Merge branch 'master' of git+ssh://git.overlays.gentoo.org/proj/sci

* 'master' of git+ssh://git.overlays.gentoo.org/proj/sci:
  bumped mpir to 1.3.0, remove old rc, adjust copyright in 1.2.2
  sci-chemistry/pymol-apbs-plugin -- fixes for some file locations
  sci-chemistry/ccpn-2.1.2.1_p100129 -- Added todays python fixes
  sci-chemistry/refmac -- Version bump
  sci-chemistry/refmac -- Version bump
  sci-chemistry/refmac -- Version bump

17 files changed, 411 insertions, 37 deletions

diff --git a/dev-libs/mpir/ChangeLog b/dev-libs/mpir/ChangeLog
index 7aed9b843..c986d879b 100644
--- a/dev-libs/mpir/ChangeLog
+++ b/dev-libs/mpir/ChangeLog
@@ -1,7 +1,21 @@
 # ChangeLog for dev-libs/mpir
-# Copyright 1999-2009 Gentoo Foundation; Distributed under the GPL v2
+# Copyright 1999-2010 Gentoo Foundation; Distributed under the GPL v2
 # $Header: $
 
+  30 Jan 2010; François Bissey <f.r.bissey@massey.ac.nz>
+  -mpir-1.3.0_rc3.ebuild, +mpir-1.3.0.ebuild,
+  +files/mpir-1.3.0-ABI-multilib.patch, +files/mpir-1.3.0-yasm.patch,
+  -files/mpir-1.3.0_rc3-yasm.patch:
+  fix copyright line in 1.2.2
+
+*mpir-1.3.0 (30 Jan 2010)
+
+  30 Jan 2010; François Bissey <f.r.bissey@massey.ac.nz>
+  -mpir-1.3.0_rc3.ebuild, +mpir-1.3.0.ebuild,
+  +files/mpir-1.3.0-ABI-multilib.patch, +files/mpir-1.3.0-yasm.patch,
+  -files/mpir-1.3.0_rc3-yasm.patch:
+  Bumped to version 1.3.0 remove old rc. Add a proper ABI patch.
+
   17 Dec 2009; Thomas Kahle <tom@gentoo.org> -mpir-1.2.1.ebuild,
   mpir-1.2.2.ebuild, +files/mpir-1.2.2-yasm.patch:
   yasm-patch for v 1.2.2, v 1.2.1 removed
diff --git a/dev-libs/mpir/Manifest b/dev-libs/mpir/Manifest
index bc720cad6..4e9b809a8 100644
--- a/dev-libs/mpir/Manifest
+++ b/dev-libs/mpir/Manifest
@@ -1,8 +1,9 @@
 AUX mpir-1.2.2-yasm.patch 2049 RMD160 33138854e9429ee5fd57fc547a50bfec02aa51bc SHA1 03a513b9a832734324bc6116cf06c4ebca17f2c3 SHA256 483aff2973c89ce78fe46ef965bbbe8e06d7ba8d75bf64c651a1e379ebebe581
-AUX mpir-1.3.0_rc3-yasm.patch 1741 RMD160 a10820ce5a350f746cab4981ccf40ca9f40e1cca SHA1 5aa4003a7ff6d3f1f4d36734acd90c41cb8b39f0 SHA256 32d1ed07d65b033c70d78cb85ae3cb551ba2f7871d50ad9f3e991abec9bcc5c1
+AUX mpir-1.3.0-ABI-multilib.patch 3903 RMD160 3f961212097a7957f2cc831929c545cfc3e80e2b SHA1 cda3a90665716132f5078eedb0fdfca2eff3d4b2 SHA256 3db2dc41f385d6c8ce9da8406a42072c8462e6e15eba0b6ff93664ef31c00957
+AUX mpir-1.3.0-yasm.patch 1741 RMD160 a10820ce5a350f746cab4981ccf40ca9f40e1cca SHA1 5aa4003a7ff6d3f1f4d36734acd90c41cb8b39f0 SHA256 32d1ed07d65b033c70d78cb85ae3cb551ba2f7871d50ad9f3e991abec9bcc5c1
 DIST mpir-1.2.2.tar.gz 4276405 RMD160 11bfa2c4de8c1131498722638f8f2e4242651918 SHA1 bd012e207f2c750dfc23af6ac25b96bdd7009354 SHA256 6e070f6a2cc104596f197ac551cac0a35f64e3de5522891db544a1417b7f908a
-DIST mpir-1.3.0-rc3.tar.gz 4276806 RMD160 61cec894b867cddb2c366adaf03027fde6079ad4 SHA1 2fba6f4883732bab13fc059a1ffc1c437aa1fbf6 SHA256 067cb2e01c886494c2576e94d3e79243514ffe791da3bf23e1a3bcd9ec4c29f2
-EBUILD mpir-1.2.2.ebuild 830 RMD160 9181292e4d9f28fbbc694ef59b942ff04d83876f SHA1 cacd1974c117bf2445bc00b36377176effaf4ea1 SHA256 b9ac9363e607e99bc2b97c5d3913cec346e1aa2720dc47e28e323e05ab39106d
-EBUILD mpir-1.3.0_rc3.ebuild 1150 RMD160 97f88858f63bdef07c0f37dfd556d8c5c11772b2 SHA1 540d99268d3436ab7432dca69c549a359c203e07 SHA256 17ee29d144dbe86b4c22a44e86b0a834041fd059880a1d3e320a92e1389b09cc
-MISC ChangeLog 771 RMD160 bb58e7d4d81e7497346da0ac86bedc56d10ad8a2 SHA1 a5fa18c8d3c506c3fcecf1b976a6f5ffca6ccb87 SHA256 318909f76693df6dd81d8006130faae7b30498b3a95df08ce5a036883cd531f5
+DIST mpir-1.3.0.tar.gz 4367474 RMD160 9961226d55e3c3266e320fff93302391bd89d0ca SHA1 ffea162c98a043720657590ef9bd5f7badfd2672 SHA256 b981d1b4ae1985c25a1070cfa401c97bea20b4aa2fb46e704bd7232fa00e5511
+EBUILD mpir-1.2.2.ebuild 830 RMD160 2c22f6a0328a998c031565f6de6a38a655804317 SHA1 a8a56a6004fdae7868504de6398698b8431451fa SHA256 edd2a1ffeeb6dc8eb69a15931a13cdb59b9347abba78bf55c3d395c650dcc150
+EBUILD mpir-1.3.0.ebuild 1534 RMD160 1ca7ca8c9ca61ca709117bbd7977a76380167e6d SHA1 6d4f81ae130ab05aa07b0c69c6343dc1604eb299 SHA256 6fd6f7ffb8cec1fd21d276c993b6baf3cba2bf851e265ea32161d96de0d94313
+MISC ChangeLog 1074 RMD160 80f50c039956bca318911952828945c64196fb0c SHA1 00f3d1594ba187fbbfd74f8a19a22517496c99cd SHA256 8de1947471110a9f05111003ff3eced9acfc2e4c44965d325ff5cce91a169112
 MISC metadata.xml 516 RMD160 dcd6e4599dfc146ef42a021dcfbaf65444d5b272 SHA1 a922010b05f992381656820c3c93697da3b30b70 SHA256 d4a7736b383f142b29166bca022254c5e4e599a3304886ca73491dd7b5954d76
diff --git a/dev-libs/mpir/files/mpir-1.3.0-ABI-multilib.patch b/dev-libs/mpir/files/mpir-1.3.0-ABI-multilib.patch
new file mode 100644
index 000000000..fba6fea2e
--- /dev/null
+++ b/dev-libs/mpir/files/mpir-1.3.0-ABI-multilib.patch
