src/rapper/Makefile.am -@@ -1,3 +1,3 @@ --SUBDIRS = libxml2 gc7.0 LOOP data -+SUBDIRS = LOOP data - - EXTRA_DIST = -diff --git a/src/rapper/configure.ac b/src/rapper/configure.ac -index 5e4ef69..11b63ec 100755 ---- a/src/rapper/configure.ac -+++ b/src/rapper/configure.ac -@@ -48,6 +48,6 @@ AM_CONDITIONAL(AMDEP, test "x$enable_dependency_tracking" != xno) - - AC_SUBST(rapper_LDFLAGS) - --AC_CONFIG_SUBDIRS([gc7.0 libxml2]) -+#AC_CONFIG_SUBDIRS([gc7.0 libxml2]) - #AC_OUTPUT(Makefile LOOP/Makefile LOOP/python/Makefile data/Makefile) - AC_OUTPUT(Makefile LOOP/Makefile data/Makefile) diff --git a/sci-libs/ccp4-libs/files/6.1.3-unbundle-libs-ng2.patch b/sci-libs/ccp4-libs/files/6.1.3-unbundle-libs-ng2.patch deleted file mode 100644 index c787df903dfc..000000000000 --- a/sci-libs/ccp4-libs/files/6.1.3-unbundle-libs-ng2.patch +++ /dev/null @@ -1,395 +0,0 @@ - lib/DiffractionImage/DiffractionImageCBF.cpp | 8 ++-- - lib/DiffractionImage/MAR/Makefile.am | 3 +- - lib/DiffractionImage/MAR/marcif.c | 3 +- - lib/DiffractionImage/Makefile.am | 68 +++++++++++++++----------- - lib/DiffractionImage/configure | 5 +-- - lib/DiffractionImage/configure.in | 7 +-- - lib/src/Makefile.in | 2 +- - lib/ssm/Makefile.am | 10 ++-- - lib/ssm/configure.ac | 30 ++--------- - src/pisa/Makefile.am | 5 +- - src/pisa/configure.ac | 30 ++---------- - src/rapper/Makefile.am | 2 +- - src/rapper/configure.ac | 2 +- - 13 files changed, 70 insertions(+), 105 deletions(-) - -diff --git a/lib/DiffractionImage/DiffractionImageCBF.cpp b/lib/DiffractionImage/DiffractionImageCBF.cpp -index 69b32b0..602e35f 100755 ---- a/lib/DiffractionImage/DiffractionImageCBF.cpp -+++ b/lib/DiffractionImage/DiffractionImageCBF.cpp -@@ -6,10 +6,10 @@ - // images. - - #include "DiffractionImage.h" --#include "cbf.h" --#include "cbf_simple.h" --#include "cbf_string.h" --#include "cbf_byte_offset.h" -+#include -+#include -+#include -+#include - - - using namespace std; -diff --git a/lib/DiffractionImage/MAR/Makefile.am b/lib/DiffractionImage/MAR/Makefile.am -index fedb7ac..89a048e 100755 ---- a/lib/DiffractionImage/MAR/Makefile.am -+++ b/lib/DiffractionImage/MAR/Makefile.am -@@ -2,7 +2,7 @@ AUTOMAKE_OPTIONS = gnu - - noinst_LTLIBRARIES = libmar.la - --AM_CPPFLAGS =-I../CBFlib/src -I../CBFlib/include -+AM_CPPFLAGS = - - libmar_la_SOURCES = mar300_header.c \ - mar345_header.c \ -@@ -12,4 +12,3 @@ libmar_la_SOURCES = mar300_header.c \ - utils.c \ - pck.c - --libmar_la_LDFLAGS = -static -diff --git a/lib/DiffractionImage/MAR/marcif.c b/lib/DiffractionImage/MAR/marcif.c -index d3f4212..2c37108 100755 ---- a/lib/DiffractionImage/MAR/marcif.c -+++ b/lib/DiffractionImage/MAR/marcif.c -@@ -31,8 +31,7 @@ - #include "marcif_header.h" - #include "mar345_header.h" - --#include --#include -+#include - - #define printe(x) printf("%s: %s: %s\n",prg,f,x) - #undef cbf_failnez -diff --git a/lib/DiffractionImage/Makefile.am b/lib/DiffractionImage/Makefile.am -index 189a1d7..6652576 100755 ---- a/lib/DiffractionImage/Makefile.am -+++ b/lib/DiffractionImage/Makefile.am -@@ -1,7 +1,9 @@ - AUTOMAKE_OPTIONS = gnu --SUBDIRS = CBFlib Bruker MAR Rigaku jpg -+SUBDIRS = Bruker MAR Rigaku - --AM_CPPFLAGS =-I./MAR -I./CBFlib/src -I./CBFlib/include -I./jpg -+SYSLIBS = -ljpeg -lcbf -+ -+AM_CPPFLAGS =-I./MAR - lib_LTLIBRARIES = libDiffImage.la - - if WANT_PYTHONMOD -@@ -35,48 +37,56 @@ libDiffImage_la_SOURCES = DiffractionImageJpeg.cpp \ - Profile.cpp \ - Peak.cpp \ - dps_peaksearch_cn.c --libDiffImage_la_LDFLAGS = -static -+libDiffImage_la_LDFLAGS = -shared $(SHARED_LIB_FLAGS) -+libDiffImage_la_LIBADD = $(SYSLIBS) \ -+ ./MAR/libmar.la ./Bruker/libbruker.la \ -+ ./Rigaku/librigaku.la - --libDiffractionImage_la_DEPENDENCIES= libDiffImage.la ./CBFlib/src/libcbf.la \ -+libDiffractionImage_la_DEPENDENCIES= libDiffImage.la \ - ./Bruker/libbruker.la ./MAR/libmar.la \ -- ./Rigaku/librigaku.la ./jpg/libjpeg.la -+ ./Rigaku/librigaku.la - libDiffractionImage_la_SOURCES = DiffractionImageTclInterface.cpp --libDiffractionImage_la_LDFLAGS = -shared --whole-archive libDiffImage.la \ -- ./CBFlib/src/libcbf.la ./Bruker/libbruker.la \ -- ./MAR/libmar.la ./Rigaku/librigaku.la ./jpg/libjpeg.la \ -- --no-whole-archive -rpath '$(libdir)' -+libDiffractionImage_la_LDFLAGS = -shared --whole-archive $(SHARED_LIB_FLAGS) -+libDiffractionImage_la_LIBADD = $(SYSLIBS) -ltcl \ -+ libDiffImage.la \ -+ ./Bruker/libbruker.la \ -+ ./MAR/libmar.la ./Rigaku/librigaku.la - --lib_DiffractionImage_la_DEPENDENCIES = libDiffImage.la ./CBFlib/src/libcbf.la \ -+lib_DiffractionImage_la_DEPENDENCIES = libDiffImage.la \ - ./Bruker/libbruker.la ./MAR/libmar.la \ -- ./Rigaku/librigaku.la ./jpg/libjpeg.la -+ ./Rigaku/librigaku.la - lib_DiffractionImage_la_SOURCES = DiffractionImagePythonInterface.cpp --lib_DiffractionImage_la_LDFLAGS = -shared --whole-archive libDiffImage.la \ -- ./CBFlib/src/libcbf.la ./Bruker/libbruker.la \ -- ./MAR/libmar.la ./Rigaku/librigaku.la ./jpg/libjpeg.la \ -- --no-whole-archive -rpath '$(libdir)' -+lib_DiffractionImage_la_LDFLAGS = -shared --whole-archive $(SHARED_LIB_FLAGS) -+lib_DiffractionImage_la_LIBADD = libDiffImage.la @PYLIB@ $(SYSLIBS) \ -+ ./Bruker/libbruker.la \ -+ ./MAR/libmar.la ./Rigaku/librigaku.la - --libDiffractionImaJ_la_DEPENDENCIES = libDiffImage.la ./CBFlib/src/libcbf.la \ -+libDiffractionImaJ_la_DEPENDENCIES = libDiffImage.la \ - ./Bruker/libbruker.la ./MAR/libmar.la \ -- ./Rigaku/librigaku.la ./jpg/libjpeg.la -+ ./Rigaku/librigaku.la - libDiffractionImaJ_la_SOURCES = DiffractionImageJavaInterface.cpp --libDiffractionImaJ_la_LDFLAGS = -shared --whole-archive libDiffImage.la \ -- ./CBFlib/src/libcbf.la ./Bruker/libbruker.la \ -- ./MAR/libmar.la ./Rigaku/librigaku.la ./jpg/libjpeg.la \ -- --no-whole-archive -rpath '$(libdir)' -+libDiffractionImaJ_la_LDFLAGS = -shared --whole-archive $(SHARED_LIB_FLAGS) -+libDiffractionImaJ_la_LIBADD = libDiffImage.la \ -+ ./Bruker/libbruker.la $(SYSLIBS) \ -+ ./MAR/libmar.la ./Rigaku/librigaku.la - - bin_PROGRAMS = automask diffdump printpeaks diff2jpeg --automask_LDADD = libDiffImage.la ./Bruker/libbruker.la ./CBFlib/src/libcbf.la \ -- ./MAR/libmar.la ./Rigaku/librigaku.la ./jpg/libjpeg.la -+automask_LDADD = libDiffImage.la ./Bruker/libbruker.la \ -+ ./MAR/libmar.la ./Rigaku/librigaku.la $(SYSLIBS) - automask_SOURCES = automask.cpp --diffdump_LDADD = libDiffImage.la ./Bruker/libbruker.la ./CBFlib/src/libcbf.la \ -- ./MAR/libmar.la ./Rigaku/librigaku.la ./jpg/libjpeg.la -+automask_LDFLAGS = $(SHARED_LIB_FLAGS) -+diffdump_LDADD = libDiffImage.la ./Bruker/libbruker.la $(SYSLIBS) \ -+ ./MAR/libmar.la ./Rigaku/librigaku.la - diffdump_SOURCES = diffdump.cpp --printpeaks_LDADD = libDiffImage.la ./Bruker/libbruker.la ./CBFlib/src/libcbf.la \ -- ./MAR/libmar.la ./Rigaku/librigaku.la ./jpg/libjpeg.la -+diffdump_LDFLAGS = $(SHARED_LIB_FLAGS) -+printpeaks_LDADD = libDiffImage.la ./Bruker/libbruker.la \ -+ ./MAR/libmar.la ./Rigaku/librigaku.la $(SYSLIBS) - printpeaks_SOURCES = printpeaks.cpp --diff2jpeg_LDADD = libDiffImage.la ./Bruker/libbruker.la ./CBFlib/src/libcbf.la \ -- ./MAR/libmar.la ./Rigaku/librigaku.la ./jpg/libjpeg.la -+printpeaks_LDFLAGS = $(SHARED_LIB_FLAGS) -+diff2jpeg_LDADD = libDiffImage.la ./Bruker/libbruker.la \ -+ ./MAR/libmar.la ./Rigaku/librigaku.la $(SYSLIBS) - diff2jpeg_SOURCES = diff2jpeg.cpp -+diff2jpeg_LDFLAGS = $(SHARED_LIB_FLAGS) - - install-data-local: - @INSTALL_DATA@ doc/DiffractionImage.doc ${CDOC} -diff --git a/lib/DiffractionImage/configure b/lib/DiffractionImage/configure -index 3fb5784..fdf9683 100755 ---- a/lib/DiffractionImage/configure -+++ b/lib/DiffractionImage/configure -@@ -21768,7 +21768,7 @@ _ACEOF - fi - - --ac_config_files="$ac_config_files Makefile CBFlib/Makefile CBFlib/src/Makefile MAR/Makefile Rigaku/Makefile Bruker/Makefile jpg/Makefile" -+ac_config_files="$ac_config_files Makefile MAR/Makefile Rigaku/Makefile Bruker/Makefile " - - - cat >confcache <<\_ACEOF -@@ -22407,12 +22407,9 @@ do - case $ac_config_target in - "depfiles") CONFIG_COMMANDS="$CONFIG_COMMANDS depfiles" ;; - "Makefile") CONFIG_FILES="$CONFIG_FILES Makefile" ;; -- "CBFlib/Makefile") CONFIG_FILES="$CONFIG_FILES CBFlib/Makefile" ;; -- "CBFlib/src/Makefile") CONFIG_FILES="$CONFIG_FILES CBFlib/src/Makefile" ;; - "MAR/Makefile") CONFIG_FILES="$CONFIG_FILES MAR/Makefile" ;; - "Rigaku/Makefile") CONFIG_FILES="$CONFIG_FILES Rigaku/Makefile" ;; - "Bruker/Makefile") CONFIG_FILES="$CONFIG_FILES Bruker/Makefile" ;; -- "jpg/Makefile") CONFIG_FILES="$CONFIG_FILES jpg/Makefile" ;; - - *) { { echo "$as_me:$LINENO: error: invalid argument: $ac_config_target" >&5 - echo "$as_me: error: invalid argument: $ac_config_target" >&2;} -diff --git a/lib/DiffractionImage/configure.in b/lib/DiffractionImage/configure.in -index 7f54b4b..16efc64 100755 ---- a/lib/DiffractionImage/configure.in -+++ b/lib/DiffractionImage/configure.in -@@ -21,6 +21,8 @@ if test -n "${PYTHON}" ; then - HAVE_PYTHON=1 - CPPFLAGS="${CPPFLAGS} -I${PYTHON_PREFIX}/include/python${PYTHON_VER}" - ]) -+ PYLIB="-lpython${PYTHON_VER}" -+ AC_SUBST(PYLIB) - fi - AC_CHECK_HEADER([tcl.h], [HAVE_TCL=1]) - -@@ -65,11 +67,8 @@ AM_CONDITIONAL([WANT_JAVA], test z${HAVE_JAVA} != z) - AC_CHECK_LIB([m], [sqrt]) - - AC_CONFIG_FILES([Makefile -- CBFlib/Makefile -- CBFlib/src/Makefile - MAR/Makefile - Rigaku/Makefile -- Bruker/Makefile -- jpg/Makefile]) -+ Bruker/Makefile]) - - AC_OUTPUT -diff --git a/lib/src/Makefile.in b/lib/src/Makefile.in -index c23f488..9579b3b 100755 ---- a/lib/src/Makefile.in -+++ b/lib/src/Makefile.in -@@ -659,7 +659,7 @@ csymlib.o: $(srcdir)/csymlib.c $(srcdir)/csymlib.h - csymlib_f.o: $(srcdir)/csymlib_f.c $(srcdir)/csymlib.h - ccp4_unitcell.o: $(srcdir)/ccp4_unitcell.c $(srcdir)/ccp4_unitcell.h - ccp4_unitcell_f.o: $(srcdir)/ccp4_unitcell_f.c $(srcdir)/ccp4_unitcell.h --hybrid_36_f.o: $(srcdir)/hybrid_36_f.c $(mmdbsrcdir)/hybrid_36.h -+hybrid_36_f.o: $(srcdir)/hybrid_36_f.c - cvecmat.o: $(srcdir)/cvecmat.c $(srcdir)/cvecmat.h - cmtzlib_python_wrap.o: $(srcdir)/cmtzlib_python_wrap.c $(srcdir)/mtzdata.h - cmaplib_python_wrap.o: $(srcdir)/cmaplib_python_wrap.c -diff --git a/lib/ssm/Makefile.am b/lib/ssm/Makefile.am -index e9554e1..a3ba33d 100755 ---- a/lib/ssm/Makefile.am -+++ b/lib/ssm/Makefile.am -@@ -1,7 +1,11 @@ -+ACLOCAL_AMFLAGS = -I macros - #libtool - lib_LTLIBRARIES = libssm.la -+libssm_la_LDFLAGS = -shared $(SHARED_LIB_FLAGS) -+libssm_la_CFLAGS = @MMDB_CFLAGS@ - libssm_la_SOURCES = ssm_superpose.cpp ss_csia.cpp ss_vxedge.cpp \ - ssm_align.cpp ss_graph.cpp -+libssm_la_LIBADD = @MMDB_LIBS@ - - #non libtool - #lib_LIBRARIES = libssm.a -@@ -16,12 +20,10 @@ superpose_SOURCES = superpose.cpp - - bin_PROGRAMS = superpose - --INCLUDES = $(MMDB_CXXFLAGS) -- --AM_LDFLAGS = $(MMDB_LIBS) -+INCLUDES = @MMDB_CFLAGS@ - - EXTRA_DIST = macros/mmdb.m4 - --superpose_LDADD = libssm.la -+superpose_LDADD = libssm.la @MMDB_LIBS@ - - libssm_a_AR = $(AR) $(AR_FLAGS) -diff --git a/lib/ssm/configure.ac b/lib/ssm/configure.ac -index 783cb46..d637d11 100755 ---- a/lib/ssm/configure.ac -+++ b/lib/ssm/configure.ac -@@ -28,31 +28,10 @@ AC_ARG_ENABLE(debug, - [ac_cv_enable_debug=no ] ) - - dnl Optional: Check for MMDB. --AM_PATH_MMDB(, -- [ if test "x$mmdb_prefix" != x ; then -- if test "x$ac_MMDB_CXXFLAGS" != x ; then -- case "$ac_MMDB_CXXFLAGS" in -- *src/mmdb ) -- ac_MMDB_LDOPTS=`echo "$ac_MMDB_CXXFLAGS" | sed s#src/mmdb#src#g` -- ;; -- *include/mmdb ) -- ac_MMDB_LDOPTS=`echo "$ac_MMDB_CXXFLAGS" | sed s#include/mmdb#lib#g` -- ;; -- *) -- esac -- MMDB_CXXFLAGS="$ac_MMDB_CXXFLAGS" -- MMDB_LIBS=`echo "$ac_MMDB_LDOPTS -lmmdb" | sed s#-I#-L#` -- AC_MSG_WARN([assuming library $MMDB_LIBS headers $MMDB_CXXFLAGS]) -- else -- MMDB_CXXFLAGS="-I$mmdb_prefix/lib/src/mmdb -I$mmdb_prefix/include/mmdb" -- MMDB_LIBS="-L$mmdb_prefix/lib/src -L$mmdb_prefix/lib -lmmdb" -- AC_MSG_WARN([assuming library $MMDB_LIBS headers $MMDB_CXXFLAGS]) -- fi -- else -- AC_MSG_WARN([mmdb not found]) -- fi -- ] --) -+ -+PKG_CHECK_MODULES([MMDB],[mmdb]) -+AC_SUBST([MMDB_CFLAGS]) -+AC_SUBST([MMDB_LIBS]) - - # Checks for typedefs, structures, and compiler characteristics. - # -@@ -67,6 +46,7 @@ AC_CHECK_FUNCS([floor pow rint sqrt]) - # test for function in m - AC_CHECK_LIB([m], [sqrt]) - -+ - AC_SUBST(AR_FLAGS) - AC_SUBST(superpose_LDFLAGS) - AM_CONDITIONAL(DEBUG, test "$ac_cv_enable_debug" = yes) -diff --git a/src/pisa/Makefile.am b/src/pisa/Makefile.am -index 094fd6b..922a131 100755 ---- a/src/pisa/Makefile.am -+++ b/src/pisa/Makefile.am -@@ -1,3 +1,4 @@ -+ACLOCAL_AMFLAGS = -I macros - SUBDIRS = molref pisastore sbase - - pkgdatadir = $(datadir)/pisa -@@ -20,8 +21,8 @@ pisa.cpp pisa_lists.cpp seq_superpose.cpp - - bin_PROGRAMS = pisa - --INCLUDES = $(MMDB_CXXFLAGS) $(SSM_CXXFLAGS) -+INCLUDES = @MMDB_CFLAGS@ $(SSM_CXXFLAGS) - --pisa_LDADD = $(SSM_LIBS) $(MMDB_LIBS) -+pisa_LDADD = $(SSM_LIBS) @MMDB_LIBS@ - - EXTRA_DIST = macros/mmdb.m4 macros/ssm.m4 pisa.cfg.in -diff --git a/src/pisa/configure.ac b/src/pisa/configure.ac -index 81afdda..4f99df6 100755 ---- a/src/pisa/configure.ac -+++ b/src/pisa/configure.ac -@@ -32,35 +32,13 @@ AC_CHECK_FUNCS([floor pow rint sqrt]) - AC_CHECK_LIB([m], [sqrt]) - - dnl Optional: Check for MMDB. --AM_PATH_MMDB(, -- [ if test "x$mmdb_prefix" != x ; then -- if test "x$ac_MMDB_CXXFLAGS" != x && test "x$ac_MMDB_LDOPTS" = x ; then -- case "$ac_MMDB_CXXFLAGS" in -- *src/mmdb ) -- ac_MMDB_LDOPTS=`echo "$ac_MMDB_CXXFLAGS" | sed s#src/mmdb#src#g` -- ;; -- *include/mmdb ) -- ac_MMDB_LDOPTS=`echo "$ac_MMDB_CXXFLAGS" | sed s#include/mmdb#lib#g` -- ;; -- *) -- esac -- MMDB_CXXFLAGS="$ac_MMDB_CXXFLAGS" -- MMDB_LIBS=`echo "$ac_MMDB_LDOPTS -lmmdb" | sed s#-I#-L#` -- AC_MSG_WARN([assuming library $MMDB_LIBS headers $MMDB_CXXFLAGS]) -- else -- MMDB_CXXFLAGS="-I$mmdb_prefix/src -I$mmdb_prefix/src/mmdb -I$mmdb_prefix/include -I$mmdb_prefix/include/mmdb" -- MMDB_LIBS="-L$mmdb_prefix/src -L$mmdb_prefix/lib -lmmdb" -- AC_MSG_WARN([assuming library $MMDB_LIBS headers $MMDB_CXXFLAGS]) -- fi -- else -- AC_MSG_ERROR([mmdb not found]) -- fi -- ] --) -+PKG_CHECK_MODULES([MMDB],[mmdb]) -+AC_SUBST([MMDB_CFLAGS]) -+AC_SUBST([MMDB_LIBS]) - - ac_saved_CXXFLAGS=$CXXFLAGS - ac_saved_LIBS=$LIBS --CXXFLAGS="$CXXFLAGS $MMDB_CXXFLAGS" -+CXXFLAGS="$CXXFLAGS $MMDB_CFLAGS" - LIBS="$MMDB_LIBS $LIBS" - AM_PATH_SSM(, - [ if test "x$ssm_prefix" != x ; then -diff --git a/src/rapper/Makefile.am b/src/rapper/Makefile.am -index e78b10d..486b931 100755 ---- a/src/rapper/Makefile.am -+++ b/src/rapper/Makefile.am -@@ -1,3 +1,3 @@ --SUBDIRS = libxml2 gc7.0 LOOP data -+SUBDIRS = LOOP data - - EXTRA_DIST = -diff --git a/src/rapper/configure.ac b/src/rapper/configure.ac -index 5e4ef69..11b63ec 100755 ---- a/src/rapper/configure.ac -+++ b/src/rapper/configure.ac -@@ -48,6 +48,6 @@ AM_CONDITIONAL(AMDEP, test "x$enable_dependency_tracking" != xno) - - AC_SUBST(rapper_LDFLAGS) - --AC_CONFIG_SUBDIRS([gc7.0 libxml2]) -+#AC_CONFIG_SUBDIRS([gc7.0 libxml2]) - #AC_OUTPUT(Makefile LOOP/Makefile LOOP/python/Makefile data/Makefile) - AC_OUTPUT(Makefile LOOP/Makefile data/Makefile) diff --git a/sci-libs/ccp4-libs/files/6.1.3-unbundle-libs.patch b/sci-libs/ccp4-libs/files/6.1.3-unbundle-libs.patch deleted file mode 100644 index 96978320163b..000000000000 --- a/sci-libs/ccp4-libs/files/6.1.3-unbundle-libs.patch +++ /dev/null @@ -1,203 +0,0 @@ -diff --git