Merge branch 'master' into jlec

* master: (36 commits)
  sci-libs/msms: Version BUmp; Bump to new distutil-r1.eclass
  app-doc/root-docs: version bump
  sci-physics/root: version bump
  sys-cluster/hpl: version bump and fixes
  fixed deps
  In sci-libs/bigdft-abi-1.0.4-r1, CUDA support made compile.
  moved to gx86
  moved to gx86
  Beautify
  Beautify
  Beautify.
  Added new package: projections
  Added new package: projections
  Bashified package name mangling.
  sys-cluster/modules: Prefix keyworded. Added tests. FHS fixes. Add bunch of fedora patches
  Fixed missing use flag.
  sci-chemistry/ucsf-tools: Fix compilation with latest gcc
  sci-chemistry/modeller: Fix lib position, #474696
  sci-chemistry/pymol: Update repo uri
  sci-chemistry/pymol: Update repo uri
  ...

11 files changed, 38 insertions, 10 deletions

diff --git a/sci-chemistry/ambertools/ChangeLog b/sci-chemistry/ambertools/ChangeLog
index f4d3a9da3..c46b0af1f 100644
--- a/sci-chemistry/ambertools/ChangeLog
+++ b/sci-chemistry/ambertools/ChangeLog
@@ -2,6 +2,9 @@
 # Copyright 1999-2013 Gentoo Foundation; Distributed under the GPL v2
 # $Header: /var/cvsroot/gentoo-x86/sci-chemistry/ambertools/ChangeLog,v 1.2 2011/08/02 14:42:37 alexxy Exp $
 
+  28 Jun 2013; Christoph Junghans <ottxor@gentoo.org> ambertools-12.ebuild:
+  fixed deps
+
   03 Mar 2013; Justin Lecher <jlec@gentoo.org> ambertools-1.5-r4.ebuild:
   Add missing multilib.eclass
 
@@ -69,4 +72,3 @@
   28 Jul 2011; Alexey Shvetsov <alexxy@gentoo.org> +ambertools-1.5-r1.ebuild,
   +files/ambertools-1.5-gentoo.patch, +metadata.xml:
   Initial import to tree
-
diff --git a/sci-chemistry/ambertools/ambertools-12.ebuild b/sci-chemistry/ambertools/ambertools-12.ebuild
index 70ea7f3c3..83242962d 100644
--- a/sci-chemistry/ambertools/ambertools-12.ebuild
+++ b/sci-chemistry/ambertools/ambertools-12.ebuild
@@ -26,7 +26,7 @@ RDEPEND="
 	sci-libs/cifparse-obj
 	sci-chemistry/mopac7
 	sci-libs/netcdf
-	sci-libs/fftw:3.0
+	>=sci-libs/fftw-3.3:3.0
 	sci-chemistry/reduce"
 DEPEND="${RDEPEND}
 	app-shells/tcsh
diff --git a/sci-chemistry/gnome-chemistry-utils/ChangeLog b/sci-chemistry/gnome-chemistry-utils/ChangeLog
index b71a1a2f3..f45e5bf6a 100644
--- a/sci-chemistry/gnome-chemistry-utils/ChangeLog
+++ b/sci-chemistry/gnome-chemistry-utils/ChangeLog
@@ -2,6 +2,10 @@
 # Copyright 1999-2013 Gentoo Foundation; Distributed under the GPL v2
 # $Header: $
 
