diff options
author | Justin Lecher <jlec@gentoo.org> | 2010-07-03 08:33:57 +0000 |
---|---|---|
committer | Justin Lecher <jlec@gentoo.org> | 2010-07-03 08:33:57 +0000 |
commit | 02021366cb6d33eeffbfcade669dc0edc1907ab0 (patch) | |
tree | 2b8dc4ab61f364149588a7821815141d51f164dd /sci-chemistry/refmac | |
parent | Convert to ruby-fakegem. (diff) | |
download | historical-02021366cb6d33eeffbfcade669dc0edc1907ab0.tar.gz historical-02021366cb6d33eeffbfcade669dc0edc1907ab0.tar.bz2 historical-02021366cb6d33eeffbfcade669dc0edc1907ab0.zip |
Version Bump, removed old
Package-Manager: portage-2.2_rc67/cvs/Linux x86_64
Diffstat (limited to 'sci-chemistry/refmac')
-rw-r--r-- | sci-chemistry/refmac/ChangeLog | 8 | ||||
-rw-r--r-- | sci-chemistry/refmac/Manifest | 11 | ||||
-rw-r--r-- | sci-chemistry/refmac/files/5.6.0080-allow-dynamic-linking.patch | 94 | ||||
-rw-r--r-- | sci-chemistry/refmac/refmac-5.6.0080.ebuild | 71 |
4 files changed, 179 insertions, 5 deletions
diff --git a/sci-chemistry/refmac/ChangeLog b/sci-chemistry/refmac/ChangeLog index 7cdbf97c470f..3a4af17923a4 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 1.12 2010/07/02 06:36:10 jlec Exp $ +# $Header: /var/cvsroot/gentoo-x86/sci-chemistry/refmac/ChangeLog,v 1.13 2010/07/03 08:33:57 jlec Exp $ + +*refmac-5.6.0080 (03 Jul 2010) + + 03 Jul 2010; Justin Lecher <jlec@gentoo.org> + +files/5.6.0080-allow-dynamic-linking.patch, +refmac-5.6.0080.ebuild: + Version Bump, removed old *refmac-5.6.0079 (02 Jul 2010) diff --git a/sci-chemistry/refmac/Manifest b/sci-chemistry/refmac/Manifest index 0371018228cc..3b93838cda68 100644 --- a/sci-chemistry/refmac/Manifest +++ b/sci-chemistry/refmac/Manifest @@ -6,9 +6,11 @@ AUX 5.5-test.log.patch 1146 RMD160 0ea6293e8ecde3b9ae12658a523e3c30a5c9f01b SHA1 AUX 5.5.0110-allow-dynamic-linking.patch 2265 RMD160 191b90c619a3a0a6cd71b819b4517d639f9912e0 SHA1 23df6c19a6fa9a41ed19d4ec36bd3130ffdb40b7 SHA256 ed10babfa6f9521b1b8e0dd574aa5fa4207d64bcd57332e97f0b35039b66942b AUX 5.6.0075-allow-dynamic-linking.patch 1447 RMD160 5b4eca9f5e03aa0dea24fe4e391c363b3600eb4a SHA1 a3e4989d6b68c77e69e1bfcb76ddbc98c6e7a157 SHA256 0e54d70ac56326422158d19268432772813d34b653b041554ac6e08981ff0140 AUX 5.6.0078-allow-dynamic-linking.patch 3254 RMD160 0136fa28503c10c07ae3e7b653c04cd1e03e3641 SHA1 8b896a003dad2ab840bd7310871fab8191930de6 SHA256 ad4c0feaefcdac5b834549f99ae69aa0b0b33c37332e7e385ee04258b4c51326 +AUX 5.6.0080-allow-dynamic-linking.patch 3680 RMD160 656b50c14ae3b8b886967c39bb73c22d5e8c9ea1 SHA1 bab840c675e4628ee2220c87859fd08f0e88b95b SHA256 1aa6c02ec0aa04e044c5627d649b09402d7d95c44752f9137f62e5d513b171d9 DIST refmac5.6_source_v5.6.0077.tar.gz 1281296 RMD160 3af10c692dcca23bce735b6b45c129c4a1c029e6 SHA1 881d3e456436e15073be495a340504770884e06f SHA256 9f5df52e5b42d5c4e83388f9acd900461c66b76b25248fb539432d4dacb38d50 DIST refmac5.6_source_v5.6.0078.tar.gz 1285576 RMD160 9d5a56a6ae5f5cd03b081607a9916ba543d258a1 SHA1 cc5543cddfbd9f4dfb9105c6472f091cffca7e38 SHA256 a23d657098d890c2ce2c20de35865f512b841c1357611ae3aca31897df1ab832 DIST refmac5.6_source_v5.6.0079.tar.gz 1285637 RMD160 462ba6f5814d724f678ca39f00b52dc4b0ac0649 SHA1 386d48b905e1297983d84f35d0ab276583494153 SHA256 47a943344962e0559ba1d3c57d0c6562cee03013a62b9c1b66dce4e574a409d7 +DIST refmac5.6_source_v5.6.0080.tar.gz 1317431 