From: Donnie Berkholz Date: Mon, 7 Aug 2006 03:42:00 +0000 (+0000) Subject: Add upstream patches. The build system won't accept LDFLAGS, so unset them. (#142183... X-Git-Url: http://git.tremily.us/?a=commitdiff_plain;h=4e495533901ec71e3fe0836bd024909c8d224337;p=gentoo.git Add upstream patches. The build system won't accept LDFLAGS, so unset them. (#142183) Source the setup script again in src_install() to make sure CBIN and CCP4_LIB get set. Not doing this breaks USE=X because the Imakefiles use them. Stop changing the value of CCP4_LIB, that was only necessary for the bindir=/usr/bin, libdir=/usr/libdir install, which was too much work. Package-Manager: portage-2.1.1_pre4-r2 --- diff --git a/sci-chemistry/ccp4/ChangeLog b/sci-chemistry/ccp4/ChangeLog index 5696511daf85..4b3519f47530 100644 --- a/sci-chemistry/ccp4/ChangeLog +++ b/sci-chemistry/ccp4/ChangeLog @@ -1,6 +1,16 @@ # ChangeLog for sci-chemistry/ccp4 # Copyright 1999-2006 Gentoo Foundation; Distributed under the GPL v2 -# $Header: /var/cvsroot/gentoo-x86/sci-chemistry/ccp4/ChangeLog,v 1.3 2006/08/05 05:06:08 dberkholz Exp $ +# $Header: /var/cvsroot/gentoo-x86/sci-chemistry/ccp4/ChangeLog,v 1.4 2006/08/07 03:42:00 dberkholz Exp $ + +*ccp4-6.0.1-r1 (07 Aug 2006) + + 07 Aug 2006; Donnie Berkholz ; + +ccp4-6.0.1-r1.ebuild: + Add upstream patches. The build system won't accept LDFLAGS, so unset them. + (#142183) Source the setup script again in src_install() to make sure CBIN + and CCP4_LIB get set. Not doing this breaks USE=X because the Imakefiles use + them. Stop changing the value of CCP4_LIB, that was only necessary for the + bindir=/usr/bin, libdir=/usr/libdir install, which was too much work. 05 Aug 2006; Donnie Berkholz ; metadata.xml: Remove myself as maintainer, anyone feel free to work on this, although I'll diff --git a/sci-chemistry/ccp4/Manifest b/sci-chemistry/ccp4/Manifest index b054adb8f587..80a4baea2e38 100644 --- a/sci-chemistry/ccp4/Manifest +++ b/sci-chemistry/ccp4/Manifest @@ -46,15 +46,31 @@ AUX pass-clipper-enablevals.patch 501 RMD160 23466922268a91570b0f64cf79809b988e3 MD5 bcdb856dae7ea7b22d130474f6c17b7d files/pass-clipper-enablevals.patch 501 RMD160 23466922268a91570b0f64cf79809b988e32689b files/pass-clipper-enablevals.patch 501 SHA256 d476c9f231fb6cdfb5e57004b393644a88016318cdeed9c33c32de25e0d91b79 files/pass-clipper-enablevals.patch 501 +DIST act.f-6July2006.diff 16544 RMD160 24f48e95ec3363a2409da122bd0eb7ef5a91da36 SHA1 97ddeead440ce5b7d59fcb8e564f3907e6462c93 SHA256 ba807b19b834d68ff121e34bbfbb113ae528db1aeebfeb7e98cbb90c64c2c3c4 +DIST anisoanl.f-r1.22-r1.24.diff 9452 RMD160 02f9561362892cbbeed24592b5ed4e3eb51ace2c SHA1 76691ac9097a4132f3618e13d41d913d92e45b9a SHA256 1308ef91c63efd1c11287f68f386a62678d1ab48ddfe6e94cefdef1c92173940 +DIST cad.f-r1.70-r1.72.diff 12196 RMD160 a18c339223c8a6a66fda4cb210f2e533fea0d240 SHA1 30da509c9b51506541b0b49adbf7836c8fc5f7d4 SHA256 ba10591643f93fb310d451aacce286d8ec9386f2e781d631f794076d1021539f DIST ccp4-6.0.1-core-src.tar.gz 59311291 RMD160 0f514fe30f22a4f6eb2e05c8bab567d2132e8fae SHA1 e8f5fb325a13375793f7610160337090af8fb9b5 SHA256 26a5704d707c3bc2fbe4c1d0804abccc1c50255005d26a8ec3a03fcba63335f2 +DIST chainsaw.cpp-11May2006.diff 4720 RMD160 62c3b3a3da0d36aa8f0c67a55c068508858eeb17 SHA1 f6a4e0cd22438a8855796e82b5492bd8870aa49c SHA256 de2d2ccd365f2992e1ba9a385f1a2fcd9e52da5ff96bcbc4fa7b4404cf0bac6e +DIST contact.f-12June2006.diff 43051 RMD160 577b454ed229be8c9b79e8c4622c870d589e2cca SHA1 aff0071b1130a3cc62b419fed5909f94a87ff9e1 SHA256 1336ea01da83aad21669b82cd3895f724db6db8d17d78acfec53154ea7ce690e +DIST molrep.f-r1.28-r1.28.2.1.diff 755 RMD160 96a37ea54606583647ff9cdc9da728ce05d30849 SHA1 7fa0302e9e4309a86aad3bebde5359af740cecd8 SHA256 