diff options
Diffstat (limited to 'sci-chemistry/ccp4-apps')
20 files changed, 0 insertions, 1987 deletions
diff --git a/sci-chemistry/ccp4-apps/Manifest b/sci-chemistry/ccp4-apps/Manifest deleted file mode 100644 index e56aec5512a2..000000000000 --- a/sci-chemistry/ccp4-apps/Manifest +++ /dev/null @@ -1,2 +0,0 @@ -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 deleted file mode 100644 index 5e1032133922..000000000000 --- a/sci-chemistry/ccp4-apps/ccp4-apps-6.1.3-r13.ebuild +++ /dev/null @@ -1,395 +0,0 @@ -# Copyright 1999-2015 Gentoo Foundation -# Distributed under the terms of the GNU General Public License v2 -# $Id$ - -EAPI=5 - -PYTHON_COMPAT=( python2_7 ) - -inherit autotools eutils fortran-2 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}/${MY_P}-core-src.tar.gz - https://dev.gentoo.org/~jlec/distfiles/${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} https://dev.gentoo.org/~jlec/science-dist/${PV}-${PATCHDATE}-updates.patch.bz2" - -for i in $(seq $PATCH_TOT); do - NAME="PATCH${i}[1]" - SRC_URI="${SRC_URI} - ${SRC}/${PV}/patches/${!NAME}" -done - -LICENSE="ccp4" -SLOT="0" -KEYWORDS="amd64 ~ppc x86 ~amd64-linux ~x86-linux" -IUSE="examples X" - -X11DEPS=" - x11-libs/libX11 - x11-libs/libXaw - x11-libs/libXt - x11-libs/libxdl_view" - -TKDEPS=" - >=dev-lang/tk-8.3:0= - >=dev-tcltk/blt-2.4 - dev-tcltk/iwidgets - dev-tcltk/itcl - dev-tcltk/itk - >=dev-tcltk/tdom-0.8 - dev-tcltk/tktreectrl" - -SCILIBS=" - ~sci-libs/ccp4-libs-${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 deleted file mode 100644 index 433a78dbd23b..000000000000 --- a/sci-chemistry/ccp4-apps/files/6.1.3-clipper-template.patch +++ /dev/null @@ -1,70 +0,0 @@ ---- 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 deleted file mode 100644 index f1df3e5e19f9..000000000000 --- a/sci-chemistry/ccp4-apps/files/6.1.3-dont-build-balbes.patch +++ /dev/null @@ -1,14 +0,0 @@ -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 deleted file mode 100644 index e62ae12adfbe..000000000000 --- a/sci-chemistry/ccp4-apps/files/6.1.3-dont-build-double-and-make-bindir.patch +++ /dev/null @@ -1,24 +0,0 @@ ---- 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 deleted file mode 100644 index f645643e1c67..000000000000 --- a/sci-chemistry/ccp4-apps/files/6.1.3-dont-build-imosflm.patch +++ /dev/null @@ -1,11 +0,0 @@ ---- 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 deleted file mode 100644 index 1d1323005540..000000000000 --- a/sci-chemistry/ccp4-apps/files/6.1.3-dont-build-libs.patch +++ /dev/null @@ -1,35 +0,0 @@ ---- 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 deleted file mode 100644 index f16b0ecb938c..000000000000 --- a/sci-chemistry/ccp4-apps/files/6.1.3-dont-build-molref.patch +++ /dev/null @@ -1,19 +0,0 @@ ---- 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 deleted file mode 100644 index af4fd8219c4f..000000000000 --- a/sci-chemistry/ccp4-apps/files/6.1.3-dont-build-scala.patch +++ /dev/null @@ -1,42 +0,0 @@ ---- ./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 deleted file mode 100644 index 3af4af503fa6..000000000000 --- a/sci-chemistry/ccp4-apps/files/6.1.3-dont-build-xia.patch +++ /dev/null @@ -1,14 +0,0 @@ ---- 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 $(REFMACTARGETS) dtrek2scala crunch2 pmf - - # targets built from .c sources: - CSIMPLE = pltdev binsort diff --git a/sci-chemistry/ccp4-apps/files/6.1.3-dont-configure.patch