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-rw-r--r--sci-libs/ccp4-libs/ChangeLog104
-rw-r--r--sci-libs/ccp4-libs/Manifest40
-rw-r--r--sci-libs/ccp4-libs/ccp4-libs-6.1.1-r4.ebuild209
-rw-r--r--sci-libs/ccp4-libs/ccp4-libs-6.1.1-r6.ebuild209
-rw-r--r--sci-libs/ccp4-libs/ccp4-libs-6.1.1-r7.ebuild214
-rw-r--r--sci-libs/ccp4-libs/ccp4-libs-6.1.1.ebuild192
-rw-r--r--sci-libs/ccp4-libs/ccp4-libs-6.1.2-r1.ebuild213
-rw-r--r--sci-libs/ccp4-libs/ccp4-libs-6.1.2.ebuild210
-rw-r--r--sci-libs/ccp4-libs/ccp4-libs-6.1.3-r1.ebuild210
-rw-r--r--sci-libs/ccp4-libs/files/6.0.2-ppc-double-define-gerror.patch11
-rw-r--r--sci-libs/ccp4-libs/files/6.1.1-dont-make-dirs-in-configure.patch87
-rw-r--r--sci-libs/ccp4-libs/files/6.1.1-glibc2.10.patch22
-rw-r--r--sci-libs/ccp4-libs/files/6.1.1-link-proberly.patch255
-rw-r--r--sci-libs/ccp4-libs/files/6.1.2-64bit.patch205
-rw-r--r--sci-libs/ccp4-libs/files/6.1.2-ccif-shared.patch33
-rw-r--r--sci-libs/ccp4-libs/files/6.1.2-dont-build-mmdb.patch26
-rw-r--r--sci-libs/ccp4-libs/files/6.1.2-dont-make-dirs-in-configure.patch87
-rw-r--r--sci-libs/ccp4-libs/files/6.1.2-glibc2.10.patch22
-rw-r--r--sci-libs/ccp4-libs/files/6.1.2-link-proberly.patch255
-rw-r--r--sci-libs/ccp4-libs/files/6.1.3-ccif-shared.patch33
-rw-r--r--sci-libs/ccp4-libs/files/6.1.3-dont-build-mmdb.patch26
-rw-r--r--sci-libs/ccp4-libs/files/6.1.3-dont-make-dirs-in-configure.patch87
-rw-r--r--sci-libs/ccp4-libs/files/6.1.3-glibc2.10.patch22
-rw-r--r--sci-libs/ccp4-libs/files/6.1.3-link-proberly.patch255
-rw-r--r--sci-libs/ccp4-libs/files/pass-clipper-enablevals.patch11
-rw-r--r--sci-libs/ccp4-libs/metadata.xml9
-rw-r--r--sci-libs/mmdb/ChangeLog14
-rw-r--r--sci-libs/mmdb/Manifest4
-rw-r--r--sci-libs/mmdb/metadata.xml8
-rw-r--r--sci-libs/mmdb/mmdb-1.21.ebuild21
-rw-r--r--x11-libs/libjwc_c/ChangeLog17
-rw-r--r--x11-libs/libjwc_c/Manifest5
-rw-r--r--x11-libs/libjwc_c/files/612-gentoo.patch20
-rw-r--r--x11-libs/libjwc_c/libjwc_c-1.1-r1.ebuild29
-rw-r--r--x11-libs/libjwc_c/metadata.xml8
-rw-r--r--x11-libs/libjwc_f/ChangeLog16
-rw-r--r--x11-libs/libjwc_f/Manifest5
-rw-r--r--x11-libs/libjwc_f/files/612-gentoo.patch100
-rw-r--r--x11-libs/libjwc_f/libjwc_f-1.1-r1.ebuild35
-rw-r--r--x11-libs/libjwc_f/metadata.xml8
40 files changed, 0 insertions, 3337 deletions
diff --git a/sci-libs/ccp4-libs/ChangeLog b/sci-libs/ccp4-libs/ChangeLog
deleted file mode 100644
index aae7ba9c7..000000000
--- a/sci-libs/ccp4-libs/ChangeLog
+++ /dev/null
@@ -1,104 +0,0 @@
-# ChangeLog for sci-libs/ccp4-libs
-# Copyright 1999-2010 Gentoo Foundation; Distributed under the GPL v2
-# $Header: $
-
-*ccp4-libs-6.1.3-r1 (30 Jan 2010)
-
- 30 Jan 2010; Justin Lecher (jlec) <jlec@j-schmitz.net>
- -ccp4-libs-6.1.3.ebuild, +ccp4-libs-6.1.3-r1.ebuild:
- Bad upstream, changed tarball w/o bumping
-
-*ccp4-libs-6.1.3 (22 Dec 2009)
-
- 22 Dec 2009; Justin Lecher (jlec) <jlec@j-schmitz.net>
- +files/6.1.3-ccif-shared.patch,
- +files/6.1.3-dont-build-mmdb.patch,
- +files/6.1.3-dont-make-dirs-in-configure.patch,
- +files/6.1.3-glibc2.10.patch, +ccp4-libs-6.1.3.ebuild,
- +files/6.1.3-link-proberly.patch:
- Version bump
-
-*ccp4-libs-6.1.2-r1 (29 Oct 2009)
-
- 29 Oct 2009; Justin Lecher (jlec) <jlec@j-schmitz.net>
- +ccp4-libs-6.1.2-r1.ebuild, +files/6.1.2-64bit.patch:
- 64bit fix in diffdump
-
- 26 Aug 2009; Justin Lecher (jlec) <jlec@j-schmitz.net>
- ccp4-libs-6.1.2.ebuild:
- QA
-
- 13 Aug 2009; Justin Lecher (jlec) <jlec@j-schmitz.net>
- ccp4-libs-6.1.2.ebuild:
- Try to libmmdb build seperatly
-
-*ccp4-libs-6.1.2 (29 Jul 2009)
-
- 29 Jul 2009; Justin Lecher (jlec) <jlec@j-schmitz.net>
- +ccp4-libs-6.1.2.ebuild, +ccp4-libs-6.1.2.ebuild.save,
- +files/6.1.2-dont-make-dirs-in-configure.patch,
- +files/6.1.2-glibc2.10.patch, +files/6.1.2-link-proberly.patch:
- Still not released 6.1.2
-
-*ccp4-libs-6.1.1-r7 (05 Jul 2009)
-
- 05 Jul 2009; Justin Lecher (jlec) <jlec@j-schmitz.net>
- +ccp4-libs-6.1.1-r7.ebuild:
- Installs now some bins which come with the libs
- superpose now is named superpose-ccp4
-
-*ccp4-libs-6.1.1-r6 (11 Jun 2009)
-
- 11 Jun 2009; Justin Lecher (jlec) <jlec@j-schmitz.net>
- +ccp4-libs-6.1.1-r6.ebuild:
- missing libm in libccp4c.so
- hopefully alinkings fixed now
-
-*ccp4-libs-6.1.1-r5 (10 Jun 2009)
-
- 10 Jun 2009; Justin Lecher (jlec) <jlec@j-schmitz.net>
- +files/6.1.1-glibc2.10.patch, +ccp4-libs-6.1.1-r5.ebuild:
- Another linking fix
-
- 03 Jun 2009; Justin Lecher (jlec) <jlec@j-schmitz.net>
- -ccp4-libs-6.1.1-r2.ebuild, -ccp4-libs-6.1.1-r3.ebuild:
- cleaned up old versions
-
-*ccp4-libs-6.1.1-r4 (03 Jun 2009)
-
- 03 Jun 2009; Justin Lecher (jlec) <jlec@j-schmitz.net>
- +ccp4-libs-6.1.1-r4.ebuild:
- glibc-2.10 getline fix
- bug 270615
-
-*ccp4-libs-6.1.1-r3 (13 May 2009)
-
- 13 May 2009; Justin Lecher (jlec) <jlec@j-schmitz.net>
- +ccp4-libs-6.1.1-r3.ebuild:
- Includes upstream updates src files from 03/04/09
- fixes bug 269504
-
-*ccp4-libs-6.1.1-r2 (29 Apr 2009)
-
- 29 Apr 2009; Justin Lecher (jlec) <jlec@j-schmitz.net>
- -ccp4-libs-6.1.1-r1.ebuild, +ccp4-libs-6.1.1-r2.ebuild:
- Fixed Path of data dir
-
-*ccp4-libs-6.1.1-r1 (26 Apr 2009)
-
- 26 Apr 2009; Justin Lecher (jlec) <jlec@j-schmitz.net>
- +ccp4-libs-6.1.1-r1.ebuild:
- excluded monomer-db to seperate ebuild
- Some QA on data dir
-
-*sci-libs/ccp4-libs-6.1.1
-
- 18 Feb 2009; Justin Lecher (jlec) <jlec@j-schmitz.net>
- -sci-libs/ccp4-libs/files/6.0.99e-clipper-mmdbold-ggc-4.3.patch,
- -sci-libs/ccp4-libs/files/6.0.99e-fix-setup-bash-incompatibility.patch,
- +sci-libs/ccp4-libs/files/6.1.1-dont-make-dirs-in-configure.patch,
- +sci-libs/ccp4-libs/files/6.1.1-clipper-mmdbold-ggc-4.3.patch,
- -sci-libs/ccp4-libs/files/6.0.99e-dont-make-dirs-in-configure.patch,
- +sci-libs/ccp4-libs/files/6.1.1-fix-setup-bash-incompatibility.patch:
- bumped to revision 6.1.1
- fix-setup-bash-incompatibility.patch now done by upstream
diff --git a/sci-libs/ccp4-libs/Manifest b/sci-libs/ccp4-libs/Manifest
deleted file mode 100644
index cb5cca424..000000000
--- a/sci-libs/ccp4-libs/Manifest
+++ /dev/null
@@ -1,40 +0,0 @@
------BEGIN PGP SIGNED MESSAGE-----
-Hash: SHA1
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-DIST ccp4-6.1.1-core-src.tar.gz 246661086 RMD160 6722367727e4b6b1f8456f1458c9aac124923a89 SHA1 9141801e021f8a5107ed1e3989840e4de849b39c SHA256 56f971e05fe4543173451e48600813492fd0081b25d4a659cb0fed1fd2529407
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-DIST ccp4-6.1.2-core-src.tar.gz 247203188 RMD160 19019c6cd37e83cf6d2d19f91979edc978d18395 SHA1 2423178d3877dd44d3671a7eb4d6666de6852cb7 SHA256 bcae870675270be410278d9a6f2ee19f9caf32b73fd969e9381a4d510f174c75
-DIST ccp4-6.1.3-core-src.tar.gz 242109897 RMD160 babe577296d19849de095d5716d4e18ac3e8a4b5 SHA1 0d5d69f66b9ae24c66e767e8493d562e50962f75 SHA256 e57cdd193e2a80a0ce94b76fa6d658b111872a9c4800b942edf585f4defcc4fe
-EBUILD ccp4-libs-6.1.1-r4.ebuild 5776 RMD160 3a36e4a2fff69e2a17028c39f8849a4cfd73c64e SHA1 7693f8aa4a3e6106876e68fcdf25fada3b2e61e5 SHA256 f541ab2ffa172978b11c91c11754be4c75bb63174e2c3a4a1990f7e8fa5ddd57
-EBUILD ccp4-libs-6.1.1-r6.ebuild 5956 RMD160 88f4d6e5c9067225501f214002bc5924bc07c1a2 SHA1 8e61890578007833d8a923eeada3bdf064354056 SHA256 1e7bde2c6f9319d699cf95565aa74bd26372b9d1275fdeaaa8ee75fb4001b30a
-EBUILD ccp4-libs-6.1.1-r7.ebuild 6093 RMD160 99176fde51fd41e7b29610a15720859e97b22d01 SHA1 6a52cfb8e4cddd9454db90bb90bad600c3b753ec SHA256 2143d0c1a7905107b9699cce41d7f33a6fedc99cf9046de33d7b42ddafdfa937
-EBUILD ccp4-libs-6.1.1.ebuild 5211 RMD160 6f3705f7ab0c48bbda073eb7dc1a283b3dcaa39a SHA1 8b09909daae034fc393b49b5fda7e06a783bcd14 SHA256 e9b4a3183a8f753ced59968b261bb655c87d13ade8c9964c71f1f2948c42067e
-EBUILD ccp4-libs-6.1.2-r1.ebuild 5841 RMD160 83d0f6b8c6635e630a45b8adcd0f7564112f0c02 SHA1 9ba4da47a9227f1f91fb3cce0b7cd99202030975 SHA256 d526dfd1368290cd15e395338655f57e33bb3fce410a6642ceefe38bef707b7d
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diff --git a/sci-libs/ccp4-libs/ccp4-libs-6.1.1-r4.ebuild b/sci-libs/ccp4-libs/ccp4-libs-6.1.1-r4.ebuild
deleted file mode 100644
index 201228553..000000000
--- a/sci-libs/ccp4-libs/ccp4-libs-6.1.1-r4.ebuild
+++ /dev/null
@@ -1,209 +0,0 @@
-# Copyright 1999-2009 Gentoo Foundation
-# Distributed under the terms of the GNU General Public License v2
-# $Header: $
-
-inherit fortran eutils gnuconfig toolchain-funcs
-
-FORTRAN="g77 gfortran ifc"
-
-SRC="ftp://ftp.ccp4.ac.uk/ccp4"
-
-UPDATE="04_03_09"
-PATCHDATE="090511"
-
-MY_P="${P/-libs}"
-
-PATCH_TOT="0"
-# Here's a little scriptlet to generate this list from the provided
-# index.patches file
-#
-# i=1; while read -a line; do [[ ${line//#} != ${line} ]] && continue;
-# echo "PATCH${i}=( ${line[1]}"; echo "${line[0]} )"; (( i++ )); done <
-# index.patches
-#PATCH1=( src/topp_
-#topp.f-r1.16.2.5-r1.16.2.6.diff )
-#PATCH2=( .
-#configure-r1.372.2.18-r1.372.2.19.diff )
-
-DESCRIPTION="Protein X-ray crystallography toolkit"
-HOMEPAGE="http://www.ccp4.ac.uk/"
-RESTRICT="mirror"
-SRC_URI="${SRC}/${PV}/${MY_P}-core-src.tar.gz
- ${SRC}/${PV}/updates/${MY_P}-src-patch-${UPDATE}.tar.gz
- http://dev.gentooexperimental.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/${!NAME}"
-done
-LICENSE="ccp4"
-SLOT="0"
-KEYWORDS="~amd64 ~ppc ~x86"
-IUSE=""
-RDEPEND="virtual/lapack
- virtual/blas
- =sci-libs/fftw-2*
- app-shells/tcsh
- !<sci-chemistry/ccp4-6.0.99
- sci-libs/monomer-db"
-DEPEND="${RDEPEND}"
-
-S="${WORKDIR}/${P/-libs}"
-
-src_unpack() {
- unpack ${A}
- cd "${S}"
-
- einfo "Applying upstream patches ..."
- for patch in $(seq $PATCH_TOT); do
- base="PATCH${patch}"
- dir=$(eval echo \${${base}[0]})
- p=$(eval echo \${${base}[1]})
- pushd "${dir}" >& /dev/null
- ccp_patch "${DISTDIR}/${p}"
- popd >& /dev/null
- done
- einfo "Done."
- echo
-
- epatch "${WORKDIR}"/${PV}-${PATCHDATE}-updates.patch
-
- einfo "Applying Gentoo patches ..."
- # These two only needed when attempting to install outside build dir via
- # --bindir and --libdir instead of straight copying after build
-
- # it attempts to install some libraries during the build
- #ccp_patch "${FILESDIR}"/${P}-install-libs-at-install-time.patch
- # hklview/ipdisp.exe/xdlmapman/ipmosflm can't find libxdl_view
- # without this patch when --libdir is set
- # Rotgen still needs more patching to find it
- #ccp_patch "${FILESDIR}"/add-xdl-libdir.patch
-
- # it tries to create libdir, bindir etc on live system in configure
- ccp_patch "${FILESDIR}"/${PV}-dont-make-dirs-in-configure.patch
-
- # gerror_ gets defined twice on ppc if you're using gfortran/g95
- ccp_patch "${FILESDIR}"/6.0.2-ppc-double-define-gerror.patch
-
- einfo "Done." # done applying Gentoo patches
- echo
-
- # glibc-2.10 getline fix
- ls -l lib/src/fsplit.c
- sed -e "s:getline:${PN/-libs}getline:g" -i lib/src/fsplit.c || die
-
- gnuconfig_update
-}
-
-src_compile() {
- # Build system is broken if we set LDFLAGS
- unset LDFLAGS
-
- # GENTOO_OSNAME can be one of:
- # irix irix64 sunos sunos64 aix hpux osf1 linux freebsd
- # linux_compaq_compilers linux_intel_compilers generic Darwin
- # ia64_linux_intel Darwin_ibm_compilers linux_ibm_compilers
- if [[ "${FORTRANC}" = "ifc" ]]; then
- if use ia64; then
- GENTOO_OSNAME="ia64_linux_intel"
- else
- # Should be valid for x86, maybe amd64
- GENTOO_OSNAME="linux_intel_compilers"
- fi
- else
- # Should be valid for x86 and amd64, at least
- GENTOO_OSNAME="linux"
- fi
-
- # Sets up env
- ln -s \
- ccp4.setup-bash \
- "${S}"/include/ccp4.setup
-
- # We agree to the license by emerging this, set in LICENSE
- sed -i \
- -e "s~^\(^agreed=\).*~\1yes~g" \
- "${S}"/configure
-
- # Fix up variables -- need to reset CCP4_MASTER at install-time
- sed -i \
- -e "s~^\(setenv CCP4_MASTER.*\)/.*~\1"${WORKDIR}"~g" \
- -e "s~^\(setenv CCP4I_TCLTK.*\)/usr/local/bin~\1/usr/bin~g" \
- "${S}"/include/ccp4.setup*
-
- # Set up variables for build
- source "${S}"/include/ccp4.setup
-
- export CC=$(tc-getCC)
- export CXX=$(tc-getCXX)
- export COPTIM=${CFLAGS}
- export CXXOPTIM=${CXXFLAGS}
- # Default to -O2 if FFLAGS is unset
- export FC=${FORTRANC}
- export FOPTIM=${FFLAGS:- -O2}
-
- # Fix linking
- export SHARE_LIB="ld -shared -soname libmmdb.so --whole-archive -o libmmdb.so libmmdb.a ../libccif.a; \
- ld -shared -soname libccp4c.so --whole-archive -o libccp4c.so libccp4c.a ../libccif.a; \
- ld -shared -soname libccp4f.so --whole-archive -o libccp4f.so libccp4f.a libmmdb.a libccp4c.a ../libccif.a -lstdc++ $(gcc-config -L | awk -F: '{for(i=1; i<=NF; i++) printf " -L%s", $i}')"
-
- # Can't use econf, configure rejects unknown options like --prefix
- ./configure \
- --onlylibs \
- --with-shared-libs \
- --with-fftw=/usr \
- --with-warnings \
- --disable-cctbx \
- --disable-clipper \
- --tmpdir="${TMPDIR}" \
- ${GENTOO_OSNAME} || die "econf failed"
- emake -j1 onlylib || die "emake failed"
-}
-
-src_install() {
- # Set up variables for build
- source "${S}"/include/ccp4.setup
-
-# Only needed when using --bindir and --libdir
- # Needed to avoid errors. Originally tried to make lib and bin
- # in configure script, now patched out by dont-make-dirs-in-configure.patch
-# dodir /usr/include /usr/$(get_libdir) /usr/bin
-
-# make install || die "install failed"
- einstall || die "install failed"
-
- # Libs
- for file in "${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
-
- # Fix libdir in all *.la files
- sed -i \
- -e "s:^\(libdir=\).*:\1\'/usr/$(get_libdir)\':g" \
- "${D}"/usr/$(get_libdir)/*.la
-
- # Data
- insinto /usr/share/ccp4/data/
- doins -r "${S}"/lib/data/{*.PARM,*.prt,*.lib,*.dic,*.idl,*.cif,*.resource,*.york,*.hist,fraglib,reference_structures} || die
- dodoc "${S}"/lib/data/*.doc
- newdoc "${S}"/lib/data/README DATA-README
-
- # Include files
- insinto /usr/include
- for i in ccp4 mmdb; do
- doins -r "${S}"/include/${i} || die
- done
-}
-
-# Epatch wrapper for bulk patching
-ccp_patch() {
- EPATCH_SINGLE_MSG=" ${1##*/} ..." epatch ${1}
-}
diff --git a/sci-libs/ccp4-libs/ccp4-libs-6.1.1-r6.ebuild b/sci-libs/ccp4-libs/ccp4-libs-6.1.1-r6.ebuild
deleted file mode 100644
index 31cbfd155..000000000
--- a/sci-libs/ccp4-libs/ccp4-libs-6.1.1-r6.ebuild
+++ /dev/null
@@ -1,209 +0,0 @@
-# Copyright 1999-2009 Gentoo Foundation
-# Distributed under the terms of the GNU General Public License v2
-# $Header: $
-
-inherit fortran eutils gnuconfig toolchain-funcs
-
-FORTRAN="g77 gfortran ifc"
-
-SRC="ftp://ftp.ccp4.ac.uk/ccp4"
-
-UPDATE="04_03_09"
-PATCHDATE="090511"
-
-MY_P="${P/-libs}"
-
-PATCH_TOT="0"
-# Here's a little scriptlet to generate this list from the provided
-# index.patches file
-#
-# i=1; while read -a line; do [[ ${line//#} != ${line} ]] && continue;
-# echo "PATCH${i}=( ${line[1]}"; echo "${line[0]} )"; (( i++ )); done <
-# index.patches
-#PATCH1=( src/topp_
-#topp.f-r1.16.2.5-r1.16.2.6.diff )
-#PATCH2=( .