0bb22cb2f8e1486ec5cc6037427e9ec66189684d74b5939757b4ebe771a61084 +DIST mtztona4.f-r1.23-r1.24.diff 882 RMD160 1b34c6caaf5356574f65f2d092196cdd788cb720 SHA1 c6bfd2c3784fb385f0455f2638cd2d8ab11aaea7 SHA256 d7cf1b6ab2015b18c6b4b310e25b706a1f420d623383c17d0b51acfb00ae679a +DIST omit.f-r1.12-r1.13.diff 2303 RMD160 5dda121b69fdc3b4e138e0b88012df1d46398d3a SHA1 0836a9fe21bf2acd87d4f87115bb1dc0645e6bb9 SHA256 14a8128809f78d2d08b81cde5f91b51a694d99b56215477a62571344024a6748 +DIST refmac5.tcl-r1.39.2.3-r1.42.diff 2464 RMD160 fca236184597ab86fc9ac7333834e68eab641dac SHA1 eecf37e89e200dcbea7544f320cd16160ab5615a SHA256 8418181bae8799d2fa5a004e84cb1c66391d0cb768df5d40b34e053aced6fd4c +DIST rotmat.f-17July2006.diff 1002 RMD160 59cc822edbdc73b24e51cff013c71e4d68927979 SHA1 31fed5d06e8c8afc719f74d50acb0e833b893202 SHA256 1ee4f3288dba6404d59f51b9f9e1b4475413f7e40991204ab39474ee559605b1 +DIST sc.f-r1.9-r1.9.2.1.diff 8783 RMD160 815d25cff0fa76f73dc43da9757ad753ec392f9c SHA1 f55e2e8c84ec8cd3b94cb703b50abff625e3a7fb SHA256 418feea2ccf0014c3c2c83ab9460873114057480fd2a1dcabe305a1b956ad86b +DIST setup.fh-r1.5-r1.5.2.1.diff 1317 RMD160 45a16b00792706553e7bf23a2f54415cd5ee1b43 SHA1 2a7417cf998b5e9fcac3b3b8a2deb05627d29d1a SHA256 637564c5723fb7de04d3a06817eec704ac708b74264716905690250e42aed146 +EBUILD ccp4-6.0.1-r1.ebuild 14020 RMD160 3341bb2f726baa0448366a8a8e43aa5c1d964520 SHA1 8bc5dd084c5e6991fb3a2a68dda5a1e87531e9cc SHA256 ca377b7488e57a86ca9fa42daa315d75107e81909c3f1692dad9b3e4b1238457 +MD5 18628222e60cc5706d1dd05346170930 ccp4-6.0.1-r1.ebuild 14020 +RMD160 3341bb2f726baa0448366a8a8e43aa5c1d964520 ccp4-6.0.1-r1.ebuild 14020 +SHA256 ca377b7488e57a86ca9fa42daa315d75107e81909c3f1692dad9b3e4b1238457 ccp4-6.0.1-r1.ebuild 14020 EBUILD ccp4-6.0.1.ebuild 13729 RMD160 5fe2a8f1d42a810e8fda14c61e970f9146ab0b96 SHA1 25638dfbe892e82daccc6f40af9479ae88d2386f SHA256 d3d7ea08c1260eff42b49ead37d935bf3c9e38eac6e8eeb4fa86b3962ed25c7c MD5 48bda08719da61345f9297bdecd1b975 ccp4-6.0.1.ebuild 13729 RMD160 5fe2a8f1d42a810e8fda14c61e970f9146ab0b96 ccp4-6.0.1.ebuild 13729 SHA256 d3d7ea08c1260eff42b49ead37d935bf3c9e38eac6e8eeb4fa86b3962ed25c7c ccp4-6.0.1.ebuild 13729 -MISC ChangeLog 1294 RMD160 df51b121891b583b5ed2902a317685f18e7d8a89 SHA1 90145ffd0591e7e91509d839342a70ef7b0b33ef SHA256 3b5bfcdfbcb9b9fc54be3a4e79e25554305de0b1ddf2fcfc42f9d57d53357b22 -MD5 6fa8d57dc71f02621a1d0666e9de950f ChangeLog 1294 -RMD160 df51b121891b583b5ed2902a317685f18e7d8a89 ChangeLog 1294 -SHA256 3b5bfcdfbcb9b9fc54be3a4e79e25554305de0b1ddf2fcfc42f9d57d53357b22 ChangeLog 1294 +MISC ChangeLog 1788 RMD160 5beca7054df8ae7edde4c03b166b588467cfc7a2 SHA1 05c937c9b1b1c7c24f5db9927f633262c9b3adb2 SHA256 51580d514db58cf543c2ed532a5b394de86f40f26e53f3eb8e9c4a87da3cbf79 +MD5 361275a4deed84589af434b422ed510b ChangeLog 1788 +RMD160 5beca7054df8ae7edde4c03b166b588467cfc7a2 ChangeLog 1788 +SHA256 51580d514db58cf543c2ed532a5b394de86f40f26e53f3eb8e9c4a87da3cbf79 ChangeLog 1788 MISC metadata.xml 156 RMD160 dc078172bfebcb25d69bdf8731714f9cce9d3e36 SHA1 da2b240a255820145b7c83a5c48e45b96b7e9ee6 SHA256 5d22100902db7507a5b5493dd4a66cdb08025faf80a2c0b75e6392315c47f900 MD5 8c623e53daafa025137077c6b65815bd metadata.xml 156 RMD160 dc078172bfebcb25d69bdf8731714f9cce9d3e36 metadata.xml 156 @@ -62,3 +78,6 @@ SHA256 5d22100902db7507a5b5493dd4a66cdb08025faf80a2c0b75e6392315c47f900 metadata MD5 af2485e5d663b3c625e3ee4f94748730 files/digest-ccp4-6.0.1 265 RMD160 72caf22fe0480a8c577d84ff2ffb3bb3a6dcadd5 files/digest-ccp4-6.0.1 265 SHA256 52ebe8c93194a9140171ac2e0d80b4750913b3e97ac1ee0f37c34ad9137deda8 files/digest-ccp4-6.0.1 265 +MD5 42c7b9d83453a9015d474ef4eaea76c1 files/digest-ccp4-6.0.1-r1 3286 +RMD160 9c65d5658b463f2aa751cb59c63d954c0b69568a files/digest-ccp4-6.0.1-r1 3286 +SHA256 