a/lib/DiffractionImage/DiffractionImageCBF.cpp b/lib/DiffractionImage/DiffractionImageCBF.cpp -index 69b32b0..602e35f 100755 ---- a/lib/DiffractionImage/DiffractionImageCBF.cpp -+++ b/lib/DiffractionImage/DiffractionImageCBF.cpp -@@ -6,10 +6,10 @@ - // images. - - #include "DiffractionImage.h" --#include "cbf.h" --#include "cbf_simple.h" --#include "cbf_string.h" --#include "cbf_byte_offset.h" -+#include -+#include -+#include -+#include - - - using namespace std; -diff --git a/lib/DiffractionImage/MAR/Makefile.in b/lib/DiffractionImage/MAR/Makefile.in -index 4264696..00c4d8d 100755 ---- a/lib/DiffractionImage/MAR/Makefile.in -+++ b/lib/DiffractionImage/MAR/Makefile.in -@@ -174,7 +174,7 @@ top_builddir = @top_builddir@ - top_srcdir = @top_srcdir@ - AUTOMAKE_OPTIONS = gnu - noinst_LTLIBRARIES = libmar.la --AM_CPPFLAGS = -I../CBFlib/src -I../CBFlib/include -+AM_CPPFLAGS = - libmar_la_SOURCES = mar300_header.c \ - mar345_header.c \ - marcif.c \ -diff --git a/lib/DiffractionImage/MAR/marcif.c b/lib/DiffractionImage/MAR/marcif.c -index d3f4212..2c37108 100755 ---- a/lib/DiffractionImage/MAR/marcif.c -+++ b/lib/DiffractionImage/MAR/marcif.c -@@ -31,8 +31,7 @@ - #include "marcif_header.h" - #include "mar345_header.h" - --#include --#include -+#include - - #define printe(x) printf("%s: %s: %s\n",prg,f,x) - #undef cbf_failnez -diff --git a/lib/DiffractionImage/Makefile.in b/lib/DiffractionImage/Makefile.in -index 8197956..807cf25 100755 ---- a/lib/DiffractionImage/Makefile.in -+++ b/lib/DiffractionImage/Makefile.in -@@ -106,23 +106,19 @@ PROGRAMS = $(bin_PROGRAMS) - am_automask_OBJECTS = automask.$(OBJEXT) - automask_OBJECTS = $(am_automask_OBJECTS) - automask_DEPENDENCIES = libDiffImage.la ./Bruker/libbruker.la \ -- ./CBFlib/src/libcbf.la ./MAR/libmar.la ./Rigaku/librigaku.la \ -- ./jpg/libjpeg.la -+ ./MAR/libmar.la ./Rigaku/librigaku.la - am_diff2jpeg_OBJECTS = diff2jpeg.$(OBJEXT) - diff2jpeg_OBJECTS = $(am_diff2jpeg_OBJECTS) - diff2jpeg_DEPENDENCIES = libDiffImage.la ./Bruker/libbruker.la \ -- ./CBFlib/src/libcbf.la ./MAR/libmar.la ./Rigaku/librigaku.la \ -- ./jpg/libjpeg.la -+ ./MAR/libmar.la ./Rigaku/librigaku.la - am_diffdump_OBJECTS = diffdump.$(OBJEXT) - diffdump_OBJECTS = $(am_diffdump_OBJECTS) - diffdump_DEPENDENCIES = libDiffImage.la ./Bruker/libbruker.la \ -- ./CBFlib/src/libcbf.la ./MAR/libmar.la ./Rigaku/librigaku.la \ -- ./jpg/libjpeg.la -+ ./MAR/libmar.la ./Rigaku/librigaku.la - am_printpeaks_OBJECTS = printpeaks.$(OBJEXT) - printpeaks_OBJECTS = $(am_printpeaks_OBJECTS) - printpeaks_DEPENDENCIES = libDiffImage.la ./Bruker/libbruker.la \ -- ./CBFlib/src/libcbf.la ./MAR/libmar.la ./Rigaku/librigaku.la \ -- ./jpg/libjpeg.la -+ ./MAR/libmar.la ./Rigaku/librigaku.la - DEFAULT_INCLUDES = -I.