diff options
207 files changed, 8 insertions, 11262 deletions
diff --git a/app-office/sc/sc-7.16-r1.ebuild b/app-office/sc/sc-7.16-r1.ebuild index d9e0962abbb8..3c3083ee7a36 100644 --- a/app-office/sc/sc-7.16-r1.ebuild +++ b/app-office/sc/sc-7.16-r1.ebuild @@ -3,6 +3,7 @@ # $Id$ EAPI=5 + inherit eutils multilib toolchain-funcs DESCRIPTION="sc is a free curses-based spreadsheet program that uses key bindings similar to vi and less" @@ -17,9 +18,7 @@ COMMON_DEPEND=">=sys-libs/ncurses-5.2" DEPEND="virtual/pkgconfig" RDEPEND=" ${COMMON_DEPEND} - !dev-lang/stratego - !<sci-chemistry/ccp4-apps-6.1.3-r4 -" + !dev-lang/stratego" src_prepare() { epatch \ diff --git a/dev-libs/libjwc_c/Manifest b/dev-libs/libjwc_c/Manifest deleted file mode 100644 index 91e153d94c90..000000000000 --- a/dev-libs/libjwc_c/Manifest +++ /dev/null @@ -1 +0,0 @@ -DIST libjwc_c-1.1.tar.gz 253637 SHA256 4e3c5406347356ac4549b2b977c8011391926470cc3556e54148070b929d9ea9 SHA512 5a095fdbf4f70d012f718d2bcd2a9689bf788801df3f3f97bead70861d08d5f6b5a9ac879e02c260974b755906d35de168646947900bcb18dad40839846d87ad WHIRLPOOL bca0bb19e2898c18f29a275c1997bf55058f5efbbc1147cb7e7a967f2eafb346c0d74975208dc6dd749ba60b256dca3c1548d9a58bd938fb19d77946a1aaa85a diff --git a/dev-libs/libjwc_c/files/612-gentoo.patch b/dev-libs/libjwc_c/files/612-gentoo.patch deleted file mode 100644 index af4a691febb9..000000000000 --- a/dev-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/dev-libs/libjwc_c/libjwc_c-1.1-r2.ebuild b/dev-libs/libjwc_c/libjwc_c-1.1-r2.ebuild deleted file mode 100644 index cc9feb0c8f9f..000000000000 --- a/dev-libs/libjwc_c/libjwc_c-1.1-r2.ebuild +++ /dev/null @@ -1,31 +0,0 @@ -# Copyright 1999-2012 Gentoo Foundation -# Distributed under the terms of the GNU General Public License v2 -# $Id$ - -EAPI=4 - -AUTOTOOLS_AUTORECONF=yes - -inherit autotools-utils - -PATCH="612" - -DESCRIPTION="additional c library for ccp4" -HOMEPAGE="http://www.ccp4.ac.uk/main.html" -SRC_URI="ftp://ftp.ccp4.ac.uk/jwc/${P}.tar.gz" - -SLOT="0" -LICENSE="GPL-2" -KEYWORDS="amd64 ppc x86 ~amd64-linux ~x86-linux ~x64-macos" -IUSE="static-libs" - -DEPEND="sci-libs/ccp4-libs" -RDEPEND="${DEPEND}" - -PATCHES=( "${FILESDIR}"/${PATCH}-gentoo.patch ) - -src_prepare() { - rm missing || die - echo "libjwc_c_la_LIBADD = -lm -lccp4f" >> Makefile.am || die - autotools-utils_src_prepare -} diff --git a/dev-libs/libjwc_c/metadata.xml b/dev-libs/libjwc_c/metadata.xml deleted file mode 100644 index d747d72a25b4..000000000000 --- a/dev-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/dev-libs/libjwc_f/Manifest b/dev-libs/libjwc_f/Manifest deleted file mode 100644 index 65e6fb796fb7..000000000000 --- a/dev-libs/libjwc_f/Manifest +++ /dev/null @@ -1 +0,0 @@ -DIST libjwc_f-1.1.tar.gz 170973 SHA256 9c05d5bac2a2e75d5fd490665c795ae31280da886e30f66cf39b3a32f2981199 SHA512 6d947e1513c137a23a4b6c2525e2a2f71c31a41f37455b9b3c97bd4c82128d5b3f4a7bfdd14aba57fbc258dcdcb8fa55e420a8573576992d0ae164bfe394f8d1 WHIRLPOOL 2652f3f43451cfb378d931ccff22a20131f2f44c40c2fe4c51ea45ef08f2e08306c1362f256c0c13014b9db3418ccbce437e4ccea41faae066c800a2ece02551 diff --git a/dev-libs/libjwc_f/files/612-gentoo.patch b/dev-libs/libjwc_f/files/612-gentoo.patch deleted file mode 100644 index e687d8bec6ea..000000000000 --- a/dev-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/dev-libs/libjwc_f/libjwc_f-1.1-r2.ebuild b/dev-libs/libjwc_f/libjwc_f-1.1-r2.ebuild deleted file mode 100644 index 69a97bf28d98..000000000000 --- a/dev-libs/libjwc_f/libjwc_f-1.1-r2.ebuild +++ /dev/null @@ -1,38 +0,0 @@ -# Copyright 1999-2012 Gentoo Foundation -# Distributed under the terms of the GNU General Public License v2 -# $Id$ - -EAPI=4 - -AUTOTOOLS_AUTORECONF=yes - -inherit autotools-utils fortran-2 - -PATCH="612" - -DESCRIPTION="Additional fortran library for ccp4" -HOMEPAGE="http://www.ccp4.ac.uk/main.html" -SRC_URI="ftp://ftp.ccp4.ac.uk/jwc/${P}.tar.gz" - -SLOT="0" -LICENSE="GPL-2" -KEYWORDS="amd64 ~ppc x86 ~amd64-linux ~x86-linux ~x64-macos" -IUSE="static-libs" - -RDEPEND=" - dev-libs/libjwc_c - sci-libs/ccp4-libs" -DEPEND="${RDEPEND}" - -PATCHES=( "${FILESDIR}"/${PATCH}-gentoo.patch ) - -src_prepare() { - rm missing || die - echo "libjwc_f_la_LIBADD = -ljwc_c -lccp4f" >> Makefile.am || die - autotools-utils_src_prepare -} - -src_install() { - autotools-utils_src_install - dohtml doc/* -} diff --git a/dev-libs/libjwc_f/metadata.xml b/dev-libs/libjwc_f/metadata.xml deleted file mode 100644 index d747d72a25b4..000000000000 --- a/dev-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> diff --git a/profiles/arch/powerpc/package.use.force b/profiles/arch/powerpc/package.use.force index d011e8fff45e..846a4b60dbf4 100644 --- a/profiles/arch/powerpc/package.use.force +++ b/profiles/arch/powerpc/package.use.force @@ -15,5 +15,4 @@ net-p2p/sancho-bin java # sci-chemistry/arp-warp-bin is not available for ppc # sci-chemistry/solve-resolve-bin is not available for ppc # sci-chemistry/cns is not available for ppc -sci-chemistry/oasis minimal sci-libs/cctbx minimal diff --git a/profiles/arch/powerpc/package.use.mask b/profiles/arch/powerpc/package.use.mask index 4a791e4a4d25..cf9c1541c081 100644 --- a/profiles/arch/powerpc/package.use.mask +++ b/profiles/arch/powerpc/package.use.mask @@ -291,12 +291,6 @@ mail-client/claws-mail pda # No media-sound/lilypond here, yet (bug #356069) app-text/asciidoc test -# Kacper Kowalik <xarthisius@gentoo.org> (16 Jan 2011) -# bug 303931 -# dev-lang/icc is not available for ppc -# sci-chemistry/arp-warp-bin is not available for ppc -sci-chemistry/ccp4 arpwarp - # Justin Lecher <jlec@gentoo.org> (01 Nov 2010) # Deps not Keyworded sci-chemistry/apbs fetk diff --git a/profiles/package.mask b/profiles/package.mask index ace39767c6f5..cdbcb01f77a9 100644 --- a/profiles/package.mask +++ b/profiles/package.mask @@ -241,41 +241,6 @@ net-firewall/shorewall6-lite =app-emulation/vmware-workstation-9* =app-emulation/vmware-modules-271* -# Justin Lecher <jlec@gentoo.org> (15 Sep 2015) -# Outdated and multiple bugs -# Use upstream installer for up to version -dev-libs/libjwc_c -dev-libs/libjwc_f -sci-chemistry/arp-warp-bin -sci-chemistry/balbes -sci-chemistry/ccp4 -sci-chemistry/ccp4-apps -sci-chemistry/ccp4i -<sci-chemistry/coot-0.8 -sci-chemistry/imosflm -sci-chemistry/makecif -sci-chemistry/molrep -sci-chemistry/mosflm -sci-chemistry/mrbump -sci-chemistry/oasis -sci-chemistry/pdb-extract -sci-chemistry/pointless -sci-chemistry/refmac -sci-chemistry/scala -sci-chemistry/sfcheck -sci-chemistry/solve-resolve-bin -sci-chemistry/xdsi -sci-chemistry/xia2 -sci-libs/balbes-db -sci-libs/cctbx -<sci-libs/coot-data-3 -sci-libs/ccp4-libs -<=sci-libs/clipper-2.1_p100511-r1 -<sci-libs/mmdb-1.25.5-r1:0 -<sci-libs/monomer-db-5.41 -<sci-libs/ssm-1.4 -x11-libs/libxdl_view - # Michał Górny <mgorny@gentoo.org> (09 Sep 2015) # Package to be used with gentoo-x86 CVS, so pretty much defunct now. # Removal in 30 days. Bug #560056. diff --git a/sci-chemistry/arp-warp-bin/Manifest b/sci-chemistry/arp-warp-bin/Manifest deleted file mode 100644 index 739b86dac839..000000000000 --- a/sci-chemistry/arp-warp-bin/Manifest +++ /dev/null @@ -1 +0,0 @@ -DIST arp_warp_7.5.tar.gz 198643246 SHA256 d16fc6775905e56e5159f4a658f654b98d94f78143a2537ba67bffaed7ef1ad8 SHA512 351ed4bad863bac63005d128c693b7dde60c03ca5e8bd449ea602646f7f856c022070e542bcacae2793fbde88d67e7b5639bedeec55eeb191017a2ec19d03768 WHIRLPOOL d4ea42179a8a406508c82320567dc39ce419a2cba8b9e6ed05739dbbf0c9aba072b720c56987c4c94806ba2772f9c8787bde898f7c76543cc4702f00b7f16532 diff --git a/sci-chemistry/arp-warp-bin/arp-warp-bin-7.5.ebuild b/sci-chemistry/arp-warp-bin/arp-warp-bin-7.5.ebuild deleted file mode 100644 index ef10d0ab3d5d..000000000000 --- a/sci-chemistry/arp-warp-bin/arp-warp-bin-7.5.ebuild +++ /dev/null @@ -1,81 +0,0 @@ -# Copyright 1999-2015 Gentoo Foundation -# Distributed under the terms of the GNU General Public License v2 -# $Id$ - -EAPI=5 - -inherit eutils prefix - -MY_P="arp_warp_${PV}" - -DESCRIPTION="Improvement and interpretation of crystallographic electron density maps" -SRC_URI="${MY_P}.tar.gz" -HOMEPAGE="http://www.embl-hamburg.de/ARP/" - -LICENSE="ArpWarp" -SLOT="0" -KEYWORDS="-* amd64 x86 ~amd64-linux ~x86-linux" -IUSE="cpu_flags_x86_sse2" - -REQUIRED_USE="cpu_flags_x86_sse2" - -RDEPEND=" - app-shells/tcsh - sci-chemistry/refmac - virtual/awk - virtual/jre - virtual/opengl - x11-libs/libX11" -DEPEND="" - -RESTRICT="fetch" - -S="${WORKDIR}/${MY_P}" - -QA_PREBUILT="opt/arp-warp-bin/bin/*" - -pkg_nofetch(){ - elog "Fill out the form at http://www.embl-hamburg.de/ARP/" - elog "and place ${A} in ${DISTDIR}" -} - -src_prepare() { - epatch "${FILESDIR}"/7.3-setup.patch - eprefixify "${S}"/share/arpwarp_setup_base.* - - sed -e '/exit/d' -i "${S}"/share/arpwarp_setup_base.* || die -} - -src_install(){ - m_type=$(uname -m) - os_type=$(uname) - - exeinto /opt/${PN}/bin/bin-${m_type}-${os_type} - doexe "${S}"/bin/bin-${m_type}-${os_type}/* "${S}"/share/*{pl,sh} - - insinto /opt/${PN}/bin/bin-${m_type}-${os_type} - doins "${S}"/share/*{gif,bmp,XYZ,bash,csh,dat,lib,tbl,llh,prm} - - insinto /etc/profile.d/ - newins "${S}"/share/arpwarp_setup_base.csh 90arpwarp_setup.csh - newins "${S}"/share/arpwarp_setup_base.bash 90arpwarp_setup.sh - - dodoc "${S}"/README manual/UserGuide${PV}.pdf - dohtml -r "${S}"/manual/html/* -} - -pkg_postinst(){ - testcommand=$(echo 3 2 | awk '{printf"%3.1f",$1/$2}') - if [ $testcommand == "1,5" ];then - ewarn "*** ERROR ***" - ewarn " 3/2=" $testcommand - ewarn "Invalid decimal separator (must be ".")" - ewarn "You need to set this correctly!!!" - echo - ewarn "One way of setting the decimal separator is:" - ewarn "setenv LC_NUMERIC C' in your .cshrc file" - ewarn "\tor" - ewarn "export LC_NUMERIC=C' in your .bashrc file" - ewarn "Otherwise please consult your system manager" - fi -} diff --git a/sci-chemistry/arp-warp-bin/files/7.3-setup.patch b/sci-chemistry/arp-warp-bin/files/7.3-setup.patch deleted file mode 100644 index faed9c1102fd..000000000000 --- a/sci-chemistry/arp-warp-bin/files/7.3-setup.patch +++ /dev/null @@ -1,30 +0,0 @@ -diff --git a/share/arpwarp_setup_base.bash b/share/arpwarp_setup_base.bash -index 29e769c..0b8a51e 100644 ---- a/share/arpwarp_setup_base.bash -+++ b/share/arpwarp_setup_base.bash -@@ -13,10 +13,10 @@ else - identifier=${nameprocessor}'-'${namesystem} - fi - # --arpwarphome="$1X" -+arpwarphome="@GENTOO_PORTAGE_EPREFIX@/opt/arp-warp-bin" - # - export warpbin=${arpwarphome}/bin/bin-${identifier} --export warpdoc=${arpwarphome}/manual -+export warpdoc=@GENTOO_PORTAGE_EPREFIX@/usr/share/doc/arp-warp-bin-7.1/html/ - export PATH=${warpbin}:${PATH} - # - # Checks for existence of $warpbin directory -diff --git a/share/arpwarp_setup_base.csh b/share/arpwarp_setup_base.csh -index 41b11e9..a4edcff 100644 ---- a/share/arpwarp_setup_base.csh -+++ b/share/arpwarp_setup_base.csh -@@ -13,7 +13,7 @@ else - set identifier = ${nameprocessor}'-'${namesystem} - endif - # --set arpwarphome = '$1X' -+set arpwarphome = '@GENTOO_PORTAGE_EPREFIX@/opt/arp-warp-bin' - # - setenv warpbin ${arpwarphome}/bin/bin-${identifier} - # diff --git a/sci-chemistry/arp-warp-bin/metadata.xml b/sci-chemistry/arp-warp-bin/metadata.xml deleted file mode 100644 index 51fdedab1b38..000000000000 --- a/sci-chemistry/arp-warp-bin/metadata.xml +++ /dev/null @@ -1,5 +0,0 @@ -<?xml version="1.0" encoding="UTF-8"?> -<!DOCTYPE pkgmetadata SYSTEM "http://www.gentoo.org/dtd/metadata.dtd"> -<pkgmetadata> - <herd>sci-chemistry</herd> -</pkgmetadata> diff --git a/sci-chemistry/balbes/Manifest b/sci-chemistry/balbes/Manifest deleted file mode 100644 index c5f8b2747027..000000000000 --- a/sci-chemistry/balbes/Manifest +++ /dev/null @@ -1,2 +0,0 @@ -DIST balbes-1.0.0_p100317.tar.gz 506464 SHA256 c5bf6c2086e1a3d7d380e5501c0cffdb91cbf77c74d2951dd345273f21921d0c SHA512 0029e459877113de212574daec8532f0d225e96772c6a777d34af94e5f11c1253ca941266e68da79e0a5c5a96416a824f76c6f1d8652d9a60a34756989cae41e WHIRLPOOL 9024490eea43ef526f00aff9f2045e2689dd6d9e7575c9fd3de2a23fc4af3ad784660df4c78c9aa6380df1dac9fbf46c8b6be105a3094761ebdd43c5cb541beb -DIST ccp4-6.1.3-core-src.tar.gz 242134076 SHA256 1e529c660e7f390ec0feca9d45caa00a2813d23156c10a2747c427117293c324 SHA512 413eba806107ebcdbd93e9122275463709133d9b2a9ce44ae57a6c2350465a47ba66ad9875237aead74f5d422c0104f58f728ab37a757b10d82cde92af444c20 WHIRLPOOL faebf8ee7920013bc3d0e83565207dca1f31ba0b5c92fe1eae4b740f70ff2031d95787fa0d545b09c853d25657c08973527e43de02fddc086988123ca2a6339c diff --git a/sci-chemistry/balbes/balbes-1.0.0_p100317-r2.ebuild b/sci-chemistry/balbes/balbes-1.0.0_p100317-r2.ebuild deleted file mode 100644 index 5334207c0229..000000000000 --- a/sci-chemistry/balbes/balbes-1.0.0_p100317-r2.ebuild +++ /dev/null @@ -1,79 +0,0 @@ -# Copyright 1999-2012 Gentoo Foundation -# Distributed under the terms of the GNU General Public License v2 -# $Id$ - -EAPI=3 - -CCP4VER="6.1.3" -PYTHON_DEPEND="2" - -inherit eutils fortran-2 python toolchain-funcs - -DESCRIPTION="Automated molecular replacement (MR) pipeline" -HOMEPAGE="http://www.ysbl.york.ac.uk/~fei/balbes/index.html" -SRC_URI=" - mirror://gentoo/${P}.tar.gz - ftp://ftp.ccp4.ac.uk/ccp4/${CCP4VER}/ccp4-${CCP4VER}-core-src.tar.gz" - -SLOT="0" -LICENSE="ccp4" -KEYWORDS="amd64 ~ppc x86 ~amd64-linux ~x86-linux" -IUSE="" - -# bundled PyXML is modified and cannot be replaced - -COMMON_DEPEND="sci-libs/ccp4-libs" -RDEPEND="${COMMON_DEPEND} - ~sci-libs/balbes-db-${CCP4VER} - !<=sci-chemistry/ccp4-apps-6.1.3-r1" -DEPEND="${COMMON_DEPEND}" - -S="${WORKDIR}"/src - -pkg_setup() { - fortran-2_pkg_setup - python_set_active_version 2 -} - -src_unpack() { - unpack ${P}.tar.gz - tar xvzf "${DISTDIR}"/ccp4-${CCP4VER}-core-src.tar.gz \ - ccp4-${CCP4VER}/share/balbes/BALBES_0.0.1/bin_py \ - ccp4-${CCP4VER}/share/balbes/BALBES_0.0.1/PyXML-0.8.4 - python_convert_shebangs 2 "${WORKDIR}"/ccp4-${CCP4VER}/share/balbes/BALBES_0.0.1/bin_py/balbes -} - -src_prepare() { - mkdir "${WORKDIR}"/bin || die - epatch "${FILESDIR}"/${PV}-makefile.patch - cd "${WORKDIR}"/ccp4-${CCP4VER}/share/balbes/BALBES_0.0.1/ - epatch "${FILESDIR}"/pyxml-0.8.4-python-2.6.patch -} - -src_compile() { - emake \ - BLANC_FORT="$(tc-getFC) ${FFLAGS}" || die - cd "${WORKDIR}"/ccp4-${CCP4VER}/share/balbes/BALBES_0.0.1/PyXML-0.8.4 - find build -delete - $(PYTHON) setup.py build - find xml/xslt test -delete -} - -src_install() { - insinto /usr/share/balbes/BALBES_0.0.1/ - doins -r \ - "${WORKDIR}"/ccp4-${CCP4VER}/share/balbes/BALBES_0.0.1/bin_py \ - "${WORKDIR}"/ccp4-${CCP4VER}/share/balbes/BALBES_0.0.1/PyXML-0.8.4 || die - dobin \ - "${WORKDIR}"/bin/* \ - "${WORKDIR}"/ccp4-${CCP4VER}/share/balbes/BALBES_0.0.1/bin_py/balbes \ - || die -} - -pkg_postinst() { - python_mod_optimize /usr/share/balbes/BALBES_0.0.1/{bin_py,PyXML-0.8.4} -} - -pkg_postrm() { - python_mod_cleanup /usr/share/balbes/BALBES_0.0.1/{bin_py,PyXML-0.8.4} -} diff --git a/sci-chemistry/balbes/files/1.0.0_p100317-makefile.patch b/sci-chemistry/balbes/files/1.0.0_p100317-makefile.patch deleted file mode 100644 index da17240642d7..000000000000 --- a/sci-chemistry/balbes/files/1.0.0_p100317-makefile.patch +++ /dev/null @@ -1,107 +0,0 @@ -diff --git a/makefile b/makefile -index baaceb5..85a7baf 100755 ---- a/makefile -+++ b/makefile -@@ -70,6 +70,15 @@ OBJDB_G = get_pdb_list.o - - #OBJDB_Z = blanc2mtz.o libutils.o - -+# incomplete targets: -+# dimer_search_db domain_search_db domain align3 -+all: search_db get_structure_db manage_db search_dm dom2ch \ -+ save_si get_pdb_list_db update_db \ -+ update_dom_db bl2mtz check_file_db fobs2cif sol_check \ -+ get_trns p2s check_cell alt_sg \ -+ align cell_list create_bins \ -+ get_pdb_list_db get_ch get_nm get_mod -+ - search_db: sdb_l - - get_structure_db: tdb_l -@@ -201,58 +210,58 @@ save_seg_id.o: save_seg_id.f - $(BLANC_FORT) -c save_seg_id.f - - sdb_l: $(OBJDB_S) -- $(BLANC_FORT) -o ../bin/search_DB $(OBJDB_S) -+ $(BLANC_FORT) ${LDFLAGS} -o ../bin/search_DB $(OBJDB_S) - tdb_l: $(OBJDB_T) -- $(BLANC_FORT) -o ../bin/get_structure_DB $(OBJDB_T) -+ $(BLANC_FORT) ${LDFLAGS} -o ../bin/get_structure_DB $(OBJDB_T) - mdb_l: $(OBJDB_M) -- $(BLANC_FORT) -o ../bin/manage_DB $(OBJDB_M) -+ $(BLANC_FORT) ${LDFLAGS} -o ../bin/manage_DB $(OBJDB_M) - mdm_l: $(OBJDB_MD) -- $(BLANC_FORT) -o ../bin/search_DOM $(OBJDB_MD) -+ $(BLANC_FORT) ${LDFLAGS} -o ../bin/search_DOM $(OBJDB_MD) - d2c_l: $(OBJDB_A) -- $(BLANC_FORT) -o ../bin/domain2chain $(OBJDB_A) -+ $(BLANC_FORT) ${LDFLAGS} -o ../bin/domain2chain $(OBJDB_A) - upd_l: $(OBJDB_U) -- $(BLANC_FORT) -o ../bin/update_DB $(OBJDB_U) -+ $(BLANC_FORT) ${LDFLAGS} -o ../bin/update_DB $(OBJDB_U) - dom_l: $(OBJDB_V) -- $(BLANC_FORT) -o ../bin/update_domain_DB $(OBJDB_V) -+ $(BLANC_FORT) ${LDFLAGS} -o ../bin/update_domain_DB $(OBJDB_V) - ddb_l: $(OBJDB_D) -- $(BLANC_FORT) -o ../bin/dimer_search $(OBJDB_D) -+ $(BLANC_FORT) ${LDFLAGS} -o ../bin/dimer_search $(OBJDB_D) - dmdb_l: $(OBJDB_N) -- $(BLANC_FORT) -o ../bin/domain_search $(OBJDB_N) -+ $(BLANC_FORT) ${LDFLAGS} -o ../bin/domain_search $(OBJDB_N) - gdb_l: $(OBJDB_G) -- $(BLANC_FORT) -o ../bin/get_pdb_list $(OBJDB_G) -+ $(BLANC_FORT) ${LDFLAGS} -o ../bin/get_pdb_list $(OBJDB_G) - b2m_l: blanc2mtz.o libutils.o -- $(BLANC_FORT) -o ../bin/blanc2mtz blanc2mtz.o libutils.o $(CLIB)/libccp4f.a $(CLIB)/libccp4c.a -+ $(BLANC_FORT) ${LDFLAGS} -o ../bin/blanc2mtz blanc2mtz.o libutils.o -lccp4f -lccp4c - f2c_l: f2cif.o libutils.o -- $(BLANC_FORT) -o ../bin/f2cif f2cif.o libutils.o -+ $(BLANC_FORT) ${LDFLAGS} -o ../bin/f2cif f2cif.o libutils.o - chf_l: check_file_DB.o libutils.o -- $(BLANC_FORT) -o ../bin/check_file_DB check_file_DB.o libutils.o -+ $(BLANC_FORT) ${LDFLAGS} -o ../bin/check_file_DB check_file_DB.o libutils.o - chc_l: check_cell_sg.o libutils.o -- $(BLANC_FORT) -o ../bin/check_cell_sg check_cell_sg.o libutils.o -+ $(BLANC_FORT) ${LDFLAGS} -o ../bin/check_cell_sg check_cell_sg.o libutils.o - asl_l: alt_sg_list.o libutils.o -- $(BLANC_FORT) -o ../bin/alt_sg_list alt_sg_list.o libutils.o -+ $(BLANC_FORT) ${LDFLAGS} -o ../bin/alt_sg_list alt_sg_list.o libutils.o - sc_l: $(OBJDB_C) -- $(BLANC_FORT) -o ../bin/solution_check $(OBJDB_C) -+ $(BLANC_FORT) ${LDFLAGS} -o ../bin/solution_check $(OBJDB_C) - gt_l: $(OBJDB_R) -- $(BLANC_FORT) -o ../bin/get_trans $(OBJDB_R) -+ $(BLANC_FORT) ${LDFLAGS} -o ../bin/get_trans $(OBJDB_R) - dmn_l: domain.o libutils.o -- $(BLANC_FORT) -o ../bin/domain domain.o libutils.o -+ $(BLANC_FORT) ${LDFLAGS} -o ../bin/domain domain.o libutils.o - pack: pdb_pack.o libutils.o -- $(BLANC_FORT) -o ../bin/pdb_pack pdb_pack.o libutils.o -+ $(BLANC_FORT) ${LDFLAGS} -o ../bin/pdb_pack pdb_pack.o libutils.o - p2s_l: $(OBJDB_P) -- $(BLANC_FORT) -o ../bin/pdb2s $(OBJDB_P) -+ $(BLANC_FORT) ${LDFLAGS} -o ../bin/pdb2s $(OBJDB_P) - aln_l: align_DB.o DB_subr.o libutils.o -- $(BLANC_FORT) -o ../bin/align_DB align_DB.o DB_subr.o libutils.o -+ $(BLANC_FORT) ${LDFLAGS} -o ../bin/align_DB align_DB.o DB_subr.o libutils.o - aln3_l: align_DB_new.o DB_subr.o libutils.o -- $(BLANC_FORT) -o ../bin/align_DB_new align_DB_new.o DB_subr.o libutils.o -+ $(BLANC_FORT) ${LDFLAGS} -o ../bin/align_DB_new align_DB_new.o DB_subr.o libutils.o - cell_l: create_cell_list.o DB_subr.o libutils.o -- $(BLANC_FORT) -o ../bin/create_cell_list create_cell_list.o DB_subr.o libutils.o -+ $(BLANC_FORT) ${LDFLAGS} -o ../bin/create_cell_list create_cell_list.o DB_subr.o libutils.o - getch_l: get_chain.o DB_subr.o libutils.o -- $(BLANC_FORT) -o ../bin/get_chain get_chain.o DB_subr.o libutils.o -+ $(BLANC_FORT) ${LDFLAGS} -o ../bin/get_chain get_chain.o DB_subr.o libutils.o - getnmr_l: get_nmr.o DB_subr.o libutils.o -- $(BLANC_FORT) -o ../bin/get_nmr get_nmr.o DB_subr.o libutils.o -+ $(BLANC_FORT) ${LDFLAGS} -o ../bin/get_nmr get_nmr.o DB_subr.o libutils.o - getmod_l: get_model.o libutils.o -- $(BLANC_FORT) -o ../bin/get_model get_model.o libutils.o -+ $(BLANC_FORT) ${LDFLAGS} -o ../bin/get_model get_model.o libutils.o - crb_l: create_binaries.o DB_subr.o libutils.o -- $(BLANC_FORT) -o ../bin/create_binaries create_binaries.o DB_subr.o libutils.o -+ $(BLANC_FORT) ${LDFLAGS} -o ../bin/create_binaries create_binaries.o DB_subr.o libutils.o - save_si_l: save_seg_id.o DB_subr.o libutils.o -- $(BLANC_FORT) -o ../bin/save_seg_id save_seg_id.o DB_subr.o libutils.o -+ $(BLANC_FORT) ${LDFLAGS} -o ../bin/save_seg_id save_seg_id.o DB_subr.o libutils.o diff --git a/sci-chemistry/balbes/files/pyxml-0.8.4-python-2.6.patch b/sci-chemistry/balbes/files/pyxml-0.8.4-python-2.6.patch deleted file mode 100644 index d29b0b6a9eb2..000000000000 --- a/sci-chemistry/balbes/files/pyxml-0.8.4-python-2.6.patch +++ /dev/null @@ -1,28 +0,0 @@ -diff -rupN PyXML-0.8.4-old/xml/xpath/ParsedAbbreviatedAbsoluteLocationPath.py PyXML-0.8.4/xml/xpath/ParsedAbbreviatedAbsoluteLocationPath.py ---- PyXML-0.8.4-old/xml/xpath/ParsedAbbreviatedAbsoluteLocationPath.py 2008-12-15 16:54:36.000000000 +0900 -+++ PyXML-0.8.4/xml/xpath/ParsedAbbreviatedAbsoluteLocationPath.py 2008-12-15 16:57:02.000000000 +0900 -@@ -24,8 +24,8 @@ class ParsedAbbreviatedAbsoluteLocationP - self._rel = rel - nt = ParsedNodeTest.ParsedNodeTest('node', '') - ppl = ParsedPredicateList.ParsedPredicateList([]) -- as = ParsedAxisSpecifier.ParsedAxisSpecifier('descendant-or-self') -- self._step = ParsedStep.ParsedStep(as, nt, ppl) -+ as_ = ParsedAxisSpecifier.ParsedAxisSpecifier('descendant-or-self') -+ self._step = ParsedStep.ParsedStep(as_, nt, ppl) - return - - def evaluate(self, context): -diff -rupN PyXML-0.8.4-old/xml/xpath/ParsedAbbreviatedRelativeLocationPath.py PyXML-0.8.4/xml/xpath/ParsedAbbreviatedRelativeLocationPath.py ---- PyXML-0.8.4-old/xml/xpath/ParsedAbbreviatedRelativeLocationPath.py 2008-12-15 16:54:36.000000000 +0900 -+++ PyXML-0.8.4/xml/xpath/ParsedAbbreviatedRelativeLocationPath.py 2008-12-15 16:58:58.000000000 +0900 -@@ -28,8 +28,8 @@ class ParsedAbbreviatedRelativeLocationP - self._right = right - nt = ParsedNodeTest.ParsedNodeTest('node','') - ppl = ParsedPredicateList.ParsedPredicateList([]) -- as = ParsedAxisSpecifier.ParsedAxisSpecifier('descendant-or-self') -- self._middle = ParsedStep.ParsedStep(as, nt, ppl) -+ as_ = ParsedAxisSpecifier.ParsedAxisSpecifier('descendant-or-self') -+ self._middle = ParsedStep.ParsedStep(as_, nt, ppl) - - def evaluate(self, context): - res = [] diff --git a/sci-chemistry/balbes/metadata.xml b/sci-chemistry/balbes/metadata.xml deleted file mode 100644 index 4bb6be5e5d0c..000000000000 --- a/sci-chemistry/balbes/metadata.xml +++ /dev/null @@ -1,18 +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@gentoo.org</email> - </maintainer> - <longdescription> - BALBES is a system for solving protein structures using x-ray - crystalographic data. Molecular Replacement(MR) is its core - scientific method. BALBES aims to integrate all components, - necessary for finding a solution structure by MR, into one system. - It consists of a database, scientific programs and a python - pipeline. The system is automated so that it needs no user's - intervention when running complicated combination of jobs such - as model searching, molecular replacement and refinement. -</longdescription> -</pkgmetadata> diff --git a/sci-chemistry/ccp4-apps/Manifest b/sci-chemistry/ccp4-apps/Manifest deleted file mode 100644 index e56aec5512a2..000000000000 --- a/sci-chemistry/ccp4-apps/Manifest +++ /dev/null @@ -1,2 +0,0 @@ -DIST 6.1.3-oasis4.0.patch.bz2 946 SHA256 12d7c5965e0c46b0f482514d9083d6be94d65eeb14ba29c17d507d5f9669f84b SHA512 7c7bf4ef90550708bf41b1831dbe71c38418b46455adb3d42ec609d287894ac9260d9671f1759f71c713ced72fa004b9808391ea6874007ac8b7d7637f349d32 WHIRLPOOL a2bc27e1e054e1717c387f3800533fa490c03d1d18d3fe3cff4676f0ec47799a1681a206e01013c1b8f8e41162303446a824b86effeef2ed73f059feb07fb820 -DIST ccp4-6.1.3-core-src.tar.gz 242134076 SHA256 1e529c660e7f390ec0feca9d45caa00a2813d23156c10a2747c427117293c324 SHA512 413eba806107ebcdbd93e9122275463709133d9b2a9ce44ae57a6c2350465a47ba66ad9875237aead74f5d422c0104f58f728ab37a757b10d82cde92af444c20 WHIRLPOOL faebf8ee7920013bc3d0e83565207dca1f31ba0b5c92fe1eae4b740f70ff2031d95787fa0d545b09c853d25657c08973527e43de02fddc086988123ca2a6339c diff --git a/sci-chemistry/ccp4-apps/ccp4-apps-6.1.3-r13.ebuild b/sci-chemistry/ccp4-apps/ccp4-apps-6.1.3-r13.ebuild deleted file mode 100644 index 5e1032133922..000000000000 --- a/sci-chemistry/ccp4-apps/ccp4-apps-6.1.3-r13.ebuild +++ /dev/null @@ -1,395 +0,0 @@ -# Copyright 1999-2015 Gentoo Foundation -# Distributed under the terms of the GNU General Public License v2 -# $Id$ - -EAPI=5 - -PYTHON_COMPAT=( python2_7 ) - -inherit autotools eutils fortran-2 flag-o-matic gnuconfig python-single-r1 toolchain-funcs - -MY_P="${PN/-apps}-${PV}" - -#UPDATE="04_03_09" -#PATCHDATE="090511" - -PATCH_TOT="0" - -DESCRIPTION="Protein X-ray crystallography toolkit" -HOMEPAGE="http://www.ccp4.ac.uk/" -SRC="ftp://ftp.ccp4.ac.uk/ccp4" -SRC_URI=" - ${SRC}/${PV}/${MY_P}-core-src.tar.gz - https://dev.gentoo.org/~jlec/distfiles/${PV}-oasis4.0.patch.bz2" -# patch tarball from upstream - [[ -n ${UPDATE} ]] && SRC_URI="${SRC_URI} ${SRC}/${PV}/updates/${P}-src-patch-${UPDATE}.tar.gz" -# patches created by us - [[ -n ${PATCHDATE} ]] && SRC_URI="${SRC_URI} https://dev.gentoo.org/~jlec/science-dist/${PV}-${PATCHDATE}-updates.patch.bz2" - -for i in $(seq $PATCH_TOT); do - NAME="PATCH${i}[1]" - SRC_URI="${SRC_URI} - ${SRC}/${PV}/patches/${!NAME}" -done - -LICENSE="ccp4" -SLOT="0" -KEYWORDS="amd64 ~ppc x86 ~amd64-linux ~x86-linux" -IUSE="examples X" - -X11DEPS=" - x11-libs/libX11 - x11-libs/libXaw - x11-libs/libXt - x11-libs/libxdl_view" - -TKDEPS=" - >=dev-lang/tk-8.3:0= - >=dev-tcltk/blt-2.4 - dev-tcltk/iwidgets - dev-tcltk/itcl - dev-tcltk/itk - >=dev-tcltk/tdom-0.8 - dev-tcltk/tktreectrl" - -SCILIBS=" - ~sci-libs/ccp4-libs-${PV} - >=sci-libs/ccp4-libs-${PV}-r7 - sci-libs/clipper - sci-libs/fftw:2.1 - sci-libs/mmdb:0 - sci-libs/ssm - virtual/blas - virtual/lapack" - -SCIAPPS=" - sci-chemistry/pdb-extract - sci-chemistry/pymol - sci-chemistry/rasmol - >=sci-chemistry/oasis-4.0-r1" - -RDEPEND=" - ${TKDEPS} - ${SCILIBS} - app-shells/tcsh - dev-python/pyxml - dev-libs/libxml2:2 - dev-libs/libjwc_c - dev-libs/libjwc_f - dev-libs/boehm-gc - !app-office/sc - !<sci-chemistry/ccp4-6.1.3 - X? ( ${X11DEPS} )" -DEPEND="${RDEPEND} - X? ( - x11-misc/imake - x11-proto/inputproto - x11-proto/xextproto - )" -PDEPEND="${SCIAPPS}" - -RESTRICT="mirror" - -S="${WORKDIR}/${MY_P}" - -pkg_setup() { - fortran-2_pkg_setup - python-single-r1_pkg_setup -} - -src_prepare() { - tc-export PKG_CONFIG - einfo "Applying upstream patches ..." - for patch in $(seq $PATCH_TOT); do - base="PATCH${patch}" - dir=$(eval echo \${${base}[0]}) - p=$(eval echo \${${base}[1]}) - pushd "${dir}" >& /dev/null - ccp_patch "${DISTDIR}/${p}" - popd >& /dev/null - done - einfo "Done." - echo - - [[ -n ${PATCHDATE} ]] && epatch "${WORKDIR}"/${PV}-${PATCHDATE}-updates.patch - - einfo "Applying Gentoo patches ..." - - # it tries to create libdir, bindir etc on live system in configure - ccp_patch "${FILESDIR}"/${PV}-dont-make-dirs-in-configure.patch - - # We already have sci-chemistry/rasmol - # Also remember to create the bindir. - ccp_patch "${FILESDIR}"/${PV}-dont-build-double-and-make-bindir.patch - - # libraries come from sci-libs/ccp4-libs - ccp_patch "${FILESDIR}"/${PV}-dont-build-libs.patch - - # We have seperate ebuilds for those - for bin in molref xia scala imosflm balbes; do - ccp_patch "${FILESDIR}"/${PV}-dont-build-${bin}.patch - done - - # don't configure what is not build - ccp_patch "${FILESDIR}"/${PV}-dont-configure.patch - - # Set python paths correctly - ccp_patch "${FILESDIR}"/${PV}-pythonpath.patch - - # Set python paths correctly - ccp_patch "${FILESDIR}"/${PV}-pisa.patch - - # Set python paths correctly - ccp_patch "${FILESDIR}"/${PV}-clipper-template.patch - - # Fix upstreams code - ccp_patch "${FILESDIR}"/${PV}-impl-dec.patch - - # Not renaming, but unbundling libs - ccp_patch "${FILESDIR}"/${PV}-rename-rapper-ng.patch - - # Use pkg-config to detect BLAS/LAPCK - ccp_patch "${FILESDIR}"/${PV}-lapack.patch - - # unbundle libs - ccp_patch "${FILESDIR}"/${PV}-unbundle.patch - - # tcl-8.6 - ccp_patch "${FILESDIR}"/${P}-tcl8.6.patch - - # Update things for oasis 4 usage - epatch "${WORKDIR}"/${PV}-oasis4.0.patch - sed 's: oasis : :g' -i src/Makefile.in || die - - einfo "Done." # done applying Gentoo patches - echo - - find ./lib/src/mmdb ./lib/ssm ./lib/clipper ./lib/fftw lib/lapack -delete - - sed \ - -e "s:/usr:${EPREFIX}/usr:g" \ - -e 's:-Wl,-rpath,$CLIB::g' \ - -e 's: -rpath $CLIB::g' \ - -e 's: -I${srcdir}/include/cpp_c_headers::g' \ - -e 's:sleep 1:sleep .2:g' \ - -e 's:\\$(XCIF_LIB):-L$srcdir/lib/ccif -lccif:g' \ - -e 's:\\$(XLAPACK_LIB):${XLAPACK_LIB}:g' \ - -e 's:\\$(CXX_LIBS):\${CXX_LIBS}:g' \ - -e 's:\\$(XLDFLAGS):\${XLDFLAGS}:g' \ - -i configure || die - - sed \ - -e '/o crunch2/s:$: ${XLAPACK_LIB}:g' \ - -i src/Makefile* || die - - find "${S}" -name "Makefile.*" \ - -exec sed -e 's|_FLAGS-|_FLAGS:-|g' -e "s:\(eval \$([[:alnum:]]*)\):\1 \$(GENTOOLDFLAGS):g" -i '{}' \; - - # Don't build refmac, sfcheck, balbes, molrep binaries; available from the standalone version - sed -i -e "/^REFMACTARGETS/s:^.*:REFMACTARGETS="":g" configure || die - - # Rapper bundles libxml2 and boehm-gc. Don't build, use or install those. - pushd src/rapper 2>/dev/null - eautoreconf - popd 2>/dev/null - - gnuconfig_update - - python_fix_shebang -f . -} - -src_configure() { - # Build system is broken if we set LDFLAGS - export GENTOOLDFLAGS="${LDFLAGS}" - unset LDFLAGS - - # These are broken with ./src/procheck/ps.f - filter-flags "-floop-*" - - # GENTOO_OSNAME can be one of: - # irix irix64 sunos sunos64 aix hpux osf1 linux freebsd - # linux_compaq_compilers linux_intel_compilers generic Darwin - # ia64_linux_intel Darwin_ibm_compilers linux_ibm_compilers - if [[ "$(tc-getFC)" = "ifort" ]]; then - if use ia64; then - GENTOO_OSNAME="ia64_linux_intel" - else - # Should be valid for x86, maybe amd64 - GENTOO_OSNAME="linux_intel_compilers" - fi - else - # Should be valid for x86 and amd64, at least - GENTOO_OSNAME="linux" - fi - - # Sets up env - ln -s \ - ccp4.setup-bash \ - "${S}"/include/ccp4.setup - - # We agree to the license by emerging this, set in LICENSE - sed -i \ - -e "s~^\(^agreed=\).*~\1yes~g" \ - "${S}"/configure || die - - # Fix up variables -- need to reset CCP4_MASTER at install-time - sed -i \ - -e "s~^\(setenv CCP4_MASTER.*\)/.*~\1${WORKDIR}~g" \ - -e "s~^\(export CCP4_MASTER.*\)/.*~\1${WORKDIR}~g" \ - -e "s~^\(.*export CBIN=.*\)\$CCP4.*~\1\$CCP4/libexec/ccp4/bin/~g" \ - -e "s~^\(.*setenv CBIN .*\)\$CCP4.*~\1\$CCP4/libexec/ccp4/bin/~g" \ - -e "s~^\(setenv CCP4I_TCLTK.*\)/usr/local/bin~\1${EPREFIX}/usr/bin~g" \ - "${S}"/include/ccp4.setup* || die - - # Set up variables for build - source "${S}"/include/ccp4.setup-sh - - export CC=$(tc-getCC) - export CXX=$(tc-getCXX) - export COPTIM=${CFLAGS} - export CXXOPTIM=${CXXFLAGS} - # Default to -O2 if FFLAGS is unset - export FC=$(tc-getFC) - export FOPTIM=${FFLAGS:- -O2} - export BINSORT_SCR="${T}" - export CCP4_MASTER="${WORKDIR}" - export CCP4I_TCLTK="${EPREFIX}/usr/bin" - export MAKE="make ${MAKEOPTS} ${EXTRA_EMAKE}" - - # Can't use econf, configure rejects unknown options like --prefix - ./configure \ - $(use_enable X x) \ - --with-shared-libs \ - --with-fftw="${EPREFIX}/usr" \ - --with-warnings \ - --disable-pdb_extract \ - --disable-cctbx \ - --disable-phaser \ - --disable-diffractionImg \ - --disable-clipper \ - --disable-ssm \ - --disable-mosflm \ - --disable-mrbump \ - --tmpdir="${TMPDIR}" \ - ${GENTOO_OSNAME} || die "configure failed" - - # We do this manually, since disabling the clipper libraries also - # disables the clipper programs - pushd src/clipper_progs 2>/dev/null - econf \ - --prefix="${S}" \ - --bindir="${ED}"/usr/libexec/ccp4/bin \ - --with-ccp4="${S}" \ - --with-clipper="${EPREFIX}/usr" \ - --with-fftw="${EPREFIX}/usr" \ - --with-mmdb="${EPREFIX}/usr" \ - CXX=$(tc-getCXX) - popd 2>/dev/null -} - -src_compile() { - # fsplit is required for the programs - pushd lib/src 2>/dev/null - emake fsplit -j1 || die - popd 2>/dev/null - - # We do this manually, since disabling the clipper libraries also - # disables the clipper programs - pushd src/clipper_progs 2>/dev/null - emake || die - popd 2>/dev/null - - emake -j1 || die "emake failed" -} - -src_install() { - # Set up variables for build - source "${S}"/include/ccp4.setup-sh - - # if we don't make this, a ton of programs fail to install - mkdir "${S}"/bin || die - - # We do this manually, since disabling the clipper libraries also - # disables the clipper programs - pushd "${S}"/src/clipper_progs 2>/dev/null - emake install || die - popd 2>/dev/null - - einstall || die "install failed" - - # Collision with sci-chemistry/mrbump - rm -f "${S}"/bin/{mrbump,pydbviewer} || die - - # Bins - exeinto /usr/libexec/ccp4/bin/ - doexe "${S}"/bin/* || die - - # Libs - for file in "${S}"/lib/*; do - if [[ -d ${file} ]]; then - continue - elif [[ -x ${file} ]]; then - dolib.so ${file} || die - else - insinto /usr/$(get_libdir) - doins ${file} || die - fi - done - - rm -f "${S}"/include/ccp4.setup* - - # smartie -- log parsing - insinto /usr/share/ccp4 - doins -r "${S}"/share/smartie || die - - # Install docs and examples - local _man - pushd "${S}"/man/cat1 > /dev/null - for _man in *; do - newman ${_man} ${_man%??}-ccp4${_man:${#_man}-2:2} - done - popd > /dev/null - - mv "${S}"/manual/README "${S}"/manual/README-manual - dodoc manual/* README CHANGES doc/* examples/README || die - - rm "${ED}"/usr/share/doc/${PF}/GNUmakefile.* - rm "${ED}"/usr/share/doc/${PF}/COPYING.* - - dohtml -r "${S}"/html/* - - if use examples; then - for i in data rnase toxd; do - docinto examples/${i} - dodoc "${S}"/examples/${i}/* - done - - docinto examples/tutorial - dohtml -r "${S}"/examples/tutorial/html examples/tutorial/tut.css - for i in data results; do - docinto examples/tutorial/${i} - dodoc "${S}"/examples/tutorial/${i}/* - done - - for i in non-runnable runnable; do - docinto examples/unix/${i} - dodoc "${S}"/examples/unix/${i}/* - done - fi - # Needed for ccp4i docs to work - dosym ../../share/doc/${PF}/examples /usr/$(get_libdir)/ccp4/examples || die - dosym ../../share/doc/${PF}/html /usr/$(get_libdir)/ccp4/html || die - - cat >> "${T}"/baubles <<- EOF - #!${EPREFIX}/bin/bash - exec "${EPYTHON}" "\${CCP4}/share/ccp4/smartie/baubles.py" - EOF - - exeinto /usr/libexec/ccp4/bin/ - doexe "${T}"/baubles || die -} - -# Epatch wrapper for bulk patching -ccp_patch() { - EPATCH_SINGLE_MSG=" ${1##*/} ..." epatch ${1} -} diff --git a/sci-chemistry/ccp4-apps/files/6.1.3-clipper-template.patch b/sci-chemistry/ccp4-apps/files/6.1.3-clipper-template.patch deleted file mode 100644 index 433a78dbd23b..000000000000 --- a/sci-chemistry/ccp4-apps/files/6.1.3-clipper-template.patch +++ /dev/null @@ -1,70 +0,0 @@ ---- src/clipper_progs/src/intensity_target.h.orig 2010-01-21 11:27:13.236795886 -0600 -+++ src/clipper_progs/src/intensity_target.h 2010-01-21 11:31:33.450686927 -0600 -@@ -70,9 +70,31 @@ - { - public: - //! constructor: takes the datalist against which to calc target -- TargetFn_scaleLogI1I2( const HKL_data<T1>& hkl_data1_, const HKL_data<T2>& hkl_data2_ ); -+ TargetFn_scaleLogI1I2( const HKL_data<T1>& hkl_data1_, const HKL_data<T2>& hkl_data2_ ) -+ { -+ hkl_data1 = &hkl_data1_; -+ hkl_data2 = &hkl_data2_; -+ } - //! return the value and derivatives of the target function -- Rderiv rderiv( const HKL_info::HKL_reference_index& ih, const ftype& intensityh ) const; -+ Rderiv rderiv( const HKL_info::HKL_reference_index& ih, const ftype& intensityh ) const -+ { -+ Rderiv result; -+ result.r = result.dr = result.dr2 = 0.0; -+ const T1& it1 = (*hkl_data1)[ih]; -+ const T2& it2 = (*hkl_data2)[ih]; -+ if ( !it1.missing() && !it2.missing() ) -+ if ( it1.I() > 1.0e-6 && it2.I() > 1.0e-6 ) { -+ const ftype eps = ih.hkl_class().epsilon(); -+ const ftype i1 = it1.I() / eps; -+ const ftype i2 = it2.I() / eps; -+ const ftype w = sqrt( i1 * i2 ); -+ const ftype d = intensityh + log(i1) - log(i2); -+ result.r = w * d * d; -+ result.dr = 2.0 * w * d; -+ result.dr2 = 2.0 * w; -+ } -+ return result; -+ } - //! the type of the function: optionally used to improve convergence - FNtype type() const { return QUADRATIC; } - private: -@@ -109,33 +131,4 @@ - return result; - } - -- // Log I1-I2 scaling -- -- template<class T1, class T2> TargetFn_scaleLogI1I2<T1,T2>::TargetFn_scaleLogI1I2( const HKL_data<T1>& hkl_data1_, const HKL_data<T2>& hkl_data2_ ) -- { -- hkl_data1 = &hkl_data1_; -- hkl_data2 = &hkl_data2_; -- } -- -- template<class T1, class T2> TargetFn_base::Rderiv TargetFn_scaleLogI1I2<T1,T2>::rderiv( const HKL_info::HKL_reference_index& ih, const ftype& intensityh ) const -- { -- Rderiv result; -- result.r = result.dr = result.dr2 = 0.0; -- const T1& it1 = (*hkl_data1)[ih]; -- const T2& it2 = (*hkl_data2)[ih]; -- if ( !it1.missing() && !it2.missing() ) -- if ( it1.I() > 1.0e-6 && it2.I() > 1.0e-6 ) { -- const ftype eps = ih.hkl_class().epsilon(); -- const ftype i1 = it1.I() / eps; -- const ftype i2 = it2.I() / eps; -- const ftype w = sqrt( i1 * i2 ); -- const ftype d = intensityh + log(i1) - log(i2); -- result.r = w * d * d; -- result.dr = 2.0 * w * d; -- result.dr2 = 2.0 * w; -- } -- return result; -- } -- -- - #endif diff --git a/sci-chemistry/ccp4-apps/files/6.1.3-dont-build-balbes.patch b/sci-chemistry/ccp4-apps/files/6.1.3-dont-build-balbes.patch deleted file mode 100644 index f1df3e5e19f9..000000000000 --- a/sci-chemistry/ccp4-apps/files/6.1.3-dont-build-balbes.patch +++ /dev/null @@ -1,14 +0,0 @@ -diff --git a/share/Makefile.in b/share/Makefile.in -index 2d4f20b..4500993 100755 ---- a/share/Makefile.in -+++ b/share/Makefile.in -@@ -18,9 +18,6 @@ install : - for i in $(MRBUMP_TARGETS); do \ - test -s $(MRBUMP_BINDIR)/$$i && $(INSTALL_PROGRAM) $(MRBUMP_BINDIR)/$$i $(bindir)/$$i || true ;\ - done -- for i in $(BALBES_TARGETS); do \ -- test -s $(BALBES_BINDIR)/$$i && $(INSTALL_PROGRAM) $(BALBES_BINDIR)/$$i $(bindir)/$$i || true ;\ -- done - - clean : ; -rm -f core *.o *~ a.out - diff --git a/sci-chemistry/ccp4-apps/files/6.1.3-dont-build-double-and-make-bindir.patch b/sci-chemistry/ccp4-apps/files/6.1.3-dont-build-double-and-make-bindir.patch deleted file mode 100644 index e62ae12adfbe..000000000000 --- a/sci-chemistry/ccp4-apps/files/6.1.3-dont-build-double-and-make-bindir.patch +++ /dev/null @@ -1,24 +0,0 @@ ---- ccp4-6.1.1/x-windows/Makefile.in 2008-08-11 19:20:01.000000000 +0200 -+++ ccp4-6.1.1/x-windows/Makefile.in.new 2009-02-27 14:32:25.000000000 +0100 -@@ -35,7 +35,7 @@ - # - # all - # --all : xdlview libjwc_c libjwc_f rotgen_ hklview xjiffy rasmol2 ipmosflm -+all : rotgen_ hklview xjiffy - # - # xdl_view - # -@@ -157,11 +157,10 @@ - # - install_obj = hklview rotgen ipmosflm - install: all -+ mkdir -p $(bindir) - $(INSTALL_PROGRAM) $(srcdir)/hklview $(bindir) - cd $(srcdir)/XCCPJIFFY ; $(MAKE) bindir=$(bindir) libdir=$(libdir) install -- $(INSTALL_PROGRAM) $(rasmol_dir)/rasmol $(bindir) - cd $(rotgen_dir); $(MAKE) install -- $(INSTALL_PROGRAM) $(mosflm_dir)/bin/ipmosflm $(bindir) - # - # clean - # diff --git a/sci-chemistry/ccp4-apps/files/6.1.3-dont-build-imosflm.patch b/sci-chemistry/ccp4-apps/files/6.1.3-dont-build-imosflm.patch deleted file mode 100644 index f645643e1c67..000000000000 --- a/sci-chemistry/ccp4-apps/files/6.1.3-dont-build-imosflm.patch +++ /dev/null @@ -1,11 +0,0 @@ ---- ccp4i/Makefile.in 2009-06-19 15:08:53.000000000 +0200 -+++ ccp4i/Makefile.in.new 2009-08-04 21:10:14.000000000 +0200 -@@ -9,7 +9,7 @@ - SHELL = /bin/sh - DESTDIR = $(prefix) - CCP4I_BINDIR = $(top_srcdir)/ccp4i/bin --CCP4I_TARGETS = ccp4i imosflm loggraph crank mapslicer -+CCP4I_TARGETS = ccp4i loggraph crank mapslicer - - install : - for i in $(CCP4I_TARGETS); do \ diff --git a/sci-chemistry/ccp4-apps/files/6.1.3-dont-build-libs.patch b/sci-chemistry/ccp4-apps/files/6.1.3-dont-build-libs.patch deleted file mode 100644 index 1d1323005540..000000000000 --- a/sci-chemistry/ccp4-apps/files/6.1.3-dont-build-libs.patch +++ /dev/null @@ -1,35 +0,0 @@ ---- Makefile.in 2009-06-19 15:13:29.000000000 +0200 -+++ Makefile.in.new 2009-08-02 23:06:41.000000000 +0200 -@@ -2,7 +2,7 @@ - # $Id$ - - SHELL = /bin/sh --DIRS = $(fftwdir) $(clipperdir) $(diffimdir) $(lapackdir) $(ccifdir) lib/src $(ssmdir) src lib/data unsupported/src x-windows share ccp4i $(prereleasedir) -+DIRS = src lib/data unsupported/src x-windows share ccp4i $(prereleasedir) - # this is for the benefit of makes that don't pass variable values in - # recursive invocations, so that you can override these values on the - # command line at the top level -@@ -69,19 +69,19 @@ - $(MAKE) -i $(MFLAGS) $(MVARS) install; else true; fi ; \ - $(MAKE) install - --srcdir : FORCE libdir -+srcdir : FORCE - if test -d src; then cd src; $(MAKE) $(MFLAGS) $(MVARS); else true; fi - - supported : srcdir - --unsupported : FORCE libdir -+unsupported : FORCE - if test -d unsupported/src; then cd unsupported/src; \ - $(MAKE) $(MFLAGS) $(MVARS); else true; fi - --datadir : FORCE libdir -+datadir : FORCE - cd lib/data; $(MAKE) $(MFLAGS) $(MVARS) - --xwindir : FORCE libdir -+xwindir : FORCE - if test -f x-windows/Makefile; then cd x-windows; \ - $(MAKE) -i $(MFLAGS) ; else true; fi - diff --git a/sci-chemistry/ccp4-apps/files/6.1.3-dont-build-molref.patch b/sci-chemistry/ccp4-apps/files/6.1.3-dont-build-molref.patch deleted file mode 100644 index f16b0ecb938c..000000000000 --- a/sci-chemistry/ccp4-apps/files/6.1.3-dont-build-molref.patch +++ /dev/null @@ -1,19 +0,0 @@ ---- src/pisa/Makefile.am 2007-07-10 10:56:05.000000000 +0200 -+++ src/pisa/Makefile.am.new 2009-06-11 21:16:51.000000000 +0200 -@@ -1,4 +1,4 @@ --SUBDIRS = molref pisastore sbase -+SUBDIRS = pisastore sbase - - pkgdatadir = $(datadir)/pisa - ---- src/pisa/Makefile.in 2009-06-12 21:12:08.000000000 +0200 -+++ src/pisa/Makefile.in.new 2009-06-12 21:41:52.000000000 +0200 -@@ -82,7 +82,7 @@ - am__quote = @am__quote@ - install_sh = @install_sh@ - pisa_LDFLAGS = @pisa_LDFLAGS@ --SUBDIRS = molref pisastore sbase -+SUBDIRS = pisastore sbase - - dist_pkgdata_DATA = pisa.cfg - diff --git a/sci-chemistry/ccp4-apps/files/6.1.3-dont-build-scala.patch b/sci-chemistry/ccp4-apps/files/6.1.3-dont-build-scala.patch deleted file mode 100644 index af4fd8219c4f..000000000000 --- a/sci-chemistry/ccp4-apps/files/6.1.3-dont-build-scala.patch +++ /dev/null @@ -1,42 +0,0 @@ ---- ./src/Makefile.in 2009-03-20 15:06:41.000000000 +0100 -+++ ./src/Makefile.in.new 2009-07-31 23:46:13.000000000 +0200 -@@ -50,7 +50,7 @@ - - # these live in subdirectories and have more than one dependency: - OTHERS = rsps anglen secstr proclean pplot gfac2pdb tplot mplot probplot rmsdev nb \ -- scala dm dmmulti stereo mapmask maprot ncsmask \ -+ dm dmmulti stereo mapmask maprot ncsmask \ - sftools tlsanl tlsextract topp toplist dyndom sc combat mlphare fffear ffjoin \ - anisoanl $(REFMACTARGETS) dtrek2scala crunch2 pmf doser mat2symop symop2mat - -@@ -637,7 +637,7 @@ - - ### scala, mapmask, maprot, ncsmask, combat - --scala mapmask maprot ncsmask combat sc dyndom: # dependencies below -+mapmask maprot ncsmask combat sc dyndom: # dependencies below - @$(SETFLAGS) pwd=`pwd` ; rm -f $@; \ - cd $(srcdir)/$@_; \ - echo $(FC) $${$@_FLAGS-"$(FFLAGS)"} -c -o $$pwd/$@.o `pwd`/$@.f ;\ -@@ -1002,21 +1002,6 @@ - proclean: $(srcdir)/procheck/clean.f $(srcdir)/procheck/brkcln.par - rmsdev: $(srcdir)/procheck/rmsdev.f $(srcdir)/procheck/rmsdev.inc - --scaladir = $(srcdir)/scala_ --scala : $(scaladir)/scala.f $(scaladir)/column.fh $(scaladir)/orient.fh \ -- $(scaladir)/params.fh $(scaladir)/rfile.fh $(scaladir)/scales.fh \ -- $(scaladir)/nbtchc.fh $(scaladir)/parameter.fh $(scaladir)/refcon.fh \ -- $(scaladir)/rundef.fh $(scaladir)/sdfacc.fh $(scaladir)/flags.fh \ -- $(scaladir)/inout.fh $(scaladir)/dump.fh $(scaladir)/tie.fh \ -- $(scaladir)/outcon.fh $(scaladir)/version.fh $(scaladir)/anomtc.fh \ -- $(scaladir)/axes.fh $(scaladir)/bigarg.fh \ -- $(scaladir)/errors.fh $(scaladir)/flow.fh $(scaladir)/glocon.fh \ -- $(scaladir)/means.fh $(scaladir)/refflg.fh $(scaladir)/stats.fh \ -- $(scaladir)/symmty.fh $(scaladir)/sharvest.fh $(scaladir)/chtml.fh \ -- $(scaladir)/htmbuf.fh $(scaladir)/sphhrm.fh $(scaladir)/crlncf.fh \ -- $(scaladir)/datasets.fh $(scaladir)/dts_storage.fh \ -- $(scaladir)/sclinimeans.fh $(scaladir)/timecor.fh -- - freemask.o: $(dmdir)/freemask.f $(dmdir)/crystal.fh $(dmdir)/cycl.fh \ - $(dmdir)/dmheader.fh $(dmdir)/io.fh $(dmdir)/output.fh \ - $(dmdir)/params.fh $(dmdir)/uvwdata.fh diff --git a/sci-chemistry/ccp4-apps/files/6.1.3-dont-build-xia.patch b/sci-chemistry/ccp4-apps/files/6.1.3-dont-build-xia.patch deleted file mode 100644 index 3af4af503fa6..000000000000 --- a/sci-chemistry/ccp4-apps/files/6.1.3-dont-build-xia.patch +++ /dev/null @@ -1,14 +0,0 @@ ---- src/Makefile.in 2009-07-05 16:50:25.000000000 +0200 -+++ src/Makefile.in.new 2009-07-05 19:38:06.000000000 +0200 -@@ -50,9 +50,9 @@ - - # these live in subdirectories and have more than one dependency: - OTHERS = rsps anglen secstr proclean pplot gfac2pdb tplot mplot probplot rmsdev nb \ -- scala dm dmmulti stereo mapmask maprot ncsmask chef \ -+ scala dm dmmulti stereo mapmask maprot ncsmask \ - sftools tlsanl tlsextract topp toplist dyndom sc combat mlphare fffear ffjoin \ -- anisoanl $(REFMACTARGETS) dtrek2scala crunch2 pmf doser mat2symop symop2mat -+ anisoanl $(REFMACTARGETS) dtrek2scala crunch2 pmf - - # targets built from .c sources: - CSIMPLE = pltdev binsort diff --git a/sci-chemistry/ccp4-apps/files/6.1.3-dont-configure.patch b/sci-chemistry/ccp4-apps/files/6.1.3-dont-configure.patch deleted file mode 100644 index 1e59578473ff..000000000000 --- a/sci-chemistry/ccp4-apps/files/6.1.3-dont-configure.patch +++ /dev/null @@ -1,111 +0,0 @@ ---- configure 2009-08-07 12:11:28.000000000 +0200 -+++ configure.new.nolib 2009-08-17 22:30:39.000000000 +0200 -@@ -3113,41 +3113,6 @@ - RX_L="$configdir/lib/rxdispencer/rx" - export RX_H RX_L - fi -- echo -- echo "Running separate configure for CCIF library." -- echo -- cd lib/ccif -- echo "Updating modification times for configuration files" -- echo "Please wait..." -- for i in configure.in aclocal.m4 configure Makefile.in; do -- touch $i && sleep 1 -- done -- echo "...done." -- -- if [ "X$LIBFOPTIM" != "X" ]; then -- FOPTIM_save=$FOPTIM -- FOPTIM=$LIBFOPTIM -- FFLAGS="${FOPTIM} ${XFFLAGS}" -- fi -- if [ "X$LIBCOPTIM" != "X" ]; then -- COPTIM_save=$COPTIM -- COPTIM=$LIBCOPTIM -- CFLAGS="${COPTIM} ${XCFLAGS}" -- fi -- ( touch /tmp/$$.cache_file 2>/dev/null && \ -- cat /dev/null > /tmp/$$.cache_file && \ -- ./configure $xopts --libdir=${libdir} --srcdir=${srcdir}/lib/ccif --cache-file=/tmp/$$.cache_file ) || \ -- ./configure $xopts --libdir=${libdir} --srcdir=${srcdir}/lib/ccif -- rm -f /tmp/$$.cache_file -- if [ "X$LIBFOPTIM" != "X" ]; then -- FOPTIM=$FOPTIM_save -- FFLAGS="${FOPTIM} ${XFFLAGS}" -- fi -- if [ "X$LIBCOPTIM" != "X" ]; then -- COPTIM=$COPTIM_save -- CFLAGS="${COPTIM} ${XCFLAGS}" -- fi -- cd ../.. - echo - echo "Returning to main configure." - echo -@@ -5094,53 +5059,6 @@ - echo "configure $xopts --exec_prefix=${prefix} --prefix=${prefix} --bindir=${bindir} --libdir=${libdir}" - ./configure $xopts --exec_prefix=${prefix} --prefix=${prefix} --bindir=${bindir} --libdir=${libdir} - echo -- echo "CCP4 configure: Running separate configure for libjwc_c library." -- echo -- cd ${srcdir}/${xwindir}/libjwc/libjwc_c -- echo "Updating modification times for configuration files in libjwc_c" -- echo "Please wait..." -- for i in configure.in Makefile.am aclocal.m4 configure Makefile.in ltconfig ltmain.sh; do -- touch $i && sleep 1 -- done -- echo "...done." -- echo -- echo "configure $xopts --exec_prefix=${prefix} --prefix=${prefix} --bindir=${bindir} --libdir=${libdir}" -- ( touch /tmp/$$.cache_file 2>/dev/null && \ -- cat /dev/null > /tmp/$$.cache_file && \ -- ./configure $xopts --exec_prefix=${prefix} --prefix=${prefix} --bindir=${bindir} --libdir=${libdir} --cache-file=/tmp/$$.cache_file ) || \ -- ./configure $xopts --exec_prefix=${prefix} --prefix=${prefix} --bindir=${bindir} --libdir=${libdir} -- rm -f /tmp/$$.cache_file -- echo -- echo "CCP4 configure: Running separate configure for libjwc_f library." -- echo -- cd ${srcdir}/${xwindir}/libjwc/libjwc_f -- # for g77 3.1 some builds do not have no-common for system libs, -- # so disable for now -- echo "Updating modification times for configuration files in libjwc_f" -- echo "Please wait..." -- for i in configure.in Makefile.am aclocal.m4 configure Makefile.in ltconfig ltmain.sh; do -- touch $i && sleep 1 -- done -- echo "...done." -- echo -- # for g77 3.1 some builds do not have no-common for system libs, -- # so disable for now -- case $system in -- Darwin* ) -- echo "configure --disable-shared --exec_prefix=${prefix} --prefix=${prefix} --bindir=${bindir} --libdir=${libdir}" -- ( touch /tmp/$$.cache_file 2>/dev/null && \ -- cat /dev/null > /tmp/$$.cache_file && \ -- ./configure --disable-shared --exec_prefix=${prefix} --prefix=${prefix} --bindir=${bindir} --libdir=${libdir} --cache-file=/tmp/$$.cache_file ) || \ -- ./configure --disable-shared --exec_prefix=${prefix} --prefix=${prefix} --bindir=${bindir} --libdir=${libdir} -- ;; -- * ) -- echo "configure $xopts --exec_prefix=${prefix} --prefix=${prefix} --bindir=${bindir} --libdir=${libdir}" -- ( touch /tmp/$$.cache_file 2>/dev/null && \ -- cat /dev/null > /tmp/$$.cache_file && \ -- ./configure $xopts --exec_prefix=${prefix} --prefix=${prefix} --bindir=${bindir} --libdir=${libdir} --cache-file=/tmp/$$.cache_file ) || \ -- ./configure $xopts --exec_prefix=${prefix} --prefix=${prefix} --bindir=${bindir} --libdir=${libdir} -- esac -- rm -f /tmp/$$.cache_file - - if test "$non_shared" = yes; then - #this is a bit of a cheat/fudge but that's life! -@@ -5210,12 +5128,6 @@ - fi - - echo -- echo "CCP4 configure: Running separate configure for Mosflm" -- echo -- cd ${srcdir}/${mosflmdir} -- echo "configure $xopts --with-ccp4-prefix=${prefix} --exec_prefix=${prefix} --prefix=${prefix} --bindir=${bindir} --libdir=${libdir}" -- ./configure $xopts --with-ccp4-prefix=${prefix} --exec_prefix=${prefix} --prefix=${prefix} --bindir=${bindir} --libdir=${libdir} -- echo - cd ../.. - echo "Returning to main configure." - echo diff --git a/sci-chemistry/ccp4-apps/files/6.1.3-dont-make-dirs-in-configure.patch b/sci-chemistry/ccp4-apps/files/6.1.3-dont-make-dirs-in-configure.patch deleted file mode 100644 index 583697cea0a1..000000000000 --- a/sci-chemistry/ccp4-apps/files/6.1.3-dont-make-dirs-in-configure.patch +++ /dev/null @@ -1,87 +0,0 @@ ---- ccp4-6.0.99e.orig/configure 2008-07-31 10:37:22.000000000 -0700 -+++ ccp4-6.0.99e/configure 2008-07-31 10:39:18.000000000 -0700 -@@ -643,45 +643,45 @@ - # echo "! Beware -- the $system installation isn't properly tested." ; } - syswarn='echo; echo "! Beware -- the $system installation is not properly tested."' - --if test -z "$onlylibs" ; then -- for i in CCP4_SCR BINSORT_SCR; do -- if ( eval test -d \$$i || eval mkdir -p \$$i ) ; then : -- else -- eval echo "! No directory \$$i and can\'t create it." -- echo " Check the value of $i." -- badvar=1 -- fi -- done -- -- for i in libdir bindir includedir; do -- if ( eval test -d \$$i || eval mkdir -p \$$i ) ; then : -- else -- eval echo "! No directory \$$i and can\'t create it." -- echo " Check