refmac bump

5 files changed, 73 insertions, 5 deletions

diff --git a/sci-chemistry/refmac/ChangeLog b/sci-chemistry/refmac/ChangeLog
index 9f39659f7..43996d93c 100644
--- a/sci-chemistry/refmac/ChangeLog
+++ b/sci-chemistry/refmac/ChangeLog
@@ -2,6 +2,24 @@
 # Copyright 1999-2009 Gentoo Foundation; Distributed under the GPL v2
 # $Header: $
 
+*refmac-5.6.0039 (23 Jun 2009)
+
+  23 Jun 2009; Justin Lecher (jlec) <jlec@j-schmitz.net>
+  -refmac-5.6.0038.ebuild, +refmac-5.6.0039.ebuild:
+  experimental version bump and changed to MAJOR.MINOR versioned patches
+
+*refmac-5.5.0099 (23 Jun 2009)
+
+  23 Jun 2009; Justin Lecher (jlec) <jlec@j-schmitz.net>
+  +refmac-5.5.0099.ebuild:
+  In cases of twin if the program first decided that there are many twin
+  operators (e.g. four) and later removed some of these operators (e.g. the
+  number of remaining twin domains is two) then highest resolution was not
+  always correct. It was related with the fact the the resolution the
+  program works with is the highest resolution after applying all twin
+  operators. If twin is not merohedral then this resolution may be different
+  from actual resolution of the data. This bug has now been fixed.
+
 *refmac-5.5.0098 (22 Jun 2009)
 