3ccb5d939d1f0386093758fe8c5cfbb54be329869df7a77b85c0653d613f0a86 files/digest-ccp4-6.0.1-r1 3286 diff --git a/sci-chemistry/ccp4/ccp4-6.0.1-r1.ebuild b/sci-chemistry/ccp4/ccp4-6.0.1-r1.ebuild new file mode 100644 index 000000000000..997e42a76d66 --- /dev/null +++ b/sci-chemistry/ccp4/ccp4-6.0.1-r1.ebuild @@ -0,0 +1,453 @@ +# Copyright 1999-2006 Gentoo Foundation +# Distributed under the terms of the GNU General Public License v2 +# $Header: /var/cvsroot/gentoo-x86/sci-chemistry/ccp4/ccp4-6.0.1-r1.ebuild,v 1.1 2006/08/07 03:42:00 dberkholz Exp $ + +inherit fortran eutils gnuconfig toolchain-funcs + +FORTRAN="g77 gfortran ifc" + +SRC="ftp://ftp.ccp4.ac.uk/ccp4" + +PATCH_TOT="12" +PATCH1=( src/mmdb_app_ + chainsaw.cpp-11May2006.diff ) +PATCH2=( src + anisoanl.f-r1.22-r1.24.diff ) +PATCH3=( src/sc_ + sc.f-r1.9-r1.9.2.1.diff ) +PATCH4=( src/sc_ + setup.fh-r1.5-r1.5.2.1.diff ) +PATCH5=( src + contact.f-12June2006.diff ) +PATCH6=( ccp4i/tasks + refmac5.tcl-r1.39.2.3-r1.42.diff ) +PATCH7=( src + act.f-6July2006.diff ) +PATCH8=( src + rotmat.f-17July2006.diff ) +PATCH9=( src/molrep_ + molrep.f-r1.28-r1.28.2.1.diff ) +PATCH10=( src + cad.f-r1.70-r1.72.diff ) +PATCH11=( src + mtztona4.f-r1.23-r1.24.diff ) +PATCH12=( src + omit.f-r1.12-r1.13.diff ) + +DESCRIPTION="Protein X-ray crystallography toolkit" +HOMEPAGE="http://www.ccp4.ac.uk/" +RESTRICT="mirror stricter" +SRC_URI="${SRC}/${PV}/packed/${P}-core-src.tar.gz" +for i in $(seq $PATCH_TOT); do + NAME="PATCH${i}[1]" + SRC_URI="${SRC_URI} + ${SRC}/${PV}/patches/${!NAME}" +done +LICENSE="ccp4" +SLOT="0" +KEYWORDS="~ppc ~x86" +IUSE="X" +# app-office/sc overlaps sc binary and man page +# We can't rename ours since the automated ccp4i interface expects it there, +# as do many scripts. app-office/sc can't rename its because that's the name +# of the package. +RDEPEND="X? ( + || ( + ( + x11-libs/libX11 + x11-libs/libXt + x11-libs/libXaw + ) + virtual/x11 + ) + ) + >=dev-lang/tcl-8.3 + >=dev-lang/tk-8.3 + >=dev-tcltk/blt-2.4 + virtual/lapack + virtual/blas + =sci-libs/fftw-2* + sci-chemistry/pdb-extract + sci-chemistry/rasmol + sci-libs/mccp4 + || ( app-shells/tcsh app-shells/csh ) + !app-office/sc" +# >=sys-apps/portage-2.1.1_pre1 for RESTRICT=stricter +# Otherwise portage dies instead of fixing RPATHs +DEPEND="${RDEPEND} + X? ( + || ( + ( + x11-misc/imake + x11-proto/inputproto + x11-proto/xextproto + ) + virtual/x11 + ) + ) + >=sys-apps/portage-2.1.1_pre1" + +S="${WORKDIR}/${PN}-${PV}" + +src_unpack() { + unpack ${A} + cd ${S} + + 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 + + einfo "Applying Gentoo patches ..." + # These two only needed when attempting to install outside build dir via + # --bindir and --libdir instead of straight copying after build + + # it attempts to install some libraries during the build + #ccp_patch ${FILESDIR}/${P}-install-libs-at-install-time.patch + # hklview/ipdisp.exe/xdlmapman/ipmosflm can't find libxdl_view + # without this patch when --libdir is set + # Rotgen still needs more patching to find it + #ccp_patch ${FILESDIR}/add-xdl-libdir.patch + + # it tries to create libdir, bindir etc on live system in configure + ccp_patch ${FILESDIR}/${PV}-dont-make-dirs-in-configure.patch + + # We already have sci-chemistry/rasmol + ccp_patch ${FILESDIR}/dont-build-rasmol.patch + + # We already have sci-chemistry/pdb-extract +# Use configure option instead +# ccp_patch ${FILESDIR}/dont-build-pdb-extract.patch + + ccp_patch ${FILESDIR}/create-mosflm-bindir.patch + ccp_patch ${FILESDIR}/make-mosflm-libdir.patch + ccp_patch ${FILESDIR}/make-mosflm-index-libdir.patch + ccp_patch ${FILESDIR}/make-mosflm-cbf-libdir.patch + ccp_patch ${FILESDIR}/make-ipmosflm-dir.patch + +# Don't use these when we aren't building phaser +# ccp_patch ${FILESDIR}/make-phaser-bindir.patch +# ccp_patch ${FILESDIR}/no-phaser-ld-assume-kernel.patch +# # scons config.py tries to chmod python on live system +# ccp_patch ${FILESDIR}/dont-chmod-python-binary.patch + + # Don't use this when we aren't building clipper + # For some reason clipper check for $enableval even when --enable is passed + ccp_patch ${FILESDIR}/pass-clipper-enablevals.patch + ccp_patch ${FILESDIR}/clipper-find-mccp4-includes.patch + + # Default to firefox browser, not 'netscape' + ccp_patch ${FILESDIR}/ccp4i-default-to-firefox.patch + + # Also use -lpthread when linking blas and lapack + # We may need more fixing to use libcblas for the C files + ccp_patch ${FILESDIR}/check-blas-lapack-pthread.patch + + # gerror_ gets defined twice on ppc if you're using gfortran/g95 + ccp_patch ${FILESDIR}/${PV}-ppc-double-define-gerror.patch + + einfo "Done." # done applying Gentoo patches + echo + + gnuconfig_update +} + +src_compile() { + # Build system is broken if we set LDFLAGS + unset LDFLAGS + + # GENTOO_OSNAME can be one of: + # irix irix64 sunos sunos64 aix hpux osf1 linux freebsd + # linux_compaq_compilers linux_intel_compilers generic Darwin + # ia64_linux_intel Darwin_ibm_compilers linux_ibm_compilers + if [[ "${FORTRANC}" = "ifc" ]]; then + if use ia64; then + GENTOO_OSNAME="ia64_linux_intel" + else + # Should be valid for x86, maybe amd64 + GENTOO_OSNAME="linux_intel_compilers" + fi + else + # Should be valid for x86 and amd64, at least + GENTOO_OSNAME="linux" + fi + + # Sets up env + ln -s \ + ccp4.setup-bash \ + ${S}/include/ccp4.setup + + # We agree to the license by emerging this, set in LICENSE + sed -i \ + -e "s~^\(^agreed=\).*~\1yes~g" \ + ${S}/configure + + # Fix up variables -- need to reset CCP4_MASTER at install-time + sed -i \ + -e "s~^\(setenv CCP4_MASTER.*\)/.*~\1${WORKDIR}~g" \ + -e "s~^\(setenv CCP4I_TCLTK.*\)/usr/local/bin~\1/usr/bin~g" \ + ${S}/include/ccp4.setup* + + # Set up variables for build + source ${S}/include/ccp4.setup + + export CC=$(tc-getCC) + export CXX=$(tc-getCXX) + export COPTIM=${CFLAGS} + export CXXOPTIM=${CXXFLAGS} + # Default to -O2 if FFLAGS is unset + export FC=${FORTRANC} + export FOPTIM=${FFLAGS:- -O2} + + # Can't use econf, configure rejects unknown options like --prefix + ./configure \ + $(use_enable X x) \ + --with-shared-libs \ + --with-fftw=/usr \ + --with-warnings \ + --disable-pdb_extract \ + --disable-cctbx \ + --disable-phaser \ + --tmpdir="${TMPDIR}" \ + ${GENTOO_OSNAME} || die "econf failed" + emake -j1 || die "emake failed" +} + +src_install() { + # Set up variables for build + source ${S}/include/ccp4.setup + +# Only needed when using --bindir and --libdir + # Needed to avoid errors. Originally tried to make lib and bin + # in configure script, now patched out by dont-make-dirs-in-configure.patch +# dodir /usr/include /usr/$(get_libdir) /usr/bin + +# make install || die "install failed" + einstall || die "install failed" + + # Fix env + sed -i \ + -e "s~^\(setenv CCP4_MASTER.*\)${WORKDIR}~\1/usr~g" \ + -e "s~^\(setenv CCP4.*\$CCP4_MASTER\).*~\1~g" \ + -e "s~^\(setenv CCP4I_TOP\).*~\1 \$CCP4/$(get_libdir)/ccp4/ccp4i~g" \ + -e "s~^\(.*setenv CINCL.*\$CCP4\).*~\1/share/ccp4/include~g" \ + -e "s~^\(.*setenv CLIBD .*\$CCP4\).*~\1/share/ccp4/data~g" \ + -e "s~^\(.*setenv CLIBD_MON .*\)\$CCP4.*~\1\$CLIBD/monomers/~g" \ + -e "s~^\(.*setenv MOLREPLIB .*\)\$CCP4.*~\1\$CLIBD/monomers/~g" \ + -e "s~^\(.*setenv CCP4_BROWSER.*\).