From 82b342ec0e5e714aa61e616027a43cb7d229c14e Mon Sep 17 00:00:00 2001 From: "Justin Lecher (jlec)" Date: Fri, 22 May 2009 09:03:13 +0200 Subject: refmac version bump --- sci-chemistry/refmac/ChangeLog | 9 +++ sci-chemistry/refmac/Manifest | 7 ++- .../files/5.5.0093-allow-dynamic-linking.patch | 66 ++++++++++++++++++++++ sci-chemistry/refmac/refmac-5.5.0090.ebuild | 47 --------------- sci-chemistry/refmac/refmac-5.5.0093.ebuild | 47 +++++++++++++++ 5 files changed, 126 insertions(+), 50 deletions(-) create mode 100644 sci-chemistry/refmac/files/5.5.0093-allow-dynamic-linking.patch delete mode 100644 sci-chemistry/refmac/refmac-5.5.0090.ebuild create mode 100644 sci-chemistry/refmac/refmac-5.5.0093.ebuild (limited to 'sci-chemistry/refmac') diff --git a/sci-chemistry/refmac/ChangeLog b/sci-chemistry/refmac/ChangeLog index b89573cc3..cd2423492 100644 --- a/sci-chemistry/refmac/ChangeLog +++ b/sci-chemistry/refmac/ChangeLog @@ -2,6 +2,15 @@ # Copyright 1999-2009 Gentoo Foundation; Distributed under the GPL v2 # $Header: $ +*refmac-5.5.0093 (22 May 2009) + + 22 May 2009; Justin Lecher (jlec) + +files/5.5.0093-allow-dynamic-linking.patch, -refmac-5.5.0090.ebuild, + +refmac-5.5.0093.ebuild: + A problem related with TLS has been fixed. The problem was that not in all + cycle TLS contributions were added to B values and that could make + refinement unstable. + *refmac-5.5.0092 (18 May 2009) 18 May 2009; Justin Lecher (jlec) diff --git a/sci-chemistry/refmac/Manifest b/sci-chemistry/refmac/Manifest index 4a9c79c8a..f696d0e5f 100644 --- a/sci-chemistry/refmac/Manifest +++ b/sci-chemistry/refmac/Manifest @@ -1,13 +1,14 @@ AUX 5.5.0092-allow-dynamic-linking.patch 2025 RMD160 b4324061b5468aedce6d37fc17049711231e677d SHA1 d04e47048302bd7df59d470a9657289871f42721 SHA256 410ffe2a7dee8dd30376355298319f7cc413fa2ff0765a1f77f02cb975e4a23a +AUX 5.5.0093-allow-dynamic-linking.patch 2025 RMD160 b4324061b5468aedce6d37fc17049711231e677d SHA1 d04e47048302bd7df59d470a9657289871f42721 SHA256 410ffe2a7dee8dd30376355298319f7cc413fa2ff0765a1f77f02cb975e4a23a AUX 5.6.0031-allow-dynamic-linking.patch 1178 RMD160 8222b326a7f2d80d1d6202f8761c9bd4bb3ac797 SHA1 07484f5c65e35823963a712ac378bc64dafc0e5d SHA256 24e40c994ce76668e62e2374e41ece1d89fb4c59ab185d3c6eb9c3e76d4610fb AUX 5.6.0033-allow-dynamic-linking.patch 1178 RMD160 8222b326a7f2d80d1d6202f8761c9bd4bb3ac797 SHA1 07484f5c65e35823963a712ac378bc64dafc0e5d SHA256 24e40c994ce76668e62e2374e41ece1d89fb4c59ab185d3c6eb9c3e76d4610fb DIST refmac5.6_source_v5.6.0033.tar.gz 1333417 RMD160 0f6072d573beb0f03df33e988d9b101b77c52d6f SHA1 5cdaa083aae142d3aba8e764c8e7c8397e3b5c77 SHA256 591ce4d141fda1086bf5797b3a134a89d2618eaa6ff3a4c9ffa10de331d6265e -DIST refmac_5.5.0090.tar.gz 1295599 RMD160 