[cvs] dists/10.7/stable/main/finkinfo/sci pdb2pqr.info,1.4,1.5

[William Scott]

Update of /cvsroot/fink/dists/10.7/stable/main/finkinfo/sci
In directory sfp-cvs-1.v30.ch3.sourceforge.com:/tmp/cvs-serv24344

Modified Files:
pdb2pqr.info 
Log Message:
added missing numpy-py27 dependency

Index: pdb2pqr.info
===
RCS file: /cvsroot/fink/dists/10.7/stable/main/finkinfo/sci/pdb2pqr.info,v
retrieving revision 1.4
retrieving revision 1.5
diff -u -d -r1.4 -r1.5
--- pdb2pqr.info3 Jul 2013 20:59:53 -   1.4
+++ pdb2pqr.info7 Oct 2013 16:54:58 -   1.5
@@ -1,11 +1,11 @@
 Package: pdb2pqr
 Version: 1.7
-Revision: 3
+Revision: 4
 UseMaxBuildJobs: false
 Source: mirror:sourceforge:%n/%n-%v.tar.gz
 Source-MD5: 058622cb2ca6ca12af04d4f11b272951
 SourceDirectory: %n-%v
-Depends: python27, gcc48-shlibs
+Depends: python27, gcc48-shlibs, numpy-py27
 BuildDepends: python, python27, gcc48
 BuildConflicts: g77, g95, fort77
 Description: Converts pdb files to pqr


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[cvs] dists/10.4/stable/main/finkinfo/sci pdb2pqr.info,1.4,1.5

[William Scott]

Update of /cvsroot/fink/dists/10.4/stable/main/finkinfo/sci
In directory sfp-cvs-1.v30.ch3.sourceforge.com:/tmp/cvs-serv30115

Modified Files:
pdb2pqr.info 
Log Message:
added missing dependency on numpy-py27

Index: pdb2pqr.info
===
RCS file: /cvsroot/fink/dists/10.4/stable/main/finkinfo/sci/pdb2pqr.info,v
retrieving revision 1.4
retrieving revision 1.5
diff -u -d -r1.4 -r1.5
--- pdb2pqr.info5 Jul 2013 01:11:55 -   1.4
+++ pdb2pqr.info7 Oct 2013 18:49:30 -   1.5
@@ -1,11 +1,11 @@
 Package: pdb2pqr
 Version: 1.7
-Revision: 3
+Revision: 4
 UseMaxBuildJobs: false
 Source: mirror:sourceforge:%n/%n-%v.tar.gz
 Source-MD5: 058622cb2ca6ca12af04d4f11b272951
 SourceDirectory: %n-%v
-Depends: python27, gcc48-shlibs
+Depends: python27, gcc48-shlibs, numpy-py27
 BuildDepends: python, python27, gcc48
 BuildConflicts: g77, g95, fort77
 Description: Converts pdb files to pqr


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[cvs] dists/10.7/stable/main/finkinfo/sci coot-pre.info,1.3,1.4

[William Scott]

Update of /cvsroot/fink/dists/10.7/stable/main/finkinfo/sci
In directory sfp-cvs-1.v30.ch3.sourceforge.com:/tmp/cvs-serv8706

Modified Files:
coot-pre.info 
Log Message:
we now need --with-enhanced-ligand-tools to build with rdkit

Index: coot-pre.info
===
RCS file: /cvsroot/fink/dists/10.7/stable/main/finkinfo/sci/coot-pre.info,v
retrieving revision 1.3
retrieving revision 1.4
diff -u -d -r1.3 -r1.4
--- coot-pre.info   22 Sep 2013 19:00:13 -  1.3
+++ coot-pre.info   3 Oct 2013 12:48:48 -   1.4
@@ -1,11 +1,11 @@
 Package: coot-pre
 Version: 0.8-pre
-Revision: 4780
+Revision: 4791
 SourceDirectory: coot-%v
 Distribution: 10.6, 10.7, 10.8
 GCC: 4.0 
 Source: 
http://www2.mrc-lmb.cam.ac.uk/Personal/pemsley/coot/source/pre-releases/coot-%v-revision-%r.tar.gz
-Source-MD5: 32680c14bc018904b01c9a83d781d13d
+Source-MD5: 03bd3f33248d54f37ab6bb69aee1ec8f
 Source2: 
http://www.ysbl.york.ac.uk/~emsley/software/extras/reference-structures.tar.gz
 Source2-MD5: 257ab90d44f1c877ada96720dbb87c13
 ###
@@ -152,7 +152,7 @@
 --with-fftw=%p --with-gnomecanvas-prefix=%p  --with-gtk2 --with-glut-prefix=%p 
 \
 --with-guile-gtk --with-guile-gtk-prefix=%p --with-gl-prefix=/usr/X11R6
 \
 --with-gtkgl-prefix=%p --with-glib-prefix=%p  --with-goocanvas-prefix=%p   
 \
---with-gsl-prefix=%p --with-guile --with-python=%p --with-pygtk=%p 
--with-enterprise-tools   
+--with-gsl-prefix=%p --with-guile --with-python=%p --with-pygtk=%p 
--with-enhanced-ligand-tools  
 
 ###
 CompileScript: 


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[cvs] dists/10.4/stable/main/finkinfo/sci coot-pre.info,1.1,1.2

[William Scott]

Update of /cvsroot/fink/dists/10.4/stable/main/finkinfo/sci
In directory sfp-cvs-1.v30.ch3.sourceforge.com:/tmp/cvs-serv15356

Modified Files:
coot-pre.info 
Log Message:
fix so it builds once again with rdkit

