diff options
| author |   Robin H. Johnson <robbat2@gentoo.org> | 2015-08-08 13:49:04 -0700 |
|---|---|---|
| committer | Robin H. Johnson <robbat2@gentoo.org> | 2015-08-08 17:38:18 -0700 |
| commit | 56bd759df1d0c750a065b8c845e93d5dfa6b549d (patch) | |
| tree | 3f91093cdb475e565ae857f1c5a7fd339e2d781e /sci-chemistry/ccp4-apps | |
| download | gentoo-56bd759df1d0c750a065b8c845e93d5dfa6b549d.tar.gz gentoo-56bd759df1d0c750a065b8c845e93d5dfa6b549d.tar.bz2 gentoo-56bd759df1d0c750a065b8c845e93d5dfa6b549d.zip | |
proj/gentoo: Initial commit
This commit represents a new era for Gentoo:
Storing the gentoo-x86 tree in Git, as converted from CVS.
This commit is the start of the NEW history.
Any historical data is intended to be grafted onto this point.
Creation process:
1. Take final CVS checkout snapshot
2. Remove ALL ChangeLog* files
3. Transform all Manifests to thin
4. Remove empty Manifests
5. Convert all stale $Header$/$Id$ CVS keywords to non-expanded Git $Id$
5.1. Do not touch files with -kb/-ko keyword flags.
Signed-off-by: Robin H. Johnson <robbat2@gentoo.org>
X-Thanks: Alec Warner <antarus@gentoo.org> - did the GSoC 2006 migration tests
X-Thanks: Robin H. Johnson <robbat2@gentoo.org> - infra guy, herding this project
X-Thanks: Nguyen Thai Ngoc Duy <pclouds@gentoo.org> - Former Gentoo developer, wrote Git features for the migration
X-Thanks: Brian Harring <ferringb@gentoo.org> - wrote much python to improve cvs2svn
X-Thanks: Rich Freeman <rich0@gentoo.org> - validation scripts
X-Thanks: Patrick Lauer <patrick@gentoo.org> - Gentoo dev, running new 2014 work in migration
X-Thanks: Michał Górny <mgorny@gentoo.org> - scripts, QA, nagging
X-Thanks: All of other Gentoo developers - many ideas and lots of paint on the bikeshed
Diffstat (limited to 'sci-chemistry/ccp4-apps')
20 files changed, 1987 insertions, 0 deletions
diff --git a/sci-chemistry/ccp4-apps/Manifest b/sci-chemistry/ccp4-apps/Manifest new file mode 100644 index 000000000000..e56aec5512a2 --- /dev/null +++ b/sci-chemistry/ccp4-apps/Manifest @@ -0,0 +1,2 @@ +DIST 6.1.3-oasis4.0.patch.bz2 946 SHA256 12d7c5965e0c46b0f482514d9083d6be94d65eeb14ba29c17d507d5f9669f84b SHA512 7c7bf4ef90550708bf41b1831dbe71c38418b46455adb3d42ec609d287894ac9260d9671f1759f71c713ced72fa004b9808391ea6874007ac8b7d7637f349d32 WHIRLPOOL a2bc27e1e054e1717c387f3800533fa490c03d1d18d3fe3cff4676f0ec47799a1681a206e01013c1b8f8e41162303446a824b86effeef2ed73f059feb07fb820 +DIST ccp4-6.1.3-core-src.tar.gz 242134076 SHA256 1e529c660e7f390ec0feca9d45caa00a2813d23156c10a2747c427117293c324 SHA512 413eba806107ebcdbd93e9122275463709133d9b2a9ce44ae57a6c2350465a47ba66ad9875237aead74f5d422c0104f58f728ab37a757b10d82cde92af444c20 WHIRLPOOL faebf8ee7920013bc3d0e83565207dca1f31ba0b5c92fe1eae4b740f70ff2031d95787fa0d545b09c853d25657c08973527e43de02fddc086988123ca2a6339c diff --git a/sci-chemistry/ccp4-apps/ccp4-apps-6.1.3-r13.ebuild b/sci-chemistry/ccp4-apps/ccp4-apps-6.1.3-r13.ebuild new file mode 100644 index 000000000000..854cc48db0cf --- /dev/null +++ b/sci-chemistry/ccp4-apps/ccp4-apps-6.1.3-r13.ebuild @@ -0,0 +1,395 @@ +# Copyright 1999-2015 Gentoo Foundation +# Distributed under the terms of the GNU General Public License v2 +# $Id$ + +EAPI=5 + +PYTHON_COMPAT=( python2_7 ) + +inherit autotools eutils fortran-2 flag-o-matic gnuconfig python-single-r1 toolchain-funcs + +MY_P="${PN/-apps}-${PV}" + +#UPDATE="04_03_09" +#PATCHDATE="090511" + +PATCH_TOT="0" + +DESCRIPTION="Protein X-ray crystallography toolkit" +HOMEPAGE="http://www.ccp4.ac.uk/" +SRC="ftp://ftp.ccp4.ac.uk/ccp4" +SRC_URI=" + ${SRC}/${PV}/${MY_P}-core-src.tar.gz + http://dev.gentoo.org/~jlec/distfiles/${PV}-oasis4.0.patch.bz2" +# patch tarball from upstream + [[ -n ${UPDATE} ]] && SRC_URI="${SRC_URI} ${SRC}/${PV}/updates/${P}-src-patch-${UPDATE}.tar.gz" +# patches created by us + [[ -n ${PATCHDATE} ]] && SRC_URI="${SRC_URI} http://dev.gentoo.org/~jlec/science-dist/${PV}-${PATCHDATE}-updates.patch.bz2" + +for i in $(seq $PATCH_TOT); do + NAME="PATCH${i}[1]" + SRC_URI="${SRC_URI} + ${SRC}/${PV}/patches/${!NAME}" +done + +LICENSE="ccp4" +SLOT="0" +KEYWORDS="amd64 ~ppc x86 ~amd64-linux ~x86-linux" +IUSE="examples X" + +X11DEPS=" + x11-libs/libX11 + x11-libs/libXaw + x11-libs/libXt + x11-libs/libxdl_view" + +TKDEPS=" + >=dev-lang/tk-8.3:0= + >=dev-tcltk/blt-2.4 + dev-tcltk/iwidgets + dev-tcltk/itcl + dev-tcltk/itk + >=dev-tcltk/tdom-0.8 + dev-tcltk/tktreectrl" + +SCILIBS=" + ~sci-libs/ccp4-libs-${PV} + >=sci-libs/ccp4-libs-${PV}-r7 + sci-libs/clipper + sci-libs/fftw:2.1 + sci-libs/mmdb:0 + sci-libs/ssm + virtual/blas + virtual/lapack" + +SCIAPPS=" + sci-chemistry/pdb-extract + sci-chemistry/pymol + sci-chemistry/rasmol + >=sci-chemistry/oasis-4.0-r1" + +RDEPEND=" + ${TKDEPS} + ${SCILIBS} + app-shells/tcsh + dev-python/pyxml + dev-libs/libxml2:2 + dev-libs/libjwc_c + dev-libs/libjwc_f + dev-libs/boehm-gc + !app-office/sc + !<sci-chemistry/ccp4-6.1.3 + X? ( ${X11DEPS} )" +DEPEND="${RDEPEND} + X? ( + x11-misc/imake + x11-proto/inputproto + x11-proto/xextproto + )" +PDEPEND="${SCIAPPS}" + +RESTRICT="mirror" + +S="${WORKDIR}/${MY_P}" + +pkg_setup() { + fortran-2_pkg_setup + python-single-r1_pkg_setup +} + +src_prepare() { + tc-export PKG_CONFIG + einfo "Applying upstream patches ..." + for patch in $(seq $PATCH_TOT); do + base="PATCH${patch}" + dir=$(eval echo \${${base}[0]}) + p=$(eval echo \${${base}[1]}) + pushd "${dir}" >& /dev/null + ccp_patch "${DISTDIR}/${p}" + popd >& /dev/null + done + einfo "Done." + echo + + [[ -n ${PATCHDATE} ]] && epatch "${WORKDIR}"/${PV}-${PATCHDATE}-updates.patch + + einfo "Applying Gentoo patches ..." + + # 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 + # Also remember to create the bindir. + ccp_patch "${FILESDIR}"/${PV}-dont-build-double-and-make-bindir.patch + + # libraries come from sci-libs/ccp4-libs + ccp_patch "${FILESDIR}"/${PV}-dont-build-libs.patch + + # We have seperate ebuilds for those + for bin in molref xia scala imosflm balbes; do + ccp_patch "${FILESDIR}"/${PV}-dont-build-${bin}.patch + done + + # don't configure what is not build + ccp_patch "${FILESDIR}"/${PV}-dont-configure.patch + + # Set python paths correctly + ccp_patch "${FILESDIR}"/${PV}-pythonpath.patch + + # Set python paths correctly + ccp_patch "${FILESDIR}"/${PV}-pisa.patch + + # Set python paths correctly + ccp_patch "${FILESDIR}"/${PV}-clipper-template.patch + + # Fix upstreams code + ccp_patch "${FILESDIR}"/${PV}-impl-dec.patch + + # Not renaming, but unbundling libs + ccp_patch "${FILESDIR}"/${PV}-rename-rapper-ng.patch + + # Use pkg-config to detect BLAS/LAPCK + ccp_patch "${FILESDIR}"/${PV}-lapack.patch + + # unbundle libs + ccp_patch "${FILESDIR}"/${PV}-unbundle.patch + + # tcl-8.6 + ccp_patch "${FILESDIR}"/${P}-tcl8.6.patch + + # Update things for oasis 4 usage + epatch "${WORKDIR}"/${PV}-oasis4.0.patch + sed 's: oasis : :g' -i src/Makefile.in || die + + einfo "Done." # done applying Gentoo patches + echo + + find ./lib/src/mmdb ./lib/ssm ./lib/clipper ./lib/fftw lib/lapack -delete + + sed \ + -e "s:/usr:${EPREFIX}/usr:g" \ + -e 's:-Wl,-rpath,$CLIB::g' \ + -e 's: -rpath $CLIB::g' \ + -e 's: -I${srcdir}/include/cpp_c_headers::g' \ + -e 's:sleep 1:sleep .2:g' \ + -e 's:\\$(XCIF_LIB):-L$srcdir/lib/ccif -lccif:g' \ + -e 's:\\$(XLAPACK_LIB):${XLAPACK_LIB}:g' \ + -e 's:\\$(CXX_LIBS):\${CXX_LIBS}:g' \ + -e 's:\\$(XLDFLAGS):\${XLDFLAGS}:g' \ + -i configure || die + + sed \ + -e '/o crunch2/s:$: ${XLAPACK_LIB}:g' \ + -i src/Makefile* || die + + find "${S}" -name "Makefile.*" \ + -exec sed -e 's|_FLAGS-|_FLAGS:-|g' -e "s:\(eval \$([[:alnum:]]*)\):\1 \$(GENTOOLDFLAGS):g" -i '{}' \; + + # Don't build refmac, sfcheck, balbes, molrep binaries; available from the standalone version + sed -i -e "/^REFMACTARGETS/s:^.*:REFMACTARGETS="":g" configure || die + + # Rapper bundles libxml2 and boehm-gc. Don't build, use or install those. + pushd src/rapper 2>/dev/null + eautoreconf + popd 2>/dev/null + + gnuconfig_update + + python_fix_shebang -f . +} + +src_configure() { + # Build system is broken if we set LDFLAGS + export GENTOOLDFLAGS="${LDFLAGS}" + unset LDFLAGS + + # These are broken with ./src/procheck/ps.f + filter-flags "-floop-*" + + # GENTOO_OSNAME can be one of: + # irix irix64 sunos sunos64 aix hpux osf1 linux freebsd + # linux_compaq_compilers linux_intel_compilers generic Darwin + # ia64_linux_intel Darwin_ibm_compilers linux_ibm_compilers + if [[ "$(tc-getFC)" = "ifort" ]]; then + if use ia64; then + GENTOO_OSNAME="ia64_linux_intel" + else + # Should be valid for x86, maybe amd64 + GENTOO_OSNAME="linux_intel_compilers" + fi + else + # Should be valid for x86 and amd64, at least + GENTOO_OSNAME="linux" + fi + + # Sets up env + ln -s \ + ccp4.setup-bash \ + "${S}"/include/ccp4.setup + + # We agree to the license by emerging this, set in LICENSE + sed -i \ + -e "s~^\(^agreed=\).*~\1yes~g" \ + "${S}"/configure || die + + # Fix up variables -- need to reset CCP4_MASTER at install-time + sed -i \ + -e "s~^\(setenv CCP4_MASTER.*\)/.*~\1${WORKDIR}~g" \ + -e "s~^\(export CCP4_MASTER.*\)/.*~\1${WORKDIR}~g" \ + -e "s~^\(.*export CBIN=.*\)\$CCP4.