-#configure-r1.372.2.18-r1.372.2.19.diff )
-
-DESCRIPTION="Protein X-ray crystallography toolkit"
-HOMEPAGE="http://www.ccp4.ac.uk/"
-RESTRICT="mirror"
-SRC_URI="${SRC}/${PV}/${MY_P}-core-src.tar.gz
- ${SRC}/${PV}/updates/${MY_P}-src-patch-${UPDATE}.tar.gz
- http://dev.gentooexperimental.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/${!NAME}"
-done
-LICENSE="ccp4"
-SLOT="0"
-KEYWORDS="~amd64 ~ppc ~x86"
-IUSE=""
-RDEPEND="virtual/lapack
- virtual/blas
- =sci-libs/fftw-2*
- app-shells/tcsh
- !<sci-chemistry/ccp4-6.0.99
- sci-libs/monomer-db"
-DEPEND="${RDEPEND}"
-
-S="${WORKDIR}/${P/-libs}"
-
-src_unpack() {
- unpack ${A}
- cd "${S}"
-
- einfo "Applying upstream patches ..."
- for patch in $(seq $PATCH_TOT); do
- base="PATCH${patch}"
- dir=$(eval echo \${${base}[0]})
- p=$(eval echo \${${base}[1]})
- pushd "${dir}" >& /dev/null
- ccp_patch "${DISTDIR}/${p}"
- popd >& /dev/null
- done
- einfo "Done."
- echo
-
- epatch "${WORKDIR}"/${PV}-${PATCHDATE}-updates.patch
-
- einfo "Applying Gentoo patches ..."
- # These two only needed when attempting to install outside build dir via
- # --bindir and --libdir instead of straight copying after build
-
- # it attempts to install some libraries during the build
- #ccp_patch "${FILESDIR}"/${P}-install-libs-at-install-time.patch
- # hklview/ipdisp.exe/xdlmapman/ipmosflm can't find libxdl_view
- # without this patch when --libdir is set
- # Rotgen still needs more patching to find it
- #ccp_patch "${FILESDIR}"/add-xdl-libdir.patch
-
- # it tries to create libdir, bindir etc on live system in configure
- ccp_patch "${FILESDIR}"/${PV}-dont-make-dirs-in-configure.patch
-
- # gerror_ gets defined twice on ppc if you're using gfortran/g95
- ccp_patch "${FILESDIR}"/6.0.2-ppc-double-define-gerror.patch
-
- einfo "Done." # done applying Gentoo patches
- echo
-
- # glibc-2.10 getline fix
- sed -e "s:getline:${PN/-libs}getline:g" -i lib/src/fsplit.c || die
- ccp_patch "${FILESDIR}"/${PV}-glibc2.10.patch
-
- gnuconfig_update
-}
-
-src_compile() {
- # Build system is broken if we set LDFLAGS
- unset LDFLAGS
-
- # GENTOO_OSNAME can be one of:
- # irix irix64 sunos sunos64 aix hpux osf1 linux freebsd
- # linux_compaq_compilers linux_intel_compilers generic Darwin
- # ia64_linux_intel Darwin_ibm_compilers linux_ibm_compilers
- if [[ "${FORTRANC}" = "ifc" ]]; then
- if use ia64; then
- GENTOO_OSNAME="ia64_linux_intel"
- else
- # Should be valid for x86, maybe amd64
- GENTOO_OSNAME="linux_intel_compilers"
- fi
- else
- # Should be valid for x86 and amd64, at least
- GENTOO_OSNAME="linux"
- fi
-
- # Sets up env
- ln -s \
- ccp4.setup-bash \
- "${S}"/include/ccp4.setup
-
- # We agree to the license by emerging this, set in LICENSE
- sed -i \
- -e "s~^\(^agreed=\).*~\1yes~g" \
- "${S}"/configure
-
- # Fix up variables -- need to reset CCP4_MASTER at install-time
- sed -i \
- -e "s~^\(setenv CCP4_MASTER.*\)/.*~\1"${WORKDIR}"~g" \
- -e "s~^\(setenv CCP4I_TCLTK.*\)/usr/local/bin~\1/usr/bin~g" \
- "${S}"/include/ccp4.setup*
-
- # Set up variables for build
- source "${S}"/include/ccp4.setup
-
- export CC=$(tc-getCC)
- export CXX=$(tc-getCXX)
- export COPTIM=${CFLAGS}
- export CXXOPTIM=${CXXFLAGS}
- # Default to -O2 if FFLAGS is unset
- export FC=${FORTRANC}
- export FOPTIM=${FFLAGS:- -O2}
-
- # Fix linking
- export SHARE_LIB="ld -shared -soname libmmdb.so --whole-archive -o libmmdb.so libmmdb.a ../libccif.a $(gcc-config -L | awk -F: '{for(i=1; i<=NF; i++) printf " -L%s", $i}'); \
- ld -shared -soname libccp4c.so --whole-archive -o libccp4c.so libccp4c.a ../libccif.a -lm $(gcc-config -L | awk -F: '{for(i=1; i<=NF; i++) printf " -L%s", $i}'); \
- ld -shared -soname libccp4f.so --whole-archive -o libccp4f.so libccp4f.a libmmdb.a libccp4c.a ../libccif.a -lstdc++ -lgfortran $(gcc-config -L | awk -F: '{for(i=1; i<=NF; i++) printf " -L%s", $i}')"
-
- # Can't use econf, configure rejects unknown options like --prefix
- ./configure \
- --onlylibs \
- --with-shared-libs \
- --with-fftw=/usr \
- --with-warnings \
- --disable-cctbx \
- --disable-clipper \
- --tmpdir="${TMPDIR}" \
- ${GENTOO_OSNAME} || die "econf failed"
- emake -j1 onlylib || die "emake failed"
-}
-
-src_install() {
- # Set up variables for build
- source "${S}"/include/ccp4.setup
-
-# Only needed when using --bindir and --libdir
- # Needed to avoid errors. Originally tried to make lib and bin
- # in configure script, now patched out by dont-make-dirs-in-configure.patch
-# dodir /usr/include /usr/$(get_libdir) /usr/bin
-
-# make install || die "install failed"
- einstall || die "install failed"
-
- # Libs
- for file in "${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
-
- # Fix libdir in all *.la files
- sed -i \
- -e "s:^\(libdir=\).*:\1\'/usr/$(get_libdir)\':g" \
- "${D}"/usr/$(get_libdir)/*.la
-
- # Data
- insinto /usr/share/ccp4/data/
- doins -r "${S}"/lib/data/{*.PARM,*.prt,*.lib,*.dic,*.idl,*.cif,*.resource,*.york,*.hist,fraglib,reference_structures} || die
- dodoc "${S}"/lib/data/*.doc
- newdoc "${S}"/lib/data/README DATA-README
-
- # Include files
- insinto /usr/include
- for i in ccp4 mmdb; do
- doins -r "${S}"/include/${i} || die
- done
-}
-
-# Epatch wrapper for bulk patching
-ccp_patch() {
- EPATCH_SINGLE_MSG=" ${1##*/} ..." epatch ${1}
-}
diff --git a/sci-libs/ccp4-libs/ccp4-libs-6.1.1-r7.ebuild b/sci-libs/ccp4-libs/ccp4-libs-6.1.1-r7.ebuild
deleted file mode 100644
index 43ddf853f..000000000
--- a/sci-libs/ccp4-libs/ccp4-libs-6.1.1-r7.ebuild
+++ /dev/null
@@ -1,214 +0,0 @@
-# Copyright 1999-2009 Gentoo Foundation
-# Distributed under the terms of the GNU General Public License v2
-# $Header: $
-
-inherit fortran eutils gnuconfig toolchain-funcs
-
-FORTRAN="g77 gfortran ifc"
-
-SRC="ftp://ftp.ccp4.ac.uk/ccp4"
-
-UPDATE="04_03_09"
-PATCHDATE="090511"
-
-MY_P="${P/-libs}"
-
-PATCH_TOT="0"
-# Here's a little scriptlet to generate this list from the provided
-# index.patches file
-#
-# i=1; while read -a line; do [[ ${line//#} != ${line} ]] && continue;
-# echo "PATCH${i}=( ${line[1]}"; echo "${line[0]} )"; (( i++ )); done <
-# index.patches
-#PATCH1=( src/topp_
-#topp.f-r1.16.2.5-r1.16.2.6.diff )
-#PATCH2=( .
-#configure-r1.372.2.18-r1.372.2.19.diff )
-
-DESCRIPTION="Protein X-ray crystallography toolkit"
-HOMEPAGE="http://www.ccp4.ac.uk/"
-RESTRICT="mirror"
-SRC_URI="${SRC}/${PV}/${MY_P}-core-src.tar.gz
- ${SRC}/${PV}/updates/${MY_P}-src-patch-${UPDATE}.tar.gz
- http://dev.gentooexperimental.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/${!NAME}"
-done
-LICENSE="ccp4"
-SLOT="0"
-KEYWORDS="~amd64 ~ppc ~x86"
-IUSE=""
-RDEPEND="virtual/lapack
- virtual/blas
- =sci-libs/fftw-2*
- app-shells/tcsh
- !<sci-chemistry/ccp4-6.0.99
- sci-libs/monomer-db"
-DEPEND="${RDEPEND}"
-
-S="${WORKDIR}/${P/-libs}"
-
-src_unpack() {
- unpack ${A}
- cd "${S}"
-
- einfo "Applying upstream patches ..."
- for patch in $(seq $PATCH_TOT); do
- base="PATCH${patch}"
- dir=$(eval echo \${${base}[0]})
- p=$(eval echo \${${base}[1]})
- pushd "${dir}" >& /dev/null
- ccp_patch "${DISTDIR}/${p}"
- popd >& /dev/null
- done
- einfo "Done."
- echo
-
- epatch "${WORKDIR}"/${PV}-${PATCHDATE}-updates.patch
-
- einfo "Applying Gentoo patches ..."
- # These two only needed when attempting to install outside build dir via
- # --bindir and --libdir instead of straight copying after build
-
- # it attempts to install some libraries during the build
- #ccp_patch "${FILESDIR}"/${P}-install-libs-at-install-time.patch
- # hklview/ipdisp.exe/xdlmapman/ipmosflm can't find libxdl_view
- # without this patch when --libdir is set
- # Rotgen still needs more patching to find it
- #ccp_patch "${FILESDIR}"/add-xdl-libdir.patch
-
- # it tries to create libdir, bindir etc on live system in configure
- ccp_patch "${FILESDIR}"/${PV}-dont-make-dirs-in-configure.patch
-
- # gerror_ gets defined twice on ppc if you're using gfortran/g95
- ccp_patch "${FILESDIR}"/6.0.2-ppc-double-define-gerror.patch
-
- einfo "Done." # done applying Gentoo patches
- echo
-
- # glibc-2.10 getline fix
- sed -e "s:getline:${PN/-libs}getline:g" -i lib/src/fsplit.c || die
- ccp_patch "${FILESDIR}"/${PV}-glibc2.10.patch
-
- gnuconfig_update
-}
-
-src_compile() {
- # Build system is broken if we set LDFLAGS
- unset LDFLAGS
-
- # GENTOO_OSNAME can be one of:
- # irix irix64 sunos sunos64 aix hpux osf1 linux freebsd
- # linux_compaq_compilers linux_intel_compilers generic Darwin
- # ia64_linux_intel Darwin_ibm_compilers linux_ibm_compilers
- if [[ "${FORTRANC}" = "ifc" ]]; then
- if use ia64; then
- GENTOO_OSNAME="ia64_linux_intel"
- else
- # Should be valid for x86, maybe amd64
- GENTOO_OSNAME="linux_intel_compilers"
- fi
- else
- # Should be valid for x86 and amd64, at least
- GENTOO_OSNAME="linux"
- fi
-
- # Sets up env
- ln -s \
- ccp4.setup-bash \
- "${S}"/include/ccp4.setup
-
- # We agree to the license by emerging this, set in LICENSE
- sed -i \
- -e "s~^\(^agreed=\).*~\1yes~g" \
- "${S}"/configure
-
- # Fix up variables -- need to reset CCP4_MASTER at install-time
- sed -i \
- -e "s~^\(setenv CCP4_MASTER.*\)/.*~\1"${WORKDIR}"~g" \
- -e "s~^\(setenv CCP4I_TCLTK.*\)/usr/local/bin~\1/usr/bin~g" \
- "${S}"/include/ccp4.setup*
-
- # Set up variables for build
- source "${S}"/include/ccp4.setup
-
- export CC=$(tc-getCC)
- export CXX=$(tc-getCXX)
- export COPTIM=${CFLAGS}
- export CXXOPTIM=${CXXFLAGS}
- # Default to -O2 if FFLAGS is unset
- export FC=${FORTRANC}
- export FOPTIM=${FFLAGS:- -O2}
-# export CCP4_SCR="${T}"
-
- # Fix linking
- export SHARE_LIB="ld -shared -soname libmmdb.so --whole-archive -o libmmdb.so libmmdb.a ../libccif.a $(gcc-config -L | awk -F: '{for(i=1; i<=NF; i++) printf " -L%s", $i}'); \
- ld -shared -soname libccp4c.so --whole-archive -o libccp4c.so libccp4c.a ../libccif.a -lm $(gcc-config -L | awk -F: '{for(i=1; i<=NF; i++) printf " -L%s", $i}'); \
- ld -shared -soname libccp4f.so --whole-archive -o libccp4f.so libccp4f.a libmmdb.a libccp4c.a ../libccif.a -lstdc++ -lgfortran $(gcc-config -L | awk -F: '{for(i=1; i<=NF; i++) printf " -L%s", $i}')"
-
- # Can't use econf, configure rejects unknown options like --prefix
- ./configure \
- --onlylibs \
- --with-shared-libs \
- --with-fftw=/usr \
- --with-warnings \
- --disable-cctbx \
- --disable-clipper \
- --tmpdir="${TMPDIR}" \
- ${GENTOO_OSNAME} || die "econf failed"
- emake -j1 onlylib || die "emake failed"
-}
-
-src_install() {
- # Set up variables for build
- source "${S}"/include/ccp4.setup
-
-# Only needed when using --bindir and --libdir
- # Needed to avoid errors. Originally tried to make lib and bin
- # in configure script, now patched out by dont-make-dirs-in-configure.patch
-# dodir /usr/include /usr/$(get_libdir) /usr/bin
-
-# make install || die "install failed"
- einstall || die "install failed"
-
- # Libs
- for file in "${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
-
- # Bins
- dobin bin/{automask,diff2jpeg,diffdump,printpeaks} || die
- newbin bin/superpose superpose-ccp4 || die
-
- # Fix libdir in all *.la files
- sed -i \
- -e "s:^\(libdir=\).*:\1\'/usr/$(get_libdir)\':g" \
- "${D}"/usr/$(get_libdir)/*.la
-
- # Data
- insinto /usr/share/ccp4/data/
- doins -r "${S}"/lib/data/{*.PARM,*.prt,*.lib,*.dic,*.idl,*.cif,*.resource,*.york,*.hist,fraglib,reference_structures} || die
- dodoc "${S}"/lib/data/*.doc
- newdoc "${S}"/lib/data/README DATA-README
-
- # Include files
- insinto /usr/include
- for i in ccp4 mmdb; do
- doins -r "${S}"/include/${i} || die
- done
-}
-
-# Epatch wrapper for bulk patching
-ccp_patch() {
- EPATCH_SINGLE_MSG=" ${1##*/} ..." epatch ${1}
-}
diff --git a/sci-libs/ccp4-libs/ccp4-libs-6.1.1.ebuild b/sci-libs/ccp4-libs/ccp4-libs-6.1.1.ebuild
deleted file mode 100644
index 871bffab1..000000000
--- a/sci-libs/ccp4-libs/ccp4-libs-6.1.1.ebuild
+++ /dev/null
@@ -1,192 +0,0 @@
-# Copyright 1999-2009 Gentoo Foundation
-# Distributed under the terms of the GNU General Public License v2
-# $Header: $
-
-inherit fortran eutils gnuconfig toolchain-funcs
-
-FORTRAN="g77 gfortran ifc"
-
-SRC="ftp://ftp.ccp4.ac.uk/ccp4"
-
-PATCH_TOT="0"
-# Here's a little scriptlet to generate this list from the provided
-# index.patches file
-#
-# i=1; while read -a line; do [[ ${line//#} != ${line} ]] && continue;
-# echo "PATCH${i}=( ${line[1]}"; echo "${line[0]} )"; (( i++ )); done <
-# index.patches
-#PATCH1=( src/topp_
-#topp.f-r1.16.2.5-r1.16.2.6.diff )
-#PATCH2=( .
-#configure-r1.372.2.18-r1.372.2.19.diff )
-
-DESCRIPTION="Protein X-ray crystallography toolkit"
-HOMEPAGE="http://www.ccp4.ac.uk/"
-RESTRICT="mirror"
-SRC_URI="${SRC}/${PV}/${P/-libs}-core-src.tar.gz"
-for i in $(seq $PATCH_TOT); do
- NAME="PATCH${i}[1]"
- SRC_URI="${SRC_URI}
- ${SRC}/${PV}/patches/${!NAME}"
-done
-LICENSE="ccp4"
-SLOT="0"
-KEYWORDS="~amd64 ~ppc ~x86"
-IUSE=""
-RDEPEND="virtual/lapack
- virtual/blas
- =sci-libs/fftw-2*
- app-shells/tcsh
- !<sci-chemistry/ccp4-6.0.99"
-DEPEND="${RDEPEND}"
-
-S="${WORKDIR}/${P/-libs}"
-
-src_unpack() {
- unpack ${A}
- cd "${S}"
-
- einfo "Applying upstream patches ..."
- for patch in $(seq $PATCH_TOT); do
- base="PATCH${patch}"
- dir=$(eval echo \${${base}[0]})
- p=$(eval echo \${${base}[1]})
- pushd "${dir}" >& /dev/null
- ccp_patch "${DISTDIR}/${p}"
- popd >& /dev/null
- done
- einfo "Done."
- echo
-
- einfo "Applying Gentoo patches ..."