the argument of --$i." -- badvar=1 -- fi -- done -- -- for i in $dotsrc $dotunsupp $dotunsuppsrc $dotdeprec $dotdeprecsrc ./lib ./lib/src ./lib/data ./ccp4i/etc/unix $mosflmdir/lib $mosflmdir/bin $mosflmdir/cbf/lib ; do -- if test -d $i || mkdir $i; then : -- else -- eval echo "! No directory $i and can\'t create it." -- badvar=1 -- fi -- done --else -- # Kludge to fool the "Makefile" target in the top-level CCP4 -- # Makefile into not trying to remake src/Makefile.in -- for i in $srcdir/src $srcdir/lib/src ; do -- if test -d $i || mkdir $i; then -- if ! test -f $i/Makefile.in ; then -- echo -- echo "onlylibs: making dummy file $i/Makefile.in" -- touch $i/Makefile.in -- fi -- fi -- done --fi -+#if test -z "$onlylibs" ; then -+# for i in CCP4_SCR BINSORT_SCR; do -+# if ( eval test -d \$$i || eval mkdir -p \$$i ) ; then : -+# else -+# eval echo "! No directory \$$i and can\'t create it." -+# echo " Check the value of $i." -+# badvar=1 -+# fi -+# done -+# -+# for i in libdir bindir includedir; do -+# if ( eval test -d \$$i || eval mkdir -p \$$i ) ; then : -+# else -+# eval echo "! No directory \$$i and can\'t create it." -+# echo " Check the argument of --$i." -+# badvar=1 -+# fi -+# done -+# -+# for i in $dotsrc $dotunsupp $dotunsuppsrc $dotdeprec $dotdeprecsrc ./lib ./lib/src ./lib/data ./ccp4i/etc/unix $mosflmdir/lib $mosflmdir/bin $mosflmdir/cbf/lib ; do -+# if test -d $i || mkdir $i; then : -+# else -+# eval echo "! No directory $i and can\'t create it." -+# badvar=1 -+# fi -+# done -+#else -+# # Kludge to fool the "Makefile" target in the top-level CCP4 -+# # Makefile into not trying to remake src/Makefile.in -+# for i in $srcdir/src $srcdir/lib/src ; do -+# if test -d $i || mkdir $i; then -+# if ! test -f $i/Makefile.in ; then -+# echo -+# echo "onlylibs: making dummy file $i/Makefile.in" -+# touch $i/Makefile.in -+# fi -+# fi -+# done -+#fi - - ### sanity checks - diff --git a/sci-chemistry/ccp4-apps/files/6.1.3-impl-dec.patch b/sci-chemistry/ccp4-apps/files/6.1.3-impl-dec.patch deleted file mode 100644 index db8236063043..000000000000 --- a/sci-chemistry/ccp4-apps/files/6.1.3-impl-dec.patch +++ /dev/null @@ -1,152 +0,0 @@ -diff --git a/lib/DiffractionImage/Bruker/FRM_LIB.c b/lib/DiffractionImage/Bruker/FRM_LIB.c -index bfda882..f821e04 100755 ---- a/lib/DiffractionImage/Bruker/FRM_LIB.c -+++ b/lib/DiffractionImage/Bruker/FRM_LIB.c -@@ -38,6 +38,8 @@ FRM_LIB: Routines for reading, writing, and handling frame files. - #include "sys/types.h" /* _open, etc. */ - #include "sys/stat.h" /* _open, etc. */ - -+#include <unistd.h> -+ - #ifndef _MSC_VER - int min(int a, int b) - { -diff --git a/lib/DiffractionImage/MAR/mar300_header.c b/lib/DiffractionImage/MAR/mar300_header.c -index 1a933de..1c40c32 100755 ---- a/lib/DiffractionImage/MAR/mar300_header.c -+++ b/lib/DiffractionImage/MAR/mar300_header.c -@@ -23,6 +23,9 @@ - */ - #include "mar300_header.h" - -+#include <sys/types.h> -+#include <unistd.h> -+ - /* - * Local functions - */ -diff --git a/lib/DiffractionImage/MAR/mar345_header.c b/lib/DiffractionImage/MAR/mar345_header.c -index a8351ea..16d0f7b 100755 ---- a/lib/DiffractionImage/MAR/mar345_header.c -+++ b/lib/DiffractionImage/MAR/mar345_header.c -@@ -32,6 +32,9 @@ - */ - #include "mar345_header.h" - -+#include <sys/types.h> -+#include <unistd.h> -+ - /* - * Definitions - */ -diff --git a/lib/DiffractionImage/MAR/nb_header.c b/lib/DiffractionImage/MAR/nb_header.c -index 07f2741..6364ca4 100755 ---- a/lib/DiffractionImage/MAR/nb_header.c -+++ b/lib/DiffractionImage/MAR/nb_header.c -@@ -20,6 +20,8 @@ - #include <io.h> - #endif - -+#include <sys/types.h> -+#include <unistd.h> - /* - * mar software include files - */ -diff --git a/lib/DiffractionImage/MAR/swap.c b/lib/DiffractionImage/MAR/swap.c -index 443bb8c..0d96b3f 100755 ---- a/lib/DiffractionImage/MAR/swap.c -+++ b/lib/DiffractionImage/MAR/swap.c -@@ -10,6 +10,9 @@ - * - **********************************************************************/ - -+#define _XOPEN_SOURCE -+#include <unistd.h> -+ - void swaplong(); - void swapshort(); - -diff --git a/lib/ccif/f_interface.c b/lib/ccif/f_interface.c -index 0f6a6b7..a09dc48 100755 ---- a/lib/ccif/f_interface.c -+++ b/lib/ccif/f_interface.c -@@ -25,6 +25,7 @@ - ********************************************************************/ - - #include "stdpccts.h" -+#include <sys/mman.h> - - /* This file is terribly organised, and badly needs re-doing. There is probably - * scope for splitting this into three modules: -diff --git a/lib/src/ccp4_general_f.c b/lib/src/ccp4_general_f.c -index 8b5d04f..74ee3f7 100755 ---- a/lib/src/ccp4_general_f.c -+++ b/lib/src/ccp4_general_f.c -@@ -26,6 +26,7 @@ - #include <string.h> - #include <stdlib.h> - #include <math.h> -+#include <time.h> - #include "ccp4_errno.h" - #include "ccp4_fortran.h" - #include "ccp4_parser.h" -diff --git a/lib/src/ccp4_program.c b/lib/src/ccp4_program.c -index 3e83d4d..bb3e975 100755 ---- a/lib/src/ccp4_program.c -+++ b/lib/src/ccp4_program.c -@@ -25,6 +25,7 @@ - #include <stdio.h> - #include <stdlib.h> - #include <string.h> -+#include <time.h> - #include "ccp4_program.h" - #include "ccp4_parser.h" - #include "ccp4_utils.h" -diff --git a/lib/src/fsplit.c b/lib/src/fsplit.c -index ee8af24..c6fb3cd 100755 ---- a/lib/src/fsplit.c -+++ b/lib/src/fsplit.c -@@ -50,6 +50,7 @@ static char sccsid[] = "@(#)fsplit.c 5.5 (Berkeley) 3/12/91"; - #include <string.h> - #include <sys/types.h> - #include <sys/stat.h> -+#include <unistd.h> - - /* - * usage: fsplit [-e efile] ... [file] -diff --git a/src/clipper_progs/src/pirate/compress42.c b/src/clipper_progs/src/pirate/compress42.c -index ea52e96..30dbd56 100755 ---- a/src/clipper_progs/src/pirate/compress42.c -+++ b/src/clipper_progs/src/pirate/compress42.c -@@ -142,6 +142,7 @@ - #include <sys/types.h> - #include <sys/stat.h> - #include <errno.h> -+#include <unistd.h> - - #ifdef DIRENT - # include <dirent.h> -diff --git a/src/mtz2cif_/mtz2cif.c b/src/mtz2cif_/mtz2cif.c -index e224430..c7b82f4 100755 ---- a/src/mtz2cif_/mtz2cif.c -+++ b/src/mtz2cif_/mtz2cif.c -@@ -28,6 +28,7 @@ - #include "cmtzlib.h" - #include "ccp4_parser.h" - #include "ccp4_general.h" -+#include "ccp4_program.h" - #include "csymlib.h" - #include "mtz2cif_lib.h" - -diff --git a/x-windows/XCCPJIFFY/xplot84driver.c b/x-windows/XCCPJIFFY/xplot84driver.c -index 67e0bf1..76526ab 100755 ---- a/x-windows/XCCPJIFFY/xplot84driver.c -+++ b/x-windows/XCCPJIFFY/xplot84driver.c -@@ -11,6 +11,7 @@ - - #include <stdio.h> - #include <sys/types.h> -+#include <stdlib.h> - - #include <X11/StringDefs.h> - #include <X11/Intrinsic.h> diff --git a/sci-chemistry/ccp4-apps/files/6.1.3-lapack.patch b/sci-chemistry/ccp4-apps/files/6.1.3-lapack.patch deleted file mode 100644 index 62892db01147..000000000000 --- a/sci-chemistry/ccp4-apps/files/6.1.3-lapack.patch +++ /dev/null @@ -1,597 +0,0 @@ -diff --git a/configure b/configure -index 833f483..bcfa62d 100755 ---- a/configure -+++ b/configure -@@ -3226,574 +3226,14 @@ else - echo - echo "Warning: this option has not been extensively tested!" - echo "Please report problems to ccp4@ccp4.ac.uk" -- # Search for vendor LAPACK/BLAS first -- if test ! "$with_netlib_lapack" ; then -- # Initialise variables to blank -- lapackdir= -- XLAPACK_LIB= -- # Possible directories to check for vendor or pre-existing LAPACK or -- # BLAS - add to these if you want to test others -- trydirs="`echo $LD_LIBRARY_PATH |sed -e s/:/\ /g` /lib /usr/lib /usr/local/lib" -- # Possible library names -- # These are the names like xxxx where the library will be libxxxx.a -- # or libxxxx.so -- echo -- echo "Guessing names for native/vendor LAPACK and/or BLAS libraries" -- echo "on this system" -- case $system in -- linux | linux64 | linux32 ) -- # linux users will usually have them in /usr/lib but don't call it -- trylapack="lapack" -- tryblas="blas" -- # if code is non_shared then this can lead to problems. both blas and lapack -- # need to be resolved even if they are not called! -- if test "$non_shared" = yes; then -- echo "You are compiling linux non_shared. This sometimes causes problems " -- echo " so checking for requirements." -- echo "Checking: try to link library against test program" -- if test -f testlink.f || test -f testlink ; then -- rm -f testlink* -- fi -- cat > testlink.f <<EOF -- PROGRAM TESTLINK --C A bit of scala code to test the linking -- real bf(3), bnorm --c -- integer maxbmt -- parameter (maxbmt = 2) -- double precision B(maxbmt,maxbmt), eigval(maxbmt), -- $ eigvec(maxbmt,maxbmt), w(5*maxbmt) -- integer m, ia, ix, istat --c -- B(1,1) = 1.00 -- B(1,2) = 1.00 -- B(2,1) = 1.00 -- B(2,2) = 1.00 --c -- m = maxbmt -- ia = maxbmt -- ix = maxbmt -- call dsyev('N', 'L', m, B, ia, eigval, w, 5*maxbmt, istat) -- end --EOF -- #firstly test without -lblas -- test_compile="$FC $FOPTIM $XFFLAGS -o testlink testlink.f -llapack" -- echo $test_compile -- if { (eval $test_compile >& /dev/null ) 2>&1; } && test -s testlink ; then -- # Compilation was okay -- echo "... only -llapack needed" -- XLAPACK_LIB="-llapack" -- # Set the next two variables so that configure -- # doesn't try to build netlib libraries -- LAPACKLIB="lapack" -- noblas=yes -- trylapack= -- tryblas= -- else -- echo "more than just -llapack needed...." -- test_compile="$FC $FOPTIM $XFFLAGS -o testlink testlink.f -llapack -lblas" -- echo $test_compile -- if { (eval $test_compile ) 2>&1; } && test -s testlink ; then -- # Compilation was okay -- echo "...-llapack and -lblas were needed" -- XLAPACK_LIB="-llapack -lblas" -- # Set the next two variables so that configure -- # doesn't try to build netlib libraries -- LAPACKLIB="lapack blas" -- noblas=no -- trylapack= -- tryblas= -- else -- echo "....could not find either lapack or blas." -- fi -- fi -- fi -- # add 64 bit libs -- case $system in -- linux64 ) trydirs="/usr/lib64 ${trydirs}" ;; -- esac -- -- ;; -- osf1) -- # OSF1 has dxml (old version) and cxml -- # which should have both lapack and blas -- trylapack="dxml cxml" -- tryblas= -- trydirs="${trydirs} /usr/shlib" -- ;; -- irix) -- # Additional search paths for IRIX -- trydirs="${trydirs} /usr/lib32" -- # SCSL should have both LAPACK and BLAS -- trylapack="scs" -- tryblas="blas" -- ;; -- irix64) -- # Additional search paths for IRIX64 -- trydirs="${trydirs} /usr/lib64" -- # SCSL should have both LAPACK and BLAS -- trylapack="scs" -- tryblas="blas" -- # Extra compiler flags? -- #XLAPACKFLAGS="-OPT:IEEE_NaN_inf=ON" -- ;; -- aix) -- # Additional search paths for AIX -- trydirs="${trydirs}" -- # AIX might have ESSL library - blas only I think -- trylapack= -- tryblas="essl" -- ;; -- hpux) -- # Additional search paths for HPUX -- trydirs="${trydirs} /opt/fortran/lib /opt/fortran/lib/pa2.0 /opt/mlib/lib/pa2.0" -- # HPUX should have both LAPACK (part of mlib) and BLAS -- trylapack="lapack" -- tryblas="blas" -- # Extra compiler flags? -- # +U77 required for ETIME function - this is already in XFFLAGS -- #XLAPACKFLAGS="+U77" -- ;; -- -- sunos | sunos64) -- # Sun has libraries with BLAS and LAPACK invoked using -- # -xlic_lib=sunperf -- trylapack= -- tryblas= -- echo "SunOs can use the Sun Performance Library (if installed)" -- echo "which has both BLAS and LAPACK 3.0" -- echo -- echo "Looking for a valid library to use..." -- echo -- # Loop over the possible library names -- try_libs="sunperf" -- for testlib in $try_libs -- do -- if test ! "$XLAPACK_LIB" ; then -- # Try running a test compile to see if this a valid library -- if test -f testlink.f || test -f testlink ; then -- rm -f testlink* -- fi -- cat > testlink.f <<EOF --c Test fortran program to link against library -- PROGRAM TESTLINK -- IMPLICIT NONE -- INTEGER A -- A = 1 -- STOP -- END --EOF -- test_compile="$FC $FOPTIM $XFFLAGS -o testlink testlink.f -dalign -xlic_lib=$testlib" -- echo $test_compile -- if { (eval $test_compile ) 2>&1; } && test -s testlink ; then -- # Compilation was okay -- echo "... -xlic_lib=$testlib is okay" -- XLAPACK_LIB="-dalign -xlic_lib=$testlib" -- # Set the next two variables so that configure -- # doesn't try to build netlib libraries -- LAPACKLIB="$testlib" -- noblas=yes -- else -- # Compilation failed -- echo "... cannot use -xlic_lib=$testlib" -- fi -- # End of test for testlib -- fi -- # End of loop over possible lib names -- done -- # Report if no suitable library was found -- if test ! "$XLAPACK_LIB" ; then -- echo -- echo "No suitable LAPACK library was found." -- echo "This may be because the Sun Performance Library is not" -- echo "installed on your system" -- echo "Contact your system administrator or Sun vendor" -- fi -- ;; -- Darwin | Darwin32 | Darwin64 ) -- # Darwin has libraries with BLAS and LAPACK invoked using -- # -framework vecLib -- echo "Darwin can use the vecLib Library (if installed)" -- echo "which has both BLAS and LAPACK 3.0" -- echo -- # This is a special case so try running a test compile -- echo "Checking: try to link library against test program" -- if test -f testlink.f || test -f testlink ; then -- rm -f testlink* -- fi -- cat > testlink.f <<EOF --c Test fortran program to link against library -- PROGRAM TESTLINK -- IMPLICIT NONE -- INTEGER A -- A = 1 -- STOP -- END --EOF -- test_compile="$FC $FOPTIM $XFFLAGS -o testlink testlink.f -framework vecLib" -- echo $test_compile -- if { (eval $test_compile ) 2>&1; } && test -s testlink ; then -- # Compilation was okay -- echo "... -framework vecLib is okay" -- XLAPACK_LIB="-framework vecLib" -- # Set the next two variables so that configure -- # doesn't try to build netlib libraries -- LAPACKLIB="vecLib" -- noblas=yes -- else --#alternative linking for vecLib libraries -- case `uname -sr` in -- *Darwin\ 7.* ) test_compile="$FC $FOPTIM $XFFLAGS -o testlink testlink.f -lcc_dynamic -Wl,-framework -Wl,vecLib" ;; -- * ) test_compile="$FC $FOPTIM $XFFLAGS -o testlink testlink.f -Wl,-framework -Wl,vecLib" ;; -- esac -- -- echo $test_compile -- if { (eval $test_compile ) 2>&1; } && test -s testlink ; then -- # Compilation was okay -- echo "... -framework vecLib is okay" -- XLAPACK_LIB="-Wl,-framework -Wl,vecLib" -- # Set the next two variables so that configure -- # doesn't try to build netlib libraries -- LAPACKLIB="-Wl,-framework -Wl,vecLib" -- noblas=yes -- else -- # Compilation failed -- echo "... cannot use -framework vecLib" -- echo -- fi -- fi -- trylapack= -- tryblas= --# try the fink installation -- trydirs="${trydirs} /sw" -- ;; -- Darwin_ibm_compilers ) -- # Darwin has libraries with BLAS and LAPACK invoked using -- # -framework vecLib -- echo "Darwin can use the vecLib Library (if installed)" -- echo "which has both BLAS and LAPACK 3.0" -- echo -- # This is a special case so try running a test compile -- echo "Checking: try to link library against test program" -- if test -f testlink.f || test -f testlink ; then -- rm -f testlink* -- fi -- cat > testlink.f <<EOF --c Test fortran program to link against library -- PROGRAM TESTLINK -- IMPLICIT NONE -- INTEGER A -- A = 1 -- STOP -- END --EOF -- case `uname -sr` in -- Darwin\ 8* ) -- XLAPACK_LIB="-L/System/Library/Frameworks/Accelerate.framework/Versions/A/Frameworks/vecLib.framework/Versions/A -lLAPACK -lBLAS" -- test_compile="$FC $FOPTIM $XFFLAGS -o testlink testlink.f $XLAPACK_LIB" -- ;; -- Darwin\ 7* ) -- XLAPACK_LIB="-L/System/Library/Frameworks/Accelerate.framework/Versions/A/Frameworks/vecLib.framework/Versions/A -lLAPACK -lBLAS" -- test_compile="$FC $FOPTIM $XFFLAGS -o testlink testlink.f -lcc_dynamic $XLAPACK_LIB" -- ;; -- *) -- XLAPACK_LIB="/System/Library/Frameworks/vecLib.Framework/Versions/Current/VecLib" -- test_compile="$FC $FOPTIM $XFFLAGS -o testlink testlink.f $XLAPACK_LIB" -- esac -- echo $test_compile -- if { (eval $test_compile ) 2>&1; } && test -s testlink ; then -- # Compilation was okay -- echo "... -framework vecLib is okay" -- # Set the next two variables so that configure -- # doesn't try to build netlib libraries -- LAPACKLIB="vecLib" -- noblas=yes -- else -- # Compilation failed -- XLAPACK_LIB="" -- echo "... cannot use -framework vecLib" -- echo -- fi -- trylapack= -- tryblas= --# try the fink installation -- trydirs="${trydirs} /sw" -- ;; -- -- Darwin_intel_compilers) -- # Darwin has libraries with BLAS and LAPACK invoked using -- # -F vecLib -- echo "Darwin can use the vecLib Library (if installed)" -- echo "which has both BLAS and LAPACK 3.0" -- echo -- # This is a special case so try running a test compile -- echo "Checking: try to link library against test program" -- if test -f testlink.f || test -f testlink ; then -- rm -f testlink* -- fi -- cat > testlink.f <<EOF --c Test fortran program to link against library -- PROGRAM TESTLINK -- IMPLICIT NONE -- INTEGER A -- A = 1 -- STOP -- END --EOF -- test_compile="$FC $FOPTIM $XFFLAGS -o testlink testlink.f -Wl,-framework -Wl,vecLib" -- echo $test_compile -- if { (eval $test_compile ) 2>&1; } && test -s testlink ; then -- # Compilation was okay -- # doesn't try to build netlib libraries -- XLAPACK_LIB="-F /System/Library/Frameworks -Qoption,ld,-framework -Qoption,ld,vecLib" -- LAPACKLIB="vecLib" -- noblas=yes -- else -- # Compilation failed -- echo "... cannot use -framework vecLib" -- echo -- fi -- trylapack= -- tryblas= --# try the fink installation -- trydirs="${trydirs} /sw" -- ;; -- --# linux_ia64_sgi_altix) --# SGI Japan -- ia64_linux_intel) -- # Additional search paths for Linux/IA64 -- trydirs="${trydirs} /opt/scsl/lib /usr/lib /usr/local/lib" -- # SCSL and MKL should have both LAPACK and BLAS -- trylapack="mkl_lapack scs lapack" -- tryblas="mkl scs blas" -- ;; -- linux_ibm_compilers ) -- trylapack="lapack" -- tryblas="blas" -- ;; -- linux64_ibm_compilers ) -- trydirs="/usr/lib64 ${trydirs}" -- trylapack="lapack" -- tryblas="blas" -- ;; -- linux_intel_compilers ) -- trydirs="/usr/lib64 ${trydirs}" -- trylapack="mkl_lapack lapack" -- tryblas="mkl blas" -- ;; -- *) -- echo "The guesses for this system may not be correct - please" -- echo "e-mail ccp4@ccp4.ac.uk if you have any extra information" -- echo -- # Default guess is just libblas -- trylapack="lapack" -- tryblas="blas" -- ;; -- esac -- # -- # Search for LAPACK libraries -- # -- # Write out what the guesses are -- if test "$trylapack" ; then -- echo "Possible LAPACK library names for this system:" -- for libname in $trylapack -- do -- echo " lib$libname" -- done -- # Possible library name extensions -- tryexts="a so dylib" -- # Now loop over all the possibilities and see if anything -- # turns up -- echo -- echo "Searching for libraries with LAPACK and BLAS:" -- for testdir in $trydirs -- do -- for testlib in $trylapack -- do -- for ext in $tryexts -- do -- if test ! "$LAPACKLIB"; then -- if test -s "$testdir/lib$testlib.$ext" ; then -- echo "...found LAPACK library: $testdir/lib$testlib.$ext" -- # Now try and link to a test program -- # This is really for IRIX where libraries can be -- # o32 or n32 -- echo " Testing: try to link library against test program" -- if test -f testlink.f || test -f testlink ; then -- rm -f testlink* -- fi -- cat > testlink.f <<EOF --c Test fortran program to link against library -- PROGRAM TESTLINK -- IMPLICIT NONE -- INTEGER A -- A = 1 -- STOP -- END --EOF -- test_compile="$FC $FOPTIM $XFFLAGS -o testlink testlink.f -L$testdir -l$testlib" -- test_ccompile="$FC $FOPTIM $XFFLAGS -o testlink testlink.f -L$testdir -l$testlib $XLDFLAGS" -- echo $test_compile -- if { (eval $test_compile ) 2>&1; } && test -s testlink ; then -- have_lapack=yes -- else --# cover clapack option -- echo $test_ccompile -- if { (eval $test_ccompile ) 2>&1; } && test -s testlink ; then -- have_lapack=yes -- fi -- fi -- if test x$have_lapack = xyes ; then -- # This one is okay -- LAPACKLIB="$testlib" -- LAPACKDIR="$testdir" -- echo "Link ok - using lib$LAPACKLIB from $LAPACKDIR" -- # -- XLAPACK_LIB="-L$LAPACKDIR -l$LAPACKLIB" -- # -- # Test to see if we need BLAS too -- # Do this by trying to compile a test program -- # Use the LSAME test for now -- echo -- echo " * Checking whether we need a separate BLAS library *" -- echo " Testing: try linking library against test program" -- cd lib/lapack/test -- if test -f testlsame ; then -- rm -f testsame testlsame.o -- fi -- test_compile="$FC $FOPTIM $XFFLAGS -o testlsame lsametst.f -L$LAPACKDIR -l$LAPACKLIB" -- test_ccompile="$FC $FOPTIM $XFFLAGS -o testlsame lsametst.f -L$LAPACKDIR -l$LAPACKLIB $XLDFLAGS" -- echo $test_compile -- if { ( eval $test_compile) 2>&1;} && test -s testlsame ; then -- have_blas=yes -- else --#cblas route -- echo $test_ccompile -- if { ( eval $test_ccompile) 2>&1;} && test -s testlsame ; then -- have_blas=yes -- fi -- fi -- if test x$have_blas = xyes ; then -- echo "Test program okay - additional separate BLAS not required" -- noblas=yes -- else -- echo "Test program failed - need a separate BLAS library" -- fi -- cd ../../.. -- else -- # Keep looking -- echo " link failed - cannot use lib$testlib" -- fi -- fi -- fi -- done -- done -- if test ! "$LAPACKLIB"; then -- echo "...nothing in $testdir" -- fi -- done -- fi -- -- # If LAPACKLIB hasn't been set at this point then no LAPACK library -- # was found -- if test ! "$LAPACKLIB" ; then -- echo -- echo "No pre-existing LAPACK library found - NetLib LAPACK will be built instead" -- make_lapack=lapacklib -- fi -- # Look for possible BLAS -- if test ! "$noblas" ; then -- if test "$tryblas" ; then -- echo -- echo "Possible BLAS library names for this system:" -- for libname in $tryblas -- do -- echo " lib$libname" -- done -- # Possible library name extensions -- tryexts="a so" -- # Now loop over all the possibilities and see if anything -- # turns up -- echo -- echo "Searching for libraries with BLAS:" -- for testdir in $trydirs -- do -- for testlib in $tryblas -- do -- for ext in $tryexts -- do -- if test ! "$BLASLIB"; then -- if test -s "$testdir/lib$testlib.$ext" ; then -- echo "...found BLAS library: $testdir/lib$testlib.$ext" -- # Now try and link to a test program -- # This is really for IRIX where libraries can be -- # o32 or n32 -- echo " Testing: try to link library against test program" -- if test -f testlink.f || test -f testlink ; then -- rm -f testlink* -- fi -- cat > testlink.f <<EOF --c Test fortran program to link against library -- PROGRAM TESTLINK -- IMPLICIT NONE -- INTEGER A -- A = 1 -- STOP -- END --EOF -- test_compile="$FC $FOPTIM $XFFLAGS -o testlink testlink.f -L$testdir -l$testlib" -- test_ccompile="$FC $FOPTIM $XFFLAGS -o testlink testlink.f -L$testdir -l$testlib $XLDFLAGS" -- echo $test_compile -- if { ( eval $test_compile) 2>&1;} && test -s testlink ; then -- have_blas=yes -- else -- echo $test_ccompile -- if { ( eval $test_compile) 2>&1;} && test -s testlink ; then -- have_blas=yes -- fi -- fi -- if test x$have_blas = xyes ; then -- # This one is okay -- BLASLIB="$testlib" -- BLASDIR="$testdir" -- BLASEXT="$ext" -- echo "Link ok - using lib$BLASLIB from $BLASDIR" -- XLAPACK_LIB="$XLAPACK_LIB -L$BLASDIR -l$BLASLIB" -- else -- # Keep looking -- echo " link failed - cannot use lib$testlib" -- fi -- fi -- fi -- done -- done -- if test ! "$BLASLIB"; then -- echo "...nothing in $testdir" -- fi -- done -- fi -- # Do we need to build BLAS too? -- if test ! "$BLASLIB" ; then -- echo -- echo "No pre-existing BLAS library was found - NetLib BLAS will be built instead" -- echo "This may result in poorer performance of the LAPACK routines" -- make_blas=blaslib -- BLASLIB=blas -- BLASDIR="$srcdir/lib/lapack" -- BLASEXT="a" -- fi -- fi -+ # gentoo is clever -+ make_blas= -+ make_lapack= -+ BLASLIB=$(${PKG_CONFIG} --libs blas) -+ LAPACKLIB=$(${PKG_CONFIG} --libs lapack) -+ XLAPACK_LIB="${BLASLIB} ${LAPACKLIB}" -+ XFFLAGS_LAPACK="$(${PKG_CONFIG} --cflags lapack blas)" - # Otherwise force building of NetLib BLAS and LAPACK libs -- else -- echo -- echo "! Force building of NetLib BLAS and LAPACK..." -- make_blas=blaslib -- make_lapack=lapacklib -- BLASLIB=blas -- BLASDIR="$srcdir/lib/lapack" -- BLASEXT="a" -- fi - # need to know if we the lapack library was linked using the C or - # fortran linker - if test -f testlink.f || test -f testlink || test -f testlink.c ; then -@@ -3916,8 +3356,8 @@ RANLIB = ${RANLIB} - INSTALL_DATA = ${INSTALL_DATA} - libdir = $libdir - # --BLASLIB = lib${BLASLIB}.${BLASEXT} --LAPACKLIB = liblapack.a -+BLASLIB = ${BLASLIB} -+LAPACKLIB = ${LAPACKLIB} - # - # These variables define targets in the main Makefile - blaslib = ${make_blas} diff --git a/sci-chemistry/ccp4-apps/files/6.1.3-pisa.patch b/sci-chemistry/ccp4-apps/files/6.1.3-pisa.patch deleted file mode 100644 index 9d8fefe965e5..000000000000 --- a/sci-chemistry/ccp4-apps/files/6.1.3-pisa.patch +++ /dev/null @@ -1,23 +0,0 @@ -diff --git a/src/pisa/sbase/Makefile.am b/src/pisa/sbase/Makefile.am -index 053e83a..4ff3394 100755 ---- a/src/pisa/sbase/Makefile.am -+++ b/src/pisa/sbase/Makefile.am -@@ -1,4 +1,4 @@ --pkgdatadir = $(datadir)/sbase -+pkgdatadir = $(datadir)/pisa/sbase - dist_pkgdata_DATA = \ - graph.sbase index.sbase struct.sbase - -diff --git a/src/pisa/sbase/Makefile.in b/src/pisa/sbase/Makefile.in -index faa3f7f..8630bd7 100755 ---- a/src/pisa/sbase/Makefile.in -+++ b/src/pisa/sbase/Makefile.in -@@ -62,7 +62,7 @@ POST_UNINSTALL = : - EXEEXT = @EXEEXT@ - OBJEXT = @OBJEXT@ - PATH_SEPARATOR = @PATH_SEPARATOR@ --pkgdatadir = $(datadir)/sbase -+pkgdatadir = $(datadir)/pisa/sbase - AMTAR = @AMTAR@ - AR_FLAGS = @AR_FLAGS@ - AWK = @AWK@ diff --git a/sci-chemistry/ccp4-apps/files/6.1.3-pythonpath.patch b/sci-chemistry/ccp4-apps/files/6.1.3-pythonpath.patch deleted file mode 100644 index 7a012be6ef02..000000000000 --- a/sci-chemistry/ccp4-apps/files/6.1.3-pythonpath.patch +++ /dev/null @@ -1,65 +0,0 @@ -diff --git a/ccp4-6.1.2/include/ccp4.setup-bash b/ccp4-6.1.2/include/ccp4.setup-bash -index 9848101..cea8ae6 100755 ---- a/ccp4-6.1.2/include/ccp4.setup-bash -+++ b/ccp4-6.1.2/include/ccp4.setup-bash -@@ -188,9 +188,9 @@ fi - #Python path for the subprocess fixed module - - if [ $ccp4_first_in_path -eq 1 ]; then -- setenv PYTHONPATH ${CCP4}/share/python:${PYTHONPATH} -+ setenv PYTHONPATH ${CCP4}/share/ccp4/smartie:${CCP4I_TOP}/python:${PYTHONPATH} - else -- setenv PYTHONPATH ${PYTHONPATH}:${CCP4}/share/python -+ setenv PYTHONPATH ${PYTHONPATH}:${CCP4}/share/ccp4/smartie:${CCP4I_TOP}/python - fi - - ### PLOT_COMMAND PRINT_COMMAND for the XCCPJIFFY programs to compile ### -diff --git a/ccp4-6.1.2/include/ccp4.setup-csh b/ccp4-6.1.2/include/ccp4.setup-csh -index 42f0820..93c2cf3 100755 ---- a/ccp4-6.1.2/include/ccp4.setup-csh -+++ b/ccp4-6.1.2/include/ccp4.setup-csh -@@ -180,9 +180,9 @@ endif - #Python path for the subprocess fixed module - if (${?PYTHONPATH}) then - if ($ccp4_first_in_path) then -- setenv PYTHONPATH ${CCP4}/share/python:${PYTHONPATH} -+ setenv PYTHONPATH ${CCP4}/share/ccp4/smartie:${CCP4I_TOP}/python:${PYTHONPATH} - else -- setenv PYTHONPATH ${PYTHONPATH}:${CCP4}/share/python -+ setenv PYTHONPATH ${PYTHONPATH}:${CCP4}/share/ccp4/smartie:${CCP4I_TOP}/python - endif - else - setenv PYTHONPATH ${CCP4}/share/python -diff --git a/ccp4-6.1.2/include/ccp4.setup-sh b/ccp4-6.1.2/include/ccp4.setup-sh -index 4396ebf..a0455bd 100755 ---- a/ccp4-6.1.2/include/ccp4.setup-sh -+++ b/ccp4-6.1.2/include/ccp4.setup-sh -@@ -228,9 +228,9 @@ test -r $CCP4/include/ccp4.msg && cat $CCP4/include/ccp4.msg - #Python path for the subprocess fixed module - - if test $ccp4_first_in_path -eq 1; then -- export PYTHONPATH=${CCP4}/share/python:${PYTHONPATH} -+ export PYTHONPATH=${CCP4}/share/ccp4/smartie:${CCP4I_TOP}/python:${PYTHONPATH} - else -- export PYTHONPATH=${PYTHONPATH}:${CCP4}/share/python -+ export PYTHONPATH=${PYTHONPATH}:${CCP4}/share/ccp4/smartie:${CCP4I_TOP}/python - fi - - ################### THE REST SHOULDN'T NEED EDITING ##################### -diff --git a/ccp4-6.1.2/include/ccp4.setup-zsh b/ccp4-6.1.2/include/ccp4.setup-zsh -index 0e5c2ce..53523f3 100755 ---- a/ccp4-6.1.2/include/ccp4.setup-zsh -+++ b/ccp4-6.1.2/include/ccp4.setup-zsh -@@ -157,10 +157,10 @@ export CLASSPATH - #Python path for the subprocess fixed module - - if ($ccp4_first_in_path) then -- PYTHONPATH=${CCP4}/share/python:${PYTHONPATH} -+ PYTHONPATH=${CCP4}/share/ccp4/smartie:${CCP4I_TOP}/python:${PYTHONPATH} - export PYTHONPATH - else -- PYTHONPATH=${PYTHONPATH}:${CCP4}/share/python -+ PYTHONPATH=${PYTHONPATH}:${CCP4}/share/ccp4/smartie:${CCP4I_TOP}/python - export PYTHONPATH - fi - diff --git a/sci-chemistry/ccp4-apps/files/6.1.3-rename-rapper-ng.patch b/sci-chemistry/ccp4-apps/files/6.1.3-rename-rapper-ng.patch deleted file mode 100644 index a5144cfa5d33..000000000000 --- a/sci-chemistry/ccp4-apps/files/6.1.3-rename-rapper-ng.patch +++ /dev/null @@ -1,60 +0,0 @@ -diff --git a/src/Makefile.in b/src/Makefile.in -index 70781f3..b2dcc25 100755 ---- a/src/Makefile.in -+++ b/src/Makefile.in -@@ -760,7 +760,7 @@ chainsawobjs = chainsaw.o - pdbcur : $(pdbcurobjs) - @$(SETFLAGS) ; rm -f pdbcur; eval $(CXX) $${mmdb_app_FLAGS-"$(CXXFLAGS)"} -o pdbcur $(pdbcurobjs) $(LDCXXFLAGS) - ncont : $(ncontobjs) -- @$(SETFLAGS) ; rm -f ncont; eval $(CXX) $${mmdb_app_FLAGS-"$(CXXFLAGS)"} -o ncont $(ncontobjs) $(LDCXXFLAGS) -+ @$(SETFLAGS) ; rm -f ncont; eval $(CXX) $${mmdb_app_FLAGS-"$(CXXFLAGS)"} -o ncont $(ncontobjs) $(LDCXXFLAGS) -lmmdb - coord_format : $(coord_formatobjs) - @$(SETFLAGS) xxx=1 ; \ - rm -f coord_format; \ -diff --git a/src/rapper/LOOP/Makefile.am b/src/rapper/LOOP/Makefile.am -index 85f212e..2608c6d 100755 ---- a/src/rapper/LOOP/Makefile.am -+++ b/src/rapper/LOOP/Makefile.am -@@ -15,12 +15,12 @@ params.cpp typed_value.cpp misc.cpp residue.cpp atom.cpp psa.cpp edm_sidechains. - hash_table.cpp surface.cpp parse.cpp band.cpp edensity.cpp read_map.cpp iterator.cpp \ - residue_range.cpp pop_search_frags.cpp saxs.cpp lib_choral.cpp pdf.cpp WeightedDistribMean.cpp - --rapper_LDADD = ../gc7.0/libgc.la ../libxml2/libxml2.la -+rapper_LDADD = @GC_LIBS@ @LIBXML_LIBS@ - - pkgdatadir = $(datadir)/rapper - dist_pkgdata_DATA = params.xml - --INCLUDES = -I. -I../gc7.0/include -I../libxml2/include -+INCLUDES = -I. @LIBXML_CFLAGS@ @GC_CFLAGS@ - #SUBDIRS = \ - #@PYTHON_USE_TRUE@ python - -diff --git a/src/rapper/Makefile.am b/src/rapper/Makefile.am -index e78b10d..486b931 100755 ---- a/src/rapper/Makefile.am -+++ b/src/rapper/Makefile.am -@@ -1,3 +1,3 @@ --SUBDIRS = libxml2 gc7.0 LOOP data -+SUBDIRS = LOOP data - - EXTRA_DIST = -diff --git a/src/rapper/configure.ac b/src/rapper/configure.ac -index 5e4ef69..268a579 100755 ---- a/src/rapper/configure.ac -+++ b/src/rapper/configure.ac -@@ -48,6 +48,13 @@ AM_CONDITIONAL(AMDEP, test "x$enable_dependency_tracking" != xno) - - AC_SUBST(rapper_LDFLAGS) - --AC_CONFIG_SUBDIRS([gc7.0 libxml2]) -+PKG_CHECK_MODULES([LIBXML],[libxml-2.0]) -+AC_SUBST([LIBXML_CFLAGS]) -+AC_SUBST([LIBXML_LIBS]) -+ -+PKG_CHECK_MODULES([GC],[bdw-gc]) -+AC_SUBST([GC_CFLAGS]) -+AC_SUBST([GC_LIBS]) -+ - #AC_OUTPUT(Makefile LOOP/Makefile LOOP/python/Makefile data/Makefile) - AC_OUTPUT(Makefile LOOP/Makefile data/Makefile) diff --git a/sci-chemistry/ccp4-apps/files/6.1.3-unbundle.patch b/sci-chemistry/ccp4-apps/files/6.1.3-unbundle.patch deleted file mode 100644 index 107cfd740238..000000000000 --- a/sci-chemistry/ccp4-apps/files/6.1.3-unbundle.patch +++ /dev/null @@ -1,131 +0,0 @@ - src/Makefile.in | 14 +++++----- - src/pisa/configure.ac | 67 +++++++++---------------------------------------- - 2 files changed, 19 insertions(+), 62 deletions(-) - -diff --git a/src/Makefile.in b/src/Makefile.in -index 70781f3..b11db04 100755 ---- a/src/Makefile.in -+++ b/src/Makefile.in -@@ -778,8 +778,8 @@ chainsaw : $(chainsawobjs) - eval $(CXX) $${mmdb_app_FLAGS-"$(CXXFLAGS)"} -o chainsaw $(chainsawobjs) $(LDCXXFLAGS) - pdbcur.o pcur_funcs.o ncont.o coord_format.o pdb_merge.o chainsaw.o: # dependencies at end - @$(SETFLAGS) xxx=1 ; \ -- echo $(CXX) -I$(mmdb_appdir) -I$(incdir) -I$(incdir)/mmdb $${mmdb_app_FLAGS-"$(CXXFLAGS)"} -c -o $@ $(mmdb_appdir)/`basename $@ .o`.cpp ; -- eval $(CXX) -I$(mmdb_appdir) -I$(incdir) -I$(incdir)/mmdb $${mmdb_app_FLAGS-"$(CXXFLAGS)"} -c -o $@ $(mmdb_appdir)/`basename $@ .o`.cpp -+ echo $(CXX) -I$(mmdb_appdir) -I$(incdir) `pkg-config --cflags mmdb` $${mmdb_app_FLAGS-"$(CXXFLAGS)"} -c -o $@ $(mmdb_appdir)/`basename $@ .o`.cpp ; -+ eval $(CXX) -I$(mmdb_appdir) -I$(incdir) `pkg-config --cflags mmdb` $${mmdb_app_FLAGS-"$(CXXFLAGS)"} -c -o $@ $(mmdb_appdir)/`basename $@ .o`.cpp - - ### bp3, afro, gcx - -@@ -813,8 +813,8 @@ gcx : libbp3 $(gcxobjs) - - $(libbp3objs) $(bp3objs) $(afroobjs) $(gcxobjs) : # dependencies at end - @$(SETFLAGS) xxx=1 ; \ -- echo $(CXX) -I$(bp3dir) -I$(incdir) -I$(incdir)/mmdb $${bp3_FLAGS-"$(CXXFLAGS)"} -c -o $@ $(bp3dir)/`basename $@ .o`.C ; \ -- eval $(CXX) -I$(bp3dir) -I$(incdir) -I$(incdir)/mmdb $${bp3_FLAGS-"$(CXXFLAGS)"} -c -o $@ $(bp3dir)/`basename $@ .o`.C -+ echo $(CXX) -I$(bp3dir) -I$(incdir) `pkg-config --cflags mmdb` $${bp3_FLAGS-"$(CXXFLAGS)"} -c -o $@ $(bp3dir)/`basename $@ .o`.C ; \ -+ eval $(CXX) -I$(bp3dir) -I$(incdir) `pkg-config --cflags mmdb` $${bp3_FLAGS-"$(CXXFLAGS)"} -c -o $@ $(bp3dir)/`basename $@ .o`.C - - ### crunch2 pmf - -@@ -853,7 +853,7 @@ cif2xml : $(cif2xmlobjs) - cross_validate : $(cross_validateobjs) - @$(SETFLAGS); rm -f cross_validate; eval $(CXX) $${harvest_app_FLAGS-"$(CXXFLAGS)"} -o cross_validate $(cross_validateobjs) $(LDCXXFLAGS) - cif2xml.o cross_validate.o : # dependencies at end -- @$(SETFLAGS); eval $(CXX) -I$(harvest_appdir) -I$(incdir) -I$(incdir)/mmdb $${harvest_app_FLAGS-"$(CXXFLAGS)"} -c -o $@ $(harvest_appdir)/`basename $@ .o`.cpp -+ @$(SETFLAGS); eval $(CXX) -I$(harvest_appdir) -I$(incdir) `pkg-config --cflags mmdb` $${harvest_app_FLAGS-"$(CXXFLAGS)"} -c -o $@ $(harvest_appdir)/`basename $@ .o`.cpp - - pdb_extractdir = $(srcdir)/harvest_app_/pdb_extract - pdb_extract_suite : -@@ -873,8 +873,8 @@ $(dev_tools_ctargets) : - $(dev_tools_cxxtargets) : - @$(SETFLAGS) xxx=1; \ - rm -f $@; \ -- echo $(CXX) $${dev_tools_FLAGS-"$(CXXFLAGS)"} -o $@ $(dev_toolsdir)/$@.cpp -I$(incdir) -I$(incdir)/mmdb $(LDCXXFLAGS) ;\ -- eval $(CXX) $${dev_tools_FLAGS-"$(CXXFLAGS)"} -o $@ $(dev_toolsdir)/$@.cpp -I$(incdir) -I$(incdir)/mmdb $(LDCXXFLAGS) -+ echo $(CXX) $${dev_tools_FLAGS-"$(CXXFLAGS)"} -o $@ $(dev_toolsdir)/$@.cpp -I$(incdir) `pkg-config --cflags mmdb` $(LDCXXFLAGS) ;\ -+ eval $(CXX) $${dev_tools_FLAGS-"$(CXXFLAGS)"} -o $@ $(dev_toolsdir)/$@.cpp -I$(incdir) `pkg-config --cflags mmdb` $(LDCXXFLAGS) - - ### mlphare - mlphare: -diff --git a/src/pisa/configure.ac b/src/pisa/configure.ac -index 81afdda..044b6f8 100755 ---- a/src/pisa/configure.ac -+++ b/src/pisa/configure.ac -@@ -31,64 +31,21 @@ AC_CHECK_FUNCS([floor pow rint sqrt]) - # test for function in m - AC_CHECK_LIB([m], [sqrt]) - --dnl Optional: Check for MMDB. --AM_PATH_MMDB(, -- [ if test "x$mmdb_prefix" != x ; then -- if test "x$ac_MMDB_CXXFLAGS" != x && test "x$ac_MMDB_LDOPTS" = x ; then -- case "$ac_MMDB_CXXFLAGS" in -- *src/mmdb ) -- ac_MMDB_LDOPTS=`echo "$ac_MMDB_CXXFLAGS" | sed s#src/mmdb#src#g` -- ;; -- *include/mmdb ) -- ac_MMDB_LDOPTS=`echo "$ac_MMDB_CXXFLAGS" | sed s#include/mmdb#lib#g` -- ;; -- *) -- esac -- MMDB_CXXFLAGS="$ac_MMDB_CXXFLAGS" -- MMDB_LIBS=`echo "$ac_MMDB_LDOPTS -lmmdb" | sed s#-I#-L#` -- AC_MSG_WARN([assuming library $MMDB_LIBS headers $MMDB_CXXFLAGS]) -- else -- MMDB_CXXFLAGS="-I$mmdb_prefix/src -I$mmdb_prefix/src/mmdb -I$mmdb_prefix/include -I$mmdb_prefix/include/mmdb" -- MMDB_LIBS="-L$mmdb_prefix/src -L$mmdb_prefix/lib -lmmdb" -- AC_MSG_WARN([assuming library $MMDB_LIBS headers $MMDB_CXXFLAGS]) -- fi -- else -- AC_MSG_ERROR([mmdb not found]) -- fi -- ] --) -+PKG_CHECK_MODULES([MMDB],[mmdb]) -+PKG_CHECK_MODULES([SSM],[ssm]) -+ -+MMDB_CXXFLAGS=${MMDB_CFLAGS} -+ -+AC_SUBST([MMDB_CFLAGS]) -+AC_SUBST([MMDB_CXXFLAGS]) -+AC_SUBST([SSM_CFLAGS]) -+ -+AC_SUBST([MMDB_LIBS]) -+AC_SUBST([SSM_LIBS]) - --ac_saved_CXXFLAGS=$CXXFLAGS --ac_saved_LIBS=$LIBS - CXXFLAGS="$CXXFLAGS $MMDB_CXXFLAGS" - LIBS="$MMDB_LIBS $LIBS" --AM_PATH_SSM(, -- [ if test "x$ssm_prefix" != x ; then -- if test "x$ac_SSM_CXXFLAGS" != x && test "x$ac_SSM_LDOPTS" = x ; then -- case "$ac_SSM_CXXFLAGS" in -- *lib/ssm ) -- ac_SSM_LDOPTS=`echo "$ac_SSM_CXXFLAGS" | sed s#lib/ssm#lib#g` -- ;; -- *include/ssm ) -- ac_SSM_LDOPTS=`echo "$ac_SSM_CXXFLAGS" | sed s#include/ssm#lib#g` -- ;; -- *) -- esac -- SSM_CXXFLAGS="$ac_SSM_CXXFLAGS" -- SSM_LIBS=`echo "$ac_SSM_LDOPTS -lssm" | sed s#-I#-L#` -- AC_MSG_WARN([assuming library $SSM_LIBS headers $SSM_CXXFLAGS]) -- else -- SSM_CXXFLAGS="-I$ssm_prefix/include/ssm -I$ssm_prefix/lib/ssm" -- SSM_LIBS="-L$ssm_prefix/lib -L$ssm_prefix/lib/ssm -lssm" -- AC_MSG_WARN([assuming library $SSM_LIBS headers $SSM_CXXFLAGS]) -- fi -- else -- AC_MSG_ERROR([ssm not found]) -- fi -- ] --) --CXXFLAGS=$ac_saved_CXXFLAGS --LIBS=$ac_saved_LIBS -+ - - # Checks for typedefs, structures, and compiler characteristics. - # diff --git a/sci-chemistry/ccp4-apps/files/ccp4-apps-6.1.3-tcl8.6.patch b/sci-chemistry/ccp4-apps/files/ccp4-apps-6.1.3-tcl8.6.patch deleted file mode 100644 index 4b98545eec83..000000000000 --- a/sci-chemistry/ccp4-apps/files/ccp4-apps-6.1.3-tcl8.6.patch +++ /dev/null @@ -1,130 +0,0 @@ - src/ccp4mapwish_/c_src/ccp4mapwish_canvas.c | 34 ++++++++++++++--------------- - 1 file changed, 17 insertions(+), 17 deletions(-) - -diff --git a/src/ccp4mapwish_/c_src/ccp4mapwish_canvas.c b/src/ccp4mapwish_/c_src/ccp4mapwish_canvas.c -index 2c9f02f..98d814a 100755 ---- a/src/ccp4mapwish_/c_src/ccp4mapwish_canvas.c -+++ b/src/ccp4mapwish_/c_src/ccp4mapwish_canvas.c -@@ -297,7 +297,7 @@ int canvas_draw_line(char *canvas, int npts, float *x, float *y, char *tags, - puts("canvas_draw_line: about to evaluate the command..."); - } - if (Tcl_Eval(interp,command) != TCL_OK) { -- printf("canvas_draw_line: error from Tcl_Eval: %s",interp->result); -+ printf("canvas_draw_line: error from Tcl_Eval: %s",Tcl_GetStringResult(interp)); - return 0; - } - if (CCP4MAPWISH_CANVAS_DIAG) -@@ -432,7 +432,7 @@ int canvas_draw_rectangle(char *canvas, int npts, float *x, float *y, - puts("canvas_draw_rectangle: about to evaluate the command..."); - } - if (Tcl_Eval(interp,command) != TCL_OK) { -- printf("canvas_draw_rectangle: error from Tcl_Eval: %s",interp->result); -+ printf("canvas_draw_rectangle: error from Tcl_Eval: %s",Tcl_GetStringResult(interp)); - printf("canvas_draw_rectangle:\ncanvas = \"%s\"\ntags = \"%s\"\ncolor = \"%s\"\nunits = \"%c\"\n",canvas,tags,color,units); - return 0; - } -@@ -536,7 +536,7 @@ int canvas_draw_label(char *canvas, char *text, float x, float y, - /* Execute the command which draws the label */ - if (CCP4MAPWISH_CANVAS_DIAG) printf("canvas_draw_label: command is: %s\n",command); - if (Tcl_Eval(interp,command) != TCL_OK) { -- printf("canvas_draw_label: error from Tcl_Eval: %s\n",interp->result); -+ printf("canvas_draw_label: error from Tcl_Eval: %s\n",Tcl_GetStringResult(interp)); - return 0; - } - -@@ -617,7 +617,7 @@ int canvas_scale_canvas(char *canvas, char *tag, float scale) - /* Execute the command which scales the canvas */ - if (CCP4MAPWISH_CANVAS_DIAG) printf("canvas_scale_canvas: command is: %s\n",command); - if (Tcl_Eval(interp,command) != TCL_OK) { -- printf("canvas_scale_canvas: error from Tcl_Eval: %s\n",interp->result); -+ printf("canvas_scale_canvas: error from Tcl_Eval: %s\n",Tcl_GetStringResult(interp)); - return 0; - } - -@@ -706,7 +706,7 @@ int canvas_shift_canvas(char *canvas) - /* Execute the command which resizes the canvas */ - if (CCP4MAPWISH_CANVAS_DIAG) printf("canvas_shift_canvas: command is: %s\n",command); - if (Tcl_Eval(interp,command) != TCL_OK) { -- printf("canvas_shift_canvas: error from Tcl_Eval: %s\n",interp->result); -+ printf("canvas_shift_canvas: error from Tcl_Eval: %s\n",Tcl_GetStringResult(interp)); - return 0; - } - -@@ -789,7 +789,7 @@ int canvas_shift_element(char *canvas, char *tag, int shiftx, int shifty) - /* Execute the command which resizes the canvas */ - if (CCP4MAPWISH_CANVAS_DIAG) printf("canvas_shift_canvas: command is: %s\n",command); - if (Tcl_Eval(interp,command) != TCL_OK) { -- printf("canvas_shift_element: error from Tcl_Eval: %s\n",interp->result); -+ printf("canvas_shift_element: error from Tcl_Eval: %s\n",Tcl_GetStringResult(interp)); - return 0; - } - -@@ -861,7 +861,7 @@ int canvas_delete(char *canvas, char *tag) - /* Execute the command which deletes the tagged items */ - if (CCP4MAPWISH_CANVAS_DIAG) printf("canvas_delete: command is: %s\n",command); - if (Tcl_Eval(interp,command) != TCL_OK) { -- printf("canvas_scale_canvas: error from Tcl_Eval: %s\n",interp->result); -+ printf("canvas_scale_canvas: error from Tcl_Eval: %s\n",Tcl_GetStringResult(interp)); - return 0; - } - -@@ -892,15 +892,15 @@ int canvas_exists(char *canvas) - - sprintf(tmpstr,"winfo exists %s",canvas); - if (Tcl_Eval(interp,tmpstr) != TCL_OK) { -- printf("canvas_exists: error from Tcl_Eval: %s",interp->result); -+ printf("canvas_exists: error from Tcl_Eval: %s",Tcl_GetStringResult(interp)); - return 0; - } - /* Extract a long int using strtol - If no conversion takes place then "endptr" will be equal - to "result" */ -- istatus = (int) strtol(interp->result,&endptr,10); -- if (strcmp(interp->result,endptr) == 0) { -- printf("canvas_exists: bad return status from winfo command \"%s\"\n",interp->result); -+ istatus = (int) strtol(Tcl_GetStringResult(interp),&endptr,10); -+ if (strcmp(Tcl_GetStringResult(interp),endptr) == 0) { -+ printf("canvas_exists: bad return status from winfo command \"%s\"\n",Tcl_GetStringResult(interp)); - return 0; - } - if (!istatus) { -@@ -930,13 +930,13 @@ float canvas_get_tk_scaling(char *canvas, char units) - - /* Execute the tk scaling command */ - if (Tcl_Eval(interp,"tk scaling") != TCL_OK) { -- printf("canvas_get_tk_scaling: error from Tcl_Eval: %s",interp->result); -+ printf("canvas_get_tk_scaling: error from Tcl_Eval: %s",Tcl_GetStringResult(interp)); - return (float) 0.0; - } - - /* Extract a float from the result */ -- tkscale = ((float) strtod(interp->result,&endptr)); -- if (strcmp(interp->result,endptr) == 0) { -+ tkscale = ((float) strtod(Tcl_GetStringResult(interp),&endptr)); -+ if (strcmp(Tcl_GetStringResult(interp),endptr) == 0) { - printf("canvas_get_tk_scaling: couldn't extract scale factor\n"); - return (float) 0.0; - } -@@ -1021,19 +1021,19 @@ int canvas_get_limits(char *canvas, int limits[4]) - - /* Evaluate the command */ - if (Tcl_Eval(interp,command) != TCL_OK) { -- printf("canvas_get_limits: error from Tcl_Eval: %s\n",interp->result); -+ printf("canvas_get_limits: error from Tcl_Eval: %s\n",Tcl_GetStringResult(interp)); - return 0; - } - - /* Process the result - it should consist of 4 integers */ - /* Use strtok which can split the string based on tokens - set by the programmer - in this case a space */ -- if (!interp->result) { -+ if (!Tcl_GetStringResult(interp)) { - puts("canvas_get_limits: failed to fetch canvas limits"); - return TCL_ERROR; - } - i = 0; -- p = strtok(interp->result," "); -+ p = strtok(Tcl_GetStringResult(interp)," "); - if (p == NULL) { - return 0; - } diff --git a/sci-chemistry/ccp4-apps/metadata.xml b/sci-chemistry/ccp4-apps/metadata.xml deleted file mode 100644 index 51fdedab1b38..000000000000 --- a/sci-chemistry/ccp4-apps/metadata.xml +++ /dev/null @@ -1,5 +0,0 @@ -<?xml version="1.0" encoding="UTF-8"?> -<!DOCTYPE pkgmetadata SYSTEM "http://www.gentoo.org/dtd/metadata.dtd"> -<pkgmetadata> - <herd>sci-chemistry</herd> -</pkgmetadata> diff --git a/sci-chemistry/ccp4/ccp4-6.1.3-r1.ebuild b/sci-chemistry/ccp4/ccp4-6.1.3-r1.ebuild deleted file mode 100644 index eea4a408b472..000000000000 --- a/sci-chemistry/ccp4/ccp4-6.1.3-r1.ebuild +++ /dev/null @@ -1,38 +0,0 @@ -# Copyright 1999-2012 Gentoo Foundation -# Distributed under the terms of the GNU General Public License v2 -# $Id$ - -EAPI=4 - -inherit fortran-2 - -DESCRIPTION="Protein X-ray crystallography toolkit -- meta package" -HOMEPAGE="http://www.ccp4.ac.uk/" -SRC_URI="" - -LICENSE="ccp4" -SLOT="0" -KEYWORDS="amd64 ~ppc x86 ~amd64-linux ~x86-linux" -IUSE="X arpwarp +balbes" - -RDEPEND=" - ~sci-chemistry/ccp4-apps-${PV}[X?] - !<=sci-chemistry/ccp4-apps-${PV}-r2 - >=sci-chemistry/molrep-11.0.00-r1 - >=sci-chemistry/mosflm-7.0.6-r2 - sci-chemistry/mrbump[X?] - >=sci-chemistry/oasis-4.0-r1 - >=sci-chemistry/pdb-extract-3.004-r2 - >=sci-chemistry/refmac-5.5.0110-r1 - >=sci-chemistry/scala-3.3.18-r1 - >=sci-chemistry/sfcheck-7.03.18-r1 - sci-chemistry/xia2 - arpwarp? ( sci-chemistry/arp-warp-bin ) - balbes? ( sci-chemistry/balbes ) - X? ( - ~sci-chemistry/ccp4i-${PV} - sci-chemistry/imosflm - sci-chemistry/pymol - sci-chemistry/rasmol - )" -DEPEND="" diff --git a/sci-chemistry/ccp4/files/6.0.1-dont-make-dirs-in-configure.patch b/sci-chemistry/ccp4/files/6.0.1-dont-make-dirs-in-configure.patch deleted file mode 100644 index 1420419ffab0..000000000000 --- a/sci-chemistry/ccp4/files/6.0.1-dont-make-dirs-in-configure.patch +++ /dev/null @@ -1,87 +0,0 @@ ---- ccp4-6.0.1.orig/configure 2006-06-10 17:30:02.000000000 -0700 -+++ ccp4-6.0.1/configure 2006-06-10 17:45:43.000000000 -0700 -@@ -623,45 +623,45 @@ - # echo "! Beware -- the $system installation isn't properly tested." ; } - syswarn='echo; echo "! Beware -- the $system installation is not properly tested."' - --if test -z "$onlylibs" ; then -- for i in CCP4_SCR BINSORT_SCR; do -- if ( eval test -d \$$i || eval mkdir -p \$$i ) ; then : -- else -- eval echo "! No directory \$$i and can\'t create it." -- echo " Check the value of $i." -- badvar=1 -- fi -- done -- -- for i in libdir bindir; do -- if ( eval test -d \$$i || eval mkdir -p \$$i ) ; then : -- else -- eval echo "! No directory \$$i and can\'t create it." -- echo " Check the argument of --$i." -- badvar=1 -- fi -- done -- -- for i in $dotsrc $dotunsupp $dotunsuppsrc ./lib ./lib/src ./lib/data ./ccp4i/etc/unix $mosflmdir/lib $mosflmdir/bin $mosflmdir/cbf/lib ; do -- if test -d $i || mkdir $i; then : -- else -- eval echo "! No directory $i and can\'t create it." -- badvar=1 -- fi -- done --else -- # Kludge to fool the "Makefile" target in the top-level CCP4 -- # Makefile into not trying to remake src/Makefile.in -- for i in $srcdir/src $srcdir/lib/src ; do -- if test -d $i || mkdir $i; then -- if ! test -f $i/Makefile.in ; then -- echo -- echo "onlylibs: making dummy file $i/Makefile.in" -- touch $i/Makefile.in -- fi -- fi -- done --fi -+#if test -z "$onlylibs" ; then -+# for i in CCP4_SCR BINSORT_SCR; do -+# if ( eval test -d \$$i || eval mkdir -p \$$i ) ; then : -+# else -+# eval echo "! No directory \$$i and can\'t create it." -+# echo " Check the value of $i." -+# badvar=1 -+# fi -+# done -+# -+# for i in libdir bindir; do -+# if ( eval test -d \$$i || eval mkdir -p \$$i ) ; then : -+# else -+# eval echo "! No directory \$$i and can\'t create it." -+# echo " Check the argument of --$i." -+# badvar=1 -+# fi -+# done -+# -+# for i in $dotsrc $dotunsupp $dotunsuppsrc ./lib ./lib/src ./lib/data ./ccp4i/etc/unix $mosflmdir/lib $mosflmdir/bin $mosflmdir/cbf/lib ; do -+# if test -d $i || mkdir $i; then : -+# else -+# eval echo "! No directory $i and can\'t create it." -+# badvar=1 -+# fi -+# done -+#else -+# # Kludge to fool the "Makefile" target in the top-level CCP4 -+# # Makefile into not trying to remake src/Makefile.in -+# for i in $srcdir/src $srcdir/lib/src ; do -+# if test -d $i || mkdir $i; then -+# if ! test -f $i/Makefile.in ; then -+# echo -+# echo "onlylibs: making dummy file $i/Makefile.in" -+# touch $i/Makefile.in -+# fi -+# fi -+# done -+#fi - - ### sanity checks - diff --git a/sci-chemistry/ccp4/files/6.0.1-ppc-double-define-gerror.patch b/sci-chemistry/ccp4/files/6.0.1-ppc-double-define-gerror.patch deleted file mode 100644 index a77d9494a05c..000000000000 --- a/sci-chemistry/ccp4/files/6.0.1-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-chemistry/ccp4/files/6.0.2-dont-make-dirs-in-configure.patch b/sci-chemistry/ccp4/files/6.0.2-dont-make-dirs-in-configure.patch deleted file mode 100644 index 1420419ffab0..000000000000 --- a/sci-chemistry/ccp4/files/6.0.2-dont-make-dirs-in-configure.patch +++ /dev/null @@ -1,87 +0,0 @@ ---- ccp4-6.0.1.orig/configure 2006-06-10 17:30:02.000000000 -0700 -+++ ccp4-6.0.1/configure 2006-06-10 17:45:43.000000000 -0700 -@@ -623,45 +623,45 @@ - # echo "! Beware -- the $system installation isn't properly tested." ; } - syswarn='echo; echo "! Beware -- the $system installation is not properly tested."' - --if test -z "$onlylibs" ; then -- for i in CCP4_SCR BINSORT_SCR; do -- if ( eval test -d \$$i || eval mkdir -p \$$i ) ; then : -- else -- eval echo "! No directory \$$i and can\'t create it." -- echo " Check the value of $i." -- badvar=1 -- fi -- done -- -- for i in libdir bindir; do -- if ( eval test -d \$$i || eval mkdir -p \$$i ) ; then : -- else -- eval echo "! No directory \$$i and can\'t create it." -- echo " Check the argument of --$i." -- badvar=1 -- fi -- done -- -- for i in $dotsrc $dotunsupp $dotunsuppsrc ./lib ./lib/src ./lib/data ./ccp4i/etc/unix $mosflmdir/lib $mosflmdir/bin $mosflmdir/cbf/lib ; do -- if test -d $i || mkdir $i; then : -- else -- eval echo "! No directory $i and can\'t create it." -- badvar=1 -- fi -- done --else -- # Kludge to fool the "Makefile" target in the top-level CCP4 -- # Makefile into not trying to remake src/Makefile.in -- for i in $srcdir/src $srcdir/lib/src ; do -- if test -d $i || mkdir $i; then -- if ! test -f $i/Makefile.in ; then -- echo -- echo "onlylibs: making dummy file $i/Makefile.in" -- touch $i/Makefile.in -- fi -- fi -- done --fi -+#if test -z "$onlylibs" ; then -+# for i in CCP4_SCR BINSORT_SCR; do -+# if ( eval test -d \$$i || eval mkdir -p \$$i ) ; then : -+# else -+# eval echo "! No directory \$$i and can\'t create it." -+# echo " Check the value of $i." -+# badvar=1 -+# fi -+# done -+# -+# for i in libdir bindir; do -+# if ( eval test -d \$$i || eval mkdir -p \$$i ) ; then : -+# else -+# eval echo "! No directory \$$i and can\'t create it." -+# echo " Check the argument of --$i." -+# badvar=1 -+# fi -+# done -+# -+# for i in $dotsrc $dotunsupp $dotunsuppsrc ./lib ./lib/src ./lib/data ./ccp4i/etc/unix $mosflmdir/lib $mosflmdir/bin $mosflmdir/cbf/lib ; do -+# if test -d $i || mkdir $i; then : -+# else -+# eval echo "! No directory $i and can\'t create it." -+# badvar=1 -+# fi -+# done -+#else -+# # Kludge to fool the "Makefile" target in the top-level CCP4 -+# # Makefile into not trying to remake src/Makefile.in -+# for i in $srcdir/src $srcdir/lib/src ; do -+# if test -d $i || mkdir $i; then -+# if ! test -f $i/Makefile.in ; then -+# echo -+# echo "onlylibs: making dummy file $i/Makefile.in" -+# touch $i/Makefile.in -+# fi -+# fi -+# done -+#fi - - ### sanity checks - diff --git a/sci-chemistry/ccp4/files/6.0.2-gcc-4.1.2-idate-fix.patch b/sci-chemistry/ccp4/files/6.0.2-gcc-4.1.2-idate-fix.patch deleted file mode 100644 index c118cc53baff..000000000000 --- a/sci-chemistry/ccp4/files/6.0.2-gcc-4.1.2-idate-fix.patch +++ /dev/null @@ -1,14 +0,0 @@ -https://bugs.gentoo.org/show_bug.cgi?id=175630 -JTRiley - ---- ccp4-6.0.2.orig/src/refmac5_/make_unix_ccp4.f 2005-09-06 07:29:56.000000000 -0400 -+++ ccp4-6.0.2.new/src/refmac5_/make_unix_ccp4.f 2007-05-02 20:03:46.000000000 -0400 -@@ -97,7 +97,7 @@ - - READ(CID,'(I2,1X,I2,1X,I2,2X)') IH(4),IH(3),IH(2) - -- CALL IDATE(IMON,IDAY,IYR) -+ CALL UIDATE(IMON,IDAY,IYR) - IF(IYR.GE.99) THEN - IYR=IYR+1900 - ELSE diff --git a/sci-chemistry/ccp4/files/6.0.2-ppc-double-define-gerror.patch b/sci-chemistry/ccp4/files/6.0.2-ppc-double-define-gerror.patch deleted file mode 100644 index a77d9494a05c..000000000000 --- a/sci-chemistry/ccp4/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-chemistry/ccp4/files/ccp4i-default-to-firefox.patch b/sci-chemistry/ccp4/files/ccp4i-default-to-firefox.patch deleted file mode 100644 index 106db895b775..000000000000 --- a/sci-chemistry/ccp4/files/ccp4i-default-to-firefox.patch +++ /dev/null @@ -1,13 +0,0 @@ ---- ccp4-5.99.5.orig/ccp4i/etc/configure.def.dist 2006-01-06 17:54:17.000000000 -0800 -+++ ccp4-5.99.5/ccp4i/etc/configure.def.dist 2006-01-06 17:54:47.000000000 -0800 -@@ -54,8 +54,8 @@ - MESSAGE _text "" - BLT_LIBRARY _text "" - MENU_LENGTH _positiveint 25 --HYPERTEXT_VIEWER _text netscape --START_NETSCAPE _text netscape -+HYPERTEXT_VIEWER _text firefox -+START_NETSCAPE _text firefox - O_MAPMAN _text mapman - MAPMAN_MAXSIZE _positiveint 4194304 - QUANTA_MBKALL _text mbkall diff --git a/sci-chemistry/ccp4/files/check-blas-lapack-pthread.patch b/sci-chemistry/ccp4/files/check-blas-lapack-pthread.patch deleted file mode 100644 index 02a2aa6d8877..000000000000 --- a/sci-chemistry/ccp4/files/check-blas-lapack-pthread.patch +++ /dev/null @@ -1,103 +0,0 @@ ---- ccp4-5.99.5.orig/configure 2006-01-17 00:35:36.000000000 -0800 -+++ ccp4-5.99.5/configure 2006-01-17 10:44:39.000000000 -0800 -@@ -2410,12 +2410,12 @@ - end - EOF - #firslty test without -lblas -- test_compile="$FC $FOPTIM $XFFLAGS -o testlink testlink.f -llapack" -+ test_compile="$FC $FOPTIM $XFFLAGS -o testlink testlink.f -llapack -lpthread" - echo $test_compile - if { (eval $test_compile >& /dev/null ) 2>&1; } && test -s testlink ; then - # Compilation was okay -- echo "... only -llapack needed" -- XLAPACK_LIB="-llapack" -+ echo "... only -llapack -lpthread needed" -+ XLAPACK_LIB="-llapack -lpthread" - # Set the next two variables so that configure - # doesn't try to build netlib libraries - LAPACKLIB="lapack" -@@ -2424,12 +2424,12 @@ - tryblas= - else - echo "more than just -llapack needed...." -- test_compile="$FC $FOPTIM $XFFLAGS -o testlink testlink.f -llapack -lblas" -+ test_compile="$FC $FOPTIM $XFFLAGS -o testlink testlink.f -llapack -lblas -lpthread" - echo $test_compile - if { (eval $test_compile ) 2>&1; } && test -s testlink ; then - # Compilation was okay -- echo "...