@@ -0,0 +1,145 @@
+--- configure.in.orig	2009-11-28 10:48:59.196977657 +0000
++++ configure.in	2009-11-28 10:54:50.717976971 +0000
+@@ -361,7 +361,7 @@
+ # hugely bloat the output.
+ 
+ 
+-AC_ARG_VAR(ABI, [desired ABI (for processors supporting more than one ABI)])
++AC_ARG_VAR(MPIRABI, [desired ABI (for processors supporting more than one ABI)])
+ 
+ # abilist needs to be non-empty, "standard" is just a generic name here
+ abilist="standard"
+@@ -1590,7 +1590,7 @@
+ 
+ cat >&AC_FD_CC <<EOF
+ User:
+-ABI=$ABI
++MPIRABI=$MPIRABI
+ CC=$CC
+ CFLAGS=$CFLAGS_or_unset
+ CPPFLAGS=$CPPFLAGS_or_unset
+@@ -1611,22 +1611,22 @@
+ # If the user specifies an ABI then it must be in $abilist, after that
+ # $abilist is restricted to just that choice.
+ #
+-if test -n "$ABI"; then
++if test -n "$MPIRABI"; then
+   found=no
+   for abi in $abilist; do
+-    if test $abi = "$ABI"; then found=yes; break; fi
++    if test $abi = "$MPIRABI"; then found=yes; break; fi
+   done
+   if test $found = no; then
+-    AC_MSG_ERROR([ABI=$ABI is not among the following valid choices: $abilist])
++    AC_MSG_ERROR([MPIRABI=$MPIRABI is not among the following valid choices: $abilist])
+   fi
+-  abilist="$ABI"
++  abilist="$MPIRABI"
+ fi
+ 
+ found_compiler=no
+ 
+ for abi in $abilist; do
+ 
+-  echo "checking ABI=$abi"
++  echo "checking MPIRABI=$abi"
+ 
+   # Suppose abilist="64 32", then for abi=64, will have abi1="_64" and
+   # abi2="_64".  For abi=32, will have abi1="_32" and abi2="".  This is how
+@@ -1879,7 +1879,7 @@
+     done
+   fi
+ 
+-  ABI="$abi"
++  MPIRABI="$abi"
+   CC="$cc"
+   CFLAGS="$cflags"
+   CPPFLAGS="$cppflags"
+@@ -1895,8 +1895,8 @@
+    AC_SUBST(GMP_CFLAGS)
+ 
+   # Could easily have this in config.h too, if desired.
+-  ABI_nodots=`echo $ABI | sed 's/\./_/'`
+-  GMP_DEFINE_RAW("define_not_for_expansion(\`HAVE_ABI_$ABI_nodots')", POST)
++  ABI_nodots=`echo $MPIRABI | sed 's/\./_/'`
++  GMP_DEFINE_RAW("define_not_for_expansion(\`HAVE_ABI_$MPIRABI_nodots')", POST)
+ 
+ 
+   # GMP_LDFLAGS substitution, selected according to ABI.
+@@ -2094,7 +2094,7 @@
+ #
+ case $host in
+   X86_PATTERN | X86_64_PATTERN)
+-    if test "$ABI" = 32; then
++    if test "$MPIRABI" = 32; then
+       case "$path $fat_path" in
+         *mmx*)   GMP_ASM_X86_MMX( , [GMP_STRIP_PATH(*mmx*)]) ;;
+       esac
+@@ -2108,7 +2108,7 @@
+ 
+ cat >&AC_FD_CC <<EOF
+ Decided:
+-ABI=$ABI
++MPIRABI=$MPIRABI
+ CC=$CC
+ CFLAGS=$CFLAGS
+ CPPFLAGS=$CPPFLAGS
+@@ -2117,7 +2117,7 @@
+ CXXFLAGS=$CXXFLAGS
+ path=$path
+ EOF
+-echo "using ABI=\"$ABI\""
++echo "using MPIRABI=\"$MPIRABI\""
+ echo "      CC=\"$CC\""
+ echo "      CFLAGS=\"$CFLAGS\""
+ echo "      CPPFLAGS=\"$CPPFLAGS\""
+@@ -2593,7 +2593,7 @@
+ 
+ 
+ if test -n "$fat_path"; then
+-  if test "$ABI" = 64; then
++  if test "$MPIRABI" = 64; then
+     fat_path="$fat_path_64"
+   fi
+ 
+@@ -3099,19 +3099,19 @@
+       GMP_INCLUDE_MPN(powerpc32/powerpc-defs.m4)
+       case $host in
+         *-*-aix*)
+-	  case $ABI in
++	  case $MPIRABI in
+ 	    64 | aix64)  GMP_INCLUDE_MPN(powerpc64/aix.m4) ;;
+             *)           GMP_INCLUDE_MPN(powerpc32/aix.m4) ;;
+           esac
+           ;;
+         *-*-linux* | *-*-*bsd*)
+-	  case $ABI in
++	  case $MPIRABI in
+ 	    mode64)      GMP_INCLUDE_MPN(powerpc64/elf.m4) ;;
+ 	    mode32 | 32) GMP_INCLUDE_MPN(powerpc32/elf.m4) ;;
+           esac
+           ;;
+         *-*-darwin*)
+-	  case $ABI in
++	  case $MPIRABI in
+ 	    mode64)      GMP_INCLUDE_MPN(powerpc64/darwin.m4) ;;
+ 	    mode32 | 32) GMP_INCLUDE_MPN(powerpc32/darwin.m4) ;;
+           esac
+@@ -3126,7 +3126,7 @@
+       GMP_INCLUDE_MPN(powerpc32/aix.m4)
+       ;;
+     sparcv9*-*-* | ultrasparc*-*-* | sparc64-*-*)
+-      case $ABI in
++      case $MPIRABI in
+         64)
+           GMP_ASM_SPARC_REGISTER
+           ;;
+@@ -3134,7 +3134,7 @@
+       ;;
+     X86_PATTERN | X86_64_PATTERN)
+       GMP_ASM_ALIGN_FILL_0x90
+-      case $ABI in
++      case $MPIRABI in
+         32)
+           GMP_INCLUDE_MPN(x86/x86-defs.m4)
+           AC_DEFINE(HAVE_HOST_CPU_FAMILY_x86)
diff --git a/dev-libs/mpir/files/mpir-1.3.0_rc3-yasm.patch b/dev-libs/mpir/files/mpir-1.3.0-yasm.patch
index 572931353..572931353 100644
--- a/dev-libs/mpir/files/mpir-1.3.0_rc3-yasm.patch
+++ b/dev-libs/mpir/files/mpir-1.3.0-yasm.patch
diff --git a/dev-libs/mpir/mpir-1.2.2.ebuild b/dev-libs/mpir/mpir-1.2.2.ebuild
index 6c0135a6a..9e1024480 100644
--- a/dev-libs/mpir/mpir-1.2.2.ebuild
+++ b/dev-libs/mpir/mpir-1.2.2.ebuild
@@ -1,4 +1,4 @@
-# Copyright 1999-2009 Gentoo Foundation
+# Copyright 1999-2010 Gentoo Foundation
 # Distributed under the terms of the GNU General Public License v2
 # $Header: $
 