- # These two only needed when attempting to install outside build dir via
- # --bindir and --libdir instead of straight copying after build
-
- # it attempts to install some libraries during the build
- #ccp_patch "${FILESDIR}"/${P}-install-libs-at-install-time.patch
- # hklview/ipdisp.exe/xdlmapman/ipmosflm can't find libxdl_view
- # without this patch when --libdir is set
- # Rotgen still needs more patching to find it
- #ccp_patch "${FILESDIR}"/add-xdl-libdir.patch
-
- # it tries to create libdir, bindir etc on live system in configure
- ccp_patch "${FILESDIR}"/${PV}-dont-make-dirs-in-configure.patch
-
- # gerror_ gets defined twice on ppc if you're using gfortran/g95
- ccp_patch "${FILESDIR}"/6.0.2-ppc-double-define-gerror.patch
-
- einfo "Done." # done applying Gentoo patches
- echo
-
- gnuconfig_update
-}
-
-src_compile() {
- # Build system is broken if we set LDFLAGS
- unset LDFLAGS
-
- # GENTOO_OSNAME can be one of:
- # irix irix64 sunos sunos64 aix hpux osf1 linux freebsd
- # linux_compaq_compilers linux_intel_compilers generic Darwin
- # ia64_linux_intel Darwin_ibm_compilers linux_ibm_compilers
- if [[ "${FORTRANC}" = "ifc" ]]; then
- if use ia64; then
- GENTOO_OSNAME="ia64_linux_intel"
- else
- # Should be valid for x86, maybe amd64
- GENTOO_OSNAME="linux_intel_compilers"
- fi
- else
- # Should be valid for x86 and amd64, at least
- GENTOO_OSNAME="linux"
- fi
-
- # Sets up env
- ln -s \
- ccp4.setup-bash \
- "${S}"/include/ccp4.setup
-
- # We agree to the license by emerging this, set in LICENSE
- sed -i \
- -e "s~^\(^agreed=\).*~\1yes~g" \
- "${S}"/configure
-
- # Fix up variables -- need to reset CCP4_MASTER at install-time
- sed -i \
- -e "s~^\(setenv CCP4_MASTER.*\)/.*~\1"${WORKDIR}"~g" \
- -e "s~^\(setenv CCP4I_TCLTK.*\)/usr/local/bin~\1/usr/bin~g" \
- "${S}"/include/ccp4.setup*
-
- # Set up variables for build
- source "${S}"/include/ccp4.setup
-
- export CC=$(tc-getCC)
- export CXX=$(tc-getCXX)
- export COPTIM=${CFLAGS}
- export CXXOPTIM=${CXXFLAGS}
- # Default to -O2 if FFLAGS is unset
- export FC=${FORTRANC}
- export FOPTIM=${FFLAGS:- -O2}
-
- # Fix linking
- export SHARE_LIB="ld -shared -soname libmmdb.so --whole-archive -o libmmdb.so libmmdb.a ../libccif.a; \
- ld -shared -soname libccp4c.so --whole-archive -o libccp4c.so libccp4c.a ../libccif.a; \
- ld -shared -soname libccp4f.so --whole-archive -o libccp4f.so libccp4f.a libmmdb.a libccp4c.a ../libccif.a -lstdc++ $(gcc-config -L | awk -F: '{for(i=1; i<=NF; i++) printf " -L%s", $i}')"
-
- # Can't use econf, configure rejects unknown options like --prefix
- ./configure \
- --onlylibs \
- --with-shared-libs \
- --with-fftw=/usr \
- --with-warnings \
- --disable-cctbx \
- --disable-clipper \
- --tmpdir="${TMPDIR}" \
- ${GENTOO_OSNAME} || die "econf failed"
- emake -j1 onlylib || die "emake failed"
-}
-
-src_install() {
- # Set up variables for build
- source "${S}"/include/ccp4.setup
-
-# Only needed when using --bindir and --libdir
- # Needed to avoid errors. Originally tried to make lib and bin
- # in configure script, now patched out by dont-make-dirs-in-configure.patch
-# dodir /usr/include /usr/$(get_libdir) /usr/bin
-
-# make install || die "install failed"
- einstall || die "install failed"
-
- # Libs
- for file in "${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
-
- # Fix libdir in all *.la files
- sed -i \
- -e "s:^\(libdir=\).*:\1\'/usr/$(get_libdir)\':g" \
- "${D}"/usr/$(get_libdir)/*.la
-
- # Data
- insinto /usr/share/ccp4
- doins -r "${S}"/lib/data || die
-
- # Include files
- insinto /usr/include
- for i in ccp4 mmdb; do
- doins -r "${S}"/include/${i} || die
- done
-}
-
-# Epatch wrapper for bulk patching
-ccp_patch() {
- EPATCH_SINGLE_MSG=" ${1##*/} ..." epatch ${1}
-}
diff --git a/sci-libs/ccp4-libs/ccp4-libs-6.1.2-r1.ebuild b/sci-libs/ccp4-libs/ccp4-libs-6.1.2-r1.ebuild
deleted file mode 100644
index 3d6ac6880..000000000
--- a/sci-libs/ccp4-libs/ccp4-libs-6.1.2-r1.ebuild
+++ /dev/null
@@ -1,213 +0,0 @@
-# Copyright 1999-2009 Gentoo Foundation
-# Distributed under the terms of the GNU General Public License v2
-# $Header: $
-
-inherit fortran eutils gnuconfig toolchain-funcs
-
-FORTRAN="g77 gfortran ifc"
-
-SRC="ftp://ftp.ccp4.ac.uk/ccp4"
-
-#UPDATE="04_03_09"
-#PATCHDATE="090511"
-
-MY_P="${P/-libs}"
-
-PATCH_TOT="0"
-# Here's a little scriptlet to generate this list from the provided
-# index.patches file
-#
-# i=1; while read -a line; do [[ ${line//#} != ${line} ]] && continue;
-# echo "PATCH${i}=( ${line[1]}"; echo "${line[0]} )"; (( i++ )); done <
-# index.patches
-#PATCH1=( src/topp_
-#topp.f-r1.16.2.5-r1.16.2.6.diff )
-#PATCH2=( .
-#configure-r1.372.2.18-r1.372.2.19.diff )
-
-DESCRIPTION="Protein X-ray crystallography toolkit"
-HOMEPAGE="http://www.ccp4.ac.uk/"
-SRC_URI="${SRC}/${PV}/${MY_P}-core-src.tar.gz"
-# 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.gentooexperimental.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/${!NAME}"
-done
-
-LICENSE="ccp4"
-SLOT="0"
-KEYWORDS="~amd64 ~x86"
-IUSE=""
-
-RDEPEND="
- app-shells/tcsh
- !<sci-chemistry/ccp4-6.0.99
- =sci-libs/fftw-2*
- sci-libs/mmdb
- sci-libs/monomer-db
- virtual/lapack
- virtual/blas"
-DEPEND="${RDEPEND}"
-
-RESTRICT="mirror"
-
-S="${WORKDIR}/${MY_P}"
-
-src_unpack() {
- unpack ${A}
- cd "${S}"
-
- einfo "Applying upstream patches ..."
- for patch in $(seq $PATCH_TOT); do
- base="PATCH${patch}"
- dir=$(eval echo \${${base}[0]})
- p=$(eval echo \${${base}[1]})
- pushd "${dir}" >& /dev/null
- ccp_patch "${DISTDIR}/${p}"
- popd >& /dev/null
- done
- einfo "Done."
- echo
-
- [[ -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
-
- # gerror_ gets defined twice on ppc if you're using gfortran/g95
- ccp_patch "${FILESDIR}"/6.0.2-ppc-double-define-gerror.patch
-
- # make creation of libccif.so smooth
- ccp_patch "${FILESDIR}"/${PV}-ccif-shared.patch
-
- # lets try to build libmmdb seperatly
- ccp_patch "${FILESDIR}"/${PV}-dont-build-mmdb.patch
-
- # 64bit long -> int32_t patch
- ccp_patch "${FILESDIR}"/${PV}-64bit.patch
-
- einfo "Done." # done applying Gentoo patches
- echo
-
- gnuconfig_update
-}
-
-src_compile() {
- # Build system is broken if we set LDFLAGS
- userldflags="${LDFLAGS}"
- export SHARED_LIB_FLAGS="${LDFLAGS}"
- unset LDFLAGS
-
- # GENTOO_OSNAME can be one of:
- # irix irix64 sunos sunos64 aix hpux osf1 linux freebsd
- # linux_compaq_compilers linux_intel_compilers generic Darwin
- # ia64_linux_intel Darwin_ibm_compilers linux_ibm_compilers
- if [[ "${FORTRANC}" = "ifc" ]]; then
- if use ia64; then
- GENTOO_OSNAME="ia64_linux_intel"
- else
- # Should be valid for x86, maybe amd64
- GENTOO_OSNAME="linux_intel_compilers"
- fi
- else
- # Should be valid for x86 and amd64, at least
- GENTOO_OSNAME="linux"
- fi
-
- # Sets up env
- ln -s \
- ccp4.setup-bash \
- "${S}"/include/ccp4.setup
-
- # We agree to the license by emerging this, set in LICENSE
- sed -i \
- -e "s~^\(^agreed=\).*~\1yes~g" \
- "${S}"/configure
-
- # Fix up variables -- need to reset CCP4_MASTER at install-time
- sed -i \
- -e "s~^\(setenv CCP4_MASTER.*\)/.*~\1"${WORKDIR}"~g" \
- -e "s~^\(setenv CCP4I_TCLTK.*\)/usr/local/bin~\1/usr/bin~g" \
- "${S}"/include/ccp4.setup*
-
- # Set up variables for build
- source "${S}"/include/ccp4.setup
-
- export CC=$(tc-getCC)
- export CXX=$(tc-getCXX)
- export COPTIM=${CFLAGS}
- export CXXOPTIM=${CXXFLAGS}
- # Default to -O2 if FFLAGS is unset
- export FC=${FORTRANC}
- export FOPTIM=${FFLAGS:- -O2}
-# export CCP4_SCR="${T}"
-
- # Fix linking
-# $(tc-getCC) ${userldflags} -shared -Wl,-soname,libmmdb.so -o libmmdb.so \${MMDBOBJS} $(gcc-config -L | awk -F: '{for(i=1; i<=NF; i++) printf " -L%s", $i}') -lm -lstdc++ && \
- export SHARE_LIB="\
- $(tc-getCC) ${userldflags} -shared -Wl,-soname,libccp4c.so -o libccp4c.so \${CORELIBOBJS} \${CGENERALOBJS} \${CUCOBJS} \${CMTZOBJS} \${CMAPOBJS} \${CSYMOBJS} -L.. -lccif $(gcc-config -L | awk -F: '{for(i=1; i<=NF; i++) printf " -L%s", $i}') -lm && \
- ${FORTRANC} ${userldflags} -shared -Wl,-soname,libccp4f.so -o libccp4f.so \${FORTRANLOBJS} \${FINTERFACEOBJS} -L.. -lccif -L. -lccp4c -lmmdb $(gcc-config -L | awk -F: '{for(i=1; i<=NF; i++) printf " -L%s", $i}') -lstdc++ -lgfortran -lm"
-
- # Can't use econf, configure rejects unknown options like --prefix
- ./configure \
- --onlylibs \
- --with-shared-libs \
- --with-fftw=/usr \
- --with-warnings \
- --disable-cctbx \
- --disable-clipper \
- --tmpdir="${TMPDIR}" \
- ${GENTOO_OSNAME} || die "econf failed"
- emake -j1 onlylib || die "emake failed"
-}
-
-src_install() {
- # Set up variables for build
- source "${S}"/include/ccp4.setup
-
- einstall || die "install failed"
-
- # 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
-
- # Bins
- dobin bin/{automask,diff2jpeg,diffdump,printpeaks} || die
- newbin bin/superpose superpose-ccp4 || die
-
- # Fix libdir in all *.la files
- sed -i \
- -e "s:^\(libdir=\).*:\1\'/usr/$(get_libdir)\':g" \
- "${D}"/usr/$(get_libdir)/*.la
-
- # Data
- insinto /usr/share/ccp4/data/
- doins -r "${S}"/lib/data/{*.PARM,*.prt,*.lib,*.dic,*.idl,*.cif,*.resource,*.york,*.hist,fraglib,reference_structures} || die
- dodoc "${S}"/lib/data/*.doc
- newdoc "${S}"/lib/data/README DATA-README
-
- # Include files
- insinto /usr/include
- for i in ccp4; do
- doins -r "${S}"/include/${i} || die
- done
-}
-
-# Epatch wrapper for bulk patching
-ccp_patch() {
- EPATCH_SINGLE_MSG=" ${1##*/} ..." epatch ${1}
-}
diff --git a/sci-libs/ccp4-libs/ccp4-libs-6.1.2.ebuild b/sci-libs/ccp4-libs/ccp4-libs-6.1.2.ebuild
deleted file mode 100644
index 7191ff805..000000000
--- a/sci-libs/ccp4-libs/ccp4-libs-6.1.2.ebuild
+++ /dev/null
@@ -1,210 +0,0 @@
-# Copyright 1999-2009 Gentoo Foundation
-# Distributed under the terms of the GNU General Public License v2
-# $Header: $
-
-inherit fortran eutils gnuconfig toolchain-funcs
-
-FORTRAN="g77 gfortran ifc"
-
-SRC="ftp://ftp.ccp4.ac.uk/ccp4"
-
-#UPDATE="04_03_09"
-#PATCHDATE="090511"
-
-MY_P="${P/-libs}"
-
-PATCH_TOT="0"
-# Here's a little scriptlet to generate this list from the provided
-# index.patches file
-#
-# i=1; while read -a line; do [[ ${line//#} != ${line} ]] && continue;
-# echo "PATCH${i}=( ${line[1]}"; echo "${line[0]} )"; (( i++ )); done <
-# index.patches
-#PATCH1=( src/topp_
-#topp.f-r1.16.2.5-r1.16.2.6.diff )
-#PATCH2=( .
-#configure-r1.372.2.18-r1.372.2.19.diff )
-
-DESCRIPTION="Protein X-ray crystallography toolkit"
-HOMEPAGE="http://www.ccp4.ac.uk/"
-SRC_URI="${SRC}/${PV}/${MY_P}-core-src.tar.gz"
-# 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.gentooexperimental.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/${!NAME}"
-done
-
-LICENSE="ccp4"
-SLOT="0"
-KEYWORDS="~amd64 ~x86"
-IUSE=""
-
-RDEPEND="
- app-shells/tcsh
- !<sci-chemistry/ccp4-6.0.99
- =sci-libs/fftw-2*
- sci-libs/mmdb
- sci-libs/monomer-db
- virtual/lapack
- virtual/blas"
-DEPEND="${RDEPEND}"
-
-RESTRICT="mirror"
-
-S="${WORKDIR}/${MY_P}"
-
-src_unpack() {
- unpack ${A}
- cd "${S}"
-
- einfo "Applying upstream patches ..."
- for patch in $(seq $PATCH_TOT); do
- base="PATCH${patch}"
- dir=$(eval echo \${${base}[0]})
- p=$(eval echo \${${base}[1]})
- pushd "${dir}" >& /dev/null
- ccp_patch "${DISTDIR}/${p}"
- popd >& /dev/null
- done
- einfo "Done."
- echo
-
- [[ -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
-
- # gerror_ gets defined twice on ppc if you're using gfortran/g95
- ccp_patch "${FILESDIR}"/6.0.2-ppc-double-define-gerror.patch
-
- # make creation of libccif.so smooth
- ccp_patch "${FILESDIR}"/${PV}-ccif-shared.patch
-
- # lets try to build libmmdb seperatly
- ccp_patch "${FILESDIR}"/${PV}-dont-build-mmdb.patch
-
- einfo "Done." # done applying Gentoo patches
- echo
-
- gnuconfig_update
-}
-
-src_compile() {
- # Build system is broken if we set LDFLAGS
- userldflags="${LDFLAGS}"
- export SHARED_LIB_FLAGS="${LDFLAGS}"
- unset LDFLAGS
-
- # GENTOO_OSNAME can be one of:
- # irix irix64 sunos sunos64 aix hpux osf1 linux freebsd
- # linux_compaq_compilers linux_intel_compilers generic Darwin
- # ia64_linux_intel Darwin_ibm_compilers linux_ibm_compilers
- if [[ "${FORTRANC}" = "ifc" ]]; then
- if use ia64; then
- GENTOO_OSNAME="ia64_linux_intel"
- else
- # Should be valid for x86, maybe amd64
- GENTOO_OSNAME="linux_intel_compilers"
- fi
- else
- # Should be valid for x86 and amd64, at least
- GENTOO_OSNAME="linux"
- fi
-
- # Sets up env
- ln -s \
- ccp4.setup-bash \
- "${S}"/include/ccp4.setup
-
- # We agree to the license by emerging this, set in LICENSE
- sed -i \
- -e "s~^\(^agreed=\).*~\1yes~g" \
- "${S}"/configure
-
- # Fix up variables -- need to reset CCP4_MASTER at install-time
- sed -i \
- -e "s~^\(setenv CCP4_MASTER.*\)/.*~\1"${WORKDIR}"~g" \
- -e "s~^\(setenv CCP4I_TCLTK.*\)/usr/local/bin~\1/usr/bin~g" \
- "${S}"/include/ccp4.setup*
-
- # Set up variables for build
- source "${S}"/include/ccp4.setup
-
- export CC=$(tc-getCC)
- export CXX=$(tc-getCXX)
- export COPTIM=${CFLAGS}
- export CXXOPTIM=${CXXFLAGS}
- # Default to -O2 if FFLAGS is unset
- export FC=${FORTRANC}
- export FOPTIM=${FFLAGS:- -O2}
-# export CCP4_SCR="${T}"
-
- # Fix linking
-# $(tc-getCC) ${userldflags} -shared -Wl,-soname,libmmdb.so -o libmmdb.so \${MMDBOBJS} $(gcc-config -L | awk -F: '{for(i=1; i<=NF; i++) printf " -L%s", $i}') -lm -lstdc++ && \
- export SHARE_LIB="\
- $(tc-getCC) ${userldflags} -shared -Wl,-soname,libccp4c.so -o libccp4c.so \${CORELIBOBJS} \${CGENERALOBJS} \${CUCOBJS} \${CMTZOBJS} \${CMAPOBJS} \${CSYMOBJS} -L.. -lccif $(gcc-config -L | awk -F: '{for(i=1; i<=NF; i++) printf " -L%s", $i}') -lm && \
- ${FORTRANC} ${userldflags} -shared -Wl,-soname,libccp4f.so -o libccp4f.so \${FORTRANLOBJS} \${FINTERFACEOBJS} -L.. -lccif -L. -lccp4c -lmmdb $(gcc-config -L | awk -F: '{for(i=1; i<=NF; i++) printf " -L%s", $i}') -lstdc++ -lgfortran -lm"
-
- # Can't use econf, configure rejects unknown options like --prefix
- ./configure \
- --onlylibs \
- --with-shared-libs \
- --with-fftw=/usr \
- --with-warnings \
- --disable-cctbx \
- --disable-clipper \
- --tmpdir="${TMPDIR}" \
- ${GENTOO_OSNAME} || die "econf failed"
- emake -j1 onlylib || die "emake failed"
-}
-
-src_install() {
- # Set up variables for build
- source "${S}"/include/ccp4.setup
-
- einstall || die "install failed"
-
- # 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
-
- # Bins
- dobin bin/{automask,diff2jpeg,diffdump,printpeaks} || die
- newbin bin/superpose superpose-ccp4 || die
-
- # Fix libdir in all *.la files
- sed -i \
- -e "s:^\(libdir=\).*:\1\'/usr/$(get_libdir)\':g" \
- "${D}"/usr/$(get_libdir)/*.la
-
- # Data
- insinto /usr/share/ccp4/data/
- doins -r "${S}"/lib/data/{*.PARM,*.prt,*.lib,*.dic,*.idl,*.cif,*.resource,*.york,*.hist,fraglib,reference_structures} || die
- dodoc "${S}"/lib/data/*.doc
- newdoc "${S}"/lib/data/README DATA-README
-
- # Include files
- insinto /usr/include
- for i in ccp4; do
- doins -r "${S}"/include/${i} || die
- done
-}
-
-# Epatch wrapper for bulk patching
-ccp_patch() {
- EPATCH_SINGLE_MSG=" ${1##*/} ..." epatch ${1}
-}
diff --git a/sci-libs/ccp4-libs/ccp4-libs-6.1.3-r1.ebuild b/sci-libs/ccp4-libs/ccp4-libs-6.1.3-r1.ebuild
deleted file mode 100644
index 39015b67a..000000000
--- a/sci-libs/ccp4-libs/ccp4-libs-6.1.3-r1.ebuild
+++ /dev/null
@@ -1,210 +0,0 @@
-# Copyright 1999-2010 Gentoo Foundation
-# Distributed under the terms of the GNU General Public License v2
-# $Header: $
-
-inherit fortran eutils gnuconfig toolchain-funcs
-
-FORTRAN="g77 gfortran ifc"
-
-SRC="ftp://ftp.ccp4.ac.uk/ccp4"
-
-#UPDATE="04_03_09"
-#PATCHDATE="090511"
-
-MY_P="${P/-libs}"
-
-PATCH_TOT="0"
-# Here's a little scriptlet to generate this list from the provided
-# index.patches file
-#
-# i=1; while read -a line; do [[ ${line//#} != ${line} ]] && continue;
-# echo "PATCH${i}=( ${line[1]}"; echo "${line[0]} )"; (( i++ )); done <
-# index.patches
-#PATCH1=( src/topp_
-#topp.f-r1.16.2.5-r1.16.2.6.diff )
-#PATCH2=( .
-#configure-r1.372.2.18-r1.372.2.19.diff )
-
-DESCRIPTION="Protein X-ray crystallography toolkit"
-HOMEPAGE="http://www.ccp4.ac.uk/"
-SRC_URI="${SRC}/${PV}/${MY_P}-core-src.tar.gz"
-# 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.gentooexperimental.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/${!NAME}"
-done
-
-LICENSE="ccp4"
-SLOT="0"
-KEYWORDS="~amd64 ~x86"
-IUSE=""
-
-RDEPEND="
- app-shells/tcsh
- !<sci-chemistry/ccp4-6.0.99
- =sci-libs/fftw-2*
- sci-libs/mmdb
- sci-libs/monomer-db
- virtual/lapack
- virtual/blas"
-DEPEND="${RDEPEND}"
-
-RESTRICT="mirror"
-
-S="${WORKDIR}/${MY_P}"
-
-src_unpack() {
- unpack ${A}
- cd "${S}"
-
- einfo "Applying upstream patches ..."
