refmac version bump

4 files changed, 79 insertions, 3 deletions

diff --git a/sci-chemistry/refmac/ChangeLog b/sci-chemistry/refmac/ChangeLog
index b89573cc3..cd2423492 100644
--- a/sci-chemistry/refmac/ChangeLog
+++ b/sci-chemistry/refmac/ChangeLog
@@ -2,6 +2,15 @@
 # Copyright 1999-2009 Gentoo Foundation; Distributed under the GPL v2
 # $Header: $
 
+*refmac-5.5.0093 (22 May 2009)
+
+  22 May 2009; Justin Lecher (jlec) <jlec@j-schmitz.net>
+  +files/5.5.0093-allow-dynamic-linking.patch, -refmac-5.5.0090.ebuild,
+  +refmac-5.5.0093.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-5.5.0092 (18 May 2009)
 
   18 May 2009; Justin Lecher (jlec) <jlec@j-schmitz.net>
diff --git a/sci-chemistry/refmac/Manifest b/sci-chemistry/refmac/Manifest
index 4a9c79c8a..f696d0e5f 100644
--- a/sci-chemistry/refmac/Manifest
+++ b/sci-chemistry/refmac/Manifest
@@ -1,13 +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 5.6.0031-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_5.5.0090.tar.gz 1295599 RMD160 8707ac700f106baaa47831a920de602c2ff9288e SHA1 aefff2001aa3922c170de5ebc87acf07ece698c9 SHA256 4f522003f3d05dbe627c5603d498ebfce76b93df81f46813fdfdd051528db7f4
 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_source_v5.6.0031.tar.gz 1331481 RMD160 ae37017abeb8ba01d8a3318e78987780e3ce5070 SHA1 6f1a6a35bf9e9efba6a60861f69b53aa728c4392 SHA256 80a6e441635df07e06a80a2bbee1bc12781c7d57dd107b83de4baebfd3f99cf4
-EBUILD refmac-5.5.0090.ebuild 1045 RMD160 ab5645566baf7d0dbac1522258377130e837d2a7 SHA1 6dacfd7d27edf0121344e255f5bda678b5701f69 SHA256 dbb5111b9ede779c6345c44400510a0d12f655d89eb0208f9e2ddc2304315c70
 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-5.6.0031.ebuild 1062 RMD160 88e1065c6899b09e943bf2b3365d36bda4fd3bc0 SHA1 c811d1771f2384347382ffb532442f2d5a1b264f SHA256 2379b4b9e19f0079fe0350f3864c7bb9a1618a48e0d6c54c0497b20f1848f61b
 EBUILD refmac-5.6.0033.ebuild 1200 RMD160 cf0754afc5ea07df2fed0baf7599dfcd32e43ada SHA1 7811acc5a91e73b0ee85a340e489f1bc95eecefb SHA256 ee98605ab90acd94b7f3e669ef41e9e4fff309cacd9cb188ddc2c7cfa360aa17
-MISC ChangeLog 2226 RMD160 dce9a453a3141a8ebbdb7f1b0f79e2a983de3ee7 SHA1 6cd8a592dd7decb53fc9f39652e7edd4c918b47e SHA256 5fecb7aa87b61f7c3547f146831d0cc86c37ac7a117d11f6399fee96d6ee2066
+MISC ChangeLog 2584 RMD160 cd19a66f42f6453582bf66e5a99da315cc7fe220 SHA1 78a40747e4f18471914469b899f27f2070edb887 SHA256 63149d11693614a7787ae24b903e44871fa6dd1dc6bff70fd8edbcd37cf45bb5
 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
new file mode 100644
index 000000000..415ba9d08
--- /dev/null
+++ b/sci-chemistry/refmac/files/5.5.0093-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-5.5.0093.ebuild
index d53653bdc..d53653bdc 100644
--- a/sci-chemistry/refmac/refmac-5.5.0090.ebuild
+++ b/sci-chemistry/refmac/refmac-5.5.0093.ebuild