diff --git a/dev-libs/mpir/mpir-1.3.0_rc3.ebuild b/dev-libs/mpir/mpir-1.3.0.ebuild
index 9678bf63a..0fde349c7 100644
--- a/dev-libs/mpir/mpir-1.3.0_rc3.ebuild
+++ b/dev-libs/mpir/mpir-1.3.0.ebuild
@@ -1,16 +1,15 @@
-# Copyright 1999-2009 Gentoo Foundation
+# Copyright 1999-2010 Gentoo Foundation
 # Distributed under the terms of the GNU General Public License v2
 # $Header: $
 
 EAPI=2
 
-inherit eutils versionator autotools
+inherit eutils autotools
 
 DESCRIPTION="MPIR is a library for arbitrary precision integer arithmetic derived from version 4.2.1 of gmp"
 HOMEPAGE="http://www.mpir.org/"
-SRC_URI="http://www.mpir.org/${PN}-$(replace_version_separator 3 -).tar.gz"
+SRC_URI="http://www.mpir.org/${P}.tar.gz"
 RESTRICT="mirror"
-S="${WORKDIR}/${PN}-$(get_version_component_range 1-3)"
 
 LICENSE="LGPL-2.1"
 SLOT="0"
@@ -25,13 +24,15 @@ RDEPEND=""
 
 src_prepare(){
 	epatch "${FILESDIR}/${P}-yasm.patch"
+	epatch "${FILESDIR}/${P}-ABI-multilib.patch"
+	# FIXME: In the same way there was QA regarding executable stacks
+	#        with GMP we have some here as well. We cannot apply the
+	#        GMP solution as yasm is used, at least on x64/amd64.
+	#        Furthermore we are able to patch config.ac.
 	eautoreconf
 }
 
 src_configure() {
-	# causes problems on amd64
-	unset ABI
-
 # beware that cpudetection aka fat binaries is x86/amd64 only.
 # It will need to be filtered when extended to other archs
 	econf \
@@ -44,3 +45,10 @@ src_install() {
 	emake DESTDIR="${D}" install || die "emake install failed"
 	dodoc ChangeLog README NEWS
 }
+
+pkg_postinst() {
+	elog "The mpir ebuild is still under development."
+	elog "Help us improve the ebuild in:"
+	elog "http://bugs.gentoo.org/show_bug.cgi?id=293383"
+	elog "This ebuild is known to have an executable atack problem"
+}
diff --git a/sci-chemistry/ccpn/ChangeLog b/sci-chemistry/ccpn/ChangeLog
index 5caa7cb0e..2cc27105f 100644
--- a/sci-chemistry/ccpn/ChangeLog
+++ b/sci-chemistry/ccpn/ChangeLog
@@ -2,6 +2,12 @@
 # Copyright 1999-2010 Gentoo Foundation; Distributed under the GPL v2
 # $Header: $
 
+*ccpn-2.1.2.1_p100129 (29 Jan 2010)
+
+  29 Jan 2010; Justin Lecher (jlec) <jlec@j-schmitz.net>
+  +ccpn-2.1.2.1_p100129.ebuild:
+  Added todays python fixes
+
 *ccpn-2.1.2.1_p100124 (24 Jan 2010)
 
