From 17e2cfd41a86ce3e6e182396994f9487d4e7667c Mon Sep 17 00:00:00 2001 From: Donnie Berkholz Date: Fri, 24 Nov 2006 10:45:41 +0000 Subject: [PATCH] Bump. Package-Manager: portage-2.1.2_rc2 --- sci-chemistry/ccp4/ChangeLog | 9 +- sci-chemistry/ccp4/Manifest | 24 +- sci-chemistry/ccp4/ccp4-6.0.2.ebuild | 423 ++++++++++++++++++ .../6.0.2-dont-make-dirs-in-configure.patch | 87 ++++ .../6.0.2-ppc-double-define-gerror.patch | 11 + sci-chemistry/ccp4/files/digest-ccp4-6.0.2 | 3 + 6 files changed, 552 insertions(+), 5 deletions(-) create mode 100644 sci-chemistry/ccp4/ccp4-6.0.2.ebuild create mode 100644 sci-chemistry/ccp4/files/6.0.2-dont-make-dirs-in-configure.patch create mode 100644 sci-chemistry/ccp4/files/6.0.2-ppc-double-define-gerror.patch create mode 100644 sci-chemistry/ccp4/files/digest-ccp4-6.0.2 diff --git a/sci-chemistry/ccp4/ChangeLog b/sci-chemistry/ccp4/ChangeLog index 00d667734a44..114f3215df60 100644 --- a/sci-chemistry/ccp4/ChangeLog +++ b/sci-chemistry/ccp4/ChangeLog @@ -1,6 +1,13 @@ # 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 1.6 2006/09/26 08:01:27 dberkholz Exp $ +# $Header: /var/cvsroot/gentoo-x86/sci-chemistry/ccp4/ChangeLog,v 1.7 2006/11/24 10:45:41 dberkholz Exp $ + +*ccp4-6.0.2 (24 Nov 2006) + + 24 Nov 2006; Donnie Berkholz ; + +files/6.0.2-dont-make-dirs-in-configure.patch, + +files/6.0.2-ppc-double-define-gerror.patch, +ccp4-6.0.2.ebuild: + Bump. 26 Sep 2006; Donnie Berkholz ; ccp4-6.0.1-r1.ebuild: Stable on x86/ppc. diff --git a/sci-chemistry/ccp4/Manifest b/sci-chemistry/ccp4/Manifest index fc81d7a94687..e8832515b164 100644 --- a/sci-chemistry/ccp4/Manifest +++ b/sci-chemistry/ccp4/Manifest @@ -6,6 +6,14 @@ AUX 6.0.1-ppc-double-define-gerror.patch 424 RMD160 4f012233446fffa61e8d775a19a0 MD5 5a2ad632f539bc7981b55b6f52b6a227 files/6.0.1-ppc-double-define-gerror.patch 424 RMD160 4f012233446fffa61e8d775a19a0dacea4ae2234 files/6.0.1-ppc-double-define-gerror.patch 424 SHA256 09c2c1e0176bee94673b21609b2b00118b2bb4f5942f3feb35c64c61c99ebc61 files/6.0.1-ppc-double-define-gerror.patch 424 +AUX 6.0.2-dont-make-dirs-in-configure.patch 2790 RMD160 904e37ab1ea20dda50f50ce8780268eb5fa52480 SHA1 f8989cb867c92def86ccd88b4d67f38578d5d80b SHA256 2dbf78513ef94d88e446042e969644ad8a8462a22e80105e7481af93003a18bf +MD5 3dc230e3cc15f5cd2a19968e8f07a9f2 files/6.0.2-dont-make-dirs-in-configure.patch 2790 +RMD160 904e37ab1ea20dda50f50ce8780268eb5fa52480 files/6.0.2-dont-make-dirs-in-configure.patch 2790 +SHA256 2dbf78513ef94d88e446042e969644ad8a8462a22e80105e7481af93003a18bf files/6.0.2-dont-make-dirs-in-configure.patch 2790 +AUX 6.0.2-ppc-double-define-gerror.patch 424 RMD160 4f012233446fffa61e8d775a19a0dacea4ae2234 SHA1 209fa1bdf1e59b4055177e343b69e487d9183fb3 SHA256 09c2c1e0176bee94673b21609b2b00118b2bb4f5942f3feb35c64c61c99ebc61 +MD5 5a2ad632f539bc7981b55b6f52b6a227 files/6.0.2-ppc-double-define-gerror.patch 424 +RMD160 4f012233446fffa61e8d775a19a0dacea4ae2234 files/6.0.2-ppc-double-define-gerror.patch 424 +SHA256 09c2c1e0176bee94673b21609b2b00118b2bb4f5942f3feb35c64c61c99ebc61 files/6.0.2-ppc-double-define-gerror.patch 424 AUX ccp4i-default-to-firefox.patch 717 RMD160 