-llapack and -lblas were needed" -- XLAPACK_LIB="-llapack -lblas" -+ echo "...-llapack, -lpthread and -lblas were needed" -+ XLAPACK_LIB="-llapack -lpthread -lblas" - # Set the next two variables so that configure - # doesn't try to build netlib libraries - LAPACKLIB="lapack blas" -@@ -2720,8 +2720,8 @@ - STOP - END - EOF -- test_compile="$FC $FOPTIM $XFFLAGS -o testlink testlink.f -L$testdir -l$testlib" -- test_ccompile="$FC $FOPTIM $XFFLAGS -o testlink testlink.f -L$testdir -l$testlib $XLDFLAGS" -+ test_compile="$FC $FOPTIM $XFFLAGS -o testlink testlink.f -L$testdir -l$testlib -lpthread" -+ test_ccompile="$FC $FOPTIM $XFFLAGS -o testlink testlink.f -L$testdir -l$testlib $XLDFLAGS -lpthread" - echo $test_compile - if { (eval $test_compile ) 2>&1; } && test -s testlink ; then - have_lapack=yes -@@ -2738,7 +2738,7 @@ - LAPACKDIR="$testdir" - echo "Link ok - using lib$LAPACKLIB from $LAPACKDIR" - # -- XLAPACK_LIB="-L$LAPACKDIR -l$LAPACKLIB" -+ XLAPACK_LIB="-L$LAPACKDIR -l$LAPACKLIB -lpthread" - # - # Test to see if we need BLAS too - # Do this by trying to compile a test program -@@ -2750,8 +2750,8 @@ - if test -f testlsame ; then - rm -f testsame testlsame.o - fi -- test_compile="$FC $FOPTIM $XFFLAGS -o testlsame lsametst.f -L$LAPACKDIR -l$LAPACKLIB" -- test_ccompile="$FC $FOPTIM $XFFLAGS -o testlsame lsametst.f -L$LAPACKDIR -l$LAPACKLIB $XLDFLAGS" -+ test_compile="$FC $FOPTIM $XFFLAGS -o testlsame lsametst.f -L$LAPACKDIR -l$LAPACKLIB -lpthread" -+ test_ccompile="$FC $FOPTIM $XFFLAGS -o testlsame lsametst.f -L$LAPACKDIR -l$LAPACKLIB $XLDFLAGS -lpthread" - echo $test_compile - if { ( eval $test_compile) 2>&1;} && test -s testlsame ; then - have_blas=yes -@@ -2830,8 +2830,8 @@ - STOP - END - EOF -- test_compile="$FC $FOPTIM $XFFLAGS -o testlink testlink.f -L$testdir -l$testlib" -- test_ccompile="$FC $FOPTIM $XFFLAGS -o testlink testlink.f -L$testdir -l$testlib $XLDFLAGS" -+ test_compile="$FC $FOPTIM $XFFLAGS -o testlink testlink.f -L$testdir -l$testlib -lpthread" -+ test_ccompile="$FC $FOPTIM $XFFLAGS -o testlink testlink.f -L$testdir -l$testlib $XLDFLAGS -lpthread" - echo $test_compile - if { ( eval $test_compile) 2>&1;} && test -s testlink ; then - have_blas=yes -@@ -3033,7 +3033,7 @@ - if test -f testlsame ; then - rm -f testsame testlsame.o - fi -- test_compile="$FC $FOPTIM $XFFLAGS -o testlsame lsametst.f -L$BLASDIR -l$BLASLIB" -+ test_compile="$FC $FOPTIM $XFFLAGS -o testlsame lsametst.f -L$BLASDIR -l$BLASLIB -lpthread" - echo $test_compile - if { ( eval $test_compile) 2>&1;} && test -s testlsame ; then - echo "Found LSAME in lib$BLASLIB" -@@ -3046,7 +3046,7 @@ - if test -f testxerbla ; then - rm -f testxerbla testxerbla.o - fi -- test_compile="$FC $FOPTIM $XFFLAGS -o testxerbla xerblatst.f -L$BLASDIR -l$BLASLIB" -+ test_compile="$FC $FOPTIM $XFFLAGS -o testxerbla xerblatst.f -L$BLASDIR -l$BLASLIB -lpthread" - echo $test_compile - if { ( eval $test_compile) 2>&1;} && test -s testxerbla ; then - # Found lsame -@@ -3080,7 +3080,7 @@ - cd ../.. - # - lapackdir=lib/lapack -- XLAPACK_LIB="-L$srcdir/lib/lapack -llapack -L$BLASDIR -l$BLASLIB" -+ XLAPACK_LIB="-L$srcdir/lib/lapack -llapack -L$BLASDIR -l$BLASLIB -lpthread" - # netlib lapack is in fortran, so we may need the fortran libraries when - # we are linking using the C or C++ compilers - case $system in diff --git a/sci-chemistry/ccp4/files/clipper-find-mccp4-includes.patch b/sci-chemistry/ccp4/files/clipper-find-mccp4-includes.patch deleted file mode 100644 index 3bf5a0652247..000000000000 --- a/sci-chemistry/ccp4/files/clipper-find-mccp4-includes.patch +++ /dev/null @@ -1,11 +0,0 @@ ---- ccp4-5.99.5/lib/clipper/configure.orig 2006-01-07 16:54:13.000000000 -0800 -+++ ccp4-5.99.5/lib/clipper/configure 2006-01-07 16:54:31.000000000 -0800 -@@ -21751,7 +21751,7 @@ - - if test "x$mccp4_prefix" != x; then - # ie. mccp4=thing was given (thing is what we're checking for) -- ac_MCCP4_CXXFLAGS="-I$mccp4_prefix/include" -+ ac_MCCP4_CXXFLAGS="-I$mccp4_prefix/include -I$mccp4_prefix/include/mccp4" - ac_MCCP4_LDOPTS="-L$mccp4_prefix/lib -lmccp4" - else - # treat as standard lib/include diff --git a/sci-chemistry/ccp4/files/create-mosflm-bindir.patch b/sci-chemistry/ccp4/files/create-mosflm-bindir.patch deleted file mode 100644 index 34d6197572fc..000000000000 --- a/sci-chemistry/ccp4/files/create-mosflm-bindir.patch +++ /dev/null @@ -1,10 +0,0 @@ ---- ccp4-5.99.5.orig/x-windows/Makefile.in 2006-01-06 12:31:02.000000000 -0800 -+++ ccp4-5.99.5/x-windows/Makefile.in 2006-01-06 12:31:30.000000000 -0800 -@@ -158,6 +158,7 @@ - install_obj = ipdisp.exe hklview xdldataman xdlmapman \ - rotgen ipmosflm - install: all -+ mkdir -p $(bindir) - $(INSTALL_PROGRAM) $(srcdir)/ipdisp.exe $(bindir) - $(INSTALL_PROGRAM) $(srcdir)/ipdisp/ipdisp $(bindir) - $(INSTALL_PROGRAM) $(srcdir)/hklview $(bindir) diff --git a/sci-chemistry/ccp4/files/dont-build-rasmol.patch b/sci-chemistry/ccp4/files/dont-build-rasmol.patch deleted file mode 100644 index 8da54fd26de8..000000000000 --- a/sci-chemistry/ccp4/files/dont-build-rasmol.patch +++ /dev/null @@ -1,19 +0,0 @@ ---- ccp4-5.99.5.orig/x-windows/Makefile.in 2005-12-05 03:06:57.000000000 -0800 -+++ ccp4-5.99.5/x-windows/Makefile.in 2005-12-05 03:07:23.000000000 -0800 -@@ -35,7 +35,7 @@ - # - # all - # --all : xdlview libjwc_c libjwc_f rotgen_ hklview ipdisp.exe xdlgjk xjiffy rasmol2 ipmosflm -+all : xdlview libjwc_c libjwc_f rotgen_ hklview ipdisp.exe xdlgjk xjiffy ipmosflm - # - # xdl_view - # -@@ -161,7 +161,6 @@ - $(INSTALL_PROGRAM) $(srcdir)/xdldataman $(bindir) - $(INSTALL_PROGRAM) $(srcdir)/xdlmapman $(bindir) - cd $(srcdir)/XCCPJIFFY ; $(MAKE) install -- $(INSTALL_PROGRAM) $(rasmol_dir)/rasmol $(bindir) - cd $(rotgen_dir); $(MAKE) install - $(INSTALL_PROGRAM) $(mosflm_dir)/bin/ipmosflm $(bindir) - cd $(xdlview_dir); $(MAKE) install diff --git a/sci-chemistry/ccp4/files/make-ipmosflm-dir.patch b/sci-chemistry/ccp4/files/make-ipmosflm-dir.patch deleted file mode 100644 index 7813141b2ec2..000000000000 --- a/sci-chemistry/ccp4/files/make-ipmosflm-dir.patch +++ /dev/null @@ -1,10 +0,0 @@ ---- ccp4-5.99.5.orig/x-windows/Mosflm/mosflm/Makefile.in 2006-01-06 00:04:12.000000000 -0800 -+++ ccp4-5.99.5/x-windows/Mosflm/mosflm/Makefile.in 2006-01-06 00:04:41.000000000 -0800 -@@ -37,6 +37,7 @@ - ${F77} ${FFLAGS} -o $@ $< - - ipmosflm: ${OBJS} -+ mkdir -p ${DPSBIN} - ${FLINK} ${FFLAGS} ${OBJS} ${LOCALLIBS} ${LIBS} \ - -o ${DPSBIN}/ipmosflm ${LDFLAGS} - diff --git a/sci-chemistry/ccp4/files/make-mosflm-cbf-libdir.patch b/sci-chemistry/ccp4/files/make-mosflm-cbf-libdir.patch deleted file mode 100644 index ae4b7633b105..000000000000 --- a/sci-chemistry/ccp4/files/make-mosflm-cbf-libdir.patch +++ /dev/null @@ -1,11 +0,0 @@ ---- ccp4-5.99.5.orig/x-windows/Mosflm/cbf/Makefile.in 2006-01-05 23:42:19.000000000 -0800 -+++ ccp4-5.99.5/x-windows/Mosflm/cbf/Makefile.in 2006-01-05 23:43:35.000000000 -0800 -@@ -132,7 +132,7 @@ - # - # CBF library - # --$(LIB)/libcbf.a: $(SOURCE) $(HEADERS) $(COMMONDEP) -+$(LIB)/libcbf.a: $(SOURCE) $(HEADERS) $(COMMONDEP) $(LIB) - $(CC) $(CFLAGS) $(INCLUDES) $(WARNINGS) -c $(SOURCE) - $(AR) cr $@ *.o - $(RANLIB) $@ diff --git a/sci-chemistry/ccp4/files/make-mosflm-index-libdir.patch b/sci-chemistry/ccp4/files/make-mosflm-index-libdir.patch deleted file mode 100644 index 97607b689672..000000000000 --- a/sci-chemistry/ccp4/files/make-mosflm-index-libdir.patch +++ /dev/null @@ -1,10 +0,0 @@ ---- ccp4-5.99.5.orig/x-windows/Mosflm/index/Makefile.in 2006-01-05 23:15:09.000000000 -0800 -+++ ccp4-5.99.5/x-windows/Mosflm/index/Makefile.in 2006-01-05 23:15:30.000000000 -0800 -@@ -76,6 +76,7 @@ - - # local version of libdps_index.a - ${LIB}/dps_index.a: ${IOBJS} ${HOBJS} -+ mkdir -p ${LIB} - ar ru ${LIB}/dps_index.a ${IOBJS} ${HOBJS} - - ${LIB}/libpeak.a: diff --git a/sci-chemistry/ccp4/files/make-mosflm-libdir.patch b/sci-chemistry/ccp4/files/make-mosflm-libdir.patch deleted file mode 100644 index eac1b9f1721e..000000000000 --- a/sci-chemistry/ccp4/files/make-mosflm-libdir.patch +++ /dev/null @@ -1,10 +0,0 @@ ---- ccp4-5.99.5.orig/x-windows/Mosflm/src/dps/index/Makefile.in 2006-01-05 22:48:47.000000000 -0800 -+++ ccp4-5.99.5/x-windows/Mosflm/src/dps/index/Makefile.in 2006-01-05 22:49:02.000000000 -0800 -@@ -42,6 +42,7 @@ - $(LOCALLIBS) $(LIBS) - - index: $(IOBJS) -+ mkdir -p $(LIBDIR) - ${AR} $(AR_FLAGS) $(LIBDIR)/libdps_index.a $(IOBJS) - chmod 644 $(LIBDIR)/libdps_index.a - diff --git a/sci-chemistry/ccp4/files/pass-clipper-enablevals.patch b/sci-chemistry/ccp4/files/pass-clipper-enablevals.patch deleted file mode 100644 index 3e1a8b0e6be8..000000000000 --- a/sci-chemistry/ccp4/files/pass-clipper-enablevals.patch +++ /dev/null @@ -1,11 +0,0 @@ ---- ccp4-5.99.5.orig/configure 2006-01-06 11:45:43.000000000 -0800 -+++ ccp4-5.99.5/configure 2006-01-06 11:46:53.000000000 -0800 -@@ -3210,7 +3210,7 @@ - #ccp4 setup - xopts="${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-chemistry/ccp4/metadata.xml b/sci-chemistry/ccp4/metadata.xml deleted file mode 100644 index d37774eb9ada..000000000000 --- a/sci-chemistry/ccp4/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> - <use> - <flag name="balbes">Install sci-chemistry/balbes</flag> - <flag name="arpwarp">Add binary arp-warp for molecular replacement</flag> - </use> -</pkgmetadata> diff --git a/sci-chemistry/ccp4i/Manifest b/sci-chemistry/ccp4i/Manifest deleted file mode 100644 index e082cb44f7fb..000000000000 --- a/sci-chemistry/ccp4i/Manifest +++ /dev/null @@ -1,3 +0,0 @@ -DIST 6.1.3-oasis4.0.patch.bz2 946 SHA256 12d7c5965e0c46b0f482514d9083d6be94d65eeb14ba29c17d507d5f9669f84b SHA512 7c7bf4ef90550708bf41b1831dbe71c38418b46455adb3d42ec609d287894ac9260d9671f1759f71c713ced72fa004b9808391ea6874007ac8b7d7637f349d32 WHIRLPOOL a2bc27e1e054e1717c387f3800533fa490c03d1d18d3fe3cff4676f0ec47799a1681a206e01013c1b8f8e41162303446a824b86effeef2ed73f059feb07fb820 -DIST ccp4-6.1.3-core-src.tar.gz 242134076 SHA256 1e529c660e7f390ec0feca9d45caa00a2813d23156c10a2747c427117293c324 SHA512 413eba806107ebcdbd93e9122275463709133d9b2a9ce44ae57a6c2350465a47ba66ad9875237aead74f5d422c0104f58f728ab37a757b10d82cde92af444c20 WHIRLPOOL faebf8ee7920013bc3d0e83565207dca1f31ba0b5c92fe1eae4b740f70ff2031d95787fa0d545b09c853d25657c08973527e43de02fddc086988123ca2a6339c -DIST ccp4i-6.1.3-arpwarp.patch.bz2 58498 SHA256 297e6f75354f3a1932302f7039bf449484c95eb41b8634ae96d93c754b47c687 SHA512 0bf18d9768b722c553e79eed04de316f6b0b4695f7678e1d850d5e22735ecc79cdb961ea76b6482457fff232892b81ce191cd48fa588ded8058184a871dffb65 WHIRLPOOL f24625941e31e951f13c94cf31e2ca061840b016aa3fd038d29710d9ca400d364467dc3fa1e42a55944d63ac7e42a0a6baa39a596c55b18610eeb552d232d1b8 diff --git a/sci-chemistry/ccp4i/ccp4i-6.1.3-r4.ebuild b/sci-chemistry/ccp4i/ccp4i-6.1.3-r4.ebuild deleted file mode 100644 index bdfba7800493..000000000000 --- a/sci-chemistry/ccp4i/ccp4i-6.1.3-r4.ebuild +++ /dev/null @@ -1,99 +0,0 @@ -# Copyright 1999-2015 Gentoo Foundation -# Distributed under the terms of the GNU General Public License v2 -# $Id$ - -EAPI=5 - -PYTHON_COMPAT=( python2_7 ) - -inherit eutils multilib python-single-r1 virtualx - -MY_PN="${PN%i}" -MY_P="${MY_PN}-${PV}" - -#UPDATE="04_03_09" -#PATCHDATE="090511" - -SRC="ftp://ftp.ccp4.ac.uk/ccp4" - -DESCRIPTION="Protein X-ray crystallography toolkit -- graphical interface" -HOMEPAGE="http://www.ccp4.ac.uk/" -SRC_URI=" - ${SRC}/${PV}/${MY_P}-core-src.tar.gz - mirror://gentoo/${P}-arpwarp.patch.bz2 - https://dev.gentoo.org/~jlec/distfiles/${PV}-oasis4.0.patch.bz2" -[[ -n ${UPDATE} ]] && SRC_URI="${SRC_URI} ${SRC}/${PV}/updates/${P}-src-patch-${UPDATE}.tar.gz" -[[ -n ${PATCHDATE} ]] && SRC_URI="${SRC_URI} https://dev.gentoo.org/~jlec/science-dist/${PV}-${PATCHDATE}-updates.patch.bz2" - -SLOT="0" -KEYWORDS="amd64 ~ppc x86 ~amd64-linux ~x86-linux" -LICENSE="ccp4" -IUSE="" - -RDEPEND=" - app-shells/tcsh - media-gfx/graphviz - >=dev-lang/tk-8.3:0 - >=dev-tcltk/blt-2.4 - sci-libs/ccp4-libs" -DEPEND="${RDEPEND}" - -S="${WORKDIR}/${MY_P}" - -PATCHES=( - "${FILESDIR}"/${PV}-fix-baubles.patch - "${WORKDIR}"/${P}-arpwarp.patch - ) - -src_prepare() { - epatch ${PATCHES[@]} - - [[ ! -z ${PATCHDATE} ]] && epatch "${WORKDIR}"/${PV}-${PATCHDATE}-updates.patch - - epatch "${WORKDIR}"/${PV}-oasis4.0.patch - python_fix_shebang ccp4i/ share/dbccp4i/ -} - -src_configure() { - : -} - -src_compile() { - : -} - -src_install() { - # rm imosflm stuff - rm -rf "${S}"/ccp4i/{bin/imosflm,imosflm} || die - - rm -rf "${S}"/ccp4i/{bin,etc}/WINDOWS || die - - # This is installed by mrbump - rm -rf "${S}"/ccp4i/{tasks/{dbviewer.tcl,mrbump.*},templates/mrbump.com,scripts/mrbump.script} || die - - # CCP4Interface - GUI - insinto /usr/$(get_libdir)/ccp4 - doins -r "${S}"/ccp4i - exeinto /usr/$(get_libdir)/ccp4/ccp4i/bin - doexe "${S}"/ccp4i/bin/* - dosym ../$(get_libdir)/ccp4/ccp4i/bin/ccp4i /usr/bin/ccp4i - - dodir /usr/$(get_libdir)/ccp4/ccp4i/unix - - # dbccp4i - insinto /usr/share/ccp4 - doins -r "${S}"/share/dbccp4i -} - -pkg_postinst() { - _ccp4-setup() { - source "${EPREFIX}/etc/profile" - export USER=root - bash "${EPREFIX}"/usr/$(get_libdir)/ccp4/ccp4i/bin/ccp4i -h > /dev/null - } - VIRTUALX_COMMAND="_ccp4-setup" virtualmake - echo "" - elog "ccp4i needs some enviromental settings. So please" - elog "\t source ${EPREFIX}/etc/profile" - echo "" -} diff --git a/sci-chemistry/ccp4i/files/6.1.3-fix-baubles.patch b/sci-chemistry/ccp4i/files/6.1.3-fix-baubles.patch deleted file mode 100644 index 2c5f659b8018..000000000000 --- a/sci-chemistry/ccp4i/files/6.1.3-fix-baubles.patch +++ /dev/null @@ -1,22 +0,0 @@ ---- ccp4i/etc/configure.def.dist 2009-01-09 16:45:08.000000000 +0100 -+++ ccp4i/etc/configure.def.dist.new 2009-07-07 23:17:26.000000000 +0200 -@@ -53,8 +53,8 @@ - RUN_IMOSFLM _text "ccp4iwish [file join [GetEnvPath CCP4I_TOP] imosflm imosflm.tcl] project [GetCurrentProjectDir [GetCurrentProject]]" - RUN_CCP4MG _text "ccp4mg" - RUN_COOT _text "coot" --RUN_BAUBLES _text "python [file join [GetEnvPath CCP4] share smartie baubles.py]" --RUN_DBVIEWER _text "wish [file join [GetEnvPath CCP4] share dbccp4i application viewer.tcl]" -+RUN_BAUBLES _text "python [file join [GetEnvPath CCP4] share ccp4 smartie baubles.py]" -+RUN_DBVIEWER _text "wish [file join [GetEnvPath DBCCP4I_TOP] application viewer.tcl]" - ENABLE_BUBBLE_HELP _logical 1 - DISABLE_TASKS _logical 1 - CCP4_SETUP_COMMAND _text setup_ccp4 -@@ -62,7 +62,7 @@ - BLT_LIBRARY _text "" - MENU_LENGTH _positiveint 25 - HYPERTEXT_VIEWER _text firefox --START_NETSCAPE _text netscape -+START_NETSCAPE _text firefox - O_MAPMAN _text mapman - MAPMAN_MAXSIZE _positiveint 4194304 - QUANTA_MBKALL _text mbkall diff --git a/sci-chemistry/ccp4i/files/6.1.3-rename-rapper.patch b/sci-chemistry/ccp4i/files/6.1.3-rename-rapper.patch deleted file mode 100644 index 9f5cfb4b635f..000000000000 --- a/sci-chemistry/ccp4i/files/6.1.3-rename-rapper.patch +++ /dev/null @@ -1,61 +0,0 @@ -diff --git a/ccp4i/scripts/check.script b/ccp4i/scripts/check.script -index def44bc..dd4bb7e 100755 ---- a/ccp4i/scripts/check.script -+++ b/ccp4i/scripts/check.script -@@ -24,7 +24,7 @@ - if $RUN_RAMPAGE { - - # Generate command line -- set cmd "[BinPath rapper]" -+ set cmd "[BinPath rappermc]" - - set rapperdatadir [FileJoin [GetEnvPath CCP4] share rapper] - set paramsfile [FileJoin $rapperdatadir params.xml] -diff --git a/ccp4i/scripts/rapper.script b/ccp4i/scripts/rapper.script -index cdae1e2..faae226 100755 ---- a/ccp4i/scripts/rapper.script -+++ b/ccp4i/scripts/rapper.script -@@ -17,7 +17,7 @@ - - #set up command line - --set cmd "[BinPath rapper]" -+set cmd "[BinPath rappermc]" - - set rapperdatadir [FileJoin [GetEnvPath CCP4] share rapper] - set paramsfile [FileJoin [GetEnvPath CCP4] share rapper params.xml] -@@ -180,7 +180,7 @@ append outfiles " $XYZOUT PROJECT" - - # Run RAPPER to join loop back to framework and out put to defined pdb file - # Also need to sort out multimodel files join - FIX ME --set cmd2 "[BinPath rapper]" -+set cmd2 "[BinPath rappermc]" - append cmd2 " $paramsfile joinpdb " - append cmd2 " --pdb2 \"$root\-loop.pdb\" " - append cmd2 " --pdb \"$root\-framework.pdb\" " -diff --git a/ccp4i/tasks/check.tcl b/ccp4i/tasks/check.tcl -index ae88ff2..ee3307b 100755 ---- a/ccp4i/tasks/check.tcl -+++ b/ccp4i/tasks/check.tcl -@@ -46,7 +46,7 @@ proc check_run { arrayname } { - # Check for Rampage program. If it is not found, we switch off the option. - # If it was the only option, script will fail with next check. - if { $array(RUN_RAMPAGE) == 1 } { -- if { [FindExecutable "rapper"] == "" } { -+ if { [FindExecutable "rappermc"] == "" } { - WarningMessage "Input Error: Rapper_Rampage program not found in system path." - set array(RUN_RAMPAGE) 0 - } -diff --git a/ccp4i/tasks/rapper.tcl b/ccp4i/tasks/rapper.tcl -index e299057..8843a3f 100755 ---- a/ccp4i/tasks/rapper.tcl -+++ b/ccp4i/tasks/rapper.tcl -@@ -28,7 +28,7 @@ proc rapper_run { arrayname } { - # Check for RAPPER program. If it is not found, we switch off the option. - # If it was the only option, script will fail with next check. - if { [regexp MODEL $build_type ] && $prog_type == "RAPPER"} { -- if { [FindExecutable "rapper"] == "" } { -+ if { [FindExecutable "rappermc"] == "" } { - WarningMessage "Input Error: RAPPER program not found in system path." - set build_type 0 - } diff --git a/sci-chemistry/ccp4i/files/6.1.3-rename-superpose.patch b/sci-chemistry/ccp4i/files/6.1.3-rename-superpose.patch deleted file mode 100644 index 74cd2b946601..000000000000 --- a/sci-chemistry/ccp4i/files/6.1.3-rename-superpose.patch +++ /dev/null @@ -1,26 +0,0 @@ -diff --git a/ccp4i/scripts/superpose.script b/ccp4i/scripts/superpose.script -index 3483c97..5027536 100755 ---- a/ccp4i/scripts/superpose.script -+++ b/ccp4i/scripts/superpose.script -@@ -21,7 +21,7 @@ - - if { [regexp SSM $SUPERPOSE_MODE ] } { - -- set cmd "[BinPath superpose] \"$XYZIN2\" -s $SSM_MOVING \"$XYZIN1\" -s $SSM_FIXED \"$XYZOUT_LOCAL\"" -+ set cmd "[BinPath superpose-ccp4] \"$XYZIN2\" -s $SSM_MOVING \"$XYZIN1\" -s $SSM_FIXED \"$XYZOUT_LOCAL\"" - set status [Execute $cmd "" program_status report ] - - } elseif { [regexp TOP $SUPERPOSE_MODE ] } { -diff --git a/ccp4i/tasks/superpose.tcl b/ccp4i/tasks/superpose.tcl -index 748bf6e..c92122a 100755 ---- a/ccp4i/tasks/superpose.tcl -+++ b/ccp4i/tasks/superpose.tcl -@@ -100,7 +100,7 @@ proc superpose_run { arrayname } { - # If user is match equivalent named residues/atoms then fit in the match fields - switch [GetValue $arrayname SUPERPOSE_MODE] \ - SSM { -- if { ![file exists [FindExecutable superpose]] } { -+ if { ![file exists [FindExecutable superpose-ccp4]] } { - WarningMessage "The program \"superpose\" is not on your path. - Check your installation for \"superpose\" program and \"ssm\" library." - return 0 diff --git a/sci-chemistry/ccp4i/files/6.1.3-rename-truncate.patch b/sci-chemistry/ccp4i/files/6.1.3-rename-truncate.patch deleted file mode 100644 index 9af60b7c5152..000000000000 --- a/sci-chemistry/ccp4i/files/6.1.3-rename-truncate.patch +++ /dev/null @@ -1,91 +0,0 @@ -diff --git a/ccp4i/crank/plugins/prep/crank_prep.tcl b/ccp4i/crank/plugins/prep/crank_prep.tcl -index 7d05905..d01f1dc 100755 ---- a/ccp4i/crank/plugins/prep/crank_prep.tcl -+++ b/ccp4i/crank/plugins/prep/crank_prep.tcl -@@ -226,7 +226,7 @@ proc run_truncate { i j } { - set script "$script\n$labout" - set script "$script\nEND\n" - -- set run_command "truncate $command << \"$script\"" -+ set run_command "ftruncate $command << \"$script\"" - puts $run_command - catch {eval exec $run_command } output - puts $output -diff --git a/ccp4i/scripts/dtrek2mtz.script b/ccp4i/scripts/dtrek2mtz.script -index e74aa0d..a2a1adb 100755 ---- a/ccp4i/scripts/dtrek2mtz.script -+++ b/ccp4i/scripts/dtrek2mtz.script -@@ -36,7 +36,7 @@ - set HKL_TRUNCATE [GetTmpFileName -ext mtz] - - CreateComScript truncate truncate_script -- set cmd "[BinPath truncate] HKLIN \"$HKLTMP\" HKLOUT \"$HKL_TRUNCATE\"" -+ set cmd "[BinPath ftruncate] HKLIN \"$HKLTMP\" HKLOUT \"$HKL_TRUNCATE\"" - set status [Execute $cmd $truncate_script program_status report] - - HandleHarvestFile $HARVEST_MODE $HARVEST_PNAME $HARVEST_DNAME truncate -diff --git a/ccp4i/scripts/import.script b/ccp4i/scripts/import.script -index 90cba83..1c90c33 100755 ---- a/ccp4i/scripts/import.script -+++ b/ccp4i/scripts/import.script -@@ -144,7 +144,7 @@ if { $FORMAT == "MTZ" } { - - set truncatemtz [GetTmpFileName -ext mtz ] - CreateComScript truncate truncate_script -- set cmd "[BinPath truncate] HKLIN \"$tmpmtz\" HKLOUT \"$truncatemtz\"" -+ set cmd "[BinPath ftruncate] HKLIN \"$tmpmtz\" HKLOUT \"$truncatemtz\"" - set status [Execute $cmd $truncate_script program_status report] - - -diff --git a/ccp4i/scripts/import_scaled.script b/ccp4i/scripts/import_scaled.script -index dcc619b..7250513 100755 ---- a/ccp4i/scripts/import_scaled.script -+++ b/ccp4i/scripts/import_scaled.script -@@ -62,7 +62,7 @@ - - } else { - CreateComScript truncate truncate_script -- set cmd "[BinPath truncate] HKLIN \"$HKLTMP\" HKLOUT \"$HKL_TRUNCATE\"" -+ set cmd "[BinPath ftruncate] HKLIN \"$HKLTMP\" HKLOUT \"$HKL_TRUNCATE\"" - set status [Execute $cmd $truncate_script program_status report] - - HandleHarvestFile $HARVEST_MODE $HARVEST_PNAME $HARVEST_DNAME truncate -diff --git a/ccp4i/scripts/scala.script b/ccp4i/scripts/scala.script -index 6940ccd..bde10d6 100755 ---- a/ccp4i/scripts/scala.script -+++ b/ccp4i/scripts/scala.script -@@ -275,7 +275,7 @@ END" - - } else { - CreateComScript truncate truncate_script -- set cmd "[BinPath truncate] HKLIN \"$HKLTMP\" HKLOUT \"$HKL_TRUNCATE\"" -+ set cmd "[BinPath ftruncate] HKLIN \"$HKLTMP\" HKLOUT \"$HKL_TRUNCATE\"" - set status [Execute $cmd $truncate_script $LOG_FILE program_status report ] - } - -diff --git a/ccp4i/scripts/scalepack2mtz.script b/ccp4i/scripts/scalepack2mtz.script -index 986e06c..a1947a6 100755 ---- a/ccp4i/scripts/scalepack2mtz.script -+++ b/ccp4i/scripts/scalepack2mtz.script -@@ -35,7 +35,7 @@ - - set HKL_TRUNCATE [GetTmpFileName -ext mtz] - CreateComScript truncate truncate_script -- set cmd "[BinPath truncate] HKLIN \"$HKLTMP\" HKLOUT \"$HKL_TRUNCATE\"" -+ set cmd "[BinPath ftruncate] HKLIN \"$HKLTMP\" HKLOUT \"$HKL_TRUNCATE\"" - set status [Execute $cmd $truncate_script program_status report] - - HandleHarvestFile $HARVEST_MODE $HARVEST_PNAME $HARVEST_DNAME truncate -diff --git a/ccp4i/scripts/truncate.script b/ccp4i/scripts/truncate.script -index e0e09ce..2d448a2 100755 ---- a/ccp4i/scripts/truncate.script -+++ b/ccp4i/scripts/truncate.script -@@ -45,7 +45,7 @@ - - CreateComScript truncate truncate_script - -- set cmd "[BinPath truncate] HKLIN \"$HKLIN\"" -+ set cmd "[BinPath ftruncate] HKLIN \"$HKLIN\"" - if { ![StringSame $INPUT_DATA AMPLITUDES] } { - append cmd " HKLOUT \"$HKL_TRUNCATE\"" - } diff --git a/sci-chemistry/ccp4i/metadata.xml b/sci-chemistry/ccp4i/metadata.xml deleted file mode 100644 index 51fdedab1b38..000000000000 --- a/sci-chemistry/ccp4i/metadata.xml +++ /dev/null @@ -1,5 +0,0 @@ -<?xml version="1.0" encoding="UTF-8"?> -<!DOCTYPE pkgmetadata SYSTEM "http://www.gentoo.org/dtd/metadata.dtd"> -<pkgmetadata> - <herd>sci-chemistry</herd> -</pkgmetadata> diff --git a/sci-chemistry/coot/coot-0.7.1-r1.ebuild b/sci-chemistry/coot/coot-0.7.1-r1.ebuild deleted file mode 100644 index 001145ee18ee..000000000000 --- a/sci-chemistry/coot/coot-0.7.1-r1.ebuild +++ /dev/null @@ -1,167 +0,0 @@ -# Copyright 1999-2015 Gentoo Foundation -# Distributed under the terms of the GNU General Public License v2 -# $Id$ - -EAPI=5 - -PYTHON_COMPAT=( python2_7 ) - -AUTOTOOLS_AUTORECONF="true" - -inherit autotools-utils python-single-r1 toolchain-funcs versionator - -MY_S2_PV=$(replace_version_separator 2 - ${PV}) -MY_S2_P=${PN}-${MY_S2_PV/pre1/pre-1} -MY_S_P=${MY_S2_P}-${PR/r/revision-} -MY_PV=${PV} -MY_P=${PN}-${MY_PV} - -DESCRIPTION="Crystallographic Object-Oriented Toolkit for model building, completion and validation" -HOMEPAGE="http://www2.mrc-lmb.cam.ac.uk/personal/pemsley/coot/" -SRC_URI=" - http://www2.mrc-lmb.cam.ac.uk/Personal/pemsley/coot/source/releases/${MY_P}.tar.gz - test? ( https://dev.gentoo.org/~jlec/distfiles/greg-data-${PV}.tar.gz )" - -SLOT="0" -LICENSE="GPL-3" -KEYWORDS="~amd64 ~x86 ~amd64-linux ~x86-linux" -IUSE="+openmp static-libs test" - -REQUIRED_USE="${PYTHON_REQUIRED_USE}" - -AUTOTOOLS_IN_SOURCE_BUILD=1 - -SCIDEPS=" - >=sci-libs/ccp4-libs-6.1 - sci-libs/clipper - >=sci-libs/coot-data-2 - >=sci-libs/gsl-1.3 - >=sci-libs/mmdb-1.23:0 - sci-libs/ssm - sci-libs/monomer-db - sci-chemistry/reduce - sci-chemistry/refmac - sci-chemistry/probe" - -XDEPS=" - gnome-base/libgnomecanvas - gnome-base/librsvg:2 - media-libs/libpng - media-libs/freeglut - x11-libs/gtk+:2 - x11-libs/goocanvas:0 - x11-libs/gtkglext" - -SCHEMEDEPS=" - dev-scheme/net-http - dev-scheme/guile-gui - >=dev-scheme/guile-lib-0.1.6 - dev-scheme/guile-www - >=x11-libs/guile-gtk-2.1" - -RDEPEND=" - ${SCIDEPS} - ${XDEPS} - ${SCHEMEDEPS} - ${PYTHON_DEPS} - dev-python/pygtk:2[${PYTHON_USEDEP}] - >=dev-libs/gmp-4.2.2-r2 - >=net-misc/curl-7.19.6 - net-dns/libidn" -DEPEND="${RDEPEND} - >=sys-devel/libtool-2.4-r2 - dev-lang/swig - sys-devel/bc - test? ( dev-scheme/greg )" - -S="${WORKDIR}/${MY_P}" - -pkg_setup() { - if use openmp; then - tc-has-openmp || die "Please use an OPENMP capable compiler" - fi - python-single-r1_pkg_setup -} - -PATCHES=( - "${FILESDIR}"/${PN}-0.7-clipper-config.patch - "${FILESDIR}"/${PN}-0.7-goocanvas.patch - "${FILESDIR}"/${PN}-0.7-mmdb-config.patch - "${FILESDIR}"/${PN}-0.7-ssm.patch - ) - -src_prepare() { - sed \ - -e "s:AM_COOT_SYS_BUILD_TYPE:COOT_SYS_BUILD_TYPE=Gentoo-Linux-${EPYTHON}-gtk2 ; AC_MSG_RESULT([\$COOT_SYS_BUILD_TYPE]); AC_SUBST(COOT_SYS_BUILD_TYPE):g" \ - -i configure.in || die - - autotools-utils_src_prepare -} - -src_configure() { - # All the --with's are used to activate various parts. - # Yes, this is broken behavior. - local myeconfargs=( - --includedir='${prefix}/include/coot' - --with-goocanvas-prefix="${EPREFIX}/usr" - --with-guile - --with-python="${EPREFIX}/usr" - --with-guile-gtk - --with-gtk2 - --with-pygtk - $(use_enable openmp) - ) - autotools-utils_src_configure -} - -src_test() { - source "${EPREFIX}/etc/profile.d/40ccp4.setup.sh" - mkdir "${T}"/coot_test - - export COOT_STANDARD_RESIDUES="${S}/standard-residues.pdb" - export COOT_SCHEME_DIR="${S}/scheme/" - export COOT_RESOURCES_FILE="${S}/cootrc" - export COOT_PIXMAPS_DIR="${S}/pixmaps/" - export COOT_DATA_DIR="${S}/" - export COOT_PYTHON_DIR="${S}/python/" - export PYTHONPATH="${COOT_PYTHON_DIR}:${PYTHONPATH}" - export PYTHONHOME="${EPREFIX}"/usr/ - export CCP4_SCR="${T}"/coot_test/ - export CLIBD_MON="${EPREFIX}/usr/share/ccp4/data/monomers/" - export SYMINFO="${S}/syminfo.lib" - - export COOT_TEST_DATA_DIR="${WORKDIR}"/greg-data - - cat > command-line-greg.scm <<- EOF - (use-modules (ice-9 greg)) - (set! greg-tools (list "greg-tests")) - (set! greg-debug #t) - (set! greg-verbose 5) - (let ((r (greg-test-run))) - (if r - (coot-real-exit 0) - (coot-real-exit 1))) - EOF - - einfo "Running test with following paths ..." - einfo "COOT_STANDARD_RESIDUES $COOT_STANDARD_RESIDUES" - einfo "COOT_SCHEME_DIR $COOT_SCHEME_DIR" - einfo "COOT_RESOURCES_FILE $COOT_RESOURCES_FILE" - einfo "COOT_PIXMAPS_DIR $COOT_PIXMAPS_DIR" - einfo "COOT_DATA_DIR $COOT_DATA_DIR" - einfo "COOT_PYTHON_DIR $COOT_PYTHON_DIR" - einfo "PYTHONPATH $PYTHONPATH" - einfo "PYTHONHOME $PYTHONHOME" - einfo "CCP4_SCR ${CCP4_SCR}" - einfo "CLIBD_MON ${CLIBD_MON}" - einfo "SYMINFO ${SYMINFO}" - - "${S}"/src/coot-real --no-graphics --script command-line-greg.scm || die - "${S}"/src/coot-real --no-graphics --script python-tests/coot_unittest.py || die -} - -src_install() { - autotools-utils_src_install - insinto /usr/share/${PN} - doins syminfo.lib -} diff --git a/sci-chemistry/coot/coot-0.7.2.ebuild b/sci-chemistry/coot/coot-0.7.2.ebuild deleted file mode 100644 index 0e14d4464539..000000000000 --- a/sci-chemistry/coot/coot-0.7.2.ebuild +++ /dev/null @@ -1,165 +0,0 @@ -# Copyright 1999-2015 Gentoo Foundation -# Distributed under the terms of the GNU General Public License v2 -# $Id$ - -EAPI=5 - -PYTHON_COMPAT=( python2_7 ) - -AUTOTOOLS_AUTORECONF="true" - -inherit autotools-utils python-single-r1 toolchain-funcs versionator - -MY_S2_PV=$(replace_version_separator 2 - ${PV}) -MY_S2_P=${PN}-${MY_S2_PV/pre1/pre-1} -MY_S_P=${MY_S2_P}-${PR/r/revision-} -MY_PV=${PV} -MY_P=${PN}-${MY_PV} - -DESCRIPTION="Crystallographic Object-Oriented Toolkit for model building, completion and validation" -HOMEPAGE="http://www2.mrc-lmb.cam.ac.uk/personal/pemsley/coot/" -SRC_URI=" - http://www2.mrc-lmb.cam.ac.uk/Personal/pemsley/coot/source/releases/${MY_P}.tar.gz - test? ( https://dev.gentoo.org/~jlec/distfiles/greg-data-${PV}.tar.gz )" - -SLOT="0" -LICENSE="GPL-3" -KEYWORDS="amd64 x86 ~amd64-linux ~x86-linux" -IUSE="+openmp static-libs test" - -REQUIRED_USE="${PYTHON_REQUIRED_USE}" - -AUTOTOOLS_IN_SOURCE_BUILD=1 - -SCIDEPS=" - >=sci-libs/ccp4-libs-6.1 - sci-libs/clipper - >=sci-libs/coot-data-2 - >=sci-libs/gsl-1.3 - >=sci-libs/mmdb-1.23:0 - sci-libs/ssm - sci-libs/monomer-db - sci-chemistry/reduce - sci-chemistry/refmac - sci-chemistry/probe" - -XDEPS=" - gnome-base/libgnomecanvas - gnome-base/librsvg:2 - media-libs/libpng - media-libs/freeglut - x11-libs/gtk+:2 - x11-libs/goocanvas:0 - x11-libs/gtkglext" - -SCHEMEDEPS=" - dev-scheme/net-http - dev-scheme/guile-gui - >=dev-scheme/guile-lib-0.1.6 - dev-scheme/guile-www - >=x11-libs/guile-gtk-2.1" - -RDEPEND=" - ${SCIDEPS} - ${XDEPS} - ${SCHEMEDEPS} - ${PYTHON_DEPS} - dev-python/pygtk:2[${PYTHON_USEDEP}] - >=dev-libs/gmp-4.2.2-r2 - >=net-misc/curl-7.19.6 - net-dns/libidn" -DEPEND="${RDEPEND} - >=sys-devel/libtool-2.4-r2 - dev-lang/swig - sys-devel/bc - test? ( dev-scheme/greg )" - -S="${WORKDIR}/${MY_P}" - -pkg_setup() { - if use openmp; then - tc-has-openmp || die "Please use an OPENMP capable compiler" - fi - python-single-r1_pkg_setup -} - -PATCHES=( - "${FILESDIR}"/${PN}-0.7-clipper-config.patch - "${FILESDIR}"/${PN}-0.7-goocanvas.patch - "${FILESDIR}"/${PN}-0.7-mmdb-config.patch - ) - -src_prepare() { - sed \ - -e "s:AM_COOT_SYS_BUILD_TYPE:COOT_SYS_BUILD_TYPE=Gentoo-Linux-${EPYTHON}-gtk2 ; AC_MSG_RESULT([\$COOT_SYS_BUILD_TYPE]); AC_SUBST(COOT_SYS_BUILD_TYPE):g" \ - -i configure.in || die - - autotools-utils_src_prepare -} - -src_configure() { - # All the --with's are used to activate various parts. - # Yes, this is broken behavior. - local myeconfargs=( - --includedir='${prefix}/include/coot' - --with-goocanvas-prefix="${EPREFIX}/usr" - --with-guile - --with-python="${EPREFIX}/usr" - --with-guile-gtk - --with-gtk2 - --with-pygtk - $(use_enable openmp) - ) - autotools-utils_src_configure -} - -src_compile() { - autotools-utils_src_compile - cp "${S}"/src/coot_gtk2.py python/coot.py || die -} - -src_test() { - source "${EPREFIX}/etc/profile.d/40ccp4.setup.sh" - mkdir "${T}"/coot_test - - export COOT_STANDARD_RESIDUES="${S}/standard-residues.pdb" - export COOT_SCHEME_DIR="${S}/scheme/" - export COOT_RESOURCES_FILE="${S}/cootrc" - export COOT_PIXMAPS_DIR="${S}/pixmaps/" - export COOT_DATA_DIR="${S}/" - export COOT_PYTHON_DIR="${S}/python/" - export PYTHONPATH="${COOT_PYTHON_DIR}:${PYTHONPATH}" - export PYTHONHOME="${EPREFIX}"/usr/ - export CCP4_SCR="${T}"/coot_test/ - export CLIBD_MON="${EPREFIX}/usr/share/ccp4/data/monomers/" - export SYMINFO="${S}/syminfo.lib" - - export COOT_TEST_DATA_DIR="${WORKDIR}"/greg-data - - cat > command-line-greg.scm <<- EOF - (use-modules (ice-9 greg)) - (set! greg-tools (list "greg-tests")) - (set! greg-debug #t) - (set! greg-verbose 5) - (let ((r (greg-test-run))) - (if r - (coot-real-exit 0) - (coot-real-exit 1))) - EOF - - einfo "Running test with following paths ..." - einfo "COOT_STANDARD_RESIDUES $COOT_STANDARD_RESIDUES" - einfo "COOT_SCHEME_DIR $COOT_SCHEME_DIR" - einfo "COOT_RESOURCES_FILE $COOT_RESOURCES_FILE" - einfo "COOT_PIXMAPS_DIR $COOT_PIXMAPS_DIR" - einfo "COOT_DATA_DIR $COOT_DATA_DIR" - einfo "COOT_PYTHON_DIR $COOT_PYTHON_DIR" - einfo "PYTHONPATH $PYTHONPATH" - einfo "PYTHONHOME $PYTHONHOME" - einfo "CCP4_SCR ${CCP4_SCR}" - einfo "CLIBD_MON ${CLIBD_MON}" - einfo "SYMINFO ${SYMINFO}" - - "${S}"/src/coot-real --no-graphics --script command-line-greg.scm || die - "${S}"/src/coot-real --no-graphics --script python-tests/coot_unittest.py || die -} diff --git a/sci-chemistry/coot/coot-0.7.ebuild b/sci-chemistry/coot/coot-0.7.ebuild deleted file mode 100644 index f5cdfa54b525..000000000000 --- a/sci-chemistry/coot/coot-0.7.ebuild +++ /dev/null @@ -1,159 +0,0 @@ -# Copyright 1999-2014 Gentoo Foundation -# Distributed under the terms of the GNU General Public License v2 -# $Id$ - -EAPI=4 - -PYTHON_DEPEND="2" - -AUTOTOOLS_AUTORECONF="true" - -inherit autotools-utils python toolchain-funcs versionator - -MY_S2_PV=$(replace_version_separator 2 - ${PV}) -MY_S2_P=${PN}-${MY_S2_PV/pre1/pre-1} -MY_S_P=${MY_S2_P}-${PR/r/revision-} -MY_PV=${PV} -MY_P=${PN}-${MY_PV} - -DESCRIPTION="Crystallographic Object-Oriented Toolkit for model building, completion and validation" -HOMEPAGE="http://www2.mrc-lmb.cam.ac.uk/personal/pemsley/coot/" -SRC_URI=" - http://www.biop.ox.ac.uk/coot/software/source/releases/${MY_P}.tar.gz - test? ( https://dev.gentoo.org/~jlec/distfiles/greg-data-${PV}.tar.gz )" - -SLOT="0" -LICENSE="GPL-3" -KEYWORDS="amd64 x86 ~amd64-linux ~x86-linux" -IUSE="+openmp static-libs test" - -AUTOTOOLS_IN_SOURCE_BUILD=1 - -SCIDEPS=" - >=sci-libs/ccp4-libs-6.1 - sci-libs/clipper - >=sci-libs/coot-data-2 - >=sci-libs/gsl-1.3 - >=sci-libs/mmdb-1.23:0 - sci-libs/ssm - <sci-libs/monomer-db-1 - sci-chemistry/reduce - <sci-chemistry/refmac-5.6 - sci-chemistry/probe" - -XDEPS=" - gnome-base/libgnomecanvas - gnome-base/librsvg:2 - media-libs/libpng - media-libs/freeglut - x11-libs/gtk+:2 - x11-libs/goocanvas:0 - x11-libs/gtkglext" - -SCHEMEDEPS=" - dev-scheme/net-http - dev-scheme/guile-gui - >=dev-scheme/guile-lib-0.1.6 - dev-scheme/guile-www - >=x11-libs/guile-gtk-2.1" - -RDEPEND=" - ${SCIDEPS} - ${XDEPS} - ${SCHEMEDEPS} - dev-python/pygtk:2 - >=dev-libs/gmp-4.2.2-r2 - >=net-misc/curl-7.19.6 - net-dns/libidn" -DEPEND="${RDEPEND} - >=sys-devel/libtool-2.4-r2 - dev-lang/swig - sys-devel/bc - test? ( dev-scheme/greg )" - -S="${WORKDIR}/${MY_P}" - -pkg_setup() { - if use openmp; then - tc-has-openmp || die "Please use an OPENMP capable compiler" - fi - python_set_active_version 2 - python_pkg_setup -} - -PATCHES=( - "${FILESDIR}"/${P}-clipper-config.patch - "${FILESDIR}"/${P}-goocanvas.patch - "${FILESDIR}"/${P}-mmdb-config.patch - "${FILESDIR}"/${P}-ssm.patch - ) - -src_prepare() { - sed \ - -e "s:AM_COOT_SYS_BUILD_TYPE:COOT_SYS_BUILD_TYPE=Gentoo-Linux-$(PYTHON)-gtk2 ; AC_MSG_RESULT([\$COOT_SYS_BUILD_TYPE]); AC_SUBST(COOT_SYS_BUILD_TYPE):g" \ - -i configure.in || die - - autotools-utils_src_prepare -} - -src_configure() { - # All the --with's are used to activate various parts. - # Yes, this is broken behavior. - local myeconfargs=( - --includedir='${prefix}/include/coot' - --with-goocanvas-prefix="${EPREFIX}/usr" - --with-guile - --with-python="${EPREFIX}/usr" - --with-guile-gtk - --with-gtk2 - --with-pygtk - $(use_enable openmp) - ) - autotools-utils_src_configure -} - -src_test() { - source "${EPREFIX}/etc/profile.d/40ccp4.setup.sh" - mkdir "${T}"/coot_test - - export COOT_STANDARD_RESIDUES="${S}/standard-residues.pdb" - export COOT_SCHEME_DIR="${S}/scheme/" - export COOT_RESOURCES_FILE="${S}/cootrc" - export COOT_PIXMAPS_DIR="${S}/pixmaps/" - export COOT_DATA_DIR="${S}/" - export COOT_PYTHON_DIR="${S}/python/" - export PYTHONPATH="${COOT_PYTHON_DIR}:${PYTHONPATH}" - export PYTHONHOME="${EPREFIX}"/usr/ - export CCP4_SCR="${T}"/coot_test/ - export CLIBD_MON="${EPREFIX}/usr/share/ccp4/data/monomers/" - export SYMINFO="${S}/syminfo.lib" - - export COOT_TEST_DATA_DIR="${WORKDIR}"/data/greg-data - - cat > command-line-greg.scm <<- EOF - (use-modules (ice-9 greg)) - (set! greg-tools (list "greg-tests")) - (set! greg-debug #t) - (set! greg-verbose 5) - (let ((r (greg-test-run))) - (if r - (coot-real-exit 0) - (coot-real-exit 1))) - EOF - - einfo "Running test with following paths ..." - einfo "COOT_STANDARD_RESIDUES $COOT_STANDARD_RESIDUES" - einfo "COOT_SCHEME_DIR $COOT_SCHEME_DIR" - einfo "COOT_RESOURCES_FILE $COOT_RESOURCES_FILE" - einfo "COOT_PIXMAPS_DIR $COOT_PIXMAPS_DIR" - einfo "COOT_DATA_DIR $COOT_DATA_DIR" - einfo "COOT_PYTHON_DIR $COOT_PYTHON_DIR" - einfo "PYTHONPATH $PYTHONPATH" - einfo "PYTHONHOME $PYTHONHOME" - einfo "CCP4_SCR ${CCP4_SCR}" - einfo "CLIBD_MON ${CLIBD_MON}" - einfo "SYMINFO ${SYMINFO}" - - "${S}"/src/coot-real --no-graphics --script command-line-greg.scm || die - "${S}"/src/coot-real --no-graphics --script python-tests/coot_unittest.py || die -} diff --git a/sci-chemistry/imosflm/Manifest b/sci-chemistry/imosflm/Manifest deleted file mode 100644 index 2ce7d893b7fd..000000000000 --- a/sci-chemistry/imosflm/Manifest +++ /dev/null @@ -1 +0,0 @@ -DIST imosflm-1.0.7.zip 941784 SHA256 b067261b4d7ef2f1f7581ddeaa08252d29f889acf89ce190eb0d8b30aa94b107 SHA512 f3163e1f71c5b1e24d6b3fbd5a040bbcebae25485d1258eef4b2725821f5f96c1260adb2bcc3ab57179d7b9b9e538ddf0494ab9b5be259b98d138fddacec8c77 WHIRLPOOL bd2b6bcdcc241fde41fe2ba99bd1e2f47bc444c46ee36a5b332d5c018b81a9d649378110a8bffa48ffc67a19b04ede7e61846b53a250e5fe3058ec0313fda80c diff --git a/sci-chemistry/imosflm/files/1.0.4-impl-dec.patch b/sci-chemistry/imosflm/files/1.0.4-impl-dec.patch deleted file mode 100644 index 5d0dd7010910..000000000000 --- a/sci-chemistry/imosflm/files/1.0.4-impl-dec.patch +++ /dev/null @@ -1,12 +0,0 @@ -diff --git a/c/tkImageLoad.c b/c/tkImageLoad.c -index e7c46f0..1496a15 100755 ---- a/c/tkImageLoad.c -+++ b/c/tkImageLoad.c -@@ -12,6 +12,7 @@ - #include <tcl.h> - #include <tk.h> - #include <assert.h> -+#include <stdlib.h> - - #define HEADER_LINE_LENGTH 512 - #define BYTES_PER_PIXEL 2 diff --git a/sci-chemistry/imosflm/files/1.0.4-tk.patch b/sci-chemistry/imosflm/files/1.0.4-tk.patch deleted file mode 100644 index a90175194eb4..000000000000 --- a/sci-chemistry/imosflm/files/1.0.4-tk.patch +++ /dev/null @@ -1,50 +0,0 @@ ---- c/tkImageLoad.c 2009-08-14 21:10:19.000000000 +0200 -+++ c/tkImageLoad.c.new 2009-08-14 21:10:55.000000000 +0200 -@@ -19,6 +19,7 @@ - //#define BLOCKED 1 - //#define UNBLOCKED 1 - #define IN_BLOCK_FLIP 1 -+#define USE_COMPOSITELESS_PHOTO_PUT_BLOCK - - /* *********************************************************************/ - ---- c/tkImageLoad.c 2009-08-14 21:13:29.000000000 +0200 -+++ c/tkImageLoad.c.new 2009-08-14 21:14:59.000000000 +0200 -@@ -272,9 +272,11 @@ - } - /* put the photo block into the image */ - #ifdef __alpha -- Tk_PhotoPutBlock(dp, &db, 0, 0, width, height); -+ Tk_PhotoPutBlock(dp, &db, 0, 0, width, height, -+ TK_PHOTO_COMPOSITE_OVERLAY); - #else -- Tk_PhotoPutBlock(dp, &db, 0, 0, width, height, TK_PHOTO_COMPOSITE_SET); -+ Tk_PhotoPutBlock(dp, &db, 0, 0, width, height, TK_PHOTO_COMPOSITE_SET, -+ TK_PHOTO_COMPOSITE_OVERLAY); - #endif - - /* Free the photo block's memory now it is finished with */ -@@ -417,9 +419,11 @@ - - /* put the photo block back into the image */ - #ifdef __alpha -- Tk_PhotoPutBlock(photo, &block, 0, 0, block.width, block.height); -+ Tk_PhotoPutBlock(photo, &block, 0, 0, block.width, block.height, -+ TK_PHOTO_COMPOSITE_OVERLAY); - #else -- Tk_PhotoPutBlock(photo, &block, 0, 0, block.width, block.height,TK_PHOTO_COMPOSITE_SET); -+ Tk_PhotoPutBlock(photo, &block, 0, 0, block.width, block.height,TK_PHOTO_COMPOSITE_SET, -+ TK_PHOTO_COMPOSITE_OVERLAY); - #endif - /* Free the photo block's memory now it is finished with */ - if (block.pixelPtr) { ---- c/tkImageLoad.c 2009-08-14 21:15:06.000000000 +0200 -+++ c/tkImageLoad.c.new 2009-08-14 21:16:53.000000000 +0200 -@@ -9,6 +9,7 @@ - \************************************************************************/ - - #include <stdio.h> -+#include <string.h> - #include <tcl.h> - #include <tk.h> - #include <assert.h> diff --git a/sci-chemistry/imosflm/files/1.0.7-libpng16.patch b/sci-chemistry/imosflm/files/1.0.7-libpng16.patch deleted file mode 100644 index 27efc6f36f4b..000000000000 --- a/sci-chemistry/imosflm/files/1.0.7-libpng16.patch +++ /dev/null @@ -1,13 +0,0 @@ -http://bugs.gentoo.org/467036 - ---- src/contrast.tcl -+++ src/contrast.tcl -@@ -3,7 +3,7 @@ - - package require palette - --image create photo ::img::pixel_count_v -data "iVBORw0KGgoAAAANSUhEUgAAAA4AAABCCAIAAAGft0AHAAAABGdBTUEAAYagMeiWXwAAASFJREFUKJGtVFEWhCAINJ9H4f4n4jD7YauAA1jGT2EwAxNyMXMppZZu3bv6Q3t3iH7ob3fOPz3wdLoi7y8V1SOZp0NE02Hm7quc6VSVaokFKzMD8qKUUd0tyEQ0z1DchNQaud+JCHclzeIDOUCle7EjcA/XPZU4Klb9y2GDY68LVe8YiAihmXT052G9SQ0+m4yN2J7EZqrvnZpheMdGRLnq5/ViddTusPeux9o5G7fdsskrV9ej8rw3I80LhNUUgqmvwCY8izozZcvo5tGt1owfoGJhoEVtgcXg2da2gJa0JYESseRJ8gvyOYSGlxUkScYFoBoJB+RZrR+H2sWx2vEQrnv0pa4HYkFqF7UHrefRdjE5zQQFAp/Nqwf8XNePZ+AHq5sOPlXtupMAAAAASUVORK5CYII=" -+image create photo ::img::pixel_count_v -data "iVBORw0KGgoAAAANSUhEUgAAAA4AAABCCAIAAAGft0AHAAAABGdBTUEAAYagMeiWXwAAASFJREFUeJytVFEWhCAINJ9H4f4n4jD7YauAA1jGT2EwAxNyMXMppZZu3bv6Q3t3iH7ob3fOPz3wdLoi7y8V1SOZp0NE02Hm7quc6VSVaokFKzMD8qKUUd0tyEQ0z1DchNQaud+JCHclzeIDOUCle7EjcA/XPZU4Klb9y2GDY68LVe8YiAihmXT052G9SQ0+m4yN2J7EZqrvnZpheMdGRLnq5/ViddTusPeux9o5G7fdsskrV9ej8rw3I80LhNUUgqmvwCY8izozZcvo5tGt1owfoGJhoEVtgcXg2da2gJa0JYESseRJ8gvyOYSGlxUkScYFoBoJB+RZrR+H2sWx2vEQrnv0pa4HYkFqF7UHrefRdjE5zQQFAp/Nqwf8XNePZ+AHq5sOPv4fGP4AAAAASUVORK5CYII=" - - class Contrast { - inherit Palette diff --git a/sci-chemistry/imosflm/imosflm-1.0.7-r1.ebuild b/sci-chemistry/imosflm/imosflm-1.0.7-r1.ebuild deleted file mode 100644 index e49667e50dc7..000000000000 --- a/sci-chemistry/imosflm/imosflm-1.0.7-r1.ebuild +++ /dev/null @@ -1,54 +0,0 @@ -# Copyright 1999-2015 Gentoo Foundation -# Distributed under the terms of the GNU General Public License v2 -# $Id$ - -EAPI=5 - -inherit eutils multilib toolchain-funcs versionator - -MY_PV="$(delete_all_version_separators ${PV})" - -DESCRIPTION="A new GUI for the Mosflm crystallographic data processing tool" -HOMEPAGE="http://www.mrc-lmb.cam.ac.uk/harry/imosflm" -SRC_URI="${HOMEPAGE}/ver${MY_PV}/downloads/${P}.zip" - -LICENSE="ccp4" -SLOT="0" -KEYWORDS="amd64 ~ppc x86 ~amd64-linux ~x86-linux" -IUSE="" - -RDEPEND=" - dev-lang/tcl:0= - >=dev-tcltk/itcl-3.3 - >=dev-tcltk/itk-3.3 - >=dev-tcltk/iwidgets-4 - >=dev-tcltk/tdom-0.8 - >=dev-tcltk/tkimg-1.3 - >=dev-tcltk/tktreectrl-2.1 - dev-tcltk/anigif - dev-tcltk/combobox - dev-tcltk/tablelist - >=sci-chemistry/mosflm-7.0.9" -DEPEND="app-arch/unzip" - -S=${WORKDIR}/${PN} - -src_prepare() { - epatch "${FILESDIR}"/${PV}-libpng16.patch -} - -src_install(){ - rm -rf lib/{*.so,anigif,combobox} - - insinto /usr/$(get_libdir)/${PN} - doins -r "${S}"/{src,bitmaps,lib} - fperms 775 /usr/$(get_libdir)/${PN}/src/imosflm - - cat >> "${T}"/23imosflm <<- EOF - IMOSFLM_VERSION="${PV}" - EOF - - doenvd "${T}"/23imosflm - - make_wrapper imosflm /usr/$(get_libdir)/${PN}/src/imosflm -} diff --git a/sci-chemistry/imosflm/metadata.xml b/sci-chemistry/imosflm/metadata.xml deleted file mode 100644 index 51fdedab1b38..000000000000 --- a/sci-chemistry/imosflm/metadata.xml +++ /dev/null @@ -1,5 +0,0 @@ -<?xml version="1.0" encoding="UTF-8"?> -<!DOCTYPE pkgmetadata SYSTEM "http://www.gentoo.org/dtd/metadata.dtd"> -<pkgmetadata> - <herd>sci-chemistry</herd> -</pkgmetadata> diff --git a/sci-chemistry/makecif/Manifest b/sci-chemistry/makecif/Manifest deleted file mode 100644 index b489a33454fd..000000000000 --- a/sci-chemistry/makecif/Manifest +++ /dev/null @@ -1 +0,0 @@ -DIST makecif-5.6.6.tar.gz 3797710 SHA256 fdcc1bee70583da3161f0d46eb792d965c04f08f0ad3033f730486550e859d1f SHA512 874c69d85b55ef22057c1113418218d7fd0a1e795f04673f3d64cd015230ab47ad8bdb0277ca9b389cc3edf397dc63c2c1cdd35837a86bc5d2a595d9ae534dbc WHIRLPOOL 5ecc1f7d06445d34e1d5d97ad98fd4c9d21db1e1611a9d89e25f0228a7b2cce5fa631b470687b3e6f7085c932cee6c5d8d4da2e6473406a22d63a26645f56be7 diff --git a/sci-chemistry/makecif/files/5.6.6-makefile.patch b/sci-chemistry/makecif/files/5.6.6-makefile.patch deleted file mode 100644 index 186abb92b7d8..000000000000 --- a/sci-chemistry/makecif/files/5.6.6-makefile.patch +++ /dev/null @@ -1,49 +0,0 @@ -diff --git a/src/makefile b/src/makefile -index 6c8264a..acdec20 100755 ---- a/src/makefile -+++ b/src/makefile -@@ -22,6 +22,8 @@ MAKEDIC = $(MAKECIF)/dic/ - # setenv BLANC_FORT "f77 -O1" - # - -+all: makecif_all libcheck_all modcheck_all emin_all -+ - clean: - rm -f temp_makecif_path.fh - rm -f ../bin/* -@@ -118,7 +120,7 @@ makecif.o: makecif.f lib_com.fh crd_com.fh - $(BLANC_FORT) -c makecif.f - - mkcif: main_makecif.o make_lib11.o make_lib12.o make_lib2.o make_vdw.o make_CIF.o make_crd1.o make_crd2.o make_new1.o make_new2.o make_rst1.o make_rst2.o make_PDB.o makecif.o make_unix.o make_subr_2.o make_subr.o set_num.o vdw_flexible.o emin.o libcheck_min.o math_refmac.o iheap_sort.o cell_symm_subrs.o subnumrec.o mol2_file.o sdf_files.o libcheck.o -- $(BLANC_FORT) -o ../bin/makecif main_makecif.o makecif.o make_vdw.o make_CIF.o make_PDB.o make_crd1.o make_crd2.o make_new1.o make_new2.o make_rst1.o make_rst2.o make_unix.o make_subr_2.o make_subr.o make_lib11.o make_lib12.o make_lib2.o set_num.o vdw_flexible.o emin.o libcheck_min.o math_refmac.o iheap_sort.o cell_symm_subrs.o subnumrec.o mol2_file.o sdf_files.o libcheck.o -+ $(BLANC_FORT) ${LDFLAGS} -o ../bin/makecif main_makecif.o makecif.o make_vdw.o make_CIF.o make_PDB.o make_crd1.o make_crd2.o make_new1.o make_new2.o make_rst1.o make_rst2.o make_unix.o make_subr_2.o make_subr.o make_lib11.o make_lib12.o make_lib2.o set_num.o vdw_flexible.o emin.o libcheck_min.o math_refmac.o iheap_sort.o cell_symm_subrs.o subnumrec.o mol2_file.o sdf_files.o libcheck.o - # ------------- - libcheck.o: libcheck.f lib_com.fh crd_com.fh - $(BLANC_FORT) -c libcheck.f -@@ -130,7 +132,7 @@ main_libcheck.o: main_libcheck.f libcheck_version.fh - $(BLANC_FORT) -c main_libcheck.f - - lbcheck: main_libcheck.o make_subr_2.o make_subr.o make_lib11.o make_lib12.o make_lib2.o libcheck.o make_PDB.o make_CIF.o make_new1.o make_new2.o make_crd1.o make_crd2.o make_unix.o set_num.o vdw_flexible.o emin.o libcheck_min.o math_refmac.o iheap_sort.o cell_symm_subrs.o subnumrec.o mol2_file.o sdf_files.o -- $(BLANC_FORT) -o ../bin/libcheck main_libcheck.o libcheck.o make_PDB.o make_CIF.o make_new1.o make_new2.o make_crd1.o make_crd2.o make_lib11.o make_lib12.o make_lib2.o make_unix.o make_subr_2.o make_subr.o set_num.o vdw_flexible.o emin.o libcheck_min.o math_refmac.o iheap_sort.o cell_symm_subrs.o subnumrec.o mol2_file.o sdf_files.o -+ $(BLANC_FORT) ${LDFLAGS} -o ../bin/libcheck main_libcheck.o libcheck.o make_PDB.o make_CIF.o make_new1.o make_new2.o make_crd1.o make_crd2.o make_lib11.o make_lib12.o make_lib2.o make_unix.o make_subr_2.o make_subr.o set_num.o vdw_flexible.o emin.o libcheck_min.o math_refmac.o iheap_sort.o cell_symm_subrs.o subnumrec.o mol2_file.o sdf_files.o - # ------------ - - emin.o: emin.f crd_com.fh atom_com.fh -@@ -143,7 +145,7 @@ main_emin.o: main_emin.f - $(BLANC_FORT) -c main_emin.f - - emn: main_emin.o emin_new.o angle_subr.o make_unix.o make_CIF.o make_subr_2.o make_subr.o -- $(BLANC_FORT) -o ../bin/emin main_emin.o emin_new.o make_CIF.o angle_subr.o make_unix.o make_subr_2.o make_subr.o -+ $(BLANC_FORT) ${LDFLAGS} -o ../bin/emin main_emin.o emin_new.o make_CIF.o angle_subr.o make_unix.o make_subr_2.o make_subr.o - - # ------------- - -@@ -155,7 +157,7 @@ main_modcheck.o: main_modcheck.f - $(BLANC_FORT) -c main_modcheck.f - - mdcheck: main_modcheck.o modcheck.o mod_subr.o make_CIF.o make_unix.o make_subr_2.o make_subr.o -- $(BLANC_FORT) -o ../bin/modcheck main_modcheck.o make_CIF.o modcheck.o mod_subr.o make_unix.o make_subr_2.o make_subr.o -+ $(BLANC_FORT) ${LDFLAGS} -o ../bin/modcheck main_modcheck.o make_CIF.o modcheck.o mod_subr.o make_unix.o make_subr_2.o make_subr.o - - - # ====================================== diff --git a/sci-chemistry/makecif/makecif-5.6.6-r1.ebuild b/sci-chemistry/makecif/makecif-5.6.6-r1.ebuild deleted file mode 100644 index 509117f300af..000000000000 --- a/sci-chemistry/makecif/makecif-5.6.6-r1.ebuild +++ /dev/null @@ -1,40 +0,0 @@ -# Copyright 1999-2013 Gentoo Foundation -# Distributed under the terms of the GNU General Public License v2 -# $Id$ - -EAPI=4 - -inherit eutils fortran-2 toolchain-funcs - -DESCRIPTION="PDB --> CIF convertor" -HOMEPAGE="http://www.ysbl.york.ac.uk/~alexei/makecif.html" -SRC_URI="mirror://gentoo/${P}.tar.gz" - -SLOT="0" -KEYWORDS="~amd64 ppc ~x86 ~amd64-linux ~x86-linux ~x64-macos ~x86-macos" -LICENSE="ccp4" -IUSE="" - -S="${WORKDIR}"/${PN} - -DEPEND="" -RDEPEND=" - !>=sci-chemistry/refmac-5.6 - sci-libs/monomer-db" - -src_prepare() { - epatch "${FILESDIR}"/${PV}-makefile.patch -} - -src_compile() { - emake -C src clean - emake \ - -C src \ - BLANC_FORT="$(tc-getFC) ${FFLAGS}" \ - LDFLAGS="${LDFLAGS}" -} - -src_install() { - dobin bin/* - dodoc readme -} diff --git a/sci-chemistry/makecif/makecif-5.6.6.ebuild b/sci-chemistry/makecif/makecif-5.6.6.ebuild deleted file mode 100644 index 3a5f70a8b259..000000000000 --- a/sci-chemistry/makecif/makecif-5.6.6.ebuild +++ /dev/null @@ -1,39 +0,0 @@ -# Copyright 1999-2012 Gentoo Foundation -# Distributed under the terms of the GNU General Public License v2 -# $Id$ - -EAPI=4 - -inherit eutils fortran-2 toolchain-funcs - -DESCRIPTION="PDB --> CIF convertor" -HOMEPAGE="http://www.ysbl.york.ac.uk/~alexei/makecif.html" -SRC_URI="mirror://gentoo/${P}.tar.gz" - -SLOT="0" -KEYWORDS="amd64 ~ppc x86 ~amd64-linux ~x86-linux" -LICENSE="ccp4" -IUSE="" - -S="${WORKDIR}"/${PN} - -DEPEND="" -RDEPEND=" - !