refmac bump

4 files changed, 124 insertions, 1 deletions

diff --git a/sci-chemistry/refmac/ChangeLog b/sci-chemistry/refmac/ChangeLog
index 81d743de2..9f39659f7 100644
--- a/sci-chemistry/refmac/ChangeLog
+++ b/sci-chemistry/refmac/ChangeLog
@@ -2,6 +2,12 @@
 # Copyright 1999-2009 Gentoo Foundation; Distributed under the GPL v2
 # $Header: $
 
+*refmac-5.5.0098 (22 Jun 2009)
+
+  22 Jun 2009; Justin Lecher (jlec) <jlec@j-schmitz.net>
+  +files/5.5-allow-dynamic-linking.patch, +refmac-5.5.0098.ebuild:
+  version bump and switch MAJOR.MINOR patches
+
 *refmac-5.6.0038 (19 Jun 2009)
 
   19 Jun 2009; Justin Lecher (jlec) <jlec@j-schmitz.net>
diff --git a/sci-chemistry/refmac/Manifest b/sci-chemistry/refmac/Manifest
index 704e61c4f..0995d224e 100644
--- a/sci-chemistry/refmac/Manifest
+++ b/sci-chemistry/refmac/Manifest
@@ -1,3 +1,4 @@
+AUX 5.5-allow-dynamic-linking.patch 2025 RMD160 b4324061b5468aedce6d37fc17049711231e677d SHA1 d04e47048302bd7df59d470a9657289871f42721 SHA256 410ffe2a7dee8dd30376355298319f7cc413fa2ff0765a1f77f02cb975e4a23a
 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
@@ -8,10 +9,12 @@ DIST refmac5.6_source_v5.6.0038.tar.gz 1482323 RMD160 cedf019c572ef3958bf1864034
 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
 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-5.6.0033.ebuild 1200 RMD160 cf0754afc5ea07df2fed0baf7599dfcd32e43ada SHA1 7811acc5a91e73b0ee85a340e489f1bc95eecefb SHA256 ee98605ab90acd94b7f3e669ef41e9e4fff309cacd9cb188ddc2c7cfa360aa17
 EBUILD refmac-5.6.0038.ebuild 1193 RMD160 d22f3798d0e15551ebb5cead888287649ad1046e SHA1 1cc508e069f7b925f83ffd2500d0841746332408 SHA256 08b1c1f63a3aefb09c030eb60aa8757af734eed715ee1d7011004d29ab4a1274
-MISC ChangeLog 4493 RMD160 f0db0021ca4408077437505fb5d5d3c479c18e87 SHA1 e4a165d4e9de3c67170d590c5d64a3e86ff4bcf0 SHA256 00d2a31463f93dc34dc442996a8a423a2864ffd5ad0c98c7a0549198c9504ad3
+MISC ChangeLog 4696 RMD160 3ce7f00f6dd1473d3990d67f8db6d8d9ad3f5b4f SHA1 802a5fab26f67dc8f02b2a73bc2d25b04e74db13 SHA256 4cba5804df91b68e9c28cdb6f9a242384a10698c1e84229208052f11875cb7da
 MISC metadata.xml 314 RMD160 d8922635160b6047732051715291e8553b513bba SHA1 b53fc6fb6cf908093794b876e729606c00351937 SHA256 50a519ddbcef4ad4f76175df36849a076d20adbb6340fdba292175b70c0d9719
diff --git a/sci-chemistry/refmac/files/5.5-allow-dynamic-linking.patch b/sci-chemistry/refmac/files/5.5-allow-dynamic-linking.patch
new file mode 100644
index 000000000..415ba9d08
--- /dev/null
+++ b/sci-chemistry/refmac/files/5.5-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-5.5.0098.ebuild b/sci-chemistry/refmac/refmac-5.5.0098.ebuild
new file mode 100644
index 000000000..f66da7081
--- /dev/null
+++ b/sci-chemistry/refmac/refmac-5.5.0098.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
+}