*~\1\$CCP4/libexec/ccp4/bin/~g" \ + -e "s~^\(.*setenv CBIN .*\)\$CCP4.*~\1\$CCP4/libexec/ccp4/bin/~g" \ + -e "s~^\(setenv CCP4I_TCLTK.*\)/usr/local/bin~\1${EPREFIX}/usr/bin~g" \ + "${S}"/include/ccp4.setup* || die + + # Set up variables for build + source "${S}"/include/ccp4.setup-sh + + export CC=$(tc-getCC) + export CXX=$(tc-getCXX) + export COPTIM=${CFLAGS} + export CXXOPTIM=${CXXFLAGS} + # Default to -O2 if FFLAGS is unset + export FC=$(tc-getFC) + export FOPTIM=${FFLAGS:- -O2} + export BINSORT_SCR="${T}" + export CCP4_MASTER="${WORKDIR}" + export CCP4I_TCLTK="${EPREFIX}/usr/bin" + export MAKE="make ${MAKEOPTS} ${EXTRA_EMAKE}" + + # Can't use econf, configure rejects unknown options like --prefix + ./configure \ + $(use_enable X x) \ + --with-shared-libs \ + --with-fftw="${EPREFIX}/usr" \ + --with-warnings \ + --disable-pdb_extract \ + --disable-cctbx \ + --disable-phaser \ + --disable-diffractionImg \ + --disable-clipper \ + --disable-ssm \ + --disable-mosflm \ + --disable-mrbump \ + --tmpdir="${TMPDIR}" \ + ${GENTOO_OSNAME} || die "configure failed" + + # We do this manually, since disabling the clipper libraries also + # disables the clipper programs + pushd src/clipper_progs 2>/dev/null + econf \ + --prefix="${S}" \ + --bindir="${ED}"/usr/libexec/ccp4/bin \ + --with-ccp4="${S}" \ + --with-clipper="${EPREFIX}/usr" \ + --with-fftw="${EPREFIX}/usr" \ + --with-mmdb="${EPREFIX}/usr" \ + CXX=$(tc-getCXX) + popd 2>/dev/null +} + +src_compile() { + # fsplit is required for the programs + pushd lib/src 2>/dev/null + emake fsplit -j1 || die + popd 2>/dev/null + + # We do this manually, since disabling the clipper libraries also + # disables the clipper programs + pushd src/clipper_progs 2>/dev/null + emake || die + popd 2>/dev/null + + emake -j1 || die "emake failed" +} + +src_install() { + # Set up variables for build + source "${S}"/include/ccp4.setup-sh + + # if we don't make this, a ton of programs fail to install + mkdir "${S}"/bin || die + + # We do this manually, since disabling the clipper libraries also + # disables the clipper programs + pushd "${S}"/src/clipper_progs 2>/dev/null + emake install || die + popd 2>/dev/null + + einstall || die "install failed" + + # Collision with sci-chemistry/mrbump + rm -f "${S}"/bin/{mrbump,pydbviewer} || die + + # Bins + exeinto /usr/libexec/ccp4/bin/ + doexe "${S}"/bin/* || die + + # Libs + for file in "${S}"/lib/*; do + if [[ -d ${file} ]]; then + continue + elif [[ -x ${file} ]]; then + dolib.so ${file} || die + else + insinto /usr/$(get_libdir) + doins ${file} || die + fi + done + + rm -f "${S}"/include/ccp4.setup* + + # smartie -- log parsing + insinto /usr/share/ccp4 + doins -r "${S}"/share/smartie || die + + # Install docs and examples + local _man + pushd "${S}"/man/cat1 > /dev/null + for _man in *; do + newman ${_man} ${_man%??}-ccp4${_man:${#_man}-2:2} + done + popd > /dev/null + + mv "${S}"/manual/README "${S}"/manual/README-manual + dodoc manual/* README CHANGES doc/* examples/README || die + + rm "${ED}"/usr/share/doc/${PF}/GNUmakefile.* + rm "${ED}"/usr/share/doc/${PF}/COPYING.* + + dohtml -r "${S}"/html/* + + if use examples; then + for i in data rnase toxd; do + docinto examples/${i} + dodoc "${S}"/examples/${i}/* + done + + docinto examples/tutorial + dohtml -r "${S}"/examples/tutorial/html examples/tutorial/tut.css + for i in data results; do + docinto examples/tutorial/${i} + dodoc "${S}"/examples/tutorial/${i}/* + done + + for i in non-runnable runnable; do + docinto examples/unix/${i} + dodoc "${S}"/examples/unix/${i}/* + done + fi + # Needed for ccp4i docs to work + dosym ../../share/doc/${PF}/examples /usr/$(get_libdir)/ccp4/examples || die + dosym ../../share/doc/${PF}/html /usr/$(get_libdir)/ccp4/html || die + + cat >> "${T}"/baubles <<- EOF + #!${EPREFIX}/bin/bash + exec "${EPYTHON}" "\${CCP4}/share/ccp4/smartie/baubles.py" + EOF + + exeinto /usr/libexec/ccp4/bin/ + doexe "${T}"/baubles || die +} + +# Epatch wrapper for bulk patching +ccp_patch() { + EPATCH_SINGLE_MSG=" ${1##*/} ..." epatch ${1} +} diff --git a/sci-chemistry/ccp4-apps/files/6.1.3-clipper-template.patch b/sci-chemistry/ccp4-apps/files/6.1.3-clipper-template.patch new file mode 100644 index 000000000000..433a78dbd23b --- /dev/null +++ b/sci-chemistry/ccp4-apps/files/6.1.3-clipper-template.patch @@ -0,0 +1,70 @@ +--- src/clipper_progs/src/intensity_target.h.orig 2010-01-21 11:27:13.236795886 -0600 ++++ src/clipper_progs/src/intensity_target.h 2010-01-21 11:31:33.450686927 -0600 +@@ -70,9 +70,31 @@ + { + public: + //! constructor: takes the datalist against which to calc target +- TargetFn_scaleLogI1I2( const HKL_data<T1>& hkl_data1_, const HKL_data<T2>& hkl_data2_ ); ++ TargetFn_scaleLogI1I2( const HKL_data<T1>& hkl_data1_, const HKL_data<T2>& hkl_data2_ ) ++ { ++ hkl_data1 = &hkl_data1_; ++ hkl_data2 = &hkl_data2_; ++ } + //! return the value and derivatives of the target function +- Rderiv rderiv( const HKL_info::HKL_reference_index& ih, const ftype& intensityh ) const; ++ Rderiv rderiv( const HKL_info::HKL_reference_index& ih, const ftype& intensityh ) const ++ { ++ Rderiv result; ++ result.r = result.dr = result.dr2 = 0.0; ++ const T1& it1 = (*hkl_data1)[ih]; ++ const T2& it2 = (*hkl_data2)[ih]; ++ if ( !it1.missing() && !it2.missing() ) ++ if ( it1.I() > 1.0e-6 && it2.I() > 1.0e-6 ) { ++ const ftype eps = ih.hkl_class().epsilon(); ++ const ftype i1 = it1.I() / eps; ++ const ftype i2 = it2.I() / eps; ++ const ftype w = sqrt( i1 * i2 ); ++ const ftype d = intensityh + log(i1) - log(i2); ++ result.r = w * d * d; ++ result.dr = 2.0 * w * d; ++ result.dr2 = 2.0 * w; ++ } ++ return result; ++ } + //! the type of the function: optionally used to improve convergence + FNtype type() const { return QUADRATIC; } + private: +@@ -109,33 +131,4 @@ + return result; + } + +- // Log I1-I2 scaling +- +- template<class T1, class T2> TargetFn_scaleLogI1I2<T1,T2>::TargetFn_scaleLogI1I2( const HKL_data<T1>& hkl_data1_, const HKL_data<T2>& hkl_data2_ ) +- { +- hkl_data1 = &hkl_data1_; +- hkl_data2 = &hkl_data2_; +- } +- +- template<class T1, class T2> TargetFn_base::Rderiv TargetFn_scaleLogI1I2<T1,T2>::rderiv( const HKL_info::HKL_reference_index& ih, const ftype& intensityh ) const +- { +- Rderiv result; +- result.r = result.dr = result.dr2 = 0.0; +- const T1& it1 = (*hkl_data1)[ih]; +- const T2& it2 = (*hkl_data2)[ih]; +- if ( !it1.missing() && !it2.missing() ) +- if ( it1.I() > 1.0e-6 && it2.I() > 1.0e-6 ) { +- const ftype eps = ih.hkl_class().epsilon(); +- const ftype i1 = it1.I() / eps; +- const ftype i2 = it2.I() / eps; +- const ftype w = sqrt( i1 * i2 ); +- const ftype d = intensityh + log(i1) - log(i2); +- result.r = w * d * d; +- result.dr = 2.0 * w * d; +- result.dr2 = 2.0 * w; +- } +- return result; +- } +- +- + #endif diff --git a/sci-chemistry/ccp4-apps/files/6.1.3-dont-build-balbes.patch b/sci-chemistry/ccp4-apps/files/6.1.3-dont-build-balbes.patch new file mode 100644 index 000000000000..f1df3e5e19f9 --- /dev/null +++ b/sci-chemistry/ccp4-apps/files/6.1.3-dont-build-balbes.patch @@ -0,0 +1,14 @@ +diff --git a/share/Makefile.in b/share/Makefile.in +index 2d4f20b..4500993 100755 +--- a/share/Makefile.in ++++ b/share/Makefile.in +@@ -18,9 +18,6 @@ install : + for i in $(MRBUMP_TARGETS); do \ + test -s $(MRBUMP_BINDIR)/$$i && $(INSTALL_PROGRAM) $(MRBUMP_BINDIR)/$$i $(bindir)/$$i || true ;\ + done +- for i in $(BALBES_TARGETS); do \ +- test -s $(BALBES_BINDIR)/$$i && $(INSTALL_PROGRAM) $(BALBES_BINDIR)/$$i $(bindir)/$$i || true ;\ +- done + + clean : ; -rm -f core *.o *~ a.out + diff --git a/sci-chemistry/ccp4-apps/files/6.1.3-dont-build-double-and-make-bindir.patch b/sci-chemistry/ccp4-apps/files/6.1.3-dont-build-double-and-make-bindir.patch new file mode 100644 index 000000000000..e62ae12adfbe --- /dev/null +++ b/sci-chemistry/ccp4-apps/files/6.1.3-dont-build-double-and-make-bindir.patch @@ -0,0 +1,24 @@ +--- ccp4-6.1.1/x-windows/Makefile.in 2008-08-11 19:20:01.000000000 +0200 ++++ ccp4-6.1.1/x-windows/Makefile.in.new 2009-02-27 14:32:25.000000000 +0100 +@@ -35,7 +35,7 @@ + # + # all + # +-all : xdlview libjwc_c libjwc_f rotgen_ hklview xjiffy rasmol2 ipmosflm ++all : rotgen_ hklview xjiffy + # + # xdl_view + # +@@ -157,11 +157,10 @@ + # + install_obj = hklview rotgen ipmosflm + install: all ++ mkdir -p $(bindir) + $(INSTALL_PROGRAM) $(srcdir)/hklview $(bindir) + cd $(srcdir)/XCCPJIFFY ; $(MAKE) bindir=$(bindir) libdir=$(libdir) install +- $(INSTALL_PROGRAM) $(rasmol_dir)/rasmol $(bindir) + cd $(rotgen_dir); $(MAKE) install +- $(INSTALL_PROGRAM) $(mosflm_dir)/bin/ipmosflm $(bindir) + # + # clean + # diff --git a/sci-chemistry/ccp4-apps/files/6.1.3-dont-build-imosflm.patch b/sci-chemistry/ccp4-apps/files/6.1.3-dont-build-imosflm.patch new file mode 100644 index 000000000000..f645643e1c67 --- /dev/null +++ b/sci-chemistry/ccp4-apps/files/6.1.3-dont-build-imosflm.patch @@ -0,0 +1,11 @@ +--- ccp4i/Makefile.in 2009-06-19 15:08:53.000000000 +0200 ++++ ccp4i/Makefile.in.new 2009-08-04 21:10:14.000000000 +0200 +@@ -9,7 +9,7 @@ + SHELL = /bin/sh + DESTDIR = $(prefix) + CCP4I_BINDIR = $(top_srcdir)/ccp4i/bin +-CCP4I_TARGETS = ccp4i imosflm loggraph crank mapslicer ++CCP4I_TARGETS = ccp4i loggraph crank mapslicer + + install : + for i in $(CCP4I_TARGETS); do \ diff --git a/sci-chemistry/ccp4-apps/files/6.1.3-dont-build-libs.patch b/sci-chemistry/ccp4-apps/files/6.1.3-dont-build-libs.patch new file mode 100644 index 000000000000..1d1323005540 --- /dev/null +++ b/sci-chemistry/ccp4-apps/files/6.1.3-dont-build-libs.patch @@ -0,0 +1,35 @@ +--- Makefile.in 2009-06-19 15:13:29.000000000 +0200 ++++ Makefile.in.new 2009-08-02 23:06:41.000000000 +0200 +@@ -2,7 +2,7 @@ + # $Id$ + + SHELL = /bin/sh +-DIRS = $(fftwdir) $(clipperdir) $(diffimdir) $(lapackdir) $(ccifdir) lib/src $(ssmdir) src lib/data unsupported/src x-windows share ccp4i $(prereleasedir) ++DIRS = src lib/data unsupported/src x-windows share ccp4i $(prereleasedir) + # this is for the benefit of makes that don't pass variable values in + # recursive invocations, so that you can override these values on the + # command line at the top level +@@ -69,19 +69,19 @@ + $(MAKE) -i $(MFLAGS) $(MVARS) install; else true; fi ; \ + $(MAKE) install + +-srcdir : FORCE libdir ++srcdir : FORCE + if test -d src; then cd src; $(MAKE) $(MFLAGS) $(MVARS); else true; fi + + supported : srcdir + +-unsupported : FORCE libdir ++unsupported : FORCE + if test -d unsupported/src; then cd unsupported/src; \ + $(MAKE) $(MFLAGS) $(MVARS); else true; fi + +-datadir : FORCE libdir ++datadir : FORCE + cd lib/data; $(MAKE) $(MFLAGS) $(MVARS) + +-xwindir : FORCE libdir ++xwindir : FORCE + if test -f x-windows/Makefile; then cd x-windows; \ + $(MAKE) -i $(MFLAGS) ; else true; fi + diff --git a/sci-chemistry/ccp4-apps/files/6.1.3-dont-build-molref.patch b/sci-chemistry/ccp4-apps/files/6.1.3-dont-build-molref.patch new file mode 100644 index 000000000000..f16b0ecb938c --- /dev/null +++ b/sci-chemistry/ccp4-apps/files/6.1.3-dont-build-molref.patch @@ -0,0 +1,19 @@ +--- src/pisa/Makefile.am 2007-07-10 10:56:05.000000000 +0200 ++++ src/pisa/Makefile.am.new 2009-06-11 21:16:51.000000000 +0200 +@@ -1,4 +1,4 @@ +-SUBDIRS = molref pisastore sbase ++SUBDIRS = pisastore sbase + + pkgdatadir = $(datadir)/pisa + +--- src/pisa/Makefile.in 2009-06-12 21:12:08.000000000 +0200 ++++ src/pisa/Makefile.in.new 2009-06-12 21:41:52.000000000 +0200 +@@ -82,7 +82,7 @@ + am__quote = @am__quote@ + install_sh = @install_sh@ + pisa_LDFLAGS = @pisa_LDFLAGS@ +-SUBDIRS = molref pisastore sbase ++SUBDIRS = pisastore sbase + + dist_pkgdata_DATA = pisa.cfg + diff --git a/sci-chemistry/ccp4-apps/files/6.1.3-dont-build-scala.patch b/sci-chemistry/ccp4-apps/files/6.1.3-dont-build-scala.patch new file mode 100644 index 000000000000..af4fd8219c4f --- /dev/null +++ b/sci-chemistry/ccp4-apps/files/6.1.3-dont-build-scala.patch @@ -0,0 +1,42 @@ +--- ./src/Makefile.in 2009-03-20 15:06:41.000000000 +0100 ++++ ./src/Makefile.in.new 2009-07-31 23:46:13.000000000 +0200 +@@ -50,7 +50,7 @@ + + # these live in subdirectories and have more than one dependency: + OTHERS = rsps anglen secstr proclean pplot gfac2pdb tplot mplot probplot rmsdev nb \ +- scala dm dmmulti stereo mapmask maprot ncsmask \ ++ dm dmmulti stereo mapmask maprot ncsmask \ + sftools tlsanl tlsextract topp toplist dyndom sc combat mlphare fffear ffjoin \ + anisoanl $(REFMACTARGETS) dtrek2scala crunch2 pmf doser mat2symop symop2mat + +@@ -637,7 +637,7 @@ + + ### scala, mapmask, maprot, ncsmask, combat + +-scala mapmask maprot ncsmask combat sc dyndom: # dependencies below ++mapmask maprot ncsmask combat sc dyndom: # dependencies below + @$(SETFLAGS) pwd=`pwd` ; rm -f $@; \ + cd $(srcdir)/$@_; \ + echo $(FC) $${$@_FLAGS-"$(FFLAGS)"} -c -o $$pwd/$@.o `pwd`/$@.f ;\ +@@ -1002,21 +1002,6 @@ + proclean: $(srcdir)/procheck/clean.f $(srcdir)/procheck/brkcln.par + rmsdev: $(srcdir)/procheck/rmsdev.f $(srcdir)/procheck/rmsdev.inc + +-scaladir = $(srcdir)/scala_ +-scala : $(scaladir)/scala.f $(scaladir)/column.fh $(scaladir)/orient.fh \ +- $(scaladir)/params.fh $(scaladir)/rfile.fh $(scaladir)/scales.fh \ +- $(scaladir)/nbtchc.fh $(scaladir)/parameter.fh $(scaladir)/refcon.fh \ +- $(scaladir)/rundef.fh $(scaladir)/sdfacc.fh $(scaladir)/flags.fh \ +- $(scaladir)/inout.fh $(scaladir)/dump.fh $(scaladir)/tie.fh \ +- $(scaladir)/outcon.fh $(scaladir)/version.fh $(scaladir)/anomtc.fh \ +- $(scaladir)/axes.fh $(scaladir)/bigarg.fh \ +- $(scaladir)/errors.fh $(scaladir)/flow.fh $(scaladir)/glocon.fh \ +- $(scaladir)/means.fh $(scaladir)/refflg.fh $(scaladir)/stats.fh \ +- $(scaladir)/symmty.fh $(scaladir)/sharvest.fh $(scaladir)/chtml.fh \ +- $(scaladir)/htmbuf.fh $(scaladir)/sphhrm.fh $(scaladir)/crlncf.fh \ +- $(scaladir)/datasets.fh $(scaladir)/dts_storage.fh \ +- $(scaladir)/sclinimeans.fh $(scaladir)/timecor.fh +- + freemask.o: $(dmdir)/freemask.f $(dmdir)/crystal.fh $(dmdir)/cycl.fh \ + $(dmdir)/dmheader.fh $(dmdir)/io.fh $(dmdir)/output.fh \ + $(dmdir)/params.fh $(dmdir)/uvwdata.fh diff --git a/sci-chemistry/ccp4-apps/files/6.1.3-dont-build-xia.patch b/sci-chemistry/ccp4-apps/files/6.1.3-dont-build-xia.patch new file mode 100644 index 000000000000..3af4af503fa6 --- /dev/null +++ b/sci-chemistry/ccp4-apps/files/6.1.3-dont-build-xia.patch @@ -0,0 +1,14 @@ +--- src/Makefile.in 2009-07-05 16:50:25.000000000 +0200 ++++ src/Makefile.in.new 2009-07-05 19:38:06.000000000 +0200 +@@ -50,9 +50,9 @@ + + # these live in subdirectories and have more than one dependency: + OTHERS = rsps anglen secstr proclean pplot gfac2pdb tplot mplot probplot rmsdev nb \ +- scala dm dmmulti stereo mapmask maprot ncsmask chef \ ++ scala dm dmmulti stereo mapmask maprot ncsmask \ + sftools tlsanl tlsextract topp toplist dyndom sc combat mlphare fffear ffjoin \ +- anisoanl $(REFMACTARGETS) dtrek2scala crunch2 pmf doser mat2symop symop2mat ++ anisoanl $(REFMACTARGETS) dtrek2scala crunch2 pmf + + # targets built from .c sources: + CSIMPLE = pltdev binsort diff --git a/sci-chemistry/ccp4-apps/files/6.1.3-dont-configure.patch b/sci-chemistry/ccp4-apps/files/6.1.3-dont-configure.patch new file mode 100644 index 000000000000..1e59578473ff --- /dev/null +++ b/sci-chemistry/ccp4-apps/files/6.1.3-dont-configure.patch @@ -0,0 +1,111 @@ +--- configure 2009-08-07 12:11:28.000000000 +0200 ++++ configure.new.nolib 2009-08-17 22:30:39.000000000 +0200 +@@ -3113,41 +3113,6 @@ + RX_L="$configdir/lib/rxdispencer/rx" + export RX_H RX_L + fi +- echo +- echo "Running separate configure for CCIF library." +- echo +- cd lib/ccif +- echo "Updating modification times for configuration files" +- echo "Please wait..." +- for i in configure.in aclocal.m4 configure Makefile.in; do +- touch $i && sleep 1 +- done +- echo "...done." +- +- if [ "X$LIBFOPTIM" != "X" ]; then +- FOPTIM_save=$FOPTIM +- FOPTIM=$LIBFOPTIM +- FFLAGS="${FOPTIM} ${XFFLAGS}" +- fi +- if [ "X$LIBCOPTIM" != "X" ]; then +- COPTIM_save=$COPTIM +- COPTIM=$LIBCOPTIM +- CFLAGS="${COPTIM} ${XCFLAGS}" +- fi +- ( touch /tmp/$$.cache_file 2>/dev/null && \ +- cat /dev/null > /tmp/$$.cache_file && \ +- ./configure $xopts --libdir=${libdir} --srcdir=${srcdir}/lib/ccif --cache-file=/tmp/$$.cache_file ) || \ +- ./configure $xopts --libdir=${libdir} --srcdir=${srcdir}/lib/ccif +- rm -f /tmp/$$.cache_file +- if [ "X$LIBFOPTIM" != "X" ]; then +- FOPTIM=$FOPTIM_save +- FFLAGS="${FOPTIM} ${XFFLAGS}" +- fi +- if [ "X$LIBCOPTIM" != "X" ]; then +- COPTIM=$COPTIM_save +- CFLAGS="${COPTIM} ${XCFLAGS}" +- fi +- cd ../.. + echo + echo "Returning to main configure." + echo +@@ -5094,53 +5059,6 @@ + echo "configure $xopts --exec_prefix=${prefix} --prefix=${prefix} --bindir=${bindir} --libdir=${libdir}" + ./configure $xopts --exec_prefix=${prefix} --prefix=${prefix} --bindir=${bindir} --libdir=${libdir} + echo +- echo "CCP4 configure: Running separate configure for libjwc_c library." +- echo +- cd ${srcdir}/${xwindir}/libjwc/libjwc_c +- echo "Updating modification times for configuration files in libjwc_c" +- echo "Please wait..." +- for i in configure.in Makefile.am aclocal.m4 configure Makefile.in ltconfig ltmain.sh; do +- touch $i && sleep 1 +- done +- echo "...done." +- echo +- echo "configure $xopts --exec_prefix=${prefix} --prefix=${prefix} --bindir=${bindir} --libdir=${libdir}" +- ( touch /tmp/$$.cache_file 2>/dev/null && \ +- cat /dev/null > /tmp/$$.cache_file && \ +- ./configure $xopts --exec_prefix=${prefix} --prefix=${prefix} --bindir=${bindir} --libdir=${libdir} --cache-file=/tmp/$$.cache_file ) || \ +- ./configure $xopts --exec_prefix=${prefix} --prefix=${prefix} --bindir=${bindir} --libdir=${libdir} +- rm -f /tmp/$$.cache_file +- echo +- echo "CCP4 configure: Running separate configure for libjwc_f library." +- echo +- cd ${srcdir}/${xwindir}/libjwc/libjwc_f +- # for g77 3.1 some builds do not have no-common for system libs, +- # so disable for now +- echo "Updating modification times for configuration files in libjwc_f" +- echo "Please wait..." +- for i in configure.in Makefile.am aclocal.m4 configure Makefile.in ltconfig ltmain.sh; do +- touch $i && sleep 1 +- done +- echo "...done." +- echo +- # for g77 3.1 some builds do not have no-common for system libs, +- # so disable for now +- case $system in +- Darwin* ) +- echo "configure --disable-shared --exec_prefix=${prefix} --prefix=${prefix} --bindir=${bindir} --libdir=${libdir}" +- ( touch /tmp/$$.cache_file 2>/dev/null && \ +- cat /dev/null > /tmp/$$.cache_file && \ +- ./configure --disable-shared --exec_prefix=${prefix} --prefix=${prefix} --bindir=${bindir} --libdir=${libdir} --cache-file=/tmp/$$.cache_file ) || \ +- ./configure --disable-shared --exec_prefix=${prefix} --prefix=${prefix} --bindir=${bindir} --libdir=${libdir} +- ;; +- * ) +- echo "configure $xopts --exec_prefix=${prefix} --prefix=${prefix} --bindir=${bindir} --libdir=${libdir}" +- ( touch /tmp/$$.cache_file 2>/dev/null && \ +- cat /dev/null > /tmp/$$.cache_file && \ +- ./configure $xopts --exec_prefix=${prefix} --prefix=${prefix} --bindir=${bindir} --libdir=${libdir} --cache-file=/tmp/$$.cache_file ) || \ +- ./configure $xopts --exec_prefix=${prefix} --prefix=${prefix} --bindir=${bindir} --libdir=${libdir} +- esac +- rm -f /tmp/$$.cache_file + + if test "$non_shared" = yes; then + #this is a bit of a cheat/fudge but that's life! +@@ -5210,12 +5128,6 @@ + fi + + echo +- echo "CCP4 configure: Running separate configure for Mosflm" +- echo +- cd ${srcdir}/${mosflmdir} +- echo "configure $xopts --with-ccp4-prefix=${prefix} --exec_prefix=${prefix} --prefix=${prefix} --bindir=${bindir} --libdir=${libdir}" +- ./configure $xopts --with-ccp4-prefix=${prefix} --exec_prefix=${prefix} --prefix=${prefix} --bindir=${bindir} --libdir=${libdir} +- echo + cd ../.. + echo "Returning to main configure." + echo diff --git a/sci-chemistry/ccp4-apps/files/6.1.3-dont-make-dirs-in-configure.patch b/sci-chemistry/ccp4-apps/files/6.1.3-dont-make-dirs-in-configure.patch new file mode 100644 index 000000000000..583697cea0a1 --- /dev/null +++ b/sci-chemistry/ccp4-apps/files/6.1.3-dont-make-dirs-in-configure.patch @@ -0,0 +1,87 @@ +--- ccp4-6.0.99e.orig/configure 2008-07-31 10:37:22.000000000 -0700 ++++ ccp4-6.0.99e/configure 2008-07-31 10:39:18.000000000 -0700 +@@ -643,45 +643,45 @@ + # echo "! Beware -- the $system installation isn't properly tested." ; } + syswarn='echo; echo "! Beware -- the $system installation is not properly tested."' + +-if test -z "$onlylibs" ; then +- for i in CCP4_SCR BINSORT_SCR; do +- if ( eval test -d \$$i || eval mkdir -p \$$i ) ; then : +- else +- eval echo "! No directory \$$i and can\'t create it." +- echo " Check the value of $i." +- badvar=1 +- fi +- done +- +- for i in libdir bindir includedir; do +- if ( eval test -d \$$i || eval mkdir -p \$$i ) ; then : +- else +- eval echo "! No directory \$$i and can\'t create it." +- echo " Check the argument of --$i." +- badvar=1 +- fi +- done +- +- for i in $dotsrc $dotunsupp $dotunsuppsrc $dotdeprec $dotdeprecsrc ./lib ./lib/src ./lib/data ./ccp4i/etc/unix $mosflmdir/lib $mosflmdir/bin $mosflmdir/cbf/lib ; do +- if test -d $i || mkdir $i; then : +- else +- eval echo "! No directory $i and can\'t create it." +- badvar=1 +- fi +- done +-else +- # Kludge to fool the "Makefile" target in the top-level CCP4 +- # Makefile into not trying to remake src/Makefile.in +- for i in $srcdir/src $srcdir/lib/src ; do +- if test -d $i || mkdir $i; then +- if ! test -f $i/Makefile.in ; then +- echo +- echo "onlylibs: making dummy file $i/Makefile.in" +- touch $i/Makefile.in +- fi +- fi +- done +-fi ++#if test -z "$onlylibs" ; then ++# for i in CCP4_SCR BINSORT_SCR; do ++# if ( eval test -d \$$i || eval mkdir -p \$$i ) ; then : ++# else ++# eval echo "! No directory \$$i and can\'t create it." ++# echo " Check the value of $i." ++# badvar=1 ++# fi ++# done ++# ++# for i in libdir bindir includedir; do ++# if ( eval test -d \$$i || eval mkdir -p \$$i ) ; then : ++# else ++# eval echo "! No directory \$$i and can\'t create it." ++# echo " Check the argument of --$i." ++# badvar=1 ++# fi ++# done ++# ++# for i in $dotsrc $dotunsupp $dotunsuppsrc $dotdeprec $dotdeprecsrc ./lib ./lib/src ./lib/data ./ccp4i/etc/unix $mosflmdir/lib $mosflmdir/bin $mosflmdir/cbf/lib ; do ++# if test -d $i || mkdir $i; then : ++# else ++# eval echo "! No directory $i and can\'t create it." ++# badvar=1 ++# fi ++# done ++#else ++# # Kludge to fool the "Makefile" target in the top-level CCP4 ++# # Makefile into not trying to remake src/Makefile.in ++# for i in $srcdir/src $srcdir/lib/src ; do ++# if test -d $i || mkdir $i; then ++# if ! test -f $i/Makefile.in ; then ++# echo ++# echo "onlylibs: making dummy file $i/Makefile.in" ++# touch $i/Makefile.in ++# fi ++# fi ++# done ++#fi + + ### sanity checks + diff --git a/sci-chemistry/ccp4-apps/files/6.1.3-impl-dec.patch b/sci-chemistry/ccp4-apps/files/6.1.3-impl-dec.patch new file mode 100644 index 000000000000..db8236063043 --- /dev/null +++ b/sci-chemistry/ccp4-apps/files/6.1.3-impl-dec.patch @@ -0,0 +1,152 @@ +diff --git a/lib/DiffractionImage/Bruker/FRM_LIB.c b/lib/DiffractionImage/Bruker/FRM_LIB.c +index bfda882..f821e04 100755 +--- a/lib/DiffractionImage/Bruker/FRM_LIB.c ++++ b/lib/DiffractionImage/Bruker/FRM_LIB.c +@@ -38,6 +38,8 @@ FRM_LIB: Routines for reading, writing, and handling frame files. + #include "sys/types.h" /* _open, etc. */ + #include "sys/stat.h" /* _open, etc. */ + ++#include <unistd.h> ++ + #ifndef _MSC_VER + int min(int a, int b) + { +diff --git a/lib/DiffractionImage/MAR/mar300_header.c b/lib/DiffractionImage/MAR/mar300_header.c +index 1a933de..1c40c32 100755 +--- a/lib/DiffractionImage/MAR/mar300_header.c ++++ b/lib/DiffractionImage/MAR/mar300_header.c +@@ -23,6 +23,9 @@ + */ + #include "mar300_header.h" + ++#include <sys/types.h> ++#include <unistd.h> ++ + /* + * Local functions + */ +diff --git a/lib/DiffractionImage/MAR/mar345_header.c b/lib/DiffractionImage/MAR/mar345_header.c +index a8351ea..16d0f7b 100755 +--- a/lib/DiffractionImage/MAR/mar345_header.c ++++ b/lib/DiffractionImage/MAR/mar345_header.c +@@ -32,6 +32,9 @@ + */ + #include "mar345_header.h" + ++#include <sys/types.h> ++#include <unistd.h> ++ + /* + * Definitions + */ +diff --git a/lib/DiffractionImage/MAR/nb_header.c b/lib/DiffractionImage/MAR/nb_header.c +index 07f2741..6364ca4 100755 +--- a/lib/DiffractionImage/MAR/nb_header.c ++++ b/lib/DiffractionImage/MAR/nb_header.c +@@ -20,6 +20,8 @@ + #include <io.h> + #endif + ++#include <sys/types.h> ++#include <unistd.h> + /* + * mar software include files + */ +diff --git a/lib/DiffractionImage/MAR/swap.c b/lib/DiffractionImage/MAR/swap.c +index 443bb8c..0d96b3f 100755 +--- a/lib/DiffractionImage/MAR/swap.c ++++ b/lib/DiffractionImage/MAR/swap.c +@@ -10,6 +10,9 @@ + * + **********************************************************************/ + ++#define _XOPEN_SOURCE ++#include <unistd.h> ++ + void swaplong(); + void swapshort(); + +diff --git a/lib/ccif/f_interface.c b/lib/ccif/f_interface.c +index 0f6a6b7..a09dc48 100755 +--- a/lib/ccif/f_interface.c ++++ b/lib/ccif/f_interface.c +@@ -25,6 +25,7 @@ + ********************************************************************/ + + #include "stdpccts.h" ++#include <sys/mman.h> + + /* This file is terribly organised, and badly needs re-doing. There is probably + * scope for splitting this into three modules: +diff --git a/lib/src/ccp4_general_f.c b/lib/src/ccp4_general_f.c +index 8b5d04f..74ee3f7 100755 +--- a/lib/src/ccp4_general_f.c ++++ b/lib/src/ccp4_general_f.c +@@ -26,6 +26,7 @@ + #include <string.h> + #include <stdlib.h> + #include <math.h> ++#include <time.h> + #include "ccp4_errno.h" + #include "ccp4_fortran.h" + #include "ccp4_parser.h" +diff --git a/lib/src/ccp4_program.c b/lib/src/ccp4_program.c +index 3e83d4d..bb3e975 100755 +--- a/lib/src/ccp4_program.c ++++ b/lib/src/ccp4_program.c +@@ -25,6 +25,7 @@ + #include <stdio.h> + #include <stdlib.h> + #include <string.h> ++#include <time.h> + #include "ccp4_program.h" + #include "ccp4_parser.h" + #include "ccp4_utils.h" +diff --git a/lib/src/fsplit.c b/lib/src/fsplit.c +index ee8af24..c6fb3cd 100755 +--- a/lib/src/fsplit.c ++++ b/lib/src/fsplit.c +@@ -50,6 +50,7 @@ static char sccsid[] = "@(#)fsplit.c 5.5 (Berkeley) 3/12/91"; + #include <string.h> + #include <sys/types.h> + #include <sys/stat.h> ++#include <unistd.h> + + /* + * usage: fsplit [-e efile] ... [file] +diff --git a/src/clipper_progs/src/pirate/compress42.c b/src/clipper_progs/src/pirate/compress42.c +index ea52e96..30dbd56 100755 +--- a/src/clipper_progs/src/pirate/compress42.c ++++ b/src/clipper_progs/src/pirate/compress42.c +@@ -142,6 +142,7 @@ + #include <sys/types.h> + #include <sys/stat.h> + #include <errno.h> ++#include <unistd.h> + + #ifdef DIRENT + # include <dirent.h> +diff --git a/src/mtz2cif_/mtz2cif.c b/src/mtz2cif_/mtz2cif.c +index e224430..c7b82f4 100755 +--- a/src/mtz2cif_/mtz2cif.c ++++ b/src/mtz2cif_/mtz2cif.c +@@ -28,6 +28,7 @@ + #include "cmtzlib.h" + #include "ccp4_parser.h" + #include "ccp4_general.h" ++#include "ccp4_program.h" + #include "csymlib.h" + #include "mtz2cif_lib.h" + +diff --git a/x-windows/XCCPJIFFY/xplot84driver.c b/x-windows/XCCPJIFFY/xplot84driver.c +index 67e0bf1..76526ab 100755 +--- a/x-windows/XCCPJIFFY/xplot84driver.c ++++ b/x-windows/XCCPJIFFY/xplot84driver.c +@@ -11,6 +11,7 @@ + + #include <stdio.h> + #include <sys/types.h> ++#include <stdlib.h> + + #include <X11/StringDefs.h> + #include <X11/Intrinsic.h> diff --git a/sci-chemistry/ccp4-apps/files/6.1.3-lapack.patch b/sci-chemistry/ccp4-apps/files/6.1.3-lapack.patch new file mode 100644 index 000000000000..62892db01147 --- /dev/null +++ b/sci-chemistry/ccp4-apps/files/6.1.3-lapack.patch @@ -0,0 +1,597 @@ +diff --git a/configure b/configure +index 833f483..bcfa62d 100755 +--- a/configure ++++ b/configure +@@ -3226,574 +3226,14 @@ else + echo + echo "Warning: this option has not been extensively tested!" + echo "Please report problems to ccp4@ccp4.ac.uk" +- # Search for vendor LAPACK/BLAS first +- if test ! "$with_netlib_lapack" ; then +- # Initialise variables to blank +- lapackdir= +- XLAPACK_LIB= +- # Possible directories to check for vendor or pre-existing LAPACK or +- # BLAS - add to these if you want to test others +- trydirs="`echo $LD_LIBRARY_PATH |sed -e s/:/\ /g` /lib /usr/lib /usr/local/lib" +- # Possible library names +- # These are the names like xxxx where the library will be libxxxx.a +- # or libxxxx.so +- echo +- echo "Guessing names for native/vendor LAPACK and/or BLAS libraries" +- echo "on this system" +- case $system in +- linux | linux64 | linux32 ) +- # linux users will usually have them in /usr/lib but don't call it +- trylapack="lapack" +- tryblas="blas" +- # if code is non_shared then this can lead to problems. both blas and lapack +- # need to be resolved even if they are not called! +- if test "$non_shared" = yes; then +- echo "You are compiling linux non_shared. This sometimes causes problems " +- echo " so checking for requirements." +- echo "Checking: try to link library against test program" +- if test -f testlink.f || test -f testlink ; then +- rm -f testlink* +- fi +- cat > testlink.f <<EOF +- PROGRAM TESTLINK +-C A bit of scala code to test the linking +- real bf(3), bnorm +-c +- integer maxbmt +- parameter (maxbmt = 2) +- double precision B(maxbmt,maxbmt), eigval(maxbmt), +- $ eigvec(maxbmt,maxbmt), w(5*maxbmt) +- integer m, ia, ix, istat +-c +- B(1,1) = 1.00 +- B(1,2) = 1.00 +- B(2,1) = 1.00 +- B(2,2) = 1.00 +-c +- m = maxbmt +- ia = maxbmt +- ix = maxbmt +- call dsyev('N', 'L', m, B, ia, eigval, w, 5*maxbmt, istat) +- end +-EOF +- #firstly test without -lblas +- test_compile="$FC $FOPTIM $XFFLAGS -o testlink testlink.f -llapack" +- 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" +- # Set the next two variables so that configure +- # doesn't try to build netlib libraries +- LAPACKLIB="lapack" +- noblas=yes +- trylapack= +- tryblas= +- else +- echo "more than just -llapack needed...." +- test_compile="$FC $FOPTIM $XFFLAGS -o testlink testlink.f -llapack -lblas" +- echo $test_compile +- if { (eval $test_compile ) 2>&1; } && test -s testlink ; then +- # Compilation was okay +- echo "...-llapack and -lblas were needed" +- XLAPACK_LIB="-llapack -lblas" +- # Set the next two variables so that configure +- # doesn't try to build netlib libraries +- LAPACKLIB="lapack blas" +- noblas=no +- trylapack= +- tryblas= +- else +- echo "....could not find either lapack or blas." +- fi +- fi +- fi +- # add 64 bit libs +- case $system in +- linux64 ) trydirs="/usr/lib64 ${trydirs}" ;; +- esac +- +- ;; +- osf1) +- # OSF1 has dxml (old version) and cxml +- # which should have both lapack and blas +- trylapack="dxml cxml" +- tryblas= +- trydirs="${trydirs} /usr/shlib" +- ;; +- irix) +- # Additional search paths for IRIX +- trydirs="${trydirs} /usr/lib32" +- # SCSL should have both LAPACK and BLAS +- trylapack="scs" +- tryblas="blas" +- ;; +- irix64) +- # Additional search paths for IRIX64 +- trydirs="${trydirs} /usr/lib64" +- # SCSL should have both LAPACK and BLAS +- trylapack="scs" +- tryblas="blas" +- # Extra compiler flags? +- #XLAPACKFLAGS="-OPT:IEEE_NaN_inf=ON" +- ;; +- aix) +- # Additional search paths for AIX +- trydirs="${trydirs}" +- # AIX might have ESSL library - blas only I think +- trylapack= +- tryblas="essl" +- ;; +- hpux) +- # Additional search paths for HPUX +- trydirs="${trydirs} /opt/fortran/lib /opt/fortran/lib/pa2.0 /opt/mlib/lib/pa2.0" +- # HPUX should have both LAPACK (part of mlib) and BLAS +- trylapack="lapack" +- tryblas="blas" +- # Extra compiler flags? +- # +U77 required for ETIME function - this is already in XFFLAGS +- #XLAPACKFLAGS="+U77" +- ;; +- +- sunos | sunos64) +- # Sun has libraries with BLAS and LAPACK invoked using +- # -xlic_lib=sunperf +- trylapack= +- tryblas= +- echo "SunOs can use the Sun Performance Library (if installed)" +- echo "which has both BLAS and LAPACK 3.0" +- echo +- echo "Looking for a valid library to use..." +- echo +- # Loop over the possible library names +- try_libs="sunperf" +- for testlib in $try_libs +- do +- if test ! "$XLAPACK_LIB" ; then +- # Try running a test compile to see if this a valid library +- if test -f testlink.f || test -f testlink ; then +- rm -f testlink* +- fi +- cat > testlink.f <<EOF +-c Test fortran program to link against library +- PROGRAM TESTLINK +- IMPLICIT NONE +- INTEGER A +- A = 1 +- STOP +- END +-EOF +- test_compile="$FC $FOPTIM $XFFLAGS -o testlink testlink.f -dalign -xlic_lib=$testlib" +- echo $test_compile +- if { (eval $test_compile ) 2>&1; } && test -s testlink ; then +- # Compilation was okay +- echo "... -xlic_lib=$testlib is okay" +- XLAPACK_LIB="-dalign -xlic_lib=$testlib" +- # Set the next two variables so that configure +- # doesn't try to build netlib libraries +- LAPACKLIB="$testlib" +- noblas=yes +- else +- # Compilation failed +- echo "... cannot use -xlic_lib=$testlib" +- fi +- # End of test for testlib +- fi +- # End of loop over possible lib names +- done +- # Report if no suitable library was found +- if test ! "$XLAPACK_LIB" ; then +- echo +- echo "No suitable LAPACK library was found." +- echo "This may be because the Sun Performance Library is not" +- echo "installed on your system" +- echo "Contact your system administrator or Sun vendor" +- fi +- ;; +- Darwin | Darwin32 | Darwin64 ) +- # Darwin has libraries with BLAS and LAPACK invoked using +- # -framework vecLib +- echo "Darwin can use the vecLib Library (if installed)" +- echo "which has both BLAS and LAPACK 3.0" +- echo +- # This is a special case so try running a test compile +- echo "Checking: try to link library against test program" +- if test -f testlink.f || test -f testlink ; then +- rm -f testlink* +- fi +- cat > testlink.f <<EOF +-c Test fortran program to link against library +- PROGRAM TESTLINK +- IMPLICIT NONE +- INTEGER A +- A = 1 +- STOP +- END +-EOF +- test_compile="$FC $FOPTIM $XFFLAGS -o testlink testlink.f -framework vecLib" +- echo $test_compile +- if { (eval $test_compile ) 2>&1; } && test -s testlink ; then +- # Compilation was okay +- echo "... -framework vecLib is okay" +- XLAPACK_LIB="-framework vecLib" +- # Set the next two variables so that configure +- # doesn't try to build netlib libraries +- LAPACKLIB="vecLib" +- noblas=yes +- else +-#alternative linking for vecLib libraries +- case `uname -sr` in +- *Darwin\ 7.* ) test_compile="$FC $FOPTIM $XFFLAGS -o testlink testlink.f -lcc_dynamic -Wl,-framework -Wl,vecLib" ;; +- * ) test_compile="$FC $FOPTIM $XFFLAGS -o testlink testlink.f -Wl,-framework -Wl,vecLib" ;; +- esac +- +- echo $test_compile +- if { (eval $test_compile ) 2>&1; } && test -s testlink ; then +- # Compilation was okay +- echo "... -framework vecLib is okay" +- XLAPACK_LIB="-Wl,-framework -Wl,vecLib" +- # Set the next two variables so that configure +- # doesn't try to build netlib libraries +- LAPACKLIB="-Wl,-framework -Wl,vecLib" +- noblas=yes +- else +- # Compilation failed +- echo "... cannot use -framework vecLib" +- echo +- fi +- fi +- trylapack= +- tryblas= +-# try the fink installation +- trydirs="${trydirs} /sw" +- ;; +- Darwin_ibm_compilers ) +- # Darwin has libraries with BLAS and LAPACK invoked using +- # -framework vecLib +- echo "Darwin can use the vecLib Library (if installed)" +- echo "which has both BLAS and LAPACK 3.0" +- echo +- # This is a special case so try running a test compile +- echo "Checking: try to link library against test program" +- if test -f testlink.f || test -f testlink ; then +- rm -f testlink* +- fi +- cat > testlink.f <<EOF +-c Test fortran program to link against library +- PROGRAM TESTLINK +- IMPLICIT NONE +- INTEGER A +- A = 1 +- STOP +- END +-EOF +- case `uname -sr` in +- Darwin\ 8* ) +- XLAPACK_LIB="-L/System/Library/Frameworks/Accelerate.framework/Versions/A/Frameworks/vecLib.framework/Versions/A -lLAPACK -lBLAS" +- test_compile="$FC $FOPTIM $XFFLAGS -o testlink testlink.f $XLAPACK_LIB" +- ;; +- Darwin\ 7* ) +- XLAPACK_LIB="-L/System/Library/Frameworks/Accelerate.framework/Versions/A/Frameworks/vecLib.framework/Versions/A -lLAPACK -lBLAS" +- test_compile="$FC $FOPTIM $XFFLAGS -o testlink testlink.f -lcc_dynamic $XLAPACK_LIB" +- ;; +- *) +- XLAPACK_LIB="/System/Library/Frameworks/vecLib.Framework/Versions/Current/VecLib" +- test_compile="$FC $FOPTIM $XFFLAGS -o testlink testlink.f $XLAPACK_LIB" +- esac +- echo $test_compile +- if { (eval $test_compile ) 