- for patch in $(seq $PATCH_TOT); do
- base="PATCH${patch}"
- dir=$(eval echo \${${base}[0]})
- p=$(eval echo \${${base}[1]})
- pushd "${dir}" >& /dev/null
- ccp_patch "${DISTDIR}/${p}"
- popd >& /dev/null
- done
- einfo "Done."
- echo
-
- [[ -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
-
- # gerror_ gets defined twice on ppc if you're using gfortran/g95
- ccp_patch "${FILESDIR}"/6.0.2-ppc-double-define-gerror.patch
-
- # make creation of libccif.so smooth
- ccp_patch "${FILESDIR}"/${PV}-ccif-shared.patch
-
- # lets try to build libmmdb seperatly
- ccp_patch "${FILESDIR}"/${PV}-dont-build-mmdb.patch
-
- einfo "Done." # done applying Gentoo patches
- echo
-
- gnuconfig_update
-}
-
-src_compile() {
- # Build system is broken if we set LDFLAGS
- userldflags="${LDFLAGS}"
- export SHARED_LIB_FLAGS="${LDFLAGS}"
- unset LDFLAGS
-
- # GENTOO_OSNAME can be one of:
- # irix irix64 sunos sunos64 aix hpux osf1 linux freebsd
- # linux_compaq_compilers linux_intel_compilers generic Darwin
- # ia64_linux_intel Darwin_ibm_compilers linux_ibm_compilers
- if [[ "${FORTRANC}" = "ifc" ]]; then
- if use ia64; then
- GENTOO_OSNAME="ia64_linux_intel"
- else
- # Should be valid for x86, maybe amd64
- GENTOO_OSNAME="linux_intel_compilers"
- fi
- else
- # Should be valid for x86 and amd64, at least
- GENTOO_OSNAME="linux"
- fi
-
- # Sets up env
- ln -s \
- ccp4.setup-bash \
- "${S}"/include/ccp4.setup
-
- # We agree to the license by emerging this, set in LICENSE
- sed -i \
- -e "s~^\(^agreed=\).*~\1yes~g" \
- "${S}"/configure
-
- # Fix up variables -- need to reset CCP4_MASTER at install-time
- sed -i \
- -e "s~^\(setenv CCP4_MASTER.*\)/.*~\1"${WORKDIR}"~g" \
- -e "s~^\(setenv CCP4I_TCLTK.*\)/usr/local/bin~\1/usr/bin~g" \
- "${S}"/include/ccp4.setup*
-
- # Set up variables for build
- source "${S}"/include/ccp4.setup
-
- export CC=$(tc-getCC)
- export CXX=$(tc-getCXX)
- export COPTIM=${CFLAGS}
- export CXXOPTIM=${CXXFLAGS}
- # Default to -O2 if FFLAGS is unset
- export FC=${FORTRANC}
- export FOPTIM=${FFLAGS:- -O2}
-# export CCP4_SCR="${T}"
-
- # Fix linking
-# $(tc-getCC) ${userldflags} -shared -Wl,-soname,libmmdb.so -o libmmdb.so \${MMDBOBJS} $(gcc-config -L | awk -F: '{for(i=1; i<=NF; i++) printf " -L%s", $i}') -lm -lstdc++ && \
- export SHARE_LIB="\
- $(tc-getCC) ${userldflags} -shared -Wl,-soname,libccp4c.so -o libccp4c.so \${CORELIBOBJS} \${CGENERALOBJS} \${CUCOBJS} \${CMTZOBJS} \${CMAPOBJS} \${CSYMOBJS} -L.. -lccif $(gcc-config -L | awk -F: '{for(i=1; i<=NF; i++) printf " -L%s", $i}') -lm && \
- ${FORTRANC} ${userldflags} -shared -Wl,-soname,libccp4f.so -o libccp4f.so \${FORTRANLOBJS} \${FINTERFACEOBJS} -L.. -lccif -L. -lccp4c -lmmdb $(gcc-config -L | awk -F: '{for(i=1; i<=NF; i++) printf " -L%s", $i}') -lstdc++ -lgfortran -lm"
-
- # Can't use econf, configure rejects unknown options like --prefix
- ./configure \
- --onlylibs \
- --with-shared-libs \
- --with-fftw=/usr \
- --with-warnings \
- --disable-cctbx \
- --disable-clipper \
- --tmpdir="${TMPDIR}" \
- ${GENTOO_OSNAME} || die "econf failed"
- emake -j1 onlylib || die "emake failed"
-}
-
-src_install() {
- # Set up variables for build
- source "${S}"/include/ccp4.setup
-
- einstall || die "install failed"
-
- # 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
-
- # Bins
- dobin bin/{automask,diff2jpeg,diffdump,printpeaks} || die
- newbin bin/superpose superpose-ccp4 || die
-
- # Fix libdir in all *.la files
- sed -i \
- -e "s:^\(libdir=\).*:\1\'/usr/$(get_libdir)\':g" \
- "${D}"/usr/$(get_libdir)/*.la
-
- # Data
- insinto /usr/share/ccp4/data/
- doins -r "${S}"/lib/data/{*.PARM,*.prt,*.lib,*.dic,*.idl,*.cif,*.resource,*.york,*.hist,fraglib,reference_structures} || die
- dodoc "${S}"/lib/data/*.doc
- newdoc "${S}"/lib/data/README DATA-README
-
- # Include files
- insinto /usr/include
- for i in ccp4; do
- doins -r "${S}"/include/${i} || die
- done
-}
-
-# Epatch wrapper for bulk patching
-ccp_patch() {
- EPATCH_SINGLE_MSG=" ${1##*/} ..." epatch ${1}
-}
diff --git a/sci-libs/ccp4-libs/files/6.0.2-ppc-double-define-gerror.patch b/sci-libs/ccp4-libs/files/6.0.2-ppc-double-define-gerror.patch
deleted file mode 100644
index a77d9494a..000000000
--- a/sci-libs/ccp4-libs/files/6.0.2-ppc-double-define-gerror.patch
+++ /dev/null
@@ -1,11 +0,0 @@
---- ccp4-6.0.1.orig/lib/src/library_f.c 2006-06-12 07:06:22.000000000 -0700
-+++ ccp4-6.0.1/lib/src/library_f.c 2006-06-12 07:21:56.000000000 -0700
-@@ -716,7 +716,7 @@
-
- #endif /* end of apple xlf support */
-
--#if ( defined (__linux__) && defined (_CALL_SYSV) )
-+#if ( defined (__linux__) && defined (_CALL_SYSV) && ! defined(G95) && ! defined (GFORTRAN) )
- /* linuxppc xlf support */
- void gerror_ (str, Lstr)
- char *str;
diff --git a/sci-libs/ccp4-libs/files/6.1.1-dont-make-dirs-in-configure.patch b/sci-libs/ccp4-libs/files/6.1.1-dont-make-dirs-in-configure.patch
deleted file mode 100644
index 583697cea..000000000
--- a/sci-libs/ccp4-libs/files/6.1.1-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 $i/Makefile.in
-+# fi
-+# fi
-+# done
-+#fi
-
- ### sanity checks
-
diff --git a/sci-libs/ccp4-libs/files/6.1.1-glibc2.10.patch b/sci-libs/ccp4-libs/files/6.1.1-glibc2.10.patch
deleted file mode 100644
index 6e3997647..000000000
--- a/sci-libs/ccp4-libs/files/6.1.1-glibc2.10.patch
+++ /dev/null
@@ -1,22 +0,0 @@
---- lib/ccif/configure.in 2009-06-10 13:52:59.000000000 +0200
-+++ lib/ccif/configure.in.new 2009-06-10 14:04:31.000000000 +0200
-@@ -363,7 +363,7 @@
- fi
- SHARED_LIB_CMD='$(LD) $(SHARED_LIB_FLAGS) -shared -soname $(SHARED_LIB_NAME) \\\
- --whole-archive '"$SHARED_LIB_RESTRICT"' $L \\\
-- $(RX_LFLAG) -o $(SHARED_LIB_NAME)'
-+ $(RX_LFLAG) -o $(SHARED_LIB_NAME) -lm'
- SHARED_LIB_EXPORTS_CMD='cp libccif-universal-ld.lis $(SHARED_LIB_EXPORTS)'
- fi
- ;;
---- lib/ccif/configure 2009-06-10 14:26:58.000000000 +0200
-+++ lib/ccif/configure.new 2009-06-10 14:43:31.000000000 +0200
-@@ -1807,7 +1807,7 @@
- SHARED_LIB_CMD='$(LD) $(SHARED_LIB_CFLAGS) -shared -soname \\\
- $(SHARED_LIB_NAME) \\\
- --whole-archive $L \\\
-- -o $(SHARED_LIB_NAME)'
-+ -o $(SHARED_LIB_NAME) -lm'
- SHARED_LIB_EXPORTS_CMD=''
- fi
- ;;
diff --git a/sci-libs/ccp4-libs/files/6.1.1-link-proberly.patch b/sci-libs/ccp4-libs/files/6.1.1-link-proberly.patch
deleted file mode 100644
index 0780314f0..000000000
--- a/sci-libs/ccp4-libs/files/6.1.1-link-proberly.patch
+++ /dev/null
@@ -1,255 +0,0 @@
---- lib/src/Makefile.in 2009-03-02 17:53:15.000000000 +0100
-+++ lib/src/Makefile.in.new 2009-03-02 17:52:09.000000000 +0100
-@@ -172,9 +172,8 @@
-
- ##### Makefile targets ######
-
--all: fsplit $(LMMDB) $(LC) $(LF) $(SCRIPT_MODULES)
-+all: fsplit $(LMMDB) LMMDB_SO $(LC) LC_SO $(LF) LF_SO $(SCRIPT_MODULES)
- # maybe create shared library
-- $(SHARE_LIB)
-
- $(LC) : $(CORELIBOBJS) $(CGENERALOBJS) $(CUCOBJS) $(CMTZOBJS) $(CMAPOBJS) $(CSYMOBJS)
- $(AR) $(LC) $?
-@@ -186,6 +185,27 @@
- $(AR) $(LF) $(FINTERFACEOBJS)
- $(RANLIB) $@
-
-+LMMDB_SO :
-+ $(CC) $(COPTIM) -shared -Wl,-soname,libmmdb.so.0 -o libmmdb.so.0.0.0 \
-+ $(MMDBOBJS) && \
-+ ln -sf libmmdb.so.0.0.0 libmmdb.so.0 && \
-+ ln -sf libmmdb.so.0.0.0 libmmdb.so
-+
-+LC_SO :
-+ $(CC) $(COPTIM) -shared -Wl,-soname,libccp4c.so.0 -o libccp4c.so.0.0.0 \
-+ $(CORELIBOBJS) $(CGENERALOBJS) $(CUCOBJS) $(CMTZOBJS) $(CMAPOBJS) $(CSYMOBJS) && \
-+ ln -sf libccp4c.so.0.0.0 libccp4c.so.0 && \
-+ ln -sf libccp4c.so.0.0.0 libccp4c.so
-+
-+LF_SO :
-+ $(FC) $(FOPTIM) -shared -Wl,-soname,libccp4f.so.0 -o libccp4f.so.0.0.0 \
-+ parser.dir/*.o ccplib.dir/*.o lgglib.dir/*.o plot84lib.dir/*.o \
-+ libhtml.dir/*.o pxxml.dir/*.o rwbrook.dir/*.o cciflib.dir/*.o \
-+ harvlib.dir/*.o keyparse.dir/*.o dna_output.dir/*.o plotsubs.dir/*.o \
-+ modlib.dir/*.o fftlib.dir/*.o unix.dir/*.o pack_f.o pack_c.o $(FINTERFACEOBJS) && \
-+ ln -sf libccp4f.so.0.0.0 libccp4f.so.0 && \
-+ ln -sf libccp4f.so.0.0.0 libccp4f.so
-+
-#@@ -186,6 +185,27 @@
-# $(AR) $(LF) $(FINTERFACEOBJS)
-# $(RANLIB) $@
-#
-#+LMMDB_SO :
-#+ $(CC) $(COPTIM) -shared -Wl,-soname,libmmdb.so.0 -o ../libmmdb.so.0.0.0 \
-#+ $(MMDBOBJS) && \
-#+ ln -sf libmmdb.so.0.0.0 ../libmmdb.so.0 && \
-#+ ln -sf libmmdb.so.0.0.0 ../libmmdb.so
-#+
-#+LC_SO :
-#+ $(CC) $(COPTIM) -shared -Wl,-soname,libccp4_c.so.0 -o ../libccp4_c.so.0.0.0 \
-#+ $(CORELIBOBJS) $(CGENERALOBJS) $(CUCOBJS) $(CMTZOBJS) $(CMAPOBJS) $(CSYMOBJS) && \
-#+ ln -sf libccp4_c.so.0.0.0 ../libccp4_c.so.0 && \
-#+ ln -sf libccp4_c.so.0.0.0 ../libccp4_c.so
-#+
-#+LF_SO :
-#+ $(FC) $(FOPTIM) -shared -Wl,-soname,libccp4_f.so.0 -o ../libccp4_f.so.0.0.0 \
-#+ parser.dir/*.o ccplib.dir/*.o lgglib.dir/*.o plot84lib.dir/*.o \
-#+ libhtml.dir/*.o pxxml.dir/*.o rwbrook.dir/*.o cciflib.dir/*.o \
-#+ harvlib.dir/*.o keyparse.dir/*.o dna_output.dir/*.o plotsubs.dir/*.o \
-#+ modlib.dir/*.o fftlib.dir/*.o unix.dir/*.o pack_f.o pack_c.o $(FINTERFACEOBJS) && \
-#+ ln -sf libccp4_f.so.0.0.0 ../libccp4_f.so.0 && \
-#+ ln -sf libccp4_f.so.0.0.0 ../libccp4_f.so
-#+
- # cmtz library only
-
- cmtz: $(LCMTZ)
-@@ -339,9 +356,7 @@
- fi
- cd parser.dir && \
- for i in `pwd`/*.$F; do \
-- $(FC) -c $(FFLAGS) $(SHARED_LIB_FFLAGS) $$i; done\
-- && $(AR) ../$(LF) *.o
-- rm -f parser.dir/*.o
-+ $(FC) -c $(FFLAGS) $(SHARED_LIB_FFLAGS) $$i; done
- parser : parser.o
- $(RANLIB) $(LF)
-
-@@ -351,9 +366,7 @@
- echo ' END' >> ccplib.dir/ccplib.$F
- cd ccplib.dir && $(fsplit_dir)/fsplit $(srcdir)/ccplib.f >/dev/null && $(RMEMPTY) && \
- for i in `pwd`/*.$F; do \
-- $(FC) -c $(FFLAGS) $(SHARED_LIB_FFLAGS) $$i; done\
-- && $(AR) ../$(LF) *.o
-- rm -f ccplib.dir/*.o
-+ $(FC) -c $(FFLAGS) $(SHARED_LIB_FFLAGS) $$i; done
- ccplib : ccplib.o
- $(RANLIB) $(LF)
-
-@@ -364,9 +377,7 @@
- @$(SETFLAGS) ; \
- cd lgglib.dir && $(fsplit_dir)/fsplit $(srcdir)/lgglib.f >/dev/null && $(RMEMPTY) && \
- for i in `pwd`/*.$F; do \
-- eval $(FC) -c $${lgglib_FLAGS-"$(FFLAGS)"} $(SHARED_LIB_FFLAGS) $$i; done\
-- && $(AR) ../$(LF) *.o
-- rm -f lgglib.dir/*.o
-+ eval $(FC) -c $${lgglib_FLAGS-"$(FFLAGS)"} $(SHARED_LIB_FFLAGS) $$i; done
- lgglib : lgglib.o
- $(RANLIB) $(LF)
-
-@@ -376,9 +387,7 @@
- echo ' END' >> plot84lib.dir/plot84lib.$F
- cd plot84lib.dir && $(fsplit_dir)/fsplit $(srcdir)/plot84lib.f >/dev/null && $(RMEMPTY) && \
- for i in `pwd`/*.$F; do \
-- $(FC) -c $(FFLAGS) $(SHARED_LIB_FFLAGS) $$i; done\
-- && $(AR) ../$(LF) *.o
-- rm -f plot84lib.dir/*.o
-+ $(FC) -c $(FFLAGS) $(SHARED_LIB_FFLAGS) $$i; done
- plot84lib : plot84lib.o
- $(RANLIB) $(LF)
-
-@@ -388,9 +397,7 @@
- echo ' END' >> libhtml.dir/libhtml.$F
- cd libhtml.dir && $(fsplit_dir)/fsplit $(srcdir)/libhtml.f >/dev/null && $(RMEMPTY) && \
- for i in `pwd`/*.$F; do \
-- $(FC) -c $(FFLAGS) $(SHARED_LIB_FFLAGS) $$i; done\
-- && $(AR) ../$(LF) *.o
-- rm -f libhtml.dir/*.o
-+ $(FC) -c $(FFLAGS) $(SHARED_LIB_FFLAGS) $$i; done
- libhtml : libhtml.o
- $(RANLIB) $(LF)
-
-@@ -400,9 +407,7 @@
- echo ' END' >> pxxml.dir/pxxml.$F
- cd pxxml.dir && $(fsplit_dir)/fsplit $(srcdir)/pxxml.f >/dev/null && $(RMEMPTY) && \
- for i in `pwd`/*.$F; do \
-- $(FC) -c $(FFLAGS) $(SHARED_LIB_FFLAGS) $$i; done\
-- && $(AR) ../$(LF) *.o
-- rm -f pxxml.dir/*.o
-+ $(FC) -c $(FFLAGS) $(SHARED_LIB_FFLAGS) $$i; done
- pxxml : pxxml.o
- $(RANLIB) $(LF)
-
-@@ -412,9 +417,7 @@
- echo ' END' >> rwbrook.dir/rwbrook.$F
- cd rwbrook.dir && $(fsplit_dir)/fsplit $(srcdir)/rwbrook.f >/dev/null && $(RMEMPTY) && \
- for i in `pwd`/*.$F; do \
-- $(FC) -c $(FFLAGS) $(SHARED_LIB_FFLAGS) $$i; done\
-- && $(AR) ../$(LF) *.o
-- rm -f rwbrook.dir/*.o
-+ $(FC) -c $(FFLAGS) $(SHARED_LIB_FFLAGS) $$i; done
- rwbrook : rwbrook.o
- $(RANLIB) $(LF)
-
-@@ -424,9 +427,7 @@
- echo ' END' >> cciflib.dir/cciflib.$F
- cd cciflib.dir && $(fsplit_dir)/fsplit $(srcdir)/cciflib.f >/dev/null && $(RMEMPTY) && \
- for i in `pwd`/*.$F; do \
-- $(FC) -c $(FFLAGS) $(SHARED_LIB_FFLAGS) -I$(srcdir) $$i; done\
-- && $(AR) ../$(LF) *.o
-- rm -f cciflib.dir/*.o
-+ $(FC) -c $(FFLAGS) $(SHARED_LIB_FFLAGS) -I$(srcdir) $$i; done
- cciflib : cciflib.o
- $(RANLIB) $(LF)
-
-@@ -440,9 +441,7 @@
- && $(AR) ../$(LF) *.o ; else \
- cd harvlib.dir && $(fsplit_dir)/fsplit $(srcdir)/harv_dummy.f >/dev/null && $(RMEMPTY) && \
- for i in `pwd`/*.$F; do \
-- $(FC) -c $(FFLAGS) $(SHARED_LIB_FFLAGS) -I$(srcdir) $$i; done\
-- && $(AR) ../$(LF) *.o ; fi
-- rm -f harvlib.dir/*.o
-+ $(FC) -c $(FFLAGS) $(SHARED_LIB_FFLAGS) -I$(srcdir) $$i; done; fi
- harvlib : harvlib.o
- $(RANLIB) $(LF)
-
-@@ -452,9 +451,7 @@
- echo ' END' >> keyparse.dir/keyparse.$F
- cd keyparse.dir && $(fsplit_dir)/fsplit $(srcdir)/keyparse.f >/dev/null && $(RMEMPTY) && \
- for i in `pwd`/*.$F; do \
-- $(FC) -c $(FFLAGS) $(SHARED_LIB_FFLAGS) $$i; done\
-- && $(AR) ../$(LF) *.o
-- rm -f keyparse.dir/*.o
-+ $(FC) -c $(FFLAGS) $(SHARED_LIB_FFLAGS) $$i; done
- keyparse : keyparse.o
- $(RANLIB) $(LF)
-
-@@ -464,9 +461,7 @@
- echo ' END' >> dna_output.dir/dna_output.$F
- cd dna_output.dir && $(fsplit_dir)/fsplit $(srcdir)/dna_output.f >/dev/null && $(RMEMPTY) && \
- for i in `pwd`/*.$F; do \
-- $(FC) -I$(srcdir) -c $(FFLAGS) $(SHARED_LIB_FFLAGS) $$i; done\
-- && $(AR) ../$(LF) *.o
-- rm -f dna_output.dir/*.o
-+ $(FC) -I$(srcdir) -c $(FFLAGS) $(SHARED_LIB_FFLAGS) $$i; done
- dna_output : dna_output.o
- $(RANLIB) $(LF)
-
-@@ -474,10 +469,9 @@
- # for ipdisp. May be useful but could be moved.
