From c6da6496bd646a96e65a7f629b143f2e8db714d8 Mon Sep 17 00:00:00 2001 From: Donnie Berkholz Date: Fri, 16 Jun 2006 20:46:02 +0000 Subject: [PATCH] Add CCP4, a popular protein X-ray crystallography toolkit. Relies on portage auto-fixing RPATHs for now, because its build system consists of a bunch of stuff thrown together into the same tarball. Package-Manager: portage-2.1.1_pre1 --- sci-chemistry/ccp4/ChangeLog | 20 + sci-chemistry/ccp4/Manifest | 64 +++ sci-chemistry/ccp4/ccp4-6.0.1.ebuild | 432 ++++++++++++++++++ .../6.0.1-dont-make-dirs-in-configure.patch | 87 ++++ .../6.0.1-ppc-double-define-gerror.patch | 11 + .../ccp4/files/ccp4i-default-to-firefox.patch | 13 + .../files/check-blas-lapack-pthread.patch | 103 +++++ .../files/clipper-find-mccp4-includes.patch | 11 + .../ccp4/files/create-mosflm-bindir.patch | 10 + sci-chemistry/ccp4/files/digest-ccp4-6.0.1 | 3 + .../ccp4/files/dont-build-rasmol.patch | 19 + .../ccp4/files/make-ipmosflm-dir.patch | 10 + .../ccp4/files/make-mosflm-cbf-libdir.patch | 11 + .../ccp4/files/make-mosflm-index-libdir.patch | 10 + .../ccp4/files/make-mosflm-libdir.patch | 10 + .../ccp4/files/pass-clipper-enablevals.patch | 11 + sci-chemistry/ccp4/metadata.xml | 9 + 17 files changed, 834 insertions(+) create mode 100644 sci-chemistry/ccp4/ChangeLog create mode 100644 sci-chemistry/ccp4/Manifest create mode 100644 sci-chemistry/ccp4/ccp4-6.0.1.ebuild create mode 100644 sci-chemistry/ccp4/files/6.0.1-dont-make-dirs-in-configure.patch create mode 100644 sci-chemistry/ccp4/files/6.0.1-ppc-double-define-gerror.patch create mode 100644 sci-chemistry/ccp4/files/ccp4i-default-to-firefox.patch create mode 100644 sci-chemistry/ccp4/files/check-blas-lapack-pthread.patch create mode 100644 sci-chemistry/ccp4/files/clipper-find-mccp4-includes.patch create mode 100644 sci-chemistry/ccp4/files/create-mosflm-bindir.patch create mode 100644 sci-chemistry/ccp4/files/digest-ccp4-6.0.1 create mode 100644 sci-chemistry/ccp4/files/dont-build-rasmol.patch create mode 100644 sci-chemistry/ccp4/files/make-ipmosflm-dir.patch create mode 100644 sci-chemistry/ccp4/files/make-mosflm-cbf-libdir.patch create mode 100644 sci-chemistry/ccp4/files/make-mosflm-index-libdir.patch create mode 100644 sci-chemistry/ccp4/files/make-mosflm-libdir.patch create mode 100644 sci-chemistry/ccp4/files/pass-clipper-enablevals.patch create mode 100644 sci-chemistry/ccp4/metadata.xml diff --git a/sci-chemistry/ccp4/ChangeLog b/sci-chemistry/ccp4/ChangeLog new file mode 100644 index 000000000000..d379184f709c --- /dev/null +++ b/sci-chemistry/ccp4/ChangeLog @@ -0,0 +1,20 @@ +# 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 1.1 2006/06/16 20:46:02 spyderous Exp $ + +*ccp4-6.0.1 (16 Jun 2006) + + 16 Jun 2006; Donnie Berkholz ; + +files/6.0.1-dont-make-dirs-in-configure.patch, + +files/6.0.1-ppc-double-define-gerror.patch, + +files/ccp4i-default-to-firefox.patch, + +files/check-blas-lapack-pthread.patch, + +files/clipper-find-mccp4-includes.patch, + +files/create-mosflm-bindir.patch, +files/dont-build-rasmol.patch, + +files/make-ipmosflm-dir.patch, +files/make-mosflm-cbf-libdir.patch, + +files/make-mosflm-index-libdir.patch, +files/make-mosflm-libdir.patch, + +files/pass-clipper-enablevals.patch, +metadata.xml, +ccp4-6.0.1.ebuild: + Add CCP4, a popular protein X-ray crystallography toolkit. Relies on portage + auto-fixing RPATHs for now, because its build system consists of a bunch of + stuff thrown together into the same tarball. + diff --git a/sci-chemistry/ccp4/Manifest b/sci-chemistry/ccp4/Manifest new file mode 100644 index 000000000000..d3ccda89b92d --- /dev/null +++ b/sci-chemistry/ccp4/Manifest @@ -0,0 +1,64 @@ +AUX 6.0.1-dont-make-dirs-in-configure.patch 2790 RMD160 904e37ab1ea20dda50f50ce8780268eb5fa52480 SHA1 f8989cb867c92def86ccd88b4d67f38578d5d80b SHA256 2dbf78513ef94d88e446042e969644ad8a8462a22e80105e7481af93003a18bf +MD5 3dc230e3cc15f5cd2a19968e8f07a9f2 files/6.0.1-dont-make-dirs-in-configure.patch 2790 +RMD160 904e37ab1ea20dda50f50ce8780268eb5fa52480 files/6.0.1-dont-make-dirs-in-configure.patch 2790 +SHA256 2dbf78513ef94d88e446042e969644ad8a8462a22e80105e7481af93003a18bf files/6.0.1-dont-make-dirs-in-configure.patch 2790 +AUX 6.0.1-ppc-double-define-gerror.patch 424 RMD160 4f012233446fffa61e8d775a19a0dacea4ae2234 SHA1 209fa1bdf1e59b4055177e343b69e487d9183fb3 SHA256 09c2c1e0176bee94673b21609b2b00118b2bb4f5942f3feb35c64c61c99ebc61 +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 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 +SHA256 40bc277d9353f13b490291fe0ba10c1180adc80a660afa5cf8f7c9449af909ae files/ccp4i-default-to-firefox.patch 717 +AUX check-blas-lapack-pthread.patch 5335 RMD160 d9818cd59333c6f40984f71a0f32249725d5ffcc SHA1 5aa0ee530975bd89dde38145297c4868ee54adbb SHA256 82a73295274b6d4cabbe00883a3e9cf6a38fe80eed8c487cd67960d073cb1231 +MD5 a9fd6533dc70e2c88e4623509e20c30b files/check-blas-lapack-pthread.patch 5335 +RMD160 d9818cd59333c6f40984f71a0f32249725d5ffcc files/check-blas-lapack-pthread.patch 5335 +SHA256 82a73295274b6d4cabbe00883a3e9cf6a38fe80eed8c487cd67960d073cb1231 files/check-blas-lapack-pthread.patch 5335 +AUX clipper-find-mccp4-includes.patch 491 RMD160 203cb5f807ede5462070d993f3e4b914992aa3e1 SHA1 f58ef6f143d751d50b55e620be877327af651fb9 SHA256 154c012c0ca75fc0da50b412b948acec53f4cecd2efd8910af73166db270e026 +MD5 cee8a62b63386a13f4276cab7bf09260 files/clipper-find-mccp4-includes.patch 491 +RMD160 203cb5f807ede5462070d993f3e4b914992aa3e1 files/clipper-find-mccp4-includes.patch 491 +SHA256 154c012c0ca75fc0da50b412b948acec53f4cecd2efd8910af73166db270e026 files/clipper-find-mccp4-includes.patch 491 +AUX create-mosflm-bindir.patch 438 RMD160 b0a210bf86de3af52c538efdf05d9ba44d7824d9 SHA1 30f45f7ac2eda5241256d31ee5073594985e5a05 SHA256 41b06cb4860b263fbc5c7c5be2aec1f859ff1cd6dd3750e5aae0410c264b1d84 +MD5 fcf801c9c9f1cc7f35294ff95776ff5e files/create-mosflm-bindir.patch 438 +RMD160 b0a210bf86de3af52c538efdf05d9ba44d7824d9 files/create-mosflm-bindir.patch 438 +SHA256 41b06cb4860b263fbc5c7c5be2aec1f859ff1cd6dd3750e5aae0410c264b1d84 files/create-mosflm-bindir.patch 438 +AUX