2>&1; } && test -s testlink ; then +- # Compilation was okay +- echo "... -framework vecLib is okay" +- # Set the next two variables so that configure +- # doesn't try to build netlib libraries +- LAPACKLIB="vecLib" +- noblas=yes +- else +- # Compilation failed +- XLAPACK_LIB="" +- echo "... cannot use -framework vecLib" +- echo +- fi +- trylapack= +- tryblas= +-# try the fink installation +- trydirs="${trydirs} /sw" +- ;; +- +- Darwin_intel_compilers) +- # Darwin has libraries with BLAS and LAPACK invoked using +- # -F vecLib +- echo "Darwin can use the vecLib Library (if installed)" +- echo "which has both BLAS and LAPACK 3.0" +- echo +- # This is a special case so try running a test compile +- echo "Checking: try to link library against test program" +- if test -f testlink.f || test -f testlink ; then +- rm -f testlink* +- fi +- cat > testlink.f <<EOF +-c Test fortran program to link against library +- PROGRAM TESTLINK +- IMPLICIT NONE +- INTEGER A +- A = 1 +- STOP +- END +-EOF +- test_compile="$FC $FOPTIM $XFFLAGS -o testlink testlink.f -Wl,-framework -Wl,vecLib" +- echo $test_compile +- if { (eval $test_compile ) 2>&1; } && test -s testlink ; then +- # Compilation was okay +- # doesn't try to build netlib libraries +- XLAPACK_LIB="-F /System/Library/Frameworks -Qoption,ld,-framework -Qoption,ld,vecLib" +- LAPACKLIB="vecLib" +- noblas=yes +- else +- # Compilation failed +- echo "... cannot use -framework vecLib" +- echo +- fi +- trylapack= +- tryblas= +-# try the fink installation +- trydirs="${trydirs} /sw" +- ;; +- +-# linux_ia64_sgi_altix) +-# SGI Japan +- ia64_linux_intel) +- # Additional search paths for Linux/IA64 +- trydirs="${trydirs} /opt/scsl/lib /usr/lib /usr/local/lib" +- # SCSL and MKL should have both LAPACK and BLAS +- trylapack="mkl_lapack scs lapack" +- tryblas="mkl scs blas" +- ;; +- linux_ibm_compilers ) +- trylapack="lapack" +- tryblas="blas" +- ;; +- linux64_ibm_compilers ) +- trydirs="/usr/lib64 ${trydirs}" +- trylapack="lapack" +- tryblas="blas" +- ;; +- linux_intel_compilers ) +- trydirs="/usr/lib64 ${trydirs}" +- trylapack="mkl_lapack lapack" +- tryblas="mkl blas" +- ;; +- *) +- echo "The guesses for this system may not be correct - please" +- echo "e-mail ccp4@ccp4.ac.uk if you have any extra information" +- echo +- # Default guess is just libblas +- trylapack="lapack" +- tryblas="blas" +- ;; +- esac +- # +- # Search for LAPACK libraries +- # +- # Write out what the guesses are +- if test "$trylapack" ; then +- echo "Possible LAPACK library names for this system:" +- for libname in $trylapack +- do +- echo " lib$libname" +- done +- # Possible library name extensions +- tryexts="a so dylib" +- # Now loop over all the possibilities and see if anything +- # turns up +- echo +- echo "Searching for libraries with LAPACK and BLAS:" +- for testdir in $trydirs +- do +- for testlib in $trylapack +- do +- for ext in $tryexts +- do +- if test ! "$LAPACKLIB"; then +- if test -s "$testdir/lib$testlib.$ext" ; then +- echo "...found LAPACK library: $testdir/lib$testlib.$ext" +- # Now try and link to a test program +- # This is really for IRIX where libraries can be +- # o32 or n32 +- echo " Testing: try to link library against test program" +- if test -f testlink.f || test -f testlink ; then +- rm -f testlink* +- fi +- cat > testlink.f <<EOF +-c Test fortran program to link against library +- PROGRAM TESTLINK +- IMPLICIT NONE +- INTEGER A +- A = 1 +- 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" +- echo $test_compile +- if { (eval $test_compile ) 2>&1; } && test -s testlink ; then +- have_lapack=yes +- else +-# cover clapack option +- echo $test_ccompile +- if { (eval $test_ccompile ) 2>&1; } && test -s testlink ; then +- have_lapack=yes +- fi +- fi +- if test x$have_lapack = xyes ; then +- # This one is okay +- LAPACKLIB="$testlib" +- LAPACKDIR="$testdir" +- echo "Link ok - using lib$LAPACKLIB from $LAPACKDIR" +- # +- XLAPACK_LIB="-L$LAPACKDIR -l$LAPACKLIB" +- # +- # Test to see if we need BLAS too +- # Do this by trying to compile a test program +- # Use the LSAME test for now +- echo +- echo " * Checking whether we need a separate BLAS library *" +- echo " Testing: try linking library against test program" +- cd lib/lapack/test +- if test -f testlsame ; then +- rm -f testsame testlsame.o +- fi +- test_compile="$FC $FOPTIM $XFFLAGS -o testlsame lsametst.f -L$LAPACKDIR -l$LAPACKLIB" +- test_ccompile="$FC $FOPTIM $XFFLAGS -o testlsame lsametst.f -L$LAPACKDIR -l$LAPACKLIB $XLDFLAGS" +- echo $test_compile +- if { ( eval $test_compile) 2>&1;} && test -s testlsame ; then +- have_blas=yes +- else +-#cblas route +- echo $test_ccompile +- if { ( eval $test_ccompile) 2>&1;} && test -s testlsame ; then +- have_blas=yes +- fi +- fi +- if test x$have_blas = xyes ; then +- echo "Test program okay - additional separate BLAS not required" +- noblas=yes +- else +- echo "Test program failed - need a separate BLAS library" +- fi +- cd ../../.. +- else +- # Keep looking +- echo " link failed - cannot use lib$testlib" +- fi +- fi +- fi +- done +- done +- if test ! "$LAPACKLIB"; then +- echo "...nothing in $testdir" +- fi +- done +- fi +- +- # If LAPACKLIB hasn't been set at this point then no LAPACK library +- # was found +- if test ! "$LAPACKLIB" ; then +- echo +- echo "No pre-existing LAPACK library found - NetLib LAPACK will be built instead" +- make_lapack=lapacklib +- fi +- # Look for possible BLAS +- if test ! "$noblas" ; then +- if test "$tryblas" ; then +- echo +- echo "Possible BLAS library names for this system:" +- for libname in $tryblas +- do +- echo " lib$libname" +- done +- # Possible library name extensions +- tryexts="a so" +- # Now loop over all the possibilities and see if anything +- # turns up +- echo +- echo "Searching for libraries with BLAS:" +- for testdir in $trydirs +- do +- for testlib in $tryblas +- do +- for ext in $tryexts +- do +- if test ! "$BLASLIB"; then +- if test -s "$testdir/lib$testlib.$ext" ; then +- echo "...found BLAS library: $testdir/lib$testlib.$ext" +- # Now try and link to a test program +- # This is really for IRIX where libraries can be +- # o32 or n32 +- echo " Testing: try to link library against test program" +- if test -f testlink.f || test -f testlink ; then +- rm -f testlink* +- fi +- cat > testlink.f <<EOF +-c Test fortran program to link against library +- PROGRAM TESTLINK +- IMPLICIT NONE +- INTEGER A +- A = 1 +- 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" +- echo $test_compile +- if { ( eval $test_compile) 2>&1;} && test -s testlink ; then +- have_blas=yes +- else +- echo $test_ccompile +- if { ( eval $test_compile) 2>&1;} && test -s testlink ; then +- have_blas=yes +- fi +- fi +- if test x$have_blas = xyes ; then +- # This one is okay +- BLASLIB="$testlib" +- BLASDIR="$testdir" +- BLASEXT="$ext" +- echo "Link ok - using lib$BLASLIB from $BLASDIR" +- XLAPACK_LIB="$XLAPACK_LIB -L$BLASDIR -l$BLASLIB" +- else +- # Keep looking +- echo " link failed - cannot use lib$testlib" +- fi +- fi +- fi +- done +- done +- if test ! "$BLASLIB"; then +- echo "...nothing in $testdir" +- fi +- done +- fi +- # Do we need to build BLAS too? +- if test ! "$BLASLIB" ; then +- echo +- echo "No pre-existing BLAS library was found - NetLib BLAS will be built instead" +- echo "This may result in poorer performance of the LAPACK routines" +- make_blas=blaslib +- BLASLIB=blas +- BLASDIR="$srcdir/lib/lapack" +- BLASEXT="a" +- fi +- fi ++ # gentoo is clever ++ make_blas= ++ make_lapack= ++ BLASLIB=$(${PKG_CONFIG} --libs blas) ++ LAPACKLIB=$(${PKG_CONFIG} --libs lapack) ++ XLAPACK_LIB="${BLASLIB} ${LAPACKLIB}" ++ XFFLAGS_LAPACK="$(${PKG_CONFIG} --cflags lapack blas)" + # Otherwise force building of NetLib BLAS and LAPACK libs +- else +- echo +- echo "! Force building of NetLib BLAS and LAPACK..." +- make_blas=blaslib +- make_lapack=lapacklib +- BLASLIB=blas +- BLASDIR="$srcdir/lib/lapack" +- BLASEXT="a" +- fi + # need to know if we the lapack library was linked using the C or + # fortran linker + if test -f testlink.f || test -f testlink || test -f testlink.c ; then +@@ -3916,8 +3356,8 @@ RANLIB = ${RANLIB} + INSTALL_DATA = ${INSTALL_DATA} + libdir = $libdir + # +-BLASLIB = lib${BLASLIB}.