- $(LF)(pack_c.o): $(srcdir)/pack_c.c $(srcdir)/pack_c.h
- $(CC) $(CFLAGS) $(SHARED_LIB_CFLAGS) -I$(srcdir) -c $(srcdir)/pack_c.c
-- $(AR) $(LF) pack_c.o && rm pack_c.o
-+ $(AR) $(LF) pack_c.o
- $(LF)(pack_f.o): $(srcdir)/pack_f.f
-- $(FC) -c $(FFLAGS) $(SHARED_LIB_FFLAGS) $(srcdir)/pack_f.$(F) && $(AR) $(LF) pack_f.o \
-- && rm pack_f.o
-+ $(FC) -c $(FFLAGS) $(SHARED_LIB_FFLAGS) $(srcdir)/pack_f.$(F) && $(AR) $(LF) pack_f.o
- pack: $(LF)(pack_c.o) $(LF)(pack_f.o)
- $(RANLIB) $(LF)
-
-@@ -488,9 +482,7 @@
- echo ' END' >> sorting_main.dir/sorting_main.$F
- cd sorting_main.dir && $(fsplit_dir)/fsplit $(srcdir)/sorting_main.f >/dev/null && $(RMEMPTY) && \
- for i in `pwd`/*.$F; do \
-- $(FC) -c $(FFLAGS) $(SHARED_LIB_FFLAGS) $$i; done\
-- && $(AR) ../$(LF) *.o
-- rm -f sorting_main.dir/*.o
-+ $(FC) -c $(FFLAGS) $(SHARED_LIB_FFLAGS) $$i; done
- sorting_main : sorting_main.o
- $(RANLIB) $(LF)
-
-@@ -500,9 +492,7 @@
- echo ' END' >> plotsubs.dir/plotsubs.$F
- cd plotsubs.dir && $(fsplit_dir)/fsplit $(srcdir)/plotsubs.f >/dev/null && $(RMEMPTY) && \
- for i in `pwd`/*.$F; do \
-- $(FC) -c $(FFLAGS) $(SHARED_LIB_FFLAGS) $$i; done\
-- && $(AR) ../$(LF) *.o
-- rm -f plotsubs.dir/*.o
-+ $(FC) -c $(FFLAGS) $(SHARED_LIB_FFLAGS) $$i; done
- plotsubs : plotsubs.o
- $(RANLIB) $(LF)
-
-@@ -512,9 +502,7 @@
- echo ' END' >> modlib.dir/modlib.$F
- cd modlib.dir && $(fsplit_dir)/fsplit $(srcdir)/modlib.f >/dev/null && $(RMEMPTY) && \
- for i in `pwd`/*.$F; do \
-- $(FC) -c $(FFLAGS) $(SHARED_LIB_FFLAGS) $$i; done\
-- && $(AR) ../$(LF) *.o
-- rm -f modlib.dir/*.o
-+ $(FC) -c $(FFLAGS) $(SHARED_LIB_FFLAGS) $$i; done
- modlib : modlib.o
- $(RANLIB) $(LF)
-
-@@ -524,9 +512,7 @@
- echo ' END' >> fftlib.dir/fftlib.$F
- cd fftlib.dir && $(fsplit_dir)/fsplit $(srcdir)/fftlib.f >/dev/null && $(RMEMPTY) && \
- for i in `pwd`/*.$F; do \
-- $(FC) -c $(FFLAGS) $(SHARED_LIB_FFLAGS) $$i; done \
-- && $(AR) ../$(LF) *.o
-- rm -f fftlib.dir/*.o
-+ $(FC) -c $(FFLAGS) $(SHARED_LIB_FFLAGS) $$i; done
- fftlib : fftlib.o
- $(RANLIB) $(LF)
-
-@@ -541,9 +527,7 @@
- echo ' END' >> unix.dir/unix.f
- cd unix.dir && $(fsplit_dir)/fsplit ../unix.f >/dev/null && $(RMEMPTY) && \
- for i in `pwd`/*.$F; do \
-- $(FC) -c $(FFLAGS) $(SHARED_LIB_FFLAGS) $$i; done\
-- && $(AR) ../$(LF) *.o
-- rm -f unix.dir/*.o
-+ $(FC) -c $(FFLAGS) $(SHARED_LIB_FFLAGS) $$i; done
- unix : unix.o
- $(RANLIB) $(LF)
-
diff --git a/sci-libs/ccp4-libs/files/6.1.2-64bit.patch b/sci-libs/ccp4-libs/files/6.1.2-64bit.patch
deleted file mode 100644
index 390600b71..000000000
--- a/sci-libs/ccp4-libs/files/6.1.2-64bit.patch
+++ /dev/null
@@ -1,205 +0,0 @@
-diff --git a/ccp4-6.1.2/lib/DiffractionImage/Rigaku/RaxisImage.h b/ccp4-6.1.2/lib/DiffractionImage/Rigaku/RaxisImage.h
-index e02b72b..8a9611c 100755
---- a/ccp4-6.1.2/lib/DiffractionImage/Rigaku/RaxisImage.h
-+++ b/ccp4-6.1.2/lib/DiffractionImage/Rigaku/RaxisImage.h
-@@ -50,6 +50,7 @@
- #include <iostream>
- #include <fstream>
- #include <sstream>
-+#include <stdint.h>
-
- /****************************************************************************
- * Definitions *
-@@ -92,7 +93,7 @@ struct RigakuHeader {
- float crnt; /* generator current (mA) */
- char focs[12]; /* focus info */
- char optc[80]; /* xray memo */
-- long cyld; /* IP shape, 0=flat,1=cylinder */
-+ int32_t cyld; /* IP shape, 0=flat,1=cylinder */
- float weis; /* Weissenberg oscillation 1 */
- char res2[56]; /* reserved space for future use */
-
-@@ -101,7 +102,7 @@ struct RigakuHeader {
- float phi0; /* datum phi angle (deg) */
- float phis; /* phi oscillation start angle (deg) */
- float phie; /* phi oscillation end angle (deg) */
-- long oscn; /* frame number */
-+ int32_t oscn; /* frame number */
- float fext; /* exposure time (min) */
- float drtx; /* direct beam X position */
- float drtz; /* direct beam Z position */
-@@ -113,31 +114,31 @@ struct RigakuHeader {
- /* This space is now used for storing the scan
- template information - tlh, 01 Feb 1999 */
-
-- long xpxl; /* number of pixels in X direction */
-- long zpxl; /* number of pixels in Z direction */
-+ int32_t xpxl; /* number of pixels in X direction */
-+ int32_t zpxl; /* number of pixels in Z direction */
- float xsiz; /* size of pixel in X direction (mm) */
- float zsiz; /* size of pixel in Z direction (mm) */
-- long rlng; /* record length (bytes) */
-- long rnum; /* number of records (lines) in image */
-- long ipst; /* starting line number */
-- long ipnm; /* IP number */
-+ int32_t rlng; /* record length (bytes) */
-+ int32_t rnum; /* number of records (lines) in image */
-+ int32_t ipst; /* starting line number */
-+ int32_t ipnm; /* IP number */
- float rato; /* photomultiplier output hi/lo ratio */
- float ft_1; /* fading time, end of exposure to start of read */
- float ft_2; /* fading time, end of exposure to end of read */
- char host[10]; /* type of computer (IRIS, VAX) => endian */
- char ip[10]; /* type of IP */
-- long dr_x; /* horizontal scanning code: 0=left->right, 1=>right->left */
-- long dr_z; /* vertical scanning code: 0=down->up, 1=up->down */
-- long drxz; /* front/back scanning code: 0=front, 1=back */
-+ int32_t dr_x; /* horizontal scanning code: 0=left->right, 1=>right->left */
-+ int32_t dr_z; /* vertical scanning code: 0=down->up, 1=up->down */
-+ int32_t drxz; /* front/back scanning code: 0=front, 1=back */
- float shft; /* pixel shift, R-AXIS V */
- float ineo; /* intensity ratio E/O R-AXIS V */
-- long majc; /* magic number to indicate next values are legit */
-- long naxs; /* Number of goniometer axes */
-+ int32_t majc; /* magic number to indicate next values are legit */
-+ int32_t naxs; /* Number of goniometer axes */
- float gvec[5][3]; /* Goniometer axis vectors */
- float gst[5]; /* Start angles for each of 5 axes */
- float gend[5]; /* End angles for each of 5 axes */
- float goff[5]; /* Offset values for each of 5 axes */
-- long saxs; /* Which axis is the scan axis? */
-+ int32_t saxs; /* Which axis is the scan axis? */
- char gnom[40]; /* Names of the axes (space or comma separated?) */
-
- /*
-@@ -148,17 +149,17 @@ struct RigakuHeader {
- char file[16]; /* */
- char cmnt[20]; /* */
- char smpl[20]; /* */
-- long iext; /* */
-- long reso; /* */
-- long save; /* */
-- long dint; /* */
-- long byte; /* */
-- long init; /* */
-- long ipus; /* */
-- long dexp; /* */
-- long expn; /* */
-- long posx[20]; /* */
-- long posy[20]; /* */
-+ int32_t iext; /* */
-+ int32_t reso; /* */
-+ int32_t save; /* */
-+ int32_t dint; /* */
-+ int32_t byte; /* */
-+ int32_t init; /* */
-+ int32_t ipus; /* */
-+ int32_t dexp; /* */
-+ int32_t expn; /* */
-+ int32_t posx[20]; /* */
-+ int32_t posy[20]; /* */
- int xray; /* */
- char res5[768]; /* reserved space for future use */
- };
-@@ -213,10 +214,10 @@ bool ReadImageBuffer(std::ifstream &InputFile,unsigned short * const pImageBuffe
- // is 2 bytes.
- unsigned short Swap(unsigned short Value);
-
-- // This routine swaps the long <VAR>Value</VAR> so that the endianness
-+ // This routine swaps the int32_t <VAR>Value</VAR> so that the endianness
- // of <VAR>Value</VAR> is reversed and then returns the swapped value.
-- // This routine assumes that the size of a long is 4 bytes.
--long Swap(long Value);
-+ // This routine assumes that the size of a int32_t is 4 bytes.
-+int32_t Swap(int32_t Value);
-
- // This routine swaps the float <VAR>Value</VAR> so that the endianness
- // of <VAR>Value</VAR> is reversed and then returns the swapped value.
-@@ -225,14 +226,14 @@ long Swap(long Value);
- float Swap(float Value);
-
- // This routine swaps the values in a Rigaku-style header,
-- // <VAR>Header</VAR> so that the endianness of the <CODE>long</CODE>
-+ // <VAR>Header</VAR> so that the endianness of the <CODE>int32_t</CODE>
- // and </CODE>float</CODE> is reversed.
- void Swap(RigakuHeader &Header);
-
-- // This routine returns a long containing the actual value of a packed
-+ // This routine returns a int32_t containing the actual value of a packed
- // R-AXIS image pixel, <VAR>PixelValue</VAR>. The Rigaku-style header
- // contains information concerning the packing scheme used.
--long UnPackPixelValue(const RigakuHeader &Header,
-+int32_t UnPackPixelValue(const RigakuHeader &Header,
- const unsigned short PixelValue);
-
- // This routine writes out pixel values for some prefined pixel positions
-diff --git a/ccp4-6.1.2/lib/DiffractionImage/Rigaku/ReadRAXISImages.cpp b/ccp4-6.1.2/lib/DiffractionImage/Rigaku/ReadRAXISImages.cpp
-index 882d93d..3df1918 100755
---- a/ccp4-6.1.2/lib/DiffractionImage/Rigaku/ReadRAXISImages.cpp
-+++ b/ccp4-6.1.2/lib/DiffractionImage/Rigaku/ReadRAXISImages.cpp
-@@ -87,7 +87,7 @@ bool ReadHeader(std::ifstream &InputFile,
-
- // Read the additional padding in the header
-
-- long size = Header.rlng-MinimumRigakuHeaderLength;
-+ int32_t size = Header.rlng-MinimumRigakuHeaderLength;
- p = new char [size];
- InputFile.read(p,size);
- delete [] p;
-@@ -108,7 +108,7 @@ bool ReadImageBuffer(std::ifstream &InputFile,unsigned short * const pImageBuffe
- // 2 bytes/pixel.
- RigakuHeader Header;
- ReadHeader(InputFile, Header);
-- long size = Header.rlng*Header.rnum/2;
-+ int32_t size = Header.rlng*Header.rnum/2;
-
- // Read in the data.
-
-@@ -153,9 +153,9 @@ unsigned short Swap(const unsigned short Value)
-
- /****************************************************************************
- ****************************************************************************/
--long Swap(const long Value)
-+int32_t Swap(const int32_t Value)
- {
-- long swap = Value;
-+ int32_t swap = Value;
- char *p = reinterpret_cast<char *>(&swap);
-
- char tmp = p[0];
-@@ -192,7 +192,7 @@ float Swap(const float Value)
- void Swap(RigakuHeader &Header)
- {
-
--// Swap the bytes in the long elements of the header.
-+// Swap the bytes in the int32_t elements of the header.
-
- Header.cyld = Swap(Header.cyld);
- Header.oscn = Swap(Header.oscn);
-@@ -257,7 +257,7 @@ void Swap(RigakuHeader &Header)
-
- /****************************************************************************
- ****************************************************************************/
--long UnPackPixelValue(const RigakuHeader &Header,
-+int32_t UnPackPixelValue(const RigakuHeader &Header,
- const unsigned short PixelValue)
- {
- // Pixels are packed so that if the most significant bit is set, then
-@@ -274,7 +274,7 @@ long UnPackPixelValue(const RigakuHeader &Header,
-
- // We only need to use the lower 15 bits of the value to uncompress it.
-
-- long Value = 0x7fff&PixelValue;
-+ int32_t Value = 0x7fff&PixelValue;
-
- // Shift the value by the ratio in the header.
-
-@@ -296,7 +296,7 @@ void OutputSamplePixelValues(const RigakuHeader &Header,
- std::cout << " First pixel (0," << Header.ipst << ") in image = " <<
- UnPackPixelValue(Header,*pImageBuffer) << std::endl;
-
-- long index = (Header.rnum/2-1)*Header.xpxl+(Header.xpxl/2-1);
-+ int32_t index = (Header.rnum/2-1)*Header.xpxl+(Header.xpxl/2-1);
- std::cout << " Middle pixel (" << Header.xpxl/2 << ',' <<
- Header.rnum/2+Header.ipst << ") in image = " <<
- UnPackPixelValue(Header,pImageBuffer[index]) << std::endl;
diff --git a/sci-libs/ccp4-libs/files/6.1.2-ccif-shared.patch b/sci-libs/ccp4-libs/files/6.1.2-ccif-shared.patch
deleted file mode 100644
index ca18d75bc..000000000
--- a/sci-libs/ccp4-libs/files/6.1.2-ccif-shared.patch
+++ /dev/null
@@ -1,33 +0,0 @@
---- configure 2009-08-04 22:35:34.000000000 +0200
-+++ configure.new 2009-08-04 22:54:32.000000000 +0200
-@@ -3136,8 +3136,8 @@
- 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/$$.cache_file ) || \
-- ./configure $xopts --libdir=${libdir} --srcdir=${srcdir}/lib/ccif
-+ ./configure $xopts --libdir=${libdir} --srcdir=${srcdir}/lib/ccif --cache-file=/tmp/$$.cache_file --enable-shared-lib ) || \
-+ ./configure $xopts --libdir=${libdir} --srcdir=${srcdir}/lib/ccif --enable-shared-lib
- rm -f /tmp/$$.cache_file
- if [ "X$LIBFOPTIM" != "X" ]; then
- FOPTIM=$FOPTIM_save
---- lib/ccif/configure 2009-08-04 22:35:37.000000000 +0200
-+++ lib/ccif/configure.new 2009-08-04 23:05:44.000000000 +0200
-@@ -5568,7 +5568,7 @@
- enable_shared_lib=no
- ;;
-
-- i?86-unknown-linux | i?86-pc-linux-gnu )
-+ i?86-unknown-linux | i?86-pc-linux-gnu | x86_64-unknown-linux-gnu)
- if test $enable_shared_lib = yes ; then
-
- SO_LOC_VAR='LD_LIBRARY_PATH'
-@@ -5585,7 +5585,7 @@
- else
- SHARED_LIB_PATH='LD_LIBRARY_PATH=`pwd`'
- fi
-- SHARED_LIB_CMD='$(CC) $(SHARED_LIB_FLAGS) -shared -Wl,-soname -Wl,$(SHARED_LIB_NAME) '"$SHARED_LIB_RESTRICT"' ${LOBJS} $(RX_LFLAG) -o $(SHARED_LIB_NAME)'
-+ SHARED_LIB_CMD='$(CC) $(SHARED_LIB_FLAGS) -shared -Wl,-soname -Wl,$(SHARED_LIB_NAME) '"$SHARED_LIB_RESTRICT"' ${LOBJS} $(RX_LFLAG) -o $(SHARED_LIB_NAME) -lm'
- # SHARED_LIB_EXPORTS_CMD='cp libccif-universal-ld.lis $(SHARED_LIB_EXPORTS)'
- SHARED_LIB_EXPORTS_CMD=''
- fi
diff --git a/sci-libs/ccp4-libs/files/6.1.2-dont-build-mmdb.patch b/sci-libs/ccp4-libs/files/6.1.2-dont-build-mmdb.patch
deleted file mode 100644
index b3fefacda..000000000
--- a/sci-libs/ccp4-libs/files/6.1.2-dont-build-mmdb.patch
+++ /dev/null
@@ -1,26 +0,0 @@
---- lib/src/Makefile.in 2009-06-18 15:44:08.000000000 +0200
-+++ lib/src/Makefile.in.new 2009-08-11 11:58:25.000000000 +0200
-@@ -176,7 +176,7 @@
-
- ##### Makefile targets ######
-
--all: fsplit $(LMMDB) $(LC) $(LF) $(SCRIPT_MODULES)
-+all: fsplit $(LC) $(LF) $(SCRIPT_MODULES)
- # maybe create shared library
- $(SHARE_LIB)
-
---- lib/src/Makefile.in 2009-06-18 15:44:08.000000000 +0200
-+++ lib/src/Makefile.in.new 2009-08-11 12:17:53.000000000 +0200
-@@ -716,11 +716,9 @@
- rm -f $(DESTDIR)$(includedir)/mmdb/$$f; \
- done
-
--install : all install-ccp4HEADERS install-mmdbHEADERS
-- $(INSTALL_DATA) `pwd`/$(LMMDB) $(libdir)/$(LMMDB)
-+install : all install-ccp4HEADERS
- $(INSTALL_DATA) `pwd`/$(LC) $(libdir)/$(LC)
- $(INSTALL_DATA) `pwd`/$(LF) $(libdir)/$(LF)
-- $(RANLIB) $(libdir)/$(LMMDB)
- $(RANLIB) $(libdir)/$(LC)
- $(RANLIB) $(libdir)/$(LF)
- $(SHARE_INST)
diff --git a/sci-libs/ccp4-libs/files/6.1.2-dont-make-dirs-in-configure.patch b/sci-libs/ccp4-libs/files/6.1.2-dont-make-dirs-in-configure.patch
deleted file mode 100644
index 583697cea..000000000
--- a/sci-libs/ccp4-libs/files/6.1.2-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 $i/Makefile.in
-+# fi
-+# fi
-+# done
-+#fi
-
- ### sanity checks
-
diff --git a/sci-libs/ccp4-libs/files/6.1.2-glibc2.10.patch b/sci-libs/ccp4-libs/files/6.1.2-glibc2.10.patch
deleted file mode 100644
index 6e3997647..000000000
--- a/sci-libs/ccp4-libs/files/6.1.2-glibc2.10.patch
+++ /dev/null
@@ -1,22 +0,0 @@
---- lib/ccif/configure.in 2009-06-10 13:52:59.000000000 +0200
-+++ lib/ccif/configure.in.new 2009-06-10 14:04:31.000000000 +0200
-@@ -363,7 +363,7 @@
- fi
- SHARED_LIB_CMD='$(LD) $(SHARED_LIB_FLAGS) -shared -soname $(SHARED_LIB_NAME) \\\
- --whole-archive '"$SHARED_LIB_RESTRICT"' $L \\\
-- $(RX_LFLAG) -o $(SHARED_LIB_NAME)'
-+ $(RX_LFLAG) -o $(SHARED_LIB_NAME) -lm'
- SHARED_LIB_EXPORTS_CMD='cp libccif-universal-ld.lis $(SHARED_LIB_EXPORTS)'
- fi
- ;;
---- lib/ccif/configure 2009-06-10 14:26:58.000000000 +0200
-+++ lib/ccif/configure.new 2009-06-10 14:43:31.000000000 +0200
-@@ -1807,7 +1807,7 @@
- SHARED_LIB_CMD='$(LD) $(SHARED_LIB_CFLAGS) -shared -soname \\\
- $(SHARED_LIB_NAME) \\\
- --whole-archive $L \\\
-- -o $(SHARED_LIB_NAME)'
-+ -o $(SHARED_LIB_NAME) -lm'
- SHARED_LIB_EXPORTS_CMD=''
- fi
- ;;
diff --git a/sci-libs/ccp4-libs/files/6.1.2-link-proberly.patch b/sci-libs/ccp4-libs/files/6.1.2-link-proberly.patch
deleted file mode 100644
index 0780314f0..000000000
--- a/sci-libs/ccp4-libs/files/6.1.2-link-proberly.patch
+++ /dev/null
@@ -1,255 +0,0 @@
---- lib/src/Makefile.in 2009-03-02 17:53:15.000000000 +0100
-+++ lib/src/Makefile.in.new 2009-03-02 17:52:09.000000000 +0100
-@@ -172,9 +172,8 @@
-
- ##### Makefile targets ######
-
--all: fsplit $(LMMDB) $(LC) $(LF) $(SCRIPT_MODULES)
-+all: fsplit $(LMMDB) LMMDB_SO $(LC) LC_SO $(LF) LF_SO $(SCRIPT_MODULES)
- # maybe create shared library
-- $(SHARE_LIB)
-
- $(LC) : $(CORELIBOBJS) $(CGENERALOBJS) $(CUCOBJS) $(CMTZOBJS) $(CMAPOBJS) $(CSYMOBJS)
- $(AR) $(LC) $?