*~\1 firefox~g" \ + ${S}/include/ccp4.setup* + + # Get rid of S instances + # Also the main clipper library is built as libclipper-core, not libclipper + sed -i \ + -e "s:${S}:${ROOT}usr:g" \ + -e "s:lclipper :lclipper-core :g" \ + ${S}/bin/clipper-config +# sed -i \ +# -e "s:${S}:${ROOT}usr:g" \ +# ${S}/$(get_libdir)/cctbx/cctbx_build/setpaths* + + # Bins + EXEDESTTREE="/usr/bin" doexe ${S}/bin/* + + # Libs + for file in ${S}/lib/*; do + if [[ -d ${file} ]]; then + continue + elif [[ -x ${file} ]]; then + dolib.so ${file} + else + INSDESTTREE="/usr/$(get_libdir)" doins ${file} + fi + done + + # Fix libdir in all *.la files + sed -i \ + -e "s:^\(libdir=\).*:\1\'/usr/$(get_libdir)\':g" \ + ${D}/usr/$(get_libdir)/*.la + + # Library symlinks + local LIBNAMES="libclipper-ccp4.so.0.0.0 + libclipper-cif.so.0.0.0 + libclipper-contrib.so.0.0.0 + libclipper-core.so.0.0.0 + libclipper-minimol.so.0.0.0 + libclipper-mmdbold.so.0.0.0 + libclipper-mmdb.so.0.0.0 + libclipper-mtz.so.1.0.0 + libclipper-phs.so.0.0.0 + libjwc_c.so.0.1.1 + libjwc_f.so.0.1.1 + libssm.so.0.0.0 + libxdl_viewextra.so.0.0.0 + libxdl_view.so.2.0.0" + + for LIBNAME in ${LIBNAMES}; do + library_dosym ${LIBNAME} + done + +# dosym libclipper-ccp4.so.0.0.0 /usr/$(get_libdir)/libclipper-ccp4.so +# dosym libclipper-ccp4.so.0.0.0 /usr/$(get_libdir)/libclipper-ccp4.so.0 +# dosym libclipper-ccp4.so.0.0.0 /usr/$(get_libdir)/libclipper-ccp4.so.0.0 +# +# dosym libclipper-cif.so.0.0.0 /usr/$(get_libdir)/libclipper-cif.so +# dosym libclipper-cif.so.0.0.0 /usr/$(get_libdir)/libclipper-cif.so.0 +# dosym libclipper-cif.so.0.0.0 /usr/$(get_libdir)/libclipper-cif.so.0.0 +# +# dosym libclipper-contrib.so.0.0.0 /usr/$(get_libdir)/libclipper-contrib.so +# dosym libclipper-contrib.so.0.0.0 /usr/$(get_libdir)/libclipper-contrib.so.0 +# dosym libclipper-contrib.so.0.0.0 /usr/$(get_libdir)/libclipper-contrib.so.0.0 +# +# dosym libclipper-core.so.0.0.0 /usr/$(get_libdir)/libclipper-core.so +# dosym libclipper-core.so.0.0.0 /usr/$(get_libdir)/libclipper-core.so.0 +# dosym libclipper-core.so.0.0.0 /usr/$(get_libdir)/libclipper-core.so.0.0 +# +# dosym libclipper-minimol.so.0.0.0 /usr/$(get_libdir)/libclipper-minimol.so +# dosym libclipper-minimol.so.0.0.0 /usr/$(get_libdir)/libclipper-minimol.so.0 +# dosym libclipper-minimol.so.0.0.0 /usr/$(get_libdir)/libclipper-minimol.so.0.0 +# +# dosym libclipper-mmdbold.so.0.0.0 /usr/$(get_libdir)/libclipper-mmdbold.so +# dosym libclipper-mmdbold.so.0.0.0 /usr/$(get_libdir)/libclipper-mmdbold.so.0 +# dosym libclipper-mmdbold.so.0.0.0 /usr/$(get_libdir)/libclipper-mmdbold.so.0.0 +# +# dosym libclipper-mmdb.so.0.0.0 /usr/$(get_libdir)/libclipper-mmdb.so +# dosym libclipper-mmdb.so.0.0.0 /usr/$(get_libdir)/libclipper-mmdb.so.0 +# dosym libclipper-mmdb.so.0.0.0 /usr/$(get_libdir)/libclipper-mmdb.so.0.0 +# +# dosym libclipper-mtz.so.1.0.0 /usr/$(get_libdir)/libclipper-mtz.so +# dosym libclipper-mtz.so.1.0.0 /usr/$(get_libdir)/libclipper-mtz.so.1 +# dosym libclipper-mtz.so.1.0.0 /usr/$(get_libdir)/libclipper-mtz.so.1.0 +# +# dosym libclipper-phs.so.0.0.0 /usr/$(get_libdir)/libclipper-phs.so +# dosym libclipper-phs.so.0.0.0 /usr/$(get_libdir)/libclipper-phs.so.0 +# dosym libclipper-phs.so.0.0.0 /usr/$(get_libdir)/libclipper-phs.so.0.0 +# +# dosym libjwc_c.so.0.1.1 /usr/$(get_libdir)/libjwc_c.so +# dosym libjwc_c.so.0.1.1 /usr/$(get_libdir)/libjwc_c.so.0 +# dosym libjwc_c.so.0.1.1 /usr/$(get_libdir)/libjwc_c.so.0.1 +# +# dosym libjwc_f.so.0.1.1 /usr/$(get_libdir)/libjwc_f.so +# dosym libjwc_f.so.0.1.1 /usr/$(get_libdir)/libjwc_f.so.0 +# dosym libjwc_f.so.0.1.1 /usr/$(get_libdir)/libjwc_f.so.0.1 +# +# dosym libssm.so.0.0.0 /usr/$(get_libdir)/libssm.so +# dosym libssm.so.0.0.0 /usr/$(get_libdir)/libssm.so.0 +# dosym libssm.so.0.0.0 /usr/$(get_libdir)/libssm.so.0.0 +# +# dosym libxdl_viewextra.so.0.0.0 /usr/$(get_libdir)/libxdl_viewextra.so +# dosym libxdl_viewextra.so.0.0.0 /usr/$(get_libdir)/libxdl_viewextra.so.0 +# dosym libxdl_viewextra.so.0.0.0 /usr/$(get_libdir)/libxdl_viewextra.so.0.0 +# +# dosym