From cbb13346d98bc9073268d8cfa084ecdc2e1de9c1 Mon Sep 17 00:00:00 2001 From: "Justin Lecher (jlec)" Date: Tue, 26 May 2009 14:36:29 +0200 Subject: version bump of refmac 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. and guile-www added bug 271283 --- dev-scheme/guile-www/ChangeLog | 32 +++++++++++ dev-scheme/guile-www/Manifest | 6 ++ dev-scheme/guile-www/guile-www-2.24.ebuild | 17 ++++++ dev-scheme/guile-www/metadata.xml | 9 +++ sci-chemistry/refmac/ChangeLog | 10 ++++ sci-chemistry/refmac/Manifest | 8 +-- .../files/5.5.0093-allow-dynamic-linking.patch | 66 ---------------------- .../files/5.5.0094-allow-dynamic-linking.patch | 66 ++++++++++++++++++++++ sci-chemistry/refmac/refmac-5.5.0093.ebuild | 47 --------------- sci-chemistry/refmac/refmac-5.5.0094.ebuild | 47 +++++++++++++++ 10 files changed, 191 insertions(+), 117 deletions(-) create mode 100644 dev-scheme/guile-www/ChangeLog create mode 100644 dev-scheme/guile-www/Manifest create mode 100644 dev-scheme/guile-www/guile-www-2.24.ebuild create mode 100644 dev-scheme/guile-www/metadata.xml delete mode 100644 sci-chemistry/refmac/files/5.5.0093-allow-dynamic-linking.patch create mode 100644 sci-chemistry/refmac/files/5.5.0094-allow-dynamic-linking.patch delete mode 100644 sci-chemistry/refmac/refmac-5.5.0093.ebuild create mode 100644 sci-chemistry/refmac/refmac-5.5.0094.ebuild diff --git a/dev-scheme/guile-www/ChangeLog b/dev-scheme/guile-www/ChangeLog new file mode 100644 index 000000000..64c6760bc --- /dev/null +++ b/dev-scheme/guile-www/ChangeLog @@ -0,0 +1,32 @@ +# ChangeLog for dev-scheme/guile-www +# Copyright 1999-2009 Gentoo Foundation; Distributed under the GPL v2 +# $Header: /var/cvsroot/gentoo-x86/dev-scheme/guile-www/ChangeLog,v 1.5 2008/07/12 12:24:56 hkbst Exp $ + +*guile-www-2.24 (26 May 2009) + + 26 May 2009; Justin Lecher (jlec) + +guile-www-2.24.ebuild, +metadata.xml: + version bump + +*guile-www-2.23 (12 Jul 2008) + + 12 Jul 2008; Marijn Schouten +guile-www-2.23.ebuild: + bump + + 10 Jan 2007; Piotr Jaroszyński guile-www-2.15.ebuild: + Dependency update: dev-util/guile -> dev-scheme/guile. + + 01 Oct 2006; Donnie Berkholz ; metadata.xml: + Transfer to sci-chemistry herd from sci. + + 26 Sep 2006; Donnie Berkholz ; + guile-www-2.15.ebuild: + Stable on x86/ppc. + +*guile-www-2.15 (16 Jun 2006) + + 16 Jun 2006; Donnie Berkholz ; +metadata.xml, + +guile-www-2.15.ebuild: + Add Guile code for HTTP, URL and CGI programming, needed for + sci-chemistry/coot. + diff --git a/dev-scheme/guile-www/Manifest b/dev-scheme/guile-www/Manifest new file mode 100644 index 000000000..6e8f82830 --- /dev/null +++ b/dev-scheme/guile-www/Manifest @@ -0,0 +1,6 @@ +DIST guile-www-2.15.tar.gz 214672 RMD160 21d8e516ea0c515e2f6e00d9f5840973b934bc06 SHA1 b05a65ff70122ffa71c5cf4c46b2602719f892dd SHA256 fc847371dd943d3b136d57f438ec2cfa5f31c6980df7573c851fa280d3c4cfc8 +DIST guile-www-2.23.tar.gz 273202 RMD160 e2455de3837815b5616ea85fd2988d6b4dbe927f SHA1 f69f968e3a5aae21aa896a0f46e3e342baea5ba4 SHA256 8593b6a9fe9d8ee08d154b9825d188ad57ca26c71c36d1fb7a855154bdbef3fa +EBUILD guile-www-2.15.ebuild 608 RMD160 c9943993427be4aa0145b3d8e2c55690748f55a0 SHA1 9ee12a2e5b1c25d1a05cffdb52c71eb2dfaa1bde SHA256 89f9d12edbf0803ac383d8bcfae430041b0591ff720387af0a30325bd06249ca +EBUILD guile-www-2.23.ebuild 601 RMD160 cb31e17a7d5119eeee8042c5b42a36ec2107d989 SHA1 094101d6e973929cd96d37866c311dec36de80b1 SHA256 a290399802f93b9b5591f708e8bef52532516f244e30974cc4866a3102cc1990 +MISC ChangeLog 887 RMD160 7063eeecb5a85878b5656d1646eec251d4a5531b SHA1 3a77adf73d221c91b83aa25e9355ef253f3cd4b9 SHA256 27276647257f559ff49deceb3c168283eaa63aeb65cbf086c31b07ef2365c991 +MISC metadata.xml 258 RMD160 f28967430de9ad28d9e5cc6666d3e507117879ee SHA1 c594a70de8bf8aa9f5766ff8bfd5135e7536d249 SHA256 b6a5e5a499c6846188743b9220fc3c518467023a1aa9dc883d29bd92fb495d75 diff --git a/dev-scheme/guile-www/guile-www-2.24.ebuild b/dev-scheme/guile-www/guile-www-2.24.ebuild new file mode 100644 index 000000000..034f1b19a --- /dev/null +++ b/dev-scheme/guile-www/guile-www-2.24.ebuild @@ -0,0 +1,17 @@ +# Copyright 1999-2009 Gentoo Foundation +# Distributed under the terms of the GNU General Public License v2 +# $Header: /var/cvsroot/gentoo-x86/dev-scheme/guile-www/guile-www-2.23.ebuild,v 1.1 2008/07/12 12:24:56 hkbst Exp $ + +DESCRIPTION="Guile Scheme modules to facilitate HTTP, URL and CGI programming" +HOMEPAGE="http://www.gnuvola.org/software/guile-www/" +SRC_URI="http://www.gnuvola.org/software/guile-www/${P}.tar.gz" +LICENSE="GPL-3" +SLOT="0" +KEYWORDS="~amd64 ~ppc ~x86" +IUSE="" +RDEPEND="dev-scheme/guile" +DEPEND="${RDEPEND}" + +src_install() { + make DESTDIR="${D}" install || die "install failed" +} diff --git a/dev-scheme/guile-www/metadata.xml b/dev-scheme/guile-www/metadata.xml new file mode 100644 index 000000000..797b6c062 --- /dev/null +++ b/dev-scheme/guile-www/metadata.xml @@ -0,0 +1,9 @@ + + + +sci-chemistry + +spyderous@gentoo.org +Donnie Berkholz + + diff --git a/sci-chemistry/refmac/ChangeLog b/sci-chemistry/refmac/ChangeLog index cd2423492..d786dfe83 100644 --- a/sci-chemistry/refmac/ChangeLog +++ b/sci-chemistry/refmac/ChangeLog @@ -2,6 +2,16 @@ # Copyright 1999-2009 Gentoo Foundation; Distributed under the GPL v2 # $Header: $ +*refmac-5.5.0094 (26 May 2009) + + 26 May 2009; Justin Lecher (jlec) + -files/5.5.0093-allow-dynamic-linking.patch, -refmac-5.5.0093.ebuild, + +files/5.5.0094-allow-dynamic-linking.patch, +refmac-5.5.0094.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-5.5.0093 (22 May 2009) 22 May 2009; Justin Lecher (jlec) diff --git a/sci-chemistry/refmac/Manifest b/sci-chemistry/refmac/Manifest index f696d0e5f..e5923c11c 100644 --- a/sci-chemistry/refmac/Manifest +++ b/sci-chemistry/refmac/Manifest @@ -1,14 +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 5.5.0094-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_5.5.0092.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_5.5.0094.tar.gz 1296698 RMD160 fc07b10be0c00627b4c4174f44e0d7a7ae0bf86c SHA1 e4f69497c174e9e60d8b7f57cf456f5aa142c906 SHA256 afb9c971d9c1721a56cd81bdae265d6a3de1860db6615109d3de6624cc9ff8d0 DIST refmac_source_v5.6.0031.tar.gz 1331481 RMD160 ae37017abeb8ba01d8a3318e78987780e3ce5070 SHA1 6f1a6a35bf9e9efba6a60861f69b53aa728c4392 SHA256 80a6e441635df07e06a80a2bbee1bc12781c7d57dd107b83de4baebfd3f99cf4 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-5.5.0094.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 2584 RMD160 cd19a66f42f6453582bf66e5a99da315cc7fe220 SHA1 78a40747e4f18471914469b899f27f2070edb887 SHA256 63149d11693614a7787ae24b903e44871fa6dd1dc6bff70fd8edbcd37cf45bb5 +MISC ChangeLog 2988 RMD160 8a8b1ecf1edeafc2d9b327ff7c51c6cf80b034e8 SHA1 5c762cb946bbd6c999a23438b61dad5a13001d62 SHA256 99df459585fbede011cdc8afd15cbf54729de33d450d63dd2883691172a0a493 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 deleted file mode 100644 index 415ba9d08..000000000 --- a/sci-chemistry/refmac/files/5.5.0093-allow-dynamic-linking.patch +++ /dev/null @@ -1,66 +0,0 @@ ---- 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) $(LLIBCIF) - - clean: - /bin/rm *.o diff --git a/sci-chemistry/refmac/files/5.5.0094-allow-dynamic-linking.patch b/sci-chemistry/refmac/files/5.5.0094-allow-dynamic-linking.patch new file mode 100644 index 000000000..415ba9d08 --- /dev/null +++ b/sci-chemistry/refmac/files/5.5.0094-allow-dynamic-linking.patch @@ -0,0 +1,66 @@ +--- makefile_refmac.inc1.orig 2008-08-01 22:17:14.000000000 -0700 ++++ makefile_refmac.inc1 2008-08-01 22:18:46.000000000 -0700 +@@ -69,9 +69,7 @@ + bridge.o \ + i0.o \ + i1.o \ +-chbevl.o \ +-$(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-5.5.0093.ebuild b/sci-chemistry/refmac/refmac-5.5.0093.ebuild deleted file mode 100644 index d53653bdc..000000000 --- a/sci-chemistry/refmac/refmac-5.5.0093.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-5.5.0094.ebuild b/sci-chemistry/refmac/refmac-5.5.0094.ebuild new file mode 100644 index 000000000..d53653bdc --- /dev/null +++ b/sci-chemistry/refmac/refmac-5.5.0094.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