-@@ -186,6 +185,27 @@
- $(AR) $(LF) $(FINTERFACEOBJS)
- $(RANLIB) $@
-
-+LMMDB_SO :
-+ $(CC) $(COPTIM) -shared -Wl,-soname,libmmdb.so.0 -o libmmdb.so.0.0.0 \
-+ $(MMDBOBJS) && \
-+ ln -sf libmmdb.so.0.0.0 libmmdb.so.0 && \
-+ ln -sf libmmdb.so.0.0.0 libmmdb.so
-+
-+LC_SO :
-+ $(CC) $(COPTIM) -shared -Wl,-soname,libccp4c.so.0 -o libccp4c.so.0.0.0 \
-+ $(CORELIBOBJS) $(CGENERALOBJS) $(CUCOBJS) $(CMTZOBJS) $(CMAPOBJS) $(CSYMOBJS) && \
-+ ln -sf libccp4c.so.0.0.0 libccp4c.so.0 && \
-+ ln -sf libccp4c.so.0.0.0 libccp4c.so
-+
-+LF_SO :
-+ $(FC) $(FOPTIM) -shared -Wl,-soname,libccp4f.so.0 -o libccp4f.so.0.0.0 \
-+ parser.dir/*.o ccplib.dir/*.o lgglib.dir/*.o plot84lib.dir/*.o \
-+ libhtml.dir/*.o pxxml.dir/*.o rwbrook.dir/*.o cciflib.dir/*.o \
-+ harvlib.dir/*.o keyparse.dir/*.o dna_output.dir/*.o plotsubs.dir/*.o \
-+ modlib.dir/*.o fftlib.dir/*.o unix.dir/*.o pack_f.o pack_c.o $(FINTERFACEOBJS) && \
-+ ln -sf libccp4f.so.0.0.0 libccp4f.so.0 && \
-+ ln -sf libccp4f.so.0.0.0 libccp4f.so
-+
-#@@ -186,6 +185,27 @@
-# $(AR) $(LF) $(FINTERFACEOBJS)
-# $(RANLIB) $@
-#
-#+LMMDB_SO :
-#+ $(CC) $(COPTIM) -shared -Wl,-soname,libmmdb.so.0 -o ../libmmdb.so.0.0.0 \
-#+ $(MMDBOBJS) && \
-#+ ln -sf libmmdb.so.0.0.0 ../libmmdb.so.0 && \
-#+ ln -sf libmmdb.so.0.0.0 ../libmmdb.so
-#+
-#+LC_SO :
-#+ $(CC) $(COPTIM) -shared -Wl,-soname,libccp4_c.so.0 -o ../libccp4_c.so.0.0.0 \
-#+ $(CORELIBOBJS) $(CGENERALOBJS) $(CUCOBJS) $(CMTZOBJS) $(CMAPOBJS) $(CSYMOBJS) && \
-#+ ln -sf libccp4_c.so.0.0.0 ../libccp4_c.so.0 && \
-#+ ln -sf libccp4_c.so.0.0.0 ../libccp4_c.so
-#+
-#+LF_SO :
-#+ $(FC) $(FOPTIM) -shared -Wl,-soname,libccp4_f.so.0 -o ../libccp4_f.so.0.0.0 \
-#+ parser.dir/*.o ccplib.dir/*.o lgglib.dir/*.o plot84lib.dir/*.o \
-#+ libhtml.dir/*.o pxxml.dir/*.o rwbrook.dir/*.o cciflib.dir/*.o \
-#+ harvlib.dir/*.o keyparse.dir/*.o dna_output.dir/*.o plotsubs.dir/*.o \
-#+ modlib.dir/*.o fftlib.dir/*.o unix.dir/*.o pack_f.o pack_c.o $(FINTERFACEOBJS) && \
-#+ ln -sf libccp4_f.so.0.0.0 ../libccp4_f.so.0 && \
-#+ ln -sf libccp4_f.so.0.0.0 ../libccp4_f.so
-#+
- # cmtz library only
-
- cmtz: $(LCMTZ)
-@@ -339,9 +356,7 @@
- fi
- cd parser.dir && \
- for i in `pwd`/*.$F; do \
-- $(FC) -c $(FFLAGS) $(SHARED_LIB_FFLAGS) $$i; done\
-- && $(AR) ../$(LF) *.o
-- rm -f parser.dir/*.o
-+ $(FC) -c $(FFLAGS) $(SHARED_LIB_FFLAGS) $$i; done
- parser : parser.o
- $(RANLIB) $(LF)
-
-@@ -351,9 +366,7 @@
- echo ' END' >> ccplib.dir/ccplib.$F
- cd ccplib.dir && $(fsplit_dir)/fsplit $(srcdir)/ccplib.f >/dev/null && $(RMEMPTY) && \
- for i in `pwd`/*.$F; do \
-- $(FC) -c $(FFLAGS) $(SHARED_LIB_FFLAGS) $$i; done\
-- && $(AR) ../$(LF) *.o
-- rm -f ccplib.dir/*.o
-+ $(FC) -c $(FFLAGS) $(SHARED_LIB_FFLAGS) $$i; done
- ccplib : ccplib.o
- $(RANLIB) $(LF)
-
-@@ -364,9 +377,7 @@
- @$(SETFLAGS) ; \
- cd lgglib.dir && $(fsplit_dir)/fsplit $(srcdir)/lgglib.f >/dev/null && $(RMEMPTY) && \
- for i in `pwd`/*.$F; do \
-- eval $(FC) -c $${lgglib_FLAGS-"$(FFLAGS)"} $(SHARED_LIB_FFLAGS) $$i; done\
-- && $(AR) ../$(LF) *.o
-- rm -f lgglib.dir/*.o
-+ eval $(FC) -c $${lgglib_FLAGS-"$(FFLAGS)"} $(SHARED_LIB_FFLAGS) $$i; done
- lgglib : lgglib.o
- $(RANLIB) $(LF)
-
-@@ -376,9 +387,7 @@
- echo ' END' >> plot84lib.dir/plot84lib.$F
- cd plot84lib.dir && $(fsplit_dir)/fsplit $(srcdir)/plot84lib.f >/dev/null && $(RMEMPTY) && \
- for i in `pwd`/*.$F; do \
-- $(FC) -c $(FFLAGS) $(SHARED_LIB_FFLAGS) $$i; done\
-- && $(AR) ../$(LF) *.o
-- rm -f plot84lib.dir/*.o
-+ $(FC) -c $(FFLAGS) $(SHARED_LIB_FFLAGS) $$i; done
- plot84lib : plot84lib.o
- $(RANLIB) $(LF)
-
-@@ -388,9 +397,7 @@
- echo ' END' >> libhtml.dir/libhtml.$F
- cd libhtml.dir && $(fsplit_dir)/fsplit $(srcdir)/libhtml.f >/dev/null && $(RMEMPTY) && \
- for i in `pwd`/*.$F; do \
-- $(FC) -c $(FFLAGS) $(SHARED_LIB_FFLAGS) $$i; done\
-- && $(AR) ../$(LF) *.o
-- rm -f libhtml.dir/*.o
-+ $(FC) -c $(FFLAGS) $(SHARED_LIB_FFLAGS) $$i; done
- libhtml : libhtml.o
- $(RANLIB) $(LF)
-
-@@ -400,9 +407,7 @@
- echo ' END' >> pxxml.dir/pxxml.$F
- cd pxxml.dir && $(fsplit_dir)/fsplit $(srcdir)/pxxml.f >/dev/null && $(RMEMPTY) && \
- for i in `pwd`/*.$F; do \
-- $(FC) -c $(FFLAGS) $(SHARED_LIB_FFLAGS) $$i; done\
-- && $(AR) ../$(LF) *.o
-- rm -f pxxml.dir/*.o
-+ $(FC) -c $(FFLAGS) $(SHARED_LIB_FFLAGS) $$i; done
- pxxml : pxxml.o
- $(RANLIB) $(LF)
-
-@@ -412,9 +417,7 @@
- echo ' END' >> rwbrook.dir/rwbrook.$F
- cd rwbrook.dir && $(fsplit_dir)/fsplit $(srcdir)/rwbrook.f >/dev/null && $(RMEMPTY) && \
- for i in `pwd`/*.$F; do \
-- $(FC) -c $(FFLAGS) $(SHARED_LIB_FFLAGS) $$i; done\
-- && $(AR) ../$(LF) *.o
-- rm -f rwbrook.dir/*.o
-+ $(FC) -c $(FFLAGS) $(SHARED_LIB_FFLAGS) $$i; done
- rwbrook : rwbrook.o
- $(RANLIB) $(LF)
-
-@@ -424,9 +427,7 @@
- echo ' END' >> cciflib.dir/cciflib.$F
- cd cciflib.dir && $(fsplit_dir)/fsplit $(srcdir)/cciflib.f >/dev/null && $(RMEMPTY) && \
- for i in `pwd`/*.$F; do \
-- $(FC) -c $(FFLAGS) $(SHARED_LIB_FFLAGS) -I$(srcdir) $$i; done\
-- && $(AR) ../$(LF) *.o
-- rm -f cciflib.dir/*.o
-+ $(FC) -c $(FFLAGS) $(SHARED_LIB_FFLAGS) -I$(srcdir) $$i; done
- cciflib : cciflib.o
- $(RANLIB) $(LF)
-
-@@ -440,9 +441,7 @@
- && $(AR) ../$(LF) *.o ; else \
- cd harvlib.dir && $(fsplit_dir)/fsplit $(srcdir)/harv_dummy.f >/dev/null && $(RMEMPTY) && \
- for i in `pwd`/*.$F; do \
-- $(FC) -c $(FFLAGS) $(SHARED_LIB_FFLAGS) -I$(srcdir) $$i; done\
-- && $(AR) ../$(LF) *.o ; fi
-- rm -f harvlib.dir/*.o
-+ $(FC) -c $(FFLAGS) $(SHARED_LIB_FFLAGS) -I$(srcdir) $$i; done; fi
- harvlib : harvlib.o
- $(RANLIB) $(LF)
-
-@@ -452,9 +451,7 @@
- echo ' END' >> keyparse.dir/keyparse.$F
- cd keyparse.dir && $(fsplit_dir)/fsplit $(srcdir)/keyparse.f >/dev/null && $(RMEMPTY) && \
- for i in `pwd`/*.$F; do \
-- $(FC) -c $(FFLAGS) $(SHARED_LIB_FFLAGS) $$i; done\
-- && $(AR) ../$(LF) *.o
-- rm -f keyparse.dir/*.o
-+ $(FC) -c $(FFLAGS) $(SHARED_LIB_FFLAGS) $$i; done
- keyparse : keyparse.o
- $(RANLIB) $(LF)
-
-@@ -464,9 +461,7 @@
- echo ' END' >> dna_output.dir/dna_output.$F
- cd dna_output.dir && $(fsplit_dir)/fsplit $(srcdir)/dna_output.f >/dev/null && $(RMEMPTY) && \
- for i in `pwd`/*.$F; do \
-- $(FC) -I$(srcdir) -c $(FFLAGS) $(SHARED_LIB_FFLAGS) $$i; done\
-- && $(AR) ../$(LF) *.o
-- rm -f dna_output.dir/*.o
-+ $(FC) -I$(srcdir) -c $(FFLAGS) $(SHARED_LIB_FFLAGS) $$i; done
- dna_output : dna_output.o
- $(RANLIB) $(LF)
-
-@@ -474,10 +469,9 @@
- # for ipdisp. May be useful but could be moved.
- $(LF)(pack_c.o): $(srcdir)/pack_c.c $(srcdir)/pack_c.h
- $(CC) $(CFLAGS) $(SHARED_LIB_CFLAGS) -I$(srcdir) -c $(srcdir)/pack_c.c
-- $(AR) $(LF) pack_c.o && rm pack_c.o
-+ $(AR) $(LF) pack_c.o
- $(LF)(pack_f.o): $(srcdir)/pack_f.f
-- $(FC) -c $(FFLAGS) $(SHARED_LIB_FFLAGS) $(srcdir)/pack_f.$(F) && $(AR) $(LF) pack_f.o \
-- && rm pack_f.o
-+ $(FC) -c $(FFLAGS) $(SHARED_LIB_FFLAGS) $(srcdir)/pack_f.$(F) && $(AR) $(LF) pack_f.o
- pack: $(LF)(pack_c.o) $(LF)(pack_f.o)
- $(RANLIB) $(LF)
-
-@@ -488,9 +482,7 @@
- echo ' END' >> sorting_main.dir/sorting_main.$F
- cd sorting_main.dir && $(fsplit_dir)/fsplit $(srcdir)/sorting_main.f >/dev/null && $(RMEMPTY) && \
- for i in `pwd`/*.$F; do \
-- $(FC) -c $(FFLAGS) $(SHARED_LIB_FFLAGS) $$i; done\
-- && $(AR) ../$(LF) *.o
-- rm -f sorting_main.dir/*.o
-+ $(FC) -c $(FFLAGS) $(SHARED_LIB_FFLAGS) $$i; done
- sorting_main : sorting_main.o
- $(RANLIB) $(LF)
-
-@@ -500,9 +492,7 @@
- echo ' END' >> plotsubs.dir/plotsubs.$F
- cd plotsubs.dir && $(fsplit_dir)/fsplit $(srcdir)/plotsubs.f >/dev/null && $(RMEMPTY) && \
- for i in `pwd`/*.$F; do \
-- $(FC) -c $(FFLAGS) $(SHARED_LIB_FFLAGS) $$i; done\
-- && $(AR) ../$(LF) *.o
-- rm -f plotsubs.dir/*.o
-+ $(FC) -c $(FFLAGS) $(SHARED_LIB_FFLAGS) $$i; done
- plotsubs : plotsubs.o
- $(RANLIB) $(LF)
-
-@@ -512,9 +502,7 @@
- echo ' END' >> modlib.dir/modlib.$F
- cd modlib.dir && $(fsplit_dir)/fsplit $(srcdir)/modlib.f >/dev/null && $(RMEMPTY) && \
- for i in `pwd`/*.$F; do \
-- $(FC) -c $(FFLAGS) $(SHARED_LIB_FFLAGS) $$i; done\
-- && $(AR) ../$(LF) *.o
-- rm -f modlib.dir/*.o
-+ $(FC) -c $(FFLAGS) $(SHARED_LIB_FFLAGS) $$i; done
- modlib : modlib.o
- $(RANLIB) $(LF)
-
-@@ -524,9 +512,7 @@
- echo ' END' >> fftlib.dir/fftlib.$F
- cd fftlib.dir && $(fsplit_dir)/fsplit $(srcdir)/fftlib.f >/dev/null && $(RMEMPTY) && \
- for i in `pwd`/*.$F; do \
-- $(FC) -c $(FFLAGS) $(SHARED_LIB_FFLAGS) $$i; done \
-- && $(AR) ../$(LF) *.o
-- rm -f fftlib.dir/*.o
-+ $(FC) -c $(FFLAGS) $(SHARED_LIB_FFLAGS) $$i; done
- fftlib : fftlib.o
- $(RANLIB) $(LF)
-
-@@ -541,9 +527,7 @@
- echo ' END' >> unix.dir/unix.f
- cd unix.dir && $(fsplit_dir)/fsplit ../unix.f >/dev/null && $(RMEMPTY) && \
- for i in `pwd`/*.$F; do \
-- $(FC) -c $(FFLAGS) $(SHARED_LIB_FFLAGS) $$i; done\
-- && $(AR) ../$(LF) *.o
-- rm -f unix.dir/*.o
-+ $(FC) -c $(FFLAGS) $(SHARED_LIB_FFLAGS) $$i; done
- unix : unix.o
- $(RANLIB) $(LF)
-
diff --git a/sci-libs/ccp4-libs/files/6.1.3-ccif-shared.patch b/sci-libs/ccp4-libs/files/6.1.3-ccif-shared.patch
deleted file mode 100644
index ca18d75bc..000000000
--- a/sci-libs/ccp4-libs/files/6.1.3-ccif-shared.patch
+++ /dev/null
@@ -1,33 +0,0 @@
---- configure 2009-08-04 22:35:34.000000000 +0200
-+++ configure.new 2009-08-04 22:54:32.000000000 +0200
-@@ -3136,8 +3136,8 @@
- 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/$$.cache_file ) || \
-- ./configure $xopts --libdir=${libdir} --srcdir=${srcdir}/lib/ccif
-+ ./configure $xopts --libdir=${libdir} --srcdir=${srcdir}/lib/ccif --cache-file=/tmp/$$.cache_file --enable-shared-lib ) || \
-+ ./configure $xopts --libdir=${libdir} --srcdir=${srcdir}/lib/ccif --enable-shared-lib
- rm -f /tmp/$$.cache_file
- if [ "X$LIBFOPTIM" != "X" ]; then
- FOPTIM=$FOPTIM_save
---- lib/ccif/configure 2009-08-04 22:35:37.000000000 +0200
-+++ lib/ccif/configure.new 2009-08-04 23:05:44.000000000 +0200
-@@ -5568,7 +5568,7 @@
- enable_shared_lib=no
- ;;
-
-- i?86-unknown-linux | i?86-pc-linux-gnu )
-+ i?86-unknown-linux | i?86-pc-linux-gnu | x86_64-unknown-linux-gnu)
- if test $enable_shared_lib = yes ; then
-
- SO_LOC_VAR='LD_LIBRARY_PATH'
-@@ -5585,7 +5585,7 @@
- else
- SHARED_LIB_PATH='LD_LIBRARY_PATH=`pwd`'
- fi
-- SHARED_LIB_CMD='$(CC) $(SHARED_LIB_FLAGS) -shared -Wl,-soname -Wl,$(SHARED_LIB_NAME) '"$SHARED_LIB_RESTRICT"' ${LOBJS} $(RX_LFLAG) -o $(SHARED_LIB_NAME)'
-+ SHARED_LIB_CMD='$(CC) $(SHARED_LIB_FLAGS) -shared -Wl,-soname -Wl,$(SHARED_LIB_NAME) '"$SHARED_LIB_RESTRICT"' ${LOBJS} $(RX_LFLAG) -o $(SHARED_LIB_NAME) -lm'
- # SHARED_LIB_EXPORTS_CMD='cp libccif-universal-ld.lis $(SHARED_LIB_EXPORTS)'
- SHARED_LIB_EXPORTS_CMD=''
- fi
diff --git a/sci-libs/ccp4-libs/files/6.1.3-dont-build-mmdb.patch b/sci-libs/ccp4-libs/files/6.1.3-dont-build-mmdb.patch
deleted file mode 100644
index b3fefacda..000000000
--- a/sci-libs/ccp4-libs/files/6.1.3-dont-build-mmdb.patch
+++ /dev/null
@@ -1,26 +0,0 @@
---- lib/src/Makefile.in 2009-06-18 15:44:08.000000000 +0200
-+++ lib/src/Makefile.in.new 2009-08-11 11:58:25.000000000 +0200
-@@ -176,7 +176,7 @@
-
- ##### Makefile targets ######
-
--all: fsplit $(LMMDB) $(LC) $(LF) $(SCRIPT_MODULES)
-+all: fsplit $(LC) $(LF) $(SCRIPT_MODULES)
- # maybe create shared library
- $(SHARE_LIB)
-
---- lib/src/Makefile.in 2009-06-18 15:44:08.000000000 +0200
-+++ lib/src/Makefile.in.new 2009-08-11 12:17:53.000000000 +0200
-@@ -716,11 +716,9 @@
- rm -f $(DESTDIR)$(includedir)/mmdb/$$f; \
- done
-
--install : all install-ccp4HEADERS install-mmdbHEADERS
-- $(INSTALL_DATA) `pwd`/$(LMMDB) $(libdir)/$(LMMDB)
-+install : all install-ccp4HEADERS
- $(INSTALL_DATA) `pwd`/$(LC) $(libdir)/$(LC)
- $(INSTALL_DATA) `pwd`/$(LF) $(libdir)/$(LF)
-- $(RANLIB) $(libdir)/$(LMMDB)
- $(RANLIB) $(libdir)/$(LC)
- $(RANLIB) $(libdir)/$(LF)
- $(SHARE_INST)
diff --git a/sci-libs/ccp4-libs/files/6.1.3-dont-make-dirs-in-configure.patch b/sci-libs/ccp4-libs/files/6.1.3-dont-make-dirs-in-configure.patch
deleted file mode 100644
index 583697cea..000000000
--- a/sci-libs/ccp4-libs/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 $i/Makefile.in
-+# fi
-+# fi
-+# done
-+#fi
-
- ### sanity checks
-
diff --git a/sci-libs/ccp4-libs/files/6.1.3-glibc2.10.patch b/sci-libs/ccp4-libs/files/6.1.3-glibc2.10.patch
deleted file mode 100644
index 6e3997647..000000000
--- a/sci-libs/ccp4-libs/files/6.1.3-glibc2.10.patch
+++ /dev/null
@@ -1,22 +0,0 @@
---- lib/ccif/configure.in 2009-06-10 13:52:59.000000000 +0200
-+++ lib/ccif/configure.in.new 2009-06-10 14:04:31.000000000 +0200
-@@ -363,7 +363,7 @@
- fi
- SHARED_LIB_CMD='$(LD) $(SHARED_LIB_FLAGS) -shared -soname $(SHARED_LIB_NAME) \\\
- --whole-archive '"$SHARED_LIB_RESTRICT"' $L \\\
-- $(RX_LFLAG) -o $(SHARED_LIB_NAME)'
-+ $(RX_LFLAG) -o $(SHARED_LIB_NAME) -lm'
- SHARED_LIB_EXPORTS_CMD='cp libccif-universal-ld.lis $(SHARED_LIB_EXPORTS)'
- fi
- ;;
---- lib/ccif/configure 2009-06-10 14:26:58.000000000 +0200
-+++ lib/ccif/configure.new 2009-06-10 14:43:31.000000000 +0200
-@@ -1807,7 +1807,7 @@
- SHARED_LIB_CMD='$(LD) $(SHARED_LIB_CFLAGS) -shared -soname \\\
- $(SHARED_LIB_NAME) \\\
- --whole-archive $L \\\
-- -o $(SHARED_LIB_NAME)'
-+ -o $(SHARED_LIB_NAME) -lm'
- SHARED_LIB_EXPORTS_CMD=''
- fi
- ;;
diff --git a/sci-libs/ccp4-libs/files/6.1.3-link-proberly.patch b/sci-libs/ccp4-libs/files/6.1.3-link-proberly.patch
deleted file mode 100644
index 0780314f0..000000000
--- a/sci-libs/ccp4-libs/files/6.1.3-link-proberly.patch
+++ /dev/null
@@ -1,255 +0,0 @@
---- lib/src/Makefile.in 2009-03-02 17:53:15.000000000 +0100
-+++ lib/src/Makefile.in.new 2009-03-02 17:52:09.000000000 +0100
-@@ -172,9 +172,8 @@
-
- ##### Makefile targets ######
-
--all: fsplit $(LMMDB) $(LC) $(LF) $(SCRIPT_MODULES)
-+all: fsplit $(LMMDB) LMMDB_SO $(LC) LC_SO $(LF) LF_SO $(SCRIPT_MODULES)
- # maybe create shared library
-- $(SHARE_LIB)
-
- $(LC) : $(CORELIBOBJS) $(CGENERALOBJS) $(CUCOBJS) $(CMTZOBJS) $(CMAPOBJS) $(CSYMOBJS)
- $(AR) $(LC) $?