Index: coot-pre.info
===
RCS file: /cvsroot/fink/dists/10.4/stable/main/finkinfo/sci/coot-pre.info,v
retrieving revision 1.1
retrieving revision 1.2
diff -u -d -r1.1 -r1.2
--- coot-pre.info   6 Sep 2013 05:40:39 -   1.1
+++ coot-pre.info   3 Oct 2013 15:36:43 -   1.2
@@ -1,11 +1,11 @@
 Package: coot-pre
 Version: 0.8-pre
-Revision: 4749
+Revision: 4791
 SourceDirectory: coot-%v
 Distribution: 10.6, 10.7, 10.8
 GCC: 4.0 
 Source: 
http://www2.mrc-lmb.cam.ac.uk/Personal/pemsley/coot/source/pre-releases/coot-%v-revision-%r.tar.gz
-Source-MD5: acbce0f1e9eaeebab24f7e33a56e4460
+Source-MD5: 03bd3f33248d54f37ab6bb69aee1ec8f
 Source2: 
http://www.ysbl.york.ac.uk/~emsley/software/extras/reference-structures.tar.gz
 Source2-MD5: 257ab90d44f1c877ada96720dbb87c13
 ###
@@ -139,11 +139,12 @@
 BuildDependsOnly: false
 NoSetCPPFLAGS: true
 NoSetLDFLAGS: true
-PatchFile: %n.patch
-PatchFile-MD5: 847c69ea1ded1d4238b66ab4840a8141
+#PatchFile: %n.patch
+#PatchFile-MD5: 32ce1999e10d267e9c61bebe0af2ea52
 PatchScript: 
-sed 's|@PREFIX@|%p|g' %{PatchFile} | patch -p1
+#sed 's|@PREFIX@|%p|g' %{PatchFile} | patch -p1
 perl -pi -e 's|CXX\=\libtool --mode\=link \$CXX\|#CXX|g' configure
+perl -pi -e 's|define coot-png-display-program \display\|define 
coot-png-display-program \open\|g' scheme/raster3d.scm
 
 ###
 ConfigureParams:   
@@ -151,7 +152,7 @@
 --with-fftw=%p --with-gnomecanvas-prefix=%p  --with-gtk2 --with-glut-prefix=%p 
 \
 --with-guile-gtk --with-guile-gtk-prefix=%p --with-gl-prefix=/usr/X11R6
 \
 --with-gtkgl-prefix=%p --with-glib-prefix=%p  --with-goocanvas-prefix=%p   
 \
---with-gsl-prefix=%p --with-guile --with-python=%p --with-pygtk=%p 
--with-enterprise-tools   
+--with-gsl-prefix=%p --with-guile --with-python=%p --with-pygtk=%p 
--with-enhanced-ligand-tools  
 
 ###
 CompileScript: 
@@ -207,8 +208,8 @@
 export SED=/usr/bin/sed
 export COOT_REFMAC_LIB_DIR=%p/share/coot/lib
 #
-NUMPROC=$(sysctl -n hw.ncpu)
-#NUMPROC=1
+# NUMPROC=$(sysctl -n hw.ncpu)
+NUMPROC=1
 make -j $NUMPROC install prefix=%i
 #
 # Clean up the 120 MB  mess, which zsh makes so much fun:


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[cvs] dists/10.7/stable/main/finkinfo/sci coot-pre.patch,1.1,NONE

[William Scott]

Update of /cvsroot/fink/dists/10.7/stable/main/finkinfo/sci
In directory sfp-cvs-1.v30.ch3.sourceforge.com:/tmp/cvs-serv4065

Removed Files:
coot-pre.patch 
Log Message:
patch now obsolete

--- coot-pre.patch DELETED ---


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[cvs] dists/10.7/stable/main/finkinfo/sci coot-pre.info,1.2,1.3

[William Scott]

Update of /cvsroot/fink/dists/10.7/stable/main/finkinfo/sci
In directory sfp-cvs-1.v30.ch3.sourceforge.com:/tmp/cvs-serv4143

Modified Files:
coot-pre.info 
Log Message:
update incorporates previous patch

Index: coot-pre.info
===
RCS file: /cvsroot/fink/dists/10.7/stable/main/finkinfo/sci/coot-pre.info,v
retrieving revision 1.2
retrieving revision 1.3
diff -u -d -r1.2 -r1.3
--- coot-pre.info   5 Sep 2013 02:35:52 -   1.2
+++ coot-pre.info   22 Sep 2013 19:00:13 -  1.3
@@ -1,11 +1,11 @@
 Package: coot-pre
 Version: 0.8-pre
-Revision: 4749
+Revision: 4780
 SourceDirectory: coot-%v
 Distribution: 10.6, 10.7, 10.8
 GCC: 4.0 
 Source: 
http://www2.mrc-lmb.cam.ac.uk/Personal/pemsley/coot/source/pre-releases/coot-%v-revision-%r.tar.gz
-Source-MD5: acbce0f1e9eaeebab24f7e33a56e4460
+Source-MD5: 32680c14bc018904b01c9a83d781d13d
 Source2: 
http://www.ysbl.york.ac.uk/~emsley/software/extras/reference-structures.tar.gz
 Source2-MD5: 257ab90d44f1c877ada96720dbb87c13
 ###
@@ -139,11 +139,12 @@
 BuildDependsOnly: false
 NoSetCPPFLAGS: true
 NoSetLDFLAGS: true
-PatchFile: %n.patch
-PatchFile-MD5: 847c69ea1ded1d4238b66ab4840a8141
+#PatchFile: %n.patch
+#PatchFile-MD5: 32ce1999e10d267e9c61bebe0af2ea52
 PatchScript: 
-sed 's|@PREFIX@|%p|g' %{PatchFile} | patch -p1
+#sed 's|@PREFIX@|%p|g' %{PatchFile} | patch -p1
 perl -pi -e 's|CXX\=\libtool --mode\=link \$CXX\|#CXX|g' configure
+perl -pi -e 's|define coot-png-display-program \display\|define 
coot-png-display-program \open\|g' scheme/raster3d.scm
 
 ###
 ConfigureParams:   


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[cvs] dists/10.7/stable/main/finkinfo/sci rdkit.info,1.8,1.9

[William Scott]

Update of /cvsroot/fink/dists/10.7/stable/main/finkinfo/sci
In directory sfp-cvs-1.v30.ch3.sourceforge.com:/tmp/cvs-serv31725

Modified Files:
rdkit.info 
Log Message:
changed from clang to gcc to get libSLNParse.1.dylib to build

Index: rdkit.info
===
RCS file: /cvsroot/fink/dists/10.7/stable/main/finkinfo/sci/rdkit.info,v
retrieving revision 1.8
retrieving revision 1.9
diff -u -d -r1.8 -r1.9
--- rdkit.info  8 Sep 2013 02:58:58 -   1.8
+++ rdkit.info  9 Sep 2013 01:28:54 -   1.9
@@ -1,6 +1,6 @@
 Package: rdkit
 Version: 2013.06.1
-Revision: 4
+Revision: 5
 Distribution: 10.6, 10.7, 10.8
 GCC: 4.0
 BuildDependsOnly: false
@@ -16,13 +16,13 @@
 similarity searches.
 