   22 Jun 2009; Justin Lecher (jlec) <jlec@j-schmitz.net>
diff --git a/sci-chemistry/refmac/Manifest b/sci-chemistry/refmac/Manifest
index 0995d224e..d87066916 100644
--- a/sci-chemistry/refmac/Manifest
+++ b/sci-chemistry/refmac/Manifest
@@ -2,19 +2,21 @@ AUX 5.5-allow-dynamic-linking.patch 2025 RMD160 b4324061b5468aedce6d37fc17049711
 AUX 5.5.0092-allow-dynamic-linking.patch 2025 RMD160 b4324061b5468aedce6d37fc17049711231e677d SHA1 d04e47048302bd7df59d470a9657289871f42721 SHA256 410ffe2a7dee8dd30376355298319f7cc413fa2ff0765a1f77f02cb975e4a23a
 AUX 5.5.0095-allow-dynamic-linking.patch 2025 RMD160 b4324061b5468aedce6d37fc17049711231e677d SHA1 d04e47048302bd7df59d470a9657289871f42721 SHA256 410ffe2a7dee8dd30376355298319f7cc413fa2ff0765a1f77f02cb975e4a23a
 AUX 5.5.0097-allow-dynamic-linking.patch 2025 RMD160 b4324061b5468aedce6d37fc17049711231e677d SHA1 d04e47048302bd7df59d470a9657289871f42721 SHA256 410ffe2a7dee8dd30376355298319f7cc413fa2ff0765a1f77f02cb975e4a23a
+AUX 5.6-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
-AUX 5.6.0038-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 refmac5.6_source_v5.6.0038.tar.gz 1482323 RMD160 cedf019c572ef3958bf1864034f98f00eda6dde3 SHA1 aa5cca7cc8527eef66b4f692a8c6bb0e2d58a0c4 SHA256 2d42d154e1990150b47e84669f7c7882344f843169c0091905a05c7e5df4aa73
+DIST refmac5.6_source_v5.6.0039.tar.gz 1482386 RMD160 c2a7d116a7764cae3e2ebfaafb95febe71f919a3 SHA1 ea7ce4d6ca5c0603bcab342a754d03c3791536dc SHA256 700ea3753d842e3b8eb154cf7e0d3c9378716c9c1f0c236078e8d182d56d2c77
 DIST refmac_5.5.0092.tar.gz 1296668 RMD160 1f48cb3d2cfc3b7e91bcde5caa212813d63b20be SHA1 35497b7986ad4861518077f5e06937851cbeb4ff SHA256 6aabf0af882605a2dc73b29f42e8dee34be0888f667befb7342576b2df84623d
 DIST refmac_5.5.0095.tar.gz 1297509 RMD160 bbf3f3cf43c6aaba08864d7e76a795c0b22395d4 SHA1 06bb2c0567e09cc04a5443f033b9c5b7d50f9515 SHA256 1e781566c320e63c3769e59e7a14ea8c7da2f81d6d88ec3a8cc196f14da8d694
 DIST refmac_5.5.0097.tar.gz 1297620 RMD160 e3e5cfe977d677f5efd0c5419d638d0fe3c20334 SHA1 873b5adbacde2fb1912d37a519acc4860c14e68a SHA256 5219949741d422244fca19d01ff675786deb08c6699f2c0e53008170ccbfcabd
 DIST refmac_5.5.0098.tar.gz 1298071 RMD160 5a7d2937727ae83327572bea5d35cca93e4fdfcc SHA1 c27c6cb0cce70ea8994b26fc26d60bb421afa84b SHA256 bd1ea457a6f6c79e56270dd128785d05403fb78263f0ec225c4a8c86f4e002c9
+DIST refmac_5.5.0099.tar.gz 1298129 RMD160 2a5820d62f590a45a6c3ca66b3691b7fb1b66bc3 SHA1 78d798fe4db63d5eb4748c905832a59ef75ddea0 SHA256 c680fa40a1417efa9f6725f45c73b7bada09a3bcf5d24993369ebccbaeea90a6
 EBUILD refmac-5.5.0092.ebuild 1045 RMD160 ab5645566baf7d0dbac1522258377130e837d2a7 SHA1 6dacfd7d27edf0121344e255f5bda678b5701f69 SHA256 dbb5111b9ede779c6345c44400510a0d12f655d89eb0208f9e2ddc2304315c70
 EBUILD refmac-5.5.0095.ebuild 1011 RMD160 c129e2b3178a6b84428233940befe445fd86a4d6 SHA1 9e99428fadbb4a28be7a7208dce74d82c13ed063 SHA256 6530e9486e2769a9f0b9c139a0e000c5661e9b64582cdbb2b7798ce001367aae
 EBUILD refmac-5.5.0097.ebuild 1033 RMD160 80c2fc2f65ac928413aa1b6de16bd1d708562272 SHA1 188fcb5b2847abe298b6c607b619fe68db93ad15 SHA256 669c5de8be79e006c30b88789e2711eb71e54da4cfb411fb9b284139c110043c
 EBUILD refmac-5.5.0098.ebuild 1080 RMD160 7829b2a9db340fcf141d450bb5ac7c69669374b4 SHA1 978647cca646c89d5f4b6c863464265b34534fc0 SHA256 8c45013ac7949cc2f3f3ed949abecc3cdaf06629b01d5b4da30ba375899451de
+EBUILD refmac-5.5.0099.ebuild 1080 RMD160 7829b2a9db340fcf141d450bb5ac7c69669374b4 SHA1 978647cca646c89d5f4b6c863464265b34534fc0 SHA256 8c45013ac7949cc2f3f3ed949abecc3cdaf06629b01d5b4da30ba375899451de
 EBUILD refmac-5.6.0033.ebuild 1200 RMD160 cf0754afc5ea07df2fed0baf7599dfcd32e43ada SHA1 7811acc5a91e73b0ee85a340e489f1bc95eecefb SHA256 ee98605ab90acd94b7f3e669ef41e9e4fff309cacd9cb188ddc2c7cfa360aa17
-EBUILD refmac-5.6.0038.ebuild 1193 RMD160 d22f3798d0e15551ebb5cead888287649ad1046e SHA1 1cc508e069f7b925f83ffd2500d0841746332408 SHA256 08b1c1f63a3aefb09c030eb60aa8757af734eed715ee1d7011004d29ab4a1274
-MISC ChangeLog 4696 RMD160 3ce7f00f6dd1473d3990d67f8db6d8d9ad3f5b4f SHA1 802a5fab26f67dc8f02b2a73bc2d25b04e74db13 SHA256 4cba5804df91b68e9c28cdb6f9a242384a10698c1e84229208052f11875cb7da
+EBUILD refmac-5.6.0039.ebuild 1228 RMD160 6959dd7c182ee0eda8ebf055b3c336ea5434a499 SHA1 95560258fb4402fde15c107722a4b976cce7a7fe SHA256 797c51f62f8cc763dba35bd89a9a997d9956669a6aa99bf64766a9af02270b24
+MISC ChangeLog 5537 RMD160 46799d82b90eb01eb2f48aaefb780ec2ba9629e4 SHA1 18c2c5d920e11a08b90a38995f4575886f6d004f SHA256 a9a202018ff4427ee0662577101666ab4b67696efb99ded54d67b3e22251006d
 MISC metadata.xml 314 RMD160 d8922635160b6047732051715291e8553b513bba SHA1 b53fc6fb6cf908093794b876e729606c00351937 SHA256 50a519ddbcef4ad4f76175df36849a076d20adbb6340fdba292175b70c0d9719
diff --git a/sci-chemistry/refmac/files/5.6.0038-allow-dynamic-linking.patch b/sci-chemistry/refmac/files/5.6-allow-dynamic-linking.patch
index c67921eab..c67921eab 100644
--- a/sci-chemistry/refmac/files/5.6.0038-allow-dynamic-linking.patch
+++ b/sci-chemistry/refmac/files/5.6-allow-dynamic-linking.patch
diff --git a/sci-chemistry/refmac/refmac-5.5.0099.ebuild b/sci-chemistry/refmac/refmac-5.5.0099.ebuild
new file mode 100644
index 000000000..f66da7081
--- /dev/null
+++ b/sci-chemistry/refmac/refmac-5.5.0099.ebuild
@@ -0,0 +1,48 @@
+# Copyright 1999-2009 Gentoo Foundation
+# Distributed under the terms of the GNU General Public License v2
+# $Header: $
+
+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"
+
+SLOT="0"
+LICENSE="ccp4"
+KEYWORDS="~amd64 ~x86"
+IUSE=""
+RESTRICT="mirror"
+
+RDEPEND="virtual/lapack
+	virtual/blas
+	sci-libs/ccp4-libs"
+DEPEND="${RDEPEND}"
+
+S="${WORKDIR}"
+
+PATCHES=(
+	"${FILESDIR}"/$(get_version_component_range 1-2 ${PV})-allow-dynamic-linking.patch
+	)
+
+src_compile() {
+	emake \
+		FC=$(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 ${i} || die
+	done
+	dosym refmac /usr/bin/refmac5 || die
+	dodoc refmac_keywords.pdf bugs_and_features.pdf || die
+}
diff --git a/sci-chemistry/refmac/refmac-5.6.0038.ebuild b/sci-chemistry/refmac/refmac-5.6.0039.ebuild
index 9e3bfd904..6d40e0bfb 100644
--- a/sci-chemistry/refmac/refmac-5.6.0038.ebuild
+++ b/sci-chemistry/refmac/refmac-5.6.0039.ebuild
@@ -26,7 +26,7 @@ DEPEND="${RDEPEND}"
 S="${WORKDIR}"
 
 PATCHES=(
-	"${FILESDIR}"/${PV}-allow-dynamic-linking.patch
+	"${FILESDIR}"/$(get_version_component_range 1-2 ${PV})-allow-dynamic-linking.patch
 )
 
 src_compile() {