626050c2ca8386e369900225f74f97fb22c3a91e SHA1 dc255e30033d1dbc422dbacd2c1814c13a003bc3 SHA256 40bc277d9353f13b490291fe0ba10c1180adc80a660afa5cf8f7c9449af909ae MD5 b7c4c90e38ef49651876128a209b4546 files/ccp4i-default-to-firefox.patch 717 RMD160 626050c2ca8386e369900225f74f97fb22c3a91e files/ccp4i-default-to-firefox.patch 717 @@ -50,6 +58,7 @@ DIST act.f-6July2006.diff 16544 RMD160 24f48e95ec3363a2409da122bd0eb7ef5a91da36 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 ccp4-6.0.2-core-src.tar.gz 62286123 RMD160 159c71c5079422d6e540e4678fb8e4f9f83fc99d SHA1 279da65beb9c2e64a80abdeb693a78879a062cf0 SHA256 b8716198b4d5c1ad3aea190180a5c56e0e80eda0386e5c99542d169da6960875 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 @@ -67,10 +76,14 @@ EBUILD ccp4-6.0.1.ebuild 13729 RMD160 5fe2a8f1d42a810e8fda14c61e970f9146ab0b96 S 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 2008 RMD160 e54d0d0031c60c95f7d881aee9a993a5ba1ed2fd SHA1 00e48e0273b9cead7dfdad20be1682d93397cc71 SHA256 fc2cc2839aa5e770a96f7fa857a8f215685e8644c024cc5b94e09c33e50737e8 -MD5 5ee9b4c15a1a288d5f21d8a9bb8a50a7 ChangeLog 2008 -RMD160 e54d0d0031c60c95f7d881aee9a993a5ba1ed2fd ChangeLog 2008 -SHA256 fc2cc2839aa5e770a96f7fa857a8f215685e8644c024cc5b94e09c33e50737e8 ChangeLog 2008 +EBUILD ccp4-6.0.2.ebuild 13483 RMD160 20043e32b6a1aae3e9431c2c5f793816ee754b7e SHA1 bdfadd46b8b9e75e3758a17d98a077b69035e167 SHA256 0f4bc1201162b9dce21254e2f9497bbc391dd3ad7bba30fd5cec8fd9376e587b +MD5 26accaf55746435d81fb5c55d1f41114 ccp4-6.0.2.ebuild 13483 +RMD160 20043e32b6a1aae3e9431c2c5f793816ee754b7e ccp4-6.0.2.ebuild 13483 +SHA256 0f4bc1201162b9dce21254e2f9497bbc391dd3ad7bba30fd5cec8fd9376e587b ccp4-6.0.2.ebuild 13483 +MISC ChangeLog 2216 RMD160 cbdef48f6f45064fa21a7a1e57b580e3899dc108 SHA1 d4fb0a46ab1a6ef736be031530329fcbae78d583 SHA256 3afb703e3805ab9c3830fa4d468fda79c16094311602fa859e2ee089580b3410 +MD5 2ebc390cdd05eabb3257b6a7b77d2309 ChangeLog 2216 +RMD160 cbdef48f6f45064fa21a7a1e57b580e3899dc108 ChangeLog 2216 +SHA256 3afb703e3805ab9c3830fa4d468fda79c16094311602fa859e2ee089580b3410 ChangeLog 2216 MISC metadata.xml 166 RMD160 4452298fd03e7c9395d1182bfe69d60a14144af6 SHA1 cb0b513473c0348f4f6f6cd9a132e4884155fddb SHA256 84c92b49702daf95eace8d2765215cbd8650da4ef776f9f700b5ce3785dec852 MD5 43628e9f5743b5c3b018a82669a76bc7 metadata.xml 166 RMD160 4452298fd03e7c9395d1182bfe69d60a14144af6 metadata.xml 166 @@ -81,3 +94,6 @@ SHA256 52ebe8c93194a9140171ac2e0d80b4750913b3e97ac1ee0f37c34ad9137deda8 files/di 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 +MD5 4197e0ed0288c715e184aa7df8a4dbd6 files/digest-ccp4-6.0.2 265 +RMD160 b7b82a63b44e956b19cd49241a49565cac594d25 files/digest-ccp4-6.0.2 265 +SHA256 a9d7f019b604fd193ac9797e76d5c3058771a16866134bdbe9b94ca137405946 files/digest-ccp4-6.0.2 265 diff --git a/sci-chemistry/ccp4/ccp4-6.0.2.ebuild b/sci-chemistry/ccp4/ccp4-6.0.2.ebuild new file mode 100644 index 000000000000..092ff624ea02 --- /dev/null +++ b/sci-chemistry/ccp4/ccp4-6.0.2.ebuild @@ -0,0 +1,423 @@ +# Copyright 1999-2006 Gentoo Foundation +# Distributed under the terms of the GNU General Public License v2 +# $Header: /var/cvsroot/gentoo-x86/sci-chemistry/ccp4/ccp4-6.0.2.ebuild,v 