dont-build-rasmol.patch 725 RMD160 2c294c46dcea586026e6d7c3936527e490bd7569 SHA1 97ac86575512776ecabb32488df6f59cf2431884 SHA256 f46b1d8d6f239f4b7c9b1d343661c98f1bc0015bc988881261b06a79a1e0c3e5 +MD5 8638a4880d926711233e53382f35205a files/dont-build-rasmol.patch 725 +RMD160 2c294c46dcea586026e6d7c3936527e490bd7569 files/dont-build-rasmol.patch 725 +SHA256 f46b1d8d6f239f4b7c9b1d343661c98f1bc0015bc988881261b06a79a1e0c3e5 files/dont-build-rasmol.patch 725 +AUX make-ipmosflm-dir.patch 375 RMD160 b359ff3028777157f6ce4cb60c5aa35b8177779e SHA1 1c23f2d56a8cfea479f5b32c842fe50d134c68c0 SHA256 2ca03ea4b4c1581be56bbac0afd3cbfe789b61a8453e50b1b477b074c6b2fd43 +MD5 5c89d8a6c5570d442a71a8c598a80f72 files/make-ipmosflm-dir.patch 375 +RMD160 b359ff3028777157f6ce4cb60c5aa35b8177779e files/make-ipmosflm-dir.patch 375 +SHA256 2ca03ea4b4c1581be56bbac0afd3cbfe789b61a8453e50b1b477b074c6b2fd43 files/make-ipmosflm-dir.patch 375 +AUX make-mosflm-cbf-libdir.patch 415 RMD160 19e275563cbd7c3d6b91630f8c554494a75d8ea0 SHA1 d264cbee4db1a1f48297ce43fef4f45e14e1aebe SHA256 475eec831306d33871f65b827b07a09dbe0ecd7b4f9e6af34a91fa4d433d56a4 +MD5 962cb5c0c55797f865254e4dc374183b files/make-mosflm-cbf-libdir.patch 415 +RMD160 19e275563cbd7c3d6b91630f8c554494a75d8ea0 files/make-mosflm-cbf-libdir.patch 415 +SHA256 475eec831306d33871f65b827b07a09dbe0ecd7b4f9e6af34a91fa4d433d56a4 files/make-mosflm-cbf-libdir.patch 415 +AUX make-mosflm-index-libdir.patch 358 RMD160 772bad5d83385adce5858f43ac9302c94cd6a6b8 SHA1 b889d238b0f3e2385ad8259ea4ea85b29d05e0d1 SHA256 5549d5208548168c0f246606802c143bd34b87ca3eb25640c6b777d9d9e4b902 +MD5 e38e0ef05c30c16148e8319e0bb0977d files/make-mosflm-index-libdir.patch 358 +RMD160 772bad5d83385adce5858f43ac9302c94cd6a6b8 files/make-mosflm-index-libdir.patch 358 +SHA256 5549d5208548168c0f246606802c143bd34b87ca3eb25640c6b777d9d9e4b902 files/make-mosflm-index-libdir.patch 358 +AUX make-mosflm-libdir.patch 371 RMD160 2ff9ddcc064b2621d241850d9774961b140d28b8 SHA1 0a4aba167b530544f6e602dab622e51fae1c7b68 SHA256 55c2978125acb3f1ba55039d171b09b6dbd13ee1dd1e4c1e48edc48e89d5c717 +MD5 703cb01ad626d4dbf4176a18ea5269a1 files/make-mosflm-libdir.patch 371 +RMD160 2ff9ddcc064b2621d241850d9774961b140d28b8 files/make-mosflm-libdir.patch 371 +SHA256 55c2978125acb3f1ba55039d171b09b6dbd13ee1dd1e4c1e48edc48e89d5c717 files/make-mosflm-libdir.patch 371 +AUX pass-clipper-enablevals.patch 501 RMD160 23466922268a91570b0f64cf79809b988e32689b SHA1 c254d31fe88ed1716a53bd549cf7aee537ca5204 SHA256 d476c9f231fb6cdfb5e57004b393644a88016318cdeed9c33c32de25e0d91b79 +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 ccp4-6.0.1-core-src.tar.gz 59311291 RMD160 0f514fe30f22a4f6eb2e05c8bab567d2132e8fae SHA1 e8f5fb325a13375793f7610160337090af8fb9b5 SHA256 26a5704d707c3bc2fbe4c1d0804abccc1c50255005d26a8ec3a03fcba63335f2 +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 1012 RMD160 f6184eb32342ca2ca1f8eb8c41e93be1ae78e27d SHA1 7154ddbef8aaca8dadacbf25ec4522dff76ee10e SHA256 5ddac215ec26b617ce72cc344c799b5070b122ff8479bf368c126eef581e7a81 +MD5 151f372b72ea8eaf0f2f3f3321819d14 