   24 Jan 2010; Justin Lecher (jlec) <jlec@j-schmitz.net>
diff --git a/sci-chemistry/ccpn/Manifest b/sci-chemistry/ccpn/Manifest
index 42d1dbd26..2a48bba78 100644
--- a/sci-chemistry/ccpn/Manifest
+++ b/sci-chemistry/ccpn/Manifest
@@ -12,6 +12,7 @@ DIST analysis2.1.0.tar.gz 18962012 RMD160 3997fe7deafd50142f60d036e82f436519efe1
 DIST analysis2.1.1.tar.gz 18972580 RMD160 17e0fca7dc6b1c272ebbff68cb2589ab3bbff9c6 SHA1 62a28269e1215c458fbf8866c2323fbc690a7ea3 SHA256 1da964a61b98e29735dce1ba75f5f1fbf76dcded3bf93aaa05a4f1c05729972a
 DIST analysis2.1.2_1.tar.gz 19227793 RMD160 f633a8338e3fbb9d8ad77c9482d63191419b0885 SHA1 f711a424da22c84295610483a6cc481d2d2161e9 SHA256 e7eda0b50c357a2b62633c473da4621ccdc48c747c59d8ccb495d57e846308fa
 DIST ccpn-update-100124.patch.bz2 21213 RMD160 51e4531acfbd57e795630e7dc6c260c2f92ce21d SHA1 8a065bb6cfa97ca88b15bac149c7af05c151fe27 SHA256 a075fa28527e1444b22340562cae4d6607d203a84cd163f404d0cc2854a66006
+DIST ccpn-update-100129.patch.bz2 23824 RMD160 845b61cdfacd59e42191303bd055c6a543970b12 SHA1 db5b66a29d86483142a7c57e46cc0b9f8539413d SHA256 357f6c2f4c912061f9b8ecbb2c857f8b37770037932829145fb4c5c38650f046
 DIST update-091012.patch.bz2 41959 RMD160 3ddb011d80935fea02fbf00fd06cadd32d86ecbc SHA1 467a41d1f634417739af09dc8a725f4b32238e5c SHA256 fe5051256f81d2f59a19b2463a7b6c5697680030b4b2823a6b6869eec85b8dbb
 DIST update-091025.patch.bz2 17170 RMD160 5b2b440b742345a815158e63e356f82cfce933f6 SHA1 569e370e819c940e904696e1ab4eae7380e035d0 SHA256 5467ccd9bb437f1d0720a02e2629120319a61d77cc246cbdbaadc89deb884a51
 DIST update-091220.patch.bz2 16551 RMD160 6a4f12c88be5e0a5af3f4ec560d4e795006ea231 SHA1 f5b1c31f82f8ae930b11ba742ea09c09a9b45d24 SHA256 e355f42fd1e82fbf39377c56472f20346aea7c5aab97df4c36c508a31b6dacb5
@@ -20,16 +21,17 @@ EBUILD ccpn-2.0.7.1-r2.ebuild 4550 RMD160 4adb7d8e25ae01b7c390475fa253e3408425e5
 EBUILD ccpn-2.1.0-r4.ebuild 4167 RMD160 63f746dd33faa4a753d24ae0fc75c31bde3c3a61 SHA1 3624b2792b39a4db868006eb0711f180abb6dcd4 SHA256 3d82036ffcda14918e6924fd8eef89e56c85d1776f359071ad15d5620708f8e7
 EBUILD ccpn-2.1.1-r1.ebuild 4195 RMD160 7e67b7712b448f098c01fbe0c19d1f5eab7a8d64 SHA1 4580a861ce8fcafe6c82254117339d3a0fc36db2 SHA256 6a945186e8d349b3d53de852b8d651889cdc092f5b3123ec3c2c40b56b75c81c
 EBUILD ccpn-2.1.2.1_p100124.ebuild 4292 RMD160 9cafce52f78af25c9e02b8770d56e466d3b67787 SHA1 632e3fc541b5b24893cea043eb00b618e931b7ba SHA256 26687db3db96cc44e15fd46d48d680b2d442b5f614824c819f5da4616e441fd8
+EBUILD ccpn-2.1.2.1_p100129.ebuild 4292 RMD160 9cafce52f78af25c9e02b8770d56e466d3b67787 SHA1 632e3fc541b5b24893cea043eb00b618e931b7ba SHA256 26687db3db96cc44e15fd46d48d680b2d442b5f614824c819f5da4616e441fd8
 EBUILD ccpn-2.1.2_p1-r3.ebuild 4083 RMD160 2867b8e5c80c0391aa7d0d4688e383bd42331394 SHA1 f6ae4acb9a7a926da7d1219cd3918bb0e7c4ffea SHA256 061cc050cff5d4e31ce808705dc3dabe4b95c7c2a747659d3670347134757582
 EBUILD ccpn-2.1.2_p1-r4.ebuild 4110 RMD160 e692383d827c067d4c6c08eae4c3ebf7acb8ea21 SHA1 2f1022b4e729c61a34a5accc50831058272d2f9c SHA256 ae931526ced750af05329f92bffe57d1fc13b5535e39bf2cb440dead74bbb26b
 EBUILD ccpn-2.1.2_p1-r5.ebuild 4225 RMD160 8680cac8119d9f1624e5c8a38aff4429e10cf24b SHA1 fa17fda2ba1864728ea672084bbb73ca9976948f SHA256 c336ae6a9ea1c310ad91487b83a62d7439ff279a5d6671c138aa6e8d4376fbf4
 EBUILD ccpn-2.1.2_p1-r6.ebuild 4225 RMD160 7337ad67feee602a5224d5d28e4e69735b8cf2e0 SHA1 c28cee175f191dcbc4acf7841089fced91bd3724 SHA256 f32e2e5c77731c5aa9fb650342f938e4b1d20fee7e402d93e7107c5330e894c4
-MISC ChangeLog 5895 RMD160 8203007d7a42a083a4257cef8f3dc9149657511c SHA1 5c27b93dd47a3c351f18f190a09fa095275a927b SHA256 2307e3362858076676788a94eb9db211e5e1e3e48a5714f74c3b26ffa8504ebc
+MISC ChangeLog 6050 RMD160 9032cc151b9ba479d331748e9567bc40989e371d SHA1 e3a0580196e5fe6ee185e83402492966fc2aa3ef SHA256 bfb9643a04ad966f0c7219688b573920ed15484d4a8a257424a2cbd75a988eb9
 MISC metadata.xml 339 RMD160 2e62dd84c66f8229f9f75832b91b3921a23386c9 SHA1 3252b1e326b3ba201266861d6461bcc069ad770e SHA256 bbb58d377587da3e6a2d4a742829e24b2c840be26d8e8da2d3f6fbf26c0143ec
 -----BEGIN PGP SIGNATURE-----
 Version: GnuPG v2.0.11 (GNU/Linux)
 