 BuildConflicts:  boost1.35.nopython, boost1.35.python26, boost1.35.python27, 
boost1.35.systempython, boost1.46.cmake, boost-jam, boost1.46.1.cmake, 
boost1.52.0.cmake
-Depends: %N-shlibs (= %v-%r), python27-shlibs, numpy-py27, sqlite3-shlibs, 
pil-py27, boost1.53.python27-shlibs, boost1.53.nopython-shlibs
+Depends: %N-shlibs (= %v-%r), python27-shlibs, numpy-py27, sqlite3-shlibs, 
pil-py27, boost1.53.python27-shlibs,  boost1.53.nopython-shlibs
 BuildDepends:  python27, numpy-py27, sqlite3-dev, cmake, boost1.53.python27
 CompileScript: 
 #!/bin/sh -efv
 mkdir build
 cd build
-cmake -DFLEX_EXECUTABLE:FILEPATH=/usr/bin/flex -DCMAKE_OSX_SYSROOT:PATH=/ 
-DCMAKE_OSX_DEPLOYMENT_TARGET:STRING= -DCMAKE_INSTALL_PREFIX=%p 
-DCMAKE_INSTALL_NAME_DIR=%p/lib/%n   -DCMAKE_PREFIX_PATH=%p  
-DBOOST_LIBRARYDIR=%p/lib/python2.7/site-packages 
-DBOOST_ROOT=%p/lib/boost-1_53 -DBoost_NO_SYSTEM_PATHS=ON 
-DPYTHON_LIBRARY=%p/lib/python2.7/config/libpython2.7.dylib  
-DPYTHON_INCLUDE_DIR=%p/include/python2.7 -DPYTHON_EXECUTABLE=%p/bin/python2.7 
..  
+CC=/usr/bin/gcc CXX=/usr/bin/g++ cmake 
-DFLEX_EXECUTABLE:FILEPATH=/usr/bin/flex -DCMAKE_OSX_SYSROOT:PATH=/ 
-DCMAKE_OSX_DEPLOYMENT_TARGET:STRING= -DCMAKE_INSTALL_PREFIX=%p 
-DCMAKE_INSTALL_NAME_DIR=%p/lib/%n   -DCMAKE_PREFIX_PATH=%p  
-DBOOST_LIBRARYDIR=%p/lib/python2.7/site-packages 
-DBOOST_ROOT=%p/lib/boost-1_53 -DBoost_NO_SYSTEM_PATHS=ON 
-DPYTHON_LIBRARY=%p/lib/python2.7/config/libpython2.7.dylib  
-DPYTHON_INCLUDE_DIR=%p/include/python2.7 -DPYTHON_EXECUTABLE=%p/bin/python2.7 
..  
 make install
 
 InstallScript: 
@@ -75,6 +75,7 @@
 %p/lib/%N/libRDGeometryLib.1.dylib1.0.0 %n  (= 
2013.06.1-1)
 %p/lib/%N/libShapeHelpers.1.dylib 1.0.0 %n  (= 
2013.06.1-1)
 %p/lib/%N/libSimDivPickers.1.dylib1.0.0 %n  (= 
2013.06.1-1)
+   %p/lib/%N/libSLNParse.1.dylib   
  1.0.0 %n  (= 2013.06.1-1)
 %p/lib/%N/libSmilesParse.1.dylib  1.0.0 %n  (= 
2013.06.1-1)
 %p/lib/%N/libSubgraphs.1.dylib1.0.0 %n  (= 
2013.06.1-1)
 %p/lib/%N/libSubstructMatch.1.dylib   1.0.0 %n  (= 
2013.06.1-1)


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[cvs] dists/10.4/stable/main/finkinfo/sci rdkit.info,1.5,1.6

[William Scott]

Update of /cvsroot/fink/dists/10.4/stable/main/finkinfo/sci
In directory sfp-cvs-1.v30.ch3.sourceforge.com:/tmp/cvs-serv31798

Modified Files:
rdkit.info 
Log Message:
build explicitly with gcc to be consistent with change in 10.7 branch

Index: rdkit.info
===
RCS file: /cvsroot/fink/dists/10.4/stable/main/finkinfo/sci/rdkit.info,v
retrieving revision 1.5
retrieving revision 1.6
diff -u -d -r1.5 -r1.6
--- rdkit.info  8 Sep 2013 03:03:44 -   1.5
+++ rdkit.info  9 Sep 2013 01:31:01 -   1.6
@@ -1,6 +1,6 @@
 Package: rdkit
 Version: 2013.06.1
-Revision: 4
+Revision: 5
 Distribution: 10.6, 10.7, 10.8
 GCC: 4.0
 BuildDependsOnly: false
@@ -16,13 +16,13 @@
 similarity searches.
 
 BuildConflicts:  boost1.35.nopython, boost1.35.python26, boost1.35.python27, 
boost1.35.systempython, boost1.46.cmake, boost-jam, boost1.46.1.cmake, 
boost1.52.0.cmake
-Depends: %N-shlibs (= %v-%r), python27-shlibs, numpy-py27, sqlite3-shlibs, 
pil-py27, boost1.53.python27-shlibs, boost1.53.nopython-shlibs
+Depends: %N-shlibs (= %v-%r), python27-shlibs, numpy-py27, sqlite3-shlibs, 
pil-py27, boost1.53.python27-shlibs,  boost1.53.nopython-shlibs
 BuildDepends:  python27, numpy-py27, sqlite3-dev, cmake, boost1.53.python27
 CompileScript: 
 #!/bin/sh -efv
 mkdir build
 cd build
-cmake -DFLEX_EXECUTABLE:FILEPATH=/usr/bin/flex -DCMAKE_OSX_SYSROOT:PATH=/ 
-DCMAKE_OSX_DEPLOYMENT_TARGET:STRING= -DCMAKE_INSTALL_PREFIX=%p 
-DCMAKE_INSTALL_NAME_DIR=%p/lib/%n   -DCMAKE_PREFIX_PATH=%p  
-DBOOST_LIBRARYDIR=%p/lib/python2.7/site-packages 
-DBOOST_ROOT=%p/lib/boost-1_53 -DBoost_NO_SYSTEM_PATHS=ON 
-DPYTHON_LIBRARY=%p/lib/python2.7/config/libpython2.7.dylib  
-DPYTHON_INCLUDE_DIR=%p/include/python2.7 -DPYTHON_EXECUTABLE=%p/bin/python2.7 
..  
+CC=/usr/bin/gcc CXX=/usr/bin/g++ cmake 
-DFLEX_EXECUTABLE:FILEPATH=/usr/bin/flex -DCMAKE_OSX_SYSROOT:PATH=/ 
-DCMAKE_OSX_DEPLOYMENT_TARGET:STRING= -DCMAKE_INSTALL_PREFIX=%p 
-DCMAKE_INSTALL_NAME_DIR=%p/lib/%n   -DCMAKE_PREFIX_PATH=%p  
-DBOOST_LIBRARYDIR=%p/lib/python2.7/site-packages 
-DBOOST_ROOT=%p/lib/boost-1_53 -DBoost_NO_SYSTEM_PATHS=ON 
-DPYTHON_LIBRARY=%p/lib/python2.7/config/libpython2.7.dylib  
-DPYTHON_INCLUDE_DIR=%p/include/python2.7 -DPYTHON_EXECUTABLE=%p/bin/python2.7 
..  
 make install
 
