refmac bump and fix the eclass usage

6 files changed, 129 insertions, 5 deletions

diff --git a/sci-chemistry/refmac/ChangeLog b/sci-chemistry/refmac/ChangeLog
index baaaecd85..e711297a9 100644
--- a/sci-chemistry/refmac/ChangeLog
+++ b/sci-chemistry/refmac/ChangeLog
@@ -2,6 +2,13 @@
 # Copyright 1999-2009 Gentoo Foundation; Distributed under the GPL v2
 # $Header: $
 
+*refmac-5.5.0097 (08 Jun 2009)
+
+  08 Jun 2009; Justin Lecher (jlec) <jlec@j-schmitz.net>
+  +files/5.5.0097-allow-dynamic-linking.patch, refmac-5.5.0095.ebuild,
+  +refmac-5.5.0097.ebuild, refmac-5.6.0036.ebuild:
+  version bump and QA of the last QA
+
   05 Jun 2009; Justin Lecher (jlec) <jlec@j-schmitz.net>
   refmac-5.5.0095.ebuild, refmac-5.6.0036.ebuild:
   make it more straight
diff --git a/sci-chemistry/refmac/Manifest b/sci-chemistry/refmac/Manifest
index 66550901b..891f1465d 100644
--- a/sci-chemistry/refmac/Manifest
+++ b/sci-chemistry/refmac/Manifest
@@ -1,14 +1,17 @@
 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 5.6.0033-allow-dynamic-linking.patch 1178 RMD160 8222b326a7f2d80d1d6202f8761c9bd4bb3ac797 SHA1 07484f5c65e35823963a712ac378bc64dafc0e5d SHA256 24e40c994ce76668e62e2374e41ece1d89fb4c59ab185d3c6eb9c3e76d4610fb
 AUX 5.6.0036-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_v5.6.0036.tar.gz 1429255 RMD160 f17c0e59dff15ea60fd04e840dbf8b28766971a9 SHA1 7f6d95b7827fa4db9909d64e1e9c781b9db51041 SHA256 aa0093e061606c93ae17aad658988c045e1c22e148c7a18256d79fb6ecbd0199
 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
 EBUILD refmac-5.5.0092.ebuild 1045 RMD160 ab5645566baf7d0dbac1522258377130e837d2a7 SHA1 6dacfd7d27edf0121344e255f5bda678b5701f69 SHA256 dbb5111b9ede779c6345c44400510a0d12f655d89eb0208f9e2ddc2304315c70
-EBUILD refmac-5.5.0095.ebuild 1011 RMD160 27697288404425d51ff787028955f1816e18fa5f SHA1 393bf0b01bb77cb17e390543e3a6aad723336cea SHA256 36cc3cffcffc18436b02e0a0e5643d531bbbcacfb238e160c2c714055692cf9d
+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-5.6.0033.ebuild 1200 RMD160 cf0754afc5ea07df2fed0baf7599dfcd32e43ada SHA1 7811acc5a91e73b0ee85a340e489f1bc95eecefb SHA256 ee98605ab90acd94b7f3e669ef41e9e4fff309cacd9cb188ddc2c7cfa360aa17
-EBUILD refmac-5.6.0036.ebuild 1165 RMD160 eb4ef3db8de20e234d25297f9034e6467c917e02 SHA1 3030348c2ce4096a0cd967271d76d502dabf0f2c SHA256 0ac362a4acb8825e7768b1b876c2dc2529feec69ae385f6022acfd80cf8bdb16
-MISC ChangeLog 3958 RMD160 2c6cb73b2a9b2ad1004fddfc57c08ee1cdc5c348 SHA1 c451eab0db8c08a15af474a3b3b1d258f84c0cd6 SHA256 48b7b8a1e5ff4bccefafa26650b7d48cbf19d9c16a6309d5b0fa2e0559e954e1
+EBUILD refmac-5.6.0036.ebuild 1165 RMD160 dbc64fbac1074e4c4c43451602c64b3f5ca12df4 SHA1 331bc1d19eacc299ad6af657048b9642d7ed0a23 SHA256 e63cdb6fc66fb5401e234014db3463f981aa33a4975ae2e9122319052529ebb6
+MISC ChangeLog 4207 RMD160 9e51edb03afe086856698e5d4f68acdb09fca8a0 SHA1 c14a5b772ab125c652967d94115af05ba9b058a9 SHA256 3f6aa4c5258739e7255f8178d89a3f49e4e0b708c084dcfe656dfcefd7762c6d
 MISC metadata.xml 314 RMD160 d8922635160b6047732051715291e8553b513bba SHA1 b53fc6fb6cf908093794b876e729606c00351937 SHA256 50a519ddbcef4ad4f76175df36849a076d20adbb6340fdba292175b70c0d9719
diff --git a/sci-chemistry/refmac/files/5.5.0097-allow-dynamic-linking.patch b/sci-chemistry/refmac/files/5.5.0097-allow-dynamic-linking.patch
new file mode 100644
index 000000000..415ba9d08
--- /dev/null
+++ b/sci-chemistry/refmac/files/5.5.0097-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-5.5.0095.ebuild b/sci-chemistry/refmac/refmac-5.5.0095.ebuild
index 8d5890ade..0c220e3fc 100644
--- a/sci-chemistry/refmac/refmac-5.5.0095.ebuild
+++ b/sci-chemistry/refmac/refmac-5.5.0095.ebuild
@@ -2,7 +2,7 @@
 # Distributed under the terms of the GNU General Public License v2
 # $Header: $
 
-inherit base fortran toolchain-funcs
+inherit fortran base toolchain-funcs
 
 DESCRIPTION="Macromolecular crystallographic refinement program"
 HOMEPAGE="http://www.ysbl.york.ac.uk/~garib/refmac/"
diff --git a/sci-chemistry/refmac/refmac-5.5.0097.ebuild b/sci-chemistry/refmac/refmac-5.5.0097.ebuild
new file mode 100644
index 000000000..64c1df9a3
--- /dev/null
+++ b/sci-chemistry/refmac/refmac-5.5.0097.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
+
+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=(
+	"${FILESDIR}"/${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-5.6.0036.ebuild b/sci-chemistry/refmac/refmac-5.6.0036.ebuild
index 4e2e62466..dcc714792 100644
--- a/sci-chemistry/refmac/refmac-5.6.0036.ebuild
+++ b/sci-chemistry/refmac/refmac-5.6.0036.ebuild
@@ -2,7 +2,7 @@
 # Distributed under the terms of the GNU General Public License v2
 # $Header: $
 
-inherit base fortran toolchain-funcs versionator
+inherit fortran base toolchain-funcs versionator
 
 MY_PV="$(get_version_component_range 1-2)"