-iEYEARECAAYFAktcFRoACgkQgAnW8HDreRZXigCfQySgfbEMRIQih5NXxAuy7Cvc
-4QMAn1e821KwiZDqI+ngZDvQPYM8nzyC
-=vxFV
+iEYEARECAAYFAktjCpUACgkQgAnW8HDreRZ0YQCg0JVIf/ZA6jpXzirSvlzzRP1P
+n9QAnRIIGMTlDON2ofIojvGolphvUX6V
+=rNR8
 -----END PGP SIGNATURE-----
diff --git a/sci-chemistry/ccpn/ccpn-2.1.2.1_p100129.ebuild b/sci-chemistry/ccpn/ccpn-2.1.2.1_p100129.ebuild
new file mode 100644
index 000000000..d0387ed5e
--- /dev/null
+++ b/sci-chemistry/ccpn/ccpn-2.1.2.1_p100129.ebuild
@@ -0,0 +1,171 @@
+# Copyright 1999-2010 Gentoo Foundation
+# Distributed under the terms of the GNU General Public License v2
+# $Header: $
+
+EAPI="2"
+
+PYTHON_USE_WITH="ssl tk"
+
+inherit eutils portability python toolchain-funcs versionator
+
+PATCHSET="${PV##*_p}"
+MY_PN="${PN}mr"
+MY_PV="$(replace_version_separator 3 _ ${PV%%_p*})"
+
+DESCRIPTION="The Collaborative Computing Project for NMR"
+SRC_URI="http://www.bio.cam.ac.uk/ccpn/download/${MY_PN}/analysis${MY_PV}.tar.gz"
+	[[ -n ${PATCHSET} ]] && SRC_URI="${SRC_URI}	http://dev.gentooexperimental.org/~jlec/distfiles/ccpn-update-${PATCHSET}.patch.bz2"
+HOMEPAGE="http://www.ccpn.ac.uk/ccpn"
+
+SLOT="0"
+LICENSE="|| ( CCPN LGPL-2.1 )"
+KEYWORDS="~amd64 ~x86"
+IUSE="+opengl"
+
+RDEPEND="
+	dev-lang/tk
+	dev-python/elementtree
+	dev-python/numpy
+	dev-tcltk/tix
+	opengl? ( virtual/glut )"
+DEPEND="${RDEPEND}"
+RESTRICT="mirror"
+
+S="${WORKDIR}"/${MY_PN}/${MY_PN}$(get_version_component_range 1-2 ${PV})
+
+pkg_setup() {
+	python_version
+}
+
+src_prepare() {
+	[[ -n ${PATCHSET} ]] && \
+		epatch "${WORKDIR}"/ccpn-update-${PATCHSET}.patch
+
+	local tk_ver
+	local myconf
+
+	tk_ver="$(best_version dev-lang/tk | cut -d- -f3 | cut -d. -f1,2)"
+
+	if use opengl; then
+		GLUT_NEED_INIT="-DNEED_GLUT_INIT"
+		IGNORE_GL_FLAG=""
+		GL_FLAG="-DUSE_GL_FALSE"
+		GL_DIR="/usr"
+		GL_LIB="-lglut -lGLU -lGL"
+		GL_INCLUDE_FLAGS="-I\$(GL_DIR)/include"
+		GL_LIB_FLAGS="-L\$(GL_DIR)/$(get_libdir)"
+
+	else
+		IGNORE_GL_FLAG="-DIGNORE_GL"
+		GL_FLAG="-DUSE_GL_FALSE"
+	fi
+
+	GLUT_NOT_IN_GL=""
+	GLUT_FLAG="\$(GLUT_NEED_INIT) \$(GLUT_NOT_IN_GL)"
+
+	sed \
+		-e "s:^\(CC =\).*:\1 $(tc-getCC):g" \
+		-e "s:^\(OPT_FLAG =\).*:\1 ${CFLAGS}:g" \
+		-e "s:^\(LINK_FLAGS =.*\):\1 ${LDFLAGS}:g" \
+		-e "s:^\(IGNORE_GL_FLAG =\).*:\1 ${IGNORE_GL_FLAG}:g" \
+		-e "s:^\(GL_FLAG =\).*:\1 ${GL_FLAG}:g" \
+		-e "s:^\(GLUT_NEED_INIT =\).*:\1 ${GLUT_NEED_INIT}:g" \
+		-e "s:^\(GLUT_NOT_IN_GL =\).*:\1:g" \
+		-e "s:^\(X11_LIB_FLAGS =\).*:\1 -L/usr/$(get_libdir):g" \
+		-e "s:^\(TCL_LIB_FLAGS =\).*:\1 -L/usr/$(get_libdir):g" \
+		-e "s:^\(TK_LIB_FLAGS =\).*:\1 -L/usr/$(get_libdir):g" \
+		-e "s:^\(PYTHON_INCLUDE_FLAGS =\).*:\1 -I\$(PYTHON_DIR)/include/python${PYVER}:g" \
+		-e "s:^\(GL_LIB_FLAGS =\).*:\1 -L/usr/$(get_libdir):g" \
+		c/environment_default.txt > c/environment.txt
+}
+
+src_compile() {
+	emake \
+		-C c \
+		all links || \
+		die "failed to compile"
+}
+
+src_install() {
+
+	local in_path
+	local gentoo_sitedir
+	local libdir
+	local files
+	local tkver
+
+	in_path=$(python_get_sitedir)/${PN}
+	gentoo_sitedir=$(python_get_sitedir)
+	libdir=$(get_libdir)
+	tkver=$(best_version dev-lang/tk | cut -d- -f3 | cut -d. -f1,2)
+
+	for wrapper in analysis dangle dataShifter eci formatConverter pipe2azara; do
+		sed -e "s:gentoo_sitedir:${gentoo_sitedir}:g" \
+		    -e "s:libdir:${libdir}:g" \
+			-e "s:tkver:${tkver}:g" \
+		    "${FILESDIR}"/${wrapper} > "${T}"/${wrapper} || die "Fail fix ${wrapper}"
+		dobin "${T}"/${wrapper} || die "Failed to install ${wrapper}"
+	done
+
+	for i in python/memops/format/compatibility/{Converters,part2/Converters2}.py; do
+		sed \
+			-e 's:#from __future__:from __future__:g' \
+			-i ${i}
+	done
+
+	insinto ${in_path}
+
+	dodir ${in_path}/c
+
+	ebegin "Installing main files"
+	doins -r data model python || die "main files installation failed"
+	eend
+
+	dohtml -r doc/* || die
+	dosym ../../../../share/doc/${PF}/html ${in_path}/doc || die
+
+	einfo "Adjusting permissions"
+
+	files="ccpnmr/c/ContourFile.so
+		ccpnmr/c/ContourLevels.so
+		ccpnmr/c/ContourStyle.so
+		ccpnmr/c/PeakList.so
+		ccpnmr/c/SliceFile.so
+		ccpnmr/c/WinPeakList.so
+		ccpnmr/c/AtomCoordList.so
+		ccpnmr/c/AtomCoord.so
+		ccpnmr/c/Bacus.so
+		ccpnmr/c/CloudUtil.so
+		ccpnmr/c/DistConstraintList.so
+		ccpnmr/c/DistConstraint.so
+		ccpnmr/c/DistForce.so
+		ccpnmr/c/Dynamics.so
+		ccpnmr/c/Midge.so
+		ccp/c/StructAtom.so
+		ccp/c/StructBond.so
+		ccp/c/StructStructure.so
+		ccp/c/StructUtil.so
+		memops/c/BlockFile.so
+		memops/c/FitMethod.so
+		memops/c/GlHandler.so
+		memops/c/MemCache.so
+		memops/c/PdfHandler.so
+		memops/c/PsHandler.so
+		memops/c/ShapeFile.so
+		memops/c/StoreFile.so
+		memops/c/StoreHandler.so
+		memops/c/TkHandler.so"
+
+	for FILE in ${files}; do
+		fperms 755 ${in_path}/python/${FILE}
+	done
+}
+
+pkg_postinst() {
+	python_need_rebuild
+	python_mod_optimize $(python_get_sitedir)/${PN}
+}
+
+pkg_postrm() {
+	python_mod_cleanup $(python_get_sitedir)/${PN}
+}
diff --git a/sci-chemistry/pymol-apbs-plugin/ChangeLog b/sci-chemistry/pymol-apbs-plugin/ChangeLog
index 8a401b5d2..262b0754b 100644
--- a/sci-chemistry/pymol-apbs-plugin/ChangeLog
+++ b/sci-chemistry/pymol-apbs-plugin/ChangeLog
@@ -2,6 +2,10 @@
 # Copyright 1999-2010 Gentoo Foundation; Distributed under the GPL v2
 # $Header: $
 