+  21 Jun 2013; Justin Lecher <jlec@gentoo.org>
+  gnome-chemistry-utils-0.14.2.ebuild, metadata.xml:
+  Fix min version of openbabel
+
   06 Apr 2013; Karl Linden (lilrc) <lilrc@users.sourceforge.net>
   gnome-chemistry-utils-0.14.2.ebuild:
   Migrate to gnome2 eclass.
diff --git a/sci-chemistry/gnome-chemistry-utils/gnome-chemistry-utils-0.14.2.ebuild b/sci-chemistry/gnome-chemistry-utils/gnome-chemistry-utils-0.14.2.ebuild
index cbaeea866..e0d8c6a23 100644
--- a/sci-chemistry/gnome-chemistry-utils/gnome-chemistry-utils-0.14.2.ebuild
+++ b/sci-chemistry/gnome-chemistry-utils/gnome-chemistry-utils-0.14.2.ebuild
@@ -23,7 +23,7 @@ RDEPEND="
 	>=gnome-extra/libgsf-1.14.9
 	>=sci-chemistry/bodr-5
 	>=sci-chemistry/chemical-mime-data-0.1.94
-	>=sci-chemistry/openbabel-2.1.0
+	>=sci-chemistry/openbabel-2.3.0
 	>=x11-libs/cairo-1.6.0
 	>=x11-libs/gdk-pixbuf-2.22.0
 	>=x11-libs/goffice-0.10.0
diff --git a/sci-chemistry/gnome-chemistry-utils/metadata.xml b/sci-chemistry/gnome-chemistry-utils/metadata.xml
index 5a8da44f4..94e01b4a7 100644
--- a/sci-chemistry/gnome-chemistry-utils/metadata.xml
+++ b/sci-chemistry/gnome-chemistry-utils/metadata.xml
@@ -1,11 +1,11 @@
 <?xml version="1.0" encoding="UTF-8"?>
 <!DOCTYPE pkgmetadata SYSTEM "http://www.gentoo.org/dtd/metadata.dtd">
 <pkgmetadata>
-	<longdescription lang="en">
+  <longdescription lang="en">
 		The Gnome Chemistry Utils provide some programs and library containing
 		GTK widgets and some C++ classes related to chemistry. 
 	</longdescription>
-	<use>
-		<flag name="gnumeric">Build pluging for gnumeric</flag>
-	</use>
+  <use>
+    <flag name="gnumeric">Build pluging for gnumeric</flag>
+  </use>
 </pkgmetadata>
diff --git a/sci-chemistry/modeller/ChangeLog b/sci-chemistry/modeller/ChangeLog
index 2817f00e5..cedd72b92 100644
--- a/sci-chemistry/modeller/ChangeLog
+++ b/sci-chemistry/modeller/ChangeLog
@@ -2,6 +2,10 @@
 # Copyright 1999-2013 Gentoo Foundation; Distributed under the GPL v2
 # $Header: $
 
+  26 Jun 2013; Justin Lecher <jlec@gentoo.org> -modeller-9.12-r1.ebuild,
+  +modeller-9.12-r2.ebuild:
+  Fix lib position, #474696
+
 *modeller-9.12-r1 (18 Jun 2013)
 
   18 Jun 2013; Justin Lecher <jlec@gentoo.org> -modeller-9.12.ebuild,
diff --git a/sci-chemistry/modeller/modeller-9.12-r1.ebuild b/sci-chemistry/modeller/modeller-9.12-r2.ebuild
index a25aa7fae..9cfd2e3d3 100644
--- a/sci-chemistry/modeller/modeller-9.12-r1.ebuild
+++ b/sci-chemistry/modeller/modeller-9.12-r2.ebuild
@@ -7,7 +7,7 @@ EAPI=5
 PYTHON_COMPAT=( python{2_6,2_7,3_2,3_3} )
 PYTHON_COMPAT=( python{2_6,2_7} )
 
-inherit distutils-r1 eutils versionator
+inherit distutils-r1 eutils multilib versionator
 