b/sci-chemistry/ccp4-apps/files/6.1.3-dont-configure.patch deleted file mode 100644 index 1e59578473ff..000000000000 --- a/sci-chemistry/ccp4-apps/files/6.1.3-dont-configure.patch +++ /dev/null @@ -1,111 +0,0 @@ ---- configure 2009-08-07 12:11:28.000000000 +0200 -+++ configure.new.nolib 2009-08-17 22:30:39.000000000 +0200 -@@ -3113,41 +3113,6 @@ - RX_L="$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 deleted file mode 100644 index 583697cea0a1..000000000000 --- a/sci-chemistry/ccp4-apps/files/6.1.3-dont-make-dirs-in-configure.patch +++ /dev/null @@ -1,87 +0,0 @@ ---- ccp4-6.0.99e.orig/configure 2008-07-31 10:37:22.000000000 -0700 -+++ ccp4-6.0.99e/configure 2008-07-31 10:39:18.000000000 -0700 -@@ -643,45 +643,45 @@ - # echo "! Beware -- the $system installation isn't properly tested." ; } - syswarn='echo; echo "! Beware -- the $system installation is not properly tested."' - --if test -z "$onlylibs" ; then -- for i in CCP4_SCR BINSORT_SCR; do -- if ( eval test -d \$$i || eval mkdir -p \$$i ) ; then : -- else -- eval echo "! No directory \$$i and can\'t create it." -- echo " Check the value of $i." -- badvar=1 -- fi -- done -- -- for i in libdir bindir includedir; do -- if ( eval test -d \$$i || eval mkdir -p \$$i ) ; then : -- else -- eval echo "! No directory \$$i and can\'t create it." -- echo " Check the argument of --$i." -- badvar=1 -- fi -- done -- -- for i in $dotsrc $dotunsupp $dotunsuppsrc $dotdeprec $dotdeprecsrc ./lib ./lib/src ./lib/data ./ccp4i/etc/unix $mosflmdir/lib $mosflmdir/bin $mosflmdir/cbf/lib ; do -- if test -d $i || mkdir $i; then : -- else -- eval echo "! No directory $i and can\'t create it." -- badvar=1 -- fi -- done --else -- # Kludge to fool the "Makefile" target in the top-level CCP4 -- # Makefile into not trying to remake src/Makefile.in -- for i in $srcdir/src $srcdir/lib/src ; do -- if test -d $i || mkdir $i; then -- if ! test -f $i/Makefile.in ; then -- echo -- echo "onlylibs: making dummy file $i/Makefile.in" -- touch $i/Makefile.in -- fi -- fi -- done --fi -+#if test -z "$onlylibs" ; then -+# for i in CCP4_SCR BINSORT_SCR; do -+# if ( eval test -d \$$i || eval mkdir -p \$$i ) ; then : -+# else -+# eval echo "! No directory \$$i and can\'t create it." -+# echo " Check the value of $i." -+# badvar=1 -+# fi -+# done -+# -+# for i in libdir bindir includedir; do -+# if ( eval test -d \$$i || eval mkdir -p \$$i ) ; then : -+# else -+# eval echo "! No directory \$$i and can\'t create it." -+# echo " Check the argument of --$i." -+# badvar=1 -+# fi -+# done -+# -+# for i in $dotsrc $dotunsupp $dotunsuppsrc $dotdeprec $dotdeprecsrc ./lib ./lib/src ./lib/data ./ccp4i/etc/unix $mosflmdir/lib $mosflmdir/bin $mosflmdir/cbf/lib ; do -+# if test -d $i || mkdir $i; then : -+# else -+# eval echo "! No directory $i and can\'t create it." -+# badvar=1 -+# fi -+# done -+#else -+# # Kludge to fool the "Makefile" target in the top-level CCP4 -+# # Makefile into not trying to remake src/Makefile.in -+# for i in $srcdir/src $srcdir/lib/src ; do -+# if test -d $i || mkdir $i; then -+# if ! test -f $i/Makefile.in ; then -+# echo -+# echo "onlylibs: making dummy file $i/Makefile.in" -+# touch $i/Makefile.in -+# fi -+# fi -+# done -+#fi - - ### sanity checks - diff --git a/sci-chemistry/ccp4-apps/files/6.1.3-impl-dec.patch b/sci-chemistry/ccp4-apps/files/6.1.3-impl-dec.patch deleted file mode 100644 index db8236063043..000000000000 --- a/sci-chemistry/ccp4-apps/files/6.1.3-impl-dec.patch +++ /dev/null @@ -1,152 +0,0 @@ -diff --git a/lib/DiffractionImage/Bruker/FRM_LIB.c b/lib/DiffractionImage/Bruker/FRM_LIB.c -index bfda882..f821e04 100755 ---- a/lib/DiffractionImage/Bruker/FRM_LIB.c -+++ b/lib/DiffractionImage/Bruker/FRM_LIB.c -@@ -38,6 +38,8 @@ FRM_LIB: Routines for reading, writing, and handling frame files. - #include "sys/types.h" /* _open, etc. */ - #include "sys/stat.h" /* _open, etc. */ - -+#include <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 deleted file mode 100644 index 62892db01147..000000000000 --- a/sci-chemistry/ccp4-apps/files/6.1.3-lapack.patch +++ /dev/null @@ -1,597 +0,0 @@ -diff --git a/configure b/configure -index 833f483..bcfa62d 100755 ---- a/configure -+++ b/configure -@@ -3226,574 +3226,14 @@ else - echo - echo "Warning: this option has not been extensively tested!" - echo "Please report problems to ccp4@ccp4.ac.uk" -- # Search for vendor LAPACK/BLAS first -- if test ! "$with_netlib_lapack" ; then -- # Initialise variables to blank -- lapackdir= -- XLAPACK_LIB= -- # Possible directories to check for vendor or pre-existing LAPACK or -- # BLAS - add to these if you want to test others -- trydirs="`echo $LD_LIBRARY_PATH |sed -e s/:/\ /g` /lib /usr/lib /usr/local/lib" -- # Possible library names -- # These are the names like xxxx where the library will be libxxxx.a -- # or libxxxx.so -- echo -- echo "Guessing names for native/vendor LAPACK and/or BLAS libraries" -- echo "on this system" -- case $system in -- linux | linux64 | linux32 ) -- # linux users will usually have them in /usr/lib but don't call it -- trylapack="lapack" -- tryblas="blas" -- # if code is non_shared then this can lead to problems. both blas and lapack -- # need to be resolved even if they are not called! -- if test "$non_shared" = yes; then -- echo "You are compiling linux non_shared. This sometimes causes problems " -- echo " so checking for requirements." -- echo "Checking: try to link library against test program" -- if test -f testlink.f || test -f testlink ; then -- rm -f testlink* -- fi -- cat > testlink.f <<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 deleted file mode 100644 index 9d8fefe965e5..000000000000 --- a/sci-chemistry/ccp4-apps/files/6.1.3-pisa.patch +++ /dev/null @@ -1,23 +0,0 @@ -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 deleted file mode 100644 index 7a012be6ef02..000000000000 --- a/sci-chemistry/ccp4-apps/files/6.1.3-pythonpath.patch +++ /dev/null @@ -1,65 +0,0 @@ -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 deleted file mode 100644 index a5144cfa5d33..000000000000 --- a/sci-chemistry/ccp4-apps/files/6.1.3-rename-rapper-ng.patch +++ /dev/null @@ -1,60 +0,0 @@ -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 deleted file mode 100644 index 107cfd740238..000000000000 --- a/sci-chemistry/ccp4-apps/files/6.1.3-unbundle.patch +++ /dev/null @@ -1,131 +0,0 @@ - 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 deleted file mode 100644 index 4b98545eec83..000000000000 --- a/sci-chemistry/ccp4-apps/files/ccp4-apps-6.1.3-tcl8.6.patch +++ /dev/null @@ -1,130 +0,0 @@ - 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 deleted file mode 100644 index 51fdedab1b38..000000000000 --- a/sci-chemistry/ccp4-apps/metadata.xml +++ /dev/null @@ -1,5 +0,0 @@ -<?xml version="1.0" encoding="UTF-8"?> -<!DOCTYPE pkgmetadata SYSTEM "http://www.gentoo.org/dtd/metadata.dtd"> -<pkgmetadata> - <herd>sci-chemistry</herd> -</pkgmetadata> |