 InstallScript: 
@@ -75,6 +75,7 @@
 %p/lib/%N/libRDGeometryLib.1.dylib1.0.0 %n  (= 
2013.06.1-1)
 %p/lib/%N/libShapeHelpers.1.dylib 1.0.0 %n  (= 
2013.06.1-1)
 %p/lib/%N/libSimDivPickers.1.dylib1.0.0 %n  (= 
2013.06.1-1)
+   %p/lib/%N/libSLNParse.1.dylib   
  1.0.0 %n  (= 2013.06.1-1)
 %p/lib/%N/libSmilesParse.1.dylib  1.0.0 %n  (= 
2013.06.1-1)
 %p/lib/%N/libSubgraphs.1.dylib1.0.0 %n  (= 
2013.06.1-1)
 %p/lib/%N/libSubstructMatch.1.dylib   1.0.0 %n  (= 
2013.06.1-1)


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[cvs] dists/10.7/stable/main/finkinfo/sci rdkit.info,1.7,1.8

[William Scott]

Update of /cvsroot/fink/dists/10.7/stable/main/finkinfo/sci
In directory sfp-cvs-1.v30.ch3.sourceforge.com:/tmp/cvs-serv11463

Modified Files:
rdkit.info 
Log Message:
added dependency on boost1.53.nopython-shlibs

Index: rdkit.info
===
RCS file: /cvsroot/fink/dists/10.7/stable/main/finkinfo/sci/rdkit.info,v
retrieving revision 1.7
retrieving revision 1.8
diff -u -d -r1.7 -r1.8
--- rdkit.info  1 Aug 2013 01:12:55 -   1.7
+++ rdkit.info  8 Sep 2013 02:58:58 -   1.8
@@ -1,6 +1,6 @@
 Package: rdkit
 Version: 2013.06.1
-Revision: 2
+Revision: 4
 Distribution: 10.6, 10.7, 10.8
 GCC: 4.0
 BuildDependsOnly: false
@@ -16,7 +16,7 @@
 similarity searches.
 
 BuildConflicts:  boost1.35.nopython, boost1.35.python26, boost1.35.python27, 
boost1.35.systempython, boost1.46.cmake, boost-jam, boost1.46.1.cmake, 
boost1.52.0.cmake
-Depends: %N-shlibs (= %v-%r), python27-shlibs, numpy-py27, sqlite3-shlibs, 
pil-py27, boost1.53.python27-shlibs
+Depends: %N-shlibs (= %v-%r), python27-shlibs, numpy-py27, sqlite3-shlibs, 
pil-py27, boost1.53.python27-shlibs, boost1.53.nopython-shlibs
 BuildDepends:  python27, numpy-py27, sqlite3-dev, cmake, boost1.53.python27
 CompileScript: 
 #!/bin/sh -efv


--
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[cvs] dists/10.4/stable/main/finkinfo/sci rdkit.info,1.4,1.5

[William Scott]

Update of /cvsroot/fink/dists/10.4/stable/main/finkinfo/sci
In directory sfp-cvs-1.v30.ch3.sourceforge.com:/tmp/cvs-serv11659

Modified Files:
rdkit.info 
Log Message:
added dependency on boost1.53.nopython-shlibs

Index: rdkit.info
===
RCS file: /cvsroot/fink/dists/10.4/stable/main/finkinfo/sci/rdkit.info,v
retrieving revision 1.4
retrieving revision 1.5
diff -u -d -r1.4 -r1.5
--- rdkit.info  7 Sep 2013 04:01:51 -   1.4
+++ rdkit.info  8 Sep 2013 03:03:44 -   1.5
@@ -1,13 +1,11 @@
 Package: rdkit
 Version: 2013.06.1
-Revision: 3
+Revision: 4
 Distribution: 10.6, 10.7, 10.8
 GCC: 4.0
 BuildDependsOnly: false
 Source: mirror:sourceforge:rdkit/RDKit_2013_06_1.tgz
 Source-MD5: 13b9ea2c4c03e04dcea055c79b3173a9
-Source2: mirror:sourceforge:boost/boost_1_53_0.tar.bz2
-Source2-MD5: a00d22605d5dbcfb4c9936a9b35bc4c2
 Description: Cheminformatics and machine-learning software 
 DescDetail: 
 A collection of cheminformatics and machine-learning software written in C++ 
@@ -17,98 +15,70 @@
 to be stored in a relational database and retrieved via substructure and 
 similarity searches.
 