ChangeLog 1012 +RMD160 f6184eb32342ca2ca1f8eb8c41e93be1ae78e27d ChangeLog 1012 +SHA256 5ddac215ec26b617ce72cc344c799b5070b122ff8479bf368c126eef581e7a81 ChangeLog 1012 +MISC metadata.xml 248 RMD160 6488d9f1ef3e05e6ac5a29ddcc818e5ead0a5230 SHA1 75a648fddef9922cdfe21fb0298a1c746190fd82 SHA256 de0ad7dc383b462c407cae015684d27c090455eac87c6f0f9ff581ef6e0b5b27 +MD5 af1bfbb0777267a03e889b08173f2757 metadata.xml 248 +RMD160 6488d9f1ef3e05e6ac5a29ddcc818e5ead0a5230 metadata.xml 248 +SHA256 de0ad7dc383b462c407cae015684d27c090455eac87c6f0f9ff581ef6e0b5b27 metadata.xml 248 +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 diff --git a/sci-chemistry/ccp4/ccp4-6.0.1.ebuild b/sci-chemistry/ccp4/ccp4-6.0.1.ebuild new file mode 100644 index 000000000000..d3a1e56b5431 --- /dev/null +++ b/sci-chemistry/ccp4/ccp4-6.0.1.ebuild @@ -0,0 +1,432 @@ +# 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.ebuild,v 1.1 2006/06/16 20:46:02 spyderous Exp $ + +inherit fortran eutils gnuconfig toolchain-funcs + +FORTRAN="g77 gfortran ifc" + +SRC="ftp://ftp.ccp4.ac.uk/ccp4" + +PATCH_TOT="0" +#PATCH1=( src +# anisoanl.f-r1.22-r1.24.diff ) +#PATCH2=( src/sc_ +# sc.f-r1.9-r1.9.2.1.diff ) +#PATCH3=( src/sc_ +# setup.fh-r1.5-r1.5.2.1.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" +# ${SRC}/${PV}/patches/${PATCH1[1]} +# ${SRC}/${PV}/patches/${PATCH2[1]} +# ${SRC}/${PV}/patches/${PATCH3[1]}" +LICENSE="ccp4" +SLOT="0" +KEYWORDS="~ppc ~x86" +IUSE="X" +# app-office/sc overlaps sc binary and man page +# We can't rename ours since the automated ccp4i interface expects it there, +# as do many scripts. app-office/sc can't rename its because that's the name +# of the package. +RDEPEND="X? ( + || ( + ( + x11-libs/libX11 + x11-libs/libXt + x11-libs/libXaw + ) + virtual/x11 + ) + ) + >=dev-lang/tcl-8.3 + >=dev-lang/tk-8.3 + >=dev-tcltk/blt-2.4 + virtual/lapack + virtual/blas + =sci-libs/fftw-2* + sci-chemistry/pdb-extract + sci-chemistry/rasmol + sci-libs/mccp4 + || ( app-shells/tcsh app-shells/csh ) + !app-office/sc" +# >=sys-apps/portage-2.1.1_pre1 for RESTRICT=stricter +# Otherwise portage dies instead of fixing RPATHs +DEPEND="${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() { + # 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=${FFLAGS:- -O2} + + # Add xdl libraries to library search path + # Note: some of configure attaches CCP4_LIB to -L, and other parts + # append libfoo.a immediately after it, so it can only be a single path. + export CCP4_LIB="${CCP4}/x-windows/xdl_view/src/.libs" + + # 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}" \ + ${GENTOO_OSNAME} || die "econf failed" + emake -j1 || die "emake failed" +} + +src_install() { +# Only needed when using --bindir and --libdir + # Needed to avoid errors. Originally tried to make lib and bin + # in configure script, now patched out by dont-make-dirs-in-configure.patch +# dodir /usr/include /usr/$(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/6.0.1-dont-make-dirs-in-configure.patch b/sci-chemistry/ccp4/files/6.0.1-dont-make-dirs-in-configure.patch