>=sci-chemistry/refmac-5.6 - sci-libs/monomer-db" - -src_prepare() { - epatch "${FILESDIR}"/${PV}-makefile.patch -} - -src_compile() { - cd src && emake clean - emake \ - BLANC_FORT="$(tc-getFC) ${FFLAGS}" \ - LDFLAGS="${LDFLAGS}" -} - -src_install() { - dobin bin/* - dodoc readme -} diff --git a/sci-chemistry/makecif/metadata.xml b/sci-chemistry/makecif/metadata.xml deleted file mode 100644 index 993c1d1ffcda..000000000000 --- a/sci-chemistry/makecif/metadata.xml +++ /dev/null @@ -1,18 +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@gentoo.org</email> - </maintainer> - <longdescription> -PDB - CIF convertor -check and create correct structure description -create the list of restraints -create dictionary description of new ligands -rebuild missing atoms -create tree like structure -also the part of REFMAC -can use additional user's dictionary -</longdescription> -</pkgmetadata> diff --git a/sci-chemistry/molrep/Manifest b/sci-chemistry/molrep/Manifest deleted file mode 100644 index d91b8a448acd..000000000000 --- a/sci-chemistry/molrep/Manifest +++ /dev/null @@ -1,2 +0,0 @@ -DIST molrep-11.0.02.tar.gz 3594084 SHA256 6acb00bc91ad76027461ce6055eda72c8de34e5243449a31d5ede9e537e9adce SHA512 e22636e2d6b5558b66877960a64c0b990bb50d9e1b42016981b64e1311f83d5942fde7c1cd2dc8462ef1be814ce94ef566028079a7a091c9b3d7300f2d6ce03f WHIRLPOOL e507108a38be703e882ab3fd25e817c53c2d57b76fce578de3d308f10a85fce7a9febed39f748667a01c631b35787955d7d0290c944d4bfabfc936eab620daaf -DIST molrep-11.0.03.tar.gz 3643087 SHA256 f4c317713b0dddf0ca883734f0bfe27600b50f8d4dd354ea8ae8245e21ce4392 SHA512 d9ff351e3754871d100c41aa9b8af48e3588768320f5ed92e536fac5e24114ca5df6497103d0b077455fc4e30e2d3d085aeb63854eb88dc8e74259b4e1683dc8 WHIRLPOOL b16e128e3ca7f1734ca79f70decab3e262d47b6a37c49e46c4c7d51f3fd8093cd3a0f20e487caeb5e9aa0a37a9fd050588cad3e99ad46e1866d05ff4a8ed0bb6 diff --git a/sci-chemistry/molrep/files/10.2.35-respect-FLAGS.patch b/sci-chemistry/molrep/files/10.2.35-respect-FLAGS.patch deleted file mode 100644 index d81ec793b510..000000000000 --- a/sci-chemistry/molrep/files/10.2.35-respect-FLAGS.patch +++ /dev/null @@ -1,61 +0,0 @@ ---- src/makefile 2009-02-27 16:51:46.492890717 +0100 -+++ src/makefile.new 2009-02-27 16:52:18.295619642 +0100 -@@ -5,8 +5,8 @@ - - BIN = $(MOLREP)/bin - --OBJS = main_molrep_mtz.o molrep.o molrep1.o molrep2.o molrep3.o molrep_prog.o molrep_prog1.o molrep_prog2.o molrep_subr.o molrep_dummy.o molrep_sym.o molrep_unix.o --OBJSL = main_molrep_mtz.o molrep.o molrep1.o molrep2.o molrep3.o molrep_prog.o molrep_prog1.o molrep_prog2.o molrep_subr.o molrep_sym.o molrep_unix.o -+OBJS = main_molrep_mtz.o molrep.o molrep1.o molrep2.o molrep3.o molrep_prog.o molrep_prog1.o molrep_prog2.o molrep_subr.o molrep_dummy.o molrep_sym_ccp4.o molrep_unix_ccp4.o -+OBJSL = main_molrep_mtz.o molrep.o molrep1.o molrep2.o molrep3.o molrep_prog.o molrep_prog1.o molrep_prog2.o molrep_subr.o molrep_sym_ccp4.o molrep_unix_ccp4.o - - - all: molrep -@@ -19,31 +19,31 @@ - # ----------------------------- - - molrep.o: molrep.f -- $(MR_FORT) -c molrep.f -+ $(MR_FORT) $(FFLAGS) -c molrep.f - molrep1.o: molrep1.f -- $(MR_FORT) -c molrep1.f -+ $(MR_FORT) $(FFLAGS) -c molrep1.f - molrep2.o: molrep2.f -- $(MR_FORT) -c molrep2.f -+ $(MR_FORT) $(FFLAGS) -c molrep2.f - molrep3.o: molrep3.f -- $(MR_FORT) -c molrep3.f -+ $(MR_FORT) $(FFLAGS) -c molrep3.f - molrep_prog.o: molrep_prog.f -- $(MR_FORT) -c molrep_prog.f -+ $(MR_FORT) $(FFLAGS) -c molrep_prog.f - molrep_prog1.o: molrep_prog1.f -- $(MR_FORT) -c molrep_prog1.f -+ $(MR_FORT) $(FFLAGS) -c molrep_prog1.f - molrep_prog2.o: molrep_prog2.f -- $(MR_FORT) -c molrep_prog2.f -+ $(MR_FORT) $(FFLAGS) -c molrep_prog2.f - molrep_subr.o: molrep_subr.f -- $(MR_FORT) -c molrep_subr.f --molrep_sym.o: molrep_sym.f -- $(MR_FORT) -c molrep_sym.f -+ $(MR_FORT) $(FFLAGS) -c molrep_subr.f -+molrep_sym_ccp4.o: molrep_sym.f -+ $(MR_FORT) $(FFLAGS) -c molrep_sym_ccp4.f - main_molrep_mtz.o: main_molrep_mtz.f molrep_version.fh molrep_keywords.fh -- $(MR_FORT) -c main_molrep_mtz.f --molrep_unix.o: molrep_unix.f -- $(MR_FORT) -c molrep_unix.f -+ $(MR_FORT) $(FFLAGS) -c main_molrep_mtz.f -+molrep_unix_ccp4.o: molrep_unix.f -+ $(MR_FORT) $(FFLAGS) -c molrep_unix_ccp4.f - molrep_dummy.o: molrep_dummy.f -- $(MR_FORT) -c molrep_dummy.f -+ $(MR_FORT) $(FFLAGS) -c molrep_dummy.f - - molrep: $(OBJS) -- $(MR_FORT) -o $(BIN)/molrep $(OBJSL) $(MR_LIBRARY) -+ $(MR_FORT) $(FFLAGS) $(LDFLAGS) -o $(BIN)/molrep $(OBJSL) $(MR_LIBRARY) - - # -------------------------------- - diff --git a/sci-chemistry/molrep/files/11.0.00-respect-FLAGS.patch b/sci-chemistry/molrep/files/11.0.00-respect-FLAGS.patch deleted file mode 100644 index c18b9a1e3f0d..000000000000 --- a/sci-chemistry/molrep/files/11.0.00-respect-FLAGS.patch +++ /dev/null @@ -1,12 +0,0 @@ -diff --git a/src/makefile b/src/makefile -index 30d0de7..10dd68f 100755 ---- a/src/makefile -+++ b/src/makefile -@@ -46,6 +46,6 @@ molrep_dummy.o: molrep_dummy.f - $(MR_FORT) -c molrep_dummy.f - - molrep: $(OBJS) -- $(MR_FORT) -o $(BIN)/molrep $(OBJSL) $(MR_LIBRARY) -+ $(MR_FORT) $(LDFLAGS) -o $(BIN)/molrep $(OBJSL) $(MR_LIBRARY) - - # -------------------------------- diff --git a/sci-chemistry/molrep/files/11.0.00-test.patch b/sci-chemistry/molrep/files/11.0.00-test.patch deleted file mode 100644 index d90cfb8c7b35..000000000000 --- a/sci-chemistry/molrep/files/11.0.00-test.patch +++ /dev/null @@ -1,191 +0,0 @@ -diff --git a/molrep_check/em.bat b/molrep_check/em.bat -index 2f0f992..96ddd75 100755 ---- a/molrep_check/em.bat -+++ b/molrep_check/em.bat -@@ -8,6 +8,8 @@ $MR_TEST/molrep -m ../em/model.pdb -f ../em/pel.map -po out/ -ps scr/ -i <<stop - # -------------------------------- - _NMON 6 - stop -+echo $? -+[[ $? ]] || exit 1 - # -------------------------------- - # - # 2. Atomic model --> EM map -@@ -20,6 +22,7 @@ $MR_TEST/molrep -m ../em/model.pdb -f ../em/pel.map -po out/ -ps scr/ -i <<stop - _NMON 6 - _prf y - stop -+[[ $? ]] || exit 1 - # -------------------------------- - # - # 3. Atomic model --> EM map -@@ -36,6 +39,7 @@ _ncs 322 - _centre 0.500 0.490 0.490 - _angles 0.0 0.0 90.0 - stop -+[[ $? ]] || exit 1 - # -------------------------------- - # - cp out/molrep.pdb hexamer.pdb -@@ -52,6 +56,7 @@ $MR_TEST/molrep -mx hexamer.pdb -f ../em/pel.map -po out/ -ps scr/ -i <<stop - # -------------------------------- - _DOM s - stop -+[[ $? ]] || exit 1 - # -------------------------------- - # - # 5. EM --> X-ray -@@ -60,6 +65,7 @@ stop - $MR_TEST/molrep -f ../em/p2.cif -m ../em/pel.map -po out/ -ps scr/ -i <<stop - # -------------------------------- - stop -+[[ $? ]] || exit 1 - # -------------------------------- - # - # 6. Placing the model to a particular orientation and position. -@@ -72,4 +78,5 @@ $MR_TEST/molrep -f ../em/p2.cif -m ../em/pel.map -po out/ -ps scr/ -i <<stop - _fun s - _file_t ../em/tab - stop -+[[ $? ]] || exit 1 - #========================================== -diff --git a/molrep_check/mr.bat b/molrep_check/mr.bat -index 284a4cd..6e00695 100755 ---- a/molrep_check/mr.bat -+++ b/molrep_check/mr.bat -@@ -10,6 +10,7 @@ - $MR_TEST/molrep -f ../data/test.mtz -m ../data/test_mod.pdb -po out/ -ps scr/ -i <<stop - # -------------------------------- - stop -+[[ $? ]] || exit 1 - # - # ================================================================= - # -@@ -26,6 +27,7 @@ _nmon 2 - _COMPL .5 - _SIM .7 - stop -+[[ $? ]] || exit 1 - # - # ================================================================= - # -@@ -46,6 +48,7 @@ $MR_TEST/molrep -f ../data/test.cif -m ../data/test_mod.pdb -mx ../data/test_mod - # -------------------------------- - _NP 3 - stop -+[[ $? ]] || exit 1 - # - # ================================================================= - # -@@ -67,6 +70,7 @@ $MR_TEST/molrep -f ../data/test.cif -m ../data/test_mod.pdb -po out/ -ps scr/ -i - _NMON 2 - _NP 3 - stop -+[[ $? ]] || exit 1 - # - # ================================================================= - # -@@ -85,6 +89,7 @@ _NPT 3 - _NPTD 3 - _DYAD D - stop -+[[ $? ]] || exit 1 - # - # ================================================================= - # -@@ -103,6 +108,7 @@ _NP 3 - _NPT 10 - _NMR 3 - stop -+[[ $? ]] || exit 1 - # - # ================================================================= - # -@@ -118,6 +124,7 @@ _PRF Y - _compl 1. - _sim .2 - stop -+[[ $? ]] || exit 1 - # - # ================================================================= - # -@@ -136,6 +143,7 @@ _ph PH - _fom FOM - # - stop -+[[ $? ]] || exit 1 - # ================================================================= - # - # 9. use sequence -@@ -145,6 +153,7 @@ stop - $MR_TEST/molrep -f ../data/s100.mtz -m ../data/monomer.pdb -s ../data/s100.seq -po out/ -ps scr/ -i <<stop - # -------------------------------- - stop -+[[ $? ]] || exit 1 - # ================================================================= - # - # 10. Locked RF -@@ -157,6 +166,7 @@ _lock y - _file_tsrf ../data/srf.tab - _nsrf 1 - stop -+[[ $? ]] || exit 1 - # ================================================================= - # - # 11. Multi-monomer search using NCS, SELF = 'A' means to compute Self RF and -@@ -169,6 +179,7 @@ $MR_TEST/molrep -f ../data/s100.mtz -m ../data/monomer.pdb -m2 ../data/monomer.p - _self a - _nsrf 1 - stop -+[[ $? ]] || exit 1 - # ================================================================= - # - # 12. use pst -@@ -179,6 +190,7 @@ $MR_TEST/molrep -f ../data/pst.mtz -m ../data/model_pst.pdb -po out/ -ps scr/ -i - # -------------------------------- - # - stop -+[[ $? ]] || exit 1 - # ================================================================= - # - # 13. space group check -@@ -189,7 +201,8 @@ $MR_TEST/molrep -f ../data/test.mtz -m ../data/test_mod.pdb -po out/ -ps scr/ -i - # -------------------------------- - _sg all - # --stop -+s[[ $? ]] || exit 1 -+top - # ========================================================== - # - # 14. Example for finding HA position by MR solution. -@@ -206,6 +219,7 @@ _SIGFD SIGFD3 - # - _FUN d - stop -+[[ $? ]] || exit 1 - # ========================================================== - # - # 15. Example for HA search by multi-copy search -@@ -225,6 +239,7 @@ _diff h - _dyad y - _nmon 4 - stop -+[[ $? ]] || exit 1 - # ========================================================== - # - # 16. Example HA for search by translation function -@@ -242,6 +257,7 @@ _FUN t - _diff h - _nmon 4 - stop -+[[ $? ]] || exit 1 - # ========================================================== - # - # 17. Example for Self RF for Heavy Atom structure in derivative. -@@ -258,4 +274,5 @@ _SIGFD SIGFD3 - _FUN r - _diff h - stop -+[[ $? ]] || exit 1 - # ========================================================== diff --git a/sci-chemistry/molrep/files/11.0.03-EOR.patch b/sci-chemistry/molrep/files/11.0.03-EOR.patch deleted file mode 100644 index 430629e8dcc1..000000000000 --- a/sci-chemistry/molrep/files/11.0.03-EOR.patch +++ /dev/null @@ -1,16 +0,0 @@ - src/molrep.f | 2 +- - 1 files changed, 1 insertions(+), 1 deletions(-) - -diff --git a/src/molrep.f b/src/molrep.f -index eac0cfc..94f74c6 100755 ---- a/src/molrep.f -+++ b/src/molrep.f -@@ -1257,7 +1257,7 @@ C CHECK_DENS_FILE( 2 ) - LEN1 = 1 - IF(LEN.GT.60) LEN1 = LEN - 59 - WRITE(LINE,'(''Input MODEL_2(fixed)_file:'',A)') -- * NAME2(LEN11:LEN) -+ * NAME2(LEN1:LEN) - CALL MSGDOC(MDoc,LINE) - - ENDIF diff --git a/sci-chemistry/molrep/metadata.xml b/sci-chemistry/molrep/metadata.xml deleted file mode 100644 index ae9ec7c5f6a4..000000000000 --- a/sci-chemistry/molrep/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-chemistry</herd> - <maintainer> - <email>jlec@gentoo.org</email> - </maintainer> -</pkgmetadata> diff --git a/sci-chemistry/molrep/molrep-11.0.02.ebuild b/sci-chemistry/molrep/molrep-11.0.02.ebuild deleted file mode 100644 index 51ff6cb26524..000000000000 --- a/sci-chemistry/molrep/molrep-11.0.02.ebuild +++ /dev/null @@ -1,57 +0,0 @@ -# Copyright 1999-2013 Gentoo Foundation -# Distributed under the terms of the GNU General Public License v2 -# $Id$ - -EAPI=4 - -inherit eutils fortran-2 multilib toolchain-funcs - -DESCRIPTION="molecular replacement program" -HOMEPAGE="http://www.ysbl.york.ac.uk/~alexei/molrep.html" -SRC_URI="mirror://gentoo/${P}.tar.gz" - -LICENSE="ccp4" -SLOT="0" -KEYWORDS="amd64 ppc x86 ~amd64-linux ~x86-linux" -IUSE="" - -RDEPEND=" - >=sci-libs/ccp4-libs-6.1.3 - sci-libs/mmdb - virtual/lapack" -DEPEND="${RDEPEND} - virtual/pkgconfig" - -S="${WORKDIR}/${PN}" - -src_prepare() { - epatch \ - "${FILESDIR}"/11.0.00-respect-FLAGS.patch \ - "${FILESDIR}"/11.0.00-test.patch -} - -src_compile() { - cd "${S}"/src - emake clean - emake \ - MR_FORT="$(tc-getFC) ${FFLAGS}" \ - FFLAGS="${FFLAGS}" \ - LDFLAGS="${LDFLAGS}" \ - MR_LIBRARY="-L${EPREFIX}/usr/$(get_libdir) -lccp4f -lccp4c $($(tc-getPKG_CONFIG) --libs mmdb lapack) -lccif -lstdc++ -lm" -} - -src_test() { - export MR_TEST="${S}/bin/" - cd "${S}"/molrep_check/work - mkdir out scr - cp ../*.bat . - bash em.bat || die - bash mr.bat || die -} - -src_install() { - exeinto /usr/libexec/ccp4/bin/ - doexe bin/${PN} - dosym ../libexec/ccp4/bin/${PN} /usr/bin/${PN} - dodoc readme doc/${PN}.rtf -} diff --git a/sci-chemistry/molrep/molrep-11.0.03-r1.ebuild b/sci-chemistry/molrep/molrep-11.0.03-r1.ebuild deleted file mode 100644 index 3373bbba6f97..000000000000 --- a/sci-chemistry/molrep/molrep-11.0.03-r1.ebuild +++ /dev/null @@ -1,59 +0,0 @@ -# Copyright 1999-2013 Gentoo Foundation -# Distributed under the terms of the GNU General Public License v2 -# $Id$ - -EAPI=4 - -inherit eutils flag-o-matic fortran-2 multilib toolchain-funcs - -DESCRIPTION="molecular replacement program" -HOMEPAGE="http://www.ysbl.york.ac.uk/~alexei/molrep.html" -SRC_URI="https://dev.gentoo.org/~jlec/distfiles/${P}.tar.gz" - -LICENSE="ccp4" -SLOT="0" -KEYWORDS="~amd64 ~ppc ~x86 ~amd64-linux ~x86-linux" -IUSE="" - -RDEPEND=" - >=sci-libs/ccp4-libs-6.1.3 - sci-libs/mmdb - virtual/lapack" -DEPEND="${RDEPEND} - virtual/pkgconfig" - -S="${WORKDIR}/${PN}" - -src_prepare() { - epatch \ - "${FILESDIR}"/11.0.00-respect-FLAGS.patch \ - "${FILESDIR}"/11.0.00-test.patch \ - "${FILESDIR}"/${PV}-EOR.patch - [[ $(tc-getFC) =~ gfortran ]] && append-fflags -fno-second-underscore -} - -src_compile() { - cd "${S}"/src - emake clean - emake \ - MR_FORT="$(tc-getFC) ${FFLAGS}" \ - FFLAGS="${FFLAGS}" \ - LDFLAGS="${LDFLAGS}" \ - MR_LIBRARY="-L${EPREFIX}/usr/$(get_libdir) -lccp4f -lccp4c $($(tc-getPKG_CONFIG) --libs mmdb lapack) -lccif -lstdc++ -lm" -} - -src_test() { - export MR_TEST="${S}/bin/" - cd "${S}"/molrep_check/work - mkdir out scr - cp ../*.bat . - bash em.bat || die - bash mr.bat || die -} - -src_install() { - exeinto /usr/libexec/ccp4/bin/ - doexe bin/${PN} - dosym ../libexec/ccp4/bin/${PN} /usr/bin/${PN} - dodoc readme doc/${PN}.rtf -} diff --git a/sci-chemistry/mosflm/Manifest b/sci-chemistry/mosflm/Manifest deleted file mode 100644 index 80df134c833e..000000000000 --- a/sci-chemistry/mosflm/Manifest +++ /dev/null @@ -1 +0,0 @@ -DIST mosflm709.tgz 3324010 SHA256 d22b05211f274b50c284d4c14fcb456c52b13344e2a48d5f45855fe87f82f6d1 SHA512 aa85f8459f280e0e1d2d54041029ef072346ecef3ffcc7724eb524469e1b77dfbd95aac8b46f2b9682d605a4e5931d9c13f1162d5f3bcff08644db7e79a6316c WHIRLPOOL b3a82858a8d2a3162bc0fcfb3bf7fb7b01cfc6bca80b34643e7c6caae54b1ef1e2b24a58617ffe2b0423ca6626d51e31b49c0dba6a82ed5c61fa10d044e0d3b8 diff --git a/sci-chemistry/mosflm/files/7.0.6-Makefile.patch b/sci-chemistry/mosflm/files/7.0.6-Makefile.patch deleted file mode 100644 index a35232f6e8c0..000000000000 --- a/sci-chemistry/mosflm/files/7.0.6-Makefile.patch +++ /dev/null @@ -1,13 +0,0 @@ ---- Makefile 2008-10-17 16:15:30.000000000 +0200 -+++ Makefile.new 2009-02-20 21:52:34.000000000 +0100 -@@ -22,7 +22,7 @@ - CBFLIBS = cbf/lib/libcbf.a - JPGLIBS = jpg/libjpeg.a - --all: $(DPSLIBS) $(CBFLIBS) $(JPGLIBS) -- cd mosflm ; make -+all: dpslibs cbflibs -+ +make -C mosflm - - ########################################################################## - diff --git a/sci-chemistry/mosflm/files/7.0.6-impl-dec.patch b/sci-chemistry/mosflm/files/7.0.6-impl-dec.patch deleted file mode 100644 index da393eb93fe6..000000000000 --- a/sci-chemistry/mosflm/files/7.0.6-impl-dec.patch +++ /dev/null @@ -1,36 +0,0 @@ -diff --git a/mosflm/bravais_fortran.c b/mosflm/bravais_fortran.c -index 3d68cad..800bd0e 100644 ---- a/mosflm/bravais_fortran.c -+++ b/mosflm/bravais_fortran.c -@@ -2,6 +2,7 @@ - #include <stdlib.h> - #include <math.h> - #include "../util/util.h" -+#include "../util/bravais.h" - - /* bravais_fortran_(): This routine converts array from FORTRAN program - to structure for call to bravais -diff --git a/mosflm/chelp.c b/mosflm/chelp.c -index b2aaefc..fa44ab0 100644 ---- a/mosflm/chelp.c -+++ b/mosflm/chelp.c -@@ -5,6 +5,7 @@ - /* modified for Linux by Joachim Meyer jmeyer@embl-heidelberg.de 1998.05.19 */ - - #include "chelp.h" -+#include <stdio.h> - - #if CALL_LIKE_HPUX - void chelp () -diff --git a/mosflm/pck.c b/mosflm/pck.c -index ec094fc..288671d 100644 ---- a/mosflm/pck.c -+++ b/mosflm/pck.c -@@ -17,6 +17,7 @@ - #include <math.h> - #include <ctype.h> - #include <string.h> -+#include <unistd.h> - - #define BYTE char - #define WORD short int diff --git a/sci-chemistry/mosflm/files/7.0.6-parallel.patch b/sci-chemistry/mosflm/files/7.0.6-parallel.patch deleted file mode 100644 index f735c7ce5cf7..000000000000 --- a/sci-chemistry/mosflm/files/7.0.6-parallel.patch +++ /dev/null @@ -1,28 +0,0 @@ ---- cbf/Makefile 2009-08-31 09:35:06.000000000 +0200 -+++ cbf/Makefile.new 2009-08-31 10:44:46.000000000 +0200 -@@ -362,6 +362,8 @@ - $(EXAMPLES)/img.h \ - $(INCLUDE)/md5.h - -+OBJ = $(subst .c,.o,$(SOURCE)) -+ - # - # Compile the library and examples - # -@@ -379,11 +381,14 @@ - $(LIB): - mkdir $(LIB) - -+ -+.c.o: $(SOURCE) $(HEADERS) -+ $(CC) $(CFLAGS) $(INCLUDES) $(WARNINGS) -c $< -+ - # - # CBF library - # --$(LIB)/libcbf.a: $(SOURCE) $(HEADERS) $(COMMONDEP) -- $(CC) $(CFLAGS) $(INCLUDES) $(WARNINGS) -c $(SOURCE) -+$(LIB)/libcbf.a: $(OBJ) $(COMMONDEP) - $(AR) cr $@ *.o - rm *.o - if [ -f $(RANLIB) ]; then $(RANLIB) $@ ; fi diff --git a/sci-chemistry/mosflm/files/7.0.7-parallel.patch b/sci-chemistry/mosflm/files/7.0.7-parallel.patch deleted file mode 100644 index df0a8b63273a..000000000000 --- a/sci-chemistry/mosflm/files/7.0.7-parallel.patch +++ /dev/null @@ -1,92 +0,0 @@ - Makefile | 21 ++++++++++----------- - cbf/Makefile | 9 +++++++-- - 2 files changed, 17 insertions(+), 13 deletions(-) - -diff --git a/Makefile b/Makefile -index 37f4c7e..51d4164 100644 ---- a/Makefile -+++ b/Makefile -@@ -22,8 +22,8 @@ DPSLIBS = lib/DPSLIB.a - CBFLIBS = cbf/lib/libcbf.a - JPGLIBS = jpg/libjpeg.a - --all: $(DPSLIBS) $(CBFLIBS) $(JPGLIBS) -- cd mosflm ; make -+all: $(DPSLIBS) -+ $(MAKE) -C mosflm - - ########################################################################## - # # -@@ -47,22 +47,21 @@ dpslibs: - - cbflibs: - rm -f `find ./cbf -name "*.a" -print` -- cd cbf ; make all ; if [ -f $(RANLIB) ]; \ -- then $(RANLIB) lib/libcbf.a; fi -+ $(MAKE) -C cbf all - - jpglibs: -- cd jpg ; if [ ! -f Makefile ]; then ./configure ; fi; make libjpeg.a -+ cd jpg ; if [ ! -f Makefile ]; then ./configure ; fi; $(MAKE) libjpeg.a - - ${DPSLIBS}: -- make dpslibs -+ $(MAKE) dpslibs - - ${CBFLIBS}: -- make cbflibs -+ $(MAKE) cbflibs - - ${JPGLIBS}: -- make jpglibs -+ $(MAKE) jpglibs - --libs: ${DPSLIBS} ${CBFLIBS} ${JPGLIBS} -+libs: ${DPSLIBS} ${CBFLIBS} - @echo "****************************************************************" - @echo " Making libraries for system ${HOSTTYPE}" - @echo "****************************************************************" -@@ -71,11 +70,11 @@ ipmosflm: libs - @echo "****************************************************************" - @echo " Making IPMOSFLM for system ${HOSTTYPE}" - @echo "****************************************************************" -- cd mosflm ; make ipmosflm -+ $(MAKE) -C mosflm ipmosflm - - force: - rm bin/ipmosflm -- make ipmosflm -+ $(MAKE) ipmosflm - - install: - @echo "the executable is in ${MOSHOME}/bin/ipmosflm" -diff --git a/cbf/Makefile b/cbf/Makefile -index e61497c..c3c94ac 100644 ---- a/cbf/Makefile -+++ b/cbf/Makefile -@@ -362,6 +362,8 @@ HEADERS = $(INCLUDE)/cbf.h \ - $(EXAMPLES)/img.h \ - $(INCLUDE)/md5.h - -+OBJ = $(subst .c,.o,$(SOURCE)) -+ - # - # Compile the library and examples - # -@@ -379,11 +381,14 @@ $(INSTALLDIR): - $(LIB): - mkdir $(LIB) - -+ -+.c.o: $(SOURCE) $(HEADERS) -+ $(CC) $(CFLAGS) $(INCLUDES) $(WARNINGS) -c $< -+ - # - # CBF library - # --$(LIB)/libcbf.a: $(SOURCE) $(HEADERS) $(COMMONDEP) -- $(CC) $(CFLAGS) $(INCLUDES) $(WARNINGS) -c $(SOURCE) -+$(LIB)/libcbf.a: $(OBJ) $(COMMONDEP) - $(AR) cr $@ *.o - rm *.o - if [ -f $(RANLIB) ]; then $(RANLIB) $@ ; fi diff --git a/sci-chemistry/mosflm/files/7.0.9-parallel.patch b/sci-chemistry/mosflm/files/7.0.9-parallel.patch deleted file mode 100644 index 38c6fc45a5c0..000000000000 --- a/sci-chemistry/mosflm/files/7.0.9-parallel.patch +++ /dev/null @@ -1,92 +0,0 @@ - Makefile | 21 ++++++++++----------- - cbf/Makefile | 9 +++++++-- - 2 files changed, 17 insertions(+), 13 deletions(-) - -diff --git a/Makefile b/Makefile -index 3d2f543..2219d8d 100644 ---- a/Makefile -+++ b/Makefile -@@ -22,8 +22,8 @@ DPSLIBS = lib/DPSLIB.a - CBFLIBS = cbf/lib/libcbf.a - JPGLIBS = jpg/libjpeg.a - --all: $(DPSLIBS) $(CBFLIBS) $(JPGLIBS) -- cd mosflm ; make -+all: $(DPSLIBS) -+ $(MAKE) -C mosflm - - dpslibs: - @-find . -name "*a" -delete -@@ -32,22 +32,21 @@ dpslibs: - - cbflibs: - @-find ./cbf -name "*.a" -delete -- cd cbf ; make all ; if [ -f $(RANLIB) ]; \ -- then $(RANLIB) lib/libcbf.a; fi -+ $(MAKE) -C cbf all - - jpglibs: -- cd jpg ; if [ ! -f Makefile ]; then ./configure ; fi; make libjpeg.a -+ cd jpg ; if [ ! -f Makefile ]; then ./configure ; fi; $(MAKE) libjpeg.a - - ${DPSLIBS}: -- make dpslibs -+ $(MAKE) dpslibs - - ${CBFLIBS}: -- make cbflibs -+ $(MAKE) cbflibs - - ${JPGLIBS}: -- make jpglibs -+ $(MAKE) jpglibs - --libs: ${DPSLIBS} ${CBFLIBS} ${JPGLIBS} -+libs: ${DPSLIBS} ${CBFLIBS} - @echo "****************************************************************" - @echo " Making libraries for system ${HOSTTYPE}" - @echo "****************************************************************" -@@ -56,11 +55,11 @@ ipmosflm: libs - @echo "****************************************************************" - @echo " Making IPMOSFLM for system ${HOSTTYPE}" - @echo "****************************************************************" -- cd mosflm ; make ipmosflm -+ $(MAKE) -C mosflm ipmosflm - - force: - @-rm -f bin/ipmosflm -- make ipmosflm -+ $(MAKE) ipmosflm - - install: - @echo "the executable is in ${MOSHOME}/bin/ipmosflm" -diff --git a/cbf/Makefile b/cbf/Makefile -index e61497c..c3c94ac 100644 ---- a/cbf/Makefile -+++ b/cbf/Makefile -@@ -362,6 +362,8 @@ HEADERS = $(INCLUDE)/cbf.h \ - $(EXAMPLES)/img.h \ - $(INCLUDE)/md5.h - -+OBJ = $(subst .c,.o,$(SOURCE)) -+ - # - # Compile the library and examples - # -@@ -379,11 +381,14 @@ $(INSTALLDIR): - $(LIB): - mkdir $(LIB) - -+ -+.c.o: $(SOURCE) $(HEADERS) -+ $(CC) $(CFLAGS) $(INCLUDES) $(WARNINGS) -c $< -+ - # - # CBF library - # --$(LIB)/libcbf.a: $(SOURCE) $(HEADERS) $(COMMONDEP) -- $(CC) $(CFLAGS) $(INCLUDES) $(WARNINGS) -c $(SOURCE) -+$(LIB)/libcbf.a: $(OBJ) $(COMMONDEP) - $(AR) cr $@ *.o - rm *.o - if [ -f $(RANLIB) ]; then $(RANLIB) $@ ; fi diff --git a/sci-chemistry/mosflm/files/mosflm-7.0.7-buffer-overflow.patch b/sci-chemistry/mosflm/files/mosflm-7.0.7-buffer-overflow.patch deleted file mode 100644 index 90158eb458d5..000000000000 --- a/sci-chemistry/mosflm/files/mosflm-7.0.7-buffer-overflow.patch +++ /dev/null @@ -1,16 +0,0 @@ - mosflm/pilatus_c.c | 2 +- - 1 files changed, 1 insertions(+), 1 deletions(-) - -diff --git a/mosflm/pilatus_c.c b/mosflm/pilatus_c.c -index 1eaae26..cce5a02 100644 ---- a/mosflm/pilatus_c.c -+++ b/mosflm/pilatus_c.c -@@ -34,7 +34,7 @@ delete them later */ - int cbf_int[16]; - long cbf_int4[16]; - double cbf_double[16]; -- char cbf_char[16][24]; -+ char cbf_char[16][32]; - /* temporary from cbfwrap.c - pilatus doesn't have these, so we'll - delete them later */ - int id, index, iindex; diff --git a/sci-chemistry/mosflm/files/mosflm-7.0.7-impl-dec.patch b/sci-chemistry/mosflm/files/mosflm-7.0.7-impl-dec.patch deleted file mode 100644 index 32f251f8e00c..000000000000 --- a/sci-chemistry/mosflm/files/mosflm-7.0.7-impl-dec.patch +++ /dev/null @@ -1,29 +0,0 @@ - mosflm/mosflm_jpeg.c | 1 + - src/dps/index/ind_gen_direct.c | 2 ++ - 2 files changed, 3 insertions(+), 0 deletions(-) - -diff --git a/mosflm/mosflm_jpeg.c b/mosflm/mosflm_jpeg.c -index 2b32b2e..54684d0 100644 ---- a/mosflm/mosflm_jpeg.c -+++ b/mosflm/mosflm_jpeg.c -@@ -76,6 +76,7 @@ G. Winter - #include <fcntl.h> - #include <stdio.h> - #include <stdlib.h> -+#include <string.h> - #if (defined _MSC_VER) - /* no need to do this for __MINGW_ (Mingw gcc) this is just about unique!*/ - #define S_IRWXU S_IREAD|S_IWRITE|S_IEXEC -diff --git a/src/dps/index/ind_gen_direct.c b/src/dps/index/ind_gen_direct.c -index 6e143df..2eea61b 100644 ---- a/src/dps/index/ind_gen_direct.c -+++ b/src/dps/index/ind_gen_direct.c -@@ -41,6 +41,8 @@ - /* #include <malloc.h> */ - #include "util.h" - #include "ind_gen_direct.h" -+#include "ind_help.h" -+#include "ind_sort_merge.h" - /* char *strcat( char *, const char *); */ - - diff --git a/sci-chemistry/mosflm/files/mosflm-7.0.9-buffer-overflow.patch b/sci-chemistry/mosflm/files/mosflm-7.0.9-buffer-overflow.patch deleted file mode 100644 index bb4a16bf30fc..000000000000 --- a/sci-chemistry/mosflm/files/mosflm-7.0.9-buffer-overflow.patch +++ /dev/null @@ -1,16 +0,0 @@ - mosflm/pilatus_c.c | 2 +- - 1 files changed, 1 insertions(+), 1 deletions(-) - -diff --git a/mosflm/pilatus_c.c b/mosflm/pilatus_c.c -index 4a85b26..9893e0c 100644 ---- a/mosflm/pilatus_c.c -+++ b/mosflm/pilatus_c.c -@@ -34,7 +34,7 @@ delete them later */ - int cbf_int[16] = {0}; - long cbf_int4[16] = {0}; - double cbf_double[16] = {0}; -- char cbf_char[16][24] = {' '}; -+ char cbf_char[16][32] = {' '}; - /* temporary from cbfwrap.c - pilatus doesn't have these, so we'll - delete them later */ - int id, index, iindex; diff --git a/sci-chemistry/mosflm/metadata.xml b/sci-chemistry/mosflm/metadata.xml deleted file mode 100644 index ae9ec7c5f6a4..000000000000 --- a/sci-chemistry/mosflm/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-chemistry</herd> - <maintainer> - <email>jlec@gentoo.org</email> - </maintainer> -</pkgmetadata> diff --git a/sci-chemistry/mosflm/mosflm-7.0.9.ebuild b/sci-chemistry/mosflm/mosflm-7.0.9.ebuild deleted file mode 100644 index 3aa74ced3d94..000000000000 --- a/sci-chemistry/mosflm/mosflm-7.0.9.ebuild +++ /dev/null @@ -1,74 +0,0 @@ -# Copyright 1999-2015 Gentoo Foundation -# Distributed under the terms of the GNU General Public License v2 -# $Id$ - -EAPI=5 - -inherit eutils fortran-2 toolchain-funcs versionator - -MY_PV="$(delete_all_version_separators)" -MY_P="${PN}${MY_PV}" - -DESCRIPTION="A program for integrating single crystal diffraction data from area detectors" -HOMEPAGE="http://www.mrc-lmb.cam.ac.uk/harry/mosflm/" -SRC_URI="${HOMEPAGE}ver${MY_PV}/build-it-yourself/${MY_P}.tgz" - -SLOT="0" -LICENSE="ccp4" -KEYWORDS="amd64 ppc x86 ~amd64-linux ~x86-linux" -IUSE="" - -RDEPEND=" - app-shells/tcsh - sci-libs/cbflib - sci-libs/ccp4-libs - sys-libs/ncurses - virtual/jpeg:0= - x11-libs/libxdl_view" -DEPEND="${RDEPEND}" - -S="${WORKDIR}/${MY_P}" - -src_prepare() { - sed \ - -e "s:../cbf/lib/libcbf.a:-lcbf -limg:g" \ - -e "s:../jpg/libjpeg.a:-ljpeg:g" \ - -i ${PN}/Makefile || die - - sed \ - -e '/jinclude.h/d' \ - -i mosflm/mosflm_jpeg.c || die - - cp DATETIME.C mosflm/datetime.c || die - - epatch \ - "${FILESDIR}"/${PV}-parallel.patch \ - "${FILESDIR}"/7.0.6-impl-dec.patch \ - "${FILESDIR}"/${P}-buffer-overflow.patch \ - "${FILESDIR}"/${PN}-7.0.7-impl-dec.patch - - rm -rf test.f {cbf,jpg}/*.{h,c} || die -} - -src_compile() { - emake \ - MOSHOME="${S}" \ - DPS="${S}" \ - FC=$(tc-getFC) \ - FLINK=$(tc-getFC) \ - CC=$(tc-getCC) \ - AR_FLAGS=vru \ - MOSLIBS="-lccp4f -lccp4c -lxdl_view $($(tc-getPKG_CONFIG) --libs ncurses) -lXt -lmmdb -lccif -lstdc++" \ - MCFLAGS="-O0 -fno-second-underscore" \ - MOSFLAGS="${FFLAGS} -fno-second-underscore" \ - FFLAGS="${FFLAGS} -fno-second-underscore" \ - CFLAGS="${CFLAGS}" \ - MOSCFLAGS="${CFLAGS}" \ - LFLAGS="${LDFLAGS}" -} - -src_install() { - exeinto /usr/libexec/ccp4/bin/ - doexe bin/ipmosflm - dosym ../libexec/ccp4/bin/ip${PN} /usr/bin/ip${PN} -} diff --git a/sci-chemistry/mrbump/Manifest b/sci-chemistry/mrbump/Manifest deleted file mode 100644 index f9887a6071b2..000000000000 --- a/sci-chemistry/mrbump/Manifest +++ /dev/null @@ -1 +0,0 @@ -DIST mrbump-0.4.4.tar.gz 9220116 SHA256 499634815cf316ca273900252dab16b91f6421b0f85a548108258f9934dccd6a SHA512 3a39159d78c4310f5a04efc7bb10ed81f6f260baa65db3615d5065c94175e33de3dbe2073de057a699efe541d59674cc927699229a4af5e8102600caea4c03d3 WHIRLPOOL adb8c583b81cce8ec7e29f203b0a33de41f42c0fae77317671593f661db8c06c56106ed4fcfdeb503c9594c8802dc1dd1a0c7da290b7d3046e8f3d8d6911f60d diff --git a/sci-chemistry/mrbump/files/0.4.4-superpose.patch b/sci-chemistry/mrbump/files/0.4.4-superpose.patch deleted file mode 100644 index c9941e9ece2a..000000000000 --- a/sci-chemistry/mrbump/files/0.4.4-superpose.patch +++ /dev/null @@ -1,11 +0,0 @@ ---- share/mrbump/include/mr/Ensemble.py 2008-07-28 16:40:47.000000000 +0200 -+++ share/mrbump/include/mr/Ensemble.py.new 2009-08-26 22:26:44.000000000 +0200 -@@ -29,7 +29,7 @@ - self.superposeEXE=os.path.join(os.environ['CBIN'], 'superpose.exe') - self.pdbsetEXE=os.path.join(os.environ['CBIN'], 'pdbset.exe') - else: -- self.superposeEXE=os.path.join(os.environ['CBIN'], 'superpose') -+ self.superposeEXE=os.path.join(os.environ['CBIN'], 'superpose-ccp4') - self.pdbsetEXE=os.path.join(os.environ['CBIN'], 'pdbset') - - self.SPxyz_template='' diff --git a/sci-chemistry/mrbump/metadata.xml b/sci-chemistry/mrbump/metadata.xml deleted file mode 100644 index 4aaae064be71..000000000000 --- a/sci-chemistry/mrbump/metadata.xml +++ /dev/null @@ -1,10 +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@gentoo.org</email> - <name>Justin Lecher (jlec)</name> - </maintainer> -</pkgmetadata> - diff --git a/sci-chemistry/mrbump/mrbump-0.4.4.ebuild b/sci-chemistry/mrbump/mrbump-0.4.4.ebuild deleted file mode 100644 index 66ec9309e1cd..000000000000 --- a/sci-chemistry/mrbump/mrbump-0.4.4.ebuild +++ /dev/null @@ -1,57 +0,0 @@ -# Copyright 1999-2012 Gentoo Foundation -# Distributed under the terms of the GNU General Public License v2 -# $Id$ - -EAPI="3" - -PYTHON_DEPEND="2" - -inherit eutils multilib python - -DESCRIPTION="An automated scheme for Molecular Replacement" -HOMEPAGE="http://www.ccp4.ac.uk/MrBUMP" -SRC_URI="${HOMEPAGE}/release/${P}.tar.gz" - -LICENSE="ccp4" -SLOT="0" -KEYWORDS="amd64 ~ppc x86 ~amd64-linux ~x86-linux" -IUSE="X perl" - -RDEPEND=">=sci-chemistry/ccp4-apps-6.1.3[X?] - || ( sci-biology/mafft - sci-biology/clustalw:2 - sci-biology/probcons - sci-biology/t-coffee ) - sci-biology/fasta - X? ( media-gfx/graphviz ) - perl? ( dev-perl/SOAP-Lite )" -DEPEND="${RDEPEND}" - -pkg_setup() { - python_set_active_version 2 -} - -src_unpack(){ - unpack ${A} - cd "${S}" - unpack ./"${PN}".tar.gz -} - -src_prepare() { - epatch "${FILESDIR}"/${PV}-superpose.patch - python_convert_shebangs 2 setup_lib/* -} - -src_install(){ - insinto /usr/$(get_libdir)/ccp4/ccp4i - doins -r ccp4i/{MrBUMP-ccp4i.tar.gz,MrBUMP/{help,scripts,tasks,templates}} || \ - die "failed to install interface" - - insinto /usr/share/${PN} - doins -r share/${PN}/{data,include} || die "failed to install mrbump data" - - dobin share/${PN}/bin/* || die "failed to install binaries" - - dodoc README.txt || die - dohtml html/mrbump_doc.html || die -} diff --git a/sci-chemistry/oasis/Manifest b/sci-chemistry/oasis/Manifest deleted file mode 100644 index e87a831c1fe3..000000000000 --- a/sci-chemistry/oasis/Manifest +++ /dev/null @@ -1 +0,0 @@ -DIST oasis4.0_Linux.zip 6714528 SHA256 56da70ce0c2750aaddf64ad2cd7852fc341d2022209484beb356b4e73dec61ba SHA512 b43b8315e8e3bc8531e11021605100f231635e2363256a19ed0f51015913221eb9e37b3891b9b1239bf83c9ada8f65a1bdc79ec5745201436f8c3b5019bd4bf7 WHIRLPOOL 24d337391997d036bd657ab22aecc77d36f7fa0af573d17433869a29640a8a10368c75ebee114071c577cc0cce34d838271147599d99e2c389088b8c6185f41b diff --git a/sci-chemistry/oasis/files/4.0-makefile.patch b/sci-chemistry/oasis/files/4.0-makefile.patch deleted file mode 100644 index f27a350a1fd2..000000000000 --- a/sci-chemistry/oasis/files/4.0-makefile.patch +++ /dev/null @@ -1,15 +0,0 @@ -diff --git a/src/Makefile b/src/Makefile -index 1e9128f..eb9edaf 100644 ---- a/src/Makefile -+++ b/src/Makefile -@@ -20,8 +20,8 @@ IRIX: - @ ${F77} -O2 -mips3 -nocpp -OPT:Olimit=1500 -w -rpath ${CCP4_LIB} -o oasis4-0 oasis4-0.f -L${CCP4_LIB}/src -lccp4f -lccp4c -lmmdb -lC -lm -L/usr/lib32 -lblas - @ ${F77} -O2 -mips3 -nocpp -OPT:Olimit=1500 -w -rpath ${CCP4_LIB} -o fnp2fp fnp2fp.f -L${CCP4_LIB}/src -lccp4f -lccp4c -lmmdb -lC -lm -L/usr/lib32 -lblas - Linux: -- @ ${F77} -O -w -fno-second-underscore -fno-globals -fno-automatic -o oasis4-0 oasis4-0.f -L${CCP4_LIB} -lccp4f -lccp4c -lmmdb -lstdc++ -lg2c -lm -L${CCP4_LIB} -- @ ${F77} -O -w -fno-second-underscore -fno-globals -fno-automatic -o fnp2fp fnp2fp.f -L${CCP4_LIB} -lccp4f -lccp4c -lmmdb -lstdc++ -lg2c -lm -L${CCP4_LIB} -+ ${F77} $(CFLAGS) $(LDFLAGS) -o oasis oasis4-0.f -L${CCP4_LIB} -lccp4f -lccp4c -lmmdb -lstdc++ -lm -L${CCP4_LIB} -+ ${F77} $(CFLAGS) $(LDFLAGS) -o fnp2fp fnp2fp.f -L${CCP4_LIB} -lccp4f -lccp4c -lmmdb -lstdc++ -lm -L${CCP4_LIB} - Darwin: - @ ${F77} -O2 -fno-second-underscore -o fnp2fp fnp2fp.f -L${CCP4_LIB} -lccp4f -lccp4c -lmmdb -lstdc++ -lgcc_s.10.5 -lSystem -lm - @ ${F77} -O2 -fno-second-underscore -o oasis4-0 oasis4-0.f -L${CCP4_LIB} -lccp4f -lccp4c -lmmdb -lstdc++ -lgcc_s.10.5 -lSystem -lm diff --git a/sci-chemistry/oasis/metadata.xml b/sci-chemistry/oasis/metadata.xml deleted file mode 100644 index 8412c2f3d312..000000000000 --- a/sci-chemistry/oasis/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-chemistry</herd> - <use> - <flag name="minimal">Restricts functionality on free software</flag> - </use> -</pkgmetadata> diff --git a/sci-chemistry/oasis/oasis-4.0-r3.ebuild b/sci-chemistry/oasis/oasis-4.0-r3.ebuild deleted file mode 100644 index 98c8aaef47b4..000000000000 --- a/sci-chemistry/oasis/oasis-4.0-r3.ebuild +++ /dev/null @@ -1,70 +0,0 @@ -# Copyright 1999-2015 Gentoo Foundation -# Distributed under the terms of the GNU General Public License v2 -# $Id$ - -EAPI=5 - -inherit eutils fortran-2 multilib toolchain-funcs - -MY_P="${PN}${PV}_Linux" - -DESCRIPTION="A direct-method program for SAD/SIR phasing" -HOMEPAGE="http://cryst.iphy.ac.cn/Project/protein/protein-I.html" -SRC_URI="https://dev.gentoo.org/~jlec/distfiles/${MY_P}.zip" - -SLOT="0" -KEYWORDS="amd64 ~ppc x86 ~amd64-linux ~x86-linux" -LICENSE="ccp4 oasis" -IUSE="examples +minimal" - -RDEPEND=" - sci-chemistry/ccp4-apps - sci-chemistry/pymol - sci-libs/mmdb:0 - sci-visualization/gnuplot - !minimal? ( - sci-chemistry/solve-resolve-bin - sci-chemistry/arp-warp-bin - )" -DEPEND="${RDEPEND} - sci-libs/ccp4-libs" - -S="${WORKDIR}"/${MY_P} - -src_prepare() { - rm bin/{fnp2fp,gnuplot,oasis4-0,seq} || die - epatch "${FILESDIR}"/${PV}-makefile.patch -} - -src_compile() { - emake \ - -C src \ - F77="$(tc-getFC)" \ - CFLAGS="${FFLAGS}" \ - CCP4_LIB="${EPREFIX}/usr/$(get_libdir)" \ - Linux -} - -src_install() { - exeinto /usr/libexec/ccp4/bin/ - doexe src/{${PN},fnp2fp} - - exeinto /usr/$(get_libdir)/${PN} - doexe bin/*.*sh - - insinto /usr/share/doc/${PF}/html - doins bin/html/* - dosym ../../share/doc/${PF}/html /usr/$(get_libdir)/${PN}/html - chmod 755 "${ED}"/usr/share/doc/${PF}/html/*.{*sh,awk} || die - - if use examples; then - insinto /usr/share/${PN} - doins -r examples - fi - - cat >> "${T}"/25oasis <<- EOF - oasisbin="${EPREFIX}/usr/$(get_libdir)/${PN}" - EOF - - doenvd "${T}"/25oasis -} diff --git a/sci-chemistry/pdb-extract/Manifest b/sci-chemistry/pdb-extract/Manifest deleted file mode 100644 index 9036c79e3e7c..000000000000 --- a/sci-chemistry/pdb-extract/Manifest +++ /dev/null @@ -1,2 +0,0 @@ -DIST pdb-extract-v3.004-prod-src.tar.gz 942450 SHA256 58bef2aba4869cdd16a79ddc588da5596a2ccd1f5c925f300b63b6d8299bb953 SHA512 4505fd615324982e741a3656d8a36ffc2cd6524c825d254e0a1ff44b3464aaf63cbdbe4f614a6ace6c0e56af8f452634152edadd0ed5305f0148856affa8cb60 WHIRLPOOL b7077431d75a31a9ac4ea41f7cb76874aa49626a19c1290126405a8cdac4d210f56929f9213512ae4f542286be5cbedc972642b9ef07a4e461ac969c6c0d965f -DIST pdb-extract-v3.11-prod-src.tar.gz 1016140 SHA256 cc56ab58e4b4f0914dcd61834cae673ade5b12688861ea5f0197a33f5939d131 SHA512 06ef4110f873d23bcf878877a8b9f714b895a5b269f8d33312387c0bcb569adb2b1d1577eebc30200d5f0d3648959450912911609dab3749e7d5eb4c84d7e12f WHIRLPOOL ea0e643e1d64f344fdd643348b0ce35143e29f27a64b9153d6645c8dbf914e193f700217c0caecb30ea300ae10f47ea09bed61811c3bb293ef63d9e45acf74d3 diff --git a/sci-chemistry/pdb-extract/files/pdb-extract-3.004-Makefile.patch b/sci-chemistry/pdb-extract/files/pdb-extract-3.004-Makefile.patch deleted file mode 100644 index 3a6f5498ffba..000000000000 --- a/sci-chemistry/pdb-extract/files/pdb-extract-3.004-Makefile.patch +++ /dev/null @@ -1,46 +0,0 @@ ---- Makefile 2008-12-05 14:36:44.000000000 +0100 -+++ Makefile.new 2008-12-05 14:37:21.000000000 +0100 -@@ -19,13 +19,7 @@ - CHECKOUT_SCRIPT_MODULE = util - CHECKOUT_SCRIPT = checkout.sh - --LIBDIRS = cifobj-common-v4.1 \ -- tables-v8.0 \ -- regex-v2.2 \ -- cif-file-v1.0 \ -- misclib-v2.2 \ -- cifparse-obj-v7.0 \ -- $(EXTRACT) -+LIBDIRS = $(EXTRACT) - - all: compile - ---- pdb-extract-v3.0/Makefile 2008-12-05 14:42:58.000000000 +0100 -+++ pdb-extract-v3.0/Makefile.new 2008-12-05 14:42:15.510315392 +0100 -@@ -6,6 +6,7 @@ - - M_INCL_DIR = ../include - M_LIB_DIR = ../lib -+M_LIB_DIR_GENTOO = @GENTOO_PORTAGE_EPREFIX@/usr/GENTOOLIBDIR - M_BIN_DIR = ../bin - - PROJ_DIR = . -@@ -37,12 +38,12 @@ - include ../etc/Makefile.platform - - # Dependent libraries for the pdbml-parser --CIF_FILE_LIB = $(M_LIB_DIR)/cif-file.a --CIFPARSE_LIB = $(M_LIB_DIR)/cifparse-obj.a --CIF_TABLE_LIB = $(M_LIB_DIR)/cif-table-obj.a --CIFOBJ_COMMON_LIB = $(M_LIB_DIR)/cifobj-common.a --REGEX_LIB = $(M_LIB_DIR)/regex.a --MISCLIB_LIB = $(M_LIB_DIR)/misclib.a -+CIF_FILE_LIB = $(M_LIB_DIR_GENTOO)/cif-file.a -+CIFPARSE_LIB = $(M_LIB_DIR_GENTOO)/cifparse-obj.a -+CIF_TABLE_LIB = $(M_LIB_DIR_GENTOO)/tables.a -+CIFOBJ_COMMON_LIB = $(M_LIB_DIR_GENTOO)/common.a -+REGEX_LIB = $(M_LIB_DIR_GENTOO)/regex.a -+MISCLIB_LIB = $(M_LIB_DIR_GENTOO)/misclib.a - - ALL_DEP_LIBS = $(CIF_FILE_LIB) $(CIFPARSE_LIB) \ - $(CIF_TABLE_LIB) $(CIFOBJ_COMMON_LIB) $(REGEX_LIB) $(MISCLIB_LIB) diff --git a/sci-chemistry/pdb-extract/files/pdb-extract-3.004-cflags-install.patch b/sci-chemistry/pdb-extract/files/pdb-extract-3.004-cflags-install.patch deleted file mode 100644 index cdf48e4784c6..000000000000 --- a/sci-chemistry/pdb-extract/files/pdb-extract-3.004-cflags-install.patch +++ /dev/null @@ -1,199 +0,0 @@ -diff -Naur pdb-extract-v3.004-prod-src/Makefile pdb-extract-v3.004-prod-src.new/Makefile ---- pdb-extract-v3.004-prod-src/Makefile 2007-09-11 11:19:46.000000000 -0400 -+++ pdb-extract-v3.004-prod-src.new/Makefile 2009-12-03 21:34:10.000000000 -0500 -@@ -52,7 +52,7 @@ - echo "------------------------------------------------------------"; \ - echo "**** Making $$libdir ****"; \ - echo "------------------------------------------------------------"; \ -- (cd $$libdir && $(MAKE) -f $(MAKEFILE) "OPT=-O" install) || exit 1; \ -+ (cd $$libdir && $(MAKE) -f $(MAKEFILE) C_OPT="${CFLAGS}" CCC_OPT="${CXXFLAGS}" F_OPT="${FFLAGS}" LDFLAGS_OPT="${LDFLAGS}" install) || exit 1; \ - done - - beta: -diff -Naur pdb-extract-v3.004-prod-src/etc/make.platform.darwin3 pdb-extract-v3.004-prod-src.new/etc/make.platform.darwin3 ---- pdb-extract-v3.004-prod-src/etc/make.platform.darwin3 2007-09-11 11:19:46.000000000 -0400 -+++ pdb-extract-v3.004-prod-src.new/etc/make.platform.darwin3 2009-12-03 21:34:10.000000000 -0500 -@@ -91,7 +91,7 @@ - DEFINES=$(GDEFINES) $(LDEFINES) - - ## Global include directories --GINCLUDES= -+GINCLUDES=-I@GENTOO_PORTAGE_EPREFIX@/usr/include/cifparse-obj - - # Collect all include directories from global include directories and - # include directories specified in module makefile -@@ -159,7 +159,7 @@ - STATIC_LINKING= - - # Linker flags --LDFLAGS=$(ABI) -w $(STATIC_LINKING) -+LDFLAGS=$(LDFLAGS_OPT) $(ABI) -w $(STATIC_LINKING) - - # Fortran linker - F77_LINKER=f77 -diff -Naur pdb-extract-v3.004-prod-src/etc/make.platform.darwin4 pdb-extract-v3.004-prod-src.new/etc/make.platform.darwin4 ---- pdb-extract-v3.004-prod-src/etc/make.platform.darwin4 2007-09-11 11:19:46.000000000 -0400 -+++ pdb-extract-v3.004-prod-src.new/etc/make.platform.darwin4 2009-12-03 21:34:10.000000000 -0500 -@@ -92,7 +92,7 @@ - DEFINES=$(GDEFINES) $(LDEFINES) - - ## Global include directories --GINCLUDES= -+GINCLUDES=-I@GENTOO_PORTAGE_EPREFIX@/usr/include/cifparse-obj - - # Collect all include directories from global include directories and - # include directories specified in module makefile -@@ -160,7 +160,7 @@ - STATIC_LINKING= - - # Linker flags --LDFLAGS=$(ABI) -w $(STATIC_LINKING) -+LDFLAGS=$(LDFLAGS_OPT) $(ABI) -w $(STATIC_LINKING) - - # Fortran linker - F77_LINKER=f77 -diff -Naur pdb-extract-v3.004-prod-src/etc/make.platform.gnu3 pdb-extract-v3.004-prod-src.new/etc/make.platform.gnu3 ---- pdb-extract-v3.004-prod-src/etc/make.platform.gnu3 2007-09-11 11:19:46.000000000 -0400 -+++ pdb-extract-v3.004-prod-src.new/etc/make.platform.gnu3 2009-12-03 21:34:10.000000000 -0500 -@@ -6,6 +6,8 @@ - ## - ########################################################################## - -+LIBDIR=@GENTOO_PORTAGE_EPREFIX@/usr/GENTOOLIBDIR -+ - #-----Lexer and Parser section-------------------------------------------# - - # Lexer executable -@@ -89,7 +91,7 @@ - DEFINES=$(GDEFINES) $(LDEFINES) - - ## Global include directories --GINCLUDES= -+GINCLUDES=-I@GENTOO_PORTAGE_EPREFIX@/usr/include/cifparse-obj - - # Collect all include directories from global include directories and - # include directories specified in module makefile -@@ -107,8 +109,8 @@ - C_WARNINGS=$(WARNINGS) - - # C compiler flags --CFLAGS=$(OPT) $(ABI) $(ANSI_C_FLAG) $(C_WARNINGS) $(DEFINES) $(INCLUDES) --CFLAGS_NONANSI=$(OPT) $(ABI) $(NON_ANSI_C_FLAG) $(C_WARNINGS) $(DEFINES) \ -+CFLAGS=$(C_OPT) $(ABI) $(ANSI_C_FLAG) $(C_WARNINGS) $(DEFINES) $(INCLUDES) -+CFLAGS_NONANSI=$(C_OPT) $(ABI) $(NON_ANSI_C_FLAG) $(C_WARNINGS) $(DEFINES) \ - $(INCLUDES) - - ## C++ compiler -@@ -128,9 +130,9 @@ - EXT=C - - # C++ compiler flags --C++FLAGS=$(OPT) $(ABI) $(ANSI_C_PLUS_FLAG) $(C_PLUS_WARNINGS) $(DEFINES) \ -+C++FLAGS=$(CCC_OPT) $(ABI) $(ANSI_C_PLUS_FLAG) $(C_PLUS_WARNINGS) $(DEFINES) \ - $(INCLUDES) --C++FLAGS_NONANSI=$(OPT) $(ABI) $(NON_ANSI_C_PLUS_FLAG) $(C_PLUS_WARNINGS) \ -+C++FLAGS_NONANSI=$(CCC_OPT) $(ABI) $(NON_ANSI_C_PLUS_FLAG) $(C_PLUS_WARNINGS) \ - $(DEFINES) $(INCLUDES) - # C++FLAGS_RELAXED should be set to avoid warnings reported by third party - # source code that is not maintained by PDB -@@ -144,7 +146,7 @@ - F77=f77 - - # Fortran compiler flags --FFLAGS=-O -u -+FFLAGS=$(F_OPT) - - # Additional Fortran libraries - F77LIBS= -@@ -154,11 +156,11 @@ - #-----Linkers section----------------------------------------------------# - - # Static linking option. If not defined, dynamic linking is used. --STATIC_LINKING=-static -+STATIC_LINKING= - - # Linker flags --LDFLAGS=$(ABI) -w $(STATIC_LINKING) --LDFLAGS_NO_STATIC=$(ABI) -w -+LDFLAGS=$(LDFLAGS_OPT) $(ABI) -w $(STATIC_LINKING) -+LDFLAGS_NO_STATIC=$(LDFLAGS_OPT) $(ABI) -w - - # Fortran linker - F77_LINKER=f77 -diff -Naur pdb-extract-v3.004-prod-src/etc/make.platform.gnu4 pdb-extract-v3.004-prod-src.new/etc/make.platform.gnu4 ---- pdb-extract-v3.004-prod-src/etc/make.platform.gnu4 2007-09-11 11:19:46.000000000 -0400 -+++ pdb-extract-v3.004-prod-src.new/etc/make.platform.gnu4 2009-12-03 21:34:10.000000000 -0500 -@@ -6,6 +6,8 @@ - ## - ########################################################################## - -+LIBDIR=@GENTOO_PORTAGE_EPREFIX@/usr/GENTOOLIBDIR -+ - #-----Lexer and Parser section-------------------------------------------# - - # Lexer executable -@@ -34,7 +36,7 @@ - - # WARNINGS_AS_ERRORS defines flags to instruct all compilers to treat all - # warnings as errors. --WARNINGS_AS_ERRORS=-Werror -+WARNINGS_AS_ERRORS= - - # ALL_WARNINGS defines flags to instruct all compilers to report all - # warnings. -@@ -90,7 +92,7 @@ - DEFINES=$(GDEFINES) $(LDEFINES) - - ## Global include directories --GINCLUDES= -+GINCLUDES=-I@GENTOO_PORTAGE_EPREFIX@/usr/include/cifparse-obj - - # Collect all include directories from global include directories and - # include directories specified in module makefile -@@ -108,8 +110,8 @@ - C_WARNINGS=$(WARNINGS) - - # C compiler flags --CFLAGS=$(OPT) $(ABI) $(ANSI_C_FLAG) $(C_WARNINGS) $(DEFINES) $(INCLUDES) --CFLAGS_NONANSI=$(OPT) $(ABI) $(NON_ANSI_C_FLAG) $(C_WARNINGS) $(DEFINES) \ -+CFLAGS=$(C_OPT) $(ABI) $(ANSI_C_FLAG) $(C_WARNINGS) $(DEFINES) $(INCLUDES) -+CFLAGS_NONANSI=$(C_OPT) $(ABI) $(NON_ANSI_C_FLAG) $(C_WARNINGS) $(DEFINES) \ - $(INCLUDES) - - ## C++ compiler -@@ -129,9 +131,9 @@ - EXT=C - - # C++ compiler flags --C++FLAGS=$(OPT) $(ABI) $(ANSI_C_PLUS_FLAG) $(C_PLUS_WARNINGS) $(DEFINES) \ -+C++FLAGS=$(CCC_OPT) $(ABI) $(ANSI_C_PLUS_FLAG) $(C_PLUS_WARNINGS) $(DEFINES) \ - $(INCLUDES) --C++FLAGS_NONANSI=$(OPT) $(ABI) $(NON_ANSI_C_PLUS_FLAG) $(C_PLUS_WARNINGS) \ -+C++FLAGS_NONANSI=$(CCC_OPT) $(ABI) $(NON_ANSI_C_PLUS_FLAG) $(C_PLUS_WARNINGS) \ - $(DEFINES) $(INCLUDES) - # C++FLAGS_RELAXED should be set to avoid warnings reported by third party - # source code that is not maintained by PDB -@@ -145,7 +147,7 @@ - F77=f77 - - # Fortran compiler flags --FFLAGS=-O -u -+FFLAGS=$(F_OPT) - - # Additional Fortran libraries - F77LIBS= -@@ -155,11 +157,11 @@ - #-----Linkers section----------------------------------------------------# - - # Static linking option. If not defined, dynamic linking is used. --STATIC_LINKING=-static -+STATIC_LINKING= - - # Linker flags --LDFLAGS=$(ABI) -w $(STATIC_LINKING) --LDFLAGS_NO_STATIC=$(ABI) -w -+LDFLAGS=$(LDFLAGS_OPT) $(ABI) -w $(STATIC_LINKING) -+LDFLAGS_NO_STATIC=$(LDFLAGS_OPT) $(ABI) -w - - # Fortran linker - F77_LINKER=f77 diff --git a/sci-chemistry/pdb-extract/files/pdb-extract-3.004-env.patch b/sci-chemistry/pdb-extract/files/pdb-extract-3.004-env.patch deleted file mode 100644 index 6506713742b6..000000000000 --- a/sci-chemistry/pdb-extract/files/pdb-extract-3.004-env.patch +++ /dev/null @@ -1,11 +0,0 @@ ---- pdb-extract-v3.0/src/extract.C 2007-09-11 17:19:48.000000000 +0200 -+++ pdb-extract-v3.0/src/extract.C.new 2008-12-05 17:49:59.000000000 +0100 -@@ -1689,7 +1689,7 @@ - open_file_error(inpfile, "get_mmcif"); - } - -- (!strcmp_case(CCP4,"yes"))? temp = getenv("CCP4"): temp = getenv("PDB_EXTRACT"); -+ (!strcmp_case(CCP4,"yes"))? temp = getenv("CCP4"): temp = getenv("PDB_EXTRACT_ROOT"); - if(temp != NULL) { - strcpy(pdb_extract, ""); - strcpy(pdb_extract_sf, ""); diff --git a/sci-chemistry/pdb-extract/files/pdb-extract-3.004-gcc-4.3.patch b/sci-chemistry/pdb-extract/files/pdb-extract-3.004-gcc-4.3.patch deleted file mode 100644 index 6907399c27df..000000000000 --- a/sci-chemistry/pdb-extract/files/pdb-extract-3.004-gcc-4.3.patch +++ /dev/null @@ -1,20 +0,0 @@ ---- cifobj-common-v4.1/src/GenString.C 2008-11-13 10:44:01.000000000 +0100 -+++ cifobj-common-v4.1/src/GenString.C.new 2008-11-13 10:43:54.000000000 +0100 -@@ -144,6 +144,7 @@ - #include <string> - #include <algorithm> - #include <sstream> -+#include <string.h> - - #include "GenString.h" - ---- tables-v8.0/src/ISTable.C 2007-09-11 17:19:47.000000000 +0200 -+++ tables-v8.0/src/ISTable.C.new 2008-11-13 10:48:18.000000000 +0100 -@@ -150,6 +150,7 @@ - #include <sstream> - #include <iostream> - #include <iomanip> -+#include <limits.h> - - #include "Exceptions.h" - #include "GenString.h" diff --git a/sci-chemistry/pdb-extract/files/pdb-extract-3.11-cflags-install.patch b/sci-chemistry/pdb-extract/files/pdb-extract-3.11-cflags-install.patch deleted file mode 100644 index 7383811b5bfd..000000000000 --- a/sci-chemistry/pdb-extract/files/pdb-extract-3.11-cflags-install.patch +++ /dev/null @@ -1,207 +0,0 @@ - Makefile | 2 +- - etc/make.platform.darwin3 | 4 ++-- - etc/make.platform.darwin4 | 4 ++-- - etc/make.platform.gnu3 | 20 +++++++++++--------- - etc/make.platform.gnu4 | 20 +++++++++++--------- - 5 files changed, 27 insertions(+), 23 deletions(-) - -diff --git a/Makefile b/Makefile -index 627d256..72c7e59 100644 ---- a/Makefile -+++ b/Makefile -@@ -52,7 +52,7 @@ compile: - echo "------------------------------------------------------------"; \ - echo "**** Making $$libdir ****"; \ - echo "------------------------------------------------------------"; \ -- (cd $$libdir && $(MAKE) -f $(MAKEFILE) "OPT=-O" install) || exit 1; \ -+ (cd $$libdir && $(MAKE) -f $(MAKEFILE) C_OPT="${CFLAGS}" CCC_OPT="${CXXFLAGS}" F_OPT="${FFLAGS}" LDFLAGS_OPT="${LDFLAGS}" install) || exit 1; \ - done - - beta: -diff --git a/etc/make.platform.darwin3 b/etc/make.platform.darwin3 -index c5f7b06..4c1c97c 100644 ---- a/etc/make.platform.darwin3 -+++ b/etc/make.platform.darwin3 -@@ -91,7 +91,7 @@ GDEFINES=$(PLATFORM) $(COMPILER) - DEFINES=$(GDEFINES) $(LDEFINES) - - ## Global include directories --GINCLUDES= -+GINCLUDES=-I@GENTOO_PORTAGE_EPREFIX@/usr/include/cifparse-obj - - # Collect all include directories from global include directories and - # include directories specified in module makefile -@@ -159,7 +159,7 @@ F77LIBS= - STATIC_LINKING= - - # Linker flags --LDFLAGS=$(ABI) -w $(STATIC_LINKING) -+LDFLAGS=$(LDFLAGS_OPT) $(ABI) -w $(STATIC_LINKING) - - # Fortran linker - F77_LINKER=f77 -diff --git a/etc/make.platform.darwin4 b/etc/make.platform.darwin4 -index 4619b34..f481fdb 100644 ---- a/etc/make.platform.darwin4 -+++ b/etc/make.platform.darwin4 -@@ -92,7 +92,7 @@ GDEFINES=$(PLATFORM) $(COMPILER) - DEFINES=$(GDEFINES) $(LDEFINES) - - ## Global include directories --GINCLUDES= -+GINCLUDES=-I@GENTOO_PORTAGE_EPREFIX@/usr/include/cifparse-obj - - # Collect all include directories from global include directories and - # include directories specified in module makefile -@@ -160,7 +160,7 @@ F77LIBS= - STATIC_LINKING= - - # Linker flags --LDFLAGS=$(ABI) -w $(STATIC_LINKING) -+LDFLAGS=$(LDFLAGS_OPT) $(ABI) -w $(STATIC_LINKING) - - # Fortran linker - F77_LINKER=f77 -diff --git a/etc/make.platform.gnu3 b/etc/make.platform.gnu3 -index 7fd442e..9bec4dc 100644 ---- a/etc/make.platform.gnu3 -+++ b/etc/make.platform.gnu3 -@@ -6,6 +6,8 @@ - ## - ########################################################################## - -+LIBDIR=@GENTOO_PORTAGE_EPREFIX@/usr/GENTOOLIBDIR -+ - #-----Lexer and Parser section-------------------------------------------# - - # Lexer executable -@@ -89,7 +91,7 @@ GDEFINES=$(PLATFORM) $(COMPILER) - DEFINES=$(GDEFINES) $(LDEFINES) - - ## Global include directories --GINCLUDES= -+GINCLUDES=-I@GENTOO_PORTAGE_EPREFIX@/usr/include/cifparse-obj - - # Collect all include directories from global include directories and - # include directories specified in module makefile -@@ -107,8 +109,8 @@ NON_ANSI_C_FLAG= - C_WARNINGS=$(WARNINGS) - - # C compiler flags --CFLAGS=$(OPT) $(ABI) $(ANSI_C_FLAG) $(C_WARNINGS) $(DEFINES) $(INCLUDES) --CFLAGS_NONANSI=$(OPT) $(ABI) $(NON_ANSI_C_FLAG) $(C_WARNINGS) $(DEFINES) \ -+CFLAGS=$(C_OPT) $(ABI) $(ANSI_C_FLAG) $(C_WARNINGS) $(DEFINES) $(INCLUDES) -+CFLAGS_NONANSI=$(C_OPT) $(ABI) $(NON_ANSI_C_FLAG) $(C_WARNINGS) $(DEFINES) \ - $(INCLUDES) - - ## C++ compiler -@@ -128,9 +130,9 @@ C_PLUS_WARNINGS=$(WARNINGS) $(NO_DEPRECATED) - EXT=C - - # C++ compiler flags --C++FLAGS=$(OPT) $(ABI) $(ANSI_C_PLUS_FLAG) $(C_PLUS_WARNINGS) $(DEFINES) \ -+C++FLAGS=$(CCC_OPT) $(ABI) $(ANSI_C_PLUS_FLAG) $(C_PLUS_WARNINGS) $(DEFINES) \ - $(INCLUDES) --C++FLAGS_NONANSI=$(OPT) $(ABI) $(NON_ANSI_C_PLUS_FLAG) $(C_PLUS_WARNINGS) \ -+C++FLAGS_NONANSI=$(CCC_OPT) $(ABI) $(NON_ANSI_C_PLUS_FLAG) $(C_PLUS_WARNINGS) \ - $(DEFINES) $(INCLUDES) - # C++FLAGS_RELAXED should be set to avoid warnings reported by third party - # source code that is not maintained by PDB -@@ -144,7 +146,7 @@ C++FLAGS_RELAXED=$(OPT) $(ABI) $(ANSI_C_PLUS_FLAG) $(NO_DEPRECATED) $(DEFINES) \ - F77=f77 - - # Fortran compiler flags --FFLAGS=-O -u -+FFLAGS=$(F_OPT) - - # Additional Fortran libraries - F77LIBS= -@@ -154,11 +156,11 @@ F77LIBS= - #-----Linkers section----------------------------------------------------# - - # Static linking option. If not defined, dynamic linking is used. --STATIC_LINKING=-static -+STATIC_LINKING= - - # Linker flags --LDFLAGS=$(ABI) -w $(STATIC_LINKING) --LDFLAGS_NO_STATIC=$(ABI) -w -+LDFLAGS=$(LDFLAGS_OPT) $(ABI) -w $(STATIC_LINKING) -+LDFLAGS_NO_STATIC=$(LDFLAGS_OPT) $(ABI) -w - - # Fortran linker - F77_LINKER=f77 -diff --git a/etc/make.platform.gnu4 b/etc/make.platform.gnu4 -index 78a0007..bc85308 100644 ---- a/etc/make.platform.gnu4 -+++ b/etc/make.platform.gnu4 -@@ -6,6 +6,8 @@ - ## - ########################################################################## - -+LIBDIR=@GENTOO_PORTAGE_EPREFIX@/usr/GENTOOLIBDIR -+ - #-----Lexer and Parser section-------------------------------------------# - - # Lexer executable -@@ -34,7 +36,7 @@ ABI= - - # WARNINGS_AS_ERRORS defines flags to instruct all compilers to treat all - # warnings as errors. --WARNINGS_AS_ERRORS=-Werror -+WARNINGS_AS_ERRORS= - - # ALL_WARNINGS defines flags to instruct all compilers to report all - # warnings. -@@ -90,7 +92,7 @@ GDEFINES=$(PLATFORM) $(COMPILER) - DEFINES=$(GDEFINES) $(LDEFINES) - - ## Global include directories --GINCLUDES= -+GINCLUDES=-I@GENTOO_PORTAGE_EPREFIX@/usr/include/cifparse-obj - - # Collect all include directories from global include directories and - # include directories specified in module makefile -@@ -108,8 +110,8 @@ NON_ANSI_C_FLAG= - C_WARNINGS=$(WARNINGS) - - # C compiler flags --CFLAGS=$(OPT) $(ABI) $(PIC) $(ANSI_C_FLAG) $(C_WARNINGS) $(DEFINES) $(INCLUDES) --CFLAGS_NONANSI=$(OPT) $(ABI) $(PIC) $(NON_ANSI_C_FLAG) $(DEFINES) $(INCLUDES) -+CFLAGS=$(C_OPT) $(ABI) $(PIC) $(ANSI_C_FLAG) $(C_WARNINGS) $(DEFINES) $(INCLUDES) -+CFLAGS_NONANSI=$(C_OPT) $(ABI) $(PIC) $(NON_ANSI_C_FLAG) $(DEFINES) $(INCLUDES) - - ## C++ compiler - ## This part defines C++ compiler information -@@ -128,9 +130,9 @@ C_PLUS_WARNINGS=$(WARNINGS) $(NO_DEPRECATED) - EXT=C - - # C++ compiler flags --C++FLAGS=$(OPT) $(ABI) $(PIC) $(ANSI_C_PLUS_FLAG) $(C_PLUS_WARNINGS) \ -+C++FLAGS=$(CCC_OPT) $(ABI) $(PIC) $(ANSI_C_PLUS_FLAG) $(C_PLUS_WARNINGS) \ - $(DEFINES) $(INCLUDES) --C++FLAGS_NONANSI=$(OPT) $(ABI) $(PIC) $(NON_ANSI_C_PLUS_FLAG) \ -+C++FLAGS_NONANSI=$(CCC_OPT) $(ABI) $(PIC) $(NON_ANSI_C_PLUS_FLAG) \ - $(C_PLUS_WARNINGS) $(DEFINES) $(INCLUDES) - - # C++FLAGS_RELAXED should be set to avoid warnings reported by third party -@@ -145,7 +147,7 @@ C++FLAGS_RELAXED=$(OPT) $(ABI) $(PIC) $(ANSI_C_PLUS_FLAG) $(NO_DEPRECATED) \ - F77=f77 - - # Fortran compiler flags --FFLAGS=-O -u -+FFLAGS=$(F_OPT) - - # Additional Fortran libraries - F77LIBS= -@@ -158,8 +160,8 @@ F77LIBS= - STATIC_LINKING= - - # Linker flags --LDFLAGS=$(ABI) -w $(STATIC_LINKING) --LDFLAGS_NO_STATIC=$(ABI) -w -+LDFLAGS=$(LDFLAGS_OPT) $(ABI) -w $(STATIC_LINKING) -+LDFLAGS_NO_STATIC=$(LDFLAGS_OPT) $(ABI) -w - - # Fortran linker - F77_LINKER=f77 diff --git a/sci-chemistry/pdb-extract/files/pdb-extract-3.11-gcc-4.7.patch b/sci-chemistry/pdb-extract/files/pdb-extract-3.11-gcc-4.7.patch deleted file mode 100644 index 5284bd745d53..000000000000 --- a/sci-chemistry/pdb-extract/files/pdb-extract-3.11-gcc-4.7.patch +++ /dev/null @@ -1,64 +0,0 @@ - common-v4.5/src/mapped_ptr_vector.C | 14 +++++++------- - 1 files changed, 7 insertions(+), 7 deletions(-) - -diff --git a/common-v4.5/src/mapped_ptr_vector.C b/common-v4.5/src/mapped_ptr_vector.C -index d7c61f3..e20a236 100644 ---- a/common-v4.5/src/mapped_ptr_vector.C -+++ b/common-v4.5/src/mapped_ptr_vector.C -@@ -263,12 +263,12 @@ void mapped_ptr_vector<T, StringCompareT>::push_back(T* inP, - _vector.push_back(inP); - - typename tIndex::value_type valuePair(inP->GetName(), -- make_pair(_vector.size() - 1, fileIndex)); -+ std::make_pair(_vector.size() - 1, fileIndex)); - - _index.insert(valuePair); - - _currentName = inP->GetName(); -- _currentIndices = make_pair(_vector.size() - 1, fileIndex); -+ _currentIndices = std::make_pair(_vector.size() - 1, fileIndex); - - } - -@@ -281,12 +281,12 @@ void mapped_ptr_vector<T, StringCompareT>::push_back(const string& name, - _vector.push_back(NULL); - - typename tIndex::value_type valuePair(name, -- make_pair(_vector.size() - 1, fileIndex)); -+ std::make_pair(_vector.size() - 1, fileIndex)); - - _index.insert(valuePair); - - _currentName = name; -- _currentIndices = make_pair(_vector.size() - 1, fileIndex); -+ _currentIndices = std::make_pair(_vector.size() - 1, fileIndex); - } - - -@@ -454,7 +454,7 @@ void mapped_ptr_vector<T, StringCompareT>::erase(const string& name) - if (is_equal(_currentName, name, keyComp)) - { - _currentName.clear(); -- _currentIndices = make_pair(_vector.size(), (unsigned int)0); -+ _currentIndices = std::make_pair(_vector.size(), (unsigned int)0); - } - - } -@@ -539,7 +539,7 @@ pair<unsigned int, unsigned int> mapped_ptr_vector<T, StringCompareT>::get_indic - if (_vector.empty()) - { - // Empty container. Return invalid index. -- return(make_pair(_vector.size(), (unsigned int)0)); -+ return(std::make_pair(_vector.size(), (unsigned int)0)); - } - - typename tIndex::key_compare keyComp = _index.key_comp(); -@@ -563,7 +563,7 @@ pair<unsigned int, unsigned int> mapped_ptr_vector<T, StringCompareT>::get_indic - else - { - // Not found. Return invalid index. -- return(make_pair(_vector.size(), (unsigned int)0)); -+ return(std::make_pair(_vector.size(), (unsigned int)0)); - } - } - diff --git a/sci-chemistry/pdb-extract/metadata.xml b/sci-chemistry/pdb-extract/metadata.xml deleted file mode 100644 index e42d0af60f42..000000000000 --- a/sci-chemistry/pdb-extract/metadata.xml +++ /dev/null @@ -1,5 +0,0 @@ -<?xml version="1.0" encoding="UTF-8"?