-BuildConflicts:  boost1.35.nopython, boost1.35.python26, boost1.35.python27, 
boost1.35.systempython, boost1.46.cmake, boost-jam, boost1.46.1.cmake
-Depends: %N-shlibs, python27-shlibs, numpy-py27, sqlite3-shlibs
-BuildDepends:  python27, numpy-py27, sqlite3-dev, cmake
+BuildConflicts:  boost1.35.nopython, boost1.35.python26, boost1.35.python27, 
boost1.35.systempython, boost1.46.cmake, boost-jam, boost1.46.1.cmake, 
boost1.52.0.cmake
+Depends: %N-shlibs (= %v-%r), python27-shlibs, numpy-py27, sqlite3-shlibs, 
pil-py27, boost1.53.python27-shlibs, boost1.53.nopython-shlibs
+BuildDepends:  python27, numpy-py27, sqlite3-dev, cmake, boost1.53.python27
 CompileScript: 
 #!/bin/sh -efv
-#
-# First build a more current boost libboost_python library and we will put it 
in the rdkit 
-# library subdirectory to avoid confusion
-#
-RDKIT_ROOT=$PWD
-cd ../boost_1_53_0
-BOOSTROOT=$PWD
-./bootstrap.sh --with-libraries=python,regex --with-python-root=%p 
--with-python=%p/bin/python2.7  --prefix=$PWD  
-# 
-./b2 install --prefix=$BOOSTROOT  
-cd lib
-# Despite the above it links to the system python, so fix that and give it a 
proper instal name id
-install_name_tool -change 
/System/Library/Frameworks/Python.framework/Versions/2.7/Python 
%p/lib/python2.7/config/libpython2.7.dylib libboost_python.dylib
-install_name_tool -id %p/lib/rdkit/libboost_python.dylib   
libboost_python.dylib
-#
-#
-install_name_tool -change 
/System/Library/Frameworks/Python.framework/Versions/2.7/Python 
%p/lib/python2.7/config/libpython2.7.dylib  libboost_regex.dylib
-install_name_tool -id %p/lib/rdkit/libboost_regex.dylib  libboost_regex.dylib
-#
-#
-# Now for rdkit itself
-#
-cd $RDKIT_ROOT 
 mkdir build
 cd build
-cmake -DCMAKE_INSTALL_PREFIX=%p -DCMAKE_INSTALL_NAME_DIR=%p/lib/%n   
-DCMAKE_PREFIX_PATH=%p   -DBOOST_ROOT=$BOOSTROOT -DBoost_NO_SYSTEM_PATHS=ON 
-DPYTHON_LIBRARY=%p/lib/python2.7/config/libpython2.7.dylib  
-DPYTHON_INCLUDE_DIR=%p/include/python2.7 -DPYTHON_EXECUTABLE=%p/bin/python2.7 
..  
-# NUMPROC=$(sysctl -n hw.ncpu)
-# make -j $NUMPROC install
- make install
-#
-# We only require the boost_python library and boost_regex library
-cp $BOOSTROOT/lib/libboost_python.dylib  
$RDKIT_ROOT/lib/libboost_python.dylib
-cp $BOOSTROOT/lib/libboost_regex.dylib   
$RDKIT_ROOT/lib/libboost_regex.dylib
-cp -R $BOOSTROOT/boost  $RDKIT_ROOT/Code/.
+cmake -DFLEX_EXECUTABLE:FILEPATH=/usr/bin/flex -DCMAKE_OSX_SYSROOT:PATH=/ 
-DCMAKE_OSX_DEPLOYMENT_TARGET:STRING= -DCMAKE_INSTALL_PREFIX=%p 
-DCMAKE_INSTALL_NAME_DIR=%p/lib/%n   -DCMAKE_PREFIX_PATH=%p  
-DBOOST_LIBRARYDIR=%p/lib/python2.7/site-packages 
-DBOOST_ROOT=%p/lib/boost-1_53 -DBoost_NO_SYSTEM_PATHS=ON 
-DPYTHON_LIBRARY=%p/lib/python2.7/config/libpython2.7.dylib  
-DPYTHON_INCLUDE_DIR=%p/include/python2.7 -DPYTHON_EXECUTABLE=%p/bin/python2.7 
..  
+make install
 
 InstallScript: 
 #!/bin/sh -efv
 mkdir -p %i/lib/python2.7/site-packages
+perl -pi -e 's|import Image|from PIL import Image|g' rdkit/sping/PIL/pidPIL.py
 cp -R rdkit %i/lib/python2.7/site-packages/.
 mkdir -p %i/lib
 cp -R lib %i/lib/%n
 mkdir -p %i/include
 cp -R Code %i/include/%n
+cp -R Contrib/PBF  %i/include/%n/.
+cp -R External/AvalonTools  %i/include/%n/.
+cp -R External/INCHI-API  %i/include/%n/.
+cp -R External/cmim-1.0  %i/include/%n/.
 
 SplitOff: 
 Package: %N-shlibs
 Description: rdkit dynamic libraries
 Files:  
-lib/%N/*.1.dylib 
-lib/%N/libboost_python.dylib   
   
-lib/%N/libboost_regex.dylib
  
+lib/%N/*.%v.dylib 
+lib/%N/*.1.dylib   
  
 
 Shlibs: 
-  

[cvs] dists/10.4/stable/main/finkinfo/sci rdkit.info,1.3,1.4

[William Scott]

Update of /cvsroot/fink/dists/10.4/stable/main/finkinfo/sci
In directory sfp-cvs-1.v30.ch3.sourceforge.com:/tmp/cvs-serv19860

Modified Files:
rdkit.info 
Log Message:
revert to previous revision

Index: rdkit.info
===
RCS file: /cvsroot/fink/dists/10.4/stable/main/finkinfo/sci/rdkit.info,v
retrieving revision 1.3
retrieving revision 1.4
diff -u -d -r1.3 -r1.4
--- rdkit.info  6 Sep 2013 05:40:39 -   1.3
+++ rdkit.info  7 Sep 2013 04:01:51 -   1.4
@@ -1,11 +1,13 @@
 Package: rdkit
 Version: 2013.06.1
-Revision: 2
+Revision: 3
 Distribution: 10.6, 10.7, 10.8
 GCC: 4.0
 BuildDependsOnly: false
 Source: mirror:sourceforge:rdkit/RDKit_2013_06_1.tgz
 Source-MD5: 13b9ea2c4c03e04dcea055c79b3173a9
+Source2: mirror:sourceforge:boost/boost_1_53_0.tar.bz2
+Source2-MD5: a00d22605d5dbcfb4c9936a9b35bc4c2
 Description: Cheminformatics and machine-learning software 
 DescDetail: 
 A collection of cheminformatics and machine-learning software written in C++ 
@@ -15,70 +17,98 @@
 to be stored in a relational database and retrieved via substructure and 
 similarity searches.
 