new file mode 100644 index 000000000000..1420419ffab0 --- /dev/null +++ b/sci-chemistry/ccp4/files/6.0.1-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/6.0.1-ppc-double-define-gerror.patch b/sci-chemistry/ccp4/files/6.0.1-ppc-double-define-gerror.patch new file mode 100644 index 000000000000..a77d9494a05c --- /dev/null +++ b/sci-chemistry/ccp4/files/6.0.1-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/ccp4i-default-to-firefox.patch b/sci-chemistry/ccp4/files/ccp4i-default-to-firefox.patch new file mode 100644 index 000000000000..106db895b775 --- /dev/null +++ b/sci-chemistry/ccp4/files/ccp4i-default-to-firefox.patch @@ -0,0 +1,13 @@ +--- ccp4-5.99.5.orig/ccp4i/etc/configure.def.dist 2006-01-06 17:54:17.000000000 -0800 ++++ ccp4-5.99.5/ccp4i/etc/configure.def.dist 2006-01-06 17:54:47.000000000 -0800 +@@ -54,8 +54,8 @@ + MESSAGE _text "" + BLT_LIBRARY _text "" + MENU_LENGTH _positiveint 25 +-HYPERTEXT_VIEWER _text netscape +-START_NETSCAPE _text netscape ++HYPERTEXT_VIEWER _text firefox ++START_NETSCAPE _text firefox + O_MAPMAN _text mapman + MAPMAN_MAXSIZE _positiveint 4194304 + QUANTA_MBKALL _text mbkall diff --git a/sci-chemistry/ccp4/files/check-blas-lapack-pthread.patch b/sci-chemistry/ccp4/files/check-blas-lapack-pthread.patch new file mode 100644 index 000000000000..02a2aa6d8877 --- /dev/null +++ b/sci-chemistry/ccp4/files/check-blas-lapack-pthread.patch @@ -0,0 +1,103 @@ +--- ccp4-5.99.5.orig/configure 2006-01-17 00:35:36.000000000 -0800 ++++ ccp4-5.99.5/configure 2006-01-17 10:44:39.000000000 -0800 +@@ -2410,12 +2410,12 @@ + end + EOF + #firslty test without -lblas +- test_compile="$FC $FOPTIM $XFFLAGS -o testlink testlink.f -llapack" ++ test_compile="$FC $FOPTIM $XFFLAGS -o testlink testlink.f -llapack -lpthread" + echo $test_compile + if { (eval $test_compile >& /dev/null ) 2>&1; } && test -s testlink ; then + # Compilation was okay +- echo "... only -llapack needed" +- XLAPACK_LIB="-llapack" ++ echo "... only -llapack -lpthread needed" ++ XLAPACK_LIB="-llapack -lpthread" + # Set the next two variables so that configure + # doesn't try to build netlib libraries + LAPACKLIB="lapack" +@@ -2424,12 +2424,12 @@ + tryblas= + else + echo "more than just -llapack needed...." +- test_compile="$FC $FOPTIM $XFFLAGS -o testlink testlink.f -llapack -lblas" ++ test_compile="$FC $FOPTIM $XFFLAGS -o testlink testlink.f -llapack -lblas -lpthread" + echo $test_compile + if { (eval $test_compile ) 2>&1; } && test -s testlink ; then + # Compilation was okay +- echo "...-llapack and -lblas were needed" +- XLAPACK_LIB="-llapack -lblas" ++ echo "...