refmac version bump to ...90

4 files changed, 123 insertions, 1 deletions

diff --git a/sci-chemistry/refmac/ChangeLog b/sci-chemistry/refmac/ChangeLog
index c15630295..18d3c480a 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-5.5.0090 (14 Apr 2009)
+
+  14 Apr 2009; Justin Lecher (jlec) <jlec@j-schmitz.net>
+  +files/5.5.0090-allow-dynamic-linking.patch, +refmac-5.5.0090.ebuild:
+  version bump fixes prossible segf
+
 *refmac-5.5.0089 (13 Mar 2009)
 
   13 Mar 2009; Justin Lecher (jlec) <jlec@j-schmitz.net>
diff --git a/sci-chemistry/refmac/Manifest b/sci-chemistry/refmac/Manifest
index ca89de782..a028c2c1d 100644
--- a/sci-chemistry/refmac/Manifest
+++ b/sci-chemistry/refmac/Manifest
@@ -1,8 +1,11 @@
 AUX 5.5.0088-allow-dynamic-linking.patch 2025 RMD160 b4324061b5468aedce6d37fc17049711231e677d SHA1 d04e47048302bd7df59d470a9657289871f42721 SHA256 410ffe2a7dee8dd30376355298319f7cc413fa2ff0765a1f77f02cb975e4a23a
 AUX 5.5.0089-allow-dynamic-linking.patch 2025 RMD160 b4324061b5468aedce6d37fc17049711231e677d SHA1 d04e47048302bd7df59d470a9657289871f42721 SHA256 410ffe2a7dee8dd30376355298319f7cc413fa2ff0765a1f77f02cb975e4a23a
+AUX 5.5.0090-allow-dynamic-linking.patch 2025 RMD160 b4324061b5468aedce6d37fc17049711231e677d SHA1 d04e47048302bd7df59d470a9657289871f42721 SHA256 410ffe2a7dee8dd30376355298319f7cc413fa2ff0765a1f77f02cb975e4a23a
 DIST refmac_5.5.0088.tar.gz 1295576 RMD160 d266a4d75bbe26701e308030c0e2a4f703bae7ab SHA1 19c1dc25fcbd81610d306f578101969e05599d0f SHA256 3b2a1954b3def25d8afa7c6749af4f6298901ca93648e9b1a9868e7b1b5b9cdf
 DIST refmac_5.5.0089.tar.gz 1295579 RMD160 f75538ac3c5e212226d2bd2b5ae4a9887b66c1bf SHA1 11acadf29aca70d30966d7d0b8ad37144107a671 SHA256 43fa6720d49f09948ec3378d666a0d0d9214bd1e9d7a17cdc5e1ba7220ac46f4
+DIST refmac_5.5.0090.tar.gz 1295599 RMD160 8707ac700f106baaa47831a920de602c2ff9288e SHA1 aefff2001aa3922c170de5ebc87acf07ece698c9 SHA256 4f522003f3d05dbe627c5603d498ebfce76b93df81f46813fdfdd051528db7f4
 EBUILD refmac-5.5.0088.ebuild 1045 RMD160 ab5645566baf7d0dbac1522258377130e837d2a7 SHA1 6dacfd7d27edf0121344e255f5bda678b5701f69 SHA256 dbb5111b9ede779c6345c44400510a0d12f655d89eb0208f9e2ddc2304315c70
 EBUILD refmac-5.5.0089.ebuild 1045 RMD160 ab5645566baf7d0dbac1522258377130e837d2a7 SHA1 6dacfd7d27edf0121344e255f5bda678b5701f69 SHA256 dbb5111b9ede779c6345c44400510a0d12f655d89eb0208f9e2ddc2304315c70
-MISC ChangeLog 716 RMD160 3fcab6c37c64ecf4ba2676f3690ec6a68e16d92a SHA1 79ff5dc11d6bfad1b0e5ba2b145b983db97676ec SHA256 1b15b1f738a2484fd0a45eb3c3f42ae44da995713ed37046ef1e621868527397
+EBUILD refmac-5.5.0090.ebuild 1045 RMD160 ab5645566baf7d0dbac1522258377130e837d2a7 SHA1 6dacfd7d27edf0121344e255f5bda678b5701f69 SHA256 dbb5111b9ede779c6345c44400510a0d12f655d89eb0208f9e2ddc2304315c70
+MISC ChangeLog 914 RMD160 a47057ea2c3aee336ed75a3e1c024a993fe6eee7 SHA1 3827ec88cbf5740e5a11a2aa60ae87d8d584e251 SHA256 3de9fc0a9e56f71808e4fda3d26df8d8a98c5aae8eab68570860ee38d189d863
 MISC metadata.xml 314 RMD160 d8922635160b6047732051715291e8553b513bba SHA1 b53fc6fb6cf908093794b876e729606c00351937 SHA256 50a519ddbcef4ad4f76175df36849a076d20adbb6340fdba292175b70c0d9719
diff --git a/sci-chemistry/refmac/files/5.5.0090-allow-dynamic-linking.patch b/sci-chemistry/refmac/files/5.5.0090-allow-dynamic-linking.patch
new file mode 100644
index 000000000..415ba9d08
--- /dev/null
+++ b/sci-chemistry/refmac/files/5.5.0090-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
new file mode 100644
index 000000000..d53653bdc
--- /dev/null
+++ b/sci-chemistry/refmac/refmac-5.5.0090.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
+}