> -<!DOCTYPE pkgmetadata SYSTEM "http://www.gentoo.org/dtd/metadata.dtd"> -<pkgmetadata> - <herd>sci-chemistry</herd> -</pkgmetadata> diff --git a/sci-chemistry/pdb-extract/pdb-extract-3.004-r2.ebuild b/sci-chemistry/pdb-extract/pdb-extract-3.004-r2.ebuild deleted file mode 100644 index 836d76f5c007..000000000000 --- a/sci-chemistry/pdb-extract/pdb-extract-3.004-r2.ebuild +++ /dev/null @@ -1,71 +0,0 @@ -# Copyright 1999-2011 Gentoo Foundation -# Distributed under the terms of the GNU General Public License v2 -# $Id$ - -EAPI=3 - -inherit eutils toolchain-funcs multilib prefix - -MY_P="${PN}-v${PV}-prod-src" - -DESCRIPTION="Tools for extracting mmCIF data from structure determination applications" -HOMEPAGE="http://sw-tools.pdb.org/apps/PDB_EXTRACT/index.html" -SRC_URI="http://sw-tools.pdb.org/apps/PDB_EXTRACT/${MY_P}.tar.gz" - -LICENSE="PDB" -SLOT="0" -KEYWORDS="amd64 ~ppc x86 ~amd64-linux ~x86-linux" -IUSE="" - -RDEPEND="!<app-text/html-xml-utils-5.3" -DEPEND="${RDEPEND} - >=sci-libs/cifparse-obj-7.025" - -S="${WORKDIR}/${MY_P}" - -src_prepare() { - epatch \ - "${FILESDIR}"/${P}-cflags-install.patch \ - "${FILESDIR}"/${P}-gcc-4.3.patch \ - "${FILESDIR}"/${P}-Makefile.patch \ - "${FILESDIR}"/${P}-env.patch - - sed -i "s:GENTOOLIBDIR:$(get_libdir):g" \ - pdb-extract-v3.0/Makefile \ - || die "Failed to fix libdir" - - # Get rid of unneeded directories, to make sure we use system files - ebegin "Deleting redundant directories" - rm -rf cif-file-v1.0 cifobj-common-v4.1 cifparse-obj-v7.0 \ - misclib-v2.2 regex-v2.2 tables-v8.0 - eend - - sed -i \ - -e "s:^\(CCC=\).*:\1$(tc-getCXX):g" \ - -e "s:^\(CC=\).*:\1$(tc-getCC):g" \ - -e "s:^\(GINCLUDES=\).*:\1-I${EPREFIX}/usr/include/cifparse-obj:g" \ - -e "s:^\(LIBDIR=\).*:\1${EPREFIX}/usr/$(get_libdir):g" \ - "${S}"/etc/make.* \ - || die "Failed to fix makefiles" - - eprefixify pdb-extract-v3.0/Makefile etc/* -} - -src_install() { - exeinto /usr/libexec/ccp4/bin - doexe bin/pdb_extract{,_sf} bin/extract \ - || die "failed to install binaries" - insinto /usr/include/rcsb - doins include/* || die "failed to install include files" - dodoc README* || die "failed to install docs" - insinto /usr/share/rcsb/ - doins -r pdb-extract-data || die "failed to install data files" - - cat >> "${T}"/envd <<- EOF - PDB_EXTRACT="${EPREFIX}/usr/share/rcsb/" - PDB_EXTRACT_ROOT="${EPREFIX}/usr/" - EOF - - newenvd "${T}"/envd 20pdb-extract \ - || die "failed to install env files" -} diff --git a/sci-chemistry/pdb-extract/pdb-extract-3.11.ebuild b/sci-chemistry/pdb-extract/pdb-extract-3.11.ebuild deleted file mode 100644 index 04351c8a125a..000000000000 --- a/sci-chemistry/pdb-extract/pdb-extract-3.11.ebuild +++ /dev/null @@ -1,60 +0,0 @@ -# Copyright 1999-2012 Gentoo Foundation -# Distributed under the terms of the GNU General Public License v2 -# $Id$ - -EAPI=4 - -inherit eutils toolchain-funcs multilib prefix - -MY_P="${PN}-v${PV}-prod-src" - -DESCRIPTION="Tools for extracting mmCIF data from structure determination applications" -HOMEPAGE="http://sw-tools.pdb.org/apps/PDB_EXTRACT/index.html" -SRC_URI="http://sw-tools.pdb.org/apps/PDB_EXTRACT/${MY_P}.tar.gz" - -LICENSE="PDB" -SLOT="0" -KEYWORDS="~amd64 ~ppc ~x86 ~amd64-linux ~x86-linux" -IUSE="" - -RDEPEND="!<app-text/html-xml-utils-5.3" -DEPEND="${RDEPEND} - >=sci-libs/cifparse-obj-7.025" - -S="${WORKDIR}/${MY_P}" - -MAKEOPTS+=" -j1" - -src_prepare() { - epatch \ - "${FILESDIR}"/${P}-cflags-install.patch \ - "${FILESDIR}"/${P}-gcc-4.7.patch \ - "${FILESDIR}"/${PN}-3.004-env.patch - - sed -i \ - -e "s:^\(CCC=\).*:\1$(tc-getCXX):g" \ - -e "s:^\(CC=\).*:\1$(tc-getCC):g" \ - -e "s:^\(GINCLUDES=\).*:\1-I${EPREFIX}/usr/include/cifparse-obj:g" \ - -e "s:^\(LIBDIR=\).*:\1${EPREFIX}/usr/$(get_libdir):g" \ - "${S}"/etc/make.* \ - || die "Failed to fix makefiles" - - eprefixify pdb-extract-v3.0/Makefile etc/* -} - -src_install() { - exeinto /usr/libexec/ccp4/bin - doexe bin/pdb_extract{,_sf} bin/extract - insinto /usr/include/rcsb - doins include/* - dodoc README* - insinto /usr/share/rcsb/ - doins -r pdb-extract-data - - cat >> "${T}"/envd <<- EOF - PDB_EXTRACT="${EPREFIX}/usr/share/rcsb/" - PDB_EXTRACT_ROOT="${EPREFIX}/usr/" - EOF - - newenvd "${T}"/envd 20pdb-extract -} diff --git a/sci-chemistry/phaser/Manifest b/sci-chemistry/phaser/Manifest deleted file mode 100644 index deb3ba972a75..000000000000 --- a/sci-chemistry/phaser/Manifest +++ /dev/null @@ -1 +0,0 @@ -DIST ccp4-6.1.13-phaser-cctbx-src.tar.gz 22021353 SHA256 e6c4365cb34da5ce2dd5f1e74b8927258064016194446163418c8a3139a4b804 SHA512 cdf36572613a6e400af0f29da501ccfd2a9f1a7e2d89162aad3fe14929816b41790bb57ba1e77976b9046c6e06a29df2748999db93a2cd0a4d1fde95ac1f9e8b WHIRLPOOL 5aa1a1c6520be90ef02be0e9de9c111a9835cda05a3549c390f62ceef7e68c8392670d91941b823c0ee94f29e6aab9d34a61b90e8bd3d4820a83daa547463fdb diff --git a/sci-chemistry/phaser/files/phaser-2.1.4-chmod.patch b/sci-chemistry/phaser/files/phaser-2.1.4-chmod.patch deleted file mode 100644 index 5311cb332785..000000000000 --- a/sci-chemistry/phaser/files/phaser-2.1.4-chmod.patch +++ /dev/null @@ -1,13 +0,0 @@ -diff --git a/lib/cctbx/cctbx_sources/libtbx/libtbx/config.py b/lib/cctbx/cctbx_sources/libtbx/libtbx/config.py -index 3b1bd3a..8939a74 100755 ---- a/lib/cctbx/cctbx_sources/libtbx/libtbx/config.py -+++ b/lib/cctbx/cctbx_sources/libtbx/libtbx/config.py -@@ -802,8 +802,6 @@ class environment: - else: - action = self.write_bin_sh_dispatcher - ext = "" -- try: os.chmod(source_file, 0755) -- except OSError: pass - target_file_ext = target_file + ext - remove_or_rename(target_file_ext) - try: action(source_file, target_file_ext) diff --git a/sci-chemistry/phaser/metadata.xml b/sci-chemistry/phaser/metadata.xml deleted file mode 100644 index 6b4826474daa..000000000000 --- a/sci-chemistry/phaser/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@gentoo.org</email> - <description>ccp4 maintainer</description> - </maintainer> -</pkgmetadata> diff --git a/sci-chemistry/phaser/phaser-2.1.4.ebuild b/sci-chemistry/phaser/phaser-2.1.4.ebuild deleted file mode 100644 index 86fa57f52603..000000000000 --- a/sci-chemistry/phaser/phaser-2.1.4.ebuild +++ /dev/null @@ -1,115 +0,0 @@ -# Copyright 1999-2015 Gentoo Foundation -# Distributed under the terms of the GNU General Public License v2 -# $Id$ - -EAPI=5 - -PYTHON_COMPAT=( python2_7 ) - -inherit eutils flag-o-matic python-single-r1 toolchain-funcs - -CCP4VER="6.1.13" - -DESCRIPTION="A program for phasing macromolecular crystal structures" -HOMEPAGE="http://www-structmed.cimr.cam.ac.uk/phaser" -SRC_URI="ftp://ftp.ccp4.ac.uk/ccp4/${CCP4VER}/ccp4-${CCP4VER}-${PN}-cctbx-src.tar.gz" - -LICENSE="|| ( phaser phaser-com ccp4 )" -SLOT="0" -#KEYWORDS="~amd64 ~x86" -KEYWORDS="" -IUSE="openmp" - -RDEPEND="" -DEPEND="${RDEPEND} - app-shells/tcsh" - -S="${WORKDIR}"/ccp4-${CCP4VER} - -src_prepare() { - epatch \ - "${FILESDIR}"/phaser-2.1.4-chmod.patch \ - "${FILESDIR}"/phaser-2.1.4-ldflags.patch - - use openmp && append-flags -fopenmp - - for i in ${CXXFLAGS}; do - OPTS="${OPTS} \"${i}\"," - done - - OPTS=${OPTS%,} - - sed -i \ - -e "s:opts = \[.*\]$:opts = \[${OPTS}\]:g" \ - "${S}"/lib/cctbx/cctbx_sources/libtbx/SConscript || die - - for i in ${LDFLAGS}; do - OPTSLD="${OPTSLD} \"${i}\"," - done - - sed -i \ - -e "s:env_etc.shlinkflags .* \"-shared\":env_etc.shlinkflags = \[ ${OPTSLD} \"-shared\"\]:g" \ - -e "s:\[\"-static:\[${OPTSLD} \"-static:g" \ - "${S}"/lib/cctbx/cctbx_sources/libtbx/SConscript || die - -} - -src_configure() { - local compiler - local mtype - local mversion - local nproc - - # Valid compilers are win32_cl, sunos_CC, unix_gcc, unix_ecc, - # unix_icc, unix_icpc, tru64_cxx, hp_ux11_aCC, irix_CC, - # darwin_c++, darwin_gcc. The build systems seems to prepend - # unix_ all by itself. Can this be derived from $(tc-getCC)? - compiler=$(expr match "$(tc-getCC)" '.*\([a-z]cc\)') - - # Breaks cross compilation. - mtype=$(src/${PN}/bin/machine_type) - mversion=$(src/${PN}/bin/machine_version) - - einfo "Creating build directory" - mkdir build - cd build - ln -sf "${S}/lib/cctbx/cctbx_sources/scons" scons - ln -sf "${S}/lib/cctbx/cctbx_sources/libtbx" libtbx - - einfo "Configuring phaser components" - $(PYTHON) "libtbx/configure.py" \ - --build=release \ - --compiler=${compiler} \ - --repository="${S}"/src/${PN}/source \ - --repository="${S}"/lib/cctbx/cctbx_sources \ - --static_libraries \ - ccp4io="${S}" \ - mmtbx \ - phaser || die "configure.py failed" -} - -src_compile() { - nproc=`echo "-j1 ${MAKEOPTS}" \ - | sed -e "s/.*\(-j\s*\|--jobs=\)\([0-9]\+\).*/\2/"` - - cd build - einfo "Setting up build environment" - source setpaths.sh - - einfo "Compiling phaser components" - libtbx.scons -j ${nproc} || die "libtbx.scons failed" -} - -src_install() { - dobin build/exe/phaser || die - - cat >> "${T}"/53${PN} <<- EOF - PHASER="${EPREFIX}/usr/bin" - PHASER_ENVIRONMENT="1" - PHASER_MTYPE="${mtype}" - PHASER_MVERSION="${mversion}" - PHASER_VERSION="${PV}" - EOF - - doenvd "${T}"/53${PN} || die -} diff --git a/sci-chemistry/pointless/Manifest b/sci-chemistry/pointless/Manifest deleted file mode 100644 index 911c44875112..000000000000 --- a/sci-chemistry/pointless/Manifest +++ /dev/null @@ -1,2 +0,0 @@ -DIST pointless-1.6.14.tar.gz 423657 SHA256 68f0c1f65239b1451310fe885c2b9d51fc558de7b43af1e584750e05dc5635d8 SHA512 9dd524a7c842edc01206450c52ca1a01e8e3ee6f9ff71742789943ee10e006b5452b0be3aa509dd16bb85f1b9c3d7954616a78ec2fef2daea7c0ab42cdaa42b9 WHIRLPOOL 5085afbd88713384039ef2c2b4b2f7fddd8f078dca9df54062b0415e970791868c61df98f4044b4e061077a73b4e129b6e5db34852d64cace48108db9c6ae50f -DIST pointless-1.6.2.tar.gz 412244 SHA256 5e09ca592ea565e8ace142fc0edff39d0ab723f4ac6e2cadd6ba571d667c80f6 SHA512 2e897a7302ba4d43da69c8ee91254b0632d8a0ae301140a144472f7e466078f0b1abd10362343d7d50d04bd86ae8b83265a20302f7aeae3dc8845f1581211ddd WHIRLPOOL 8953806f68684e882717673ec18263f0ac2093f3cb2cac573b20886f5f0d60c67b756f74bdb3555342bb3d287021b7c70b20c53f0e38e687a5914df935ae35cd diff --git a/sci-chemistry/pointless/files/1.5.1-gcc4.4.patch b/sci-chemistry/pointless/files/1.5.1-gcc4.4.patch deleted file mode 100644 index ca67dbd3f336..000000000000 --- a/sci-chemistry/pointless/files/1.5.1-gcc4.4.patch +++ /dev/null @@ -1,12 +0,0 @@ -diff --git a/string_util.hh b/string_util.hh -index 66af6f3..047512b 100644 ---- a/string_util.hh -+++ b/string_util.hh -@@ -3,6 +3,7 @@ - - #include <string> - #include <vector> -+#include <stdio.h> - #include "range.hh" - - //====================================================================== diff --git a/sci-chemistry/pointless/metadata.xml b/sci-chemistry/pointless/metadata.xml deleted file mode 100644 index ae9ec7c5f6a4..000000000000 --- a/sci-chemistry/pointless/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-chemistry</herd> - <maintainer> - <email>jlec@gentoo.org</email> - </maintainer> -</pkgmetadata> diff --git a/sci-chemistry/pointless/pointless-1.6.14-r1.ebuild b/sci-chemistry/pointless/pointless-1.6.14-r1.ebuild deleted file mode 100644 index d983cb290242..000000000000 --- a/sci-chemistry/pointless/pointless-1.6.14-r1.ebuild +++ /dev/null @@ -1,56 +0,0 @@ -# Copyright 1999-2015 Gentoo Foundation -# Distributed under the terms of the GNU General Public License v2 -# $Id$ - -EAPI=5 - -PYTHON_COMPAT=( python2_7 ) - -inherit eutils fortran-2 multilib python-single-r1 toolchain-funcs - -DESCRIPTION="Scores crystallographic Laue and space groups" -HOMEPAGE="ftp://ftp.mrc-lmb.cam.ac.uk/pub/pre/pointless.html" -SRC_URI="ftp://ftp.mrc-lmb.cam.ac.uk/pub/pre/${P}.tar.gz" - -SLOT="0" -LICENSE="ccp4" -KEYWORDS="~amd64 ~ppc ~x86 ~amd64-linux ~x86-linux" -IUSE="" - -REQUIRED_USE="${PYTHON_REQUIRED_USE}" - -DEPEND=" - sci-chemistry/ccp4-apps - >=sci-libs/ccp4-libs-6.1.3-r10 - sci-libs/clipper - sci-libs/fftw:2.1 - sci-libs/mmdb - >=sci-libs/cctbx-2010.03.29.2334-r3[${PYTHON_USEDEP}]" -RDEPEND="${DEPEND}" - -S="${WORKDIR}" - -src_prepare() { - epatch "${FILESDIR}"/1.5.1-gcc4.4.patch -} - -src_compile() { - emake \ - -f Makefile.make \ - CC=$(tc-getCC) \ - CXX=$(tc-getCXX) \ - CFLAGS="${CFLAGS}" \ - CXXFLAGS="${CXXFLAGS}" \ - LFLAGS="${LDFLAGS}" \ - CLIB="${EPREFIX}/usr/$(get_libdir)" \ - CCTBX_VERSION=2010 \ - ICCP4=-I"${EPREFIX}/usr/include/ccp4" \ - ITBX="-I${EPREFIX}/usr/include" \ - ICLPR="-I${EPREFIX}/$(python_get_sitedir)/" \ - LTBX="-L${EPREFIX}/usr/$(get_libdir)/cctbx/cctbx_build/lib -lcctbx" \ - SLIB="-L${EPREFIX}/usr/$(get_libdir) -lgfortran" -} - -src_install() { - dobin pointless othercell -} diff --git a/sci-chemistry/pointless/pointless-1.6.14.ebuild b/sci-chemistry/pointless/pointless-1.6.14.ebuild deleted file mode 100644 index 158bde017aea..000000000000 --- a/sci-chemistry/pointless/pointless-1.6.14.ebuild +++ /dev/null @@ -1,60 +0,0 @@ -# Copyright 1999-2012 Gentoo Foundation -# Distributed under the terms of the GNU General Public License v2 -# $Id$ - -EAPI="3" - -PYTHON_DEPEND="2" - -inherit eutils fortran-2 multilib python toolchain-funcs - -DESCRIPTION="Scores crystallographic Laue and space groups" -HOMEPAGE="ftp://ftp.mrc-lmb.cam.ac.uk/pub/pre/pointless.html" -SRC_URI="ftp://ftp.mrc-lmb.cam.ac.uk/pub/pre/${P}.tar.gz" - -SLOT="0" -LICENSE="ccp4" -KEYWORDS="~amd64 ~ppc ~x86 ~amd64-linux ~x86-linux" -IUSE="" - -DEPEND=" - sci-chemistry/ccp4-apps - >=sci-libs/ccp4-libs-6.1.3-r10 - sci-libs/clipper - sci-libs/fftw:2.1 - sci-libs/mmdb - >=sci-libs/cctbx-2010.03.29.2334-r3" -RDEPEND="${DEPEND}" - -S="${WORKDIR}" - -pkg_setup() { - fortran-2_pkg_setup - python_set_active_version 2 -} - -src_prepare() { - epatch "${FILESDIR}"/1.5.1-gcc4.4.patch -} - -src_compile() { - emake \ - -f Makefile.make \ - CC=$(tc-getCC) \ - CXX=$(tc-getCXX) \ - CFLAGS="${CFLAGS}" \ - CXXFLAGS="${CXXFLAGS}" \ - LFLAGS="${LDFLAGS}" \ - CLIB="${EPREFIX}/usr/$(get_libdir)" \ - CCTBX_VERSION=2010 \ - ICCP4=-I"${EPREFIX}/usr/include/ccp4" \ - ITBX="-I${EPREFIX}/usr/include" \ - ICLPR="-I${EPREFIX}/$(python_get_sitedir)/" \ - LTBX="-L${EPREFIX}/usr/$(get_libdir)/cctbx/cctbx_build/lib -lcctbx" \ - SLIB="-L${EPREFIX}/usr/$(get_libdir) -lgfortran" \ - || die -} - -src_install() { - dobin pointless othercell || die -} diff --git a/sci-chemistry/pointless/pointless-1.6.2.ebuild b/sci-chemistry/pointless/pointless-1.6.2.ebuild deleted file mode 100644 index 2b9f0ad4faa0..000000000000 --- a/sci-chemistry/pointless/pointless-1.6.2.ebuild +++ /dev/null @@ -1,60 +0,0 @@ -# Copyright 1999-2012 Gentoo Foundation -# Distributed under the terms of the GNU General Public License v2 -# $Id$ - -EAPI=4 - -PYTHON_DEPEND="2" - -inherit eutils fortran-2 multilib python toolchain-funcs - -DESCRIPTION="Scores crystallographic Laue and space groups" -HOMEPAGE="ftp://ftp.mrc-lmb.cam.ac.uk/pub/pre/pointless.html" -SRC_URI="ftp://ftp.mrc-lmb.cam.ac.uk/pub/pre/${P}.tar.gz" - -SLOT="0" -LICENSE="ccp4" -KEYWORDS="amd64 ~ppc x86 ~amd64-linux ~x86-linux" -IUSE="" - -DEPEND=" - sci-chemistry/ccp4-apps - >=sci-libs/ccp4-libs-6.1.3-r10 - sci-libs/clipper - sci-libs/fftw:2.1 - sci-libs/mmdb - >=sci-libs/cctbx-2010.03.29.2334-r3" -RDEPEND="${DEPEND}" - -S="${WORKDIR}" - -pkg_setup() { - fortran-2_pkg_setup - python_pkg_setup - python_set_active_version 2 -} - -src_prepare() { - epatch "${FILESDIR}"/1.5.1-gcc4.4.patch -} - -src_compile() { - emake \ - -f Makefile.make \ - CC=$(tc-getCC) \ - CXX=$(tc-getCXX) \ - CFLAGS="${CFLAGS}" \ - CXXFLAGS="${CXXFLAGS}" \ - LFLAGS="${LDFLAGS}" \ - CLIB="${EPREFIX}/usr/$(get_libdir)" \ - CCTBX_VERSION=2010 \ - ICCP4=-I"${EPREFIX}/usr/include/ccp4" \ - ITBX="-I${EPREFIX}/usr/include" \ - ICLPR="-I${EPREFIX}/$(python_get_sitedir)/" \ - LTBX="-L${EPREFIX}/usr/$(get_libdir)/cctbx/cctbx_build/lib -lcctbx" \ - SLIB="-L${EPREFIX}/usr/$(get_libdir) -lgfortran" -} - -src_install() { - dobin pointless othercell -} diff --git a/sci-chemistry/refmac/Manifest b/sci-chemistry/refmac/Manifest deleted file mode 100644 index ba3def103020..000000000000 --- a/sci-chemistry/refmac/Manifest +++ /dev/null @@ -1,2 +0,0 @@ -DIST refmac_5.5.0110.tar.gz 1326832 SHA256 1353fb1042586ec8fa37d0a90f274890d0ccc02377af5216200662338dfe08ca SHA512 7e7fd1a7d2d11ef5f2e08cae61da62ecfe6978730ce4ca80f8b00be9bdad5e7d0ad493e1b8d57d64f1393f2017a87b8342e2607b08bc4018def798038a111728 WHIRLPOOL 587260eebd2df3115ba01ee03c11ab773d7316100a09af1f259f7795a139f978d94c569b8e4ab85982c2eeda628e643376231bdca5311fc8c7d2de5b65a033ac -DIST test-framework.tar.gz 130933173 SHA256 df050a2a29da80518cb0616a0bbeb82298ea0721549348d15353bf0f66240605 SHA512 3ef8253f472c5a481f836291afb80746ad73858e130130b848851b6b5dc53ada3b78c9f853af1c46fa22f469f2ce2f3248f5f760950e118610922c0429a7da16 WHIRLPOOL 022c1b493ecd35e769b44d1e52a351b4883682ef9759626bac36e26cc61078d95de0ec2531ed706897c683c38727139fa7a13d06b64c597026817ed79612d16d diff --git a/sci-chemistry/refmac/files/5.5-test.log.patch b/sci-chemistry/refmac/files/5.5-test.log.patch deleted file mode 100644 index 61858be357a0..000000000000 --- a/sci-chemistry/refmac/files/5.5-test.log.patch +++ /dev/null @@ -1,32 +0,0 @@ ---- test-framework/refmac5/test_refmac5.py 2009-06-29 15:45:37.000000000 +0200 -+++ test-framework/refmac5/test_refmac5.py.new 2009-06-29 15:48:05.000000000 +0200 -@@ -88,7 +88,8 @@ - 'make hydr no', - 'labin IP=IMEAN SIGIP=SIGIMEAN FREE=FreeR_flag', - 'labout FC=FC PHIC=PHIC'], -- working_directory = self.test_dir) -+ working_directory = self.test_dir, -+ log_file = 'test_twinned_refinement.log') - - self.assertEqual(status, 0) - -@@ -123,7 +124,8 @@ - 'weight auto', - 'ncyc 20', - 'labout FC=FC PHIC=PHIC'], -- working_directory = self.test_dir) -+ working_directory = self.test_dir, -+ log_file = 'test_4_domain_tls.log') - - self.assertEqual(status, 0) - -@@ -156,7 +158,8 @@ - 'anomalous form SE -9.9 3.9', - 'anomalous wavelength 0.97966', - 'labout FC=FC PHIC=PHIC'], -- working_directory = self.test_dir) -+ working_directory = self.test_dir, -+ log_file = 'test_sad_refinement.log') - - self.assertEqual(status, 0) - diff --git a/sci-chemistry/refmac/files/5.5.0110-allow-dynamic-linking.patch b/sci-chemistry/refmac/files/5.5.0110-allow-dynamic-linking.patch deleted file mode 100644 index 1efbaa04d9e6..000000000000 --- a/sci-chemistry/refmac/files/5.5.0110-allow-dynamic-linking.patch +++ /dev/null @@ -1,84 +0,0 @@ -diff --git a/makefile b/makefile -index 66d4cee..5270677 100644 ---- a/makefile -+++ b/makefile -@@ -9,7 +9,7 @@ XFFLAGS = -fno-second-underscore -static - XCFLAGS = -DGFORTRAN -DPROTOTYPE - FFLAGS = $(FOPTIM) $(XFFLAGS) - CFLAGS = $(COPTIM) $(XCFLAGS) --CPPFLAGS = $(CFLAGS) -+CPPFLAGS = $(CXXFLAGS) $(XCFLAGS) - - LLIBCIF = - LLIBCCP = $(CLIB)/libccp4f.a $(CLIB)/libccp4c.a -diff --git a/makefile_refmac.inc1 b/makefile_refmac.inc1 -index 371d84d..557077f 100644 ---- a/makefile_refmac.inc1 -+++ b/makefile_refmac.inc1 -@@ -68,9 +68,7 @@ messy_pdb.o \ - bridge.o \ - i0.o \ - i1.o \ --chbevl.o \ --$(LLIBCIF) \ --$(LLIBLAPACK) -+chbevl.o - #$(LLIBCCP) \ - #crt0.o \ - #heavy.o \ -@@ -95,8 +93,7 @@ make_unix_ccp4.o \ - emin.o \ - libcheck_min.o \ - mol2_file.o \ --sdf_files.o \ --$(LLIBCCP) -+sdf_files.o - - SUBM = \ - main_makecif.o \ -@@ -116,9 +113,7 @@ make_rst2.o \ - make_PDB.o \ - makecif.o \ - make_unix_ccp4.o \ --make_vdw.o \ --$(LLIBCCP) \ --$(LLIBCIF) -+make_vdw.o - - SUBT = \ - tlsgroups.o \ -@@ -142,9 +137,7 @@ make_refmac_dummy.o \ - inout_routines.o \ - errwrt_1.o \ - linalgebra.o \ --subnumrec.o \ --$(LLIBCCP) \ --$(LLIBCIF) -+subnumrec.o - #-------------------------------------------------------------------------------- - - ed = echo 'g/^CMDW-5.0/s// /@w@q@' | tr "@" "\012" | ed -s -@@ -154,18 +147,19 @@ ed = echo 'g/^CMDW-5.0/s// /@w@q@' | tr "@" "\012" | ed -s - all: refmac libcheck makecif - - refmac: $(SUBR) -- $(FC) $(FFLAGS) $(LDFLAGF)-o refmac${VERSION} ${SUBR} $(LLIBOTHERS) $(LLIBCCP) -+ $(FC) $(FFLAGS) $(LDFLAGS) -o refmac${VERSION} ${SUBR} $(LLIBOTHERS) $(LLIBCCP) $(LLIBCIF) $(LLIBLAPACK) - - libcheck: $(SUBL) -- $(FC) $(FFLAGS) -o libcheck${VERSION} $(SUBL) -+ $(FC) $(FFLAGS) $(LDFLAGS) -o libcheck${VERSION} $(SUBL) $(LLIBCCP) - - makecif: $(SUBM) -- $(FC) $(FFLAGS) -o makecif${VERSION} $(SUBM) -+ $(FC) $(FFLAGS) $(LDFLAGS) -o makecif${VERSION} $(SUBM) $(LLIBCCP) $(LLIBCIF) - - tlsgroups: $(SUBT) -- $(FC) $(FFLAGS) -o tlsgroups${VERSION} $(SUBT) -+ $(FC) $(FFLAGS) $(LDFLAGS) -o tlsgroups${VERSION} $(SUBT) $(LLIBCCP) $(LLIBCIF) - - clean: - /bin/rm *.o - - bridge.o: bridge.cpp llhood.h covmat.h Gauss.h tabfunc.h -+ $(CXX) $(CXXFLAGS) -c bridge.cpp diff --git a/sci-chemistry/refmac/files/5.5.0110-gcc4.6.patch b/sci-chemistry/refmac/files/5.5.0110-gcc4.6.patch deleted file mode 100644 index 3969cc9c8586..000000000000 --- a/sci-chemistry/refmac/files/5.5.0110-gcc4.6.patch +++ /dev/null @@ -1,17 +0,0 @@ - hkon_secder_tch.f | 3 ++- - 1 files changed, 2 insertions(+), 1 deletions(-) - -diff --git a/hkon_secder_tch.f b/hkon_secder_tch.f -index 31794b0..86d2cdf 100644 ---- a/hkon_secder_tch.f -+++ b/hkon_secder_tch.f -@@ -3724,7 +3724,8 @@ c---External functions and subprutines - INTEGER NWORKSPACE - REAL*8 TOLER - REAL*8 WORKSPACE(300) -- REAL LSTLSQ,D2DF_WEIGHT -+ REAL*8 D2DF_WEIGHT -+ REAL LSTLSQ - C - INTEGER IBIN,IBIN_S - INTEGER I,J,K diff --git a/sci-chemistry/refmac/files/5.6.0110-allow-dynamic-linking.patch b/sci-chemistry/refmac/files/5.6.0110-allow-dynamic-linking.patch deleted file mode 100644 index 9998b759c664..000000000000 --- a/sci-chemistry/refmac/files/5.6.0110-allow-dynamic-linking.patch +++ /dev/null @@ -1,341 +0,0 @@ - makefile_refmac.inc1 | 215 ++++++++++++++++++++++++-------------------------- - 1 files changed, 104 insertions(+), 111 deletions(-) - -diff --git a/makefile_refmac.inc1 b/makefile_refmac.inc1 -index 0f8bd63..e59fbfb 100644 ---- a/makefile_refmac.inc1 -+++ b/makefile_refmac.inc1 -@@ -96,9 +96,7 @@ bridge.o \ - i0.o \ - i1.o \ - chbevl.o \ --make_unix_ccp4.o \ --$(LLIBCIF) \ --$(LLIBLAPACK) -+make_unix_ccp4.o - - - SUBL = \ -@@ -133,9 +131,7 @@ cell_symm_subrs.o \ - iheap_sort.o \ - linalgebra.o \ - math_refmac.o \ --subnumrec.o \ --$(LLIBLAPACK) \ --$(LLIBCCP) -+subnumrec.o - - SUB_FREE = \ - freer_twin.o \ -@@ -145,9 +141,7 @@ subnumrec.o \ - libT.o \ - iheap_sort.o \ - cell_symm_subrs.o \ --math_refmac.o \ --$(LLIBLAPACK) \ --$(LLIBCCP) -+math_refmac.o - - SUB_HEADER = header2matr.o - #-------------------------------------------------------------------------------- -@@ -185,41 +179,41 @@ rharvest_mod.o: rharvest_mod.f90 - twin77mod.o: twin77mod.f - $(FC) $(FFLAGS) -c twin77mod.f - --gibbs_gm_sampler.o: linalgebra_f90.f90 gibbs_gm_sampler.f90 -- $(FC) $(FFLAGS) -c linalgebra_f90.f90 gibbs_gm_sampler.f90 -+gibbs_gm_sampler.o: linalgebra_f90.o gibbs_gm_sampler.f90 -+ $(FC) $(FFLAGS) -c gibbs_gm_sampler.f90 - --max_with_twins.o: restr_files.f90 max_with_twins.f weights.f90 agreem.f90 -- $(FC) $(FFLAGS) -c restr_files.f90 weights.f90 agreem.f90 max_with_twins.f -+max_with_twins.o: restr_files.o max_with_twins.f weights.o agreem.o -+ $(FC) $(FFLAGS) -c max_with_twins.f - --merohedr_twin.o: restr_files.f90 merohedr_twin.f -- $(FC) $(FFLAGS) -c restr_files.f90 merohedr_twin.f -+merohedr_twin.o: restr_files.o merohedr_twin.f -+ $(FC) $(FFLAGS) -c merohedr_twin.f - --ls_scaling_twin_save.o: restr_files.f90 ls_scaling_twin_save.f weights.f90 agreem.f90 -- $(FC) $(FFLAGS) -c restr_files.f90 weights.f90 agreem.f90 ls_scaling_twin_save.f -+ls_scaling_twin_save.o: restr_files.o ls_scaling_twin_save.f weights.o agreem.o -+ $(FC) $(FFLAGS) -c ls_scaling_twin_save.f - --ml_params_refine.o: restr_files.f90 ml_params_refine.f weights.f90 agreem.f90 -- $(FC) $(FFLAGS) -c restr_files.f90 weights.f90 agreem.f90 ml_params_refine.f -+ml_params_refine.o: restr_files.o ml_params_refine.f weights.o agreem.o -+ $(FC) $(FFLAGS) -c ml_params_refine.f - --optimise_solvent_all.o: optimise_solvent_all.f90 agreem.f90 -- $(FC) $(FFLAGS) -c optimise_solvent_all.f90 agreem.f90 -+optimise_solvent_all.o: optimise_solvent_all.f90 agreem.o -+ $(FC) $(FFLAGS) -c optimise_solvent_all.f90 - --ncs_rest.o: ncs_rest_mod.f90 restr_files.f90 ncs_ncs_generate.f90 ncs_rest.f weights.f90 -- $(FC) $(FFLAGS) -c ncs_rest_mod.f90 restr_files.f90 ncs_ncs_generate.f90 weights.f90 ncs_rest.f -+ncs_rest.o: ncs_rest_mod.o restr_files.o ncs_ncs_generate.o ncs_rest.f weights.o -+ $(FC) $(FFLAGS) -c ncs_rest.f - --ncs_ncs_generate.o: ncs_ncs_generate.f90 align_refmac.f90 -- $(FC) $(FFLAGS) -c ncs_ncs_generate.f90 align_refmac.f90 -+ncs_ncs_generate.o: ncs_ncs_generate.f90 align_refmac.o -+ $(FC) $(FFLAGS) -c ncs_ncs_generate.f90 - --lsq_exp2.o: ncs_rest_mod.f90 restr_files.f90 dist_routines.f90 ncs_simil.f90 ridge.f90 local_tls.f90 lsq_exp2.f weights.f90 rharvest_mod.f90 -- $(FC) $(FFLAGS) -c ncs_rest_mod.f90 restr_files.f90 dist_routines.f90 ncs_simil.f90 ridge.f90 local_tls.f90 lsq_exp2.f weights.f90 rharvest_mod.f90 -+lsq_exp2.o: ncs_rest_mod.o restr_files.o dist_routines.o ncs_simil.o ridge.o local_tls.o lsq_exp2.f weights.o rharvest_mod.o -+ $(FC) $(FFLAGS) -c lsq_exp2.f - --vdw_and_contacts.o: ncs_rest_mod.f90 vdw_and_contacts.f local_tls.f90 ridge.f90 restr_files.f90 weights.f90 agreem.f90 -- $(FC) $(FFLAGS) -c ncs_rest_mod.f90 restr_files.f90 ridge.f90 local_tls.f90 weights.f90 agreem.f90 vdw_and_contacts.f -+vdw_and_contacts.o: ncs_rest_mod.o vdw_and_contacts.f local_tls.o ridge.o restr_files.o weights.o agreem.o -+ $(FC) $(FFLAGS) -c vdw_and_contacts.f - - dist_routines.o: dist_routines.f90 - $(FC) $(FFLAGS) -c dist_routines.f90 - --ncs_simil.o: ncs_rest_mod.f90 ncs_simil.f90 -- $(FC) $(FFLAGS) -c ncs_rest_mod.f90 ncs_simil.f90 -+ncs_simil.o: ncs_rest_mod.o ncs_simil.f90 -+ $(FC) $(FFLAGS) -c ncs_simil.f90 - - ridge.o: ridge.f90 - $(FC) $(FFLAGS) -c ridge.f90 -@@ -227,140 +221,138 @@ ridge.o: ridge.f90 - align_refmac.o: align_refmac.f90 - $(FC) $(FFLAGS) -c align_refmac.f90 - --rigid_allocate.o: restr_files.f90 rigid_allocate.f agreem.f90 -- $(FC) $(FFLAGS) -c restr_files.f90 agreem.f90 rigid_allocate.f -+rigid_allocate.o: restr_files.o rigid_allocate.f agreem.o -+ $(FC) $(FFLAGS) -c rigid_allocate.f - --tls_allocate.o: restr_files.f90 tls_allocate.f weights.f90 agreem.f90 -- $(FC) $(FFLAGS) -c restr_files.f90 weights.f90 agreem.f90 tls_allocate.f -+tls_allocate.o: restr_files.o tls_allocate.f weights.o agreem.o -+ $(FC) $(FFLAGS) -c tls_allocate.f - --hkon_secder_tch.o: ridge.f90 gibbs_gm_sampler.f90 ncs_rest_mod.f90 hkon_secder_tch.f local_tls.f90 ncs_simil.f90 optimise_solvent_all.f90 \ -- restr_files.f90 weights.f90 agreem.f90 rharvest_mod.f90 -- $(FC) $(FFLAGS) -c ridge.f90 gibbs_gm_sampler.f90 ncs_rest_mod.f90 restr_files.f90 optimise_solvent_all.f90 ncs_simil.f90 local_tls.f90 \ -- hkon_secder_tch.f weights.f90 agreem.f90 rharvest_mod.f90 -+hkon_secder_tch.o: ridge.o gibbs_gm_sampler.o ncs_rest_mod.o hkon_secder_tch.f local_tls.o ncs_simil.o optimise_solvent_all.o \ -+ restr_files.o weights.o agreem.o rharvest_mod.o -+ $(FC) $(FFLAGS) -c hkon_secder_tch.f - --oppro_allocate.o: ncs_rest_mod.f90 oppro_allocate.f filter_params.f90 optimise_solvent_all.f90 restr_files.f90 weights.f90 -- $(FC) $(FFLAGS) -c ncs_rest_mod.f90 restr_files.f90 optimise_solvent_all.f90 filter_params.f90 weights.f90 oppro_allocate.f -+oppro_allocate.o: ncs_rest_mod.o oppro_allocate.f filter_params.o optimise_solvent_all.o restr_files.o weights.o -+ $(FC) $(FFLAGS) -c oppro_allocate.f - --read_extra_restraints.o: restr_files.f90 read_extra_restraints.f weights.f90 -- $(FC) $(FFLAGS) -c restr_files.f90 weights.f90 read_extra_restraints.f -+read_extra_restraints.o: restr_files.o read_extra_restraints.f weights.o -+ $(FC) $(FFLAGS) -c read_extra_restraints.f - --coords.o: coords.f90 atomf77mod.f -- $(FC) $(FFLAGS) -c atomf77mod.f coords.f90 -+coords.o: coords.f90 atomf77mod.o -+ $(FC) $(FFLAGS) -c coords.f90 - - --ls_scaling_double.o: ls_scaling_double.f weights.f90 agreem.f90 -- $(FC) $(FFLAGS) -c ls_scaling_double.f weights.f90 agreem.f90 -+ls_scaling_double.o: ls_scaling_double.f weights.o agreem.o -+ $(FC) $(FFLAGS) -c ls_scaling_double.f - --fast_hessian_tabulation.o: fast_hessian_tabulation.f weights.f90 -- $(FC) $(FFLAGS) -c fast_hessian_tabulation.f weights.f90 -+fast_hessian_tabulation.o: fast_hessian_tabulation.f weights.o -+ $(FC) $(FFLAGS) -c fast_hessian_tabulation.f - --calc_stats_twin.o: calc_stats_twin.f weights.f90 agreem.f90 rharvest_mod.f90 -- $(FC) $(FFLAGS) -c calc_stats_twin.f weights.f90 agreem.f90 rharvest_mod.f90 -+calc_stats_twin.o: calc_stats_twin.f weights.o agreem.o rharvest_mod.o -+ $(FC) $(FFLAGS) -c calc_stats_twin.f - --refpre_twin.o: refpre_twin.f coords.f90 automorphism.f90 restr_files.f90 weights.f90 agreem.f90 rharvest_mod.f90 -- $(FC) $(FFLAGS) -c restr_files.f90 coords.f90 automorphism.f90 weights.f90 agreem.f90 rharvest_mod.f90 refpre_twin.f -+refpre_twin.o: refpre_twin.f coords.o automorphism.o restr_files.o weights.o agreem.o rharvest_mod.o -+ $(FC) $(FFLAGS) -c refpre_twin.f - - --decide_twin_opers_0.o: restr_files.f90 decide_twin_opers_0.f -- $(FC) $(FFLAGS) -c restr_files.f90 decide_twin_opers_0.f -+decide_twin_opers_0.o: restr_files.o decide_twin_opers_0.f -+ $(FC) $(FFLAGS) -c decide_twin_opers_0.f - - automorphism.o: automorphism.f90 - $(FC) $(FFLAGS) -c automorphism.f90 - --mtz_write_twin.o: mtz_write_twin.f filter_params.f90 restr_files.f90 weights.f90 agreem.f90 -- $(FC) $(FFLAGS) -c restr_files.f90 filter_params.f90 weights.f90 agreem.f90 mtz_write_twin.f -+mtz_write_twin.o: mtz_write_twin.f filter_params.o restr_files.o weights.o agreem.o -+ $(FC) $(FFLAGS) -c mtz_write_twin.f - - filter_params.o: filter_params.f90 - $(FC) $(FFLAGS) -c filter_params.f90 - --rcard_tor1.o: ncs_rest_mod.f90 rcard_tor1.f filter_params.f90 local_tls.f90 ridge.f90 optimise_solvent_all.f90 restr_files.f90 weights.f90 \ -- agreem.f90 rharvest_mod.f90 ncs_constr.f90 -- $(FC) $(FFLAGS) -c ncs_rest_mod.f90 restr_files.f90 optimise_solvent_all.f90 filter_params.f90 local_tls.f90 ridge.f90 weights.f90 \ -- agreem.f90 rharvest_mod.f90 ncs_constr.f90 rcard_tor1.f -+rcard_tor1.o: ncs_rest_mod.o rcard_tor1.f filter_params.o local_tls.o ridge.o optimise_solvent_all.o restr_files.o weights.o \ -+ agreem.o rharvest_mod.o ncs_constr.o -+ $(FC) $(FFLAGS) -c rcard_tor1.f - --inout_routines.o: restr_files.f90 inout_routines.f -- $(FC) $(FFLAGS) -c restr_files.f90 inout_routines.f -+inout_routines.o: restr_files.o inout_routines.f -+ $(FC) $(FFLAGS) -c inout_routines.f - --local_tls.o: local_tls.f90 linalgebra_f90.f90 -- $(FC) $(FFLAGS) -c linalgebra_f90.f90 local_tls.f90 -+local_tls.o: local_tls.f90 linalgebra_f90.o -+ $(FC) $(FFLAGS) -c local_tls.f90 - - linalgebra_f90.o: linalgebra_f90.f90 - $(FC) $(FFLAGS) -c linalgebra_f90.f90 - --make_refmac_dummy.o: restr_files.f90 ncs_rest_mod.f90 make_refmac_dummy.f optimise_solvent_all.f90 weights.f90 agreem.f90 rharvest_mod.f90 -- $(FC) $(FFLAGS) -c restr_files.f90 ncs_rest_mod.f90 weights.f90 agreem.f90 rharvest_mod.f90 optimise_solvent_all.f90 make_refmac_dummy.f -+make_refmac_dummy.o: restr_files.o ncs_rest_mod.o make_refmac_dummy.f optimise_solvent_all.o weights.o agreem.o rharvest_mod.o -+ $(FC) $(FFLAGS) -c make_refmac_dummy.f - --ml_scaling_double.o: ml_scaling_double.f optimise_solvent_all.f90 weights.f90 agreem.f90 rharvest_mod.f90 -- $(FC) $(FFLAGS) -c optimise_solvent_all.f90 weights.f90 agreem.f90 rharvest_mod.f90 ml_scaling_double.f -+ml_scaling_double.o: ml_scaling_double.f optimise_solvent_all.o weights.o agreem.o rharvest_mod.o -+ $(FC) $(FFLAGS) -c ml_scaling_double.f - --refall_twin.o: refall_twin.f optimise_solvent_all.f90 restr_files.f90 weights.f90 agreem.f90 rharvest_mod.f90 -- $(FC) $(FFLAGS) -c restr_files.f90 optimise_solvent_all.f90 weights.f90 agreem.f90 rharvest_mod.f90 refall_twin.f -+refall_twin.o: refall_twin.f optimise_solvent_all.o restr_files.f90 weights.o agreem.o rharvest_mod.o -+ $(FC) $(FFLAGS) -c refall_twin.f - --rharvest_subr.o: ncs_rest_mod.f90 rharvest_subr.f optimise_solvent_all.f90 weights.f90 agreem.f90 rharvest_mod.f90 -- $(FC) $(FFLAGS) -c ncs_rest_mod.f90 optimise_solvent_all.f90 weights.f90 agreem.f90 rharvest_mod.f90 rharvest_subr.f -+rharvest_subr.o: ncs_rest_mod.o rharvest_subr.f optimise_solvent_all.o weights.o agreem.o rharvest_mod.o -+ $(FC) $(FFLAGS) -c rharvest_subr.f - --solvent_contr_mask.o: solvent_contr_mask.f optimise_solvent_all.f90 weights.f90 agreem.f90 rharvest_mod.f90 ncs_constr.f90 -- $(FC) $(FFLAGS) -c optimise_solvent_all.f90 weights.f90 agreem.f90 rharvest_mod.f90 ncs_constr.f90 solvent_contr_mask.f -+solvent_contr_mask.o: solvent_contr_mask.f optimise_solvent_all.o weights.o agreem.o rharvest_mod.o ncs_constr.o -+ $(FC) $(FFLAGS) -c solvent_contr_mask.f - --subag_scale_hessian.o: subag_scale_hessian.f optimise_solvent_all.f90 restr_files.f90 weights.f90 agreem.f90 rharvest_mod.f90 ncs_constr.f90 -- $(FC) $(FFLAGS) -c restr_files.f90 optimise_solvent_all.f90 weights.f90 agreem.f90 rharvest_mod.f90 ncs_constr.f90 subag_scale_hessian.f -+subag_scale_hessian.o: subag_scale_hessian.f optimise_solvent_all.o restr_files.o weights.o agreem.o rharvest_mod.o ncs_constr.o -+ $(FC) $(FFLAGS) -c subag_scale_hessian.f - --aniso_ref_eigen.o: aniso_ref_eigen.f ncs_constr.f90 -- $(FC) $(FFLAGS) -c ncs_constr.f90 aniso_ref_eigen.f -+aniso_ref_eigen.o: aniso_ref_eigen.f ncs_constr.o -+ $(FC) $(FFLAGS) -c aniso_ref_eigen.f - --subcf_scale1.o: subcf_scale1.f optimise_solvent_all.f90 weights.f90 agreem.f90 rharvest_mod.f90 -- $(FC) $(FFLAGS) -c optimise_solvent_all.f90 weights.f90 agreem.f90 rharvest_mod.f90 subcf_scale1.f -+subcf_scale1.o: subcf_scale1.f optimise_solvent_all.o weights.o agreem.o rharvest_mod.o -+ $(FC) $(FFLAGS) -c subcf_scale1.f - --bvalue_routines.o: bvalue_routines.f90 restr_files.f90 atomf77mod.f -- $(FC) $(FFLAGS) -c restr_files.f90 atomf77mod.f bvalue_routines.f90 -+bvalue_routines.o: bvalue_routines.f90 restr_files.o atomf77mod.o -+ $(FC) $(FFLAGS) -c bvalue_routines.f90 - --newentry_idealise.o:: newentry_idealise.f weights.f90 -- $(FC) $(FFLAGS) -c newentry_idealise.f weights.f90 -+newentry_idealise.o:: newentry_idealise.f weights.o -+ $(FC) $(FFLAGS) -c newentry_idealise.f - --occupancy_only_refine.o: occupancy_only_refine.f agreem.f90 rharvest_mod.f90 -- $(FC) $(FFLAGS) -c occupancy_only_refine.f agreem.f90 rharvest_mod.f90 -+occupancy_only_refine.o: occupancy_only_refine.f agreem.o rharvest_mod.o -+ $(FC) $(FFLAGS) -c occupancy_only_refine.f - --refmac_completeness.o: weights.f90 agreem.f90 rharvest_mod.f90 refmac_completeness.f90 -- $(FC) $(FFLAGS) -c weights.f90 agreem.f90 rharvest_mod.f90 refmac_completeness.f90 -+refmac_completeness.o: weights.o agreem.o rharvest_mod.o refmac_completeness.f90 -+ $(FC) $(FFLAGS) -c refmac_completeness.f90 - --refmac_xml.o: refmac_xml.f optimise_solvent_all.f90 restr_files.f90 bvalue_routines.f90 weights.f90 agreem.f90 rharvest_mod.f90 -- $(FC) $(FFLAGS) -c bvalue_routines.f90 restr_files.f90 optimise_solvent_all.f90 weights.f90 agreem.f90 rharvest_mod.f90 refmac_xml.f -+refmac_xml.o: refmac_xml.f optimise_solvent_all.o restr_files.o bvalue_routines.o weights.o agreem.o rharvest_mod.o -+ $(FC) $(FFLAGS) -c refmac_xml.f - - hkl_pack.o: hkl_pack.f90 - $(FC) $(FFLAGS) -c hkl_pack.f90 - --extra_eigen.o: extra_eigen.f agreem.f90 ncs_constr.f90 -- $(FC) $(FFLAGS) -c extra_eigen.f agreem.f90 ncs_constr.f90 -+extra_eigen.o: extra_eigen.f agreem.o ncs_constr.o -+ $(FC) $(FFLAGS) -c extra_eigen.f - --subvag.o: subvag.f hkl_pack.f90 -- $(FC) $(FFLAGS) -c hkl_pack.f90 subvag.f -+subvag.o: subvag.f hkl_pack.o -+ $(FC) $(FFLAGS) -c subvag.f - --make_PDB.o: make_PDB.f ncs_constr.f90 -- $(FC) $(FFLAGS) -c ncs_constr.f90 make_PDB.f -+make_PDB.o: make_PDB.f ncs_constr.o -+ $(FC) $(FFLAGS) -c make_PDB.f - --make_CIF.o: make_CIF.f ncs_constr.f90 -- $(FC) $(FFLAGS) -c ncs_constr.f90 make_CIF.f -+make_CIF.o: make_CIF.f ncs_constr.o -+ $(FC) $(FFLAGS) -c make_CIF.f - - refmac: $(SUBR) -- $(FC) $(FFLAGS) -o refmac${VERSION} ${SUBR} $(LLIBOTHERS) $(LLIBCCP) -+ $(FC) $(FFLAGS) $(LDFLAGS) -o refmac${VERSION} ${SUBR} $(LLIBOTHERS) $(LLIBCCP) $(LLIBCIF) $(LLIBLAPACK) - --mol2_file.o: mol2_file.f odb_files.f90 -- $(FC) $(FFLAGS) -c odb_files.f90 mol2_file.f -+mol2_file.o: mol2_file.f odb_files.o -+ $(FC) $(FFLAGS) -c mol2_file.f - --odb_files.o: odb_files.f90 elements_module.f90 enerf77mod.f -- $(FC) $(FFLAGS) -c elements_module.f90 enerf77mod.f odb_files.f90 -+odb_files.o: odb_files.f90 elements_module.o enerf77mod.o -+ $(FC) $(FFLAGS) -c odb_files.f90 - - elements_module.o: elements_module.f90 - $(FC) $(FFLAGS) -c elements_module.f90 - --make_lib2.o: make_lib2.f odb_files.f90 -- $(FC) $(FFLAGS) -c odb_files.f90 make_lib2.f -+make_lib2.o: make_lib2.f odb_files.o -+ $(FC) $(FFLAGS) -c make_lib2.f - - pdb2libcheck.o: pdb2libcheck.f90 - $(FC) $(FFLAGS) -c pdb2libcheck.f90 - --libcheck.o: libcheck.f elements_module.f90 pdb2libcheck.f90 -- $(FC) $(FFLAGS) -c elements_module.f90 pdb2libcheck.f90 libcheck.f -+libcheck.o: libcheck.f elements_module.o pdb2libcheck.o -+ $(FC) $(FFLAGS) -c libcheck.f - - header2matr.o: header2matr.f90 - $(FC) $(FFLAGS) -c header2matr.f90 -@@ -369,16 +361,17 @@ freer_twin.o: freer_twin.f90 - $(FC) $(FFLAGS) -c freer_twin.f90 - - libcheck: $(SUBL) -- $(FC) $(FFLAGS) -o libcheck${VERSION} $(SUBL) -+ $(FC) $(FFLAGS) $(LDFLAGS) -o libcheck${VERSION} $(SUBL) $(LLIBCCP) $(LLIBCIF) $(LLIBLAPACK) - - free_twin: $(SUB_FREE) -- $(FC) $(FFLAGS) -o FreeTwin${VERSION} $(SUB_FREE) -+ $(FC) $(FFLAGS) $(LDFLAGS) -o FreeTwin${VERSION} $(SUB_FREE) $(LLIBCCP) $(LLIBLAPACK) - - - header2matr: $(SUB_HEADER) -- $(FC) $(FFLAGS) -o header2matr${VERSION} $(SUB_HEADER) -+ $(FC) $(FFLAGS) $(LDFLAGS) -o header2matr${VERSION} $(SUB_HEADER) - - clean: - /bin/rm *.o *.mod - - bridge.o: bridge.cpp llhood.h covmat.h Gauss.h tabfunc.h -+ $(CXX) $(CXXFLAGS) -c bridge.cpp diff --git a/sci-chemistry/refmac/files/5.6.0116-allow-dynamic-linking.patch b/sci-chemistry/refmac/files/5.6.0116-allow-dynamic-linking.patch deleted file mode 100644 index 9998b759c664..000000000000 --- a/sci-chemistry/refmac/files/5.6.0116-allow-dynamic-linking.patch +++ /dev/null @@ -1,341 +0,0 @@ - makefile_refmac.inc1 | 215 ++++++++++++++++++++++++-------------------------- - 1 files changed, 104 insertions(+), 111 deletions(-) - -diff --git a/makefile_refmac.inc1 b/makefile_refmac.inc1 -index 0f8bd63..e59fbfb 100644 ---- a/makefile_refmac.inc1 -+++ b/makefile_refmac.inc1 -@@ -96,9 +96,7 @@ bridge.o \ - i0.o \ - i1.o \ - chbevl.o \ --make_unix_ccp4.o \ --$(LLIBCIF) \ --$(LLIBLAPACK) -+make_unix_ccp4.o - - - SUBL = \ -@@ -133,9 +131,7 @@ cell_symm_subrs.o \ - iheap_sort.o \ - linalgebra.o \ - math_refmac.o \ --subnumrec.o \ --$(LLIBLAPACK) \ --$(LLIBCCP) -+subnumrec.o - - SUB_FREE = \ - freer_twin.o \ -@@ -145,9 +141,7 @@ subnumrec.o \ - libT.o \ - iheap_sort.o \ - cell_symm_subrs.o \ --math_refmac.o \ --$(LLIBLAPACK) \ --$(LLIBCCP) -+math_refmac.o - - SUB_HEADER = header2matr.o - #-------------------------------------------------------------------------------- -@@ -185,41 +179,41 @@ rharvest_mod.o: rharvest_mod.f90 - twin77mod.o: twin77mod.f - $(FC) $(FFLAGS) -c twin77mod.f - --gibbs_gm_sampler.o: linalgebra_f90.f90 gibbs_gm_sampler.f90 -- $(FC) $(FFLAGS) -c linalgebra_f90.f90 gibbs_gm_sampler.f90 -+gibbs_gm_sampler.o: linalgebra_f90.o gibbs_gm_sampler.f90 -+ $(FC) $(FFLAGS) -c gibbs_gm_sampler.f90 - --max_with_twins.o: restr_files.f90 max_with_twins.f weights.f90 agreem.f90 -- $(FC) $(FFLAGS) -c restr_files.f90 weights.f90 agreem.f90 max_with_twins.f -+max_with_twins.o: restr_files.o max_with_twins.f weights.o agreem.o -+ $(FC) $(FFLAGS) -c max_with_twins.f - --merohedr_twin.o: restr_files.f90 merohedr_twin.f -- $(FC) $(FFLAGS) -c restr_files.f90 merohedr_twin.f -+merohedr_twin.o: restr_files.o merohedr_twin.f -+ $(FC) $(FFLAGS) -c merohedr_twin.f - --ls_scaling_twin_save.o: restr_files.f90 ls_scaling_twin_save.f weights.f90 agreem.f90 -- $(FC) $(FFLAGS) -c restr_files.f90 weights.f90 agreem.f90 ls_scaling_twin_save.f -+ls_scaling_twin_save.o: restr_files.o ls_scaling_twin_save.f weights.o agreem.o -+ $(FC) $(FFLAGS) -c ls_scaling_twin_save.f - --ml_params_refine.o: restr_files.f90 ml_params_refine.f weights.f90 agreem.f90 -- $(FC) $(FFLAGS) -c restr_files.f90 weights.f90 agreem.f90 ml_params_refine.f -+ml_params_refine.o: restr_files.o ml_params_refine.f weights.o agreem.o -+ $(FC) $(FFLAGS) -c ml_params_refine.f - --optimise_solvent_all.o: optimise_solvent_all.f90 agreem.f90 -- $(FC) $(FFLAGS) -c optimise_solvent_all.f90 agreem.f90 -+optimise_solvent_all.o: optimise_solvent_all.f90 agreem.o -+ $(FC) $(FFLAGS) -c optimise_solvent_all.f90 - --ncs_rest.o: ncs_rest_mod.f90 restr_files.f90 ncs_ncs_generate.f90 ncs_rest.f weights.f90 -- $(FC) $(FFLAGS) -c ncs_rest_mod.f90 restr_files.f90 ncs_ncs_generate.f90 weights.f90 ncs_rest.f -+ncs_rest.o: ncs_rest_mod.o restr_files.o ncs_ncs_generate.o ncs_rest.f weights.o -+ $(FC) $(FFLAGS) -c ncs_rest.f - --ncs_ncs_generate.o: ncs_ncs_generate.f90 align_refmac.f90 -- $(FC) $(FFLAGS) -c ncs_ncs_generate.f90 align_refmac.f90 -+ncs_ncs_generate.o: ncs_ncs_generate.f90 align_refmac.o -+ $(FC) $(FFLAGS) -c ncs_ncs_generate.f90 - --lsq_exp2.o: ncs_rest_mod.f90 restr_files.f90 dist_routines.f90 ncs_simil.f90 ridge.f90 local_tls.f90 lsq_exp2.f weights.f90 rharvest_mod.f90 -- $(FC) $(FFLAGS) -c ncs_rest_mod.f90 restr_files.f90 dist_routines.f90 ncs_simil.f90 ridge.f90 local_tls.f90 lsq_exp2.f weights.f90 rharvest_mod.f90 -+lsq_exp2.o: ncs_rest_mod.o restr_files.o dist_routines.o ncs_simil.o ridge.o local_tls.o lsq_exp2.f weights.o rharvest_mod.o -+ $(FC) $(FFLAGS) -c lsq_exp2.f - --vdw_and_contacts.o: ncs_rest_mod.f90 vdw_and_contacts.f local_tls.f90 ridge.f90 restr_files.f90 weights.f90 agreem.f90 -- $(FC) $(FFLAGS) -c ncs_rest_mod.f90 restr_files.f90 ridge.f90 local_tls.f90 weights.f90 agreem.f90 vdw_and_contacts.f -+vdw_and_contacts.o: ncs_rest_mod.o vdw_and_contacts.f local_tls.o ridge.o restr_files.o weights.o agreem.o -+ $(FC) $(FFLAGS) -c vdw_and_contacts.f - - dist_routines.o: dist_routines.f90 - $(FC) $(FFLAGS) -c dist_routines.f90 - --ncs_simil.o: ncs_rest_mod.f90 ncs_simil.f90 -- $(FC) $(FFLAGS) -c ncs_rest_mod.f90 ncs_simil.f90 -+ncs_simil.o: ncs_rest_mod.o ncs_simil.f90 -+ $(FC) $(FFLAGS) -c ncs_simil.f90 - - ridge.o: ridge.f90 - $(FC) $(FFLAGS) -c ridge.f90 -@@ -227,140 +221,138 @@ ridge.o: ridge.f90 - align_refmac.o: align_refmac.f90 - $(FC) $(FFLAGS) -c align_refmac.f90 - --rigid_allocate.o: restr_files.f90 rigid_allocate.f agreem.f90 -- $(FC) $(FFLAGS) -c restr_files.f90 agreem.f90 rigid_allocate.f -+rigid_allocate.o: restr_files.o rigid_allocate.f agreem.o -+ $(FC) $(FFLAGS) -c rigid_allocate.f - --tls_allocate.o: restr_files.f90 tls_allocate.f weights.f90 agreem.f90 -- $(FC) $(FFLAGS) -c restr_files.f90 weights.f90 agreem.f90 tls_allocate.f -+tls_allocate.o: restr_files.o tls_allocate.f weights.o agreem.o -+ $(FC) $(FFLAGS) -c tls_allocate.f - --hkon_secder_tch.o: ridge.f90 gibbs_gm_sampler.f90 ncs_rest_mod.f90 hkon_secder_tch.f local_tls.f90 ncs_simil.f90 optimise_solvent_all.f90 \ -- restr_files.f90 weights.f90 agreem.f90 rharvest_mod.f90 -- $(FC) $(FFLAGS) -c ridge.f90 gibbs_gm_sampler.f90 ncs_rest_mod.f90 restr_files.f90 optimise_solvent_all.f90 ncs_simil.f90 local_tls.f90 \ -- hkon_secder_tch.f weights.f90 agreem.f90 rharvest_mod.f90 -+hkon_secder_tch.o: ridge.o gibbs_gm_sampler.o ncs_rest_mod.o hkon_secder_tch.f local_tls.o ncs_simil.o optimise_solvent_all.o \ -+ restr_files.o weights.o agreem.o rharvest_mod.o -+ $(FC) $(FFLAGS) -c hkon_secder_tch.f - --oppro_allocate.o: ncs_rest_mod.f90 oppro_allocate.f filter_params.f90 optimise_solvent_all.f90 restr_files.f90 weights.f90 -- $(FC) $(FFLAGS) -c ncs_rest_mod.f90 restr_files.f90 optimise_solvent_all.f90 filter_params.f90 weights.f90 oppro_allocate.f -+oppro_allocate.o: ncs_rest_mod.o oppro_allocate.f filter_params.o optimise_solvent_all.o restr_files.o weights.o -+ $(FC) $(FFLAGS) -c oppro_allocate.f - --read_extra_restraints.o: restr_files.f90 read_extra_restraints.f weights.f90 -- $(FC) $(FFLAGS) -c restr_files.f90 weights.f90 read_extra_restraints.f -+read_extra_restraints.o: restr_files.o read_extra_restraints.f weights.o -+ $(FC) $(FFLAGS) -c read_extra_restraints.f - --coords.o: coords.f90 atomf77mod.f -- $(FC) $(FFLAGS) -c atomf77mod.f coords.f90 -+coords.o: coords.f90 atomf77mod.o -+ $(FC) $(FFLAGS) -c