+  29 Jan 2010; Justin Lecher (jlec) <jlec@j-schmitz.net>
+  pymol-apbs-plugin-0_p11.ebuild, pymol-apbs-plugin-9999.ebuild:
+  fixes for some file locations
+
 *pymol-apbs-plugin-9999 (28 Jan 2010)
 *pymol-apbs-plugin-0_p11 (28 Jan 2010)
 
diff --git a/sci-chemistry/pymol-apbs-plugin/Manifest b/sci-chemistry/pymol-apbs-plugin/Manifest
index 4c021e470..9b7b3a808 100644
--- a/sci-chemistry/pymol-apbs-plugin/Manifest
+++ b/sci-chemistry/pymol-apbs-plugin/Manifest
@@ -2,14 +2,14 @@
 Hash: SHA1
 
 DIST pymol-apbs-plugin-0_p11.py 102097 RMD160 1ab4b3a9caa2f1e2a3a42b1072c91eea1c6be31c SHA1 3678bd0e329efd5401304e9434014f6712be1374 SHA256 ed2e5c7eaa0a0c81cf12092fd58c949bbfce93b5c1acd3d880f812823a66a450
-EBUILD pymol-apbs-plugin-0_p11.ebuild 1126 RMD160 64afe0a01e46b6ada1b9cb0ed5b44637d59555ac SHA1 6f766b3cec406cd87865cf7a790ddd9866d13005 SHA256 0cad4f7d5c510ba0c78530e98dd58aa7e9bc4259d13a21cc4ec04c465fe0d2c2
-EBUILD pymol-apbs-plugin-9999.ebuild 1062 RMD160 abb8c8aa8dccfc414e8b4bbd5029a7723855e2b8 SHA1 37997702681381371c0c99fa012df1b3976bc35d SHA256 23f2397f2d23883b30376efa6feb71a5dbc58ff03a09b8ffe3223a31651dd585
-MISC ChangeLog 377 RMD160 5b7b7841452407b7c9a7b979aa472b7d19ff1c1b SHA1 29aa700459c032e657cbf7dd79a2d1b3eb696fba SHA256 a3523d151d6c4b093b6c3e9c05cbc885a6cbd73a96fda1eb79521ffb8e1da261
+EBUILD pymol-apbs-plugin-0_p11.ebuild 1259 RMD160 aa4ab2d2d3fb68a746d37676f5bc21e9eed1a629 SHA1 8a9fd61e08622b4901bb35e8b5709b8cfeeb222a SHA256 23707f07179df0adc96cd283e2692b7bb981977f10ee33be6caf411634ed9040
+EBUILD pymol-apbs-plugin-9999.ebuild 1195 RMD160 c6d506b64c2997142b950b6657e0ef75844f5392 SHA1 5a1cb56fe9b29f7c72ebfbec2a697a3f8dde9c49 SHA256 9f5bb4c1dd5dd4c4f200f3a7734c719990f77613eaac1aa4b98543588239d7ec
+MISC ChangeLog 532 RMD160 3e9a6f98fdb4a91ce56907190a30e7489183e907 SHA1 19c7b5f8fc778c381903e5a22bbf33d3bf72a62a SHA256 3dbaffda60a5aba35a97d3c31248992334c2030a3c4a7be3931224852a2cd05c
 MISC metadata.xml 215 RMD160 bc9c07aa91f2f175542244e4e4522a73558210a1 SHA1 facb283386de1c0b6b938cdcd4dde04d1694298b SHA256 13f32353652adbd3d934d41381cfc2cacc9e1127c508cebc73806cc1026ee80c
 -----BEGIN PGP SIGNATURE-----
 Version: GnuPG v2.0.11 (GNU/Linux)
 
-iEYEARECAAYFAktiFPYACgkQgAnW8HDreRaXGACfba3/fgZokDh5/YtC+vElxiB8
-gW8An33Es1lLI0hNTmWQdniKIT165vf+
-=A8Tt
+iEYEARECAAYFAktjGUQACgkQgAnW8HDreRZPUgCeIa7bkaHDJJO/5qlOy/Vx9e/c
+kaIAoK1WnL4aRIs3LiW55GCyB96bfFpe
+=EBAR
 -----END PGP SIGNATURE-----
diff --git a/sci-chemistry/pymol-apbs-plugin/pymol-apbs-plugin-0_p11.ebuild b/sci-chemistry/pymol-apbs-plugin/pymol-apbs-plugin-0_p11.ebuild
index 5c2de9b27..0b7afe517 100644
--- a/sci-chemistry/pymol-apbs-plugin/pymol-apbs-plugin-0_p11.ebuild
+++ b/sci-chemistry/pymol-apbs-plugin/pymol-apbs-plugin-0_p11.ebuild
@@ -29,8 +29,10 @@ src_unpack() {
 
 src_install() {
 	sed \
-		-e "s:^APBS_PSIZE_LOCATION.*:APBS_PSIZE_LOCATION = \"$(python_get_sitedir)/pdb2pqr/src/psize.py\":g" \
-		-e "s:^APBS_PDB2PQR_LOCATION.*:APBS_PDB2PQR_LOCATION = \"$(python_get_sitedir)/pdb2pqr/pdb2pqr.py\":g" \
+		-e "s:^APBS_BINARY_LOCATION.*:APBS_BINARY_LOCATION = \"${EPREFIX}/usr/bin/apbs\":g" \
+		-e "s:^APBS_PSIZE_LOCATION.*:APBS_PSIZE_LOCATION = \"$(python_get_sitedir)/pdb2pqr/src/\":g" \
+		-e "s:^APBS_PDB2PQR_LOCATION.*:APBS_PDB2PQR_LOCATION = \"$(python_get_sitedir)/pdb2pqr/\":g" \
+		-e "s:^TEMPORARY_FILE_DIR.*:TEMPORARY_FILE_DIR = \"./\":g" \
 		-i ${P}.py
 
 	insinto $(python_get_sitedir)/pmg_tk/startup/
diff --git a/sci-chemistry/pymol-apbs-plugin/pymol-apbs-plugin-9999.ebuild b/sci-chemistry/pymol-apbs-plugin/pymol-apbs-plugin-9999.ebuild
index 594391035..705c44be5 100644
--- a/sci-chemistry/pymol-apbs-plugin/pymol-apbs-plugin-9999.ebuild
+++ b/sci-chemistry/pymol-apbs-plugin/pymol-apbs-plugin-9999.ebuild
@@ -25,8 +25,10 @@ DEPEND="${RDEPEND}"
 