-BuildConflicts:  boost1.35.nopython, boost1.35.python26, boost1.35.python27, 
boost1.35.systempython, boost1.46.cmake, boost-jam, boost1.46.1.cmake, 
boost1.52.0.cmake
-Depends: %N-shlibs (= %v-%r), python27-shlibs, numpy-py27, sqlite3-shlibs, 
pil-py27, boost1.53.python27-shlibs
-BuildDepends:  python27, numpy-py27, sqlite3-dev, cmake, boost1.53.python27
+BuildConflicts:  boost1.35.nopython, boost1.35.python26, boost1.35.python27, 
boost1.35.systempython, boost1.46.cmake, boost-jam, boost1.46.1.cmake
+Depends: %N-shlibs, python27-shlibs, numpy-py27, sqlite3-shlibs
+BuildDepends:  python27, numpy-py27, sqlite3-dev, cmake
 CompileScript: 
 #!/bin/sh -efv
+#
+# First build a more current boost libboost_python library and we will put it 
in the rdkit 
+# library subdirectory to avoid confusion
+#
+RDKIT_ROOT=$PWD
+cd ../boost_1_53_0
+BOOSTROOT=$PWD
+./bootstrap.sh --with-libraries=python,regex --with-python-root=%p 
--with-python=%p/bin/python2.7  --prefix=$PWD  
+# 
+./b2 install --prefix=$BOOSTROOT  
+cd lib
+# Despite the above it links to the system python, so fix that and give it a 
proper instal name id
+install_name_tool -change 
/System/Library/Frameworks/Python.framework/Versions/2.7/Python 
%p/lib/python2.7/config/libpython2.7.dylib libboost_python.dylib
+install_name_tool -id %p/lib/rdkit/libboost_python.dylib   
libboost_python.dylib
+#
+#
+install_name_tool -change 
/System/Library/Frameworks/Python.framework/Versions/2.7/Python 
%p/lib/python2.7/config/libpython2.7.dylib  libboost_regex.dylib
+install_name_tool -id %p/lib/rdkit/libboost_regex.dylib  libboost_regex.dylib
+#
+#
+# Now for rdkit itself
+#
+cd $RDKIT_ROOT 
 mkdir build
 cd build
-cmake -DFLEX_EXECUTABLE:FILEPATH=/usr/bin/flex -DCMAKE_OSX_SYSROOT:PATH=/ 
-DCMAKE_OSX_DEPLOYMENT_TARGET:STRING= -DCMAKE_INSTALL_PREFIX=%p 
-DCMAKE_INSTALL_NAME_DIR=%p/lib/%n   -DCMAKE_PREFIX_PATH=%p  
-DBOOST_LIBRARYDIR=%p/lib/python2.7/site-packages 
-DBOOST_ROOT=%p/lib/boost-1_53 -DBoost_NO_SYSTEM_PATHS=ON 
-DPYTHON_LIBRARY=%p/lib/python2.7/config/libpython2.7.dylib  
-DPYTHON_INCLUDE_DIR=%p/include/python2.7 -DPYTHON_EXECUTABLE=%p/bin/python2.7 
..  
-make install
+cmake -DCMAKE_INSTALL_PREFIX=%p -DCMAKE_INSTALL_NAME_DIR=%p/lib/%n   
-DCMAKE_PREFIX_PATH=%p   -DBOOST_ROOT=$BOOSTROOT -DBoost_NO_SYSTEM_PATHS=ON 
-DPYTHON_LIBRARY=%p/lib/python2.7/config/libpython2.7.dylib  
-DPYTHON_INCLUDE_DIR=%p/include/python2.7 -DPYTHON_EXECUTABLE=%p/bin/python2.7 
..  
+# NUMPROC=$(sysctl -n hw.ncpu)
+# make -j $NUMPROC install
+ make install
+#
+# We only require the boost_python library and boost_regex library
+cp $BOOSTROOT/lib/libboost_python.dylib  
$RDKIT_ROOT/lib/libboost_python.dylib
+cp $BOOSTROOT/lib/libboost_regex.dylib   
$RDKIT_ROOT/lib/libboost_regex.dylib
+cp -R $BOOSTROOT/boost  $RDKIT_ROOT/Code/.
 
 InstallScript: 
 #!/bin/sh -efv
 mkdir -p %i/lib/python2.7/site-packages
-perl -pi -e 's|import Image|from PIL import Image|g' rdkit/sping/PIL/pidPIL.py
 cp -R rdkit %i/lib/python2.7/site-packages/.
 mkdir -p %i/lib
 cp -R lib %i/lib/%n
 mkdir -p %i/include
 cp -R Code %i/include/%n
-cp -R Contrib/PBF  %i/include/%n/.
-cp -R External/AvalonTools  %i/include/%n/.
-cp -R External/INCHI-API  %i/include/%n/.
-cp -R External/cmim-1.0  %i/include/%n/.
 
 SplitOff: 
 Package: %N-shlibs
 Description: rdkit dynamic libraries
 Files:  
-lib/%N/*.%v.dylib 
-lib/%N/*.1.dylib   
  
+lib/%N/*.1.dylib 
+lib/%N/libboost_python.dylib   
   
+lib/%N/libboost_regex.dylib
  
 
 Shlibs: 
-%p/lib/%N/libAlignment.1.dylib 

[cvs] dists/10.7/stable/main/finkinfo/sci coot.info, 1.27, 1.28 coot-pre.info, 1.1, 1.2 refmac.info, 1.2, 1.3

[William Scott]

Update of /cvsroot/fink/dists/10.7/stable/main/finkinfo/sci
In directory sfp-cvs-1.v30.ch3.sourceforge.com:/tmp/cvs-serv15233

Modified Files:
coot.info coot-pre.info refmac.info 
Log Message:
fixed cheesy nonrobust symlink hack in coot for refmac monomer lib

Index: coot.info
===
RCS file: /cvsroot/fink/dists/10.7/stable/main/finkinfo/sci/coot.info,v
retrieving revision 1.27
retrieving revision 1.28
diff -u -d -r1.27 -r1.28
--- coot.info   27 Aug 2013 16:43:41 -  1.27
+++ coot.info   5 Sep 2013 02:35:51 -   1.28
@@ -1,6 +1,6 @@
 Package: coot
 Version: 0.7.1.0  
-Revision: 6
+Revision: 7
 SourceDirectory: %n-0.7.1
 Distribution: 10.6, 10.7, 10.8
 GCC: 4.0 
@@ -141,7 +141,6 @@
 PatchFile-MD5: ac51a219f71aae370e33b68dbd80030d
 PatchScript: 
 sed 's|@PREFIX@|%p|g' %{PatchFile} | patch -p1
-#perl -pi -e 's|ccp4c=ccp4c|ccp4c=gpp4|g' configure
 perl -pi -e 's|CXX\=\libtool --mode\=link \$CXX\|#CXX|g' configure
 
 ###
@@ -227,10 +226,6 @@
 install_name_tool -change 
/System/Library/Frameworks/Python.framework/Versions/2.6/Python  
%p/lib/python2.6/config/libpython2.6.dylib %i/bin/coot-real
fi
 