1.1 2006/11/24 10:45:41 dberkholz Exp $ + +inherit fortran eutils gnuconfig toolchain-funcs + +FORTRAN="g77 gfortran ifc" + +SRC="ftp://ftp.ccp4.ac.uk/ccp4" + +PATCH_TOT="0" +#PATCH1=( src/mmdb_app_ +# chainsaw.cpp-11May2006.diff ) +#PATCH2=( src +# anisoanl.f-r1.22-r1.24.diff ) + +DESCRIPTION="Protein X-ray crystallography toolkit" +HOMEPAGE="http://www.ccp4.ac.uk/" +RESTRICT="mirror stricter" +SRC_URI="${SRC}/${PV}/source/${P}-core-src.tar.gz" +for i in $(seq $PATCH_TOT); do + NAME="PATCH${i}[1]" + SRC_URI="${SRC_URI} + ${SRC}/${PV}/patches/${!NAME}" +done +LICENSE="ccp4" +SLOT="0" +KEYWORDS="~ppc ~x86" +IUSE="X" +# app-office/sc overlaps sc binary and man page +# We can't rename ours since the automated ccp4i interface expects it there, +# as do many scripts. app-office/sc can't rename its because that's the name +# of the package. +RDEPEND="X? ( + x11-libs/libX11 + x11-libs/libXt + x11-libs/libXaw + ) + >=dev-lang/tcl-8.3 + >=dev-lang/tk-8.3 + >=dev-tcltk/blt-2.4 + virtual/lapack + virtual/blas + =sci-libs/fftw-2* + sci-chemistry/pdb-extract + sci-chemistry/rasmol + sci-libs/mccp4 + || ( app-shells/tcsh app-shells/csh ) + !app-office/sc" +# >=sys-apps/portage-2.1.1_pre1 for RESTRICT=stricter +# Otherwise portage dies instead of fixing RPATHs +DEPEND="${RDEPEND} + X? ( + x11-misc/imake + x11-proto/inputproto + x11-proto/xextproto + ) + >=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/6.0.2-dont-make-dirs-in-configure.patch b/sci-chemistry/ccp4/files/6.0.2-dont-make-dirs-in-configure.patch new file mode 100644 index 000000000000..1420419ffab0 --- /dev/null +++ b/sci-chemistry/ccp4/files/6.0.2-dont-make-dirs-in-configure.patch @@ -0,0 +1,87 @@ +--- ccp4-6.0.1.orig/configure 2006-06-10 17:30:02.000000000 -0700 ++++ ccp4-6.0.1/configure 2006-06-10 17:45:43.000000000 -0700 +@@ -623,45 +623,45 @@ + # 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 $i." +- badvar=1 +- fi +- done +- +- for i in libdir bindir; do +- if ( eval test -d \$$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 ./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 $i." ++# badvar=1 ++# fi ++# done ++# ++# for i in libdir bindir; do ++# if ( eval test -d \$$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 ./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-chemistry/ccp4/files/6.0.2-ppc-double-define-gerror.patch b/sci-chemistry/ccp4/files/6.0.2-ppc-double-define-gerror.patch new file mode 100644 index 000000000000..a77d9494a05c --- /dev/null +++ b/sci-chemistry/ccp4/files/6.0.2-ppc-double-define-gerror.patch @@ -0,0 +1,11 @@ +--- 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-chemistry/ccp4/files/digest-ccp4-6.0.2 b/sci-chemistry/ccp4/files/digest-ccp4-6.0.2 new file mode 100644 index 000000000000..2f4e81e11fb4 --- /dev/null +++ b/sci-chemistry/ccp4/files/digest-ccp4-6.0.2 @@ -0,0 +1,3 @@ +MD5 a47ae8b8e6fa76eef7f17baa85e8dc16 ccp4-6.0.2-core-src.tar.gz 62286123 +RMD160 159c71c5079422d6e540e4678fb8e4f9f83fc99d ccp4-6.0.2-core-src.tar.gz 62286123 +SHA256 b8716198b4d5c1ad3aea190180a5c56e0e80eda0386e5c99542d169da6960875 ccp4-6.0.2-core-src.tar.gz 62286123 -- 2.26.2