 src_install() {
 	sed \
-		-e "s:^APBS_PSIZE_LOCATION.*:APBS_PSIZE_LOCATION = \"$(python_get_sitedir)/pdb2pqr/src/psize.py\":g" \
-		-e "s:^APBS_PDB2PQR_LOCATION.*:APBS_PDB2PQR_LOCATION = \"$(python_get_sitedir)/pdb2pqr/pdb2pqr.py\":g" \
+		-e "s:^APBS_BINARY_LOCATION.*:APBS_BINARY_LOCATION = \"${EPREFIX}/usr/bin/apbs\":g" \
+		-e "s:^APBS_PSIZE_LOCATION.*:APBS_PSIZE_LOCATION = \"$(python_get_sitedir)/pdb2pqr/src/\":g" \
+		-e "s:^APBS_PDB2PQR_LOCATION.*:APBS_PDB2PQR_LOCATION = \"$(python_get_sitedir)/pdb2pqr/\":g" \
+		-e "s:^TEMPORARY_FILE_DIR.*:TEMPORARY_FILE_DIR = \"./\":g" \
 		-i src/apbsplugin.py
 
 	insinto $(python_get_sitedir)/pmg_tk/startup/
diff --git a/sci-chemistry/refmac/ChangeLog b/sci-chemistry/refmac/ChangeLog
index ea93f988f..dbebc6c0c 100644
--- a/sci-chemistry/refmac/ChangeLog
+++ b/sci-chemistry/refmac/ChangeLog
@@ -2,6 +2,25 @@
 # Copyright 1999-2010 Gentoo Foundation; Distributed under the GPL v2
 # $Header: $
 
+*refmac-5.6.0055 (28 Jan 2010)
+
+  28 Jan 2010; Justin Lecher (jlec) <jlec@j-schmitz.net>
+  -refmac-5.6.0054.ebuild, +refmac-5.6.0055.ebuild:
+  Version bump
+
+*refmac-5.6.0054 (28 Jan 2010)
+
+  28 Jan 2010; Justin Lecher (jlec) <jlec@j-schmitz.net>
+  files/5.6-allow-dynamic-linking.patch, -refmac-5.6.0051.ebuild,
+  +refmac-5.6.0054.ebuild:
+  Version bump
+
+*refmac-5.6.0051 (22 Jan 2010)
+
+  22 Jan 2010; Justin Lecher (jlec) <jlec@j-schmitz.net>
+  -refmac-5.6.0050.ebuild, +refmac-5.6.0051.ebuild:
+  Version bump
+
 *refmac-5.6.0050 (16 Jan 2010)
 