RMD160 13f306092428bf87a29fa456c03f33c318183110 SHA1 17796be16dbbf4d442fed8814edbf6bb175a4aaf SHA256 cae4017c5a75b185c99a5460c96386978f7959c28c870b80ec9df272f9b3da53 DIST refmac_5.5.0109.tar.gz 1326779 RMD160 3b603c13638407cceb907bd43ac0a971b587c116 SHA1 3cc35a55df71bac4de3eec9cf0e690e221ae3c86 SHA256 38d416c94e1f86a0676d48d7ddaeb4af272970b8cd6b084e70aa38481327c59e DIST refmac_5.5.0110.tar.gz 1326832 RMD160 6613ca8b70e54e7827f8ff02b7d497560cb83e39 SHA1 ba2e38db6c88550bd901b474de881d6514b4d74e SHA256 1353fb1042586ec8fa37d0a90f274890d0ccc02377af5216200662338dfe08ca DIST test-framework.tar.gz 130933173 RMD160 7122539dc713615dca2ddaddfd8d152cd22624d0 SHA1 1d3e3019a67afb9b2346e919c859d402d3250fea SHA256 df050a2a29da80518cb0616a0bbeb82298ea0721549348d15353bf0f66240605 @@ -18,12 +20,13 @@ EBUILD refmac-5.5.0110.ebuild 1805 RMD160 80e546666e72290365c99c542abcef90a3394b EBUILD refmac-5.6.0077.ebuild 1789 RMD160 e5433f715ae0693c4ccbf65cb44f64b988199ea2 SHA1 dfaa458bfa184ffc2118bcc13e0a3b30caa472e8 SHA256 f23cc970ed7fc6766fddd8ceef788c58fd254bbe2be53f9df14561a06c13b1be EBUILD refmac-5.6.0078.ebuild 1786 RMD160 3a75889780b1118f2481991a56b95e62ab8363c4 SHA1 537ab12d16126fff356781f66b1d3aa2edb49117 SHA256 e43fce8f9a0fd05c6a02edb534c09a31017b2bf9274886ee0755993078e23520 EBUILD refmac-5.6.0079.ebuild 1792 RMD160 e013a579d25f02149d1a990f8169ed612a072cde SHA1 f203e1bf374ec9af4ed37f6cbeea33ce15cfd998 SHA256 987d7ab0ab86168df29edc608d02d1dddea421bac0ee8e93541eee035894b112 -MISC ChangeLog 2118 RMD160 9d29943905e4c531444d90704cf5c08a3de7c093 SHA1 c6fb45ebe54ca76d0812d9d3053a1616c0d8ce52 SHA256 18ac25d0a5833d72d2e395471e971fba2cb83a91c4298b282cd11262c4c09126 +EBUILD refmac-5.6.0080.ebuild 1786 RMD160 5851ff9ac4b5fbb60bbc76baca5a2cf060ed5d69 SHA1 5eeaef1b03d2bda2be97fe43defd5e0602661750 SHA256 c891536606c9ad16198d181a6938012b2c1c6b0fde35bfedb96d44a6e1ec8eb5 +MISC ChangeLog 2298 RMD160 b65adc697a377c370b2275e83ff3c4cc44ad32d8 SHA1 cf3fa1dfbeac6429243ab89ec7d4f83879ab8d69 SHA256 c3e010266bfa745733f40683fa9ab453ed30fdae14f9059e711f8a9d3a39a8c6 MISC metadata.xml 311 RMD160 df83b13d491a71b729455b664088d89ddbde1c8c SHA1 fffd2a5645181aa12ac9b6f74da9a011cdcf1b97 SHA256 782521c7e16d7eec82d7b7e7c43102806e7f72bc7366401808b1e1ac6e26045a -----BEGIN PGP SIGNATURE----- Version: GnuPG v2.0.15 (GNU/Linux) -iEYEARECAAYFAkwtiOAACgkQgAnW8HDreRZohgCgscTQpdqwNR6liq/y/mnIVEaa -z7gAnizgag7dLFTSIWFzhVBiWnuKsH/q -=k6cS +iEYEARECAAYFAkwu9fsACgkQgAnW8HDreRZogACgkbhbQUMLMAGX71l1JRLhx6P8 +TjcAn097ZkMwXIygOIhbAcfgPmFIK72+ +=eBOK -----END PGP SIGNATURE----- diff --git a/sci-chemistry/refmac/files/5.6.0080-allow-dynamic-linking.patch b/sci-chemistry/refmac/files/5.6.0080-allow-dynamic-linking.patch new file mode 100644 index 000000000000..6f5d1c6efe98 --- /dev/null +++ b/sci-chemistry/refmac/files/5.6.0080-allow-dynamic-linking.patch @@ -0,0 +1,94 @@ +diff --git a/makefile_refmac.inc1 b/makefile_refmac.inc1 +index 3f858c8..04e6790 100644 +--- a/makefile_refmac.inc1 ++++ b/makefile_refmac.inc1 +@@ -89,9 +89,7 @@ messy_pdb.o \ + bridge.o \ + i0.o \ + i1.o \ +-chbevl.o \ +-$(LLIBCIF) \ +-$(LLIBLAPACK) ++chbevl.o + + + SUBL = \ +@@ -124,9 +122,7 @@ cell_symm_subrs.o \ + iheap_sort.o \ + linalgebra.o \ + math_refmac.o \ +-subnumrec.o \ +-$(LLIBLAPACK) \ +-$(LLIBCCP) ++subnumrec.o + + #-------------------------------------------------------------------------------- + +@@ -150,7 +146,7 @@ twin77mod.o: twin77mod.f + $(FC) $(FFLAGS) -c twin77mod.f + + +-optimise_solvent_all.o: optimise_solvent_all.f90 ++optimise_solvent_all.o: optimise_solvent_all.f90 atomf77mod.o + $(FC) $(FFLAGS) -c optimise_solvent_all.f90 + + ncs_rest.o: ncs_ncs_generate.f90 ncs_rest.f +@@ -178,7 +174,7 @@ align_refmac.o: align_refmac.f90 + $(FC) $(FFLAGS) -c align_refmac.f90 + + +-hkon_secder_tch.o: hkon_secder_tch.f local_tls.f90 ncs_simil.f90 optimise_solvent_all.f90 ++hkon_secder_tch.o: hkon_secder_tch.f local_tls.f90 ncs_simil.f90 optimise_solvent_all.f90 optimise_solvent_all.o + $(FC) $(FFLAGS) -c optimise_solvent_all.f90 ncs_simil.f90 local_tls.f90 hkon_secder_tch.f + + oppro_allocate.o: oppro_allocate.f filter_params.f90 optimise_solvent_all.f90 +@@ -220,8 +216,8 @@ refall_twin.o: refall_twin.f optimise_solvent_all.f90 + rharvest.o: rharvest.f optimise_solvent_all.f90 + $(FC) $(FFLAGS) -c optimise_solvent_all.f90 rharvest.f + +-solvent_contr_mask.o: solvent_contr_mask.f optimise_solvent_all.f90 +- $(FC) $(FFLAGS) -c optimise_solvent_all.f90 solvent_contr_mask.f ++solvent_contr_mask.o: solvent_contr_mask.f optimise_solvent_all.f90 atomf77mod.o ++ $(FC) $(FFLAGS) -c atomf77mod.f optimise_solvent_all.f90 solvent_contr_mask.f + + subag_scale_hessian.o: subag_scale_hessian.f optimise_solvent_all.f90 + $(FC) $(FFLAGS) -c optimise_solvent_all.f90 subag_scale_hessian.f +@@ -229,7 +225,7 @@ subag_scale_hessian.o: subag_scale_hessian.f optimise_solvent_all.f90 + subcf_scale1.o: subcf_scale1.f optimise_solvent_all.f90 + $(FC) $(FFLAGS) -c optimise_solvent_all.f90 subcf_scale1.f + +-refmac_xml.o: refmac_xml.f optimise_solvent_all.f90 ++refmac_xml.o: refmac_xml.f optimise_solvent_all.f90 optimise_solvent_all.o + $(FC) $(FFLAGS) -c optimise_solvent_all.f90 refmac_xml.f + + hkl_pack.o: hkl_pack.f90 +@@ -239,9 +235,9 @@ subvag.o: subvag.f hkl_pack.f90 + $(FC) $(FFLAGS) -c hkl_pack.f90 subvag.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 ++mol2_file.o: mol2_file.f odb_files.o + $(FC) $(FFLAGS) -c odb_files.f90 mol2_file.f + + odb_files.o: odb_files.f90 elements_module.f90 enerf77mod.f +@@ -250,7 +246,7 @@ odb_files.o: odb_files.f90 elements_module.f90 enerf77mod.f + elements_module.o: elements_module.f90 + $(FC) $(FFLAGS) -c elements_module.f90 + +-make_lib2.o: make_lib2.f odb_files.f90 ++make_lib2.o: make_lib2.f odb_files.o + $(FC) $(FFLAGS) -c odb_files.f90 make_lib2.f + + pdb2libcheck.o: pdb2libcheck.f90 +@@ -260,7 +256,7 @@ 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-5.6.0080.ebuild b/sci-chemistry/refmac/refmac-5.6.0080.ebuild new file mode 100644 index 000000000000..8f6bdbfaa1ce --- /dev/null +++ b/sci-chemistry/refmac/refmac-5.6.0080.ebuild @@ -0,0 +1,71 @@ +# 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-5.6.0080.ebuild,v 1.1 2010/07/03 08:33:57 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}${MY_PV}.tar.gz + test? ( http://dev.gentooexperimental.org/~jlec/distfiles/test-framework.tar.gz )" + +SLOT="0" +LICENSE="ccp4" +KEYWORDS="~amd64 ~x86 ~amd64-linux ~x86-linux" +IUSE="test" + +RDEPEND=" + sci-libs/ccp4-libs + sci-libs/mmdb + >sci-libs/monomer-db-1 + virtual/blas + virtual/lapack" +DEPEND="${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 +} |