coords.f90 - - --ls_scaling_double.o: ls_scaling_double.f weights.f90 agreem.f90 -- $(FC) $(FFLAGS) -c ls_scaling_double.f weights.f90 agreem.f90 -+ls_scaling_double.o: ls_scaling_double.f weights.o agreem.o -+ $(FC) $(FFLAGS) -c ls_scaling_double.f - --fast_hessian_tabulation.o: fast_hessian_tabulation.f weights.f90 -- $(FC) $(FFLAGS) -c fast_hessian_tabulation.f weights.f90 -+fast_hessian_tabulation.o: fast_hessian_tabulation.f weights.o -+ $(FC) $(FFLAGS) -c fast_hessian_tabulation.f - --calc_stats_twin.o: calc_stats_twin.f weights.f90 agreem.f90 rharvest_mod.f90 -- $(FC) $(FFLAGS) -c calc_stats_twin.f weights.f90 agreem.f90 rharvest_mod.f90 -+calc_stats_twin.o: calc_stats_twin.f weights.o agreem.o rharvest_mod.o -+ $(FC) $(FFLAGS) -c calc_stats_twin.f - --refpre_twin.o: refpre_twin.f coords.f90 automorphism.f90 restr_files.f90 weights.f90 agreem.f90 rharvest_mod.f90 -- $(FC) $(FFLAGS) -c restr_files.f90 coords.f90 automorphism.f90 weights.f90 agreem.f90 rharvest_mod.f90 refpre_twin.f -+refpre_twin.o: refpre_twin.f coords.o automorphism.o restr_files.o weights.o agreem.o rharvest_mod.o -+ $(FC) $(FFLAGS) -c refpre_twin.f - - --decide_twin_opers_0.o: restr_files.f90 decide_twin_opers_0.f -- $(FC) $(FFLAGS) -c restr_files.f90 decide_twin_opers_0.f -+decide_twin_opers_0.o: restr_files.o decide_twin_opers_0.f -+ $(FC) $(FFLAGS) -c decide_twin_opers_0.f - - automorphism.o: automorphism.f90 - $(FC) $(FFLAGS) -c automorphism.f90 - --mtz_write_twin.o: mtz_write_twin.f filter_params.f90 restr_files.f90 weights.f90 agreem.f90 -- $(FC) $(FFLAGS) -c restr_files.f90 filter_params.f90 weights.f90 agreem.f90 mtz_write_twin.f -+mtz_write_twin.o: mtz_write_twin.f filter_params.o restr_files.o weights.o agreem.o -+ $(FC) $(FFLAGS) -c mtz_write_twin.f - - filter_params.o: filter_params.f90 - $(FC) $(FFLAGS) -c filter_params.f90 - --rcard_tor1.o: ncs_rest_mod.f90 rcard_tor1.f filter_params.f90 local_tls.f90 ridge.f90 optimise_solvent_all.f90 restr_files.f90 weights.f90 \ -- agreem.f90 rharvest_mod.f90 ncs_constr.f90 -- $(FC) $(FFLAGS) -c ncs_rest_mod.f90 restr_files.f90 optimise_solvent_all.f90 filter_params.f90 local_tls.f90 ridge.f90 weights.f90 \ -- agreem.f90 rharvest_mod.f90 ncs_constr.f90 rcard_tor1.f -+rcard_tor1.o: ncs_rest_mod.o rcard_tor1.f filter_params.o local_tls.o ridge.o optimise_solvent_all.o restr_files.o weights.o \ -+ agreem.o rharvest_mod.o ncs_constr.o -+ $(FC) $(FFLAGS) -c rcard_tor1.f - --inout_routines.o: restr_files.f90 inout_routines.f -- $(FC) $(FFLAGS) -c restr_files.f90 inout_routines.f -+inout_routines.o: restr_files.o inout_routines.f -+ $(FC) $(FFLAGS) -c inout_routines.f - --local_tls.o: local_tls.f90 linalgebra_f90.f90 -- $(FC) $(FFLAGS) -c linalgebra_f90.f90 local_tls.f90 -+local_tls.o: local_tls.f90 linalgebra_f90.o -+ $(FC) $(FFLAGS) -c local_tls.f90 - - linalgebra_f90.o: linalgebra_f90.f90 - $(FC) $(FFLAGS) -c linalgebra_f90.f90 - --make_refmac_dummy.o: restr_files.f90 ncs_rest_mod.f90 make_refmac_dummy.f optimise_solvent_all.f90 weights.f90 agreem.f90 rharvest_mod.f90 -- $(FC) $(FFLAGS) -c restr_files.f90 ncs_rest_mod.f90 weights.f90 agreem.f90 rharvest_mod.f90 optimise_solvent_all.f90 make_refmac_dummy.f -+make_refmac_dummy.o: restr_files.o ncs_rest_mod.o make_refmac_dummy.f optimise_solvent_all.o weights.o agreem.o rharvest_mod.o -+ $(FC) $(FFLAGS) -c make_refmac_dummy.f - --ml_scaling_double.o: ml_scaling_double.f optimise_solvent_all.f90 weights.f90 agreem.f90 rharvest_mod.f90 -- $(FC) $(FFLAGS) -c optimise_solvent_all.f90 weights.f90 agreem.f90 rharvest_mod.f90 ml_scaling_double.f -+ml_scaling_double.o: ml_scaling_double.f optimise_solvent_all.o weights.o agreem.o rharvest_mod.o -+ $(FC) $(FFLAGS) -c ml_scaling_double.f - --refall_twin.o: refall_twin.f optimise_solvent_all.f90 restr_files.f90 weights.f90 agreem.f90 rharvest_mod.f90 -- $(FC) $(FFLAGS) -c restr_files.f90 optimise_solvent_all.f90 weights.f90 agreem.f90 rharvest_mod.f90 refall_twin.f -+refall_twin.o: refall_twin.f optimise_solvent_all.o restr_files.f90 weights.o agreem.o rharvest_mod.o -+ $(FC) $(FFLAGS) -c refall_twin.f - --rharvest_subr.o: ncs_rest_mod.f90 rharvest_subr.f optimise_solvent_all.f90 weights.f90 agreem.f90 rharvest_mod.f90 -- $(FC) $(FFLAGS) -c ncs_rest_mod.f90 optimise_solvent_all.f90 weights.f90 agreem.f90 rharvest_mod.f90 rharvest_subr.f -+rharvest_subr.o: ncs_rest_mod.o rharvest_subr.f optimise_solvent_all.o weights.o agreem.o rharvest_mod.o -+ $(FC) $(FFLAGS) -c rharvest_subr.f - --solvent_contr_mask.o: solvent_contr_mask.f optimise_solvent_all.f90 weights.f90 agreem.f90 rharvest_mod.f90 ncs_constr.f90 -- $(FC) $(FFLAGS) -c optimise_solvent_all.f90 weights.f90 agreem.f90 rharvest_mod.f90 ncs_constr.f90 solvent_contr_mask.f -+solvent_contr_mask.o: solvent_contr_mask.f optimise_solvent_all.o weights.o agreem.o rharvest_mod.o ncs_constr.o -+ $(FC) $(FFLAGS) -c solvent_contr_mask.f - --subag_scale_hessian.o: subag_scale_hessian.f optimise_solvent_all.f90 restr_files.f90 weights.f90 agreem.f90 rharvest_mod.f90 ncs_constr.f90 -- $(FC) $(FFLAGS) -c restr_files.f90 optimise_solvent_all.f90 weights.f90 agreem.f90 rharvest_mod.f90 ncs_constr.f90 subag_scale_hessian.f -+subag_scale_hessian.o: subag_scale_hessian.f optimise_solvent_all.o restr_files.o weights.o agreem.o rharvest_mod.o ncs_constr.o -+ $(FC) $(FFLAGS) -c subag_scale_hessian.f - --aniso_ref_eigen.o: aniso_ref_eigen.f ncs_constr.f90 -- $(FC) $(FFLAGS) -c ncs_constr.f90 aniso_ref_eigen.f -+aniso_ref_eigen.o: aniso_ref_eigen.f ncs_constr.o -+ $(FC) $(FFLAGS) -c aniso_ref_eigen.f - --subcf_scale1.o: subcf_scale1.f optimise_solvent_all.f90 weights.f90 agreem.f90 rharvest_mod.f90 -- $(FC) $(FFLAGS) -c optimise_solvent_all.f90 weights.f90 agreem.f90 rharvest_mod.f90 subcf_scale1.f -+subcf_scale1.o: subcf_scale1.f optimise_solvent_all.o weights.o agreem.o rharvest_mod.o -+ $(FC) $(FFLAGS) -c subcf_scale1.f - --bvalue_routines.o: bvalue_routines.f90 restr_files.f90 atomf77mod.f -- $(FC) $(FFLAGS) -c restr_files.f90 atomf77mod.f bvalue_routines.f90 -+bvalue_routines.o: bvalue_routines.f90 restr_files.o atomf77mod.o -+ $(FC) $(FFLAGS) -c bvalue_routines.f90 - --newentry_idealise.o:: newentry_idealise.f weights.f90 -- $(FC) $(FFLAGS) -c newentry_idealise.f weights.f90 -+newentry_idealise.o:: newentry_idealise.f weights.o -+ $(FC) $(FFLAGS) -c newentry_idealise.f - --occupancy_only_refine.o: occupancy_only_refine.f agreem.f90 rharvest_mod.f90 -- $(FC) $(FFLAGS) -c occupancy_only_refine.f agreem.f90 rharvest_mod.f90 -+occupancy_only_refine.o: occupancy_only_refine.f agreem.o rharvest_mod.o -+ $(FC) $(FFLAGS) -c occupancy_only_refine.f - --refmac_completeness.o: weights.f90 agreem.f90 rharvest_mod.f90 refmac_completeness.f90 -- $(FC) $(FFLAGS) -c weights.f90 agreem.f90 rharvest_mod.f90 refmac_completeness.f90 -+refmac_completeness.o: weights.o agreem.o rharvest_mod.o refmac_completeness.f90 -+ $(FC) $(FFLAGS) -c refmac_completeness.f90 - --refmac_xml.o: refmac_xml.f optimise_solvent_all.f90 restr_files.f90 bvalue_routines.f90 weights.f90 agreem.f90 rharvest_mod.f90 -- $(FC) $(FFLAGS) -c bvalue_routines.f90 restr_files.f90 optimise_solvent_all.f90 weights.f90 agreem.f90 rharvest_mod.f90 refmac_xml.f -+refmac_xml.o: refmac_xml.f optimise_solvent_all.o restr_files.o bvalue_routines.o weights.o agreem.o rharvest_mod.o -+ $(FC) $(FFLAGS) -c refmac_xml.f - - hkl_pack.o: hkl_pack.f90 - $(FC) $(FFLAGS) -c hkl_pack.f90 - --extra_eigen.o: extra_eigen.f agreem.f90 ncs_constr.f90 -- $(FC) $(FFLAGS) -c extra_eigen.f agreem.f90 ncs_constr.f90 -+extra_eigen.o: extra_eigen.f agreem.o ncs_constr.o -+ $(FC) $(FFLAGS) -c extra_eigen.f - --subvag.o: subvag.f hkl_pack.f90 -- $(FC) $(FFLAGS) -c hkl_pack.f90 subvag.f -+subvag.o: subvag.f hkl_pack.o -+ $(FC) $(FFLAGS) -c subvag.f - --make_PDB.o: make_PDB.f ncs_constr.f90 -- $(FC) $(FFLAGS) -c ncs_constr.f90 make_PDB.f -+make_PDB.o: make_PDB.f ncs_constr.o -+ $(FC) $(FFLAGS) -c make_PDB.f - --make_CIF.o: make_CIF.f ncs_constr.f90 -- $(FC) $(FFLAGS) -c ncs_constr.f90 make_CIF.f -+make_CIF.o: make_CIF.f ncs_constr.o -+ $(FC) $(FFLAGS) -c make_CIF.f - - refmac: $(SUBR) -- $(FC) $(FFLAGS) -o refmac${VERSION} ${SUBR} $(LLIBOTHERS) $(LLIBCCP) -+ $(FC) $(FFLAGS) $(LDFLAGS) -o refmac${VERSION} ${SUBR} $(LLIBOTHERS) $(LLIBCCP) $(LLIBCIF) $(LLIBLAPACK) - --mol2_file.o: mol2_file.f odb_files.f90 -- $(FC) $(FFLAGS) -c odb_files.f90 mol2_file.f -+mol2_file.o: mol2_file.f odb_files.o -+ $(FC) $(FFLAGS) -c mol2_file.f - --odb_files.o: odb_files.f90 elements_module.f90 enerf77mod.f -- $(FC) $(FFLAGS) -c elements_module.f90 enerf77mod.f odb_files.f90 -+odb_files.o: odb_files.f90 elements_module.o enerf77mod.o -+ $(FC) $(FFLAGS) -c odb_files.f90 - - elements_module.o: elements_module.f90 - $(FC) $(FFLAGS) -c elements_module.f90 - --make_lib2.o: make_lib2.f odb_files.f90 -- $(FC) $(FFLAGS) -c odb_files.f90 make_lib2.f -+make_lib2.o: make_lib2.f odb_files.o -+ $(FC) $(FFLAGS) -c make_lib2.f - - pdb2libcheck.o: pdb2libcheck.f90 - $(FC) $(FFLAGS) -c pdb2libcheck.f90 - --libcheck.o: libcheck.f elements_module.f90 pdb2libcheck.f90 -- $(FC) $(FFLAGS) -c elements_module.f90 pdb2libcheck.f90 libcheck.f -+libcheck.o: libcheck.f elements_module.o pdb2libcheck.o -+ $(FC) $(FFLAGS) -c libcheck.f - - header2matr.o: header2matr.f90 - $(FC) $(FFLAGS) -c header2matr.f90 -@@ -369,16 +361,17 @@ freer_twin.o: freer_twin.f90 - $(FC) $(FFLAGS) -c freer_twin.f90 - - libcheck: $(SUBL) -- $(FC) $(FFLAGS) -o libcheck${VERSION} $(SUBL) -+ $(FC) $(FFLAGS) $(LDFLAGS) -o libcheck${VERSION} $(SUBL) $(LLIBCCP) $(LLIBCIF) $(LLIBLAPACK) - - free_twin: $(SUB_FREE) -- $(FC) $(FFLAGS) -o FreeTwin${VERSION} $(SUB_FREE) -+ $(FC) $(FFLAGS) $(LDFLAGS) -o FreeTwin${VERSION} $(SUB_FREE) $(LLIBCCP) $(LLIBLAPACK) - - - header2matr: $(SUB_HEADER) -- $(FC) $(FFLAGS) -o header2matr${VERSION} $(SUB_HEADER) -+ $(FC) $(FFLAGS) $(LDFLAGS) -o header2matr${VERSION} $(SUB_HEADER) - - clean: - /bin/rm *.o *.mod - - bridge.o: bridge.cpp llhood.h covmat.h Gauss.h tabfunc.h -+ $(CXX) $(CXXFLAGS) -c bridge.cpp diff --git a/sci-chemistry/refmac/metadata.xml b/sci-chemistry/refmac/metadata.xml deleted file mode 100644 index c0432fefe855..000000000000 --- a/sci-chemistry/refmac/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@gentoo.org</email> - <name>Justin Lecher (jlec)</name> - </maintainer> -</pkgmetadata> diff --git a/sci-chemistry/refmac/refmac-5.5.0110-r3.ebuild b/sci-chemistry/refmac/refmac-5.5.0110-r3.ebuild deleted file mode 100644 index eb8e87018219..000000000000 --- a/sci-chemistry/refmac/refmac-5.5.0110-r3.ebuild +++ /dev/null @@ -1,85 +0,0 @@ -# Copyright 1999-2014 Gentoo Foundation -# Distributed under the terms of the GNU General Public License v2 -# $Id$ - -EAPI=4 - -inherit eutils fortran-2 flag-o-matic toolchain-funcs versionator - -DESCRIPTION="Macromolecular crystallographic refinement program" -HOMEPAGE="http://www.ysbl.york.ac.uk/~garib/refmac" -SRC_URI=" - ${HOMEPAGE}/data/refmac_stable/refmac_${PV}.tar.gz - test? ( http://dev.gentooexperimental.org/~jlec/distfiles/test-framework.tar.gz )" - -SLOT="0" -LICENSE="ccp4" -KEYWORDS="amd64 ppc x86 ~amd64-linux ~x86-linux" -IUSE="test" - -RDEPEND=" - sci-chemistry/makecif - >=sci-libs/ccp4-libs-6.1.3-r7 - sci-libs/mmdb - <sci-libs/monomer-db-1 - virtual/blas - virtual/lapack" -DEPEND="${RDEPEND} - virtual/pkgconfig" - -FORTRAN_STANDARD="77 90" - -S="${WORKDIR}" - -PATCHES=( - "${FILESDIR}"/${PV}-allow-dynamic-linking.patch - "${FILESDIR}"/${PV}-gcc4.6.patch - ) - -src_prepare() { - epatch ${PATCHES[@]} - - use test && epatch "${FILESDIR}"/$(get_version_component_range 1-2 ${PV})-test.log.patch - [[ ${FC} == *gfortran* ]] && \ - append-fflags -fno-second-underscore && \ - append-cflags -DGFORTRAN -DPROTOTYPE && \ - append-libs -lgfortran -lgfortranbegin -lstdc++ - [[ ${FC} == *ifort* ]] && \ - append-libs -lstdc++ -} - -src_compile() { - emake \ - FC=$(tc-getFC) \ - CC=$(tc-getCC) \ - CXX=$(tc-getCXX) \ - COPTIM="${CFLAGS}" \ - FOPTIM="${FFLAGS:- -O2}" \ - VERSION="" \ - XFFLAGS="" \ - XCFLAGS="" \ - LLIBCCP="-lccp4f -lccp4c -lccif $($(tc-getPKG_CONFIG) --libs mmdb)" \ - LLIBLAPACK="$($(tc-getPKG_CONFIG) --libs lapack blas)" \ - LLIBOTHERS="${LIBS}" \ - ${PN} libcheck -} - -src_test() { - einfo "Starting tests ..." - source "${EPREFIX}/etc/profile.d/40ccp4.setup.sh" - export PATH="${WORKDIR}/test-framework/scripts:${S}:${PATH}" - export CCP4_TEST="${WORKDIR}"/test-framework - export CCP4_SCR="${T}" - ln -sf refmac "${S}"/refmac5 - sed '/^ANISOU/d' -i ${CCP4_TEST}/data/pdb/1vr7.pdb - ccp4-run-thorough-tests -v test_refmac5 || die -} - -src_install() { - exeinto /usr/libexec/ccp4/bin/ - doexe ${PN} - dosym refmac /usr/libexec/ccp4/bin/refmac5 - dosym ../libexec/ccp4/bin/${PN} /usr/bin/${PN} - dosym refmac /usr/bin/refmac5 - dodoc refmac_keywords.pdf bugs_and_features.pdf -} diff --git a/sci-chemistry/scala/Manifest b/sci-chemistry/scala/Manifest deleted file mode 100644 index e03416a28733..000000000000 --- a/sci-chemistry/scala/Manifest +++ /dev/null @@ -1 +0,0 @@ -DIST scala-3.3.20.tar.gz 368628 SHA256 0efb108923a4d21fdc75d7ee92567e4bac4ae409f8798fbabd8142b5b026e976 SHA512 9f9812527013d87c80101333baf7ee646f6b3c665cdb477bb4e633c0a1fa57b31b6327913cf712e961c4484a9d9edf1aab5f3cfc66e6834aca1e970a4e0ca898 WHIRLPOOL 7d6082872a9f2f992186a2626dbf7ccd9f827b1322d1399b41ebc1b07267a46cfed5f7ea085403415c01eba4fc44e9d51983080537db04b227469d6871f8f1f9 diff --git a/sci-chemistry/scala/files/3.3.18-gcc4.6.patch b/sci-chemistry/scala/files/3.3.18-gcc4.6.patch deleted file mode 100644 index 0bb3d40d479a..000000000000 --- a/sci-chemistry/scala/files/3.3.18-gcc4.6.patch +++ /dev/null @@ -1,17 +0,0 @@ - scala.f | 3 ++- - 1 files changed, 2 insertions(+), 1 deletions(-) - -diff --git a/scala.f b/scala.f -index d7e1cbe..8ed6fd2 100644 ---- a/scala.f -+++ b/scala.f -@@ -3955,7 +3955,8 @@ c line buffer - character*40 key, value - character*200 realfilename - -- integer intfp, i2swap, lenstr -+ integer intfp, lenstr -+ integer*2 i2swap - external intfp, i2swap, lenstr - logical litend - external litend diff --git a/sci-chemistry/scala/files/Makefile.am b/sci-chemistry/scala/files/Makefile.am deleted file mode 100644 index 49fd61180ef0..000000000000 --- a/sci-chemistry/scala/files/Makefile.am +++ /dev/null @@ -1,7 +0,0 @@ - -LIBS = -lccp4f $(LAPACK_LIBS) - -bin_PROGRAMS = scala - -scala_SOURCES = scala.f - diff --git a/sci-chemistry/scala/files/configure.ac b/sci-chemistry/scala/files/configure.ac deleted file mode 100644 index 35c4c7fdd194..000000000000 --- a/sci-chemistry/scala/files/configure.ac +++ /dev/null @@ -1,14 +0,0 @@ -# -*- Autoconf -*- -# Process this file with autoconf to produce a configure script. - -AC_PREREQ(2.59) -AC_INIT(scala, https://bugs.gentoo.org/) -AC_CONFIG_SRCDIR([scala.f]) -AM_INIT_AUTOMAKE([foreign]) - -PKG_CHECK_MODULES([LAPACK],[lapack]) - -# Checks for programs. -AC_PROG_FC -AC_PROG_F77 -AC_OUTPUT([Makefile]) diff --git a/sci-chemistry/scala/metadata.xml b/sci-chemistry/scala/metadata.xml deleted file mode 100644 index 2c9359ab3513..000000000000 --- a/sci-chemistry/scala/metadata.xml +++ /dev/null @@ -1,13 +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@gentoo.org</email> - </maintainer> - <longdescription> -This program scales together multiple observations of reflections from -Xray difraction experiments, and merges multiple observations into an -average intensity. -</longdescription> -</pkgmetadata> diff --git a/sci-chemistry/scala/scala-3.3.20.ebuild b/sci-chemistry/scala/scala-3.3.20.ebuild deleted file mode 100644 index 3555cc29a9d1..000000000000 --- a/sci-chemistry/scala/scala-3.3.20.ebuild +++ /dev/null @@ -1,38 +0,0 @@ -# Copyright 1999-2015 Gentoo Foundation -# Distributed under the terms of the GNU General Public License v2 -# $Id$ - -EAPI=4 - -inherit autotools fortran-2 - -DESCRIPTION="Scale together multiple observations of reflections" -HOMEPAGE="http://www.ccp4.ac.uk/dist/html/scala.html" -SRC_URI="ftp://ftp.mrc-lmb.cam.ac.uk/pub/pre/${P}.tar.gz" - -LICENSE="ccp4" -SLOT="0" -KEYWORDS="amd64 ppc x86 ~amd64-linux ~x86-linux" -IUSE="" - -RDEPEND=" - !<sci-chemistry/ccp4-6.1.2 - !dev-lang/scala-bin - !dev-lang/scala - sci-libs/ccp4-libs - virtual/lapack" -DEPEND="${RDEPEND} - virtual/pkgconfig" - -src_prepare() { - cp "${FILESDIR}"/{configure.ac,Makefile.am} "${S}" - eautoreconf -} - -src_install() { - exeinto /usr/libexec/ccp4/bin/ - doexe ${PN} - dosym ../libexec/ccp4/bin/${PN} /usr/bin/${PN} - dodoc ${PN}.doc - dohtml ${PN}.html -} diff --git a/sci-chemistry/sfcheck/Manifest b/sci-chemistry/sfcheck/Manifest deleted file mode 100644 index 77615cec106b..000000000000 --- a/sci-chemistry/sfcheck/Manifest +++ /dev/null @@ -1 +0,0 @@ -DIST sfcheck-7.03.18.tar.gz 535707 SHA256 def9ceec86fc50f35b9a729e6f84b45a83560e2c6c20a5105647182e10313148 SHA512 256aa1690e0f5ca6aca0483a7d00c1deeb7b77701d950771a134532a658f7c3189bc6abec620ea6da2af200fc879ac9ff07ef7f4ba8614b6cd4e8455a11bed93 WHIRLPOOL 7b9f99f1a8387c5bc63bdab2078d3fcfab4146046429c56503760ca12a1898e944b5aa3c42b358d303206487e5d493bdcb77fe1795490779e7bd79b8b66a2d7a diff --git a/sci-chemistry/sfcheck/files/7.03.17-ldflags.patch b/sci-chemistry/sfcheck/files/7.03.17-ldflags.patch deleted file mode 100644 index 4163cb52ac1e..000000000000 --- a/sci-chemistry/sfcheck/files/7.03.17-ldflags.patch +++ /dev/null @@ -1,12 +0,0 @@ -diff --git a/src/makefile b/src/makefile -index ab43d7d..37e469f 100755 ---- a/src/makefile -+++ b/src/makefile -@@ -60,6 +60,6 @@ main_sfcheck_ccp4.o: main_sfcheck_ccp4.f sfch_version.fh - $(MR_FORT) -c main_sfcheck_ccp4.f - - sfcheck: $(OBJS) -- $(MR_FORT) -o $(BIN)/sfcheck $(OBJSL) $(MR_LIBRARY) -+ $(MR_FORT) $(LDFLAGS) -o $(BIN)/sfcheck $(OBJSL) $(MR_LIBRARY) - - # ---------------------------------------- diff --git a/sci-chemistry/sfcheck/metadata.xml b/sci-chemistry/sfcheck/metadata.xml deleted file mode 100644 index 9ac9ffdb3a41..000000000000 --- a/sci-chemistry/sfcheck/metadata.xml +++ /dev/null @@ -1,5 +0,0 @@ -<?xml version="1.0" encoding="UTF-8"?> -<!DOCTYPE pkgmetadata SYSTEM "http://www.gentoo.org/dtd/metadata.dtd"> -<pkgmetadata> -<herd>sci-chemistry</herd> -</pkgmetadata> diff --git a/sci-chemistry/sfcheck/sfcheck-7.03.18-r1.ebuild b/sci-chemistry/sfcheck/sfcheck-7.03.18-r1.ebuild deleted file mode 100644 index e18673d0923e..000000000000 --- a/sci-chemistry/sfcheck/sfcheck-7.03.18-r1.ebuild +++ /dev/null @@ -1,42 +0,0 @@ -# Copyright 1999-2012 Gentoo Foundation -# Distributed under the terms of the GNU General Public License v2 -# $Id$ - -EAPI=4 - -inherit eutils fortran-2 toolchain-funcs - -DESCRIPTION="Program for assessing the agreement between the atomic model and X-ray data or EM map" -HOMEPAGE="http://www.ysbl.york.ac.uk/~alexei/sfcheck.html" -#SRC_URI="http://www.ysbl.york.ac.uk/~alexei/downloads/sfcheck.tar.gz" -SRC_URI="mirror://gentoo/${P}.tar.gz" - -SLOT="0" -LICENSE="ccp4" -KEYWORDS="amd64 ~ppc x86 ~amd64-linux ~x86-linux" -IUSE="" - -RDEPEND="sci-libs/ccp4-libs" -DEPEND="${RDEPEND} - !<sci-chmistry/ccp4-apps-6.1.3" - -S="${WORKDIR}"/${PN} - -src_prepare() { - epatch "${FILESDIR}"/7.03.17-ldflags.patch - - emake -C src clean -} - -src_compile() { - MR_FORT="$(tc-getFC) ${FFLAGS}" \ - MR_LIBRARY="-lccp4f" \ - emake -C src all -} - -src_install() { - exeinto /usr/libexec/ccp4/bin/ - doexe bin/${PN} - dosym ../libexec/ccp4/bin/${PN} /usr/bin/${PN} - dodoc readme ${PN}.com.gz doc/${PN}* -} diff --git a/sci-chemistry/solve-resolve-bin/Manifest b/sci-chemistry/solve-resolve-bin/Manifest deleted file mode 100644 index 43fcf716e995..000000000000 --- a/sci-chemistry/solve-resolve-bin/Manifest +++ /dev/null @@ -1,2 +0,0 @@ -DIST solve-2.13-linux-64.tar.gz 74444830 SHA256 e03250bb550686fc6e5f59d4e885b83b88cd342dfb4975eb31ddf95d9515650e SHA512 8f20715c3fb73940f03ba8a4bb3528f89ba01520cacead001796609bc15259ab7ab7f2d4960ea97efc43029863bc31e630c9e93f528a233652928220dafe0b4d WHIRLPOOL 125efe76024148656f3bb357ad1bc78d17f51eb8268c83241f4da9a94356170d0259fe48fadf6bf1ffe4b10b57bb27ed79199063dc95d0eef8d9e22de653c84a -DIST solve-2.13-linux.tar.gz 71902534 SHA256 975466fe92d8f6256de20ea0b5101876f3e5a7e3093199946c9f4824236c79d3 SHA512 a3a779ada33bd189fc8c3e6fdc424ef9c032c5540138cce52e0c8dcf5a12847b1325402a2c1715ed4ab217f433169d3612c724f2d178ead576afc44ec4839c6a WHIRLPOOL 0fec411b795a107610e620586cba511a0cbf50400e0bdfef872b22ee05e3992fcc0a4b1cf1d84d450bbeb3838a7bc9633acd8f4cf97d5e4b7a01e6e7959ccd7c diff --git a/sci-chemistry/solve-resolve-bin/metadata.xml b/sci-chemistry/solve-resolve-bin/metadata.xml deleted file mode 100644 index ae9ec7c5f6a4..000000000000 --- a/sci-chemistry/solve-resolve-bin/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-chemistry</herd> - <maintainer> - <email>jlec@gentoo.org</email> - </maintainer> -</pkgmetadata> diff --git a/sci-chemistry/solve-resolve-bin/solve-resolve-bin-2.13.ebuild b/sci-chemistry/solve-resolve-bin/solve-resolve-bin-2.13.ebuild deleted file mode 100644 index 6deae178afdd..000000000000 --- a/sci-chemistry/solve-resolve-bin/solve-resolve-bin-2.13.ebuild +++ /dev/null @@ -1,68 +0,0 @@ -# Copyright 1999-2015 Gentoo Foundation -# Distributed under the terms of the GNU General Public License v2 -# $Id$ - -EAPI=5 - -inherit eutils - -DESCRIPTION="Automated crystallographic structure solution for MIR, SAD, and MAD" -HOMEPAGE="http://www.solve.lanl.gov/index.html" -SRC_URI=" - x86? ( https://solve.lanl.gov/pub/solve/${PV}/solve-${PV}-linux.tar.gz ) - amd64? ( https://solve.lanl.gov/pub/solve/${PV}/solve-${PV}-linux-64.tar.gz )" - -SLOT="0" -LICENSE="solve" -KEYWORDS="-* x86 amd64" -IUSE="examples" - -RDEPEND="sci-libs/ccp4-libs" -DEPEND="" - -RESTRICT="mirror" - -S="${WORKDIR}"/solve-${PV} - -QA_PREBUILT="opt/solve-resolve/bin/*" - -src_install(){ - local IN_PATH="/opt/solve-resolve/" - - exeinto ${IN_PATH}bin/ - doexe bin/* - - insinto ${IN_PATH}lib/ - doins -r lib/{*sym,sym*,hist*,*dat,segments,patterns} - - docinto html - dodoc -r lib/html/* - - sed \ - -e 's:/usr/local/lib/solve/:${EPREFIX}/opt/solve-resolve/lib/:' \ - -i lib/examples_solve/p9/solve* || die - if use examples; then - sed \ - -e 's:/usr/local/lib/resolve/:${EPREFIX}/opt/solve-resolve/lib/:' \ - -i lib/examples_resolve/{resolve.csh,prime_and_switch.csh} || die - insinto /usr/share/${PF}/ - doins -r lib/examples_*solve - fi - - cat >> "${T}"/20solve-resolve <<- EOF - CCP4_OPEN="UNKNOWN" - SYMOP="${EPREFIX}/usr/share/ccp4/data/symop.lib" - SYMINFO="${EPREFIX}/usr/share/ccp4/data/syminfo.lib" - SOLVEDIR="${EPREFIX}/${IN_PATH}lib/" - PATH="${EPREFIX}/${IN_PATH}bin" - EOF - - doenvd "${T}"/20solve-resolve -} - -pkg_postinst(){ - einfo "Get a valid license key from" - einfo "http://solve.lanl.gov/license.html" - einfo "and place it in" - einfo "${EPREFIX}${IN_PATH}lib/" -} diff --git a/sci-chemistry/xdsi/Manifest b/sci-chemistry/xdsi/Manifest deleted file mode 100644 index e33598d79364..000000000000 --- a/sci-chemistry/xdsi/Manifest +++ /dev/null @@ -1 +0,0 @@ -DIST xdsi_0.92.tar.gz 886028 SHA256 416403f167d26b56965283b407783ea80927ace533df76e330b51ca37c9bb9e4 diff --git a/sci-chemistry/xdsi/files/0.92-gentoo.patch b/sci-chemistry/xdsi/files/0.92-gentoo.patch deleted file mode 100644 index f4a37ff1838d..000000000000 --- a/sci-chemistry/xdsi/files/0.92-gentoo.patch +++ /dev/null @@ -1,27 +0,0 @@ - xdsi | 6 +++--- - 1 files changed, 3 insertions(+), 3 deletions(-) - -diff --git a/xdsi b/xdsi -index cbedee8..1037913 100755 ---- a/xdsi -+++ b/xdsi -@@ -20,8 +20,8 @@ - #################################################################### - # These are the only two things you should change# - --set Templates "/mydir/templates" --set initial "/mydir/SLS-2009" -+set Templates "GENTOOTEMPLATE" -+set initial "./" - - - #################################################################### -@@ -121,7 +121,7 @@ your system administrator." - } - - --CheckExecutables "kpdf gnuplot xds_par xdsstat xds-viewer-0.6 convert pointless ipmosflm VIEW" -+CheckExecutables "kpdf gnuplot xds_par xds-viewer convert pointless ipmosflm" - - #wm resizable . 0 0 - diff --git a/sci-chemistry/xdsi/metadata.xml b/sci-chemistry/xdsi/metadata.xml deleted file mode 100644 index 431fb2be13b4..000000000000 --- a/sci-chemistry/xdsi/metadata.xml +++ /dev/null @@ -1,17 +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@gentoo.org</email> - </maintainer> - <longdescription> -XDSi offers you the possibility to process all your datasets in a given directory with minimum effort. -* You just have to provide it with a resultdirectory and the directory where your frames are stored. -* All datasets consisting of more than 100 frames within the given directory and all its subdirectories will be processed. -* For each dataset a space group assignment is done using POINTLESS of the CCP4 software package -* Plots of the most informative statistics of INTEGRATE.LP, CORRECT.LP and XDSSTAT.LP are generated for each dataset -* A plot comparing Rmeas, I/sig and Completeness of all the processed datasets is generated -* You can also generate plots for datasets that have been processed using XDS without XDSi -</longdescription> -</pkgmetadata> diff --git a/sci-chemistry/xdsi/xdsi-0.92-r1.ebuild b/sci-chemistry/xdsi/xdsi-0.92-r1.ebuild deleted file mode 100644 index 6a6c9bb7ec8b..000000000000 --- a/sci-chemistry/xdsi/xdsi-0.92-r1.ebuild +++ /dev/null @@ -1,54 +0,0 @@ -# Copyright 1999-2015 Gentoo Foundation -# Distributed under the terms of the GNU General Public License v2 -# $Id$ - -EAPI=5 - -inherit eutils - -DESCRIPTION="A crude interface for running the XDS" -HOMEPAGE="http://strucbio.biologie.uni-konstanz.de/xdswiki/index.php/Xdsi" -SRC_URI="ftp://turn5.biologie.uni-konstanz.de/pub/${PN}_${PV}.tar.gz" - -LICENSE="all-rights-reserved" -SLOT="0" -KEYWORDS="~amd64 ~x86 ~amd64-linux ~x86-linux" -IUSE="" - -RDEPEND=" - app-text/mupdf - dev-lang/tk - || ( media-gfx/imagemagick media-gfx/graphicsmagick[imagemagick] ) - sci-chemistry/mosflm - sci-chemistry/pointless - sci-chemistry/xds-bin[smp] - sci-visualization/gnuplot - sci-visualization/xds-viewer" -# Need to clarified for licensing -# sci-chemistry/xdsstat-bin -DEPEND="" - -RESTRICT="mirror bindist" - -S="${WORKDIR}" - -src_prepare() { - epatch "${FILESDIR}"/${PV}-gentoo.patch - sed \ - -e "s:GENTOOTEMPLATE:${EPREFIX}/usr/share/${PN}/templates:g" \ - -e "s:kpdf:mupdf:g" \ - -e "s:xds-viewer-0.6:xds-viewer:g" \ - -i ${PN} || die -} - -src_install() { - dobin ${PN} - insinto /usr/share/${PN}/templates - doins templates/{*.INP,bohr*,fortran,pauli,info.png,*.pck,tablesf_xdsi} - dodoc templates/*.pdf -} - -pkg_postinst() { - elog "Documentation can be found here:" - elog "ftp://turn14.biologie.uni-konstanz.de/pub/xdsi/xdsi_doc_print.pdf" -} diff --git a/sci-chemistry/xia2/Manifest b/sci-chemistry/xia2/Manifest deleted file mode 100644 index 52cb6c13f104..000000000000 --- a/sci-chemistry/xia2/Manifest +++ /dev/null @@ -1,6 +0,0 @@ -DIST xia2-0.3.1.0.tar.bz2 3389906 SHA256 32f1866bc17b093cbf157ec7bc217e47d059957104b20c88ed1b5c3706fc7e28 SHA512 cd595147164e4a281431a1d5a7298588001bb11662b517a5f95366e7b0ba4fdb33adf88dd2672c8c2ee84f48356fccb7cbd07667d5f04417a1564c7ea9f878c5 WHIRLPOOL e5493526d3075a5c61ce582a3bf42e2b4a2a73d7a28b1c8df786f0bdf5c8b1eaee986a60f379559ba556f256057794211a6c1e812b785aa9fe3179357b24b0da -DIST xia2-0.3.1.6.tar.bz2 3464982 SHA256 fde814a763e6666a1618d01569c19d574f1bf71d754dc3960beeb13c35dd201f SHA512 d00ba2c42c88d01522859839cbee6a93662ed7f89fb146babffa1dd5d6af12ca72cc146157e0dc88bba1d6543f8509fc9027e1c42ed3ae15dd3e168ca18e1858 WHIRLPOOL ccedcbf910ec5bed637739f7519e14eb249b89ae6ccd83a632ab8571a3af62f1f168f8dfd88287fed9fe927b98230e083a0d2d4525f47bc49c4074375a46a796 -DIST xia2-0.3.1.7.tar.bz2 3650285 SHA256 54beb26396c4b6ecb343544c777c2505238385f2127482d035d2c47b24a7fcf1 SHA512 d25788e6564b0f8f4c8e6723347b7691277b01192ead8f37bc7e6d1cdfbee5b22a1329f4ff82d9287875df2de1358e738de08c6a4d19353ccb40c31343dce7bd WHIRLPOOL 1c7306a54a5262632e0319a289f57610badea3945b61653039c78772399557f895ea57e02bbff6804704df8a08f4aa35fce7746e9e03807143d0e395bcd93c75 -DIST xia2-0.3.3.1.tar.bz2 3074989 SHA256 f1bf94cd9305f768fea1b541ac53d66917126e92620263a96f9c23923ec829c4 SHA512 656abd51dc6764dee16423e2ea75f590e7a04046c5ac60ce013615c91b3fd41c0089351ceb948203643bff442753773aa639b036efc089ce26592b52b187f656 WHIRLPOOL f11a6bba359ce9f3095d2993fb331a8c70a44bc1ef31dc08663ee63372db995047d5e1b4693808a347eedeb487a1b799c4e080c05416786209f62e7b619ddec8 -DIST xia2-0.3.3.3.tar.bz2 2919316 SHA256 3cf09fcf9d2c0ea6d6cb8cf66a3c5af752b4345af6a882e2d398424cf3b4b0d3 SHA512 913b5a6e24c3c070cc36b404b987331d8de99756d0f598ef485ba5fef3b4bc42d17bf4b4e648d5c99f014872d554b94880a7542dfb9ab6969e272ec986127561 WHIRLPOOL 5f19e3b06df7d5a83d75296fe9c9956f5c0b995cd5d10f1adb66e519d9dbcdd73edcbec53acb90aede6f2955bbd88991d6283af9a3578ad26a686e8530bfdffa -DIST xia2-0.3.4.0.tar.bz2 21404771 SHA256 20afe3d24c35446ef8c8944974d684229f053d3916e96e46766d8eefa4c5fabf SHA512 7d2444cb2acfcd2d7ca4c37d5714e7c249ffc419e9d7e1dbb33ccf18adc07f05a2b043af5aee721c64639b991dbbfd356181630229e91e0f871489870f9a8d51 WHIRLPOOL 14759e436d42e4b5ae558616d297f41eb9a345b19df4a4d02d2cb3c61937320d9161343b126b393049319ab6e37dc3890566b1bd3f2bff1a29cd108931640a90 diff --git a/sci-chemistry/xia2/files/0.3.1.0-fix-syntax.patch b/sci-chemistry/xia2/files/0.3.1.0-fix-syntax.patch deleted file mode 100644 index 9d92af7e33ce..000000000000 --- a/sci-chemistry/xia2/files/0.3.1.0-fix-syntax.patch +++ /dev/null @@ -1,61 +0,0 @@ -diff --git a/xia2-0.3.1.0/Applications/xia2find.py b/xia2-0.3.1.0/Applications/xia2find.py -index 1a3b0e2..e0b8a1e 100755 ---- a/xia2-0.3.1.0/Applications/xia2find.py -+++ b/xia2-0.3.1.0/Applications/xia2find.py -@@ -38,7 +38,7 @@ from Schema.Sweep import SweepFactory - from Experts.FindImages import image2template_directory - - known_image_extensions = ['img', 'mccd', 'mar2300', 'mar1200', 'mar3450', -- 'osc', 'cbf', 'mar2000']] -+ 'osc', 'cbf', 'mar2000'] - known_sweeps = { } - - def is_image_name(file): -diff --git a/xia2-0.3.1.0/Experts/DRStrategyExpert.py b/xia2-0.3.1.0/Experts/DRStrategyExpert.py -index 28b1dc3..dba3ef7 100644 ---- a/xia2-0.3.1.0/Experts/DRStrategyExpert.py -+++ b/xia2-0.3.1.0/Experts/DRStrategyExpert.py -@@ -48,24 +48,24 @@ strategy_dict = { - 'default':{ - 'score':1, - 'pipeline':{ -- 'indexer':'labelit', 'integrater':'xds', 'scaler':'xds-hybrid'} -+ 'indexer':'labelit', 'integrater':'xds', 'scaler':'xds-hybrid'}, - 'depends-on':['labelit.screen', 'xds', 'xscale', 'scala', 'combat', - 'pointless-1.1.0.4']}, - 'default':{ - 'score':2, - 'pipeline':{ -- 'indexer':'labelit', 'integrater':'mosflm', 'scaler':'mosflm'} -+ 'indexer':'labelit', 'integrater':'mosflm', 'scaler':'mosflm'}, - 'depends-on':['labelit.screen', 'mosflm', 'scala', 'reindex', - 'pointless-1.1.0.4']}, - 'mosaic':{ - 'score':1, - 'pipeline':{ -- 'indexer':'labelit', 'integrater':'xds', 'scaler':'xds-hybrid'} -+ 'indexer':'labelit', 'integrater':'xds', 'scaler':'xds-hybrid'}, - 'depends-on':['labelit.screen', 'xds', 'xscale', 'scala', 'combat', - 'pointless-1.1.0.4']}, - 'mosaic':{ - 'score':2, - 'pipeline':{ -- 'indexer':'xds', 'integrater':'xds', 'scaler':'xds'} -+ 'indexer':'xds', 'integrater':'xds', 'scaler':'xds'}, - 'depends-on':['xds', 'xscale']} - } -diff --git a/xia2core-0.3.1.0/Python/Examples/CCP4/Cad.py b/xia2core-0.3.1.0/Python/Examples/CCP4/Cad.py -index 88f9218..5fb6f2a 100644 ---- a/xia2core-0.3.1.0/Python/Examples/CCP4/Cad.py -+++ b/xia2core-0.3.1.0/Python/Examples/CCP4/Cad.py -@@ -49,8 +49,8 @@ def Cad(DriverType = None): - self.add_command_line(hklin) - - self.set_task('Rewriting reflections %s => %s' % -- ` (os.path.split(hklin)[-1], -- ` os.path.split(self.getHklout())[-1])) -+ (os.path.split(hklin)[-1], -+ os.path.split(self.getHklout())[-1])) - - self.start() - diff --git a/sci-chemistry/xia2/files/0.3.1.6-fix-syntax.patch b/sci-chemistry/xia2/files/0.3.1.6-fix-syntax.patch deleted file mode 100644 index 7770a53c4451..000000000000 --- a/sci-chemistry/xia2/files/0.3.1.6-fix-syntax.patch +++ /dev/null @@ -1,61 +0,0 @@ -diff --git a/xia2-0.3.1.6/Applications/xia2find.py b/xia2-0.3.1.6/Applications/xia2find.py -index 1a3b0e2..e0b8a1e 100755 ---- a/xia2-0.3.1.6/Applications/xia2find.py -+++ b/xia2-0.3.1.6/Applications/xia2find.py -@@ -38,7 +38,7 @@ from Schema.Sweep import SweepFactory - from Experts.FindImages import image2template_directory - - known_image_extensions = ['img', 'mccd', 'mar2300', 'mar1200', 'mar3450', -- 'osc', 'cbf', 'mar2000']] -+ 'osc', 'cbf', 'mar2000'] - known_sweeps = { } - - def is_image_name(file): -diff --git a/xia2-0.3.1.6/Experts/DRStrategyExpert.py b/xia2-0.3.1.6/Experts/DRStrategyExpert.py -index 28b1dc3..dba3ef7 100644 ---- a/xia2-0.3.1.6/Experts/DRStrategyExpert.py -+++ b/xia2-0.3.1.6/Experts/DRStrategyExpert.py -@@ -48,24 +48,24 @@ strategy_dict = { - 'default':{ - 'score':1, - 'pipeline':{ -- 'indexer':'labelit', 'integrater':'xds', 'scaler':'xds-hybrid'} -+ 'indexer':'labelit', 'integrater':'xds', 'scaler':'xds-hybrid'}, - 'depends-on':['labelit.screen', 'xds', 'xscale', 'scala', 'combat', - 'pointless-1.1.0.4']}, - 'default':{ - 'score':2, - 'pipeline':{ -- 'indexer':'labelit', 'integrater':'mosflm', 'scaler':'mosflm'} -+ 'indexer':'labelit', 'integrater':'mosflm', 'scaler':'mosflm'}, - 'depends-on':['labelit.screen', 'mosflm', 'scala', 'reindex', - 'pointless-1.1.0.4']}, - 'mosaic':{ - 'score':1, - 'pipeline':{ -- 'indexer':'labelit', 'integrater':'xds', 'scaler':'xds-hybrid'} -+ 'indexer':'labelit', 'integrater':'xds', 'scaler':'xds-hybrid'}, - 'depends-on':['labelit.screen', 'xds', 'xscale', 'scala', 'combat', - 'pointless-1.1.0.4']}, - 'mosaic':{ - 'score':2, - 'pipeline':{ -- 'indexer':'xds', 'integrater':'xds', 'scaler':'xds'} -+ 'indexer':'xds', 'integrater':'xds', 'scaler':'xds'}, - 'depends-on':['xds', 'xscale']} - } -diff --git a/xia2core-0.3.1.6/Python/Examples/CCP4/Cad.py b/xia2core-0.3.1.6/Python/Examples/CCP4/Cad.py -index 88f9218..5fb6f2a 100644 ---- a/xia2core-0.3.1.6/Python/Examples/CCP4/Cad.py -+++ b/xia2core-0.3.1.6/Python/Examples/CCP4/Cad.py -@@ -49,8 +49,8 @@ def Cad(DriverType = None): - self.add_command_line(hklin) - - self.set_task('Rewriting reflections %s => %s' % -- ` (os.path.split(hklin)[-1], -- ` os.path.split(self.getHklout())[-1])) -+ (os.path.split(hklin)[-1], -+ os.path.split(self.getHklout())[-1])) - - self.start() - diff --git a/sci-chemistry/xia2/files/0.3.1.7-fix-syntax.patch b/sci-chemistry/xia2/files/0.3.1.7-fix-syntax.patch deleted file mode 100644 index ec8ada48aad1..000000000000 --- a/sci-chemistry/xia2/files/0.3.1.7-fix-syntax.patch +++ /dev/null @@ -1,61 +0,0 @@ -diff --git a/xia2-0.3.1.7/Applications/xia2find.py b/xia2-0.3.1.7/Applications/xia2find.py -index 1a3b0e2..e0b8a1e 100755 ---- a/xia2-0.3.1.7/Applications/xia2find.py -+++ b/xia2-0.3.1.7/Applications/xia2find.py -@@ -38,7 +38,7 @@ from Schema.Sweep import SweepFactory - from Experts.FindImages import image2template_directory - - known_image_extensions = ['img', 'mccd', 'mar2300', 'mar1200', 'mar3450', -- 'osc', 'cbf', 'mar2000']] -+ 'osc', 'cbf', 'mar2000'] - known_sweeps = { } - - def is_image_name(file): -diff --git a/xia2-0.3.1.7/Experts/DRStrategyExpert.py b/xia2-0.3.1.7/Experts/DRStrategyExpert.py -index 28b1dc3..dba3ef7 100644 ---- a/xia2-0.3.1.7/Experts/DRStrategyExpert.py -+++ b/xia2-0.3.1.7/Experts/DRStrategyExpert.py -@@ -48,24 +48,24 @@ strategy_dict = { - 'default':{ - 'score':1, - 'pipeline':{ -- 'indexer':'labelit', 'integrater':'xds', 'scaler':'xds-hybrid'} -+ 'indexer':'labelit', 'integrater':'xds', 'scaler':'xds-hybrid'}, - 'depends-on':['labelit.screen', 'xds', 'xscale', 'scala', 'combat', - 'pointless-1.1.0.4']}, - 'default':{ - 'score':2, - 'pipeline':{ -- 'indexer':'labelit', 'integrater':'mosflm', 'scaler':'mosflm'} -+ 'indexer':'labelit', 'integrater':'mosflm', 'scaler':'mosflm'}, - 'depends-on':['labelit.screen', 'mosflm', 'scala', 'reindex', - 'pointless-1.1.0.4']}, - 'mosaic':{ - 'score':1, - 'pipeline':{ -- 'indexer':'labelit', 'integrater':'xds', 'scaler':'xds-hybrid'} -+ 'indexer':'labelit', 'integrater':'xds', 'scaler':'xds-hybrid'}, - 'depends-on':['labelit.screen', 'xds', 'xscale', 'scala', 'combat', - 'pointless-1.1.0.4']}, - 'mosaic':{ - 'score':2, - 'pipeline':{ -- 'indexer':'xds', 'integrater':'xds', 'scaler':'xds'} -+ 'indexer':'xds', 'integrater':'xds', 'scaler':'xds'}, - 'depends-on':['xds', 'xscale']} - } -diff --git a/xia2core-0.3.1.7/Python/Examples/CCP4/Cad.py b/xia2core-0.3.1.7/Python/Examples/CCP4/Cad.py -index 88f9218..5fb6f2a 100644 ---- a/xia2core-0.3.1.7/Python/Examples/CCP4/Cad.py -+++ b/xia2core-0.3.1.7/Python/Examples/CCP4/Cad.py -@@ -49,8 +49,8 @@ def Cad(DriverType = None): - self.add_command_line(hklin) - - self.set_task('Rewriting reflections %s => %s' % -- ` (os.path.split(hklin)[-1], -- ` os.path.split(self.getHklout())[-1])) -+ (os.path.split(hklin)[-1], -+ os.path.split(self.getHklout())[-1])) - - self.start() - diff --git a/sci-chemistry/xia2/files/0.3.3.1-fix-syntax.patch b/sci-chemistry/xia2/files/0.3.3.1-fix-syntax.patch deleted file mode 100644 index 36cf6bb60d1d..000000000000 --- a/sci-chemistry/xia2/files/0.3.3.1-fix-syntax.patch +++ /dev/null @@ -1,61 +0,0 @@ -diff --git a/xia2-0.3.3.0/Applications/xia2find.py b/xia2-0.3.3.0/Applications/xia2find.py -index 1a3b0e2..e0b8a1e 100755 ---- a/xia2-0.3.3.1/Applications/xia2find.py -+++ b/xia2-0.3.3.1/Applications/xia2find.py -@@ -38,7 +38,7 @@ from Schema.Sweep import SweepFactory - from Experts.FindImages import image2template_directory - - known_image_extensions = ['img', 'mccd', 'mar2300', 'mar1200', 'mar3450', -- 'osc', 'cbf', 'mar2000']] -+ 'osc', 'cbf', 'mar2000'] - known_sweeps = { } - - def is_image_name(file): -diff --git a/xia2-0.3.3.0/Experts/DRStrategyExpert.py b/xia2-0.3.3.0/Experts/DRStrategyExpert.py -index 28b1dc3..dba3ef7 100644 ---- a/xia2-0.3.3.1/Experts/DRStrategyExpert.py -+++ b/xia2-0.3.3.1/Experts/DRStrategyExpert.py -@@ -48,24 +48,24 @@ strategy_dict = { - 'default':{ - 'score':1, - 'pipeline':{ -- 'indexer':'labelit', 'integrater':'xds', 'scaler':'xds-hybrid'} -+ 'indexer':'labelit', 'integrater':'xds', 'scaler':'xds-hybrid'}, - 'depends-on':['labelit.screen', 'xds', 'xscale', 'scala', 'combat', - 'pointless-1.1.0.4']}, - 'default':{ - 'score':2, - 'pipeline':{ -- 'indexer':'labelit', 'integrater':'mosflm', 'scaler':'mosflm'} -+ 'indexer':'labelit', 'integrater':'mosflm', 'scaler':'mosflm'}, - 'depends-on':['labelit.screen', 'mosflm', 'scala', 'reindex', - 'pointless-1.1.0.4']}, - 'mosaic':{ - 'score':1, - 'pipeline':{ -- 'indexer':'labelit', 'integrater':'xds', 'scaler':'xds-hybrid'} -+ 'indexer':'labelit', 'integrater':'xds', 'scaler':'xds-hybrid'}, - 'depends-on':['labelit.screen', 'xds', 'xscale', 'scala', 'combat', - 'pointless-1.1.0.4']}, - 'mosaic':{ - 'score':2, - 'pipeline':{ -- 'indexer':'xds', 'integrater':'xds', 'scaler':'xds'} -+ 'indexer':'xds', 'integrater':'xds', 'scaler':'xds'}, - 'depends-on':['xds', 'xscale']} - } -diff --git a/xia2core-0.3.3.0/Python/Examples/CCP4/Cad.py b/xia2core-0.3.3.0/Python/Examples/CCP4/Cad.py -index 88f9218..5fb6f2a 100644 ---- a/xia2core-0.3.3.1/Python/Examples/CCP4/Cad.py -+++ b/xia2core-0.3.3.1/Python/Examples/CCP4/Cad.py -@@ -49,8 +49,8 @@ def Cad(DriverType = None): - self.add_command_line(hklin) - - self.set_task('Rewriting reflections %s => %s' % -- ` (os.path.split(hklin)[-1], -- ` os.path.split(self.getHklout())[-1])) -+ (os.path.split(hklin)[-1], -+ os.path.split(self.getHklout())[-1])) - - self.start() - diff --git a/sci-chemistry/xia2/files/0.3.3.3-fix-syntax.patch b/sci-chemistry/xia2/files/0.3.3.3-fix-syntax.patch deleted file mode 100644 index 53cacbb5c681..000000000000 --- a/sci-chemistry/xia2/files/0.3.3.3-fix-syntax.patch +++ /dev/null @@ -1,28 +0,0 @@ -diff --git a/xia2-0.3.3.0/Applications/xia2find.py b/xia2-0.3.3.0/Applications/xia2find.py -index 1a3b0e2..e0b8a1e 100755 ---- a/xia2-0.3.3.3/Applications/xia2find.py -+++ b/xia2-0.3.3.3/Applications/xia2find.py -@@ -38,7 +38,7 @@ from Schema.Sweep import SweepFactory - from Experts.FindImages import image2template_directory - - known_image_extensions = ['img', 'mccd', 'mar2300', 'mar1200', 'mar3450', -- 'osc', 'cbf', 'mar2000']] -+ 'osc', 'cbf', 'mar2000'] - known_sweeps = { } - - def is_image_name(file): -diff --git a/xia2core-0.3.3.0/Python/Examples/CCP4/Cad.py b/xia2core-0.3.3.0/Python/Examples/CCP4/Cad.py -index 88f9218..5fb6f2a 100644 ---- a/xia2core-0.3.3.3/Python/Examples/CCP4/Cad.py -+++ b/xia2core-0.3.3.3/Python/Examples/CCP4/Cad.py -@@ -49,8 +49,8 @@ def Cad(DriverType = None): - self.add_command_line(hklin) - - self.set_task('Rewriting reflections %s => %s' % -- ` (os.path.split(hklin)[-1], -- ` os.path.split(self.getHklout())[-1])) -+ (os.path.split(hklin)[-1], -+ os.path.split(self.getHklout())[-1])) - - self.start() - diff --git a/sci-chemistry/xia2/files/0.3.4.0-fix-syntax.patch b/sci-chemistry/xia2/files/0.3.4.0-fix-syntax.patch deleted file mode 100644 index 9ba4c94495ea..000000000000 --- a/sci-chemistry/xia2/files/0.3.4.0-fix-syntax.patch +++ /dev/null @@ -1,28 +0,0 @@ -diff --git a/xia2-0.3.3.0/Applications/xia2find.py b/xia2-0.3.3.0/Applications/xia2find.py -index 1a3b0e2..e0b8a1e 100755 ---- a/xia2-0.3.4.0/Applications/xia2find.py -+++ b/xia2-0.3.4.0/Applications/xia2find.py -@@ -38,7 +38,7 @@ from Schema.Sweep import SweepFactory - from Experts.FindImages import image2template_directory - - known_image_extensions = ['img', 'mccd', 'mar2300', 'mar1200', 'mar3450', -- 'osc', 'cbf', 'mar2000']] -+ 'osc', 'cbf', 'mar2000'] - known_sweeps = { } - - def is_image_name(file): -diff --git a/xia2core-0.3.3.0/Python/Examples/CCP4/Cad.py b/xia2core-0.3.3.0/Python/Examples/CCP4/Cad.py -index 88f9218..5fb6f2a 100644 ---- a/xia2core-0.3.4.0/Python/Examples/CCP4/Cad.py -+++ b/xia2core-0.3.4.0/Python/Examples/CCP4/Cad.py -@@ -49,8 +49,8 @@ def Cad(DriverType = None): - self.add_command_line(hklin) - - self.set_task('Rewriting reflections %s => %s' % -- ` (os.path.split(hklin)[-1], -- ` os.path.split(self.getHklout())[-1])) -+ (os.path.split(hklin)[-1], -+ os.path.split(self.getHklout())[-1])) - - self.start() - diff --git a/sci-chemistry/xia2/metadata.xml b/sci-chemistry/xia2/metadata.xml deleted file mode 100644 index 9ac9ffdb3a41..000000000000 --- a/sci-chemistry/xia2/metadata.xml +++ /dev/null @@ -1,5 +0,0 @@ -<?xml version="1.0" encoding="UTF-8"?> -<!DOCTYPE pkgmetadata SYSTEM "http://www.gentoo.org/dtd/metadata.dtd"> -<pkgmetadata> -<herd>sci-chemistry</herd> -</pkgmetadata> diff --git a/sci-chemistry/xia2/xia2-0.3.1.0.ebuild b/sci-chemistry/xia2/xia2-0.3.1.0.ebuild deleted file mode 100644 index 33b3d841acfa..000000000000 --- a/sci-chemistry/xia2/xia2-0.3.1.0.ebuild +++ /dev/null @@ -1,59 +0,0 @@ -# Copyright 1999-2011 Gentoo Foundation -# Distributed under the terms of the GNU General Public License v2 -# $Id$ - -EAPI="3" - -inherit eutils python - -DESCRIPTION="An automated data reduction system for crystallography" -HOMEPAGE="http://www.ccp4.ac.uk/xia/" -SRC_URI="http://www.ccp4.ac.uk/${PN}/${P}.tar.bz2" - -LICENSE="BSD" -SLOT="0" -KEYWORDS="~amd64 ~x86" -IUSE="" - -RDEPEND=" - >=sci-chemistry/ccp4-apps-6.1.2 - sci-chemistry/mosflm - sci-chemistry/pointless - >=sci-libs/ccp4-libs-6.1.2 - sci-libs/cctbx" -DEPEND="${RDEPEND}" - -src_prepare() { - find . -name '*.bat' | xargs rm || die - - epatch "${FILESDIR}"/${PV}-fix-syntax.patch -} - -src_install() { - rm -rf ${P}/binaries ${PN}core-${PV}/Test || die - - insinto /usr/share/ccp4/XIAROOT/ - doins -r * || die - - # Set programs executable -# fperms cannot handle wildcards - chmod 755 "${ED}"/usr/share/ccp4/XIAROOT/${P}/Applications/* || die - chmod 644 "${ED}"/usr/share/ccp4/XIAROOT/${P}/Applications/*.py || die - - cat >> "${T}"/23XIA <<- EOF - XIA2_HOME="${EPREFIX}"/usr/share/ccp4/XIAROOT - XIA2CORE_ROOT="${EPREFIX}"/usr/share/ccp4/XIAROOT/xia2core-${PV} - XIA2_ROOT="${EPREFIX}"/usr/share/ccp4/XIAROOT/xia2-${PV} - PATH="${EPREFIX}"/usr/share/ccp4/XIAROOT/xia2-${PV}/Applications - EOF - - doenvd "${T}"/23XIA -} - -pkg_postinst() { - python_mod_optimize /usr/share/ccp4/XIAROOT -} - -pkg_postrm() { - python_mod_cleanup /usr/share/ccp4/XIAROOT -} diff --git a/sci-chemistry/xia2/xia2-0.3.1.6.ebuild b/sci-chemistry/xia2/xia2-0.3.1.6.ebuild deleted file mode 100644 index 537735e1351f..000000000000 --- a/sci-chemistry/xia2/xia2-0.3.1.6.ebuild +++ /dev/null @@ -1,66 +0,0 @@ -# Copyright 1999-2011 Gentoo Foundation -# Distributed under the terms of the GNU General Public License v2 -# $Id$ - -EAPI="3" - -PYTHON_DEPEND="2" - -inherit eutils python - -DESCRIPTION="An automated data reduction system for crystallography" -HOMEPAGE="http://www.ccp4.ac.uk/xia/" -SRC_URI="http://www.ccp4.ac.uk/${PN}/${P}.tar.bz2" - -LICENSE="BSD" -SLOT="0" -KEYWORDS="~amd64 ~x86 ~amd64-linux ~x86-linux" -IUSE="" - -RDEPEND=" - >=sci-chemistry/ccp4-apps-6.1.2 - sci-chemistry/mosflm - sci-chemistry/pointless - >=sci-libs/ccp4-libs-6.1.2 - sci-libs/cctbx" -DEPEND="${RDEPEND}" - -pkg_setup() { - python_set_active_version 2 -} - -src_prepare() { - find . -name '*.bat' -delete || die - - epatch "${FILESDIR}"/${PV}-fix-syntax.patch - python_convert_shebangs -r $(python_get_version) . -} - -src_install() { - rm -rf ${P}/binaries ${PN}core-${PV}/Test || die - - insinto /usr/share/ccp4/XIAROOT/ - doins -r * || die - - # Set programs executable -# fperms cannot handle wildcards - chmod 755 "${ED}"/usr/share/ccp4/XIAROOT/${P}/Applications/* || die - chmod 644 "${ED}"/usr/share/ccp4/XIAROOT/${P}/Applications/*.py || die - - cat >> "${T}"/23XIA <<- EOF - XIA2_HOME="${EPREFIX}"/usr/share/ccp4/XIAROOT - XIA2CORE_ROOT="${EPREFIX}"/usr/share/ccp4/XIAROOT/xia2core-${PV} - XIA2_ROOT="${EPREFIX}"/usr/share/ccp4/XIAROOT/xia2-${PV} - PATH="${EPREFIX}"/usr/share/ccp4/XIAROOT/xia2-${PV}/Applications - EOF - - doenvd "${T}"/23XIA -} - -pkg_postinst() { - python_mod_optimize /usr/share/ccp4/XIAROOT -} - -pkg_postrm() { - python_mod_cleanup /usr/share/ccp4/XIAROOT -} diff --git a/sci-chemistry/xia2/xia2-0.3.1.7.ebuild b/sci-chemistry/xia2/xia2-0.3.1.7.ebuild deleted file mode 100644 index 16fbf797d1b4..000000000000 --- a/sci-chemistry/xia2/xia2-0.3.1.7.ebuild +++ /dev/null @@ -1,66 +0,0 @@ -# Copyright 1999-2011 Gentoo Foundation -# Distributed under the terms of the GNU General Public License v2 -# $Id$ - -EAPI="3" - -PYTHON_DEPEND="2" - -inherit eutils python - -DESCRIPTION="An automated data reduction system for crystallography" -HOMEPAGE="http://www.ccp4.ac.uk/xia/" -SRC_URI="http://www.ccp4.ac.uk/${PN}/${P}.tar.bz2" - -LICENSE="BSD" -SLOT="0" -KEYWORDS="~amd64 ~ppc ~x86 ~amd64-linux ~x86-linux" -IUSE="" - -RDEPEND=" - >=sci-chemistry/ccp4-apps-6.1.2 - sci-chemistry/mosflm - sci-chemistry/pointless - >=sci-libs/ccp4-libs-6.1.2 - sci-libs/cctbx" -DEPEND="${RDEPEND}" - -pkg_setup() { - python_set_active_version 2 -} - -src_prepare() { - find . -name '*.bat' -delete || die - - epatch "${FILESDIR}"/${PV}-fix-syntax.patch - python_convert_shebangs -r $(python_get_version) . -} - -src_install() { - rm -rf ${P}/binaries ${PN}core-${PV}/Test || die - - insinto /usr/share/ccp4/XIAROOT/ - doins -r * || die - - # Set programs executable -# fperms cannot handle wildcards - chmod 755 "${ED}"/usr/share/ccp4/XIAROOT/${P}/Applications/* || die - chmod 644 "${ED}"/usr/share/ccp4/XIAROOT/${P}/Applications/*.py || die - - cat >> "${T}"/23XIA <<- EOF - XIA2_HOME="${EPREFIX}"/usr/share/ccp4/XIAROOT - XIA2CORE_ROOT="${EPREFIX}"/usr/share/ccp4/XIAROOT/xia2core-${PV} - XIA2_ROOT="${EPREFIX}"/usr/share/ccp4/XIAROOT/xia2-${PV} - PATH="${EPREFIX}"/usr/share/ccp4/XIAROOT/xia2-${PV}/Applications - EOF - - doenvd "${T}"/23XIA -} - -pkg_postinst() { - python_mod_optimize /usr/share/ccp4/XIAROOT -} - -pkg_postrm() { - python_mod_cleanup /usr/share/ccp4/XIAROOT -} diff --git a/sci-chemistry/xia2/xia2-0.3.3.1.ebuild b/sci-chemistry/xia2/xia2-0.3.3.1.ebuild deleted file mode 100644 index 26fb7d0d4c83..000000000000 --- a/sci-chemistry/xia2/xia2-0.3.3.1.ebuild +++ /dev/null @@ -1,70 +0,0 @@ -# Copyright 1999-2012 Gentoo Foundation -# Distributed under the terms of the GNU General Public License v2 -# $Id$ - -EAPI=3 - -PYTHON_DEPEND="2" - -inherit eutils python - -DESCRIPTION="An automated data reduction system for crystallography" -HOMEPAGE="http://www.ccp4.ac.uk/xia/" -SRC_URI="http://www.ccp4.ac.uk/${PN}/${P}.tar.bz2" - -LICENSE="BSD" -SLOT="0" -KEYWORDS="amd64 ~ppc x86 ~amd64-linux ~x86-linux" -IUSE="" - -RDEPEND=" - >=sci-chemistry/ccp4-apps-6.1.2 - sci-chemistry/mosflm - sci-chemistry/pointless - >=sci-libs/ccp4-libs-6.1.2 - sci-libs/cctbx" -DEPEND="${RDEPEND}" - -pkg_setup() { - python_set_active_version 2 -} - -src_prepare() { - find . -name '*.bat' -delete || die - - epatch "${FILESDIR}"/${PV}-fix-syntax.patch - python_convert_shebangs -r $(python_get_version) . -} - -src_install() { - rm -rf ${P}/binaries ${PN}core-${PV}/Test || die - - insinto /usr/share/ccp4/XIAROOT/ - doins -r * || die - - # Set programs executable -# fperms cannot handle wildcards - chmod 755 "${ED}"/usr/share/ccp4/XIAROOT/${P}/Applications/* || die - chmod 644 "${ED}"/usr/share/ccp4/XIAROOT/${P}/Applications/*.py || die - - cat >> "${T}"/23XIA <<- EOF - XIA2_HOME="${EPREFIX}/usr/share/ccp4/XIAROOT" - XIA2CORE_ROOT="${EPREFIX}/usr/share/ccp4/XIAROOT/xia2core-${PV}" - XIA2_ROOT="${EPREFIX}/usr/share/ccp4/XIAROOT/xia2-${PV}" - PATH="${EPREFIX}/usr/share/ccp4/XIAROOT/xia2-${PV}/Applications" - EOF - - doenvd "${T}"/23XIA -} - -pkg_postinst() { - python_mod_optimize /usr/share/ccp4/XIAROOT - echo "" - elog "In order to use the package, you need to" - elog "\t source ${EPREFIX}/etc/profile" - echo "" -} - -pkg_postrm() { - python_mod_cleanup /usr/share/ccp4/XIAROOT -} diff --git a/sci-chemistry/xia2/xia2-0.3.3.3.ebuild b/sci-chemistry/xia2/xia2-0.3.3.3.ebuild deleted file mode 100644 index 60778aa75fb9..000000000000 --- a/sci-chemistry/xia2/xia2-0.3.3.3.ebuild +++ /dev/null @@ -1,70 +0,0 @@ -# Copyright 1999-2011 Gentoo Foundation -# Distributed under the terms of the GNU General Public License v2 -# $Id$ - -EAPI=3 - -PYTHON_DEPEND="2" - -inherit eutils python - -DESCRIPTION="An automated data reduction system for crystallography" -HOMEPAGE="http://www.ccp4.ac.uk/xia/" -SRC_URI="http://www.ccp4.ac.uk/${PN}/${P}.tar.bz2" - -LICENSE="BSD" -SLOT="0" -KEYWORDS="~amd64 ~ppc ~x86 ~amd64-linux ~x86-linux" -IUSE="" - -RDEPEND=" - >=sci-chemistry/ccp4-apps-6.1.2 - sci-chemistry/mosflm - sci-chemistry/pointless - >=sci-libs/ccp4-libs-6.1.2 - sci-libs/cctbx" -DEPEND="${RDEPEND}" - -pkg_setup() { - python_set_active_version 2 -} - -src_prepare() { - find . -name '*.bat' -delete || die - - epatch "${FILESDIR}"/${PV}-fix-syntax.patch - python_convert_shebangs -r $(python_get_version) . -} - -src_install() { - rm -rf ${P}/binaries ${PN}core-${PV}/Test || die - - insinto /usr/share/ccp4/XIAROOT/ - doins -r * || die - - # Set programs executable -# fperms cannot handle wildcards - chmod 755 "${ED}"/usr/share/ccp4/XIAROOT/${P}/Applications/* || die - chmod 644 "${ED}"/usr/share/ccp4/XIAROOT/${P}/Applications/*.py || die - - cat >> "${T}"/23XIA <<- EOF - XIA2_HOME="${EPREFIX}/usr/share/ccp4/XIAROOT" - XIA2CORE_ROOT="${EPREFIX}/usr/share/ccp4/XIAROOT/xia2core-${PV}" - XIA2_ROOT="${EPREFIX}/usr/share/ccp4/XIAROOT/xia2-${PV}" - PATH="${EPREFIX}/usr/share/ccp4/XIAROOT/xia2-${PV}/Applications" - EOF - - doenvd "${T}"/23XIA -} - -pkg_postinst() { - python_mod_optimize /usr/share/ccp4/XIAROOT - echo "" - elog "In order to use the package, you need to" - elog "\t source ${EPREFIX}/etc/profile" - echo "" -} - -pkg_postrm() { - python_mod_cleanup /usr/share/ccp4/XIAROOT -} diff --git a/sci-chemistry/xia2/xia2-0.3.4.0.ebuild b/sci-chemistry/xia2/xia2-0.3.4.0.ebuild deleted file mode 100644 index 1d27abd355dc..000000000000 --- a/sci-chemistry/xia2/xia2-0.3.4.0.ebuild +++ /dev/null @@ -1,70 +0,0 @@ -# Copyright 1999-2012 Gentoo Foundation -# Distributed under the terms of the GNU General Public License v2 -# $Id$ - -EAPI=3 - -PYTHON_DEPEND="2" - -inherit eutils python - -DESCRIPTION="An automated data reduction system for crystallography" -HOMEPAGE="http://www.ccp4.ac.uk/xia/" -SRC_URI="http://www.ccp4.ac.uk/${PN}/${P}.tar.bz2" - -LICENSE="BSD" -SLOT="0" -KEYWORDS="~amd64 ~ppc ~x86 ~amd64-linux ~x86-linux" -IUSE="" - -RDEPEND=" - >=sci-chemistry/ccp4-apps-6.1.2 - sci-chemistry/mosflm - sci-chemistry/pointless - >=sci-libs/ccp4-libs-6.1.2 - sci-libs/cctbx" -DEPEND="${RDEPEND}" - -pkg_setup() { - python_set_active_version 2 -} - -src_prepare() { - find . -name '*.bat' -delete || die - - epatch "${FILESDIR}"/${PV}-fix-syntax.patch - python_convert_shebangs -r $(python_get_version) . -} - -src_install() { - rm -rf ${P}/binaries ${PN}core-${PV}/Test || die - - insinto /usr/share/ccp4/XIAROOT/ - doins -r * || die - - # Set programs executable -# fperms cannot handle wildcards - chmod 755 "${ED}"/usr/share/ccp4/XIAROOT/${P}/Applications/* || die - chmod 644 "${ED}"/usr/share/ccp4/XIAROOT/${P}/Applications/*.py || die - - cat >> "${T}"/23XIA <<- EOF - XIA2_HOME="${EPREFIX}/usr/share/ccp4/XIAROOT" - XIA2CORE_ROOT="${EPREFIX}/usr/share/ccp4/XIAROOT/xia2core-${PV}" - XIA2_ROOT="${EPREFIX}/usr/share/ccp4/XIAROOT/xia2-${PV}" - PATH="${EPREFIX}/usr/share/ccp4/XIAROOT/xia2-${PV}/Applications" - EOF - - doenvd "${T}"/23XIA -} - -pkg_postinst() { - python_mod_optimize /usr/share/ccp4/XIAROOT - echo "" - elog "In order to use the package, you need to" - elog "\t source ${EPREFIX}/etc/profile" - echo "" -} - -pkg_postrm() { - python_mod_cleanup /usr/share/ccp4/XIAROOT -} diff --git a/sci-libs/balbes-db/Manifest b/sci-libs/balbes-db/Manifest deleted file mode 100644 index 86fed7e6ab9e..000000000000 --- a/sci-libs/balbes-db/Manifest +++ /dev/null @@ -1 +0,0 @@ -DIST ccp4-6.1.3-balbesdb-10-11-08.tar.gz 600856059 SHA256 5606fc5e131138b56fa3a1afce014225a6c07826b99587f132f6c337585f4f0d SHA512 5b7f3b3465312da72ff4816c96244252a6f0bf039fde8ff772ea683e6317053d903cdc2b3b86b78e8edbb1c766d1b3676048ac4e7d4d0db29ed7bf62dfb00ab2 WHIRLPOOL 9a01610c9767aece4c9cc052a8aa2fd5dff9c9967f11688f5e6e206a82e2714751e086a7ddbe6a99da23b70163c7b096f57d281eebe53b8dd7cdb18faed23d63 diff --git a/sci-libs/balbes-db/balbes-db-6.1.3-r1.ebuild b/sci-libs/balbes-db/balbes-db-6.1.3-r1.ebuild deleted file mode 100644 index bd973c5120d7..000000000000 --- a/sci-libs/balbes-db/balbes-db-6.1.3-r1.ebuild +++ /dev/null @@ -1,47 +0,0 @@ -# Copyright 1999-2015 Gentoo Foundation -# Distributed under the terms of the GNU General Public License v2 -# $Id$ - -EAPI=5 - -MY_P="ccp4-${PV}" - -SRC="ftp://ftp.ccp4.ac.uk/ccp4" -VERSION="10-11-08" - -DESCRIPTION="The database for the BALBES automated crystallographic molecular replacement pipeline" -HOMEPAGE="http://www.ysbl.york.ac.uk/~fei/balbes/" -SRC_URI="${SRC}/${PV}/${MY_P}-${PN/-/}-${VERSION}.tar.gz" - -LICENSE="ccp4" -SLOT="0" -KEYWORDS="amd64 ~ppc x86 ~amd64-linux ~x86-linux ~x64-macos ~x86-macos" -IUSE="" - -RDEPEND=" - >=dev-python/pyxml-0.8.4 - sci-libs/monomer-db" -DEPEND="${RDEPEND}" -RESTRICT="binchecks strip" - -S="${WORKDIR}/${MY_P}" - -src_install() { - dodir /usr/share/balbes/BALBES_0.0.1 - rm -rf share/balbes/BALBES_0.0.1/dic || die - # We don't want to wait around to copy all this, or suck up double - # the disk space - einfo "Installing files, which can take some time ..." - mv "${S}"/share/balbes/BALBES_0.0.1/* "${ED}"/usr/share/balbes/BALBES_0.0.1/ || die - # db files shouldn't be executable - find "${ED}"/usr/share/balbes/BALBES_0.0.1/ \ - -type f \ - -exec chmod 664 '{}' \; || die - dosym ../../ccp4/data/monomers /usr/share/balbes/BALBES_0.0.1/dic - - cat >> "${T}"/20balbes <<- EOF - BALBES_ROOT="${EPREFIX}/usr/share/balbes/BALBES_0.0.1/" - EOF - - doenvd "${T}"/20balbes -} diff --git a/sci-libs/balbes-db/metadata.xml b/sci-libs/balbes-db/metadata.xml deleted file mode 100644 index 51fdedab1b38..000000000000 --- a/sci-libs/balbes-db/metadata.xml +++ /dev/null @@ -1,5 +0,0 @@ -<?xml version="1.0" encoding="UTF-8"?