-# This consolidates the refmac monomer library
-mkdir -p %i/share/coot/lib/data
-ln -s %p/share/refmac/monomers/ener_lib.cif%i/share/coot/lib/.
-ln -s %p/share/refmac/monomers %i/share/coot/lib/data/.
 # Reference structures should be in %i/share/coot/reference-structures
 cp -R ../reference-structures %i/share/coot/.
 cp -R * %i/share/coot/etc/.
@@ -241,7 +236,7 @@
 echo '#!/bin/sh -f '   %i/bin/coot
 echo 'export GUILE_WARN_DEPRECATED=no'  %i/bin/coot
 echo export LC_NUMERIC=C%i/bin/coot
-echo export COOT_REFMAC_LIB_DIR=%p/share/coot/lib   %i/bin/coot
+echo export COOT_REFMAC_LIB_DIR=%p/share/refmac %i/bin/coot
 echo export COOT_PYTHON_DIR=%p/share/coot/python%i/bin/coot
 echo 'export COOT_SBASE_DIR=%p/share/ccp4'  %i/bin/coot
 echo 'export CLIBD=%p/share/ccp4'   %i/bin/coot
  

Index: refmac.info
===
RCS file: /cvsroot/fink/dists/10.7/stable/main/finkinfo/sci/refmac.info,v
retrieving revision 1.2
retrieving revision 1.3
diff -u -d -r1.2 -r1.3
--- refmac.info 29 Aug 2013 23:14:20 -  1.2
+++ refmac.info 5 Sep 2013 02:35:52 -   1.3
@@ -1,6 +1,6 @@
 Package: refmac
 Version: 5.7.0032
-Revision: 2
+Revision: 3
 Source: 
http://www2.mrc-lmb.cam.ac.uk/groups/murshudov/content/%n/SourceEtal/%n5.7_source_v%v.tar.gz
 Source-MD5: 6bde74d6fc1c7f32026ced6fd8741c99 
 Source2: 
http://www2.mrc-lmb.cam.ac.uk/groups/murshudov/content/%n/Dictionary/%n_dictionary_v5.41.tar.gz
@@ -20,12 +20,12 @@
 InstallScript: 
 #!/bin/bash -efv
 mkdir -p %i/bin
-mkdir -p   %i/share/%n
+mkdir -p   %i/share/%n/data
 mkdir -p   %i/etc/profile.d
 cp refmac5 %i/bin/.
 cp refmac5 %i/bin/%n
 touch   %i/share/%n/environ.def   %i/share/%n/default.def   
-cp -R monomers  %i/share/%n/.
+cp -R monomers  %i/share/%n/data/.
 #
 echo 'if [[ ! -f  ${CINCL}/environ.def ]];then'   
%i/etc/profile.d/refmac.sh
 echo 'export CINCL=%p/share/%n'  
%i/etc/profile.d/refmac.sh
@@ -38,7 +38,7 @@
 echo 'endif' 
%i/etc/profile.d/refmac.csh
 
 RunTimeVars: 
-CLIBD_MON: %p/share/%n/monomers/
+CLIBD_MON: %p/share/%n/data/monomers/
 SYMINFO: %p/share/ccp4/syminfo.lib
 ATOMSF: %p/share/ccp4/atomsf.lib
 

Index: coot-pre.info
===
RCS file: /cvsroot/fink/dists/10.7/stable/main/finkinfo/sci/coot-pre.info,v
retrieving revision 1.1
retrieving revision 1.2
diff -u -d -r1.1 -r1.2
--- coot-pre.info   27 Aug 2013 16:48:24 -  1.1
+++ coot-pre.info   5 Sep 2013 02:35:52 -   1.2
@@ -1,11 +1,11 @@
 Package: coot-pre
 Version: 0.8-pre
-Revision: 4747
+Revision: 4749
 SourceDirectory: coot-%v
 Distribution: 10.6, 10.7, 10.8
 GCC: 4.0 
 Source: 
http://www2.mrc-lmb.cam.ac.uk/Personal/pemsley/coot/source/pre-releases/coot-%v-revision-%r.tar.gz
-Source-MD5: 049a0af2bbeda5d4a9761c682f74c8a0
+Source-MD5: acbce0f1e9eaeebab24f7e33a56e4460
 Source2: 
http://www.ysbl.york.ac.uk/~emsley/software/extras/reference-structures.tar.gz
 Source2-MD5: 257ab90d44f1c877ada96720dbb87c13
 ###
@@ -228,10 +228,6 @@
 install_name_tool -change 
/System/Library/Frameworks/Python.framework/Versions/2.6/Python  
%p/lib/python2.6/config/libpython2.6.dylib %i/bin/coot-real
fi
 
-# This consolidates the refmac monomer library
-mkdir -p 

[cvs] dists/10.7/stable/main/finkinfo/sci refmac.info,1.1,1.2

[William Scott]

Update of /cvsroot/fink/dists/10.7/stable/main/finkinfo/sci
In directory sfp-cvs-1.v30.ch3.sourceforge.com:/tmp/cvs-serv32528

Modified Files:
refmac.info 
Log Message:
refmac csh script error corrected in profile.d file

Index: refmac.info
===
RCS file: /cvsroot/fink/dists/10.7/stable/main/finkinfo/sci/refmac.info,v
retrieving revision 1.1
retrieving revision 1.2
diff -u -d -r1.1 -r1.2
--- refmac.info 15 Aug 2013 01:36:21 -  1.1
+++ refmac.info 29 Aug 2013 23:14:20 -  1.2
@@ -1,6 +1,6 @@
 Package: refmac
 Version: 5.7.0032
-Revision: 1
+Revision: 2
 Source: 
http://www2.mrc-lmb.cam.ac.uk/groups/murshudov/content/%n/SourceEtal/%n5.7_source_v%v.tar.gz
 Source-MD5: 6bde74d6fc1c7f32026ced6fd8741c99 
 Source2: 
http://www2.mrc-lmb.cam.ac.uk/groups/murshudov/content/%n/Dictionary/%n_dictionary_v5.41.tar.gz
@@ -32,7 +32,7 @@
 echo 'export CCP4_SCR=/tmp/$USER; mkdir -p $CCP4_SCR'
%i/etc/profile.d/refmac.sh
 echo 'fi'
%i/etc/profile.d/refmac.sh
 #
-echo 'if ( ! -d  ${CINCL} ) then' 
%i/etc/profile.d/refmac.csh
+echo 'if ( ! $?CINCL ) then'  
%i/etc/profile.d/refmac.csh
 echo 'setenv CINCL %p/share/%n'  
%i/etc/profile.d/refmac.csh
 echo 'setenv CCP4_SCR /tmp/$USER; mkdir -p $CCP4_SCR'
%i/etc/profile.d/refmac.csh
 echo 'endif' 
%i/etc/profile.d/refmac.csh