   16 Jan 2010; Justin Lecher (jlec) <jlec@j-schmitz.net>
diff --git a/sci-chemistry/refmac/Manifest b/sci-chemistry/refmac/Manifest
index 15ba153bb..869016052 100644
--- a/sci-chemistry/refmac/Manifest
+++ b/sci-chemistry/refmac/Manifest
@@ -5,17 +5,17 @@ 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 1325 RMD160 437aabe9c6fbdffeb56d249063ebd9fd269ad7a2 SHA1 2e0ceeb5d2a330d152fc4a0cbfae6c677e01a57f SHA256 f93e7e27ce665e3358bbb9097fc9d93b4ec61c9b3eb0c190935bb1b6cca5cbdf
+AUX 5.6-allow-dynamic-linking.patch 1321 RMD160 fbf71730de0ff6e1702533f998d9c18a3c768066 SHA1 943848aa7e9c0aecd02066751176e668c409f5b6 SHA256 ef489c7d2a27300c92dfada7a914386b9736b8f98dd4197d2cfe35ac3ec2d729
 AUX 5.6.0033-allow-dynamic-linking.patch 1178 RMD160 8222b326a7f2d80d1d6202f8761c9bd4bb3ac797 SHA1 07484f5c65e35823963a712ac378bc64dafc0e5d SHA256 24e40c994ce76668e62e2374e41ece1d89fb4c59ab185d3c6eb9c3e76d4610fb
 AUX test.log.patch 1146 RMD160 0ea6293e8ecde3b9ae12658a523e3c30a5c9f01b SHA1 d026fdea6a487754f7e48ec24bcf4851a613b6d1 SHA256 d2c2a09f44e525dc255bc2ac93ca4194b24ca1fe58c31f0e3b5c32e439dfe2e7
 AUX twin.inp 91 RMD160 0848ddf8ebdb6e0dd327f9d01d89f86007ac1859 SHA1 bdef4076010499cae0d0c886138e2230b835481a SHA256 172706f6ef1b7a85636a176d18e73611406f29ca8d84f1d82a6120daa8f956e6
-DIST refmac5.6_source_v5.6.0050.tar.gz 1251575 RMD160 175f93d292cfa6e225acd240727e3733cdf1c45e SHA1 75245e12dbaf8fd210ac7601bc92d4e78fa8d1c2 SHA256 cfbc2a5278c4765f4e7f9862defdaee0ba528e51de72ba92fdb1ee22ed33fdc9
+DIST refmac5.6_source_v5.6.0055.tar.gz 1252732 RMD160 74d5a556dec55c01c437f5ae188bc947b83dfb95 SHA1 6e80734f5455728d280f851d8e6289cbb63d07ad SHA256 b7659d1f21d7030a8d7b4e4e2994dc5bfcede85b1e67851022ee4f3fab257e71
 DIST refmac_5.5.0102.tar.gz 1298285 RMD160 0a33e10ad498f9d516aa174ceddf8f860ec1711f SHA1 b6291eb524b419434cd851d8b3b6e9ef6845695f SHA256 435614b4aa946fa4e982237d76f814ac6459e5de7db003009563b8d6a2e3aa9f
 DIST refmac_5.5.0105.tar.gz 1326353 RMD160 39928431ed7efdfd300855f43bf6323dc723a12c SHA1 511002586bec3966d8693d7f1c43496c9bdeda1f SHA256 4a65b1dc1ceaf216415612d80b1ba14dec2793bc29e7c2008c03773f1003205f
 DIST refmac_5.5.0106.tar.gz 1326422 RMD160 16207e528aea426efd70f7dca290b45eedda9050 SHA1 64bdc4ff6cb06c207a2382c4873092c9a4db0c8c SHA256 fe5d618a1aecbae8089cc0f0d2e8d6cdbd5e0afc4fca6c9783e393cabe6f63ce
 DIST refmac_5.5.0107.tar.gz 1326419 RMD160 360fe2dd88d31fc1b1afc077a15e469a1d8bdc13 SHA1 ab60eb466a46e7dae033225416e9883b8884c14b SHA256 aa605a689a194d596b0651f5116796d43d6e3967a6c496873bcdc712802a5fe8
 DIST refmac_5.5.0108.tar.gz 1326723 RMD160 0c896be0980aa15f4879563c69bad649af340831 SHA1 4de851b1723a62f2d58c312d3c62b4cb7423fa32 SHA256 8480cea31c707263455daf94d8f6ff2c485d0ac642dc86bd8609d9bffe6883c0
-DIST refmac_5.5.0109.tar.gz 1326779 RMD160 3b603c13638407cceb907bd43ac0a971b587c116 SHA1 3cc35a55df71bac4de3eec9cf0e690e221ae3c86 SHA256 38d416c94e1f86a0676d48d7ddaeb4af272970b8cd6b084e70aa38481327c59e
+DIST refmac_5.5.0109.tar.gz 1326744 RMD160 f88c466fb7fec331e2b4d49993e641e520d7eb78 SHA1 a9d0ae26e6e1b2e11c95947adb6bd6fb7daf0eb8 SHA256 5d575c53c358afcc4695856c94c6eee5f9e589c4a430f32c5733e2cd0097078b
 DIST test-framework.tar.gz 130933173 RMD160 7122539dc713615dca2ddaddfd8d152cd22624d0 SHA1 1d3e3019a67afb9b2346e919c859d402d3250fea SHA256 df050a2a29da80518cb0616a0bbeb82298ea0721549348d15353bf0f66240605
 EBUILD refmac-5.5.0102.ebuild 1584 RMD160 4fac2468c57c9ed9b34baf07a644103939b45c51 SHA1 2293bb927f5b6476317e5a485dbaa2cad60fbb2f SHA256 066766d009f97adb3d447f077ae4577bd5893d2af76c186ab06b4b16f47f41ec
 EBUILD refmac-5.5.0105.ebuild 1584 RMD160 4fac2468c57c9ed9b34baf07a644103939b45c51 SHA1 2293bb927f5b6476317e5a485dbaa2cad60fbb2f SHA256 066766d009f97adb3d447f077ae4577bd5893d2af76c186ab06b4b16f47f41ec
@@ -23,13 +23,13 @@ EBUILD refmac-5.5.0106.ebuild 1584 RMD160 4fac2468c57c9ed9b34baf07a644103939b45c
 EBUILD refmac-5.5.0107.ebuild 1584 RMD160 4fac2468c57c9ed9b34baf07a644103939b45c51 SHA1 2293bb927f5b6476317e5a485dbaa2cad60fbb2f SHA256 066766d009f97adb3d447f077ae4577bd5893d2af76c186ab06b4b16f47f41ec
 EBUILD refmac-5.5.0108.ebuild 1584 RMD160 4fac2468c57c9ed9b34baf07a644103939b45c51 SHA1 2293bb927f5b6476317e5a485dbaa2cad60fbb2f SHA256 066766d009f97adb3d447f077ae4577bd5893d2af76c186ab06b4b16f47f41ec
 EBUILD refmac-5.5.0109.ebuild 1584 RMD160 4fac2468c57c9ed9b34baf07a644103939b45c51 SHA1 2293bb927f5b6476317e5a485dbaa2cad60fbb2f SHA256 066766d009f97adb3d447f077ae4577bd5893d2af76c186ab06b4b16f47f41ec
-EBUILD refmac-5.6.0050.ebuild 1575 RMD160 c1197c01f5adca1c1ee428737e89d08609696daf SHA1 f7b9c6b46e894be4557b50f30cecf08153145564 SHA256 5937ea0f8a69af2fddceac63d7541b576e3f3aefb42b2073ea33f9fe71ff7d05
-MISC ChangeLog 8060 RMD160 566f95277c1b30e46dbe3a1c7e02b57963cecd95 SHA1 85bb8af16d3b7fd8be6b0ff9100c940ead4df4f4 SHA256 9588d71391a041c08ff6091ec43196e0a0d523bb19a990d543f9d255f79869d9
+EBUILD refmac-5.6.0055.ebuild 1575 RMD160 c1197c01f5adca1c1ee428737e89d08609696daf SHA1 f7b9c6b46e894be4557b50f30cecf08153145564 SHA256 5937ea0f8a69af2fddceac63d7541b576e3f3aefb42b2073ea33f9fe71ff7d05
+MISC ChangeLog 8572 RMD160 b3970ba5db3867c49e5bb4bf04b61af2632a3ebc SHA1 6d5cbf1ce38cc4f15c4ceee8c7f85f054cf23889 SHA256 c3fc2f19a57fb103623d83c460f9b6c0bd6d0399e9af8d3eb328b09e272999ce
 MISC metadata.xml 314 RMD160 d8922635160b6047732051715291e8553b513bba SHA1 b53fc6fb6cf908093794b876e729606c00351937 SHA256 50a519ddbcef4ad4f76175df36849a076d20adbb6340fdba292175b70c0d9719
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diff --git a/sci-chemistry/refmac/files/5.6-allow-dynamic-linking.patch b/sci-chemistry/refmac/files/5.6-allow-dynamic-linking.patch
index c1bbbc16e..b6ad38ac8 100644
--- a/sci-chemistry/refmac/files/5.6-allow-dynamic-linking.patch
+++ b/sci-chemistry/refmac/files/5.6-allow-dynamic-linking.patch
@@ -28,7 +28,7 @@ index 79d408e..e66c887 100644
  	$(FC) $(FFLAGS) -c ncs_simil.f90 hkon_secder_tch.f
  
  refmac:	$(SUBR)
--	$(FC) $(FFLAGS) -pg -o refmac${VERSION}   ${SUBR} $(LLIBOTHERS) $(LLIBCCP)
+-	$(FC) $(FFLAGS) -o refmac${VERSION}   ${SUBR} $(LLIBOTHERS) $(LLIBCCP)
 +	$(FC) $(FFLAGS) $(LDFLAGS) -o refmac${VERSION}   ${SUBR} $(LLIBOTHERS) $(LLIBCCP) $(LLIBCIF) $(LLIBLAPACK)
  
  libcheck:	$(SUBL)
diff --git a/sci-chemistry/refmac/refmac-5.6.0050.ebuild b/sci-chemistry/refmac/refmac-5.6.0055.ebuild
index 693c5cb49..693c5cb49 100644
--- a/sci-chemistry/refmac/refmac-5.6.0050.ebuild
+++ b/sci-chemistry/refmac/refmac-5.6.0055.ebuild