-@@ -186,6 +185,27 @@
- $(AR) $(LF) $(FINTERFACEOBJS)
- $(RANLIB) $@
-
-+LMMDB_SO :
-+ $(CC) $(COPTIM) -shared -Wl,-soname,libmmdb.so.0 -o libmmdb.so.0.0.0 \
-+ $(MMDBOBJS) && \
-+ ln -sf libmmdb.so.0.0.0 libmmdb.so.0 && \
-+ ln -sf libmmdb.so.0.0.0 libmmdb.so
-+
-+LC_SO :
-+ $(CC) $(COPTIM) -shared -Wl,-soname,libccp4c.so.0 -o libccp4c.so.0.0.0 \
-+ $(CORELIBOBJS) $(CGENERALOBJS) $(CUCOBJS) $(CMTZOBJS) $(CMAPOBJS) $(CSYMOBJS) && \
-+ ln -sf libccp4c.so.0.0.0 libccp4c.so.0 && \
-+ ln -sf libccp4c.so.0.0.0 libccp4c.so
-+
-+LF_SO :
-+ $(FC) $(FOPTIM) -shared -Wl,-soname,libccp4f.so.0 -o libccp4f.so.0.0.0 \
-+ parser.dir/*.o ccplib.dir/*.o lgglib.dir/*.o plot84lib.dir/*.o \
-+ libhtml.dir/*.o pxxml.dir/*.o rwbrook.dir/*.o cciflib.dir/*.o \
-+ harvlib.dir/*.o keyparse.dir/*.o dna_output.dir/*.o plotsubs.dir/*.o \
-+ modlib.dir/*.o fftlib.dir/*.o unix.dir/*.o pack_f.o pack_c.o $(FINTERFACEOBJS) && \
-+ ln -sf libccp4f.so.0.0.0 libccp4f.so.0 && \
-+ ln -sf libccp4f.so.0.0.0 libccp4f.so
-+
-#@@ -186,6 +185,27 @@
-# $(AR) $(LF) $(FINTERFACEOBJS)
-# $(RANLIB) $@
-#
-#+LMMDB_SO :
-#+ $(CC) $(COPTIM) -shared -Wl,-soname,libmmdb.so.0 -o ../libmmdb.so.0.0.0 \
-#+ $(MMDBOBJS) && \
-#+ ln -sf libmmdb.so.0.0.0 ../libmmdb.so.0 && \
-#+ ln -sf libmmdb.so.0.0.0 ../libmmdb.so
-#+
-#+LC_SO :
-#+ $(CC) $(COPTIM) -shared -Wl,-soname,libccp4_c.so.0 -o ../libccp4_c.so.0.0.0 \
-#+ $(CORELIBOBJS) $(CGENERALOBJS) $(CUCOBJS) $(CMTZOBJS) $(CMAPOBJS) $(CSYMOBJS) && \
-#+ ln -sf libccp4_c.so.0.0.0 ../libccp4_c.so.0 && \
-#+ ln -sf libccp4_c.so.0.0.0 ../libccp4_c.so
-#+
-#+LF_SO :
-#+ $(FC) $(FOPTIM) -shared -Wl,-soname,libccp4_f.so.0 -o ../libccp4_f.so.0.0.0 \
-#+ parser.dir/*.o ccplib.dir/*.o lgglib.dir/*.o plot84lib.dir/*.o \
-#+ libhtml.dir/*.o pxxml.dir/*.o rwbrook.dir/*.o cciflib.dir/*.o \
-#+ harvlib.dir/*.o keyparse.dir/*.o dna_output.dir/*.o plotsubs.dir/*.o \
-#+ modlib.dir/*.o fftlib.dir/*.o unix.dir/*.o pack_f.o pack_c.o $(FINTERFACEOBJS) && \
-#+ ln -sf libccp4_f.so.0.0.0 ../libccp4_f.so.0 && \
-#+ ln -sf libccp4_f.so.0.0.0 ../libccp4_f.so
-#+
- # cmtz library only
-
- cmtz: $(LCMTZ)
-@@ -339,9 +356,7 @@
- fi
- cd parser.dir && \
- for i in `pwd`/*.$F; do \
-- $(FC) -c $(FFLAGS) $(SHARED_LIB_FFLAGS) $$i; done\
-- && $(AR) ../$(LF) *.o
-- rm -f parser.dir/*.o
-+ $(FC) -c $(FFLAGS) $(SHARED_LIB_FFLAGS) $$i; done
- parser : parser.o
- $(RANLIB) $(LF)
-
-@@ -351,9 +366,7 @@
- echo ' END' >> ccplib.dir/ccplib.$F
- cd ccplib.dir && $(fsplit_dir)/fsplit $(srcdir)/ccplib.f >/dev/null && $(RMEMPTY) && \
- for i in `pwd`/*.$F; do \
-- $(FC) -c $(FFLAGS) $(SHARED_LIB_FFLAGS) $$i; done\
-- && $(AR) ../$(LF) *.o
-- rm -f ccplib.dir/*.o
-+ $(FC) -c $(FFLAGS) $(SHARED_LIB_FFLAGS) $$i; done
- ccplib : ccplib.o
- $(RANLIB) $(LF)
-
-@@ -364,9 +377,7 @@
- @$(SETFLAGS) ; \
- cd lgglib.dir && $(fsplit_dir)/fsplit $(srcdir)/lgglib.f >/dev/null && $(RMEMPTY) && \
- for i in `pwd`/*.$F; do \
-- eval $(FC) -c $${lgglib_FLAGS-"$(FFLAGS)"} $(SHARED_LIB_FFLAGS) $$i; done\
-- && $(AR) ../$(LF) *.o
-- rm -f lgglib.dir/*.o
-+ eval $(FC) -c $${lgglib_FLAGS-"$(FFLAGS)"} $(SHARED_LIB_FFLAGS) $$i; done
- lgglib : lgglib.o
- $(RANLIB) $(LF)
-
-@@ -376,9 +387,7 @@
- echo ' END' >> plot84lib.dir/plot84lib.$F
- cd plot84lib.dir && $(fsplit_dir)/fsplit $(srcdir)/plot84lib.f >/dev/null && $(RMEMPTY) && \
- for i in `pwd`/*.$F; do \
-- $(FC) -c $(FFLAGS) $(SHARED_LIB_FFLAGS) $$i; done\
-- && $(AR) ../$(LF) *.o
-- rm -f plot84lib.dir/*.o
-+ $(FC) -c $(FFLAGS) $(SHARED_LIB_FFLAGS) $$i; done
- plot84lib : plot84lib.o
- $(RANLIB) $(LF)
-
-@@ -388,9 +397,7 @@
- echo ' END' >> libhtml.dir/libhtml.$F
- cd libhtml.dir && $(fsplit_dir)/fsplit $(srcdir)/libhtml.f >/dev/null && $(RMEMPTY) && \
- for i in `pwd`/*.$F; do \
-- $(FC) -c $(FFLAGS) $(SHARED_LIB_FFLAGS) $$i; done\
-- && $(AR) ../$(LF) *.o
-- rm -f libhtml.dir/*.o
-+ $(FC) -c $(FFLAGS) $(SHARED_LIB_FFLAGS) $$i; done
- libhtml : libhtml.o
- $(RANLIB) $(LF)
-
-@@ -400,9 +407,7 @@
- echo ' END' >> pxxml.dir/pxxml.$F
- cd pxxml.dir && $(fsplit_dir)/fsplit $(srcdir)/pxxml.f >/dev/null && $(RMEMPTY) && \
- for i in `pwd`/*.$F; do \
-- $(FC) -c $(FFLAGS) $(SHARED_LIB_FFLAGS) $$i; done\
-- && $(AR) ../$(LF) *.o
-- rm -f pxxml.dir/*.o
-+ $(FC) -c $(FFLAGS) $(SHARED_LIB_FFLAGS) $$i; done
- pxxml : pxxml.o
- $(RANLIB) $(LF)
-
-@@ -412,9 +417,7 @@
- echo ' END' >> rwbrook.dir/rwbrook.$F
- cd rwbrook.dir && $(fsplit_dir)/fsplit $(srcdir)/rwbrook.f >/dev/null && $(RMEMPTY) && \
- for i in `pwd`/*.$F; do \
-- $(FC) -c $(FFLAGS) $(SHARED_LIB_FFLAGS) $$i; done\
-- && $(AR) ../$(LF) *.o
-- rm -f rwbrook.dir/*.o
-+ $(FC) -c $(FFLAGS) $(SHARED_LIB_FFLAGS) $$i; done
- rwbrook : rwbrook.o
- $(RANLIB) $(LF)
-
-@@ -424,9 +427,7 @@
- echo ' END' >> cciflib.dir/cciflib.$F
- cd cciflib.dir && $(fsplit_dir)/fsplit $(srcdir)/cciflib.f >/dev/null && $(RMEMPTY) && \
- for i in `pwd`/*.$F; do \
-- $(FC) -c $(FFLAGS) $(SHARED_LIB_FFLAGS) -I$(srcdir) $$i; done\
-- && $(AR) ../$(LF) *.o
-- rm -f cciflib.dir/*.o
-+ $(FC) -c $(FFLAGS) $(SHARED_LIB_FFLAGS) -I$(srcdir) $$i; done
- cciflib : cciflib.o
- $(RANLIB) $(LF)
-
-@@ -440,9 +441,7 @@
- && $(AR) ../$(LF) *.o ; else \
- cd harvlib.dir && $(fsplit_dir)/fsplit $(srcdir)/harv_dummy.f >/dev/null && $(RMEMPTY) && \
- for i in `pwd`/*.$F; do \
-- $(FC) -c $(FFLAGS) $(SHARED_LIB_FFLAGS) -I$(srcdir) $$i; done\
-- && $(AR) ../$(LF) *.o ; fi
-- rm -f harvlib.dir/*.o
-+ $(FC) -c $(FFLAGS) $(SHARED_LIB_FFLAGS) -I$(srcdir) $$i; done; fi
- harvlib : harvlib.o
- $(RANLIB) $(LF)
-
-@@ -452,9 +451,7 @@
- echo ' END' >> keyparse.dir/keyparse.$F
- cd keyparse.dir && $(fsplit_dir)/fsplit $(srcdir)/keyparse.f >/dev/null && $(RMEMPTY) && \
- for i in `pwd`/*.$F; do \
-- $(FC) -c $(FFLAGS) $(SHARED_LIB_FFLAGS) $$i; done\
-- && $(AR) ../$(LF) *.o
-- rm -f keyparse.dir/*.o
-+ $(FC) -c $(FFLAGS) $(SHARED_LIB_FFLAGS) $$i; done
- keyparse : keyparse.o
- $(RANLIB) $(LF)
-
-@@ -464,9 +461,7 @@
- echo ' END' >> dna_output.dir/dna_output.$F
- cd dna_output.dir && $(fsplit_dir)/fsplit $(srcdir)/dna_output.f >/dev/null && $(RMEMPTY) && \
- for i in `pwd`/*.$F; do \
-- $(FC) -I$(srcdir) -c $(FFLAGS) $(SHARED_LIB_FFLAGS) $$i; done\
-- && $(AR) ../$(LF) *.o
-- rm -f dna_output.dir/*.o
-+ $(FC) -I$(srcdir) -c $(FFLAGS) $(SHARED_LIB_FFLAGS) $$i; done
- dna_output : dna_output.o
- $(RANLIB) $(LF)
-
-@@ -474,10 +469,9 @@
- # for ipdisp. May be useful but could be moved.