-llapack, -lpthread and -lblas were needed" ++ XLAPACK_LIB="-llapack -lpthread -lblas" + # Set the next two variables so that configure + # doesn't try to build netlib libraries + LAPACKLIB="lapack blas" +@@ -2720,8 +2720,8 @@ + STOP + END + EOF +- test_compile="$FC $FOPTIM $XFFLAGS -o testlink testlink.f -L$testdir -l$testlib" +- test_ccompile="$FC $FOPTIM $XFFLAGS -o testlink testlink.f -L$testdir -l$testlib $XLDFLAGS" ++ test_compile="$FC $FOPTIM $XFFLAGS -o testlink testlink.f -L$testdir -l$testlib -lpthread" ++ test_ccompile="$FC $FOPTIM $XFFLAGS -o testlink testlink.f -L$testdir -l$testlib $XLDFLAGS -lpthread" + echo $test_compile + if { (eval $test_compile ) 2>&1; } && test -s testlink ; then + have_lapack=yes +@@ -2738,7 +2738,7 @@ + LAPACKDIR="$testdir" + echo "Link ok - using lib$LAPACKLIB from $LAPACKDIR" + # +- XLAPACK_LIB="-L$LAPACKDIR -l$LAPACKLIB" ++ XLAPACK_LIB="-L$LAPACKDIR -l$LAPACKLIB -lpthread" + # + # Test to see if we need BLAS too + # Do this by trying to compile a test program +@@ -2750,8 +2750,8 @@ + if test -f testlsame ; then + rm -f testsame testlsame.o + fi +- test_compile="$FC $FOPTIM $XFFLAGS -o testlsame lsametst.f -L$LAPACKDIR -l$LAPACKLIB" +- test_ccompile="$FC $FOPTIM $XFFLAGS -o testlsame lsametst.f -L$LAPACKDIR -l$LAPACKLIB $XLDFLAGS" ++ test_compile="$FC $FOPTIM $XFFLAGS -o testlsame lsametst.f -L$LAPACKDIR -l$LAPACKLIB -lpthread" ++ test_ccompile="$FC $FOPTIM $XFFLAGS -o testlsame lsametst.f -L$LAPACKDIR -l$LAPACKLIB $XLDFLAGS -lpthread" + echo $test_compile + if { ( eval $test_compile) 2>&1;} && test -s testlsame ; then + have_blas=yes +@@ -2830,8 +2830,8 @@ + STOP + END + EOF +- test_compile="$FC $FOPTIM $XFFLAGS -o testlink testlink.f -L$testdir -l$testlib" +- test_ccompile="$FC $FOPTIM $XFFLAGS -o testlink testlink.f -L$testdir -l$testlib $XLDFLAGS" ++ test_compile="$FC $FOPTIM $XFFLAGS -o testlink testlink.f -L$testdir -l$testlib -lpthread" ++ test_ccompile="$FC $FOPTIM $XFFLAGS -o testlink testlink.f -L$testdir -l$testlib $XLDFLAGS -lpthread" + echo $test_compile + if { ( eval $test_compile) 2>&1;} && test -s testlink ; then + have_blas=yes +@@ -3033,7 +3033,7 @@ + if test -f testlsame ; then + rm -f testsame testlsame.o + fi +- test_compile="$FC $FOPTIM $XFFLAGS -o testlsame lsametst.f -L$BLASDIR -l$BLASLIB" ++ test_compile="$FC $FOPTIM $XFFLAGS -o testlsame lsametst.f -L$BLASDIR -l$BLASLIB -lpthread" + echo $test_compile + if { ( eval $test_compile) 2>&1;} && test -s testlsame ; then + echo "Found LSAME in lib$BLASLIB" +@@ -3046,7 +3046,7 @@ + if test -f testxerbla ; then + rm -f testxerbla testxerbla.o + fi +- test_compile="$FC $FOPTIM $XFFLAGS -o testxerbla xerblatst.f -L$BLASDIR -l$BLASLIB" ++ test_compile="$FC $FOPTIM $XFFLAGS -o testxerbla xerblatst.f -L$BLASDIR -l$BLASLIB -lpthread" + echo $test_compile + if { ( eval $test_compile) 2>&1;} && test -s testxerbla ; then + # Found lsame +@@ -3080,7 +3080,7 @@ + cd ../.. + # + lapackdir=lib/lapack +- XLAPACK_LIB="-L$srcdir/lib/lapack -llapack -L$BLASDIR -l$BLASLIB" ++ XLAPACK_LIB="-L$srcdir/lib/lapack -llapack -L$BLASDIR -l$BLASLIB -lpthread" + # netlib lapack is in fortran, so we may need the fortran libraries when + # we are linking using the C or C++ compilers + case $system in diff --git a/sci-chemistry/ccp4/files/clipper-find-mccp4-includes.patch b/sci-chemistry/ccp4/files/clipper-find-mccp4-includes.patch new file mode 100644 index 000000000000..3bf5a0652247 --- /dev/null +++ b/sci-chemistry/ccp4/files/clipper-find-mccp4-includes.patch @@ -0,0 +1,11 @@ +--- ccp4-5.99.5/lib/clipper/configure.orig 2006-01-07 16:54:13.000000000 -0800 ++++ ccp4-5.99.5/lib/clipper/configure 2006-01-07 16:54:31.000000000 -0800 +@@ -21751,7 +21751,7 @@ + + if test "x$mccp4_prefix" != x; then + # ie. mccp4=thing was given (thing is what we're checking for) +- ac_MCCP4_CXXFLAGS="-I$mccp4_prefix/include" ++ ac_MCCP4_CXXFLAGS="-I$mccp4_prefix/include -I$mccp4_prefix/include/mccp4" + ac_MCCP4_LDOPTS="-L$mccp4_prefix/lib -lmccp4" + else + # treat as standard lib/include diff --git a/sci-chemistry/ccp4/files/create-mosflm-bindir.patch b/sci-chemistry/ccp4/files/create-mosflm-bindir.patch new file mode 100644 index 000000000000..34d6197572fc --- /dev/null +++ b/sci-chemistry/ccp4/files/create-mosflm-bindir.patch @@ -0,0 +1,10 @@ +--- ccp4-5.99.5.orig/x-windows/Makefile.in 2006-01-06 12:31:02.000000000 -0800 ++++ ccp4-5.99.5/x-windows/Makefile.in 2006-01-06 12:31:30.000000000 -0800 +@@ -158,6 +158,7 @@ + install_obj = ipdisp.exe hklview xdldataman xdlmapman \ + rotgen ipmosflm + install: all ++ mkdir -p $(bindir) + $(INSTALL_PROGRAM) $(srcdir)/ipdisp.exe $(bindir) + $(INSTALL_PROGRAM) $(srcdir)/ipdisp/ipdisp $(bindir) + $(INSTALL_PROGRAM) $(srcdir)/hklview $(bindir) diff --git a/sci-chemistry/ccp4/files/digest-ccp4-6.0.1 b/sci-chemistry/ccp4/files/digest-ccp4-6.0.1 new file mode 100644 index 000000000000..acc5dc94a96a --- /dev/null +++ b/sci-chemistry/ccp4/files/digest-ccp4-6.0.1 @@ -0,0 +1,3 @@ +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 diff --git a/sci-chemistry/ccp4/files/dont-build-rasmol.patch b/sci-chemistry/ccp4/files/dont-build-rasmol.patch new file mode 100644 index 000000000000..8da54fd26de8 --- /dev/null +++ b/sci-chemistry/ccp4/files/dont-build-rasmol.patch @@ -0,0 +1,19 @@ +--- ccp4-5.99.5.orig/x-windows/Makefile.in 2005-12-05 03:06:57.000000000 -0800 ++++ ccp4-5.99.5/x-windows/Makefile.in 2005-12-05 03:07:23.000000000 -0800 +@@ -35,7 +35,7 @@ + # + # all + # +-all : xdlview libjwc_c libjwc_f rotgen_ hklview ipdisp.exe xdlgjk xjiffy rasmol2 ipmosflm ++all : xdlview libjwc_c libjwc_f rotgen_ hklview ipdisp.exe xdlgjk xjiffy ipmosflm + # + # xdl_view + # +@@ -161,7 +161,6 @@ + $(INSTALL_PROGRAM) $(srcdir)/xdldataman $(bindir) + $(INSTALL_PROGRAM) $(srcdir)/xdlmapman $(bindir) + cd $(srcdir)/XCCPJIFFY ; $(MAKE) install +- $(INSTALL_PROGRAM) $(rasmol_dir)/rasmol $(bindir) + cd $(rotgen_dir); $(MAKE) install + $(INSTALL_PROGRAM) $(mosflm_dir)/bin/ipmosflm $(bindir) + cd $(xdlview_dir); $(MAKE) install diff --git a/sci-chemistry/ccp4/files/make-ipmosflm-dir.patch b/sci-chemistry/ccp4/files/make-ipmosflm-dir.patch new file mode 100644 index 000000000000..7813141b2ec2 --- /dev/null +++ b/sci-chemistry/ccp4/files/make-ipmosflm-dir.patch @@ -0,0 +1,10 @@ +--- ccp4-5.99.5.orig/x-windows/Mosflm/mosflm/Makefile.in 2006-01-06 00:04:12.000000000 -0800 ++++ ccp4-5.99.5/x-windows/Mosflm/mosflm/Makefile.in 2006-01-06 00:04:41.000000000 -0800 +@@ -37,6 +37,7 @@ + ${F77} ${FFLAGS} -o $@ $< + + ipmosflm: ${OBJS} ++ mkdir -p ${DPSBIN} + ${FLINK} ${FFLAGS} ${OBJS} ${LOCALLIBS} ${LIBS} \ + -o ${DPSBIN}/ipmosflm ${LDFLAGS} + diff --git a/sci-chemistry/ccp4/files/make-mosflm-cbf-libdir.patch b/sci-chemistry/ccp4/files/make-mosflm-cbf-libdir.patch new file mode 100644 index 000000000000..ae4b7633b105 --- /dev/null +++ b/sci-chemistry/ccp4/files/make-mosflm-cbf-libdir.patch @@ -0,0 +1,11 @@ +--- ccp4-5.99.5.orig/x-windows/Mosflm/cbf/Makefile.in 2006-01-05 23:42:19.000000000 -0800 ++++ ccp4-5.99.5/x-windows/Mosflm/cbf/Makefile.in 2006-01-05 23:43:35.000000000 -0800 +@@ -132,7 +132,7 @@ + # + # CBF library + # +-$(LIB)/libcbf.a: $(SOURCE) $(HEADERS) $(COMMONDEP) ++$(LIB)/libcbf.a: $(SOURCE) $(HEADERS) $(COMMONDEP) $(LIB) + $(CC) $(CFLAGS) $(INCLUDES) $(WARNINGS) -c $(SOURCE) + $(AR) cr $@ *.o + $(RANLIB) $@ diff --git a/sci-chemistry/ccp4/files/make-mosflm-index-libdir.patch b/sci-chemistry/ccp4/files/make-mosflm-index-libdir.patch new file mode 100644 index 000000000000..97607b689672 --- /dev/null +++ b/sci-chemistry/ccp4/files/make-mosflm-index-libdir.patch @@ -0,0 +1,10 @@ +--- ccp4-5.99.5.orig/x-windows/Mosflm/index/Makefile.in 2006-01-05 23:15:09.000000000 -0800 ++++ ccp4-5.99.5/x-windows/Mosflm/index/Makefile.in 2006-01-05 23:15:30.000000000 -0800 +@@ -76,6 +76,7 @@ + + # local version of libdps_index.a + ${LIB}/dps_index.a: ${IOBJS} ${HOBJS} ++ mkdir -p ${LIB} + ar ru ${LIB}/dps_index.a ${IOBJS} ${HOBJS} + + ${LIB}/libpeak.a: diff --git a/sci-chemistry/ccp4/files/make-mosflm-libdir.patch b/sci-chemistry/ccp4/files/make-mosflm-libdir.patch new file mode 100644 index 000000000000..eac1b9f1721e --- /dev/null +++ b/sci-chemistry/ccp4/files/make-mosflm-libdir.patch @@ -0,0 +1,10 @@ +--- ccp4-5.99.5.orig/x-windows/Mosflm/src/dps/index/Makefile.in 2006-01-05 22:48:47.000000000 -0800 ++++ ccp4-5.99.5/x-windows/Mosflm/src/dps/index/Makefile.in 2006-01-05 22:49:02.000000000 -0800 +@@ -42,6 +42,7 @@ + $(LOCALLIBS) $(LIBS) + + index: $(IOBJS) ++ mkdir -p $(LIBDIR) + ${AR} $(AR_FLAGS) $(LIBDIR)/libdps_index.a $(IOBJS) + chmod 644 $(LIBDIR)/libdps_index.a + diff --git a/sci-chemistry/ccp4/files/pass-clipper-enablevals.patch b/sci-chemistry/ccp4/files/pass-clipper-enablevals.patch new file mode 100644 index 000000000000..3e1a8b0e6be8 --- /dev/null +++ b/sci-chemistry/ccp4/files/pass-clipper-enablevals.patch @@ -0,0 +1,11 @@ +--- ccp4-5.99.5.orig/configure 2006-01-06 11:45:43.000000000 -0800 ++++ ccp4-5.99.5/configure 2006-01-06 11:46:53.000000000 -0800 +@@ -3210,7 +3210,7 @@ + #ccp4 setup + xopts="${xopts} --with-ccp4=${srcdir}" + #interface setup +- xopts="${xopts} --enable-mmdb --enable-cif --enable-ccp4 --enable-minimol" ++ xopts="${xopts} --enable-mmdb --enable-cif --enable-ccp4 --enable-minimol --enable-mmdbold --enable-mtz --with-mccp4=/usr" + echo + echo "********* CLIPPER CONFIGURATION ***********" + echo diff --git a/sci-chemistry/ccp4/metadata.xml b/sci-chemistry/ccp4/metadata.xml new file mode 100644 index 000000000000..211b8bd0f0a4 --- /dev/null +++ b/sci-chemistry/ccp4/metadata.xml @@ -0,0 +1,9 @@ + + + +sci + +spyderous@gentoo.org +Donnie Berkholz + + -- 2.26.2