@am__isrc@ - depcomp = $(SHELL) $(top_srcdir)/depcomp - am__depfiles_maybe = depfiles -@@ -284,8 +280,8 @@ target_alias = @target_alias@ - top_builddir = @top_builddir@ - top_srcdir = @top_srcdir@ - AUTOMAKE_OPTIONS = gnu --SUBDIRS = CBFlib Bruker MAR Rigaku jpg --AM_CPPFLAGS = -I./MAR -I./CBFlib/src -I./CBFlib/include -I./jpg -+SUBDIRS = Bruker MAR Rigaku -+AM_CPPFLAGS = -I./MAR - lib_LTLIBRARIES = libDiffImage.la $(am__append_1) $(am__append_2) \ - $(am__append_3) - libDiffImage_la_SOURCES = DiffractionImageJpeg.cpp \ -@@ -311,50 +307,50 @@ libDiffImage_la_SOURCES = DiffractionImageJpeg.cpp \ - dps_peaksearch_cn.c - - libDiffImage_la_LDFLAGS = -static --libDiffractionImage_la_DEPENDENCIES = libDiffImage.la ./CBFlib/src/libcbf.la \ -+libDiffractionImage_la_DEPENDENCIES = libDiffImage.la \ - ./Bruker/libbruker.la ./MAR/libmar.la \ -- ./Rigaku/librigaku.la ./jpg/libjpeg.la -+ ./Rigaku/librigaku.la - - libDiffractionImage_la_SOURCES = DiffractionImageTclInterface.cpp - libDiffractionImage_la_LDFLAGS = -shared --whole-archive libDiffImage.la \ -- ./CBFlib/src/libcbf.la ./Bruker/libbruker.la \ -- ./MAR/libmar.la ./Rigaku/librigaku.la ./jpg/libjpeg.la \ -+ -lcbf ./Bruker/libbruker.la \ -+ ./MAR/libmar.la ./Rigaku/librigaku.la -ljpeg \ - --no-whole-archive -rpath '$(libdir)' - --lib_DiffractionImage_la_DEPENDENCIES = libDiffImage.la ./CBFlib/src/libcbf.la \ -+lib_DiffractionImage_la_DEPENDENCIES = libDiffImage.la \ - ./Bruker/libbruker.la ./MAR/libmar.la \ -- ./Rigaku/librigaku.la ./jpg/libjpeg.la -+ ./Rigaku/librigaku.la - - lib_DiffractionImage_la_SOURCES = DiffractionImagePythonInterface.cpp - lib_DiffractionImage_la_LDFLAGS = -shared --whole-archive libDiffImage.la \ -- ./CBFlib/src/libcbf.la ./Bruker/libbruker.la \ -- ./MAR/libmar.la ./Rigaku/librigaku.la ./jpg/libjpeg.la \ -+ -lcbf ./Bruker/libbruker.la \ -+ ./MAR/libmar.la ./Rigaku/librigaku.la -ljpeg \ - --no-whole-archive -rpath '$(libdir)' - --libDiffractionImaJ_la_DEPENDENCIES = libDiffImage.la ./CBFlib/src/libcbf.la \ -+libDiffractionImaJ_la_DEPENDENCIES = libDiffImage.la \ - ./Bruker/libbruker.la ./MAR/libmar.la \ -- ./Rigaku/librigaku.la ./jpg/libjpeg.la -+ ./Rigaku/librigaku.la - - libDiffractionImaJ_la_SOURCES = DiffractionImageJavaInterface.cpp - libDiffractionImaJ_la_LDFLAGS = -shared --whole-archive libDiffImage.la \ -- ./CBFlib/src/libcbf.la ./Bruker/libbruker.la \ -- ./MAR/libmar.la ./Rigaku/librigaku.la ./jpg/libjpeg.la \ -+ -lcbf ./Bruker/libbruker.la \ -+ ./MAR/libmar.la ./Rigaku/librigaku.la -ljpeg \ - --no-whole-archive -rpath '$(libdir)' - --automask_LDADD = libDiffImage.la ./Bruker/libbruker.la ./CBFlib/src/libcbf.la \ -- ./MAR/libmar.la ./Rigaku/librigaku.la ./jpg/libjpeg.la -+automask_LDADD = libDiffImage.la ./Bruker/libbruker.la -lcbf \ -+ ./MAR/libmar.la ./Rigaku/librigaku.la -ljpeg - - automask_SOURCES = automask.cpp --diffdump_LDADD = libDiffImage.la ./Bruker/libbruker.la ./CBFlib/src/libcbf.la \ -- ./MAR/libmar.la ./Rigaku/librigaku.la ./jpg/libjpeg.la -+diffdump_LDADD = libDiffImage.la ./Bruker/libbruker.la -lcbf \ -+ ./MAR/libmar.la ./Rigaku/librigaku.la -ljpeg - - diffdump_SOURCES = diffdump.cpp --printpeaks_LDADD = libDiffImage.la ./Bruker/libbruker.la ./CBFlib/src/libcbf.la \ -- ./MAR/libmar.la ./Rigaku/librigaku.la ./jpg/libjpeg.la -+printpeaks_LDADD = libDiffImage.la ./Bruker/libbruker.la -lcbf \ -+ ./MAR/libmar.la ./Rigaku/librigaku.la -ljpeg - - printpeaks_SOURCES = printpeaks.cpp --diff2jpeg_LDADD = libDiffImage.la ./Bruker/libbruker.la ./CBFlib/src/libcbf.la \ -- ./MAR/libmar.la ./Rigaku/librigaku.la ./jpg/libjpeg.la -+diff2jpeg_LDADD = libDiffImage.la ./Bruker/libbruker.la -lcbf \ -+ ./MAR/libmar.la ./Rigaku/librigaku.la -ljpeg - - diff2jpeg_SOURCES = diff2jpeg.cpp - all: all-recursive -diff --git a/lib/DiffractionImage/configure b/lib/DiffractionImage/configure -index 3fb5784..fdf9683 100755 ---- a/lib/DiffractionImage/configure -+++ b/lib/DiffractionImage/configure -@@ -21768,7 +21768,7 @@ _ACEOF - fi - - --ac_config_files="$ac_config_files Makefile CBFlib/Makefile CBFlib/src/Makefile MAR/Makefile Rigaku/Makefile Bruker/Makefile jpg/Makefile" -+ac_config_files="$ac_config_files Makefile MAR/Makefile Rigaku/Makefile Bruker/Makefile " - - - cat >confcache <<\_ACEOF -@@ -22407,12 +22407,9 @@ do - case $ac_config_target in - "depfiles") CONFIG_COMMANDS="$CONFIG_COMMANDS depfiles" ;; - "Makefile") CONFIG_FILES="$CONFIG_FILES Makefile" ;; -- "CBFlib/Makefile") CONFIG_FILES="$CONFIG_FILES CBFlib/Makefile" ;; -- "CBFlib/src/Makefile") CONFIG_FILES="$CONFIG_FILES CBFlib/src/Makefile" ;; - "MAR/Makefile") CONFIG_FILES="$CONFIG_FILES MAR/Makefile" ;; - "Rigaku/Makefile") CONFIG_FILES="$CONFIG_FILES Rigaku/Makefile" ;; - "Bruker/Makefile") CONFIG_FILES="$CONFIG_FILES Bruker/Makefile" ;; -- "jpg/Makefile") CONFIG_FILES="$CONFIG_FILES jpg/Makefile" ;; - - *) { { echo "$as_me:$LINENO: error: invalid argument: $ac_config_target" >&5 - echo "$as_me: error: invalid argument: $ac_config_target" >&2;} -diff --git a/lib/DiffractionImage/configure.in b/lib/DiffractionImage/configure.in -index 7f54b4b..69b10e1 100755 ---- a/lib/DiffractionImage/configure.in -+++ b/lib/DiffractionImage/configure.in -@@ -65,11 +65,8 @@ AM_CONDITIONAL([WANT_JAVA], test z${HAVE_JAVA} != z) - AC_CHECK_LIB([m], [sqrt]) - - AC_CONFIG_FILES([Makefile -- CBFlib/Makefile -- CBFlib/src/Makefile - MAR/Makefile - Rigaku/Makefile -- Bruker/Makefile -- jpg/Makefile]) -+ Bruker/Makefile]) - - AC_OUTPUT diff --git a/sci-libs/ccp4-libs/files/ccp4-libs-6.1.3-force.patch b/sci-libs/ccp4-libs/files/ccp4-libs-6.1.3-force.patch deleted file mode 100644 index 367d53e3e4f6..000000000000 --- a/sci-libs/ccp4-libs/files/ccp4-libs-6.1.3-force.patch +++ /dev/null @@ -1,16 +0,0 @@ - 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); \ diff --git a/sci-libs/ccp4-libs/files/ccp4-libs-6.1.3-format-security.patch b/sci-libs/ccp4-libs/files/ccp4-libs-6.1.3-format-security.patch deleted file mode 100644 index caf62bb652e2..000000000000 --- a/sci-libs/ccp4-libs/files/ccp4-libs-6.1.3-format-security.patch +++ /dev/null @@ -1,16 +0,0 @@ - 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); - } - } - diff --git a/sci-libs/ccp4-libs/metadata.xml b/sci-libs/ccp4-libs/metadata.xml deleted file mode 100644 index c0432fefe855..000000000000 --- a/sci-libs/ccp4-libs/metadata.xml +++ /dev/null @@ -1,9 +0,0 @@ - - - - sci-chemistry - - jlec@gentoo.org - Justin Lecher (jlec) - - -- cgit v1.2.3-65-gdbad