${BLASEXT} +-LAPACKLIB = liblapack.a ++BLASLIB = ${BLASLIB} ++LAPACKLIB = ${LAPACKLIB} + # + # These variables define targets in the main Makefile + blaslib = ${make_blas} diff --git a/sci-chemistry/ccp4-apps/files/6.1.3-pisa.patch b/sci-chemistry/ccp4-apps/files/6.1.3-pisa.patch new file mode 100644 index 000000000000..9d8fefe965e5 --- /dev/null +++ b/sci-chemistry/ccp4-apps/files/6.1.3-pisa.patch @@ -0,0 +1,23 @@ +diff --git a/src/pisa/sbase/Makefile.am b/src/pisa/sbase/Makefile.am +index 053e83a..4ff3394 100755 +--- a/src/pisa/sbase/Makefile.am ++++ b/src/pisa/sbase/Makefile.am +@@ -1,4 +1,4 @@ +-pkgdatadir = $(datadir)/sbase ++pkgdatadir = $(datadir)/pisa/sbase + dist_pkgdata_DATA = \ + graph.sbase index.sbase struct.sbase + +diff --git a/src/pisa/sbase/Makefile.in b/src/pisa/sbase/Makefile.in +index faa3f7f..8630bd7 100755 +--- a/src/pisa/sbase/Makefile.in ++++ b/src/pisa/sbase/Makefile.in +@@ -62,7 +62,7 @@ POST_UNINSTALL = : + EXEEXT = @EXEEXT@ + OBJEXT = @OBJEXT@ + PATH_SEPARATOR = @PATH_SEPARATOR@ +-pkgdatadir = $(datadir)/sbase ++pkgdatadir = $(datadir)/pisa/sbase + AMTAR = @AMTAR@ + AR_FLAGS = @AR_FLAGS@ + AWK = @AWK@ diff --git a/sci-chemistry/ccp4-apps/files/6.1.3-pythonpath.patch b/sci-chemistry/ccp4-apps/files/6.1.3-pythonpath.patch new file mode 100644 index 000000000000..7a012be6ef02 --- /dev/null +++ b/sci-chemistry/ccp4-apps/files/6.1.3-pythonpath.patch @@ -0,0 +1,65 @@ +diff --git a/ccp4-6.1.2/include/ccp4.setup-bash b/ccp4-6.1.2/include/ccp4.setup-bash +index 9848101..cea8ae6 100755 +--- a/ccp4-6.1.2/include/ccp4.setup-bash ++++ b/ccp4-6.1.2/include/ccp4.setup-bash +@@ -188,9 +188,9 @@ fi + #Python path for the subprocess fixed module + + if [ $ccp4_first_in_path -eq 1 ]; then +- setenv PYTHONPATH ${CCP4}/share/python:${PYTHONPATH} ++ setenv PYTHONPATH ${CCP4}/share/ccp4/smartie:${CCP4I_TOP}/python:${PYTHONPATH} + else +- setenv PYTHONPATH ${PYTHONPATH}:${CCP4}/share/python ++ setenv PYTHONPATH ${PYTHONPATH}:${CCP4}/share/ccp4/smartie:${CCP4I_TOP}/python + fi + + ### PLOT_COMMAND PRINT_COMMAND for the XCCPJIFFY programs to compile ### +diff --git a/ccp4-6.1.2/include/ccp4.setup-csh b/ccp4-6.1.2/include/ccp4.setup-csh +index 42f0820..93c2cf3 100755 +--- a/ccp4-6.1.2/include/ccp4.setup-csh ++++ b/ccp4-6.1.2/include/ccp4.setup-csh +@@ -180,9 +180,9 @@ endif + #Python path for the subprocess fixed module + if (${?PYTHONPATH}) then + if ($ccp4_first_in_path) then +- setenv PYTHONPATH ${CCP4}/share/python:${PYTHONPATH} ++ setenv PYTHONPATH ${CCP4}/share/ccp4/smartie:${CCP4I_TOP}/python:${PYTHONPATH} + else +- setenv PYTHONPATH ${PYTHONPATH}:${CCP4}/share/python ++ setenv PYTHONPATH ${PYTHONPATH}:${CCP4}/share/ccp4/smartie:${CCP4I_TOP}/python + endif + else + setenv PYTHONPATH ${CCP4}/share/python +diff --git a/ccp4-6.1.2/include/ccp4.setup-sh b/ccp4-6.1.2/include/ccp4.setup-sh +index 4396ebf..a0455bd 100755 +--- a/ccp4-6.1.2/include/ccp4.setup-sh ++++ b/ccp4-6.1.2/include/ccp4.setup-sh +@@ -228,9 +228,9 @@ test -r $CCP4/include/ccp4.msg && cat $CCP4/include/ccp4.msg + #Python path for the subprocess fixed module + + if test $ccp4_first_in_path -eq 1; then +- export PYTHONPATH=${CCP4}/share/python:${PYTHONPATH} ++ export PYTHONPATH=${CCP4}/share/ccp4/smartie:${CCP4I_TOP}/python:${PYTHONPATH} + else +- export PYTHONPATH=${PYTHONPATH}:${CCP4}/share/python ++ export PYTHONPATH=${PYTHONPATH}:${CCP4}/share/ccp4/smartie:${CCP4I_TOP}/python + fi + + ################### THE REST SHOULDN'T NEED EDITING ##################### +diff --git a/ccp4-6.1.2/include/ccp4.setup-zsh b/ccp4-6.1.2/include/ccp4.setup-zsh +index 0e5c2ce..53523f3 100755 +--- a/ccp4-6.1.2/include/ccp4.setup-zsh ++++ b/ccp4-6.1.2/include/ccp4.setup-zsh +@@ -157,10 +157,10 @@ export CLASSPATH + #Python path for the subprocess fixed module + + if ($ccp4_first_in_path) then +- PYTHONPATH=${CCP4}/share/python:${PYTHONPATH} ++ PYTHONPATH=${CCP4}/share/ccp4/smartie:${CCP4I_TOP}/python:${PYTHONPATH} + export PYTHONPATH + else +- PYTHONPATH=${PYTHONPATH}:${CCP4}/share/python ++ PYTHONPATH=${PYTHONPATH}:${CCP4}/share/ccp4/smartie:${CCP4I_TOP}/python + export PYTHONPATH + fi + diff --git a/sci-chemistry/ccp4-apps/files/6.1.3-rename-rapper-ng.patch b/sci-chemistry/ccp4-apps/files/6.1.3-rename-rapper-ng.patch new file mode 100644 index 000000000000..a5144cfa5d33 --- /dev/null +++ b/sci-chemistry/ccp4-apps/files/6.1.3-rename-rapper-ng.patch @@ -0,0 +1,60 @@ +diff --git a/src/Makefile.in b/src/Makefile.in +index 70781f3..b2dcc25 100755 +--- a/src/Makefile.in ++++ b/src/Makefile.in +@@ -760,7 +760,7 @@ chainsawobjs = chainsaw.o + pdbcur : $(pdbcurobjs) + @$(SETFLAGS) ; rm -f pdbcur; eval $(CXX) $${mmdb_app_FLAGS-"$(CXXFLAGS)"} -o pdbcur $(pdbcurobjs) $(LDCXXFLAGS) + ncont : $(ncontobjs) +- @$(SETFLAGS) ; rm -f ncont; eval $(CXX) $${mmdb_app_FLAGS-"$(CXXFLAGS)"} -o ncont $(ncontobjs) $(LDCXXFLAGS) ++ @$(SETFLAGS) ; rm -f ncont; eval $(CXX) $${mmdb_app_FLAGS-"$(CXXFLAGS)"} -o ncont $(ncontobjs) $(LDCXXFLAGS) -lmmdb + coord_format : $(coord_formatobjs) + @$(SETFLAGS) xxx=1 ; \ + rm -f coord_format; \ +diff --git a/src/rapper/LOOP/Makefile.am b/src/rapper/LOOP/Makefile.am +index 85f212e..2608c6d 100755 +--- a/src/rapper/LOOP/Makefile.am ++++ b/src/rapper/LOOP/Makefile.am +@@ -15,12 +15,12 @@ params.cpp typed_value.cpp misc.cpp residue.cpp atom.cpp psa.cpp edm_sidechains. + hash_table.cpp surface.cpp parse.cpp band.cpp edensity.cpp read_map.cpp iterator.cpp \ + residue_range.cpp pop_search_frags.cpp saxs.cpp lib_choral.cpp pdf.cpp WeightedDistribMean.cpp + +-rapper_LDADD = ../gc7.0/libgc.la ../libxml2/libxml2.la ++rapper_LDADD = @GC_LIBS@ @LIBXML_LIBS@ + + pkgdatadir = $(datadir)/rapper + dist_pkgdata_DATA = params.xml + +-INCLUDES = -I. -I../gc7.0/include -I../libxml2/include ++INCLUDES = -I. @LIBXML_CFLAGS@ @GC_CFLAGS@ + #SUBDIRS = \ + #@PYTHON_USE_TRUE@ python + +diff --git a/src/rapper/Makefile.am b/src/rapper/Makefile.am +index e78b10d..486b931 100755 +--- a/src/rapper/Makefile.am ++++ b/src/rapper/Makefile.am +@@ -1,3 +1,3 @@ +-SUBDIRS = libxml2 gc7.0 LOOP data ++SUBDIRS = LOOP data + + EXTRA_DIST = +diff --git a/src/rapper/configure.ac b/src/rapper/configure.ac +index 5e4ef69..268a579 100755 +--- a/src/rapper/configure.ac ++++ b/src/rapper/configure.ac +@@ -48,6 +48,13 @@ AM_CONDITIONAL(AMDEP, test "x$enable_dependency_tracking" != xno) + + AC_SUBST(rapper_LDFLAGS) + +-AC_CONFIG_SUBDIRS([gc7.0 libxml2]) ++PKG_CHECK_MODULES([LIBXML],[libxml-2.0]) ++AC_SUBST([LIBXML_CFLAGS]) ++AC_SUBST([LIBXML_LIBS]) ++ ++PKG_CHECK_MODULES([GC],[bdw-gc]) ++AC_SUBST([GC_CFLAGS]) ++AC_SUBST([GC_LIBS]) ++ + #AC_OUTPUT(Makefile LOOP/Makefile LOOP/python/Makefile data/Makefile) + AC_OUTPUT(Makefile LOOP/Makefile data/Makefile) diff --git a/sci-chemistry/ccp4-apps/files/6.1.3-unbundle.patch b/sci-chemistry/ccp4-apps/files/6.1.3-unbundle.patch new file mode 100644 index 000000000000..107cfd740238 --- /dev/null +++ b/sci-chemistry/ccp4-apps/files/6.1.3-unbundle.patch @@ -0,0 +1,131 @@ + src/Makefile.in | 14 +++++----- + src/pisa/configure.ac | 67 +++++++++---------------------------------------- + 2 files changed, 19 insertions(+), 62 deletions(-) + +diff --git a/src/Makefile.in b/src/Makefile.in +index 70781f3..b11db04 100755 +--- a/src/Makefile.in ++++ b/src/Makefile.in +@@ -778,8 +778,8 @@ chainsaw : $(chainsawobjs) + eval $(CXX) $${mmdb_app_FLAGS-"$(CXXFLAGS)"} -o chainsaw $(chainsawobjs) $(LDCXXFLAGS) + pdbcur.o pcur_funcs.o ncont.o coord_format.o pdb_merge.o chainsaw.o: # dependencies at end + @$(SETFLAGS) xxx=1 ; \ +- echo $(CXX) -I$(mmdb_appdir) -I$(incdir) -I$(incdir)/mmdb $${mmdb_app_FLAGS-"$(CXXFLAGS)"} -c -o $@ $(mmdb_appdir)/`basename $@ .o`.cpp ; +- eval $(CXX) -I$(mmdb_appdir) -I$(incdir) -I$(incdir)/mmdb $${mmdb_app_FLAGS-"$(CXXFLAGS)"} -c -o $@ $(mmdb_appdir)/`basename $@ .o`.cpp ++ echo $(CXX) -I$(mmdb_appdir) -I$(incdir) `pkg-config --cflags mmdb` $${mmdb_app_FLAGS-"$(CXXFLAGS)"} -c -o $@ $(mmdb_appdir)/`basename $@ .o`.cpp ; ++ eval $(CXX) -I$(mmdb_appdir) -I$(incdir) `pkg-config --cflags mmdb` $${mmdb_app_FLAGS-"$(CXXFLAGS)"} -c -o $@ $(mmdb_appdir)/`basename $@ .o`.cpp + + ### bp3, afro, gcx + +@@ -813,8 +813,8 @@ gcx : libbp3 $(gcxobjs) + + $(libbp3objs) $(bp3objs) $(afroobjs) $(gcxobjs) : # dependencies at end + @$(SETFLAGS) xxx=1 ; \ +- echo $(CXX) -I$(bp3dir) -I$(incdir) -I$(incdir)/mmdb $${bp3_FLAGS-"$(CXXFLAGS)"} -c -o $@ $(bp3dir)/`basename $@ .o`.C ; \ +- eval $(CXX) -I$(bp3dir) -I$(incdir) -I$(incdir)/mmdb $${bp3_FLAGS-"$(CXXFLAGS)"} -c -o $@ $(bp3dir)/`basename $@ .o`.C ++ echo $(CXX) -I$(bp3dir) -I$(incdir) `pkg-config --cflags mmdb` $${bp3_FLAGS-"$(CXXFLAGS)"} -c -o $@ $(bp3dir)/`basename $@ .o`.C ; \ ++ eval $(CXX) -I$(bp3dir) -I$(incdir) `pkg-config --cflags mmdb` $${bp3_FLAGS-"$(CXXFLAGS)"} -c -o $@ $(bp3dir)/`basename $@ .o`.C + + ### crunch2 pmf + +@@ -853,7 +853,7 @@ cif2xml : $(cif2xmlobjs) + cross_validate : $(cross_validateobjs) + @$(SETFLAGS); rm -f cross_validate; eval $(CXX) $${harvest_app_FLAGS-"$(CXXFLAGS)"} -o cross_validate $(cross_validateobjs) $(LDCXXFLAGS) + cif2xml.o cross_validate.o : # dependencies at end +- @$(SETFLAGS); eval $(CXX) -I$(harvest_appdir) -I$(incdir) -I$(incdir)/mmdb $${harvest_app_FLAGS-"$(CXXFLAGS)"} -c -o $@ $(harvest_appdir)/`basename $@ .o`.cpp ++ @$(SETFLAGS); eval $(CXX) -I$(harvest_appdir) -I$(incdir) `pkg-config --cflags mmdb` $${harvest_app_FLAGS-"$(CXXFLAGS)"} -c -o $@ $(harvest_appdir)/`basename $@ .o`.cpp + + pdb_extractdir = $(srcdir)/harvest_app_/pdb_extract + pdb_extract_suite : +@@ -873,8 +873,8 @@ $(dev_tools_ctargets) : + $(dev_tools_cxxtargets) : + @$(SETFLAGS) xxx=1; \ + rm -f $@; \ +- echo $(CXX) $${dev_tools_FLAGS-"$(CXXFLAGS)"} -o $@ $(dev_toolsdir)/$@.cpp -I$(incdir) -I$(incdir)/mmdb $(LDCXXFLAGS) ;\ +- eval $(CXX) $${dev_tools_FLAGS-"$(CXXFLAGS)"} -o $@ $(dev_toolsdir)/$@.cpp -I$(incdir) -I$(incdir)/mmdb $(LDCXXFLAGS) ++ echo $(CXX) $${dev_tools_FLAGS-"$(CXXFLAGS)"} -o $@ $(dev_toolsdir)/$@.cpp -I$(incdir) `pkg-config --cflags mmdb` $(LDCXXFLAGS) ;\ ++ eval $(CXX) $${dev_tools_FLAGS-"$(CXXFLAGS)"} -o $@ $(dev_toolsdir)/$@.cpp -I$(incdir) `pkg-config --cflags mmdb` $(LDCXXFLAGS) + + ### mlphare + mlphare: +diff --git a/src/pisa/configure.ac b/src/pisa/configure.ac +index 81afdda..044b6f8 100755 +--- a/src/pisa/configure.ac ++++ b/src/pisa/configure.ac +@@ -31,64 +31,21 @@ AC_CHECK_FUNCS([floor pow rint sqrt]) + # test for function in m + AC_CHECK_LIB([m], [sqrt]) + +-dnl Optional: Check for MMDB. +-AM_PATH_MMDB(, +- [ if test "x$mmdb_prefix" != x ; then +- if test "x$ac_MMDB_CXXFLAGS" != x && test "x$ac_MMDB_LDOPTS" = x ; then +- case "$ac_MMDB_CXXFLAGS" in +- *src/mmdb ) +- ac_MMDB_LDOPTS=`echo "$ac_MMDB_CXXFLAGS" | sed s#src/mmdb#src#g` +- ;; +- *include/mmdb ) +- ac_MMDB_LDOPTS=`echo "$ac_MMDB_CXXFLAGS" | sed s#include/mmdb#lib#g` +- ;; +- *) +- esac +- MMDB_CXXFLAGS="$ac_MMDB_CXXFLAGS" +- MMDB_LIBS=`echo "$ac_MMDB_LDOPTS -lmmdb" | sed s#-I#-L#` +- AC_MSG_WARN([assuming library $MMDB_LIBS headers $MMDB_CXXFLAGS]) +- else +- MMDB_CXXFLAGS="-I$mmdb_prefix/src -I$mmdb_prefix/src/mmdb -I$mmdb_prefix/include -I$mmdb_prefix/include/mmdb" +- MMDB_LIBS="-L$mmdb_prefix/src -L$mmdb_prefix/lib -lmmdb" +- AC_MSG_WARN([assuming library $MMDB_LIBS headers $MMDB_CXXFLAGS]) +- fi +- else +- AC_MSG_ERROR([mmdb not found]) +- fi +- ] +-) ++PKG_CHECK_MODULES([MMDB],[mmdb]) ++PKG_CHECK_MODULES([SSM],[ssm]) ++ ++MMDB_CXXFLAGS=${MMDB_CFLAGS} ++ ++AC_SUBST([MMDB_CFLAGS]) ++AC_SUBST([MMDB_CXXFLAGS]) ++AC_SUBST([SSM_CFLAGS]) ++ ++AC_SUBST([MMDB_LIBS]) ++AC_SUBST([SSM_LIBS]) + +-ac_saved_CXXFLAGS=$CXXFLAGS +-ac_saved_LIBS=$LIBS + CXXFLAGS="$CXXFLAGS $MMDB_CXXFLAGS" + LIBS="$MMDB_LIBS $LIBS" +-AM_PATH_SSM(, +- [ if test "x$ssm_prefix" != x ; then +- if test "x$ac_SSM_CXXFLAGS" != x && test "x$ac_SSM_LDOPTS" = x ; then +- case "$ac_SSM_CXXFLAGS" in +- *lib/ssm ) +- ac_SSM_LDOPTS=`echo "$ac_SSM_CXXFLAGS" | sed s#lib/ssm#lib#g` +- ;; +- *include/ssm ) +- ac_SSM_LDOPTS=`echo "$ac_SSM_CXXFLAGS" | sed s#include/ssm#lib#g` +- ;; +- *) +- esac +- SSM_CXXFLAGS="$ac_SSM_CXXFLAGS" +- SSM_LIBS=`echo "$ac_SSM_LDOPTS -lssm" | sed s#-I#-L#` +- AC_MSG_WARN([assuming library $SSM_LIBS headers $SSM_CXXFLAGS]) +- else +- SSM_CXXFLAGS="-I$ssm_prefix/include/ssm -I$ssm_prefix/lib/ssm" +- SSM_LIBS="-L$ssm_prefix/lib -L$ssm_prefix/lib/ssm -lssm" +- AC_MSG_WARN([assuming library $SSM_LIBS headers $SSM_CXXFLAGS]) +- fi +- else +- AC_MSG_ERROR([ssm not found]) +- fi +- ] +-) +-CXXFLAGS=$ac_saved_CXXFLAGS +-LIBS=$ac_saved_LIBS ++ + + # Checks for typedefs, structures, and compiler characteristics. + # diff --git a/sci-chemistry/ccp4-apps/files/ccp4-apps-6.1.3-tcl8.6.patch b/sci-chemistry/ccp4-apps/files/ccp4-apps-6.1.3-tcl8.6.patch new file mode 100644 index 000000000000..4b98545eec83 --- /dev/null +++ b/sci-chemistry/ccp4-apps/files/ccp4-apps-6.1.3-tcl8.6.patch @@ -0,0 +1,130 @@ + src/ccp4mapwish_/c_src/ccp4mapwish_canvas.c | 34 ++++++++++++++--------------- + 1 file changed, 17 insertions(+), 17 deletions(-) + +diff --git a/src/ccp4mapwish_/c_src/ccp4mapwish_canvas.c b/src/ccp4mapwish_/c_src/ccp4mapwish_canvas.c +index 2c9f02f..98d814a 100755 +--- a/src/ccp4mapwish_/c_src/ccp4mapwish_canvas.c ++++ b/src/ccp4mapwish_/c_src/ccp4mapwish_canvas.c +@@ -297,7 +297,7 @@ int canvas_draw_line(char *canvas, int npts, float *x, float *y, char *tags, + puts("canvas_draw_line: about to evaluate the command..."); + } + if (Tcl_Eval(interp,command) != TCL_OK) { +- printf("canvas_draw_line: error from Tcl_Eval: %s",interp->result); ++ printf("canvas_draw_line: error from Tcl_Eval: %s",Tcl_GetStringResult(interp)); + return 0; + } + if (CCP4MAPWISH_CANVAS_DIAG) +@@ -432,7 +432,7 @@ int canvas_draw_rectangle(char *canvas, int npts, float *x, float *y, + puts("canvas_draw_rectangle: about to evaluate the command..."); + } + if (Tcl_Eval(interp,command) != TCL_OK) { +- printf("canvas_draw_rectangle: error from Tcl_Eval: %s",interp->result); ++ printf("canvas_draw_rectangle: error from Tcl_Eval: %s",Tcl_GetStringResult(interp)); + printf("canvas_draw_rectangle:\ncanvas = \"%s\"\ntags = \"%s\"\ncolor = \"%s\"\nunits = \"%c\"\n",canvas,tags,color,units); + return 0; + } +@@ -536,7 +536,7 @@ int canvas_draw_label(char *canvas, char *text, float x, float y, + /* Execute the command which draws the label */ + if (CCP4MAPWISH_CANVAS_DIAG) printf("canvas_draw_label: command is: %s\n",command); + if (Tcl_Eval(interp,command) != TCL_OK) { +- printf("canvas_draw_label: error from Tcl_Eval: %s\n",interp->result); ++ printf("canvas_draw_label: error from Tcl_Eval: %s\n",Tcl_GetStringResult(interp)); + return 0; + } + +@@ -617,7 +617,7 @@ int canvas_scale_canvas(char *canvas, char *tag, float scale) + /* Execute the command which scales the canvas */ + if (CCP4MAPWISH_CANVAS_DIAG) printf("canvas_scale_canvas: command is: %s\n",command); + if (Tcl_Eval(interp,command) != TCL_OK) { +- printf("canvas_scale_canvas: error from Tcl_Eval: %s\n",interp->result); ++ printf("canvas_scale_canvas: error from Tcl_Eval: %s\n",Tcl_GetStringResult(interp)); + return 0; + } + +@@ -706,7 +706,7 @@ int canvas_shift_canvas(char *canvas) + /* Execute the command which resizes the canvas */ + if (CCP4MAPWISH_CANVAS_DIAG) printf("canvas_shift_canvas: command is: %s\n",command); + if (Tcl_Eval(interp,command) != TCL_OK) { +- printf("canvas_shift_canvas: error from Tcl_Eval: %s\n",interp->result); ++ printf("canvas_shift_canvas: error from Tcl_Eval: %s\n",Tcl_GetStringResult(interp)); + return 0; + } + +@@ -789,7 +789,7 @@ int canvas_shift_element(char *canvas, char *tag, int shiftx, int shifty) + /* Execute the command which resizes the canvas */ + if (CCP4MAPWISH_CANVAS_DIAG) printf("canvas_shift_canvas: command is: %s\n",command); + if (Tcl_Eval(interp,command) != TCL_OK) { +- printf("canvas_shift_element: error from Tcl_Eval: %s\n",interp->result); ++ printf("canvas_shift_element: error from Tcl_Eval: %s\n",Tcl_GetStringResult(interp)); + return 0; + } + +@@ -861,7 +861,7 @@ int canvas_delete(char *canvas, char *tag) + /* Execute the command which deletes the tagged items */ + if (CCP4MAPWISH_CANVAS_DIAG) printf("canvas_delete: command is: %s\n",command); + if (Tcl_Eval(interp,command) != TCL_OK) { +- printf("canvas_scale_canvas: error from Tcl_Eval: %s\n",interp->result); ++ printf("canvas_scale_canvas: error from Tcl_Eval: %s\n",Tcl_GetStringResult(interp)); + return 0; + } + +@@ -892,15 +892,15 @@ int canvas_exists(char *canvas) + + sprintf(tmpstr,"winfo exists %s",canvas); + if (Tcl_Eval(interp,tmpstr) != TCL_OK) { +- printf("canvas_exists: error from Tcl_Eval: %s",interp->result); ++ printf("canvas_exists: error from Tcl_Eval: %s",Tcl_GetStringResult(interp)); + return 0; + } + /* Extract a long int using strtol + If no conversion takes place then "endptr" will be equal + to "result" */ +- istatus = (int) strtol(interp->result,&endptr,10); +- if (strcmp(interp->result,endptr) == 0) { +- printf("canvas_exists: bad return status from winfo command \"%s\"\n",interp->result); ++ istatus = (int) strtol(Tcl_GetStringResult(interp),&endptr,10); ++ if (strcmp(Tcl_GetStringResult(interp),endptr) == 0) { ++ printf("canvas_exists: bad return status from winfo command \"%s\"\n",Tcl_GetStringResult(interp)); + return 0; + } + if (!istatus) { +@@ -930,13 +930,13 @@ float canvas_get_tk_scaling(char *canvas, char units) + + /* Execute the tk scaling command */ + if (Tcl_Eval(interp,"tk scaling") != TCL_OK) { +- printf("canvas_get_tk_scaling: error from Tcl_Eval: %s",interp->result); ++ printf("canvas_get_tk_scaling: error from Tcl_Eval: %s",Tcl_GetStringResult(interp)); + return (float) 0.0; + } + + /* Extract a float from the result */ +- tkscale = ((float) strtod(interp->result,&endptr)); +- if (strcmp(interp->result,endptr) == 0) { ++ tkscale = ((float) strtod(Tcl_GetStringResult(interp),&endptr)); ++ if (strcmp(Tcl_GetStringResult(interp),endptr) == 0) { + printf("canvas_get_tk_scaling: couldn't extract scale factor\n"); + return (float) 0.0; + } +@@ -1021,19 +1021,19 @@ int canvas_get_limits(char *canvas, int limits[4]) + + /* Evaluate the command */ + if (Tcl_Eval(interp,command) != TCL_OK) { +- printf("canvas_get_limits: error from Tcl_Eval: %s\n",interp->result); ++ printf("canvas_get_limits: error from Tcl_Eval: %s\n",Tcl_GetStringResult(interp)); + return 0; + } + + /* Process the result - it should consist of 4 integers */ + /* Use strtok which can split the string based on tokens + set by the programmer - in this case a space */ +- if (!interp->result) { ++ if (!Tcl_GetStringResult(interp)) { + puts("canvas_get_limits: failed to fetch canvas limits"); + return TCL_ERROR; + } + i = 0; +- p = strtok(interp->result," "); ++ p = strtok(Tcl_GetStringResult(interp)," "); + if (p == NULL) { + return 0; + } diff --git a/sci-chemistry/ccp4-apps/metadata.xml b/sci-chemistry/ccp4-apps/metadata.xml new file mode 100644 index 000000000000..51fdedab1b38 --- /dev/null +++ b/sci-chemistry/ccp4-apps/metadata.xml @@ -0,0 +1,5 @@ +<?xml version="1.0" encoding="UTF-8"?> +<!DOCTYPE pkgmetadata SYSTEM "http://www.gentoo.org/dtd/metadata.dtd"> +<pkgmetadata> + <herd>sci-chemistry</herd> +</pkgmetadata> |