 DESCRIPTION="Homology or comparative modeling of protein three-dimensional structures"
 HOMEPAGE="http://salilab.org/modeller/"
@@ -83,6 +83,7 @@ python_install_all(){
 	exeinto ${INPATH}/lib/${EXECTYPE}/
 	doexe lib/${EXECTYPE}/lib*
 	dosym libmodeller.so.8 ${INPATH}/lib/${EXECTYPE}/libmodeller.so
+	dosym ../../${INPATH}/lib/${EXECTYPE}/libmodeller.so.8 /usr/$(get_libdir)/libmodeller.so.8
 
 	use doc && HTML_DOCS=( doc/. )
 	distutils-r1_python_install_all
diff --git a/sci-chemistry/pymol/ChangeLog b/sci-chemistry/pymol/ChangeLog
index f5e0f9b41..80bd47e8c 100644
--- a/sci-chemistry/pymol/ChangeLog
+++ b/sci-chemistry/pymol/ChangeLog
@@ -2,6 +2,9 @@
 # Copyright 1999-2013 Gentoo Foundation; Distributed under the GPL v2
 # $Header: $
 
+  26 Jun 2013; Justin Lecher <jlec@gentoo.org> pymol-9999.ebuild:
+  Update repo uri
+
   25 Mar 2013; Justin Lecher <jlec@gentoo.org> pymol-9999.ebuild, metadata.xml:
   Sync with tree
 
diff --git a/sci-chemistry/pymol/pymol-9999.ebuild b/sci-chemistry/pymol/pymol-9999.ebuild
index 564732c2f..57b5715bd 100644
--- a/sci-chemistry/pymol/pymol-9999.ebuild
+++ b/sci-chemistry/pymol/pymol-9999.ebuild
@@ -12,7 +12,7 @@ inherit distutils-r1 fdo-mime subversion versionator
 DESCRIPTION="A Python-extensible molecular graphics system"
 HOMEPAGE="http://pymol.sourceforge.net/"
 SRC_URI="http://dev.gentoo.org/~jlec/distfiles/${PN}-icons.tar.xz"
-ESVN_REPO_URI="https://pymol.svn.sourceforge.net/svnroot/pymol/trunk/pymol"
+ESVN_REPO_URI="svn://svn.code.sf.net/p/pymol/code/trunk/pymol"
 
 LICENSE="PSF-2.2"
 SLOT="0"
diff --git a/sci-chemistry/ucsf-tools/ChangeLog b/sci-chemistry/ucsf-tools/ChangeLog
index 758f3fd1d..397511d37 100644
--- a/sci-chemistry/ucsf-tools/ChangeLog
+++ b/sci-chemistry/ucsf-tools/ChangeLog
@@ -2,6 +2,9 @@
 # Copyright 1999-2013 Gentoo Foundation; Distributed under the GPL v2
 # $Header: $
 
+  26 Jun 2013; Justin Lecher <jlec@gentoo.org> ucsf-tools-9999.ebuild:
+  Fix compilation with latest gcc
+
   23 Apr 2013; Justin Lecher <jlec@gentoo.org> ucsf-tools-9999.ebuild,
   metadata.xml:
   Fix metadata, #466774; bump EAPI; set restricter license
diff --git a/sci-chemistry/ucsf-tools/ucsf-tools-9999.ebuild b/sci-chemistry/ucsf-tools/ucsf-tools-9999.ebuild
index bacdbce91..127745d4b 100644
--- a/sci-chemistry/ucsf-tools/ucsf-tools-9999.ebuild
+++ b/sci-chemistry/ucsf-tools/ucsf-tools-9999.ebuild
@@ -6,7 +6,7 @@ EAPI=5
 
 AUTOTOOLS_AUTORECONF=y
 
-inherit autotools-utils
+inherit autotools-utils flag-o-matic
 
 DESCRIPTION="The USF program suite"
 HOMEPAGE="http://xray.bmc.uu.se/usf/"
@@ -30,3 +30,14 @@ src_unpack() {
 	cd "${S}"
 	unpack mark-20110912.tgz
 }
+
+src_prepare() {
+	local src
+	append-fflags -ffixed-line-length-132
+	for src in \
+		ave coma comap comdem dataman essens imp lsqman mama mapfix \
+		mapman mave ncs6d o2d prof solex spancsi; do
+			mv ${src}/${src}.{f,F} || die
+	done
+	autotools-utils_src_prepare
+}