diff options
author | Justin Lecher <jlec@gentoo.org> | 2010-05-16 12:56:16 +0000 |
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committer | Justin Lecher <jlec@gentoo.org> | 2010-05-16 12:56:16 +0000 |
commit | 38e371c007d764f186b688b501dacd52c5e2752a (patch) | |
tree | be2fb17993dbdd25810fdcf3f71d6aac72e384d6 /sci-chemistry | |
parent | RESTRICT PY ABI 2.5 (diff) | |
download | gentoo-2-38e371c007d764f186b688b501dacd52c5e2752a.tar.gz gentoo-2-38e371c007d764f186b688b501dacd52c5e2752a.tar.bz2 gentoo-2-38e371c007d764f186b688b501dacd52c5e2752a.zip |
Version Bump
(Portage version: 2.2_rc67/cvs/Linux x86_64)
Diffstat (limited to 'sci-chemistry')
-rw-r--r-- | sci-chemistry/refmac/ChangeLog | 8 | ||||
-rw-r--r-- | sci-chemistry/refmac/files/5.6.0075-allow-dynamic-linking.patch | 45 | ||||
-rw-r--r-- | sci-chemistry/refmac/refmac-5.6.0075.ebuild | 70 |
3 files changed, 122 insertions, 1 deletions
diff --git a/sci-chemistry/refmac/ChangeLog b/sci-chemistry/refmac/ChangeLog index 6dcfcb34a444..d6716faaab6d 100644 --- a/sci-chemistry/refmac/ChangeLog +++ b/sci-chemistry/refmac/ChangeLog @@ -1,6 +1,12 @@ # ChangeLog for sci-chemistry/refmac # Copyright 1999-2010 Gentoo Foundation; Distributed under the GPL v2 -# $Header: /var/cvsroot/gentoo-x86/sci-chemistry/refmac/ChangeLog,v 1.5 2010/05/13 10:06:31 jlec Exp $ +# $Header: /var/cvsroot/gentoo-x86/sci-chemistry/refmac/ChangeLog,v 1.6 2010/05/16 12:56:16 jlec Exp $ + +*refmac-5.6.0075 (16 May 2010) + + 16 May 2010; Justin Lecher <jlec@gentoo.org> + +files/5.6.0075-allow-dynamic-linking.patch, +refmac-5.6.0075.ebuild: + Version bump *refmac-5.5.0110 (13 May 2010) diff --git a/sci-chemistry/refmac/files/5.6.0075-allow-dynamic-linking.patch b/sci-chemistry/refmac/files/5.6.0075-allow-dynamic-linking.patch new file mode 100644 index 000000000000..e86a3a69dfd8 --- /dev/null +++ b/sci-chemistry/refmac/files/5.6.0075-allow-dynamic-linking.patch @@ -0,0 +1,45 @@ +diff --git a/makefile_refmac.inc1 b/makefile_refmac.inc1 +index 97791e0..6c43c5d 100644 +--- a/makefile_refmac.inc1 ++++ b/makefile_refmac.inc1 +@@ -83,9 +83,7 @@ messy_pdb.o \ + bridge.o \ + i0.o \ + i1.o \ +-chbevl.o \ +-$(LLIBCIF) \ +-$(LLIBLAPACK) ++chbevl.o + + + SUBL = \ +@@ -118,9 +116,8 @@ cell_symm_subrs.o \ + iheap_sort.o \ + linalgebra.o \ + math_refmac.o \ +-subnumrec.o \ +-$(LLIBLAPACK) \ +-$(LLIBCCP) ++subnumrec.o ++ + + #-------------------------------------------------------------------------------- + +@@ -188,7 +185,7 @@ linalgebra_f90.o: linalgebra_f90.f90 + $(FC) $(FFLAGS) -c linalgebra_f90.f90 + + 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 +@@ -209,7 +206,7 @@ libcheck.o: libcheck.f elements_module.f90 pdb2libcheck.f90 + $(FC) $(FFLAGS) -c elements_module.f90 pdb2libcheck.f90 libcheck.f + + libcheck: $(SUBL) +- $(FC) $(FFLAGS) -o libcheck${VERSION} $(SUBL) ++ $(FC) $(FFLAGS) $(LDFLAGS) -o libcheck${VERSION} $(SUBL) $(LLIBCCP) $(LLIBCIF) $(LLIBLAPACK) + + clean: + /bin/rm *.o diff --git a/sci-chemistry/refmac/refmac-5.6.0075.ebuild b/sci-chemistry/refmac/refmac-5.6.0075.ebuild new file mode 100644 index 000000000000..233956daad4e --- /dev/null +++ b/sci-chemistry/refmac/refmac-5.6.0075.ebuild @@ -0,0 +1,70 @@ +# Copyright 1999-2010 Gentoo Foundation +# Distributed under the terms of the GNU General Public License v2 +# $Header: /var/cvsroot/gentoo-x86/sci-chemistry/refmac/refmac-5.6.0075.ebuild,v 1.1 2010/05/16 12:56:16 jlec Exp $ + +EAPI="2" + +inherit fortran base toolchain-funcs versionator + +MY_PV="$(get_version_component_range 1-2)_source_v${PV}" + +DESCRIPTION="Macromolecular crystallographic refinement program" +HOMEPAGE="http://www.ysbl.york.ac.uk/~garib/refmac/" +SRC_URI="${HOMEPAGE}data/refmac_experimental/${PN}${MY_PV}.tar.gz + test? ( http://dev.gentooexperimental.org/~jlec/distfiles/test-framework.tar.gz )" + +SLOT="0" +LICENSE="ccp4" +KEYWORDS="~amd64 ~x86 ~amd64-linux ~x86-linux" +IUSE="test" + +RDEPEND=" + sci-libs/ccp4-libs + sci-libs/mmdb + virtual/blas + virtual/lapack" +DEPEND="${RDEPEND}" + +S="${WORKDIR}" + +PATCHES=( + "${FILESDIR}"/${PV}-allow-dynamic-linking.patch + ) + +src_prepare() { + base_src_prepare + use test && epatch "${FILESDIR}"/5.5-test.log.patch +} + +src_compile() { + emake \ + FC=$(tc-getFC) \ + CC=$(tc-getCC) \ + CXX=$(tc-getCXX) \ + COPTIM="${CFLAGS}" \ + FOPTIM="${FFLAGS:- -O2}" \ + VERSION="" \ + XFFLAGS="-fno-second-underscore" \ + LLIBCCP="-lccp4f -lccp4c -lccif -lmmdb -lstdc++" \ + LLIBLAPACK="$(pkg-config --libs lapack blas)" \ + || die +} + +src_test() { + einfo "Starting tests ..." + 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() { + for i in refmac libcheck; do + exeinto /usr/libexec/ccp4/bin/ + doexe ${i} || die + dosym ../libexec/ccp4/bin/${i} /usr/bin/${i} + done + dosym refmac /usr/bin/refmac5 || die +} |