8707ac700f106baaa47831a920de602c2ff9288e SHA1 aefff2001aa3922c170de5ebc87acf07ece698c9 SHA256 4f522003f3d05dbe627c5603d498ebfce76b93df81f46813fdfdd051528db7f4 DIST refmac_5.5.0092.tar.gz 1296668 RMD160 1f48cb3d2cfc3b7e91bcde5caa212813d63b20be SHA1 35497b7986ad4861518077f5e06937851cbeb4ff SHA256 6aabf0af882605a2dc73b29f42e8dee34be0888f667befb7342576b2df84623d +DIST refmac_5.5.0093.tar.gz 1296667 RMD160 90af8a0af9f5e28597b6005fdfa84c909371aa94 SHA1 ab562cc2ff858378ad35090b9619aaa109b40ab2 SHA256 79ab195b9244dc30953febad24a10d0687067a1d10e3224fafce83be928026f8 DIST refmac_source_v5.6.0031.tar.gz 1331481 RMD160 ae37017abeb8ba01d8a3318e78987780e3ce5070 SHA1 6f1a6a35bf9e9efba6a60861f69b53aa728c4392 SHA256 80a6e441635df07e06a80a2bbee1bc12781c7d57dd107b83de4baebfd3f99cf4 -EBUILD refmac-5.5.0090.ebuild 1045 RMD160 ab5645566baf7d0dbac1522258377130e837d2a7 SHA1 6dacfd7d27edf0121344e255f5bda678b5701f69 SHA256 dbb5111b9ede779c6345c44400510a0d12f655d89eb0208f9e2ddc2304315c70 EBUILD refmac-5.5.0092.ebuild 1045 RMD160 ab5645566baf7d0dbac1522258377130e837d2a7 SHA1 6dacfd7d27edf0121344e255f5bda678b5701f69 SHA256 dbb5111b9ede779c6345c44400510a0d12f655d89eb0208f9e2ddc2304315c70 +EBUILD refmac-5.5.0093.ebuild 1045 RMD160 ab5645566baf7d0dbac1522258377130e837d2a7 SHA1 6dacfd7d27edf0121344e255f5bda678b5701f69 SHA256 dbb5111b9ede779c6345c44400510a0d12f655d89eb0208f9e2ddc2304315c70 EBUILD refmac-5.6.0031.ebuild 1062 RMD160 88e1065c6899b09e943bf2b3365d36bda4fd3bc0 SHA1 c811d1771f2384347382ffb532442f2d5a1b264f SHA256 2379b4b9e19f0079fe0350f3864c7bb9a1618a48e0d6c54c0497b20f1848f61b EBUILD refmac-5.6.0033.ebuild 1200 RMD160 cf0754afc5ea07df2fed0baf7599dfcd32e43ada SHA1 7811acc5a91e73b0ee85a340e489f1bc95eecefb SHA256 ee98605ab90acd94b7f3e669ef41e9e4fff309cacd9cb188ddc2c7cfa360aa17 -MISC ChangeLog 2226 RMD160 dce9a453a3141a8ebbdb7f1b0f79e2a983de3ee7 SHA1 6cd8a592dd7decb53fc9f39652e7edd4c918b47e SHA256 5fecb7aa87b61f7c3547f146831d0cc86c37ac7a117d11f6399fee96d6ee2066 +MISC ChangeLog 2584 RMD160 cd19a66f42f6453582bf66e5a99da315cc7fe220 SHA1 78a40747e4f18471914469b899f27f2070edb887 SHA256 63149d11693614a7787ae24b903e44871fa6dd1dc6bff70fd8edbcd37cf45bb5 MISC metadata.xml 314 RMD160 d8922635160b6047732051715291e8553b513bba SHA1 b53fc6fb6cf908093794b876e729606c00351937 SHA256 50a519ddbcef4ad4f76175df36849a076d20adbb6340fdba292175b70c0d9719 diff --git a/sci-chemistry/refmac/files/5.5.0093-allow-dynamic-linking.patch b/sci-chemistry/refmac/files/5.5.0093-allow-dynamic-linking.patch new file mode 100644 index 000000000..415ba9d08 --- /dev/null +++ b/sci-chemistry/refmac/files/5.5.0093-allow-dynamic-linking.patch @@ -0,0 +1,66 @@ +--- makefile_refmac.inc1.orig 2008-08-01 22:17:14.000000000 -0700 ++++ makefile_refmac.inc1 2008-08-01 22:18:46.000000000 -0700 +@@ -69,9 +69,7 @@ + bridge.o \ + i0.o \ + i1.o \ +-chbevl.o \ +-$(LLIBCIF) \ +-$(LLIBLAPACK) ++chbevl.o + #$(LLIBCCP) \ + #crt0.o \ + +@@ -95,8 +93,7 @@ + emin.o \ + libcheck_min.o \ + mol2_file.o \ +-sdf_files.o \ +-$(LLIBCCP) ++sdf_files.o + + SUBM = \ + main_makecif.o \ +@@ -116,9 +113,7 @@ + make_PDB.o \ + makecif.o \ + make_unix_ccp4.o \ +-make_vdw.o \ +-$(LLIBCCP) \ +-$(LLIBCIF) ++make_vdw.o + + SUBT = \ + tlsgroups.o \ +@@ -142,9 +137,7 @@ + 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 @@ + all: refmac libcheck makecif + + refmac: $(SUBR) +- $(FC) $(FFLAGS) -o refmac${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-5.5.0090.ebuild b/sci-chemistry/refmac/refmac-5.5.0090.ebuild deleted file mode 100644 index d53653bdc..000000000 --- a/sci-chemistry/refmac/refmac-5.5.0090.ebuild +++ /dev/null @@ -1,47 +0,0 @@ -# Copyright 1999-2009 Gentoo Foundation -# Distributed under the terms of the GNU General Public License v2 -# $Header: $ - -inherit eutils fortran toolchain-funcs - -DESCRIPTION="Macromolecular crystallographic refinement program" -HOMEPAGE="http://www.ysbl.york.ac.uk/~garib/refmac/" -SRC_URI="${HOMEPAGE}data/refmac_stable/refmac_${PV}.tar.gz" -LICENSE="ccp4" -SLOT="0" -KEYWORDS="~amd64 ~x86" -IUSE="" -RESTRICT="mirror" -RDEPEND="virtual/lapack - virtual/blas - sci-libs/ccp4-libs" -DEPEND="${RDEPEND}" -S="${WORKDIR}" - -src_unpack() { - unpack ${A} - cd "${S}" - epatch "${FILESDIR}"/${PV}-allow-dynamic-linking.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_install() { - for i in refmac libcheck makecif; do - dobin ${i} || die - done - dosym refmac /usr/bin/refmac5 || die - dodoc refmac_keywords.pdf || die -} diff --git a/sci-chemistry/refmac/refmac-5.5.0093.ebuild b/sci-chemistry/refmac/refmac-5.5.0093.ebuild new file mode 100644 index 000000000..d53653bdc --- /dev/null +++ b/sci-chemistry/refmac/refmac-5.5.0093.ebuild @@ -0,0 +1,47 @@ +# Copyright 1999-2009 Gentoo Foundation +# Distributed under the terms of the GNU General Public License v2 +# $Header: $ + +inherit eutils fortran toolchain-funcs + +DESCRIPTION="Macromolecular crystallographic refinement program" +HOMEPAGE="http://www.ysbl.york.ac.uk/~garib/refmac/" +SRC_URI="${HOMEPAGE}data/refmac_stable/refmac_${PV}.tar.gz" +LICENSE="ccp4" +SLOT="0" +KEYWORDS="~amd64 ~x86" +IUSE="" +RESTRICT="mirror" +RDEPEND="virtual/lapack + virtual/blas + sci-libs/ccp4-libs" +DEPEND="${RDEPEND}" +S="${WORKDIR}" + +src_unpack() { + unpack ${A} + cd "${S}" + epatch "${FILESDIR}"/${PV}-allow-dynamic-linking.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_install() { + for i in refmac libcheck makecif; do + dobin ${i} || die + done + dosym refmac /usr/bin/refmac5 || die + dodoc refmac_keywords.pdf || die +} -- cgit v1.2.3-65-gdbad