libxdl_view.so.2.0.0 /usr/$(get_libdir)/libxdl_view.so +# dosym libxdl_view.so.2.0.0 /usr/$(get_libdir)/libxdl_view.so.2 +# dosym libxdl_view.so.2.0.0 /usr/$(get_libdir)/libxdl_view.so.2.0 + + # Environment files, setup scripts, etc. + INSDESTTREE="/usr/share/ccp4/include" doins ${S}/include/* + + # CCP4Interface - GUI + INSDESTTREE="/usr/$(get_libdir)/ccp4" doins -r ${S}/ccp4i + EXEDESTTREE="/usr/$(get_libdir)/ccp4/ccp4i/bin" doexe ${S}/ccp4i/bin/* + + # Data + INSDESTTREE="/usr/share/ccp4" doins -r ${S}/lib/data + + # Include files + for i in ccp4 clipper mmdb ssm; do + INSDESTTREE="/usr/include" doins -r ${S}/include/${i} + done + + # Install docs and examples + + doman ${S}/man/cat1/* + + mv ${S}/manual/README ${S}/manual/README-manual + dodoc ${S}/manual/* + + dodoc ${S}/README ${S}/CHANGES + + dodoc ${S}/doc/* + rm ${D}/usr/share/doc/${PF}/GNUmakefile.gz + rm ${D}/usr/share/doc/${PF}/COPYING.gz + + dohtml -r ${S}/html/* + dodoc ${S}/examples/README + + # Fix wrongly installed HTML pages from clipper + dohtml "${D}"/usr/html/* + rm -rf "${D}"/usr/html + + for i in data rnase toxd; do + DOCDESTTREE="examples/${i}" dodoc ${S}/examples/${i}/* + done + + DOCDESTTREE="examples/tutorial" dohtml -r ${S}/examples/tutorial/html + DOCDESTTREE="examples/tutorial" dohtml examples/tutorial/tut.css + for i in data results; do + DOCDESTTREE="examples/tutorial/${i}" dodoc ${S}/examples/tutorial/${i}/* + done + + for i in non-runnable runnable; do + DOCDESTTREE="examples/unix/${i}" dodoc ${S}/examples/unix/${i} + done + + # Needed for ccp4i docs to work + dosym ../../share/doc/${PF}/examples /usr/$(get_libdir)/ccp4/examples + dosym ../../share/doc/${PF}/html /usr/$(get_libdir)/ccp4/html + + # Fix overlaps with other packages + rm ${D}/usr/share/man/man1/rasmol.1.gz +} + +pkg_postinst() { + einfo "The Web browser defaults to firefox. Change CCP4_BROWSER" + einfo "in /usr/share/ccp4/include/ccp4.setup* to modify this." + + ewarn "Set your .bashrc or other shell login file to source" + ewarn "one of the ccp4.setup* files in ${ROOT}usr/share/ccp4/include." + ewarn "CCP4 will not work without this." +} + +# Epatch wrapper for bulk patching +ccp_patch() { + EPATCH_SINGLE_MSG=" ${1##*/} ..." epatch ${1} +} + +# Links libname.so, libname.so.major and libname.so.major.minor +# to libname.so.major.minor.micro +library_dosym() { + local LIBNAME LIBDIR SUFFIX CORE_LIBNAME LIB_MAJOR LIB_MINOR LIB_VERSIONS + + LIBNAME=${1} + LIBDIR=${2:-/usr/$(get_libdir)} + + # Tag / on the end of libdir if needed + if [[ ${LIBDIR:$((${#LIBDIR}-1)):1} != "/" ]]; then + LIBDIR="${LIBDIR}/" + fi + + if [[ "${LIBNAME}" != *.so.* ]]; then + msg="library_dosym() requires a shared, versioned library as an argument" + eerror "$msg" + die "$msg" + fi + + SUFFIX=${LIBNAME##*so.} + CORE_LIBNAME=${LIBNAME%.so.*} + CORE_LIBNAME="${CORE_LIBNAME}.so" + LIB_MAJOR=${SUFFIX%%.*} + LIB_MINOR=${SUFFIX#*.} + LIB_MINOR=${SUFFIX%%.*} + LIB_VERSIONS="${LIB_MAJOR} ${LIB_MAJOR}.${LIB_MINOR}" + for LIB_SUFFIX in .${LIB_MAJOR} .${LIB_MAJOR}.${LIB_MINOR} ""; do + einfo "Calling dosym ${LIBNAME} ${LIBDIR} ${CORE_LIBNAME} ${LIB_SUFFIX}" + dosym ${LIBNAME} ${LIBDIR}${CORE_LIBNAME}${LIB_SUFFIX} + done +} diff --git a/sci-chemistry/ccp4/files/digest-ccp4-6.0.1-r1 b/sci-chemistry/ccp4/files/digest-ccp4-6.0.1-r1 new file mode 100644 index 000000000000..e83d992ca239 --- /dev/null +++ b/sci-chemistry/ccp4/files/digest-ccp4-6.0.1-r1 @@ -0,0 +1,39 @@ +MD5 21f240d6cf7c743b8062f3765105031c act.f-6July2006.diff 16544 +RMD160 24f48e95ec3363a2409da122bd0eb7ef5a91da36 act.f-6July2006.diff 16544 +SHA256 ba807b19b834d68ff121e34bbfbb113ae528db1aeebfeb7e98cbb90c64c2c3c4 act.f-6July2006.diff 16544 +MD5 31d485acdd0c5e83a4d3d637aa83f808 anisoanl.f-r1.22-r1.24.diff 9452 +RMD160 