From: Justin Lecher Date: Thu, 13 May 2010 09:59:22 +0000 (+0000) Subject: Version Bump X-Git-Url: http://git.tremily.us/?a=commitdiff_plain;h=3e53f623707b3736ab806f2fa9374f65274bc3dc;p=gentoo.git Version Bump Package-Manager: portage-2.2_rc67/cvs/Linux x86_64 --- diff --git a/sci-chemistry/refmac/ChangeLog b/sci-chemistry/refmac/ChangeLog index 6383d6808eb0..30c1710d47e7 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 1.3 2010/03/28 20:43:07 jlec Exp $ +# $Header: /var/cvsroot/gentoo-x86/sci-chemistry/refmac/ChangeLog,v 1.4 2010/05/13 09:59:22 jlec Exp $ + +*refmac-5.5.0110 (13 May 2010) + + 13 May 2010; Justin Lecher + +files/5.5.0110-allow-dynamic-linking.patch, +refmac-5.5.0110.ebuild: + Version Bump 28 Mar 2010; Justin Lecher refmac-5.5.0109.ebuild: Keyworded for ~x86-linux ~amd64-linux diff --git a/sci-chemistry/refmac/Manifest b/sci-chemistry/refmac/Manifest index 1b07abc3f74f..05cca5439c6e 100644 --- a/sci-chemistry/refmac/Manifest +++ b/sci-chemistry/refmac/Manifest @@ -3,15 +3,18 @@ Hash: SHA1 AUX 5.5-allow-dynamic-linking.patch 2025 RMD160 b4324061b5468aedce6d37fc17049711231e677d SHA1 d04e47048302bd7df59d470a9657289871f42721 SHA256 410ffe2a7dee8dd30376355298319f7cc413fa2ff0765a1f77f02cb975e4a23a AUX 5.5-test.log.patch 1146 RMD160 0ea6293e8ecde3b9ae12658a523e3c30a5c9f01b SHA1 d026fdea6a487754f7e48ec24bcf4851a613b6d1 SHA256 d2c2a09f44e525dc255bc2ac93ca4194b24ca1fe58c31f0e3b5c32e439dfe2e7 +AUX 5.5.0110-allow-dynamic-linking.patch 2265 RMD160 191b90c619a3a0a6cd71b819b4517d639f9912e0 SHA1 23df6c19a6fa9a41ed19d4ec36bd3130ffdb40b7 SHA256 ed10babfa6f9521b1b8e0dd574aa5fa4207d64bcd57332e97f0b35039b66942b 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 EBUILD refmac-5.5.0109.ebuild 1736 RMD160 4db9926be6b3cb3d17e7e1dd1bbf56d2bf34271a SHA1 daf39f7a3d57471dbaf2c217ca49fb38a36dd911 SHA256 26ce3f5cdddae57f5f6b35ed835cb826f8f3d4de3f645abec040754cc92fff9e -MISC ChangeLog 672 RMD160 debf5af13a4e8043ee87f5eec0ab8f350a9fe1da SHA1 acbd171de3cac9a91f421e21b3c51232d79f1d07 SHA256 f7e742ebab04dc7592ee15c5536fc360fd7da72ba695ac8116fe3c686b72ab13 +EBUILD refmac-5.5.0110.ebuild 1701 RMD160 883737572c45172240906385abd54cfe8b951046 SHA1 232c1a1e96fdd29b0a92ff27c4326e37be785cd8 SHA256 dfcab3e1100049e6af534c3d2803114ff2a64fc47a0b533ffd90f0ec11febe23 +MISC ChangeLog 839 RMD160 ec3b096c7acbcad631b82983c307ad833922193a SHA1 bce52666de418a198c24299d650a9eb977db6bdf SHA256 8585f199d9bf4b1a7aaaf7a257e7ea34ca7e72c7efc38a841f21a636fc50b0ee MISC metadata.xml 311 RMD160 df83b13d491a71b729455b664088d89ddbde1c8c SHA1 fffd2a5645181aa12ac9b6f74da9a011cdcf1b97 SHA256 782521c7e16d7eec82d7b7e7c43102806e7f72bc7366401808b1e1ac6e26045a -----BEGIN PGP SIGNATURE----- Version: GnuPG v2.0.14 (GNU/Linux) -iEYEARECAAYFAkuvv2EACgkQgAnW8HDreRYn1wCeJOTBAuFmnxvfeuC+usq4gq08 -OjUAn0Mmy9b/ccmCxo+9EXFvGmDoZr8Y -=+E4q +iEYEARECAAYFAkvrzYQACgkQgAnW8HDreRZy0QCgolSmun4tJtRWrXYDiE6vJkd9 +tZAAn1fQG9g1H7wG2+hnzan+jr6SJNnM +=N0a/ -----END PGP SIGNATURE----- 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 new file mode 100644 index 000000000000..480d6025575a --- /dev/null +++ b/sci-chemistry/refmac/files/5.5.0110-allow-dynamic-linking.patch @@ -0,0 +1,68 @@ +diff --git a/makefile_refmac.inc1 b/makefile_refmac.inc1 +index 371d84d..643bf5e 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 +@@ -154,16 +147,16 @@ 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 diff --git a/sci-chemistry/refmac/refmac-5.5.0110.ebuild b/sci-chemistry/refmac/refmac-5.5.0110.ebuild new file mode 100644 index 000000000000..0fbf693c30d6 --- /dev/null +++ b/sci-chemistry/refmac/refmac-5.5.0110.ebuild @@ -0,0 +1,67 @@ +# 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-5.5.0110.ebuild,v 1.1 2010/05/13 09:59:22 jlec Exp $ + +EAPI="2" + +inherit fortran base 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 ~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 "${FILESDIR}"/$(get_version_component_range 1-2 ${PV})-test.log.patch +} + +src_compile() { + emake \ + FC=$(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="-llapack -lblas" \ + || 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 makecif; do + dobin ${i} || die + done + dosym refmac /usr/bin/refmac5 || die + dodoc refmac_keywords.pdf bugs_and_features.pdf || die +}