- $(LF)(pack_c.o): $(srcdir)/pack_c.c $(srcdir)/pack_c.h
- $(CC) $(CFLAGS) $(SHARED_LIB_CFLAGS) -I$(srcdir) -c $(srcdir)/pack_c.c
-- $(AR) $(LF) pack_c.o && rm pack_c.o
-+ $(AR) $(LF) pack_c.o
- $(LF)(pack_f.o): $(srcdir)/pack_f.f
-- $(FC) -c $(FFLAGS) $(SHARED_LIB_FFLAGS) $(srcdir)/pack_f.$(F) && $(AR) $(LF) pack_f.o \
-- && rm pack_f.o
-+ $(FC) -c $(FFLAGS) $(SHARED_LIB_FFLAGS) $(srcdir)/pack_f.$(F) && $(AR) $(LF) pack_f.o
- pack: $(LF)(pack_c.o) $(LF)(pack_f.o)
- $(RANLIB) $(LF)
-
-@@ -488,9 +482,7 @@
- echo ' END' >> sorting_main.dir/sorting_main.$F
- cd sorting_main.dir && $(fsplit_dir)/fsplit $(srcdir)/sorting_main.f >/dev/null && $(RMEMPTY) && \
- for i in `pwd`/*.$F; do \
-- $(FC) -c $(FFLAGS) $(SHARED_LIB_FFLAGS) $$i; done\
-- && $(AR) ../$(LF) *.o
-- rm -f sorting_main.dir/*.o
-+ $(FC) -c $(FFLAGS) $(SHARED_LIB_FFLAGS) $$i; done
- sorting_main : sorting_main.o
- $(RANLIB) $(LF)
-
-@@ -500,9 +492,7 @@
- echo ' END' >> plotsubs.dir/plotsubs.$F
- cd plotsubs.dir && $(fsplit_dir)/fsplit $(srcdir)/plotsubs.f >/dev/null && $(RMEMPTY) && \
- for i in `pwd`/*.$F; do \
-- $(FC) -c $(FFLAGS) $(SHARED_LIB_FFLAGS) $$i; done\
-- && $(AR) ../$(LF) *.o
-- rm -f plotsubs.dir/*.o
-+ $(FC) -c $(FFLAGS) $(SHARED_LIB_FFLAGS) $$i; done
- plotsubs : plotsubs.o
- $(RANLIB) $(LF)
-
-@@ -512,9 +502,7 @@
- echo ' END' >> modlib.dir/modlib.$F
- cd modlib.dir && $(fsplit_dir)/fsplit $(srcdir)/modlib.f >/dev/null && $(RMEMPTY) && \
- for i in `pwd`/*.$F; do \
-- $(FC) -c $(FFLAGS) $(SHARED_LIB_FFLAGS) $$i; done\
-- && $(AR) ../$(LF) *.o
-- rm -f modlib.dir/*.o
-+ $(FC) -c $(FFLAGS) $(SHARED_LIB_FFLAGS) $$i; done
- modlib : modlib.o
- $(RANLIB) $(LF)
-
-@@ -524,9 +512,7 @@
- echo ' END' >> fftlib.dir/fftlib.$F
- cd fftlib.dir && $(fsplit_dir)/fsplit $(srcdir)/fftlib.f >/dev/null && $(RMEMPTY) && \
- for i in `pwd`/*.$F; do \
-- $(FC) -c $(FFLAGS) $(SHARED_LIB_FFLAGS) $$i; done \
-- && $(AR) ../$(LF) *.o
-- rm -f fftlib.dir/*.o
-+ $(FC) -c $(FFLAGS) $(SHARED_LIB_FFLAGS) $$i; done
- fftlib : fftlib.o
- $(RANLIB) $(LF)
-
-@@ -541,9 +527,7 @@
- echo ' END' >> unix.dir/unix.f
- cd unix.dir && $(fsplit_dir)/fsplit ../unix.f >/dev/null && $(RMEMPTY) && \
- for i in `pwd`/*.$F; do \
-- $(FC) -c $(FFLAGS) $(SHARED_LIB_FFLAGS) $$i; done\
-- && $(AR) ../$(LF) *.o
-- rm -f unix.dir/*.o
-+ $(FC) -c $(FFLAGS) $(SHARED_LIB_FFLAGS) $$i; done
- unix : unix.o
- $(RANLIB) $(LF)
-
diff --git a/sci-libs/ccp4-libs/files/pass-clipper-enablevals.patch b/sci-libs/ccp4-libs/files/pass-clipper-enablevals.patch
deleted file mode 100644
index 3e1a8b0e6..000000000
--- a/sci-libs/ccp4-libs/files/pass-clipper-enablevals.patch
+++ /dev/null
@@ -1,11 +0,0 @@
---- ccp4-5.99.5.orig/configure 2006-01-06 11:45:43.000000000 -0800
-+++ ccp4-5.99.5/configure 2006-01-06 11:46:53.000000000 -0800
-@@ -3210,7 +3210,7 @@
- #ccp4 setup
- xopts="${xopts} --with-ccp4=${srcdir}"
- #interface setup
-- xopts="${xopts} --enable-mmdb --enable-cif --enable-ccp4 --enable-minimol"
-+ xopts="${xopts} --enable-mmdb --enable-cif --enable-ccp4 --enable-minimol --enable-mmdbold --enable-mtz --with-mccp4=/usr"
- echo
- echo "********* CLIPPER CONFIGURATION ***********"
- echo
diff --git a/sci-libs/ccp4-libs/metadata.xml b/sci-libs/ccp4-libs/metadata.xml
deleted file mode 100644
index c1ba80b18..000000000
--- a/sci-libs/ccp4-libs/metadata.xml
+++ /dev/null
@@ -1,9 +0,0 @@
-<?xml version="1.0" encoding="UTF-8"?>
-<!DOCTYPE pkgmetadata SYSTEM "http://www.gentoo.org/dtd/metadata.dtd">
-<pkgmetadata>
-<herd>sci-chemistry</herd>
- <maintainer>
- <email>jlec@j-schmitz.net</email>
- <name>Justin Lecher (jlec)</name>
- </maintainer>
-</pkgmetadata>
diff --git a/sci-libs/mmdb/ChangeLog b/sci-libs/mmdb/ChangeLog
deleted file mode 100644
index 842dbcbf9..000000000
--- a/sci-libs/mmdb/ChangeLog
+++ /dev/null
@@ -1,14 +0,0 @@
-# ChangeLog for sci-libs/mmdb
-# Copyright 1999-2009 Gentoo Foundation; Distributed under the GPL v2
-# $Header: $
-
- 15 Aug 2009; Justin Lecher (jlec) <jlec@j-schmitz.net> mmdb-1.21.ebuild:
- buildtime blocker against <sci-libs/ccp4-libs-6.1.2 added
-
-*mmdb-1.21 (10 Aug 2009)
-
- 10 Aug 2009; Justin Lecher (jlec) <jlec@j-schmitz.net> +mmdb-1.21.ebuild,
- +metadata.xml:
- version bump
- license changed to GPL-2 LGPL-3
-
diff --git a/sci-libs/mmdb/Manifest b/sci-libs/mmdb/Manifest
deleted file mode 100644
index f8a8d6dfd..000000000
--- a/sci-libs/mmdb/Manifest
+++ /dev/null
@@ -1,4 +0,0 @@
-DIST mmdb-1.21.tar.gz 675301 RMD160 9feb5660ffb79289a796bde5e5effffc3e81a4af SHA1 cc17a4f12448e21ce9d0c772b269b42d417113fb SHA256 508dcb4bc3a8f9552d930edf019cd2a3750c5fa794d8a95e6a22eaeaeb5ab0be
-EBUILD mmdb-1.21.ebuild 541 RMD160 697f700e44d84fd2567fc5cbb7d1603ba182f56c SHA1 549797f40b7f2fe00b2a7c13ffa0354233a0223d SHA256 b11bd7421ae0befce86c38d3cf550411f7c4c346b17c1f9c86ffc9a211ec5c58
-MISC ChangeLog 419 RMD160 9f33d0073fd13df5eaf760d854802c0cebfa3209 SHA1 9abf2990b898adf322cc894c96bdc7677e425dbb SHA256 3b340f8a3dd53e806bbd98109f7361a4f4250db0d7e17d15356c9d45cb567233
-MISC metadata.xml 215 RMD160 bc9c07aa91f2f175542244e4e4522a73558210a1 SHA1 facb283386de1c0b6b938cdcd4dde04d1694298b SHA256 13f32353652adbd3d934d41381cfc2cacc9e1127c508cebc73806cc1026ee80c
diff --git a/sci-libs/mmdb/metadata.xml b/sci-libs/mmdb/metadata.xml
deleted file mode 100644
index efb490d78..000000000
--- a/sci-libs/mmdb/metadata.xml
+++ /dev/null
@@ -1,8 +0,0 @@
-<?xml version="1.0" encoding="UTF-8"?>
-<!DOCTYPE pkgmetadata SYSTEM "http://www.gentoo.org/dtd/metadata.dtd">
-<pkgmetadata>
-<herd>sci</herd>
-<maintainer>
- <email>sci@gentoo.org</email>
-</maintainer>
-</pkgmetadata>
diff --git a/sci-libs/mmdb/mmdb-1.21.ebuild b/sci-libs/mmdb/mmdb-1.21.ebuild
deleted file mode 100644
index c21944e4f..000000000
--- a/sci-libs/mmdb/mmdb-1.21.ebuild
+++ /dev/null
@@ -1,21 +0,0 @@
-# Copyright 1999-2009 Gentoo Foundation
-# Distributed under the terms of the GNU General Public License v2
-# $Header: $
-
-EAPI="2"
-
-DESCRIPTION="The Coordinate Library is designed to assist CCP4 developers in working with coordinate files"
-HOMEPAGE="http://www.ebi.ac.uk/~keb/cldoc/"
-SRC_URI="http://www.ysbl.york.ac.uk/~emsley/software/${P}.tar.gz"
-
-LICENSE="GPL-2 LGPL-3"
-SLOT="0"
-KEYWORDS="~amd64 ~x86"
-IUSE=""
-
-DEPEND="!!<sci-libs/ccp4-libs-6.1.2"
-RDEPEND=""
-
-src_install() {
- emake DESTDIR="${D}" install || die "emake install failed"
-}
diff --git a/x11-libs/libjwc_c/ChangeLog b/x11-libs/libjwc_c/ChangeLog
deleted file mode 100644
index ad87038af..000000000
--- a/x11-libs/libjwc_c/ChangeLog
+++ /dev/null
@@ -1,17 +0,0 @@
-# ChangeLog for x11-libs/libjwc_c
-# Copyright 1999-2009 Gentoo Foundation; Distributed under the GPL v2
-# $Header: $
-
-*libjwc_c-1.1-r1 (17 Aug 2009)
-
- 17 Aug 2009; Justin Lecher (jlec) <jlec@j-schmitz.net>
- -libjwc_c-1.1.ebuild, +libjwc_c-1.1-r1.ebuild,
- +files/libjwc_c-1.1_p6.1.2.patch:
- as-needed fix
-
-*libjwc_c-1.1 (27 Feb 2009)
-
- 27 Feb 2009; Justin Lecher (jlec) <jlec@j-schmitz.net> +metadata.xml,
- +libjwc_c-1.1.ebuild:
- Initial checkin
-
diff --git a/x11-libs/libjwc_c/Manifest b/x11-libs/libjwc_c/Manifest
deleted file mode 100644
index 7eb1ede73..000000000
--- a/x11-libs/libjwc_c/Manifest
+++ /dev/null
@@ -1,5 +0,0 @@
-AUX 612-gentoo.patch 804 RMD160 69c659d6e251b69740f72b229f24f1aa75ec5364 SHA1 c58d82b1d561fbd681bf9c98d19911e76b76054f SHA256 7772a77657832119f6051cf63185d46533004e4d612a7e089dba8b1ae85a92de
-DIST libjwc_c-1.1.tar.gz 253637 RMD160 a7cee4a3509f51720d0061d7134eb7fdbdccdea7 SHA1 5f689410136194d2972994fa2e78468dee6833a9 SHA256 4e3c5406347356ac4549b2b977c8011391926470cc3556e54148070b929d9ea9
-EBUILD libjwc_c-1.1-r1.ebuild 531 RMD160 ed6856ff72975825a02c5710df1d286336d8b8b2 SHA1 6db3212de3de1113035e6fb4956cc6517df2051b SHA256 def84279f6886757876fc235bb19624565392b8754955c90baede6c7e6d34d39
-MISC ChangeLog 453 RMD160 a809f9f4991e83cb8fa019548a4b981d339fde0d SHA1 0ea117d7c797bc3b226af92f91eec8a9501d17a9 SHA256 9248d5a01efe40e8c3c65e34a6637870777919f910ab0b011acc75201427ef41
-MISC metadata.xml 215 RMD160 bc9c07aa91f2f175542244e4e4522a73558210a1 SHA1 facb283386de1c0b6b938cdcd4dde04d1694298b SHA256 13f32353652adbd3d934d41381cfc2cacc9e1127c508cebc73806cc1026ee80c
diff --git a/x11-libs/libjwc_c/files/612-gentoo.patch b/x11-libs/libjwc_c/files/612-gentoo.patch
deleted file mode 100644
index af4a691fe..000000000
--- a/x11-libs/libjwc_c/files/612-gentoo.patch
+++ /dev/null
@@ -1,20 +0,0 @@
-diff -Nu libjwc_c-1.1/imglib.c libjwc_c/imglib.c
---- libjwc_c-1.1/imglib.c 1999-08-17 15:58:11.000000000 +0200
-+++ libjwc_c/imglib.c 2004-06-03 14:24:05.000000000 +0200
-@@ -4259,7 +4259,7 @@
- {
-
- /* Note: In this routine the first local axis is called 'x' and the
-- second logal axi is called 'y' */
-+ second local axis is called 'y' */
-
- int mxcent; /* Current max no. of elements in active
- spots array */
-@@ -4469,6 +4469,7 @@
-
- /* skipping condition */
-
-+ iymid = (actspots[j].iyend+actspots[j].iybeg)/2;
- itmp = abs(iymid-actspots[j].iycent);
- if (abs((actspots[j].iyend+actspots[j].iybeg) -(iel+ibl))>
- abs((actspots[j].iyend-actspots[j].iybeg) +(iel-ibl))&&
diff --git a/x11-libs/libjwc_c/libjwc_c-1.1-r1.ebuild b/x11-libs/libjwc_c/libjwc_c-1.1-r1.ebuild
deleted file mode 100644
index 71033f5c3..000000000
--- a/x11-libs/libjwc_c/libjwc_c-1.1-r1.ebuild
+++ /dev/null
@@ -1,29 +0,0 @@
-# Copyright 1999-2009 Gentoo Foundation
-# Distributed under the terms of the GNU General Public License v2
-# $Header: $
-
-EAPI="2"
-
-inherit autotools eutils
-
-PATCH="612"
-
-DESCRIPTION="additional c library for ccp4"
-HOMEPAGE="http://www.ccp4.ac.uk/main.html"
-SRC_URI="ftp://ftp.ccp4.ac.uk/jwc/${P}.tar.gz"
-
-SLOT="0"
-LICENSE="GPL-2"
-KEYWORDS="~amd64 ~x86"
-IUSE=""
-
-src_prepare() {
- epatch "${FILESDIR}"/${PATCH}-gentoo.patch
- rm missing || die
- eautoreconf
-}
-
-src_install() {
- emake DESTDIR="${D}" install || die
- dodoc README NEWS
-}
diff --git a/x11-libs/libjwc_c/metadata.xml b/x11-libs/libjwc_c/metadata.xml
deleted file mode 100644
index efb490d78..000000000
--- a/x11-libs/libjwc_c/metadata.xml
+++ /dev/null
@@ -1,8 +0,0 @@
-<?xml version="1.0" encoding="UTF-8"?>
-<!DOCTYPE pkgmetadata SYSTEM "http://www.gentoo.org/dtd/metadata.dtd">
-<pkgmetadata>
-<herd>sci</herd>
-<maintainer>
- <email>sci@gentoo.org</email>
-</maintainer>
-</pkgmetadata>
diff --git a/x11-libs/libjwc_f/ChangeLog b/x11-libs/libjwc_f/ChangeLog
deleted file mode 100644
index baf2ca0f1..000000000
--- a/x11-libs/libjwc_f/ChangeLog
+++ /dev/null
@@ -1,16 +0,0 @@
-# ChangeLog for x11-libs/libjwc_f
-# Copyright 1999-2009 Gentoo Foundation; Distributed under the GPL v2
-# $Header: $
-
-*libjwc_f-1.1-r1 (17 Aug 2009)
-
- 17 Aug 2009; Justin Lecher (jlec) <jlec@j-schmitz.net>
- +files/612-gentoo.patch, -libjwc_f-1.1.ebuild, +libjwc_f-1.1-r1.ebuild:
- add patch untill 6.1.2
-
-*libjwc_f-1.1 (27 Feb 2009)
-
- 27 Feb 2009; Justin Lecher (jlec) <jlec@j-schmitz.net> +metadata.xml,
- +libjwc_f-1.1.ebuild:
- Initial checkin
-
diff --git a/x11-libs/libjwc_f/Manifest b/x11-libs/libjwc_f/Manifest
deleted file mode 100644
index c039a1d69..000000000
--- a/x11-libs/libjwc_f/Manifest
+++ /dev/null
@@ -1,5 +0,0 @@
-AUX 612-gentoo.patch 2779 RMD160 8ea985d29ed03a5d7106b8f475ba629d523dc62f SHA1 b62d1c805455e69add3d457f78bfb897ea1a3801 SHA256 1320119153eb08c7bba844c7c320d9d63758ba2d816ad61c11b5ca2c65ef975e
-DIST libjwc_f-1.1.tar.gz 170973 RMD160 9fc0fc38aafa1611c13dfd963b903f4bd901e436 SHA1 f68c54e6062fec63f71eb612689626b4efc2e642 SHA256 9c05d5bac2a2e75d5fd490665c795ae31280da886e30f66cf39b3a32f2981199
-EBUILD libjwc_f-1.1-r1.ebuild 595 RMD160 084d06f14bbfb4090a992c2f695ed7f6d922846b SHA1 51befdb2c75e300d2d779d6f066d4f9ee6f4f3eb SHA256 5f5ab6f049c7986a0c197c1ba8c3442a8cbb576aff392519e7ae6ee2287f2271
-MISC ChangeLog 451 RMD160 8b934a8e0b7ea5b482702e66ab255c9a1e0abd60 SHA1 9759c6d5d3a8886cd6012f1feeeb754dea07b838 SHA256 18506d0e0415a45ee58886b394db63d19cd4df25360f9d858b8febfc53531a62
-MISC metadata.xml 215 RMD160 bc9c07aa91f2f175542244e4e4522a73558210a1 SHA1 facb283386de1c0b6b938cdcd4dde04d1694298b SHA256 13f32353652adbd3d934d41381cfc2cacc9e1127c508cebc73806cc1026ee80c
diff --git a/x11-libs/libjwc_f/files/612-gentoo.patch b/x11-libs/libjwc_f/files/612-gentoo.patch
deleted file mode 100644
index e687d8bec..000000000
--- a/x11-libs/libjwc_f/files/612-gentoo.patch
+++ /dev/null
@@ -1,100 +0,0 @@
-diff -Nu libjwc_f-1.1/configure.in ccp4-6.1.2/x-windows/libjwc/libjwc_f/configure.in
---- libjwc_f-1.1/configure.in 1999-10-21 16:07:14.000000000 +0200
-+++ ccp4-6.1.2/x-windows/libjwc/libjwc_f/configure.in 2004-03-11 17:31:45.000000000 +0100
-@@ -8,6 +8,7 @@
- AC_CANONICAL_SYSTEM
-
- AM_INIT_AUTOMAKE(libjwc_f, 1.1)
-+AM_MAINTAINER_MODE
-
- case ${with_g77} in
- "yes" ) CC="gcc" GCC=yes F77=g77 ;;
-@@ -17,7 +18,7 @@
- AC_PROG_F77
-
- AC_PROG_INSTALL
--AC_PROG_RANLIB
-+AC_PROG_LIBTOOL
-
- case "$target" in
- *irix6* )
-@@ -26,8 +27,9 @@
- case "$FFLAGS" in
- *-64* ) ;; # assume they meant it
- *-o32* | *-32* ) ;; # presumably OK
-- * ) FFLAGS="$FFLAGS -o32 -O -g3"
-- CFLAGS=-32
-+ *-n32* ) ;;
-+ * ) FFLAGS="$FFLAGS -n32 -O -g3"
-+ CFLAGS=-n32
- AC_MSG_WARN([
-
- *** Using compiler flag -o32 for probable compatibility with
-@@ -47,8 +49,33 @@
- *** See the INSTALL file for more info.
- ])
- fi ;;
-+ *linux* )
-+ case $F77 in
-+ g77*)
-+ case "$FFLAGS" in
-+ *no-second-underscore* ) ;; # presumably OK
-+ * ) FFLAGS="$FFLAGS -fno-second-underscore -fno-globals" ;;
-+ esac
-+ esac ;;
-+ *darwin* )
-+ case $F77 in
-+ g77*)
-+ case "$FFLAGS" in
-+ *no-second-underscore* ) ;; # presumably OK
-+ * ) FFLAGS="$FFLAGS -fno-second-underscore -fno-globals" ;;
-+ esac
-+#mac g77 currently goes not handle -fno-common
-+ enable_shared=no;
-+ esac ;;
- * )
- esac
-+# efc, version 7.1 at least does not support soname, so use CC
-+case "$F77" in
-+ *efc ) F77LD=${F77LD:-'${CC}'} ;;
-+ * ) F77LD=${F77LD:-'${F77}'}
-+esac
-+
-+AC_SUBST(F77LD)
-
- AM_PROG_LIBTOOL
-
-Common subdirectories: libjwc_f-1.1/doc and ccp4-6.1.2/x-windows/libjwc/libjwc_f/doc
-diff -Nu libjwc_f-1.1/opn_scr.f ccp4-6.1.2/x-windows/libjwc/libjwc_f/opn_scr.f
---- libjwc_f-1.1/opn_scr.f 1999-09-07 12:50:13.000000000 +0200
-+++ ccp4-6.1.2/x-windows/libjwc/libjwc_f/opn_scr.f 2000-10-25 13:03:09.000000000 +0200
-@@ -16,6 +16,6 @@
- C
- C====== Open the file
- C
-- OPEN (IUN_SCR, STATUS='SCRATCH')
-- RETURN
-+C OPEN (IUN_SCR, STATUS='SCRATCH')
-+ CALL CCPDPN(IUN_SCR,'JWCSCR','SCRATCH','U',0, IFAIL)
- END
-diff -Nu libjwc_f-1.1/rpf_dstar.f ccp4-6.1.2/x-windows/libjwc/libjwc_f/rpf_dstar.f
---- libjwc_f-1.1/rpf_dstar.f 1999-07-09 13:39:38.000000000 +0200
-+++ ccp4-6.1.2/x-windows/libjwc/libjwc_f/rpf_dstar.f 2004-06-04 12:10:59.000000000 +0200
-@@ -376,7 +376,8 @@
- INR_FLAG = 2
- PHIW = 0.0
- END IF
-- ELSE
-+ RETURN
-+ ENDIF
- C
- C---- Calculate distance of edge of spot from sphere at end of rotation
- Crotgen.for
-@@ -418,7 +419,6 @@
- INR_FLAG = 4
- 40 RETURN
- END IF
-- END IF
- END IF
- RETURN
- END
diff --git a/x11-libs/libjwc_f/libjwc_f-1.1-r1.ebuild b/x11-libs/libjwc_f/libjwc_f-1.1-r1.ebuild
deleted file mode 100644
index 8a55f5297..000000000
--- a/x11-libs/libjwc_f/libjwc_f-1.1-r1.ebuild
+++ /dev/null
@@ -1,35 +0,0 @@
-# Copyright 1999-2009 Gentoo Foundation
-# Distributed under the terms of the GNU General Public License v2
-# $Header: $
-
-EAPI="2"
-
-inherit autotools eutils fortran
-
-FORTRAN="g77 gfortran ifc"
-
-PATCH="612"
-
-DESCRIPTION="additional c library for ccp4"
-HOMEPAGE="http://www.ccp4.ac.uk/main.html"
-SRC_URI="ftp://ftp.ccp4.ac.uk/jwc/${P}.tar.gz"
-
-LICENSE="GPL-2"
-
-SLOT="0"
-KEYWORDS="~amd64 ~x86"
-
-IUSE=""
-RDEPEND=""
-DEPEND="${RDEPEND}"
-
-src_prepare() {
- epatch "${FILESDIR}"/${PATCH}-gentoo.patch
- eautoreconf
-}
-
-src_install() {
- emake DESTDIR="${D}" install || die
- dodoc NEWS README
- dohtml doc/*
-}
diff --git a/x11-libs/libjwc_f/metadata.xml b/x11-libs/libjwc_f/metadata.xml
deleted file mode 100644
index efb490d78..000000000
--- a/x11-libs/libjwc_f/metadata.xml
+++ /dev/null
@@ -1,8 +0,0 @@
-<?xml version="1.0" encoding="UTF-8"?>
-<!DOCTYPE pkgmetadata SYSTEM "http://www.gentoo.org/dtd/metadata.dtd">
-<pkgmetadata>
-<herd>sci</herd>
-<maintainer>
- <email>sci@gentoo.org</email>
-</maintainer>
-</pkgmetadata>