02f9561362892cbbeed24592b5ed4e3eb51ace2c anisoanl.f-r1.22-r1.24.diff 9452 +SHA256 1308ef91c63efd1c11287f68f386a62678d1ab48ddfe6e94cefdef1c92173940 anisoanl.f-r1.22-r1.24.diff 9452 +MD5 d48a142e1417f848fa512a1aa45e3b10 cad.f-r1.70-r1.72.diff 12196 +RMD160 a18c339223c8a6a66fda4cb210f2e533fea0d240 cad.f-r1.70-r1.72.diff 12196 +SHA256 ba10591643f93fb310d451aacce286d8ec9386f2e781d631f794076d1021539f cad.f-r1.70-r1.72.diff 12196 +MD5 bd3ff43388b58841de79bcc23ebf81e3 ccp4-6.0.1-core-src.tar.gz 59311291 +RMD160 0f514fe30f22a4f6eb2e05c8bab567d2132e8fae ccp4-6.0.1-core-src.tar.gz 59311291 +SHA256 26a5704d707c3bc2fbe4c1d0804abccc1c50255005d26a8ec3a03fcba63335f2 ccp4-6.0.1-core-src.tar.gz 59311291 +MD5 99247535ed72ddd60f715388a8bb9cc6 chainsaw.cpp-11May2006.diff 4720 +RMD160 62c3b3a3da0d36aa8f0c67a55c068508858eeb17 chainsaw.cpp-11May2006.diff 4720 +SHA256 de2d2ccd365f2992e1ba9a385f1a2fcd9e52da5ff96bcbc4fa7b4404cf0bac6e chainsaw.cpp-11May2006.diff 4720 +MD5 dcb1dea5587990b19d5ad5b095919905 contact.f-12June2006.diff 43051 +RMD160 577b454ed229be8c9b79e8c4622c870d589e2cca contact.f-12June2006.diff 43051 +SHA256 1336ea01da83aad21669b82cd3895f724db6db8d17d78acfec53154ea7ce690e contact.f-12June2006.diff 43051 +MD5 193b367d9b0e5567ce59f5c4b0118ec4 molrep.f-r1.28-r1.28.2.1.diff 755 +RMD160 96a37ea54606583647ff9cdc9da728ce05d30849 molrep.f-r1.28-r1.28.2.1.diff 755 +SHA256 0bb22cb2f8e1486ec5cc6037427e9ec66189684d74b5939757b4ebe771a61084 molrep.f-r1.28-r1.28.2.1.diff 755 +MD5 7007d645629a666e16161bfe9ce45cfc mtztona4.f-r1.23-r1.24.diff 882 +RMD160 1b34c6caaf5356574f65f2d092196cdd788cb720 mtztona4.f-r1.23-r1.24.diff 882 +SHA256 d7cf1b6ab2015b18c6b4b310e25b706a1f420d623383c17d0b51acfb00ae679a mtztona4.f-r1.23-r1.24.diff 882 +MD5 35e064c2e674abf496cda9546858218b omit.f-r1.12-r1.13.diff 2303 +RMD160 5dda121b69fdc3b4e138e0b88012df1d46398d3a omit.f-r1.12-r1.13.diff 2303 +SHA256 14a8128809f78d2d08b81cde5f91b51a694d99b56215477a62571344024a6748 omit.f-r1.12-r1.13.diff 2303 +MD5 7a3cb3be5eb751c26d524d6e6b7d3afa refmac5.tcl-r1.39.2.3-r1.42.diff 2464 +RMD160 fca236184597ab86fc9ac7333834e68eab641dac refmac5.tcl-r1.39.2.3-r1.42.diff 2464 +SHA256 8418181bae8799d2fa5a004e84cb1c66391d0cb768df5d40b34e053aced6fd4c refmac5.tcl-r1.39.2.3-r1.42.diff 2464 +MD5 de8c82181951b3579a160932ae8ddedd rotmat.f-17July2006.diff 1002 +RMD160 59cc822edbdc73b24e51cff013c71e4d68927979 rotmat.f-17July2006.diff 1002 +SHA256 1ee4f3288dba6404d59f51b9f9e1b4475413f7e40991204ab39474ee559605b1 rotmat.f-17July2006.diff 1002 +MD5 b966473250ed75716cc88cf0aee67348 sc.f-r1.9-r1.9.2.1.diff 8783 +RMD160 815d25cff0fa76f73dc43da9757ad753ec392f9c sc.f-r1.9-r1.9.2.1.diff 8783 +SHA256 418feea2ccf0014c3c2c83ab9460873114057480fd2a1dcabe305a1b956ad86b sc.f-r1.9-r1.9.2.1.diff 8783 +MD5 fb9252300a46f3d81776661b39c00d4e setup.fh-r1.5-r1.5.2.1.diff 1317 +RMD160 45a16b00792706553e7bf23a2f54415cd5ee1b43 setup.fh-r1.5-r1.5.2.1.diff 1317 +SHA256 637564c5723fb7de04d3a06817eec704ac708b74264716905690250e42aed146 setup.fh-r1.5-r1.5.2.1.diff 1317 diff --git a/sci-chemistry/raster3d/Manifest b/sci-chemistry/raster3d/Manifest index 4470c43d4a09..03ab0c98236b 100644 --- a/sci-chemistry/raster3d/Manifest +++ b/sci-chemistry/raster3d/Manifest @@ -1,22 +1,22 @@ -AUX raster3d-gcc-4.1-gentoo.patch 2423 RMD160 4ebc09f61759a2ef79239141197ad2ee1890c23a SHA1 a9cf625be7ba6e88499f2b753c693f86509d6ae1 SHA256 5b95136918411d0f33f31289d791c78046c5728950dafcf90dcbb52f100b18bc size 2423 +AUX raster3d-gcc-4.1-gentoo.patch 2423 RMD160 4ebc09f61759a2ef79239141197ad2ee1890c23a SHA1 a9cf625be7ba6e88499f2b753c693f86509d6ae1 SHA256 5b95136918411d0f33f31289d791c78046c5728950dafcf90dcbb52f100b18bc MD5 f359b8a66da6a239d4597dbfba835a5e files/raster3d-gcc-4.1-gentoo.patch 2423 RMD160 