> -<!DOCTYPE pkgmetadata SYSTEM "http://www.gentoo.org/dtd/metadata.dtd"> -<pkgmetadata> - <herd>sci-chemistry</herd> -</pkgmetadata> diff --git a/sci-libs/ccp4-libs/Manifest b/sci-libs/ccp4-libs/Manifest deleted file mode 100644 index 9d3fe2806365..000000000000 --- a/sci-libs/ccp4-libs/Manifest +++ /dev/null @@ -1 +0,0 @@ -DIST ccp4-6.1.3-core-src.tar.gz 242134076 SHA256 1e529c660e7f390ec0feca9d45caa00a2813d23156c10a2747c427117293c324 SHA512 413eba806107ebcdbd93e9122275463709133d9b2a9ce44ae57a6c2350465a47ba66ad9875237aead74f5d422c0104f58f728ab37a757b10d82cde92af444c20 WHIRLPOOL faebf8ee7920013bc3d0e83565207dca1f31ba0b5c92fe1eae4b740f70ff2031d95787fa0d545b09c853d25657c08973527e43de02fddc086988123ca2a6339c diff --git a/sci-libs/ccp4-libs/ccp4-libs-6.1.3-r16.ebuild b/sci-libs/ccp4-libs/ccp4-libs-6.1.3-r16.ebuild deleted file mode 100644 index dcd741637048..000000000000 --- a/sci-libs/ccp4-libs/ccp4-libs-6.1.3-r16.ebuild +++ /dev/null @@ -1,359 +0,0 @@ -# Copyright 1999-2015 Gentoo Foundation -# Distributed under the terms of the GNU General Public License v2 -# $Id$ - -EAPI=5 - -PYTHON_COMPAT=( python2_7 ) - -inherit autotools eutils fortran-2 gnuconfig multilib python-single-r1 toolchain-funcs - -SRC="ftp://ftp.ccp4.ac.uk/ccp4" - -#UPDATE="04_03_09" -#PATCHDATE="090511" - -MY_P="${P/-libs}" - -PATCH_TOT="0" - -DESCRIPTION="Protein X-ray crystallography toolkit - Libraries" -HOMEPAGE="http://www.ccp4.ac.uk/" -SRC_URI="${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} https://dev.gentoo.org/~jlec/science-dist/${PV}-${PATCHDATE}-updates.patch.bz2" - -for i in $(seq $PATCH_TOT); do - NAME="PATCH${i}[1]" - SRC_URI="${SRC_URI} - ${SRC}/${PV}/patches/${!NAME}" -done - -LICENSE="ccp4" -SLOT="0" -KEYWORDS="amd64 ppc x86 ~amd64-linux ~x86-linux" -IUSE="minimal" - -REQUIRED_USE="${PYTHON_REQUIRED_USE}" - -RDEPEND=" - ${PYTHON_DEPS} - !<sci-chemistry/ccp4-6.1.3 - !<sci-chemistry/ccp4-apps-${PV}-r10 - app-shells/tcsh - dev-lang/tcl:0 - >=sci-libs/cbflib-0.9.2.2 - sci-libs/fftw:2.1 - sci-libs/mmdb:0 - sci-libs/monomer-db - sci-libs/ssm - virtual/jpeg:0= - virtual/lapack - virtual/blas" -DEPEND="${RDEPEND} - virtual/pkgconfig" - -S="${WORKDIR}/${MY_P}" - -MAKEOPTS+=" -j1" - -pkg_setup() { - fortran-2_pkg_setup - python-single-r1_pkg_setup -} - -src_prepare() { - tc-export PKG_CONFIG RANLIB AR - - sed \ - -e "/^AR/s:ar:$(tc-getAR):g" \ - -i lib/src/Makefile.in src/Makefile.in src/ccp4mapwish_/Makefile.in lib/ccif/Makefile.in || die - - 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 ..." - # fix buffer overflows wrt bug 339706 - ccp_patch "${FILESDIR}"/${PV}-overflows.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 "${FILESDIR}"/6.0.2-ppc-double-define-gerror.patch - - # make creation of libccif.so smooth - ccp_patch "${FILESDIR}"/${PV}-ccif-shared.patch - - # lets try to build libmmdb seperatly - ccp_patch "${FILESDIR}"/${PV}-dont-build-mmdb.patch - - # unbundle libjpeg and cbflib - ccp_patch "${FILESDIR}"/${PV}-unbundle-libs-ng2.patch - - # Fix missing DESTIDR - # not installing during build - ccp_patch "${FILESDIR}"/${PV}-noinstall.patch - sed \ - -e '/SHARE_INST/s:$(libdir):$(DESTDIR)/$(libdir):g' \ - -i configure || die - - # Fix upstreams code - ccp_patch "${FILESDIR}"/${PV}-impl-dec.patch - - # use pkg-config to detect BLAS/LAPACK - ccp_patch "${FILESDIR}"/${PV}-lapack.patch - - # proto type changing in version 0.9.2.2 - ccp_patch "${FILESDIR}"/${PV}-cbf.patch - - # proto type changing in version 0.9.2.2 - ccp_patch "${FILESDIR}"/${PV}-no-pypath.patch - - ccp_patch "${FILESDIR}"/${P}-force.patch - - ccp_patch "${FILESDIR}"/${P}-format-security.patch - - einfo "Done." # done applying Gentoo patches - echo - - # not needed, we have it extra - rm -rf src/rapper/{libxml2,gc7.0} || die - - sed \ - -e "s:/usr:${EPREFIX}/usr:g" \ - -e 's:-Wl,-rpath,$CLIB::g' \ - -e 's: -rpath $CLIB::g' \ - -e 's: -I${srcdir}/include/cpp_c_headers::g' \ - -e 's:sleep 1:sleep .2:g' \ - -i configure || die - - gnuconfig_update - - for i in lib/DiffractionImage src/rapper src/pisa; do - pushd ${i} > /dev/null - sed 's:-g::g' -i configure* || die - [[ -f configure.in ]] && mv configure.{in,ac} - eautoreconf - popd > /dev/null - done - - ## unbundle libssm - sed -e '/libdir/s:ssm::g' -i Makefile.in || die - find ./lib/src/mmdb ./lib/ssm ./lib/clipper ./lib/fftw lib/lapack -delete || die -} - -src_configure() { - rm -rf lib/DiffractionImage/{jpg,CBFlib} || die - - # Build system is broken if we set LDFLAGS - userldflags="${LDFLAGS}" - export SHARED_LIB_FLAGS="${LDFLAGS}" - unset LDFLAGS - - # GENTOO_OSNAME can be one of: - # irix irix64 sunos sunos64 aix hpux osf1 linux freebsd - # linux_compaq_compilers linux_intel_compilers generic Darwin - # ia64_linux_intel Darwin_ibm_compilers linux_ibm_compilers - if [[ "$(tc-getFC)" = "ifort" ]]; then - if use ia64; then - GENTOO_OSNAME="ia64_linux_intel" - else - # Should be valid for x86, maybe amd64 - GENTOO_OSNAME="linux_intel_compilers" - fi - else - # Should be valid for x86 and amd64, at least - GENTOO_OSNAME="linux" - fi - - # Sets up env - ln -s \ - ccp4.setup-bash \ - "${S}"/include/ccp4.setup || die - - # We agree to the license by emerging this, set in LICENSE - sed -i \ - -e "s~^\(^agreed=\).*~\1yes~g" \ - "${S}"/configure || die - - # Fix up variables -- need to reset CCP4_MASTER at install-time - sed -i \ - -e "s~^\(setenv CCP4_MASTER.*\)/.*~\1${WORKDIR}~g" \ - -e "s~^\(export CCP4_MASTER.*\)/.*~\1${WORKDIR}~g" \ - -e "s~^\(.*export CBIN=.*\)\$CCP4.*~\1\$CCP4/libexec/ccp4/bin/~g" \ - -e "s~^\(.*setenv CBIN .*\)\$CCP4.*~\1\$CCP4/libexec/ccp4/bin/~g" \ - -e "s~^\(setenv CCP4I_TCLTK.*\)/usr/local/bin~\1${EPREFIX}/usr/bin~g" \ - "${S}"/include/ccp4.setup* || die - - # Set up variables for build - source "${S}"/include/ccp4.setup-sh - - export CC=$(tc-getCC) - export CXX=$(tc-getCXX) - export COPTIM=${CFLAGS} - export CXXOPTIM=${CXXFLAGS} - # Default to -O2 if FFLAGS is unset - export FC=$(tc-getFC) - export FOPTIM=${FFLAGS:- -O2} - - export SHARE_LIB="\ - $(tc-getCC) ${userldflags} -shared -Wl,-soname,libccp4c.so -o libccp4c.so \${CORELIBOBJS} \${CGENERALOBJS} \${CUCOBJS} \${CMTZOBJS} \${CMAPOBJS} \${CSYMOBJS} -L../ccif/ -lccif $(gcc-config -L | awk -F: '{for(i=1; i<=NF; i++) printf " -L%s", $i}') -lm && \ - $(tc-getFC) ${userldflags} -shared -Wl,-soname,libccp4f.so -o libccp4f.so \${FORTRANLOBJS} \${FINTERFACEOBJS} -L../ccif/ -lccif -L. -lccp4c $($(tc-getPKG_CONFIG) --libs mmdb) $(gcc-config -L | awk -F: '{for(i=1; i<=NF; i++) printf " -L%s", $i}') -lstdc++ -lgfortran -lm" - - # Can't use econf, configure rejects unknown options like --prefix - ./configure \ - --onlylibs \ - --with-shared-libs \ - --with-fftw="${EPREFIX}/usr" \ - --with-warnings \ - --disable-cctbx \ - --disable-clipper \ - --disable-ssm \ - --tmpdir="${TMPDIR}" \ - --bindir="${EPREFIX}/usr/libexec/ccp4/bin/" \ - --libdir="${EPREFIX}/usr/$(get_libdir)" \ - ${GENTOO_OSNAME} || die "configure failed" -} - -src_compile() { - emake DESTDIR="${D}" onlylib -} - -src_install() { - # Set up variables for build - source "${S}"/include/ccp4.setup-sh - - emake \ - DESTDIR="${D}" \ - includedir="${EPREFIX}/usr/include" \ - library_includedir="${EPREFIX}/usr/include" \ - install - - sed \ - -e "330,1000d" \ - -i "${S}"/include/ccp4.setup-sh || die - - sed \ - -e "378,1000d" \ - -i "${S}"/include/ccp4.setup-csh || die - - sed \ - -e "s:-${PV/-r*/}::g" \ - -e "s:^\(.*export CCP4_MASTER=\).*:\1${EPREFIX}/usr:g" \ - -e "s:^\(.*setenv CCP4_MASTER\).*:\1 ${EPREFIX}/usr:g" \ - -e "s:^\(.*export CCP4=\).*CCP4_MASTER.*:\1${EPREFIX}/usr:g" \ - -e "s:^\(.*setenv CCP4\).*CCP4_MASTER.*:\1 ${EPREFIX}/usr:g" \ - -e "s:^\(.*export CCP4_SCR=\).*:\1${EPREFIX}/tmp:g" \ - -e "s:^\(.*setenv CCP4_SCR \).*:\1${EPREFIX}/tmp:g" \ - -e "s:^\(.*export BINSORT_SCR=\).*:\1${EPREFIX}/tmp:g" \ - -e "s:^\(.*setenv BINSORT_SCR \).*:\1${EPREFIX}/tmp:g" \ - -e "s:^\(.*export CCP4I_TOP=\).*:\1${EPREFIX}/usr/$(get_libdir)/ccp4/ccp4i:g" \ - -e "s:^\(.*setenv CCP4I_TOP \).*:\1${EPREFIX}/usr/$(get_libdir)/ccp4/ccp4i:g" \ - -e "s:^\(.*export CCP4I_TCLTK=\).*:\1${EPREFIX}/usr/bin:g" \ - -e "s:^\(.*setenv CCP4I_TCLTK \).*:\1${EPREFIX}/usr/bin:g" \ - -e "s:^\(.*export CCP4I_HELP=\).*:\1${EPREFIX}/usr/$(get_libdir)/ccp4/ccp4i/help:g" \ - -e "s:^\(.*setenv CCP4I_HELP \).*:\1${EPREFIX}/usr/$(get_libdir)/ccp4/ccp4i/help:g" \ - -e "s:^\(.*export CBIN=\).*:\1${EPREFIX}/usr/libexec/ccp4/bin:g" \ - -e "s:^\(.*setenv CBIN \).*:\1${EPREFIX}/usr/libexec/ccp4/bin:g" \ - -e "s:^\(.*export CCP4_BIN=\).*:\1${EPREFIX}/usr/libexec/ccp4/bin:g" \ - -e "s:^\(.*setenv CCP4_BIN \).*:\1${EPREFIX}/usr/libexec/ccp4/bin:g" \ - -e "s:^\(.*export CLIBD_MON=\).*:\1${EPREFIX}/usr/share/ccp4/data/monomers/:g" \ - -e "s:^\(.*setenv CLIBD_MON \).*:\1${EPREFIX}/usr/share/ccp4/data/monomers/:g" \ - -e "s:^\(.*export CLIBD=\).*:\1${EPREFIX}/usr/share/ccp4/data:g" \ - -e "s:^\(.*setenv CLIBD \).*:\1${EPREFIX}/usr/share/ccp4/data:g" \ - -e "s:^\(.*export CCP4_LIB=\).*:\1${EPREFIX}/usr/$(get_libdir):g" \ - -e "s:^\(.*setenv CCP4_LIB \).*:\1${EPREFIX}/usr/$(get_libdir):g" \ - -e "s:^\(.*export CCP4_BROWSER=\).*:\1firefox:g" \ - -e "s:^\(.*setenv CCP4_BROWSER \).*:\1firefox:g" \ - -e "s:^\(.*export MANPATH=\).*:\1\${MANPATH}:g" \ - -e "s:^\(.*setenv MANPATH \).*:\1\${MANPATH}:g" \ - -e "s:^\(.*export DBCCP4I_TOP=\).*:\1${EPREFIX}/usr/share/ccp4/dbccp4i:g" \ - -e "s:^\(.*setenv DBCCP4I_TOP \).*:\1${EPREFIX}/usr/share/ccp4/dbccp4i:g" \ - -e "s:^\(.*export MOLREPLIB=\).*:\1${EPREFIX}/usr/share/ccp4/data/monomers/:g" \ - -e "s:^\(.*setenv MOLREPLIB \).*:\1${EPREFIX}/usr/share/ccp4/data/monomers/:g" \ - -e "s:^\(.*export CDOC=\).*:\1${EPREFIX}/usr/share/doc:g" \ - -e "s:^\(.*setenv CDOC \).*:\1${EPREFIX}/usr/share/doc:g" \ - -e "s:^\(.*export CEXAM=\).*:\1${EPREFIX}/usr/share/doc/examples:g" \ - -e "s:^\(.*setenv CEXAM \).*:\1${EPREFIX}/usr/share/doc/examples:g" \ - -e "s:^\(.*export CINCL=\).*:\1${EPREFIX}/usr/share/ccp4/include:g" \ - -e "s:^\(.*setenv CINCL \).*:\1${EPREFIX}/usr/share/ccp4/include:g" \ - -e "s:\$CLIB/font84.dat:\"${EPREFIX}/usr/$(get_libdir)/font84.dat\":g" \ - -e "s:\$CLIB/cif_mmdic.lib:\"${EPREFIX}/usr/$(get_libdir)/cif_mmdic.lib\":g" \ - -e '/# .*LD_LIBRARY_PATH specifies/,/^$/d' \ - -e '/CLIB=/d' \ - -e '/CLIB /d' \ - -e '/CLIBS=/d' \ - -e '/CLIBS /d' \ - -e "/alias/d" \ - -e "/CCP4_HELPDIR/d" \ - -e "/IMOSFLM_VERSION/d" \ - -i "${S}"/include/ccp4.setup* || die - - # Don't check for updates on every sourcing of /etc/profile - sed -i \ - -e "s:\(eval python.*\):#\1:g" \ - "${S}"/include/ccp4.setup* || die - - # Libs - for file in "${S}"/lib/*; do - if [[ -d ${file} ]]; then - continue - elif [[ -x ${file} ]]; then - dolib.so ${file} - else - insinto /usr/$(get_libdir) - doins ${file} - fi - done - - prune_libtool_files - - sed \ - -e 's:test "LD_LIBRARY_PATH":test "$LD_LIBRARY_PATH":g' \ - -i "${S}"/include/ccp4.setup-sh || die - - if ! use minimal; then - # Setup scripts - insinto /etc/profile.d - newins "${S}"/include/ccp4.setup-csh 40ccp4.setup.csh - newins "${S}"/include/ccp4.setup-sh 40ccp4.setup.sh - - # Data - insinto /usr/share/ccp4/data/ - doins -r "${S}"/lib/data/{*.PARM,*.prt,*.lib,*.dic,*.idl,*.cif,*.resource,*.york,*.hist,fraglib,reference_structures} - - # Environment files, setup scripts, etc. - rm -rf "${S}"/include/{ccp4.setup*,COPYING,cpp_c_headers} || die - insinto /usr/share/ccp4/ - doins -r "${S}"/include - fi - - rm -f "${S}"/include/ccp4.setup* || die - - dodoc "${S}"/lib/data/*.doc - newdoc "${S}"/lib/data/README DATA-README -} - -pkg_postinst() { - einfo "The Web browser defaults to firefox. Change CCP4_BROWSER" - einfo "in ${EPREFIX}/etc/profile.d/40ccp4.setup* to modify this." -} - -# 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 a77d9494a05c..000000000000 --- 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/6.1.3-cbf.patch b/sci-libs/ccp4-libs/files/6.1.3-cbf.patch deleted file mode 100644 index 6930fcad766a..000000000000 --- a/sci-libs/ccp4-libs/files/6.1.3-cbf.patch +++ /dev/null @@ -1,16 +0,0 @@ - lib/DiffractionImage/DiffractionImageCBF.cpp | 2 +- - 1 files changed, 1 insertions(+), 1 deletions(-) - -diff --git a/lib/DiffractionImage/DiffractionImageCBF.cpp b/lib/DiffractionImage/DiffractionImageCBF.cpp -index 69b32b0..3ffee26 100755 ---- a/lib/DiffractionImage/DiffractionImageCBF.cpp -+++ b/lib/DiffractionImage/DiffractionImageCBF.cpp -@@ -62,7 +62,7 @@ namespace DI - int* tmpimg; - tmpimg=new int[height*width]; - test= cbf_decompress_byte_offset ((void *)tmpimg,sizeof(int),sign, -- nelements,&nread,0,32,sign,ccbbff,0, -+ nelements,&nread,0,0,32,sign,ccbbff,0, - byte_ord.c_str(),2,(size_t) width, - (size_t) height,1,(size_t) padding); - for(int i=0;i<height*width;i++) 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 ca18d75bc840..000000000000 --- 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 b3147ad81bbf..000000000000 --- a/sci-libs/ccp4-libs/files/6.1.3-dont-build-mmdb.patch +++ /dev/null @@ -1,24 +0,0 @@ -diff --git a/lib/src/Makefile.in b/lib/src/Makefile.in -index c23f488..b32dd1e 100755 ---- a/lib/src/Makefile.in -+++ b/lib/src/Makefile.in -@@ -176,7 +176,7 @@ $(mmdbsrcdir)/mmdb_sbase0.h $(mmdbsrcdir)/hybrid_36.h - - ##### Makefile targets ###### - --all: fsplit $(LMMDB) $(LC) $(LF) $(SCRIPT_MODULES) -+all: fsplit $(LC) $(LF) $(SCRIPT_MODULES) - # maybe create shared library - $(SHARE_LIB) - -@@ -717,10 +717,8 @@ uninstall-mmdbHEADERS: - done - - install : all install-ccp4HEADERS install-mmdbHEADERS -- $(INSTALL_DATA) `pwd`/$(LMMDB) $(libdir)/$(LMMDB) - $(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 583697cea0a1..000000000000 --- 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 6e3997647955..000000000000 --- 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-impl-dec.patch b/sci-libs/ccp4-libs/files/6.1.3-impl-dec.patch deleted file mode 100644 index 8bfa7db8cbff..000000000000 --- a/sci-libs/ccp4-libs/files/6.1.3-impl-dec.patch +++ /dev/null @@ -1,140 +0,0 @@ -diff --git a/lib/DiffractionImage/Bruker/FRM_LIB.c b/lib/DiffractionImage/Bruker/FRM_LIB.c -index bfda882..f821e04 100755 ---- a/lib/DiffractionImage/Bruker/FRM_LIB.c -+++ b/lib/DiffractionImage/Bruker/FRM_LIB.c -@@ -38,6 +38,8 @@ FRM_LIB: Routines for reading, writing, and handling frame files. - #include "sys/types.h" /* _open, etc. */ - #include "sys/stat.h" /* _open, etc. */ - -+#include <unistd.h> -+ - #ifndef _MSC_VER - int min(int a, int b) - { -diff --git a/lib/DiffractionImage/MAR/mar300_header.c b/lib/DiffractionImage/MAR/mar300_header.c -index 1a933de..1c40c32 100755 ---- a/lib/DiffractionImage/MAR/mar300_header.c -+++ b/lib/DiffractionImage/MAR/mar300_header.c -@@ -23,6 +23,9 @@ - */ - #include "mar300_header.h" - -+#include <sys/types.h> -+#include <unistd.h> -+ - /* - * Local functions - */ -diff --git a/lib/DiffractionImage/MAR/mar345_header.c b/lib/DiffractionImage/MAR/mar345_header.c -index a8351ea..16d0f7b 100755 ---- a/lib/DiffractionImage/MAR/mar345_header.c -+++ b/lib/DiffractionImage/MAR/mar345_header.c -@@ -32,6 +32,9 @@ - */ - #include "mar345_header.h" - -+#include <sys/types.h> -+#include <unistd.h> -+ - /* - * Definitions - */ -diff --git a/lib/DiffractionImage/MAR/nb_header.c b/lib/DiffractionImage/MAR/nb_header.c -index 07f2741..6364ca4 100755 ---- a/lib/DiffractionImage/MAR/nb_header.c -+++ b/lib/DiffractionImage/MAR/nb_header.c -@@ -20,6 +20,8 @@ - #include <io.h> - #endif - -+#include <sys/types.h> -+#include <unistd.h> - /* - * mar software include files - */ -diff --git a/lib/DiffractionImage/MAR/swap.c b/lib/DiffractionImage/MAR/swap.c -index 443bb8c..0d96b3f 100755 ---- a/lib/DiffractionImage/MAR/swap.c -+++ b/lib/DiffractionImage/MAR/swap.c -@@ -10,6 +10,9 @@ - * - **********************************************************************/ - -+#define _XOPEN_SOURCE -+#include <unistd.h> -+ - void swaplong(); - void swapshort(); - -diff --git a/lib/ccif/f_interface.c b/lib/ccif/f_interface.c -index 0f6a6b7..a09dc48 100755 ---- a/lib/ccif/f_interface.c -+++ b/lib/ccif/f_interface.c -@@ -25,6 +25,7 @@ - ********************************************************************/ - - #include "stdpccts.h" -+#include <sys/mman.h> - - /* This file is terribly organised, and badly needs re-doing. There is probably - * scope for splitting this into three modules: -diff --git a/lib/src/ccp4_general_f.c b/lib/src/ccp4_general_f.c -index 8b5d04f..74ee3f7 100755 ---- a/lib/src/ccp4_general_f.c -+++ b/lib/src/ccp4_general_f.c -@@ -26,6 +26,7 @@ - #include <string.h> - #include <stdlib.h> - #include <math.h> -+#include <time.h> - #include "ccp4_errno.h" - #include "ccp4_fortran.h" - #include "ccp4_parser.h" -diff --git a/lib/src/ccp4_program.c b/lib/src/ccp4_program.c -index 3e83d4d..bb3e975 100755 ---- a/lib/src/ccp4_program.c -+++ b/lib/src/ccp4_program.c -@@ -25,6 +25,7 @@ - #include <stdio.h> - #include <stdlib.h> - #include <string.h> -+#include <time.h> - #include "ccp4_program.h" - #include "ccp4_parser.h" - #include "ccp4_utils.h" -diff --git a/lib/src/fsplit.c b/lib/src/fsplit.c -index ee8af24..c6fb3cd 100755 ---- a/lib/src/fsplit.c -+++ b/lib/src/fsplit.c -@@ -50,6 +50,7 @@ static char sccsid[] = "@(#)fsplit.c 5.5 (Berkeley) 3/12/91"; - #include <string.h> - #include <sys/types.h> - #include <sys/stat.h> -+#include <unistd.h> - - /* - * usage: fsplit [-e efile] ... [file] -diff --git a/src/clipper_progs/src/pirate/compress42.c b/src/clipper_progs/src/pirate/compress42.c -index ea52e96..30dbd56 100755 ---- a/src/clipper_progs/src/pirate/compress42.c -+++ b/src/clipper_progs/src/pirate/compress42.c -@@ -142,6 +142,7 @@ - #include <sys/types.h> - #include <sys/stat.h> - #include <errno.h> -+#include <unistd.h> - - #ifdef DIRENT - # include <dirent.h> -diff --git a/src/mtz2cif_/mtz2cif.c b/src/mtz2cif_/mtz2cif.c -index e224430..c7b82f4 100755 ---- a/src/mtz2cif_/mtz2cif.c -+++ b/src/mtz2cif_/mtz2cif.c -@@ -28,6 +28,7 @@ - #include "cmtzlib.h" - #include "ccp4_parser.h" - #include "ccp4_general.h" -+#include "ccp4_program.h" - #include "csymlib.h" - #include "mtz2cif_lib.h" - diff --git a/sci-libs/ccp4-libs/files/6.1.3-lapack.patch b/sci-libs/ccp4-libs/files/6.1.3-lapack.patch deleted file mode 100644 index 0463b3719525..000000000000 --- a/sci-libs/ccp4-libs/files/6.1.3-lapack.patch +++ /dev/null @@ -1,597 +0,0 @@ -diff --git a/configure b/configure -index 833f483..bcfa62d 100755 ---- a/configure -+++ b/configure -@@ -3226,574 +3226,14 @@ else - echo - echo "Warning: this option has not been extensively tested!" - echo "Please report problems to ccp4@ccp4.ac.uk" -- # Search for vendor LAPACK/BLAS first -- if test ! "$with_netlib_lapack" ; then -- # Initialise variables to blank -- lapackdir= -- XLAPACK_LIB= -- # Possible directories to check for vendor or pre-existing LAPACK or -- # BLAS - add to these if you want to test others -- trydirs="`echo $LD_LIBRARY_PATH |sed -e s/:/\ /g` /lib /usr/lib /usr/local/lib" -- # Possible library names -- # These are the names like xxxx where the library will be libxxxx.a -- # or libxxxx.so -- echo -- echo "Guessing names for native/vendor LAPACK and/or BLAS libraries" -- echo "on this system" -- case $system in -- linux | linux64 | linux32 ) -- # linux users will usually have them in /usr/lib but don't call it -- trylapack="lapack" -- tryblas="blas" -- # if code is non_shared then this can lead to problems. both blas and lapack -- # need to be resolved even if they are not called! -- if test "$non_shared" = yes; then -- echo "You are compiling linux non_shared. This sometimes causes problems " -- echo " so checking for requirements." -- echo "Checking: try to link library against test program" -- if test -f testlink.f || test -f testlink ; then -- rm -f testlink* -- fi -- cat > testlink.f <<EOF -- PROGRAM TESTLINK --C A bit of scala code to test the linking -- real bf(3), bnorm --c -- integer maxbmt -- parameter (maxbmt = 2) -- double precision B(maxbmt,maxbmt), eigval(maxbmt), -- $ eigvec(maxbmt,maxbmt), w(5*maxbmt) -- integer m, ia, ix, istat --c -- B(1,1) = 1.00 -- B(1,2) = 1.00 -- B(2,1) = 1.00 -- B(2,2) = 1.00 --c -- m = maxbmt -- ia = maxbmt -- ix = maxbmt -- call dsyev('N', 'L', m, B, ia, eigval, w, 5*maxbmt, istat) -- end --EOF -- #firstly test without -lblas -- test_compile="$FC $FOPTIM $XFFLAGS -o testlink testlink.f -llapack" -- echo $test_compile -- if { (eval $test_compile >& /dev/null ) 2>&1; } && test -s testlink ; then -- # Compilation was okay -- echo "... only -llapack needed" -- XLAPACK_LIB="-llapack" -- # Set the next two variables so that configure -- # doesn't try to build netlib libraries -- LAPACKLIB="lapack" -- noblas=yes -- trylapack= -- tryblas= -- else -- echo "more than just -llapack needed...." -- test_compile="$FC $FOPTIM $XFFLAGS -o testlink testlink.f -llapack -lblas" -- echo $test_compile -- if { (eval $test_compile ) 2>&1; } && test -s testlink ; then -- # Compilation was okay -- echo "...-llapack and -lblas were needed" -- XLAPACK_LIB="-llapack -lblas" -- # Set the next two variables so that configure -- # doesn't try to build netlib libraries -- LAPACKLIB="lapack blas" -- noblas=no -- trylapack= -- tryblas= -- else -- echo "....could not find either lapack or blas." -- fi -- fi -- fi -- # add 64 bit libs -- case $system in -- linux64 ) trydirs="/usr/lib64 ${trydirs}" ;; -- esac -- -- ;; -- osf1) -- # OSF1 has dxml (old version) and cxml -- # which should have both lapack and blas -- trylapack="dxml cxml" -- tryblas= -- trydirs="${trydirs} /usr/shlib" -- ;; -- irix) -- # Additional search paths for IRIX -- trydirs="${trydirs} /usr/lib32" -- # SCSL should have both LAPACK and BLAS -- trylapack="scs" -- tryblas="blas" -- ;; -- irix64) -- # Additional search paths for IRIX64 -- trydirs="${trydirs} /usr/lib64" -- # SCSL should have both LAPACK and BLAS -- trylapack="scs" -- tryblas="blas" -- # Extra compiler flags? -- #XLAPACKFLAGS="-OPT:IEEE_NaN_inf=ON" -- ;; -- aix) -- # Additional search paths for AIX -- trydirs="${trydirs}" -- # AIX might have ESSL library - blas only I think -- trylapack= -- tryblas="essl" -- ;; -- hpux) -- # Additional search paths for HPUX -- trydirs="${trydirs} /opt/fortran/lib /opt/fortran/lib/pa2.0 /opt/mlib/lib/pa2.0" -- # HPUX should have both LAPACK (part of mlib) and BLAS -- trylapack="lapack" -- tryblas="blas" -- # Extra compiler flags? -- # +U77 required for ETIME function - this is already in XFFLAGS -- #XLAPACKFLAGS="+U77" -- ;; -- -- sunos | sunos64) -- # Sun has libraries with BLAS and LAPACK invoked using -- # -xlic_lib=sunperf -- trylapack= -- tryblas= -- echo "SunOs can use the Sun Performance Library (if installed)" -- echo "which has both BLAS and LAPACK 3.0" -- echo -- echo "Looking for a valid library to use..." -- echo -- # Loop over the possible library names -- try_libs="sunperf" -- for testlib in $try_libs -- do -- if test ! "$XLAPACK_LIB" ; then -- # Try running a test compile to see if this a valid library -- if test -f testlink.f || test -f testlink ; then -- rm -f testlink* -- fi -- cat > testlink.f <<EOF --c Test fortran program to link against library -- PROGRAM TESTLINK -- IMPLICIT NONE -- INTEGER A -- A = 1 -- STOP -- END --EOF -- test_compile="$FC $FOPTIM $XFFLAGS -o testlink testlink.f -dalign -xlic_lib=$testlib" -- echo $test_compile -- if { (eval $test_compile ) 2>&1; } && test -s testlink ; then -- # Compilation was okay -- echo "... -xlic_lib=$testlib is okay" -- XLAPACK_LIB="-dalign -xlic_lib=$testlib" -- # Set the next two variables so that configure -- # doesn't try to build netlib libraries -- LAPACKLIB="$testlib" -- noblas=yes -- else -- # Compilation failed -- echo "... cannot use -xlic_lib=$testlib" -- fi -- # End of test for testlib -- fi -- # End of loop over possible lib names -- done -- # Report if no suitable library was found -- if test ! "$XLAPACK_LIB" ; then -- echo -- echo "No suitable LAPACK library was found." -- echo "This may be because the Sun Performance Library is not" -- echo "installed on your system" -- echo "Contact your system administrator or Sun vendor" -- fi -- ;; -- Darwin | Darwin32 | Darwin64 ) -- # Darwin has libraries with BLAS and LAPACK invoked using -- # -framework vecLib -- echo "Darwin can use the vecLib Library (if installed)" -- echo "which has both BLAS and LAPACK 3.0" -- echo -- # This is a special case so try running a test compile -- echo "Checking: try to link library against test program" -- if test -f testlink.f || test -f testlink ; then -- rm -f testlink* -- fi -- cat > testlink.f <<EOF --c Test fortran program to link against library -- PROGRAM TESTLINK -- IMPLICIT NONE -- INTEGER A -- A = 1 -- STOP -- END --EOF -- test_compile="$FC $FOPTIM $XFFLAGS -o testlink testlink.f -framework vecLib" -- echo $test_compile -- if { (eval $test_compile ) 2>&1; } && test -s testlink ; then -- # Compilation was okay -- echo "... -framework vecLib is okay" -- XLAPACK_LIB="-framework vecLib" -- # Set the next two variables so that configure -- # doesn't try to build netlib libraries -- LAPACKLIB="vecLib" -- noblas=yes -- else --#alternative linking for vecLib libraries -- case `uname -sr` in -- *Darwin\ 7.* ) test_compile="$FC $FOPTIM $XFFLAGS -o testlink testlink.f -lcc_dynamic -Wl,-framework -Wl,vecLib" ;; -- * ) test_compile="$FC $FOPTIM $XFFLAGS -o testlink testlink.f -Wl,-framework -Wl,vecLib" ;; -- esac -- -- echo $test_compile -- if { (eval $test_compile ) 2>&1; } && test -s testlink ; then -- # Compilation was okay -- echo "... -framework vecLib is okay" -- XLAPACK_LIB="-Wl,-framework -Wl,vecLib" -- # Set the next two variables so that configure -- # doesn't try to build netlib libraries -- LAPACKLIB="-Wl,-framework -Wl,vecLib" -- noblas=yes -- else -- # Compilation failed -- echo "... cannot use -framework vecLib" -- echo -- fi -- fi -- trylapack= -- tryblas= --# try the fink installation -- trydirs="${trydirs} /sw" -- ;; -- Darwin_ibm_compilers ) -- # Darwin has libraries with BLAS and LAPACK invoked using -- # -framework vecLib -- echo "Darwin can use the vecLib Library (if installed)" -- echo "which has both BLAS and LAPACK 3.0" -- echo -- # This is a special case so try running a test compile -- echo "Checking: try to link library against test program" -- if test -f testlink.f || test -f testlink ; then -- rm -f testlink* -- fi -- cat > testlink.f <<EOF --c Test fortran program to link against library -- PROGRAM TESTLINK -- IMPLICIT NONE -- INTEGER A -- A = 1 -- STOP -- END --EOF -- case `uname -sr` in -- Darwin\ 8* ) -- XLAPACK_LIB="-L/System/Library/Frameworks/Accelerate.framework/Versions/A/Frameworks/vecLib.framework/Versions/A -lLAPACK -lBLAS" -- test_compile="$FC $FOPTIM $XFFLAGS -o testlink testlink.f $XLAPACK_LIB" -- ;; -- Darwin\ 7* ) -- XLAPACK_LIB="-L/System/Library/Frameworks/Accelerate.framework/Versions/A/Frameworks/vecLib.framework/Versions/A -lLAPACK -lBLAS" -- test_compile="$FC $FOPTIM $XFFLAGS -o testlink testlink.f -lcc_dynamic $XLAPACK_LIB" -- ;; -- *) -- XLAPACK_LIB="/System/Library/Frameworks/vecLib.Framework/Versions/Current/VecLib" -- test_compile="$FC $FOPTIM $XFFLAGS -o testlink testlink.f $XLAPACK_LIB" -- esac -- echo $test_compile -- if { (eval $test_compile ) 2>&1; } && test -s testlink ; then -- # Compilation was okay -- echo "... -framework vecLib is okay" -- # Set the next two variables so that configure -- # doesn't try to build netlib libraries -- LAPACKLIB="vecLib" -- noblas=yes -- else -- # Compilation failed -- XLAPACK_LIB="" -- echo "... cannot use -framework vecLib" -- echo -- fi -- trylapack= -- tryblas= --# try the fink installation -- trydirs="${trydirs} /sw" -- ;; -- -- Darwin_intel_compilers) -- # Darwin has libraries with BLAS and LAPACK invoked using -- # -F vecLib -- echo "Darwin can use the vecLib Library (if installed)" -- echo "which has both BLAS and LAPACK 3.0" -- echo -- # This is a special case so try running a test compile -- echo "Checking: try to link library against test program" -- if test -f testlink.f || test -f testlink ; then -- rm -f testlink* -- fi -- cat > testlink.f <<EOF --c Test fortran program to link against library -- PROGRAM TESTLINK -- IMPLICIT NONE -- INTEGER A -- A = 1 -- STOP -- END --EOF -- test_compile="$FC $FOPTIM $XFFLAGS -o testlink testlink.f -Wl,-framework -Wl,vecLib" -- echo $test_compile -- if { (eval $test_compile ) 2>&1; } && test -s testlink ; then -- # Compilation was okay -- # doesn't try to build netlib libraries -- XLAPACK_LIB="-F /System/Library/Frameworks -Qoption,ld,-framework -Qoption,ld,vecLib" -- LAPACKLIB="vecLib" -- noblas=yes -- else -- # Compilation failed -- echo "... cannot use -framework vecLib" -- echo -- fi -- trylapack= -- tryblas= --# try the fink installation -- trydirs="${trydirs} /sw" -- ;; -- --# linux_ia64_sgi_altix) --# SGI Japan -- ia64_linux_intel) -- # Additional search paths for Linux/IA64 -- trydirs="${trydirs} /opt/scsl/lib /usr/lib /usr/local/lib" -- # SCSL and MKL should have both LAPACK and BLAS -- trylapack="mkl_lapack scs lapack" -- tryblas="mkl scs blas" -- ;; -- linux_ibm_compilers ) -- trylapack="lapack" -- tryblas="blas" -- ;; -- linux64_ibm_compilers ) -- trydirs="/usr/lib64 ${trydirs}" -- trylapack="lapack" -- tryblas="blas" -- ;; -- linux_intel_compilers ) -- trydirs="/usr/lib64 ${trydirs}" -- trylapack="mkl_lapack lapack" -- tryblas="mkl blas" -- ;; -- *) -- echo "The guesses for this system may not be correct - please" -- echo "e-mail ccp4@ccp4.ac.uk if you have any extra information" -- echo -- # Default guess is just libblas -- trylapack="lapack" -- tryblas="blas" -- ;; -- esac -- # -- # Search for LAPACK libraries -- # -- # Write out what the guesses are -- if test "$trylapack" ; then -- echo "Possible LAPACK library names for this system:" -- for libname in $trylapack -- do -- echo " lib$libname" -- done -- # Possible library name extensions -- tryexts="a so dylib" -- # Now loop over all the possibilities and see if anything -- # turns up -- echo -- echo "Searching for libraries with LAPACK and BLAS:" -- for testdir in $trydirs -- do -- for testlib in $trylapack -- do -- for ext in $tryexts -- do -- if test ! "$LAPACKLIB"; then -- if test -s "$testdir/lib$testlib.$ext" ; then -- echo "...found LAPACK library: $testdir/lib$testlib.$ext" -- # Now try and link to a test program -- # This is really for IRIX where libraries can be -- # o32 or n32 -- echo " Testing: try to link library against test program" -- if test -f testlink.f || test -f testlink ; then -- rm -f testlink* -- fi -- cat > testlink.f <<EOF --c Test fortran program to link against library -- PROGRAM TESTLINK -- IMPLICIT NONE -- INTEGER A -- A = 1 -- STOP -- END --EOF -- test_compile="$FC $FOPTIM $XFFLAGS -o testlink testlink.f -L$testdir -l$testlib" -- test_ccompile="$FC $FOPTIM $XFFLAGS -o testlink testlink.f -L$testdir -l$testlib $XLDFLAGS" -- echo $test_compile -- if { (eval $test_compile ) 2>&1; } && test -s testlink ; then -- have_lapack=yes -- else --# cover clapack option -- echo $test_ccompile -- if { (eval $test_ccompile ) 2>&1; } && test -s testlink ; then -- have_lapack=yes -- fi -- fi -- if test x$have_lapack = xyes ; then -- # This one is okay -- LAPACKLIB="$testlib" -- LAPACKDIR="$testdir" -- echo "Link ok - using lib$LAPACKLIB from $LAPACKDIR" -- # -- XLAPACK_LIB="-L$LAPACKDIR -l$LAPACKLIB" -- # -- # Test to see if we need BLAS too -- # Do this by trying to compile a test program -- # Use the LSAME test for now -- echo -- echo " * Checking whether we need a separate BLAS library *" -- echo " Testing: try linking library against test program" -- cd lib/lapack/test -- if test -f testlsame ; then -- rm -f testsame testlsame.o -- fi -- test_compile="$FC $FOPTIM $XFFLAGS -o testlsame lsametst.f -L$LAPACKDIR -l$LAPACKLIB" -- test_ccompile="$FC $FOPTIM $XFFLAGS -o testlsame lsametst.f -L$LAPACKDIR -l$LAPACKLIB $XLDFLAGS" -- echo $test_compile -- if { ( eval $test_compile) 2>&1;} && test -s testlsame ; then -- have_blas=yes -- else --#cblas route -- echo $test_ccompile -- if { ( eval $test_ccompile) 2>&1;} && test -s testlsame ; then -- have_blas=yes -- fi -- fi -- if test x$have_blas = xyes ; then -- echo "Test program okay - additional separate BLAS not required" -- noblas=yes -- else -- echo "Test program failed - need a separate BLAS library" -- fi -- cd ../../.. -- else -- # Keep looking -- echo " link failed - cannot use lib$testlib" -- fi -- fi -- fi -- done -- done -- if test ! "$LAPACKLIB"; then -- echo "...nothing in $testdir" -- fi -- done -- fi -- -- # If LAPACKLIB hasn't been set at this point then no LAPACK library -- # was found -- if test ! "$LAPACKLIB" ; then -- echo -- echo "No pre-existing LAPACK library found - NetLib LAPACK will be built instead" -- make_lapack=lapacklib -- fi -- # Look for possible BLAS -- if test ! "$noblas" ; then -- if test "$tryblas" ; then -- echo -- echo "Possible BLAS library names for this system:" -- for libname in $tryblas -- do -- echo " lib$libname" -- done -- # Possible library name extensions -- tryexts="a so" -- # Now loop over all the possibilities and see if anything -- # turns up -- echo -- echo "Searching for libraries with BLAS:" -- for testdir in $trydirs -- do -- for testlib in $tryblas -- do -- for ext in $tryexts -- do -- if test ! "$BLASLIB"; then -- if test -s "$testdir/lib$testlib.$ext" ; then -- echo "...found BLAS library: $testdir/lib$testlib.$ext" -- # Now try and link to a test program -- # This is really for IRIX where libraries can be -- # o32 or n32 -- echo " Testing: try to link library against test program" -- if test -f testlink.f || test -f testlink ; then -- rm -f testlink* -- fi -- cat > testlink.f <<EOF --c Test fortran program to link against library -- PROGRAM TESTLINK -- IMPLICIT NONE -- INTEGER A -- A = 1 -- STOP -- END --EOF -- test_compile="$FC $FOPTIM $XFFLAGS -o testlink testlink.f -L$testdir -l$testlib" -- test_ccompile="$FC $FOPTIM $XFFLAGS -o testlink testlink.f -L$testdir -l$testlib $XLDFLAGS" -- echo $test_compile -- if { ( eval $test_compile) 2>&1;} && test -s testlink ; then -- have_blas=yes -- else -- echo $test_ccompile -- if { ( eval $test_compile) 2>&1;} && test -s testlink ; then -- have_blas=yes -- fi -- fi -- if test x$have_blas = xyes ; then -- # This one is okay -- BLASLIB="$testlib" -- BLASDIR="$testdir" -- BLASEXT="$ext" -- echo "Link ok - using lib$BLASLIB from $BLASDIR" -- XLAPACK_LIB="$XLAPACK_LIB -L$BLASDIR -l$BLASLIB" -- else -- # Keep looking -- echo " link failed - cannot use lib$testlib" -- fi -- fi -- fi -- done -- done -- if test ! "$BLASLIB"; then -- echo "...nothing in $testdir" -- fi -- done -- fi -- # Do we need to build BLAS too? -- if test ! "$BLASLIB" ; then -- echo -- echo "No pre-existing BLAS library was found - NetLib BLAS will be built instead" -- echo "This may result in poorer performance of the LAPACK routines" -- make_blas=blaslib -- BLASLIB=blas -- BLASDIR="$srcdir/lib/lapack" -- BLASEXT="a" -- fi -- fi -+ # gentoo is clever -+ make_blas= -+ make_lapack= -+ BLASLIB=$(${PKG_CONFIG} --libs lapack) -+ LAPACKLIB=$(${PKG_CONFIG} --libs lapack) -+ XLAPACK_LIB="${BLASLIB} ${LAPACKLIB}" -+ XFFLAGS_LAPACK="$(${PKG_CONFIG} --cflags lapack blas)" - # Otherwise force building of NetLib BLAS and LAPACK libs -- else -- echo -- echo "! Force building of NetLib BLAS and LAPACK..." -- make_blas=blaslib -- make_lapack=lapacklib -- BLASLIB=blas -- BLASDIR="$srcdir/lib/lapack" -- BLASEXT="a" -- fi - # need to know if we the lapack library was linked using the C or - # fortran linker - if test -f testlink.f || test -f testlink || test -f testlink.c ; then -@@ -3916,8 +3356,8 @@ RANLIB = ${RANLIB} - INSTALL_DATA = ${INSTALL_DATA} - libdir = $libdir - # --BLASLIB = lib${BLASLIB}.${BLASEXT} --LAPACKLIB = liblapack.a -+BLASLIB = ${BLASLIB} -+LAPACKLIB = ${LAPACKLIB} - # - # These variables define targets in the main Makefile - blaslib = ${make_blas} diff --git a/sci-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 24a0a2d8e4a2..000000000000 --- a/sci-libs/ccp4-libs/files/6.1.3-link-proberly.patch +++ /dev/null @@ -1,230 +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 -+ - # 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-no-pypath.patch b/sci-libs/ccp4-libs/files/6.1.3-no-pypath.patch deleted file mode 100644 index 6a0cb5be7c3d..000000000000 --- a/sci-libs/ccp4-libs/files/6.1.3-no-pypath.patch +++ /dev/null @@ -1,87 +0,0 @@ - include/ccp4.setup-bash | 8 -------- - include/ccp4.setup-csh | 11 ----------- - include/ccp4.setup-sh | 8 -------- - include/ccp4.setup-zsh | 10 ---------- - 4 files changed, 37 deletions(-) - -diff --git a/include/ccp4.setup-bash b/include/ccp4.setup-bash -index 3a67791..80aef23 100755 ---- a/include/ccp4.setup-bash -+++ b/include/ccp4.setup-bash -@@ -185,14 +185,6 @@ else - fi - fi - --#Python path for the subprocess fixed module -- --if [ $ccp4_first_in_path -eq 1 ]; then -- setenv PYTHONPATH ${CCP4}/share/python:${PYTHONPATH} --else -- setenv PYTHONPATH ${PYTHONPATH}:${CCP4}/share/python --fi -- - ### PLOT_COMMAND PRINT_COMMAND for the XCCPJIFFY programs to compile ### - setenv PLOT_COMMAND 'lp -s -dmicrolaser' - setenv PRINT_COMMAND 'lp -s -denscript' -diff --git a/include/ccp4.setup-csh b/include/ccp4.setup-csh -index 10d3ab8..72cc479 100755 ---- a/include/ccp4.setup-csh -+++ b/include/ccp4.setup-csh -@@ -177,17 +177,6 @@ else - endif - endif - --#Python path for the subprocess fixed module --if (${?PYTHONPATH}) then -- if ($ccp4_first_in_path) then -- setenv PYTHONPATH ${CCP4}/share/python:${PYTHONPATH} -- else -- setenv PYTHONPATH ${PYTHONPATH}:${CCP4}/share/python -- endif --else -- setenv PYTHONPATH ${CCP4}/share/python --endif -- - ### PLOT_COMMAND PRINT_COMMAND for the XCCPJIFFY programs to compile ### - setenv PLOT_COMMAND 'lp -s -dmicrolaser' - setenv PRINT_COMMAND 'lp -s -denscript' -diff --git a/include/ccp4.setup-sh b/include/ccp4.setup-sh -index 2298bba..44643ab 100755 ---- a/include/ccp4.setup-sh -+++ b/include/ccp4.setup-sh -@@ -225,14 +225,6 @@ test -r $CCP4/include/ccp4.msg && cat $CCP4/include/ccp4.msg - - ################### EXPERIENCED USERS STOP HERE ##################### - --#Python path for the subprocess fixed module -- --if test $ccp4_first_in_path -eq 1; then -- export PYTHONPATH=${CCP4}/share/python:${PYTHONPATH} --else -- export PYTHONPATH=${PYTHONPATH}:${CCP4}/share/python --fi -- - ################### THE REST SHOULDN'T NEED EDITING ##################### - - ### dbCCP4i database handler setup ### -diff --git a/include/ccp4.setup-zsh b/include/ccp4.setup-zsh -index 660b35b..e453db9 100755 ---- a/include/ccp4.setup-zsh -+++ b/include/ccp4.setup-zsh -@@ -154,16 +154,6 @@ export CCP4_BIN=$CBIN - CLASSPATH=$CBIN:$CLASSPATH # edit this if necessary - export CLASSPATH - --#Python path for the subprocess fixed module -- --if ($ccp4_first_in_path) then -- PYTHONPATH=${CCP4}/share/python:${PYTHONPATH} -- export PYTHONPATH --else -- PYTHONPATH=${PYTHONPATH}:${CCP4}/share/python -- export PYTHONPATH --fi -- - ### PLOT_COMMAND PRINT_COMMAND for the XCCPJIFFY programs to compile ### - export PLOT_COMMAND='lpr' - export PRINT_COMMAND='lpr' diff --git a/sci-libs/ccp4-libs/files/6.1.3-noinstall.patch b/sci-libs/ccp4-libs/files/6.1.3-noinstall.patch deleted file mode 100644 index c1479f2b1155..000000000000 --- a/sci-libs/ccp4-libs/files/6.1.3-noinstall.patch +++ /dev/null @@ -1,142 +0,0 @@ -diff --git a/Makefile.in b/Makefile.in -index ac552fe..fab1a87 100755 ---- a/Makefile.in -+++ b/Makefile.in -@@ -30,8 +30,7 @@ lapacklib : FORCE - - cciflib : FORCE - if test -n "$(ccifdir)"; then cd $(ccifdir); \ -- $(MAKE) $(MFLAGS) $(MVARS); else true; fi; \ -- $(MAKE) install -+ $(MAKE) $(MFLAGS) $(MVARS); else true; fi - - cctbx: FORCE - if test -n "$(cctbxdir)"; then cd $(top_srcdir)/$(cctbxdir); \ -@@ -40,8 +39,7 @@ cctbx: FORCE - libdir : FORCE lapacklib cciflib libccp4 clipper ssm diffractionImg - - libccp4: FORCE -- cd lib/src; $(MAKE) $(MFLAGS) $(MVARS) ; \ -- $(MAKE) install -+ cd lib/src; $(MAKE) $(MFLAGS) $(MVARS) - - share : FORCE - cd share; $(MAKE) $(MFLAGS) $(MVARS) -@@ -51,18 +49,15 @@ ccp4i : FORCE - - clipper: FORCE fftw - if test -n "$(clipperdir)"; then cd $(top_srcdir)/lib/clipper/clipper; \ -- $(MAKE) -i $(MFLAGS) $(MVARS); else true; fi ; \ -- $(MAKE) install -+ $(MAKE) -i $(MFLAGS) $(MVARS); else true; fi - - diffractionImg: - if test -n "$(diffimdir)"; then cd $(top_srcdir)/$(diffimdir); \ -- $(MAKE) -i $(MFLAGS) $(MVARS); else true; fi ; \ -- $(MAKE) install -+ $(MAKE) -i $(MFLAGS) $(MVARS); else true; fi - - ssm: - if test -n "$(ssmdir)"; then cd $(top_srcdir)/$(ssmdir); \ -- $(MAKE) -i $(MFLAGS) $(MVARS); else true; fi ; \ -- $(MAKE) install -+ $(MAKE) -i $(MFLAGS) $(MVARS); else true; fi - - fftw: FORCE - if test -n "$(fftwdir)"; then cd $(top_srcdir)/lib/fftw; \ -@@ -79,7 +74,7 @@ unsupported : FORCE libdir - $(MAKE) $(MFLAGS) $(MVARS); else true; fi - - datadir : FORCE libdir -- cd lib/data; $(MAKE) $(MFLAGS) $(MVARS) -+ cd lib/data; $(MAKE) $(MFLAGS) $(MVARS) font84.dat - - xwindir : FORCE libdir - if test -f x-windows/Makefile; then cd x-windows; \ -diff --git a/lib/ccif/Makefile.in b/lib/ccif/Makefile.in -index 975f1d9..75eda9f 100755 ---- a/lib/ccif/Makefile.in -+++ b/lib/ccif/Makefile.in -@@ -371,11 +371,11 @@ condition.h condition_list.h: $(srcdir)/condition.list $(srcdir)/condition.awk - # - - install : all -- $(INSTALL_DATA) `pwd`/$L $(libdir)/$L -- $(INSTALL_DATA) `pwd`/$(CIFMMLIB) $(libdir)/$(CIFMMLIB) -- $(RANLIB) $(libdir)/$L -+ $(RANLIB) $L -+ $(INSTALL_DATA) `pwd`/$L $(DESTDIR)/$(libdir)/$L -+ $(INSTALL_DATA) `pwd`/$(CIFMMLIB) $(DESTDIR)$(libdir)/$(CIFMMLIB) - if (test -f $(SHARED_LIB_NAME)); then \ -- $(INSTALL_DATA) `pwd`/$(SHARED_LIB_NAME) $(libdir)/$(SHARED_LIB_NAME); \ -+ $(INSTALL_DATA) `pwd`/$(SHARED_LIB_NAME) $(DESTDIR)/$(libdir)/$(SHARED_LIB_NAME); \ - fi - - uninstall : -diff --git a/lib/data/Makefile.in b/lib/data/Makefile.in -index cc25c5c..017502d 100755 ---- a/lib/data/Makefile.in -+++ b/lib/data/Makefile.in -@@ -30,9 +30,9 @@ font84.dat : fontpack $(srcdir)/font84.ascii - - install : all - -rm -f font84.dat -- test -f font84.ascii || $(LNS) $(srcdir)/font84.ascii . -- ./fontpack -- $(INSTALL) `pwd`/font84.dat $(libdir)/font84.dat -+ test -f font84.ascii || $(LNS) $(DESTDIR)/$(srcdir)/font84.ascii . -+ LD_LIBRARY_PATH="../src:../ccif" ./fontpack -+ $(INSTALL) `pwd`/font84.dat $(DESTDIR)/$(libdir)/font84.dat - - uninstall : - -rm -f $(libdir)/font84.dat -diff --git a/lib/src/Makefile.in b/lib/src/Makefile.in -index b32dd1e..6aa107d 100755 ---- a/lib/src/Makefile.in -+++ b/lib/src/Makefile.in -@@ -685,7 +685,7 @@ testlib : $(srcdir)/testlib.f $(LF) - # - - install-ccp4HEADERS: $(ccp4_HEADERS) -- if test ! -d $(DESTDIR)$(includedir)/ccp4; then mkdir $(DESTDIR)$(includedir)/ccp4; fi -+ if test ! -d $(DESTDIR)$(includedir)/ccp4; then mkdir -p $(DESTDIR)$(includedir)/ccp4; fi - @list='$(ccp4_HEADERS)'; for p in $$list; do \ - if test -f "$$p"; then d=; else d="$(srcdir)/"; fi; \ - f="`echo $$p | sed -e 's|^.*/||'`"; \ -@@ -716,11 +716,11 @@ uninstall-mmdbHEADERS: - rm -f $(DESTDIR)$(includedir)/mmdb/$$f; \ - done - --install : all install-ccp4HEADERS install-mmdbHEADERS -- $(INSTALL_DATA) `pwd`/$(LC) $(libdir)/$(LC) -- $(INSTALL_DATA) `pwd`/$(LF) $(libdir)/$(LF) -- $(RANLIB) $(libdir)/$(LC) -- $(RANLIB) $(libdir)/$(LF) -+install : all install-ccp4HEADERS -+ $(RANLIB) $(LC) -+ $(RANLIB) $(LF) -+ $(INSTALL_DATA) `pwd`/$(LC) $(DESTDIR)/$(libdir)/$(LC) -+ $(INSTALL_DATA) `pwd`/$(LF) $(DESTDIR)/$(libdir)/$(LF) - $(SHARE_INST) - - uninstall : uninstall-ccp4HEADERS uninstall-mmdbHEADERS -diff --git a/lib/ssm/Makefile.in b/lib/ssm/Makefile.in -index 27d3aa2..0a14fe5 100755 ---- a/lib/ssm/Makefile.in -+++ b/lib/ssm/Makefile.in -@@ -375,12 +375,12 @@ distclean-libtool: - uninstall-info-am: - install-library_includeHEADERS: $(library_include_HEADERS) - @$(NORMAL_INSTALL) -- test -z "$(library_includedir)" || $(mkdir_p) "$(DESTDIR)$(library_includedir)" -+ test -z "$(library_includedir)" || $(mkdir_p) "$(DESTDIR)$(library_includedir)/ssm" - @list='$(library_include_HEADERS)'; for p in $$list; do \ - if test -f "$$p"; then d=; else d="$(srcdir)/"; fi; \ - f=$(am__strip_dir) \ -- echo " $(library_includeHEADERS_INSTALL) '$$d$$p' '$(DESTDIR)$(library_includedir)/$$f'"; \ -- $(library_includeHEADERS_INSTALL) "$$d$$p" "$(DESTDIR)$(library_includedir)/$$f"; \ -+ echo " $(library_includeHEADERS_INSTALL) '$$d$$p' '$(DESTDIR)$(library_includedir)/ssm/$$f'"; \ -+ $(library_includeHEADERS_INSTALL) "$$d$$p" "$(DESTDIR)$(library_includedir)/ssm/$$f"; \ - done - - uninstall-library_includeHEADERS: diff --git a/sci-libs/ccp4-libs/files/6.1.3-overflows.patch b/sci-libs/ccp4-libs/files/6.1.3-overflows.patch deleted file mode 100644 index 0e3c941d1cc2..000000000000 --- a/sci-libs/ccp4-libs/files/6.1.3-overflows.patch +++ /dev/null @@ -1,35 +0,0 @@ -Fix overflows and array subscript above array bounds - -http://bugs.gentoo.org/show_bug.cgi?id=339706 - ---- ccp4-6.1.3/lib/ccif/f_interface.c -+++ ccp4-6.1.3/lib/ccif/f_interface.c -@@ -926,7 +926,7 @@ - #endif - - { -- char logname_c[81]; -+ char logname_c[MAXFLEN]; - size_t Length; - int unit; - CIF_FILE_LIST file_list_entry; -@@ -4064,7 +4064,7 @@ - #endif - - { -- char lognam_c[81], *blknam_c; -+ char lognam_c[MAXFLEN], *blknam_c; - size_t loglen, blklen; - int i, j, new; - ---- ccp4-6.1.3/lib/src/ccp4_diskio_f.c -+++ ccp4-6.1.3/lib/src/ccp4_diskio_f.c -@@ -705,7 +705,7 @@ - log_name = strdup("diskio.dft"); - if (!(file_name = getenv(log_name))) - file_name = log_name; -- for ( *istrm = 1; *istrm == MAXFILES; *istrm++) -+ for ( *istrm = 1; *istrm < MAXFILES; *istrm++) - if (!strcmp(file_name,_ioChannels[*istrm]->iobj->name)) break; - } - if (*istrm != MAXFILES) { diff --git a/sci-libs/ccp4-libs/files/6.1.3-unbundle-libs-ng.patch b/sci-libs/ccp4-libs/files/6.1.3-unbundle-libs-ng.patch deleted file mode 100644 index 4271d5b76aec..000000000000 --- a/sci-libs/ccp4-libs/files/6.1.3-unbundle-libs-ng.patch +++ /dev/null @@ -1,367 +0,0 @@ -diff --git a/lib/DiffractionImage/DiffractionImageCBF.cpp b/lib/DiffractionImage/DiffractionImageCBF.cpp -index 69b32b0..602e35f 100755 ---- a/lib/DiffractionImage/DiffractionImageCBF.cpp -+++ b/lib/DiffractionImage/DiffractionImageCBF.cpp -@@ -6,10 +6,10 @@ - // images. - - #include "DiffractionImage.h" --#include "cbf.h" --#include "cbf_simple.h" --#include "cbf_string.h" --#include "cbf_byte_offset.h" -+#include <cbflib/cbf.h> -+#include <cbflib/cbf_simple.h> -+#include <cbflib/cbf_string.h> -+#include <cbflib/cbf_byte_offset.h> - - - using namespace std; -diff --git a/lib/DiffractionImage/MAR/Makefile.am b/lib/DiffractionImage/MAR/Makefile.am -index fedb7ac..89a048e 100755 ---- a/lib/DiffractionImage/MAR/Makefile.am -+++ b/lib/DiffractionImage/MAR/Makefile.am -@@ -2,7 +2,7 @@ AUTOMAKE_OPTIONS = gnu - - noinst_LTLIBRARIES = libmar.la - --AM_CPPFLAGS =-I../CBFlib/src -I../CBFlib/include -+AM_CPPFLAGS = - - libmar_la_SOURCES = mar300_header.c \ - mar345_header.c \ -@@ -12,4 +12,3 @@ libmar_la_SOURCES = mar300_header.c \ - utils.c \ - pck.c - --libmar_la_LDFLAGS = -static -diff --git a/lib/DiffractionImage/MAR/marcif.c b/lib/DiffractionImage/MAR/marcif.c -index d3f4212..2c37108 100755 ---- a/lib/DiffractionImage/MAR/marcif.c -+++ b/lib/DiffractionImage/MAR/marcif.c -@@ -31,8 +31,7 @@ - #include "marcif_header.h" - #include "mar345_header.h" - --#include <cbf.h> --#include <img.h> -+#include <cbflib/cbf.h> - - #define printe(x) printf("%s: %s: %s\n",prg,f,x) - #undef cbf_failnez -diff --git a/lib/DiffractionImage/Makefile.am b/lib/DiffractionImage/Makefile.am -index 189a1d7..6652576 100755 ---- a/lib/DiffractionImage/Makefile.am -+++ b/lib/DiffractionImage/Makefile.am -@@ -1,7 +1,9 @@ - AUTOMAKE_OPTIONS = gnu --SUBDIRS = CBFlib Bruker MAR Rigaku jpg -+SUBDIRS = Bruker MAR Rigaku - --AM_CPPFLAGS =-I./MAR -I./CBFlib/src -I./CBFlib/include -I./jpg -+SYSLIBS = -ljpeg -lcbf -+ -+AM_CPPFLAGS =-I./MAR - lib_LTLIBRARIES = libDiffImage.la - - if WANT_PYTHONMOD -@@ -35,48 +37,56 @@ libDiffImage_la_SOURCES = DiffractionImageJpeg.cpp \ - Profile.cpp \ - Peak.cpp \ - dps_peaksearch_cn.c --libDiffImage_la_LDFLAGS = -static -+libDiffImage_la_LDFLAGS = -shared $(SHARED_LIB_FLAGS) -+libDiffImage_la_LIBADD = $(SYSLIBS) \ -+ ./MAR/libmar.la ./Bruker/libbruker.la \ -+ ./Rigaku/librigaku.la - --libDiffractionImage_la_DEPENDENCIES= libDiffImage.la ./CBFlib/src/libcbf.la \ -+libDiffractionImage_la_DEPENDENCIES= libDiffImage.la \ - ./Bruker/libbruker.la ./MAR/libmar.la \ -- ./Rigaku/librigaku.la ./jpg/libjpeg.la -+ ./Rigaku/librigaku.la - libDiffractionImage_la_SOURCES = DiffractionImageTclInterface.cpp --libDiffractionImage_la_LDFLAGS = -shared --whole-archive libDiffImage.la \ -- ./CBFlib/src/libcbf.la ./Bruker/libbruker.la \ -- ./MAR/libmar.la ./Rigaku/librigaku.la ./jpg/libjpeg.la \ -- --no-whole-archive -rpath '$(libdir)' -+libDiffractionImage_la_LDFLAGS = -shared --whole-archive $(SHARED_LIB_FLAGS) -+libDiffractionImage_la_LIBADD = $(SYSLIBS) -ltcl \ -+ libDiffImage.la \ -+ ./Bruker/libbruker.la \ -+ ./MAR/libmar.la ./Rigaku/librigaku.la - --lib_DiffractionImage_la_DEPENDENCIES = libDiffImage.la ./CBFlib/src/libcbf.la \ -+lib_DiffractionImage_la_DEPENDENCIES = libDiffImage.la \ - ./Bruker/libbruker.la ./MAR/libmar.la \ -- ./Rigaku/librigaku.la ./jpg/libjpeg.la -+ ./Rigaku/librigaku.la - lib_DiffractionImage_la_SOURCES = DiffractionImagePythonInterface.cpp --lib_DiffractionImage_la_LDFLAGS = -shared --whole-archive libDiffImage.la \ -- ./CBFlib/src/libcbf.la ./Bruker/libbruker.la \ -- ./MAR/libmar.la ./Rigaku/librigaku.la ./jpg/libjpeg.la \ -- --no-whole-archive -rpath '$(libdir)' -+lib_DiffractionImage_la_LDFLAGS = -shared --whole-archive $(SHARED_LIB_FLAGS) -+lib_DiffractionImage_la_LIBADD = libDiffImage.la @PYLIB@ $(SYSLIBS) \ -+ ./Bruker/libbruker.la \ -+ ./MAR/libmar.la ./Rigaku/librigaku.la - --libDiffractionImaJ_la_DEPENDENCIES = libDiffImage.la ./CBFlib/src/libcbf.la \ -+libDiffractionImaJ_la_DEPENDENCIES = libDiffImage.la \ - ./Bruker/libbruker.la ./MAR/libmar.la \ -- ./Rigaku/librigaku.la ./jpg/libjpeg.la -+ ./Rigaku/librigaku.la - libDiffractionImaJ_la_SOURCES = DiffractionImageJavaInterface.cpp --libDiffractionImaJ_la_LDFLAGS = -shared --whole-archive libDiffImage.la \ -- ./CBFlib/src/libcbf.la ./Bruker/libbruker.la \ -- ./MAR/libmar.la ./Rigaku/librigaku.la ./jpg/libjpeg.la \ -- --no-whole-archive -rpath '$(libdir)' -+libDiffractionImaJ_la_LDFLAGS = -shared --whole-archive $(SHARED_LIB_FLAGS) -+libDiffractionImaJ_la_LIBADD = libDiffImage.la \ -+ ./Bruker/libbruker.la $(SYSLIBS) \ -+ ./MAR/libmar.la ./Rigaku/librigaku.la - - bin_PROGRAMS = automask diffdump printpeaks diff2jpeg --automask_LDADD = libDiffImage.la ./Bruker/libbruker.la ./CBFlib/src/libcbf.la \ -- ./MAR/libmar.la ./Rigaku/librigaku.la ./jpg/libjpeg.la -+automask_LDADD = libDiffImage.la ./Bruker/libbruker.la \ -+ ./MAR/libmar.la ./Rigaku/librigaku.la $(SYSLIBS) - automask_SOURCES = automask.cpp --diffdump_LDADD = libDiffImage.la ./Bruker/libbruker.la ./CBFlib/src/libcbf.la \ -- ./MAR/libmar.la ./Rigaku/librigaku.la ./jpg/libjpeg.la -+automask_LDFLAGS = $(SHARED_LIB_FLAGS) -+diffdump_LDADD = libDiffImage.la ./Bruker/libbruker.la $(SYSLIBS) \ -+ ./MAR/libmar.la ./Rigaku/librigaku.la - diffdump_SOURCES = diffdump.cpp --printpeaks_LDADD = libDiffImage.la ./Bruker/libbruker.la ./CBFlib/src/libcbf.la \ -- ./MAR/libmar.la ./Rigaku/librigaku.la ./jpg/libjpeg.la -+diffdump_LDFLAGS = $(SHARED_LIB_FLAGS) -+printpeaks_LDADD = libDiffImage.la ./Bruker/libbruker.la \ -+ ./MAR/libmar.la ./Rigaku/librigaku.la $(SYSLIBS) - printpeaks_SOURCES = printpeaks.cpp --diff2jpeg_LDADD = libDiffImage.la ./Bruker/libbruker.la ./CBFlib/src/libcbf.la \ -- ./MAR/libmar.la ./Rigaku/librigaku.la ./jpg/libjpeg.la -+printpeaks_LDFLAGS = $(SHARED_LIB_FLAGS) -+diff2jpeg_LDADD = libDiffImage.la ./Bruker/libbruker.la \ -+ ./MAR/libmar.la ./Rigaku/librigaku.la $(SYSLIBS) - diff2jpeg_SOURCES = diff2jpeg.cpp -+diff2jpeg_LDFLAGS = $(SHARED_LIB_FLAGS) - - install-data-local: - @INSTALL_DATA@ doc/DiffractionImage.doc ${CDOC} -diff --git a/lib/DiffractionImage/configure b/lib/DiffractionImage/configure -index 3fb5784..fdf9683 100755 ---- a/lib/DiffractionImage/configure -+++ b/lib/DiffractionImage/configure -@@ -21768,7 +21768,7 @@ _ACEOF - fi - - --ac_config_files="$ac_config_files Makefile CBFlib/Makefile CBFlib/src/Makefile MAR/Makefile Rigaku/Makefile Bruker/Makefile jpg/Makefile" -+ac_config_files="$ac_config_files Makefile MAR/Makefile Rigaku/Makefile Bruker/Makefile " - - - cat >confcache <<\_ACEOF -@@ -22407,12 +22407,9 @@ do - case $ac_config_target in - "depfiles") CONFIG_COMMANDS="$CONFIG_COMMANDS depfiles" ;; - "Makefile") CONFIG_FILES="$CONFIG_FILES Makefile" ;; -- "CBFlib/Makefile") CONFIG_FILES="$CONFIG_FILES CBFlib/Makefile" ;; -- "CBFlib/src/Makefile") CONFIG_FILES="$CONFIG_FILES CBFlib/src/Makefile" ;; - "MAR/Makefile") CONFIG_FILES="$CONFIG_FILES MAR/Makefile" ;; - "Rigaku/Makefile") CONFIG_FILES="$CONFIG_FILES Rigaku/Makefile" ;; - "Bruker/Makefile") CONFIG_FILES="$CONFIG_FILES Bruker/Makefile" ;; -- "jpg/Makefile") CONFIG_FILES="$CONFIG_FILES jpg/Makefile" ;; - - *) { { echo "$as_me:$LINENO: error: invalid argument: $ac_config_target" >&5 - echo "$as_me: error: invalid argument: $ac_config_target" >&2;} -diff --git a/lib/DiffractionImage/configure.in b/lib/DiffractionImage/configure.in -index 7f54b4b..16efc64 100755 ---- a/lib/DiffractionImage/configure.in -+++ b/lib/DiffractionImage/configure.in -@@ -21,6 +21,8 @@ if test -n "${PYTHON}" ; then - HAVE_PYTHON=1 - CPPFLAGS="${CPPFLAGS} -I${PYTHON_PREFIX}/include/python${PYTHON_VER}" - ]) -+ PYLIB="-lpython${PYTHON_VER}" -+ AC_SUBST(PYLIB) - fi - AC_CHECK_HEADER([tcl.h], [HAVE_TCL=1]) - -@@ -65,11 +67,8 @@ AM_CONDITIONAL([WANT_JAVA], test z${HAVE_JAVA} != z) - AC_CHECK_LIB([m], [sqrt]) - - AC_CONFIG_FILES([Makefile -- CBFlib/Makefile -- CBFlib/src/Makefile - MAR/Makefile - Rigaku/Makefile -- Bruker/Makefile -- jpg/Makefile]) -+ Bruker/Makefile]) - - AC_OUTPUT -diff --git a/lib/ssm/Makefile.am b/lib/ssm/Makefile.am -index e9554e1..a3ba33d 100755 ---- a/lib/ssm/Makefile.am -+++ b/lib/ssm/Makefile.am -@@ -1,7 +1,11 @@ -+ACLOCAL_AMFLAGS = -I macros - #libtool - lib_LTLIBRARIES = libssm.la -+libssm_la_LDFLAGS = -shared $(SHARED_LIB_FLAGS) -+libssm_la_CFLAGS = @MMDB_CFLAGS@ - libssm_la_SOURCES = ssm_superpose.cpp ss_csia.cpp ss_vxedge.cpp \ - ssm_align.cpp ss_graph.cpp -+libssm_la_LIBADD = @MMDB_LIBS@ - - #non libtool - #lib_LIBRARIES = libssm.a -@@ -16,12 +20,10 @@ superpose_SOURCES = superpose.cpp - - bin_PROGRAMS = superpose - --INCLUDES = $(MMDB_CXXFLAGS) -- --AM_LDFLAGS = $(MMDB_LIBS) -+INCLUDES = @MMDB_CFLAGS@ - - EXTRA_DIST = macros/mmdb.m4 - --superpose_LDADD = libssm.la -+superpose_LDADD = libssm.la @MMDB_LIBS@ - - libssm_a_AR = $(AR) $(AR_FLAGS) -diff --git a/lib/ssm/configure.ac b/lib/ssm/configure.ac -index 783cb46..d637d11 100755 ---- a/lib/ssm/configure.ac -+++ b/lib/ssm/configure.ac -@@ -28,31 +28,10 @@ AC_ARG_ENABLE(debug, - [ac_cv_enable_debug=no ] ) - - dnl Optional: Check for MMDB. --AM_PATH_MMDB(, -- [ if test "x$mmdb_prefix" != x ; then -- if test "x$ac_MMDB_CXXFLAGS" != x ; then -- case "$ac_MMDB_CXXFLAGS" in -- *src/mmdb ) -- ac_MMDB_LDOPTS=`echo "$ac_MMDB_CXXFLAGS" | sed s#src/mmdb#src#g` -- ;; -- *include/mmdb ) -- ac_MMDB_LDOPTS=`echo "$ac_MMDB_CXXFLAGS" | sed s#include/mmdb#lib#g` -- ;; -- *) -- esac -- MMDB_CXXFLAGS="$ac_MMDB_CXXFLAGS" -- MMDB_LIBS=`echo "$ac_MMDB_LDOPTS -lmmdb" | sed s#-I#-L#` -- AC_MSG_WARN([assuming library $MMDB_LIBS headers $MMDB_CXXFLAGS]) -- else -- MMDB_CXXFLAGS="-I$mmdb_prefix/lib/src/mmdb -I$mmdb_prefix/include/mmdb" -- MMDB_LIBS="-L$mmdb_prefix/lib/src -L$mmdb_prefix/lib -lmmdb" -- AC_MSG_WARN([assuming library $MMDB_LIBS headers $MMDB_CXXFLAGS]) -- fi -- else -- AC_MSG_WARN([mmdb not found]) -- fi -- ] --) -+ -+PKG_CHECK_MODULES([MMDB],[mmdb]) -+AC_SUBST([MMDB_CFLAGS]) -+AC_SUBST([MMDB_LIBS]) - - # Checks for typedefs, structures, and compiler characteristics. - # -@@ -67,6 +46,7 @@ AC_CHECK_FUNCS([floor pow rint sqrt]) - # test for function in m - AC_CHECK_LIB([m], [sqrt]) - -+ - AC_SUBST(AR_FLAGS) - AC_SUBST(superpose_LDFLAGS) - AM_CONDITIONAL(DEBUG, test "$ac_cv_enable_debug" = yes) -diff --git a/src/pisa/Makefile.am b/src/pisa/Makefile.am -index 094fd6b..922a131 100755 ---- a/src/pisa/Makefile.am -+++ b/src/pisa/Makefile.am -@@ -1,3 +1,4 @@ -+ACLOCAL_AMFLAGS = -I macros - SUBDIRS = molref pisastore sbase - - pkgdatadir = $(datadir)/pisa -@@ -20,8 +21,8 @@ pisa.cpp pisa_lists.cpp seq_superpose.cpp - - bin_PROGRAMS = pisa - --INCLUDES = $(MMDB_CXXFLAGS) $(SSM_CXXFLAGS) -+INCLUDES = @MMDB_CFLAGS@ $(SSM_CXXFLAGS) - --pisa_LDADD = $(SSM_LIBS) $(MMDB_LIBS) -+pisa_LDADD = $(SSM_LIBS) @MMDB_LIBS@ - - EXTRA_DIST = macros/mmdb.m4 macros/ssm.m4 pisa.cfg.in -diff --git a/src/pisa/configure.ac b/src/pisa/configure.ac -index 81afdda..4f99df6 100755 ---- a/src/pisa/configure.ac -+++ b/src/pisa/configure.ac -@@ -32,35 +32,13 @@ AC_CHECK_FUNCS([floor pow rint sqrt]) - AC_CHECK_LIB([m], [sqrt]) - - dnl Optional: Check for MMDB. --AM_PATH_MMDB(, -- [ if test "x$mmdb_prefix" != x ; then -- if test "x$ac_MMDB_CXXFLAGS" != x && test "x$ac_MMDB_LDOPTS" = x ; then -- case "$ac_MMDB_CXXFLAGS" in -- *src/mmdb ) -- ac_MMDB_LDOPTS=`echo "$ac_MMDB_CXXFLAGS" | sed s#src/mmdb#src#g` -- ;; -- *include/mmdb ) -- ac_MMDB_LDOPTS=`echo "$ac_MMDB_CXXFLAGS" | sed s#include/mmdb#lib#g` -- ;; -- *) -- esac -- MMDB_CXXFLAGS="$ac_MMDB_CXXFLAGS" -- MMDB_LIBS=`echo "$ac_MMDB_LDOPTS -lmmdb" | sed s#-I#-L#` -- AC_MSG_WARN([assuming library $MMDB_LIBS headers $MMDB_CXXFLAGS]) -- else -- MMDB_CXXFLAGS="-I$mmdb_prefix/src -I$mmdb_prefix/src/mmdb -I$mmdb_prefix/include -I$mmdb_prefix/include/mmdb" -- MMDB_LIBS="-L$mmdb_prefix/src -L$mmdb_prefix/lib -lmmdb" -- AC_MSG_WARN([assuming library $MMDB_LIBS headers $MMDB_CXXFLAGS]) -- fi -- else -- AC_MSG_ERROR([mmdb not found]) -- fi -- ] --) -+PKG_CHECK_MODULES([MMDB],[mmdb]) -+AC_SUBST([MMDB_CFLAGS]) -+AC_SUBST([MMDB_LIBS]) - - ac_saved_CXXFLAGS=$CXXFLAGS - ac_saved_LIBS=$LIBS --CXXFLAGS="$CXXFLAGS $MMDB_CXXFLAGS" -+CXXFLAGS="$CXXFLAGS $MMDB_CFLAGS" - LIBS="$MMDB_LIBS $LIBS" - AM_PATH_SSM(, - [ if test "x$ssm_prefix" != x ; then -diff --git a/src/rapper/Makefile.am b/src/rapper/Makefile.am -index e78b10d..486b931 100755 ---- a/src/rapper/Makefile.am -+++ b/src/rapper/Makefile.am -@@ -1,3 +1,3 @@ --SUBDIRS = libxml2 gc7.0 LOOP data -+SUBDIRS = LOOP data - - EXTRA_DIST = -diff --git a/src/rapper/configure.ac b/src/rapper/configure.ac -index 5e4ef69..11b63ec 100755 ---- a/src/rapper/configure.ac -+++ b/src/rapper/configure.ac -@@ -48,6 +48,6 @@ AM_CONDITIONAL(AMDEP, test "x$enable_dependency_tracking" != xno) - - AC_SUBST(rapper_LDFLAGS) - --AC_CONFIG_SUBDIRS([gc7.0 libxml2]) -+#AC_CONFIG_SUBDIRS([gc7.0 libxml2]) - #AC_OUTPUT(Makefile LOOP/Makefile LOOP/python/Makefile data/Makefile) - AC_OUTPUT(Makefile LOOP/Makefile data/Makefile) diff --git a/sci-libs/ccp4-libs/files/6.1.3-unbundle-libs-ng2.patch b/sci-libs/ccp4-libs/files/6.1.3-unbundle-libs-ng2.patch deleted file mode 100644 index c787df903dfc..000000000000 --- a/sci-libs/ccp4-libs/files/6.1.3-unbundle-libs-ng2.patch +++ /dev/null @@ -1,395 +0,0 @@ - lib/DiffractionImage/DiffractionImageCBF.cpp | 8 ++-- - lib/DiffractionImage/MAR/Makefile.am | 3 +- - lib/DiffractionImage/MAR/marcif.c | 3 +- - lib/DiffractionImage/Makefile.am | 68 +++++++++++++++----------- - lib/DiffractionImage/configure | 5 +-- - lib/DiffractionImage/configure.in | 7 +-- - lib/src/Makefile.in | 2 +- - lib/ssm/Makefile.am | 10 ++-- - lib/ssm/configure.ac | 30 ++--------- - src/pisa/Makefile.am | 5 +- - src/pisa/configure.ac | 30 ++---------- - src/rapper/Makefile.am | 2 +- - src/rapper/configure.ac | 2 +- - 13 files changed, 70 insertions(+), 105 deletions(-) - -diff --git a/lib/DiffractionImage/DiffractionImageCBF.cpp b/lib/DiffractionImage/DiffractionImageCBF.cpp -index 69b32b0..602e35f 100755 ---- a/lib/DiffractionImage/DiffractionImageCBF.cpp -+++ b/lib/DiffractionImage/DiffractionImageCBF.cpp -@@ -6,10 +6,10 @@ - // images. - - #include "DiffractionImage.h" --#include "cbf.h" --#include "cbf_simple.h" --#include "cbf_string.h" --#include "cbf_byte_offset.h" -+#include <cbflib/cbf.h> -+#include <cbflib/cbf_simple.h> -+#include <cbflib/cbf_string.h> -+#include <cbflib/cbf_byte_offset.h> - - - using namespace std; -diff --git a/lib/DiffractionImage/MAR/Makefile.am b/lib/DiffractionImage/MAR/Makefile.am -index fedb7ac..89a048e 100755 ---- a/lib/DiffractionImage/MAR/Makefile.am -+++ b/lib/DiffractionImage/MAR/Makefile.am -@@ -2,7 +2,7 @@ AUTOMAKE_OPTIONS = gnu - - noinst_LTLIBRARIES = libmar.la - --AM_CPPFLAGS =-I../CBFlib/src -I../CBFlib/include -+AM_CPPFLAGS = - - libmar_la_SOURCES = mar300_header.c \ - mar345_header.c \ -@@ -12,4 +12,3 @@ libmar_la_SOURCES = mar300_header.c \ - utils.c \ - pck.c - --libmar_la_LDFLAGS = -static -diff --git a/lib/DiffractionImage/MAR/marcif.c b/lib/DiffractionImage/MAR/marcif.c -index d3f4212..2c37108 100755 ---- a/lib/DiffractionImage/MAR/marcif.c -+++ b/lib/DiffractionImage/MAR/marcif.c -@@ -31,8 +31,7 @@ - #include "marcif_header.h" - #include "mar345_header.h" - --#include <cbf.h> --#include <img.h> -+#include <cbflib/cbf.h> - - #define printe(x) printf("%s: %s: %s\n",prg,f,x) - #undef cbf_failnez -diff --git a/lib/DiffractionImage/Makefile.am b/lib/DiffractionImage/Makefile.am -index 189a1d7..6652576 100755 ---- a/lib/DiffractionImage/Makefile.am -+++ b/lib/DiffractionImage/Makefile.am -@@ -1,7 +1,9 @@ - AUTOMAKE_OPTIONS = gnu --SUBDIRS = CBFlib Bruker MAR Rigaku jpg -+SUBDIRS = Bruker MAR Rigaku - --AM_CPPFLAGS =-I./MAR -I./CBFlib/src -I./CBFlib/include -I./jpg -+SYSLIBS = -ljpeg -lcbf -+ -+AM_CPPFLAGS =-I./MAR - lib_LTLIBRARIES = libDiffImage.la - - if WANT_PYTHONMOD -@@ -35,48 +37,56 @@ libDiffImage_la_SOURCES = DiffractionImageJpeg.cpp \ - Profile.cpp \ - Peak.cpp \ - dps_peaksearch_cn.c --libDiffImage_la_LDFLAGS = -static -+libDiffImage_la_LDFLAGS = -shared $(SHARED_LIB_FLAGS) -+libDiffImage_la_LIBADD = $(SYSLIBS) \ -+ ./MAR/libmar.la ./Bruker/libbruker.la \ -+ ./Rigaku/librigaku.la - --libDiffractionImage_la_DEPENDENCIES= libDiffImage.la ./CBFlib/src/libcbf.la \ -+libDiffractionImage_la_DEPENDENCIES= libDiffImage.la \ - ./Bruker/libbruker.la ./MAR/libmar.la \ -- ./Rigaku/librigaku.la ./jpg/libjpeg.la -+ ./Rigaku/librigaku.la - libDiffractionImage_la_SOURCES = DiffractionImageTclInterface.cpp --libDiffractionImage_la_LDFLAGS = -shared --whole-archive libDiffImage.la \ -- ./CBFlib/src/libcbf.la ./Bruker/libbruker.la \ -- ./MAR/libmar.la ./Rigaku/librigaku.la ./jpg/libjpeg.la \ -- --no-whole-archive -rpath '$(libdir)' -+libDiffractionImage_la_LDFLAGS = -shared --whole-archive $(SHARED_LIB_FLAGS) -+libDiffractionImage_la_LIBADD = $(SYSLIBS) -ltcl \ -+ libDiffImage.la \ -+ ./Bruker/libbruker.la \ -+ ./MAR/libmar.la ./Rigaku/librigaku.la - --lib_DiffractionImage_la_DEPENDENCIES = libDiffImage.la ./CBFlib/src/libcbf.la \ -+lib_DiffractionImage_la_DEPENDENCIES = libDiffImage.la \ - ./Bruker/libbruker.la ./MAR/libmar.la \ -- ./Rigaku/librigaku.la ./jpg/libjpeg.la -+ ./Rigaku/librigaku.la - lib_DiffractionImage_la_SOURCES = DiffractionImagePythonInterface.cpp --lib_DiffractionImage_la_LDFLAGS = -shared --whole-archive libDiffImage.la \ -- ./CBFlib/src/libcbf.la ./Bruker/libbruker.la \ -- ./MAR/libmar.la ./Rigaku/librigaku.la ./jpg/libjpeg.la \ -- --no-whole-archive -rpath '$(libdir)' -+lib_DiffractionImage_la_LDFLAGS = -shared --whole-archive $(SHARED_LIB_FLAGS) -+lib_DiffractionImage_la_LIBADD = libDiffImage.la @PYLIB@ $(SYSLIBS) \ -+ ./Bruker/libbruker.la \ -+ ./MAR/libmar.la ./Rigaku/librigaku.la - --libDiffractionImaJ_la_DEPENDENCIES = libDiffImage.la ./CBFlib/src/libcbf.la \ -+libDiffractionImaJ_la_DEPENDENCIES = libDiffImage.la \ - ./Bruker/libbruker.la ./MAR/libmar.la \ -- ./Rigaku/librigaku.la ./jpg/libjpeg.la -+ ./Rigaku/librigaku.la - libDiffractionImaJ_la_SOURCES = DiffractionImageJavaInterface.cpp --libDiffractionImaJ_la_LDFLAGS = -shared --whole-archive libDiffImage.la \ -- ./CBFlib/src/libcbf.la ./Bruker/libbruker.la \ -- ./MAR/libmar.la ./Rigaku/librigaku.la ./jpg/libjpeg.la \ -- --no-whole-archive -rpath '$(libdir)' -+libDiffractionImaJ_la_LDFLAGS = -shared --whole-archive $(SHARED_LIB_FLAGS) -+libDiffractionImaJ_la_LIBADD = libDiffImage.la \ -+ ./Bruker/libbruker.la $(SYSLIBS) \ -+ ./MAR/libmar.la ./Rigaku/librigaku.la - - bin_PROGRAMS = automask diffdump printpeaks diff2jpeg --automask_LDADD = libDiffImage.la ./Bruker/libbruker.la ./CBFlib/src/libcbf.la \ -- ./MAR/libmar.la ./Rigaku/librigaku.la ./jpg/libjpeg.la -+automask_LDADD = libDiffImage.la ./Bruker/libbruker.la \ -+ ./MAR/libmar.la ./Rigaku/librigaku.la $(SYSLIBS) - automask_SOURCES = automask.cpp --diffdump_LDADD = libDiffImage.la ./Bruker/libbruker.la ./CBFlib/src/libcbf.la \ -- ./MAR/libmar.la ./Rigaku/librigaku.la ./jpg/libjpeg.la -+automask_LDFLAGS = $(SHARED_LIB_FLAGS) -+diffdump_LDADD = libDiffImage.la ./Bruker/libbruker.la $(SYSLIBS) \ -+ ./MAR/libmar.la ./Rigaku/librigaku.la - diffdump_SOURCES = diffdump.cpp --printpeaks_LDADD = libDiffImage.la ./Bruker/libbruker.la ./CBFlib/src/libcbf.la \ -- ./MAR/libmar.la ./Rigaku/librigaku.la ./jpg/libjpeg.la -+diffdump_LDFLAGS = $(SHARED_LIB_FLAGS) -+printpeaks_LDADD = libDiffImage.la ./Bruker/libbruker.la \ -+ ./MAR/libmar.la ./Rigaku/librigaku.la $(SYSLIBS) - printpeaks_SOURCES = printpeaks.cpp --diff2jpeg_LDADD = libDiffImage.la ./Bruker/libbruker.la ./CBFlib/src/libcbf.la \ -- ./MAR/libmar.la ./Rigaku/librigaku.la ./jpg/libjpeg.la -+printpeaks_LDFLAGS = $(SHARED_LIB_FLAGS) -+diff2jpeg_LDADD = libDiffImage.la ./Bruker/libbruker.la \ -+ ./MAR/libmar.la ./Rigaku/librigaku.la $(SYSLIBS) - diff2jpeg_SOURCES = diff2jpeg.cpp -+diff2jpeg_LDFLAGS = $(SHARED_LIB_FLAGS) - - install-data-local: - @INSTALL_DATA@ doc/DiffractionImage.doc ${CDOC} -diff --git a/lib/DiffractionImage/configure b/lib/DiffractionImage/configure -index 3fb5784..fdf9683 100755 ---- a/lib/DiffractionImage/configure -+++ b/lib/DiffractionImage/configure -@@ -21768,7 +21768,7 @@ _ACEOF - fi - - --ac_config_files="$ac_config_files Makefile CBFlib/Makefile CBFlib/src/Makefile MAR/Makefile Rigaku/Makefile Bruker/Makefile jpg/Makefile" -+ac_config_files="$ac_config_files Makefile MAR/Makefile Rigaku/Makefile Bruker/Makefile " - - - cat >confcache <<\_ACEOF -@@ -22407,12 +22407,9 @@ do - case $ac_config_target in - "depfiles") CONFIG_COMMANDS="$CONFIG_COMMANDS depfiles" ;; - "Makefile") CONFIG_FILES="$CONFIG_FILES Makefile" ;; -- "CBFlib/Makefile") CONFIG_FILES="$CONFIG_FILES CBFlib/Makefile" ;; -- "CBFlib/src/Makefile") CONFIG_FILES="$CONFIG_FILES CBFlib/src/Makefile" ;; - "MAR/Makefile") CONFIG_FILES="$CONFIG_FILES MAR/Makefile" ;; - "Rigaku/Makefile") CONFIG_FILES="$CONFIG_FILES Rigaku/Makefile" ;; - "Bruker/Makefile") CONFIG_FILES="$CONFIG_FILES Bruker/Makefile" ;; -- "jpg/Makefile") CONFIG_FILES="$CONFIG_FILES jpg/Makefile" ;; - - *) { { echo "$as_me:$LINENO: error: invalid argument: $ac_config_target" >&5 - echo "$as_me: error: invalid argument: $ac_config_target" >&2;} -diff --git a/lib/DiffractionImage/configure.in b/lib/DiffractionImage/configure.in -index 7f54b4b..16efc64 100755 ---- a/lib/DiffractionImage/configure.in -+++ b/lib/DiffractionImage/configure.in -@@ -21,6 +21,8 @@ if test -n "${PYTHON}" ; then - HAVE_PYTHON=1 - CPPFLAGS="${CPPFLAGS} -I${PYTHON_PREFIX}/include/python${PYTHON_VER}" - ]) -+ PYLIB="-lpython${PYTHON_VER}" -+ AC_SUBST(PYLIB) - fi - AC_CHECK_HEADER([tcl.h], [HAVE_TCL=1]) - -@@ -65,11 +67,8 @@ AM_CONDITIONAL([WANT_JAVA], test z${HAVE_JAVA} != z) - AC_CHECK_LIB([m], [sqrt]) - - AC_CONFIG_FILES([Makefile -- CBFlib/Makefile -- CBFlib/src/Makefile - MAR/Makefile - Rigaku/Makefile -- Bruker/Makefile -- jpg/Makefile]) -+ Bruker/Makefile]) - - AC_OUTPUT -diff --git a/lib/src/Makefile.in b/lib/src/Makefile.in -index c23f488..9579b3b 100755 ---- a/lib/src/Makefile.in -+++ b/lib/src/Makefile.in -@@ -659,7 +659,7 @@ csymlib.o: $(srcdir)/csymlib.c $(srcdir)/csymlib.h - csymlib_f.o: $(srcdir)/csymlib_f.c $(srcdir)/csymlib.h - ccp4_unitcell.o: $(srcdir)/ccp4_unitcell.c $(srcdir)/ccp4_unitcell.h - ccp4_unitcell_f.o: $(srcdir)/ccp4_unitcell_f.c $(srcdir)/ccp4_unitcell.h --hybrid_36_f.o: $(srcdir)/hybrid_36_f.c $(mmdbsrcdir)/hybrid_36.h -+hybrid_36_f.o: $(srcdir)/hybrid_36_f.c - cvecmat.o: $(srcdir)/cvecmat.c $(srcdir)/cvecmat.h - cmtzlib_python_wrap.o: $(srcdir)/cmtzlib_python_wrap.c $(srcdir)/mtzdata.h - cmaplib_python_wrap.o: $(srcdir)/cmaplib_python_wrap.c -diff --git a/lib/ssm/Makefile.am b/lib/ssm/Makefile.am -index e9554e1..a3ba33d 100755 ---- a/lib/ssm/Makefile.am -+++ b/lib/ssm/Makefile.am -@@ -1,7 +1,11 @@ -+ACLOCAL_AMFLAGS = -I macros - #libtool - lib_LTLIBRARIES = libssm.la -+libssm_la_LDFLAGS = -shared $(SHARED_LIB_FLAGS) -+libssm_la_CFLAGS = @MMDB_CFLAGS@ - libssm_la_SOURCES = ssm_superpose.cpp ss_csia.cpp ss_vxedge.cpp \ - ssm_align.cpp ss_graph.cpp -+libssm_la_LIBADD = @MMDB_LIBS@ - - #non libtool - #lib_LIBRARIES = libssm.a -@@ -16,12 +20,10 @@ superpose_SOURCES = superpose.cpp - - bin_PROGRAMS = superpose - --INCLUDES = $(MMDB_CXXFLAGS) -- --AM_LDFLAGS = $(MMDB_LIBS) -+INCLUDES = @MMDB_CFLAGS@ - - EXTRA_DIST = macros/mmdb.m4 - --superpose_LDADD = libssm.la -+superpose_LDADD = libssm.la @MMDB_LIBS@ - - libssm_a_AR = $(AR) $(AR_FLAGS) -diff --git a/lib/ssm/configure.ac b/lib/ssm/configure.ac -index 783cb46..d637d11 100755 ---- a/lib/ssm/configure.ac -+++ b/lib/ssm/configure.ac -@@ -28,31 +28,10 @@ AC_ARG_ENABLE(debug, - [ac_cv_enable_debug=no ] ) - - dnl Optional: Check for MMDB. --AM_PATH_MMDB(, -- [ if test "x$mmdb_prefix" != x ; then -- if test "x$ac_MMDB_CXXFLAGS" != x ; then -- case "$ac_MMDB_CXXFLAGS" in -- *src/mmdb ) -- ac_MMDB_LDOPTS=`echo "$ac_MMDB_CXXFLAGS" | sed s#src/mmdb#src#g` -- ;; -- *include/mmdb ) -- ac_MMDB_LDOPTS=`echo "$ac_MMDB_CXXFLAGS" | sed s#include/mmdb#lib#g` -- ;; -- *) -- esac -- MMDB_CXXFLAGS="$ac_MMDB_CXXFLAGS" -- MMDB_LIBS=`echo "$ac_MMDB_LDOPTS -lmmdb" | sed s#-I#-L#` -- AC_MSG_WARN([assuming library $MMDB_LIBS headers $MMDB_CXXFLAGS]) -- else -- MMDB_CXXFLAGS="-I$mmdb_prefix/lib/src/mmdb -I$mmdb_prefix/include/mmdb" -- MMDB_LIBS="-L$mmdb_prefix/lib/src -L$mmdb_prefix/lib -lmmdb" -- AC_MSG_WARN([assuming library $MMDB_LIBS headers $MMDB_CXXFLAGS]) -- fi -- else -- AC_MSG_WARN([mmdb not found]) -- fi -- ] --) -+ -+PKG_CHECK_MODULES([MMDB],[mmdb]) -+AC_SUBST([MMDB_CFLAGS]) -+AC_SUBST([MMDB_LIBS]) - - # Checks for typedefs, structures, and compiler characteristics. - # -@@ -67,6 +46,7 @@ AC_CHECK_FUNCS([floor pow rint sqrt]) - # test for function in m - AC_CHECK_LIB([m], [sqrt]) - -+ - AC_SUBST(AR_FLAGS) - AC_SUBST(superpose_LDFLAGS) - AM_CONDITIONAL(DEBUG, test "$ac_cv_enable_debug" = yes) -diff --git a/src/pisa/Makefile.am b/src/pisa/Makefile.am -index 094fd6b..922a131 100755 ---- a/src/pisa/Makefile.am -+++ b/src/pisa/Makefile.am -@@ -1,3 +1,4 @@ -+ACLOCAL_AMFLAGS = -I macros - SUBDIRS = molref pisastore sbase - - pkgdatadir = $(datadir)/pisa -@@ -20,8 +21,8 @@ pisa.cpp pisa_lists.cpp seq_superpose.cpp - - bin_PROGRAMS = pisa - --INCLUDES = $(MMDB_CXXFLAGS) $(SSM_CXXFLAGS) -+INCLUDES = @MMDB_CFLAGS@ $(SSM_CXXFLAGS) - --pisa_LDADD = $(SSM_LIBS) $(MMDB_LIBS) -+pisa_LDADD = $(SSM_LIBS) @MMDB_LIBS@ - - EXTRA_DIST = macros/mmdb.m4 macros/ssm.m4 pisa.cfg.in -diff --git a/src/pisa/configure.ac b/src/pisa/configure.ac -index 81afdda..4f99df6 100755 ---- a/src/pisa/configure.ac -+++ b/src/pisa/configure.ac -@@ -32,35 +32,13 @@ AC_CHECK_FUNCS([floor pow rint sqrt]) - AC_CHECK_LIB([m], [sqrt]) - - dnl Optional: Check for MMDB. --AM_PATH_MMDB(, -- [ if test "x$mmdb_prefix" != x ; then -- if test "x$ac_MMDB_CXXFLAGS" != x && test "x$ac_MMDB_LDOPTS" = x ; then -- case "$ac_MMDB_CXXFLAGS" in -- *src/mmdb ) -- ac_MMDB_LDOPTS=`echo "$ac_MMDB_CXXFLAGS" | sed s#src/mmdb#src#g` -- ;; -- *include/mmdb ) -- ac_MMDB_LDOPTS=`echo "$ac_MMDB_CXXFLAGS" | sed s#include/mmdb#lib#g` -- ;; -- *) -- esac -- MMDB_CXXFLAGS="$ac_MMDB_CXXFLAGS" -- MMDB_LIBS=`echo "$ac_MMDB_LDOPTS -lmmdb" | sed s#-I#-L#` -- AC_MSG_WARN([assuming library $MMDB_LIBS headers $MMDB_CXXFLAGS]) -- else -- MMDB_CXXFLAGS="-I$mmdb_prefix/src -I$mmdb_prefix/src/mmdb -I$mmdb_prefix/include -I$mmdb_prefix/include/mmdb" -- MMDB_LIBS="-L$mmdb_prefix/src -L$mmdb_prefix/lib -lmmdb" -- AC_MSG_WARN([assuming library $MMDB_LIBS headers $MMDB_CXXFLAGS]) -- fi -- else -- AC_MSG_ERROR([mmdb not found]) -- fi -- ] --) -+PKG_CHECK_MODULES([MMDB],[mmdb]) -+AC_SUBST([MMDB_CFLAGS]) -+AC_SUBST([MMDB_LIBS]) - - ac_saved_CXXFLAGS=$CXXFLAGS - ac_saved_LIBS=$LIBS --CXXFLAGS="$CXXFLAGS $MMDB_CXXFLAGS" -+CXXFLAGS="$CXXFLAGS $MMDB_CFLAGS" - LIBS="$MMDB_LIBS $LIBS" - AM_PATH_SSM(, - [ if test "x$ssm_prefix" != x ; then -diff --git a/src/rapper/Makefile.am b/src/rapper/Makefile.am -index e78b10d..486b931 100755 ---- a/src/rapper/Makefile.am -+++ b/src/rapper/Makefile.am -@@ -1,3 +1,3 @@ --SUBDIRS = libxml2 gc7.0 LOOP data -+SUBDIRS = LOOP data - - EXTRA_DIST = -diff --git a/src/rapper/configure.ac b/src/rapper/configure.ac -index 5e4ef69..11b63ec 100755 ---- a/src/rapper/configure.ac -+++ b/src/rapper/configure.ac -@@ -48,6 +48,6 @@ AM_CONDITIONAL(AMDEP, test "x$enable_dependency_tracking" != xno) - - AC_SUBST(rapper_LDFLAGS) - --AC_CONFIG_SUBDIRS([gc7.0 libxml2]) -+#AC_CONFIG_SUBDIRS([gc7.0 libxml2]) - #AC_OUTPUT(Makefile LOOP/Makefile LOOP/python/Makefile data/Makefile) - AC_OUTPUT(Makefile LOOP/Makefile data/Makefile) diff --git a/sci-libs/ccp4-libs/files/6.1.3-unbundle-libs.patch b/sci-libs/ccp4-libs/files/6.1.3-unbundle-libs.patch deleted file mode 100644 index 96978320163b..000000000000 --- a/sci-libs/ccp4-libs/files/6.1.3-unbundle-libs.patch +++ /dev/null @@ -1,203 +0,0 @@ -diff --git a/lib/DiffractionImage/DiffractionImageCBF.cpp b/lib/DiffractionImage/DiffractionImageCBF.cpp -index 69b32b0..602e35f 100755 ---- a/lib/DiffractionImage/DiffractionImageCBF.cpp -+++ b/lib/DiffractionImage/DiffractionImageCBF.cpp -@@ -6,10 +6,10 @@ - // images. - - #include "DiffractionImage.h" --#include "cbf.h" --#include "cbf_simple.h" --#include "cbf_string.h" --#include "cbf_byte_offset.h" -+#include <cbflib/cbf.h> -+#include <cbflib/cbf_simple.h> -+#include <cbflib/cbf_string.h> -+#include <cbflib/cbf_byte_offset.h> - - - using namespace std; -diff --git a/lib/DiffractionImage/MAR/Makefile.in b/lib/DiffractionImage/MAR/Makefile.in -index 4264696..00c4d8d 100755 ---- a/lib/DiffractionImage/MAR/Makefile.in -+++ b/lib/DiffractionImage/MAR/Makefile.in -@@ -174,7 +174,7 @@ top_builddir = @top_builddir@ - top_srcdir = @top_srcdir@ - AUTOMAKE_OPTIONS = gnu - noinst_LTLIBRARIES = libmar.la --AM_CPPFLAGS = -I../CBFlib/src -I../CBFlib/include -+AM_CPPFLAGS = - libmar_la_SOURCES = mar300_header.c \ - mar345_header.c \ - marcif.c \ -diff --git a/lib/DiffractionImage/MAR/marcif.c b/lib/DiffractionImage/MAR/marcif.c -index d3f4212..2c37108 100755 ---- a/lib/DiffractionImage/MAR/marcif.c -+++ b/lib/DiffractionImage/MAR/marcif.c -@@ -31,8 +31,7 @@ - #include "marcif_header.h" - #include "mar345_header.h" - --#include <cbf.h> --#include <img.h> -+#include <cbflib/cbf.h> - - #define printe(x) printf("%s: %s: %s\n",prg,f,x) - #undef cbf_failnez -diff --git a/lib/DiffractionImage/Makefile.in b/lib/DiffractionImage/Makefile.in -index 8197956..807cf25 100755 ---- a/lib/DiffractionImage/Makefile.in -+++ b/lib/DiffractionImage/Makefile.in -@@ -106,23 +106,19 @@ PROGRAMS = $(bin_PROGRAMS) - am_automask_OBJECTS = automask.$(OBJEXT) - automask_OBJECTS = $(am_automask_OBJECTS) - automask_DEPENDENCIES = libDiffImage.la ./Bruker/libbruker.la \ -- ./CBFlib/src/libcbf.la ./MAR/libmar.la ./Rigaku/librigaku.la \ -- ./jpg/libjpeg.la -+ ./MAR/libmar.la ./Rigaku/librigaku.la - am_diff2jpeg_OBJECTS = diff2jpeg.$(OBJEXT) - diff2jpeg_OBJECTS = $(am_diff2jpeg_OBJECTS) - diff2jpeg_DEPENDENCIES = libDiffImage.la ./Bruker/libbruker.la \ -- ./CBFlib/src/libcbf.la ./MAR/libmar.la ./Rigaku/librigaku.la \ -- ./jpg/libjpeg.la -+ ./MAR/libmar.la ./Rigaku/librigaku.la - am_diffdump_OBJECTS = diffdump.$(OBJEXT) - diffdump_OBJECTS = $(am_diffdump_OBJECTS) - diffdump_DEPENDENCIES = libDiffImage.la ./Bruker/libbruker.la \ -- ./CBFlib/src/libcbf.la ./MAR/libmar.la ./Rigaku/librigaku.la \ -- ./jpg/libjpeg.la -+ ./MAR/libmar.la ./Rigaku/librigaku.la - am_printpeaks_OBJECTS = printpeaks.$(OBJEXT) - printpeaks_OBJECTS = $(am_printpeaks_OBJECTS) - printpeaks_DEPENDENCIES = libDiffImage.la ./Bruker/libbruker.la \ -- ./CBFlib/src/libcbf.la ./MAR/libmar.la ./Rigaku/librigaku.la \ -- ./jpg/libjpeg.la -+ ./MAR/libmar.la ./Rigaku/librigaku.la - DEFAULT_INCLUDES = -I.@am__isrc@ - depcomp = $(SHELL) $(top_srcdir)/depcomp - am__depfiles_maybe = depfiles -@@ -284,8 +280,8 @@ target_alias = @target_alias@ - top_builddir = @top_builddir@ - top_srcdir = @top_srcdir@ - AUTOMAKE_OPTIONS = gnu --SUBDIRS = CBFlib Bruker MAR Rigaku jpg --AM_CPPFLAGS = -I./MAR -I./CBFlib/src -I./CBFlib/include -I./jpg -+SUBDIRS = Bruker MAR Rigaku -+AM_CPPFLAGS = -I./MAR - lib_LTLIBRARIES = libDiffImage.la $(am__append_1) $(am__append_2) \ - $(am__append_3) - libDiffImage_la_SOURCES = DiffractionImageJpeg.cpp \ -@@ -311,50 +307,50 @@ libDiffImage_la_SOURCES = DiffractionImageJpeg.cpp \ - dps_peaksearch_cn.c - - libDiffImage_la_LDFLAGS = -static --libDiffractionImage_la_DEPENDENCIES = libDiffImage.la ./CBFlib/src/libcbf.la \ -+libDiffractionImage_la_DEPENDENCIES = libDiffImage.la \ - ./Bruker/libbruker.la ./MAR/libmar.la \ -- ./Rigaku/librigaku.la ./jpg/libjpeg.la -+ ./Rigaku/librigaku.la - - libDiffractionImage_la_SOURCES = DiffractionImageTclInterface.cpp - libDiffractionImage_la_LDFLAGS = -shared --whole-archive libDiffImage.la \ -- ./CBFlib/src/libcbf.la ./Bruker/libbruker.la \ -- ./MAR/libmar.la ./Rigaku/librigaku.la ./jpg/libjpeg.la \ -+ -lcbf ./Bruker/libbruker.la \ -+ ./MAR/libmar.la ./Rigaku/librigaku.la -ljpeg \ - --no-whole-archive -rpath '$(libdir)' - --lib_DiffractionImage_la_DEPENDENCIES = libDiffImage.la ./CBFlib/src/libcbf.la \ -+lib_DiffractionImage_la_DEPENDENCIES = libDiffImage.la \ - ./Bruker/libbruker.la ./MAR/libmar.la \ -- ./Rigaku/librigaku.la ./jpg/libjpeg.la -+ ./Rigaku/librigaku.la - - lib_DiffractionImage_la_SOURCES = DiffractionImagePythonInterface.cpp - lib_DiffractionImage_la_LDFLAGS = -shared --whole-archive libDiffImage.la \ -- ./CBFlib/src/libcbf.la ./Bruker/libbruker.la \ -- ./MAR/libmar.la ./Rigaku/librigaku.la ./jpg/libjpeg.la \ -+ -lcbf ./Bruker/libbruker.la \ -+ ./MAR/libmar.la ./Rigaku/librigaku.la -ljpeg \ - --no-whole-archive -rpath '$(libdir)' - --libDiffractionImaJ_la_DEPENDENCIES = libDiffImage.la ./CBFlib/src/libcbf.la \ -+libDiffractionImaJ_la_DEPENDENCIES = libDiffImage.la \ - ./Bruker/libbruker.la ./MAR/libmar.la \ -- ./Rigaku/librigaku.la ./jpg/libjpeg.la -+ ./Rigaku/librigaku.la - - libDiffractionImaJ_la_SOURCES = DiffractionImageJavaInterface.cpp - libDiffractionImaJ_la_LDFLAGS = -shared --whole-archive libDiffImage.la \ -- ./CBFlib/src/libcbf.la ./Bruker/libbruker.la \ -- ./MAR/libmar.la ./Rigaku/librigaku.la ./jpg/libjpeg.la \ -+ -lcbf ./Bruker/libbruker.la \ -+ ./MAR/libmar.la ./Rigaku/librigaku.la -ljpeg \ - --no-whole-archive -rpath '$(libdir)' - --automask_LDADD = libDiffImage.la ./Bruker/libbruker.la ./CBFlib/src/libcbf.la \ -- ./MAR/libmar.la ./Rigaku/librigaku.la ./jpg/libjpeg.la -+automask_LDADD = libDiffImage.la ./Bruker/libbruker.la -lcbf \ -+ ./MAR/libmar.la ./Rigaku/librigaku.la -ljpeg - - automask_SOURCES = automask.cpp --diffdump_LDADD = libDiffImage.la ./Bruker/libbruker.la ./CBFlib/src/libcbf.la \ -- ./MAR/libmar.la ./Rigaku/librigaku.la ./jpg/libjpeg.la -+diffdump_LDADD = libDiffImage.la ./Bruker/libbruker.la -lcbf \ -+ ./MAR/libmar.la ./Rigaku/librigaku.la -ljpeg - - diffdump_SOURCES = diffdump.cpp --printpeaks_LDADD = libDiffImage.la ./Bruker/libbruker.la ./CBFlib/src/libcbf.la \ -- ./MAR/libmar.la ./Rigaku/librigaku.la ./jpg/libjpeg.la -+printpeaks_LDADD = libDiffImage.la ./Bruker/libbruker.la -lcbf \ -+ ./MAR/libmar.la ./Rigaku/librigaku.la -ljpeg - - printpeaks_SOURCES = printpeaks.cpp --diff2jpeg_LDADD = libDiffImage.la ./Bruker/libbruker.la ./CBFlib/src/libcbf.la \ -- ./MAR/libmar.la ./Rigaku/librigaku.la ./jpg/libjpeg.la -+diff2jpeg_LDADD = libDiffImage.la ./Bruker/libbruker.la -lcbf \ -+ ./MAR/libmar.la ./Rigaku/librigaku.la -ljpeg - - diff2jpeg_SOURCES = diff2jpeg.cpp - all: all-recursive -diff --git a/lib/DiffractionImage/configure b/lib/DiffractionImage/configure -index 3fb5784..fdf9683 100755 ---- a/lib/DiffractionImage/configure -+++ b/lib/DiffractionImage/configure -@@ -21768,7 +21768,7 @@ _ACEOF - fi - - --ac_config_files="$ac_config_files Makefile CBFlib/Makefile CBFlib/src/Makefile MAR/Makefile Rigaku/Makefile Bruker/Makefile jpg/Makefile" -+ac_config_files="$ac_config_files Makefile MAR/Makefile Rigaku/Makefile Bruker/Makefile " - - - cat >confcache <<\_ACEOF -@@ -22407,12 +22407,9 @@ do - case $ac_config_target in - "depfiles") CONFIG_COMMANDS="$CONFIG_COMMANDS depfiles" ;; - "Makefile") CONFIG_FILES="$CONFIG_FILES Makefile" ;; -- "CBFlib/Makefile") CONFIG_FILES="$CONFIG_FILES CBFlib/Makefile" ;; -- "CBFlib/src/Makefile") CONFIG_FILES="$CONFIG_FILES CBFlib/src/Makefile" ;; - "MAR/Makefile") CONFIG_FILES="$CONFIG_FILES MAR/Makefile" ;; - "Rigaku/Makefile") CONFIG_FILES="$CONFIG_FILES Rigaku/Makefile" ;; - "Bruker/Makefile") CONFIG_FILES="$CONFIG_FILES Bruker/Makefile" ;; -- "jpg/Makefile") CONFIG_FILES="$CONFIG_FILES jpg/Makefile" ;; - - *) { { echo "$as_me:$LINENO: error: invalid argument: $ac_config_target" >&5 - echo "$as_me: error: invalid argument: $ac_config_target" >&2;} -diff --git a/lib/DiffractionImage/configure.in b/lib/DiffractionImage/configure.in -index 7f54b4b..69b10e1 100755 ---- a/lib/DiffractionImage/configure.in -+++ b/lib/DiffractionImage/configure.in -@@ -65,11 +65,8 @@ AM_CONDITIONAL([WANT_JAVA], test z${HAVE_JAVA} != z) - AC_CHECK_LIB([m], [sqrt]) - - AC_CONFIG_FILES([Makefile -- CBFlib/Makefile -- CBFlib/src/Makefile - MAR/Makefile - Rigaku/Makefile -- Bruker/Makefile -- jpg/Makefile]) -+ Bruker/Makefile]) - - AC_OUTPUT diff --git a/sci-libs/ccp4-libs/files/ccp4-libs-6.1.3-force.patch b/sci-libs/ccp4-libs/files/ccp4-libs-6.1.3-force.patch deleted file mode 100644 index 367d53e3e4f6..000000000000 --- a/sci-libs/ccp4-libs/files/ccp4-libs-6.1.3-force.patch +++ /dev/null @@ -1,16 +0,0 @@ - Makefile.in | 2 +- - 1 file changed, 1 insertion(+), 1 deletion(-) - -diff --git a/Makefile.in b/Makefile.in -index 60033eb..13ddbd0 100755 ---- a/Makefile.in -+++ b/Makefile.in -@@ -53,7 +53,7 @@ clipper: FORCE fftw - - diffractionImg: - if test -n "$(diffimdir)"; then cd $(top_srcdir)/$(diffimdir); \ -- $(MAKE) -i $(MFLAGS) $(MVARS); else true; fi -+ $(MAKE) $(MFLAGS) $(MVARS); fi - - ssm: - if test -n "$(ssmdir)"; then cd $(top_srcdir)/$(ssmdir); \ diff --git a/sci-libs/ccp4-libs/files/ccp4-libs-6.1.3-format-security.patch b/sci-libs/ccp4-libs/files/ccp4-libs-6.1.3-format-security.patch deleted file mode 100644 index caf62bb652e2..000000000000 --- a/sci-libs/ccp4-libs/files/ccp4-libs-6.1.3-format-security.patch +++ /dev/null @@ -1,16 +0,0 @@ - lib/DiffractionImage/DiffractionImagePythonInterface.cpp | 2 +- - 1 file changed, 1 insertion(+), 1 deletion(-) - -diff --git a/lib/DiffractionImage/DiffractionImagePythonInterface.cpp b/lib/DiffractionImage/DiffractionImagePythonInterface.cpp -index f729fc5..4c24e82 100755 ---- a/lib/DiffractionImage/DiffractionImagePythonInterface.cpp -+++ b/lib/DiffractionImage/DiffractionImagePythonInterface.cpp -@@ -867,7 +867,7 @@ SWIG_Python_AddErrorMsg(const char* mesg) - Py_DECREF(old_str); - Py_DECREF(value); - } else { -- PyErr_Format(PyExc_RuntimeError, mesg); -+ PyErr_Format(PyExc_RuntimeError, "%s", mesg); - } - } - diff --git a/sci-libs/ccp4-libs/metadata.xml b/sci-libs/ccp4-libs/metadata.xml deleted file mode 100644 index c0432fefe855..000000000000 --- 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@gentoo.org</email> - <name>Justin Lecher (jlec)</name> - </maintainer> -</pkgmetadata> diff --git a/sci-libs/clipper/clipper-2.1_p100511-r1.ebuild b/sci-libs/clipper/clipper-2.1_p100511-r1.ebuild deleted file mode 100644 index 1757c6960b83..000000000000 --- a/sci-libs/clipper/clipper-2.1_p100511-r1.ebuild +++ /dev/null @@ -1,58 +0,0 @@ -# Copyright 1999-2013 Gentoo Foundation -# Distributed under the terms of the GNU General Public License v2 -# $Id$ - -EAPI=4 - -AUTOTOOLS_AUTORECONF=true - -inherit autotools-utils eutils flag-o-matic - -MY_PV=${PV/_p/-} -MY_P="${PN}-${MY_PV}" - -DESCRIPTION="Object-oriented libraries for crystallographic data and crystallographic computation" -HOMEPAGE="http://www.ysbl.york.ac.uk/~cowtan/clipper/clipper.html" -SRC_URI="http://www.ysbl.york.ac.uk/~cowtan/clipper/${MY_P}-ac.tar.gz" - -LICENSE="LGPL-2.1" -SLOT="0" -KEYWORDS="amd64 ppc x86 ~amd64-linux ~x86-linux" -IUSE="debug static-libs" - -RDEPEND=" - sci-libs/ccp4-libs - sci-libs/fftw - sci-libs/mmdb" -DEPEND="${RDEPEND}" - -S="${WORKDIR}"/${PN}-2.1 - -PATCHES=( - "${FILESDIR}"/20091215-missing-var.patch - "${FILESDIR}"/${PV}-makefile.patch - "${FILESDIR}"/${P}-outofsourcebuild.patch - ) - -src_configure() { - # Recommended on ccp4bb/coot ML to fix crashes when calculating maps - # on 64-bit systems - append-flags -fno-strict-aliasing - - local myeconfargs=( - --enable-ccp4 - --enable-cif - --enable-cns - --enable-contrib - --enable-minimol - --enable-mmdb - --enable-phs - --with-mmdb="${EPREFIX}/usr" - $(use_enable debug) - ) - autotools-utils_src_configure -} - -src_test() { - emake -C "${AUTOTOOLS_BUILD_DIR}"/examples check -} diff --git a/sci-libs/coot-data/coot-data-2-r1.ebuild b/sci-libs/coot-data/coot-data-2-r1.ebuild deleted file mode 100644 index 1640d461d019..000000000000 --- a/sci-libs/coot-data/coot-data-2-r1.ebuild +++ /dev/null @@ -1,33 +0,0 @@ -# Copyright 1999-2013 Gentoo Foundation -# Distributed under the terms of the GNU General Public License v2 -# $Id$ - -EAPI=5 - -DESCRIPTION="Data for the Crystallographic Object-Oriented Toolkit" -HOMEPAGE="http://www.biop.ox.ac.uk/coot/" -#SRC_URI="http://lmb.bioch.ox.ac.uk/coot/software/dependencies/reference-structures.tar.gz" -SRC_URI="mirror://gentoo/reference-structures-${PV}.tar.gz" - -LICENSE="GPL-3" -SLOT="0" -KEYWORDS="amd64 ppc x86 ~amd64-linux ~x86-linux ~x64-macos ~x86-macos" -IUSE="" - -RESTRICT="binchecks strip" - -S="${WORKDIR}" - -src_install() { - insinto /usr/share/coot - doins -r reference-structures - - # Coot looks in the wrong spot for the monomer library - # Listens to ccp4's CCP4_LIB rather than CLIBD_MON - cat >> "${T}"/coot <<- EOF - COOT_REFMAC_LIB_DIR="${EPREFIX}/usr/share/ccp4/" - COOT_REF_STRUCTS="${EPREFIX}/usr/share/coot/reference-structures/" - EOF - - newenvd "${T}"/coot 20coot -} diff --git a/sci-libs/coot-data/coot-data-2.ebuild b/sci-libs/coot-data/coot-data-2.ebuild deleted file mode 100644 index 2b7d33178adb..000000000000 --- a/sci-libs/coot-data/coot-data-2.ebuild +++ /dev/null @@ -1,33 +0,0 @@ -# Copyright 1999-2011 Gentoo Foundation -# Distributed under the terms of the GNU General Public License v2 -# $Id$ - -EAPI="3" - -DESCRIPTION="Data for the Crystallographic Object-Oriented Toolkit" -HOMEPAGE="http://www.biop.ox.ac.uk/coot/" -#SRC_URI="http://www.ysbl.york.ac.uk/~emsley/software/extras/reference-structures.tar.gz" -SRC_URI="mirror://gentoo/reference-structures-${PV}.tar.gz" - -LICENSE="GPL-3" -SLOT="0" -KEYWORDS="amd64 ~ppc x86 ~amd64-linux ~x86-linux ~x64-macos ~x86-macos" -IUSE="" - -RESTRICT="binchecks strip" - -S="${WORKDIR}" - -src_install() { - insinto /usr/share/coot - doins -r reference-structures || die - - # Coot looks in the wrong spot for the monomer library - # Listens to ccp4's CCP4_LIB rather than CLIBD_MON - cat >> "${T}"/coot <<- EOF - COOT_REFMAC_LIB_DIR="${EPREFIX}/usr/share/ccp4/" - COOT_REF_STRUCTS="${EPREFIX}/usr/share/coot/reference-structures/" - EOF - - newenvd "${T}"/coot 20coot || die -} diff --git a/sci-libs/mmdb/mmdb-1.24.ebuild b/sci-libs/mmdb/mmdb-1.24.ebuild deleted file mode 100644 index f44a3ae67ee1..000000000000 --- a/sci-libs/mmdb/mmdb-1.24.ebuild +++ /dev/null @@ -1,45 +0,0 @@ -# Copyright 1999-2015 Gentoo Foundation -# Distributed under the terms of the GNU General Public License v2 -# $Id$ - -EAPI=4 - -inherit autotools-utils - -DESCRIPTION="The Coordinate Library, designed to assist CCP4 developers in working with coordinate files" -HOMEPAGE="https://launchpad.net/mmdb/" -SRC_URI=" - http://www.ysbl.york.ac.uk/~emsley/software/${P}.tar.gz - https://launchpad.net/mmdb/1.23/${PV}/+download/${P}.tar.gz" - -LICENSE="GPL-2 LGPL-3" -SLOT="0" -KEYWORDS="amd64 ppc x86 ~amd64-linux ~x86-linux ~x64-macos ~x86-macos" -IUSE="static-libs" - -DEPEND="!<sci-libs/ccp4-libs-6.1.3" -RDEPEND="" - -src_install() { - autotools-utils_src_install - - # create missing mmdb.pc - cat >> "${T}"/mmdb.pc <<- EOF - prefix=${EPREFIX}/usr - exec_prefix=${EPREFIX}/usr - libdir=${EPREFIX}/usr/$(get_libdir) - includedir=${EPREFIX}/usr/include/mmdb - - Name: ${PN} - Description: Macromolecular coordinate library - Version: ${PV} - Requires: - Conflicts: - Libs: -L"${EPREFIX}/usr/$(get_libdir)" -lmmdb - Cflags: -I"${EPREFIX}/usr/include/mmdb" - - EOF - - insinto /usr/$(get_libdir)/pkgconfig - doins "${T}"/mmdb.pc -} diff --git a/sci-libs/mmdb/mmdb-1.25.5-r1.ebuild b/sci-libs/mmdb/mmdb-1.25.5-r1.ebuild index 8cae49d97a8c..6389827c63ee 100644 --- a/sci-libs/mmdb/mmdb-1.25.5-r1.ebuild +++ b/sci-libs/mmdb/mmdb-1.25.5-r1.ebuild @@ -15,7 +15,4 @@ SLOT="0" KEYWORDS="~amd64 ~ppc ~x86 ~amd64-linux ~x86-linux ~x64-macos ~x86-macos" IUSE="static-libs" -DEPEND="!<sci-libs/ccp4-libs-6.1.3" -RDEPEND="" - PATCHES=( "${FILESDIR}"/${P}-include-path.patch ) diff --git a/sci-libs/mmdb/mmdb-1.25.5.ebuild b/sci-libs/mmdb/mmdb-1.25.5.ebuild deleted file mode 100644 index 9be8cec5a894..000000000000 --- a/sci-libs/mmdb/mmdb-1.25.5.ebuild +++ /dev/null @@ -1,19 +0,0 @@ -# Copyright 1999-2014 Gentoo Foundation -# Distributed under the terms of the GNU General Public License v2 -# $Id$ - -EAPI=5 - -inherit autotools-utils - -DESCRIPTION="The Coordinate Library, designed to assist CCP4 developers in working with coordinate files" -HOMEPAGE="https://launchpad.net/mmdb/" -SRC_URI="ftp://ftp.ccp4.ac.uk/opensource/${P}.tar.gz" - -LICENSE="GPL-2 LGPL-3" -SLOT="0" -KEYWORDS="~amd64 ~ppc ~x86 ~amd64-linux ~x86-linux ~x64-macos ~x86-macos" -IUSE="static-libs" - -DEPEND="!<sci-libs/ccp4-libs-6.1.3" -RDEPEND="" diff --git a/sci-libs/monomer-db/monomer-db-0.090729.ebuild b/sci-libs/monomer-db/monomer-db-0.090729.ebuild deleted file mode 100644 index 6513cbc0404c..000000000000 --- a/sci-libs/monomer-db/monomer-db-0.090729.ebuild +++ /dev/null @@ -1,31 +0,0 @@ -# Copyright 1999-2015 Gentoo Foundation -# Distributed under the terms of the GNU General Public License v2 -# $Id$ - -EAPI=5 - -DESCRIPTION="Monomer library used for macromolecular structure building and refinement" -HOMEPAGE="http://www.ccp4.ac.uk/" -# SRC_URI="http://www.ysbl.york.ac.uk/~garib/refmac/data/refmac_dictionary.tar.gz" -SRC_URI="https://dev.gentoo.org/~jlec/science-dist/${P}.tar.gz" - -LICENSE="ccp4" -SLOT="0" -KEYWORDS="amd64 ppc x86 ~amd64-linux ~x86-linux" -IUSE="" - -RDEPEND="!<sci-chemistry/ccp4-6.1.3" -DEPEND="${RDEPEND}" - -RESTRICT="binchecks strip" - -S="${WORKDIR}"/dic - -src_install() { - insinto /usr/share/ccp4/data/monomers/ - for i in {a..z} {1..9} *list *.cif *.txt; do - doins -r ${i} - done - docinto html - dodoc *.html -} diff --git a/sci-libs/ssm/ssm-1.1.ebuild b/sci-libs/ssm/ssm-1.1.ebuild deleted file mode 100644 index d247077313dd..000000000000 --- a/sci-libs/ssm/ssm-1.1.ebuild +++ /dev/null @@ -1,31 +0,0 @@ -# Copyright 1999-2014 Gentoo Foundation -# Distributed under the terms of the GNU General Public License v2 -# $Id$ - -EAPI=5 - -inherit autotools eutils - -DESCRIPTION="A macromolecular coordinate superposition library" -HOMEPAGE="https://launchpad.net/ssm" -SRC_URI="https://launchpad.net/${PN}/trunk/${PV}/+download/${P}.tar.gz" - -LICENSE="LGPL-2.1" -SLOT="0" -KEYWORDS="amd64 ppc x86 ~amd64-linux ~x86-linux" -IUSE="static-libs" - -DEPEND=">=sci-libs/mmdb-1.23:0" -RDEPEND="${DEPEND} - !<sci-libs/ccp4-libs-6.1.3-r10" - -src_prepare() { - epatch \ - "${FILESDIR}"/${P}-mmdb.patch \ - "${FILESDIR}"/${P}-pc.patch - eautoreconf -} - -src_configure() { - econf $(use_enable static-libs static) -} diff --git a/sys-apps/coreutils/coreutils-8.20.ebuild b/sys-apps/coreutils/coreutils-8.20.ebuild index 48946b218753..96434764771c 100644 --- a/sys-apps/coreutils/coreutils-8.20.ebuild +++ b/sys-apps/coreutils/coreutils-8.20.ebuild @@ -34,7 +34,7 @@ RDEPEND="!static? ( ${LIB_DEPEND//\[static-libs]} ) !sys-apps/mktemp !<app-forensics/tct-1.18-r1 !<net-fs/netatalk-2.0.3-r4 - !<sci-chemistry/ccp4-6.1.1" +" DEPEND="${RDEPEND} static? ( ${LIB_DEPEND} ) app-arch/xz-utils" diff --git a/sys-apps/coreutils/coreutils-8.21.ebuild b/sys-apps/coreutils/coreutils-8.21.ebuild index 92fccdf5c8ae..fdaa4c2de1cb 100644 --- a/sys-apps/coreutils/coreutils-8.21.ebuild +++ b/sys-apps/coreutils/coreutils-8.21.ebuild @@ -36,7 +36,7 @@ RDEPEND="!static? ( ${LIB_DEPEND//\[static-libs]} ) !sys-apps/mktemp !<app-forensics/tct-1.18-r1 !<net-fs/netatalk-2.0.3-r4 - !<sci-chemistry/ccp4-6.1.1" +" DEPEND="${RDEPEND} static? ( ${LIB_DEPEND} ) app-arch/xz-utils" diff --git a/sys-apps/coreutils/coreutils-8.22-r1.ebuild b/sys-apps/coreutils/coreutils-8.22-r1.ebuild index 940d49ea1f3a..78fcad4daacc 100644 --- a/sys-apps/coreutils/coreutils-8.22-r1.ebuild +++ b/sys-apps/coreutils/coreutils-8.22-r1.ebuild @@ -34,7 +34,7 @@ RDEPEND="!static? ( ${LIB_DEPEND//\[static-libs]} ) !sys-apps/mktemp !<app-forensics/tct-1.18-r1 !<net-fs/netatalk-2.0.3-r4 - !<sci-chemistry/ccp4-6.1.1" +" DEPEND="${RDEPEND} static? ( ${LIB_DEPEND} ) app-arch/xz-utils" diff --git a/sys-apps/coreutils/coreutils-8.22.ebuild b/sys-apps/coreutils/coreutils-8.22.ebuild index 5f3370ca2ed1..d570dee30b43 100644 --- a/sys-apps/coreutils/coreutils-8.22.ebuild +++ b/sys-apps/coreutils/coreutils-8.22.ebuild @@ -34,7 +34,7 @@ RDEPEND="!static? ( ${LIB_DEPEND//\[static-libs]} ) !sys-apps/mktemp !<app-forensics/tct-1.18-r1 !<net-fs/netatalk-2.0.3-r4 - !<sci-chemistry/ccp4-6.1.1" +" DEPEND="${RDEPEND} static? ( ${LIB_DEPEND} ) app-arch/xz-utils" diff --git a/sys-apps/coreutils/coreutils-8.23.ebuild b/sys-apps/coreutils/coreutils-8.23.ebuild index 9d7ebab1a069..bfb0c9bc167c 100644 --- a/sys-apps/coreutils/coreutils-8.23.ebuild +++ b/sys-apps/coreutils/coreutils-8.23.ebuild @@ -40,7 +40,7 @@ RDEPEND="!static? ( ${LIB_DEPEND//\[static-libs]} ) !sys-apps/mktemp !<app-forensics/tct-1.18-r1 !<net-fs/netatalk-2.0.3-r4 - !<sci-chemistry/ccp4-6.1.1" +" DEPEND="${RDEPEND} static? ( ${LIB_DEPEND} ) app-arch/xz-utils" diff --git a/sys-apps/coreutils/coreutils-8.24.ebuild b/sys-apps/coreutils/coreutils-8.24.ebuild index f5f6bd0d946e..5b88e1c96f5f 100644 --- a/sys-apps/coreutils/coreutils-8.24.ebuild +++ b/sys-apps/coreutils/coreutils-8.24.ebuild @@ -40,7 +40,7 @@ RDEPEND="!static? ( ${LIB_DEPEND//\[static-libs]} ) !sys-apps/mktemp !<app-forensics/tct-1.18-r1 !<net-fs/netatalk-2.0.3-r4 - !<sci-chemistry/ccp4-6.1.1" +" DEPEND="${RDEPEND} static? ( ${LIB_DEPEND} ) app-arch/xz-utils" diff --git a/x11-libs/libxdl_view/Manifest b/x11-libs/libxdl_view/Manifest deleted file mode 100644 index 8f5dc9db9b31..000000000000 --- a/x11-libs/libxdl_view/Manifest +++ /dev/null @@ -1 +0,0 @@ -DIST libxdl_view-4.2.tar.gz 857566 SHA256 826adc9c6d6706ffc6f9b52e6f7871e3ebf397837010a75daa971812f162d0b3 SHA512 1ea461cc27e53e94b89cdeef9fc435342d66f618f52a6bb936ff2c7ee63fbc89ecbbecfb4da0209ec8969f09b422af3690408dc61470299ce23e3cf84b202266 WHIRLPOOL 212c7e9f09c804bf58445a116ad75d343f6cd8e393e88ed2b2fcd4f311bd59f8a803c7fbf2d3c3a799cc7e88a9ba55f6e148c07a4956b8c6f22a0398f4b8e91f diff --git a/x11-libs/libxdl_view/files/4.2-as-needed.patch b/x11-libs/libxdl_view/files/4.2-as-needed.patch deleted file mode 100644 index a59d1997c2e5..000000000000 --- a/x11-libs/libxdl_view/files/4.2-as-needed.patch +++ /dev/null @@ -1,16 +0,0 @@ -diff --git a/Makefile.am b/Makefile.am -index 347bb21..cbb04db 100644 ---- a/Makefile.am -+++ b/Makefile.am -@@ -19,7 +19,11 @@ lib_LTLIBRARIES = libxdl_view.la libxdl_viewextra.la - ## The initial value of this was a mistake! - ## See the libtool doc. - libxdl_view_la_LDFLAGS = -version-info 2:0:0 -+libxdl_view_la_LIBADD = -lX11 -lXt -lm -+ - libxdl_viewextra_la_LDFLAGS = -version-info 0:0:0 -+libxdl_viewextra_la_DEPENDENCIES = libxdl_view.la -+libxdl_viewextra_la_LIBADD = -lm -lxdl_view -ljwc_c - - EXTRA_DIST = doc/xdl_view_icon.gif doc/xdl_view_top.gif \ - doc/xdl_view_top.html doc/xdl_view_updates.html \ diff --git a/x11-libs/libxdl_view/files/4.2-impl-dec.patch b/x11-libs/libxdl_view/files/4.2-impl-dec.patch deleted file mode 100644 index 418143777338..000000000000 --- a/x11-libs/libxdl_view/files/4.2-impl-dec.patch +++ /dev/null @@ -1,13 +0,0 @@ -diff --git a/Makefile.am b/Makefile.am -index 347bb21..aa41ba3 100644 ---- a/Makefile.am -+++ b/Makefile.am -@@ -3,6 +3,8 @@ - - ## Process this file with automake. - -+CFLAGS += -std=c99 -L.libs -+ - libxdl_view_la_SOURCES = xdl_base_fr.c xdl_blank_obj.c xdl_image.c \ - xdl_bg.c xdl_img_rd.c xdl_film_img.c xdl_io_window.c \ - xdl_menu_area.c xdl_text_tab.c xdl_panel_itm.c \ diff --git a/x11-libs/libxdl_view/libxdl_view-4.2-r2.ebuild b/x11-libs/libxdl_view/libxdl_view-4.2-r2.ebuild deleted file mode 100644 index 6a9900710a5c..000000000000 --- a/x11-libs/libxdl_view/libxdl_view-4.2-r2.ebuild +++ /dev/null @@ -1,32 +0,0 @@ -# Copyright 1999-2012 Gentoo Foundation -# Distributed under the terms of the GNU General Public License v2 -# $Id$ - -EAPI=4 - -AUTOTOOLS_AUTORECONF=yes - -inherit autotools-utils - -DESCRIPTION="An X-Windows Based Toolkit" -HOMEPAGE="http://www.ccp4.ac.uk/dist/x-windows/xdl_view/doc/xdl_view_top.html" -SRC_URI="ftp://ftp.ccp4.ac.uk/jwc/${P}.tar.gz" - -LICENSE="GPL-2" -SLOT="0" -KEYWORDS="amd64 ppc x86 ~amd64-linux ~x86-linux ~x64-macos ~x86-macos" -IUSE="static-libs" - -RDEPEND=" - dev-libs/libjwc_c - x11-libs/libXt" -DEPEND="${RDEPEND}" - -PATCHES=( - "${FILESDIR}"/${PV}-impl-dec.patch - "${FILESDIR}"/${PV}-as-needed.patch ) - -src_prepare() { - rm missing || die - autotools-utils_src_prepare -} diff --git a/x11-libs/libxdl_view/metadata.xml b/x11-libs/libxdl_view/metadata.xml deleted file mode 100644 index d747d72a25b4..000000000000 --- a/x11-libs/libxdl_view/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> |