4ebc09f61759a2ef79239141197ad2ee1890c23a files/raster3d-gcc-4.1-gentoo.patch 2423 SHA256 5b95136918411d0f33f31289d791c78046c5728950dafcf90dcbb52f100b18bc files/raster3d-gcc-4.1-gentoo.patch 2423 -DIST Raster3D_2.6e.tar.gz 1757896 RMD160 38e9d48f3a24a409226b35e2d2c2f6394330f9e4 SHA256 a7b18b456c557bbcc4ee274edb1728d36691195dba463b79b1795ac7ff9b5c93 size 1757896 -DIST Raster3D_2.7c.tar.gz 1727387 RMD160 ebb41c0504646b8d965dbccad0f3cee1bfad0244 SHA256 7d5c450e83865fbafecbab3caabf38a8560b6c41982948a3b0e34d79c2c3381a size 1727387 -EBUILD raster3d-2.6e.ebuild 1381 RMD160 5e436e37d6b084eb297b9556585150c75d57597c SHA1 54880249f1eb90004d022a209b2d8797c477433b SHA256 41a9c020def2c9b94fbee0e7b0272991cef755a3e88d80678e64eaf339106a4b size 1381 +DIST Raster3D_2.6e.tar.gz 1757896 RMD160 38e9d48f3a24a409226b35e2d2c2f6394330f9e4 SHA256 a7b18b456c557bbcc4ee274edb1728d36691195dba463b79b1795ac7ff9b5c93 +DIST Raster3D_2.7c.tar.gz 1727387 RMD160 ebb41c0504646b8d965dbccad0f3cee1bfad0244 SHA256 7d5c450e83865fbafecbab3caabf38a8560b6c41982948a3b0e34d79c2c3381a +EBUILD raster3d-2.6e.ebuild 1381 RMD160 5e436e37d6b084eb297b9556585150c75d57597c SHA1 54880249f1eb90004d022a209b2d8797c477433b SHA256 41a9c020def2c9b94fbee0e7b0272991cef755a3e88d80678e64eaf339106a4b MD5 e2fd65185f0124e78febbf57d89ee724 raster3d-2.6e.ebuild 1381 RMD160 5e436e37d6b084eb297b9556585150c75d57597c raster3d-2.6e.ebuild 1381 SHA256 41a9c020def2c9b94fbee0e7b0272991cef755a3e88d80678e64eaf339106a4b raster3d-2.6e.ebuild 1381 -EBUILD raster3d-2.7c.ebuild 1736 RMD160 98a824b42fd33637b5191b043709fe425023ccc8 SHA1 d87afde96cf99e7dee0f6262124153d9d92b426c SHA256 f2d1d1151e11eddeecab2d33cb964cf14b5a5ce26b51533fae7a3b55d9b48912 size 1736 -MD5 11e68dac0e355466e3b9098e33271562 raster3d-2.7c.ebuild 1736 -RMD160 98a824b42fd33637b5191b043709fe425023ccc8 raster3d-2.7c.ebuild 1736 -SHA256 f2d1d1151e11eddeecab2d33cb964cf14b5a5ce26b51533fae7a3b55d9b48912 raster3d-2.7c.ebuild 1736 -MISC ChangeLog 1771 RMD160 86a50616847e86d133e4cb46f570e02922acbcf3 SHA1 fc2d122a87f08289224488781638bf733d801fa7 SHA256 4e94b39b2e3fcf2f70d824a4226f3dd740c8558e1e5000556d63411d71a761f9 size 1771 -MD5 95f18e894a4634c3741e33b75e6230a0 ChangeLog 1771 -RMD160 86a50616847e86d133e4cb46f570e02922acbcf3 ChangeLog 1771 -SHA256 4e94b39b2e3fcf2f70d824a4226f3dd740c8558e1e5000556d63411d71a761f9 ChangeLog 1771 -MISC metadata.xml 156 RMD160 dc078172bfebcb25d69bdf8731714f9cce9d3e36 SHA1 da2b240a255820145b7c83a5c48e45b96b7e9ee6 SHA256 5d22100902db7507a5b5493dd4a66cdb08025faf80a2c0b75e6392315c47f900 size 156 +EBUILD raster3d-2.7c.ebuild 1734 RMD160 8be900b1c723a0ce7a83633c5d774320a9dff2ca SHA1 27b9c76ae36d38d1fa1fcafd5b53b2d5d2958f63 SHA256 e2acdc2178c9240c01b992df332f3fdf981d74096024cdd9fe17f08c582f656a +MD5 6a34ef18bf8e644c5670d9eb6a63f8e4 raster3d-2.7c.ebuild 1734 +RMD160 8be900b1c723a0ce7a83633c5d774320a9dff2ca raster3d-2.7c.ebuild 1734 +SHA256 e2acdc2178c9240c01b992df332f3fdf981d74096024cdd9fe17f08c582f656a raster3d-2.7c.ebuild 1734 +MISC ChangeLog 1880 RMD160 287fd071bae8ad21f36037e1e3e5ce888caa2dbf SHA1 ef8949203240fbafe74bf70a4b2cf98bcffafaf8 SHA256 458ad40160fb147472e12ae652583733d7b997a8d656feb751bc631fbabc1e1b +MD5 a3ed20f4c75e04aa382cb5d47a6219c0 ChangeLog 1880 +RMD160 287fd071bae8ad21f36037e1e3e5ce888caa2dbf ChangeLog 1880 +SHA256 458ad40160fb147472e12ae652583733d7b997a8d656feb751bc631fbabc1e1b ChangeLog 1880 +MISC metadata.xml 156 RMD160 dc078172bfebcb25d69bdf8731714f9cce9d3e36 SHA1 da2b240a255820145b7c83a5c48e45b96b7e9ee6 SHA256 5d22100902db7507a5b5493dd4a66cdb08025faf80a2c0b75e6392315c47f900 MD5 8c623e53daafa025137077c6b65815bd metadata.xml 156 RMD160 dc078172bfebcb25d69bdf8731714f9cce9d3e36 metadata.xml 156 SHA256 5d22100902db7507a5b5493dd4a66cdb08025faf80a2c0b75e6392315c47f900 metadata.xml 156