--
Learn the latest--Visual Studio 2012, SharePoint 2013, SQL 2012, more!
Discover the easy way to master current and previous Microsoft technologies
and advance your career. Get an incredible 1,500+ hours of step-by-step
tutorial videos with LearnDevNow. Subscribe today and save!
http://pubads.g.doubleclick.net/gampad/clk?id=58040911iu=/4140/ostg.clktrk
___
Fink-commits mailing list
Fink-commits@lists.sourceforge.net
http://news.gmane.org/gmane.os.apple.fink.cvs

[cvs] dists/10.7/stable/main/finkinfo/sci clipper.patch, NONE, 1.1 clipper.info, 1.6, 1.7

[William Scott]

Update of /cvsroot/fink/dists/10.7/stable/main/finkinfo/sci
In directory sfp-cvs-1.v30.ch3.sourceforge.com:/tmp/cvs-serv11916

Modified Files:
clipper.info 
Added Files:
clipper.patch 
Log Message:
clipper bug fix for cif file i/o bug causing coot to seg fault

--- NEW FILE: clipper.patch ---
--- clipper-2.1.20130601/clipper/cif/cif_data_io.cpp2012-03-07 
03:59:51.0 -0800
+++ clipper-2.1-fixup/clipper/cif/cif_data_io.cpp   2012-07-16 
07:18:48.0 -0700
@@ -66,8 +66,7 @@
 {
mode = NONE;
 
-   // Argh, bug. It's things like this that make me dislike object
-   // oriented programming - Magic happens behind your back.  The
+   // The
// problem was that we were trying to import into f_phi_i in
// close_read() when f_phi_i had not been initialised by calling
// import_hkl_data for it (because it comes from a function that
@@ -80,7 +79,11 @@
f_sigf_i = NULL;
f_phi_i  = NULL;
rfree_i  = NULL;
-  
+   d_sigd_i = NULL;
+   ABCD_i   = NULL;
+   I_sigI_i = NULL;
+   f_sigf_ano_i = NULL;
+   
// set these when we find them
clipper_cell_set_flag = 0; 
clipper_reso_set_flag = 0; 
@@ -184,9 +187,13 @@
  Message::message( Message_fatal( CIFfile: no file open for read ) );
 
   // make sure the data list is sized
-  if ( f_sigf_i != NULL ) f_sigf_i-update();
-  if (  f_phi_i != NULL )  f_phi_i-update();
-  if (  rfree_i != NULL )  rfree_i-update();
+  if ( f_sigf_i != NULL ) f_sigf_i-update();
+  if (  f_phi_i != NULL )  f_phi_i-update();
+  if (  rfree_i != NULL )  rfree_i-update();
+  if ( d_sigd_i != NULL ) d_sigd_i-update();
+  if (   ABCD_i != NULL )   ABCD_i-update();
+  if ( I_sigI_i != NULL ) I_sigI_i-update();
+  if ( f_sigf_ano_i != NULL ) f_sigf_ano_i-update();
 
   int ret_val = 0;
   int n_calc_data = 0; 
@@ -288,29 +295,32 @@
}
 
// RFree flag
-   char *s = mmCIFLoop-GetString(status, j, ierr_rfree_flag);
-   if (! ierr_rfree_flag) { 
-  x1[0] = -1;
-  if (s) {
- // std::cout  read status :  s  :  std::endl;
- if (strncmp(s, o, 1)) {
-x1[0] = 1;
- } else {
-if (strncmp(s, f, 1)) {
-   x1[0] = 0;
+   if (rfree_i) { 
+  char *s = mmCIFLoop-GetString(status, j, ierr_rfree_flag);
+  if (! ierr_rfree_flag) { 
+ x1[0] = -1; 
+ if (s) {
+// std::cout  read status :  s  :  
std::endl;
+// could be also x; not observed, just listed
+if (! strncmp(s, o, 1)) {
+   x1[0] = 1;
+} else {
+   if (! strncmp(s, f, 1)) {
+  x1[0] = 0;
+   }
 }
  }
+ // 
+ // Every output reflection gets one of these, even if
+ // it is set to -1.  Is that the correct thing to do?
+ // I have looked at over 200 recent sf mmCIFs and if
+ // the contain conventional data then they all have
+ // the status flag.
+ //
+ // However, SFS from EM data do not
+ // 
+ rfree_i-data_import( HKL(h,k,l), x1);
   }
-  // 
-  // Every output reflection gets one of these, even if
-  // it is set to -1.  Is that the correct thing to do?
-  // I have looked at over 200 recent sf mmCIFs and if
-  // the contain conventional data then they all have
-  // the status flag.
-  //
-  // However, SFS from EM data do not
-  // 
-  rfree_i-data_import( HKL(h,k,l), x1);
}
 


Index: clipper.info
===
RCS file: /cvsroot/fink/dists/10.7/stable/main/finkinfo/sci/clipper.info,v
retrieving revision 1.6
retrieving revision 1.7
diff -u -d -r1.6 -r1.7
--- clipper.info9 Aug 2013 04:09:02 -   1.6
+++ clipper.info28 Aug 2013 16:10:17 -  1.7
@@ -1,7 +1,7 @@
 Package: clipper
 Epoch: 1
 Version: 2.1.20130601
-Revision: 1
+Revision: 2
 GCC:4.0
 BuildDepends: 
 fftw (= 2.1.5-1010) | fftw-mpi (= 2.1.5-1010), 
@@ -19,6 +19,8 @@
 Source: ftp://ftp.ccp4.ac.uk/opensource/%n-%v.tar.gz
 Source-MD5: 2e0d3faec7cc5a1eb377392122e6e254
 SourceDirectory: %n-%v
+PatchFile: %n.patch 
+Patchfile-MD5: 986698b06772d70cfd2fe06f296f8210
 DocFiles: README AUTHORS COPYING ChangeLog
 Description: Object-oriented crystallographic libraries
 DescDetail: 

[cvs] dists/10.7/stable/main/finkinfo/sci coot.info, 1.26, 1.27 libccp4.info, 1.2, 1.3

[William Scott]

Update of /cvsroot/fink/dists/10.7/stable/main/finkinfo/sci
In directory sfp-cvs-1.v30.ch3.sourceforge.com:/tmp/cvs-serv14511

Modified Files:
coot.info libccp4.info 
Log Message:
added missing srs files to libccp4 and changed coot dependency accordingly

Index: libccp4.info
===
RCS file: /cvsroot/fink/dists/10.7/stable/main/finkinfo/sci/libccp4.info,v
retrieving revision 1.2
retrieving revision 1.3
diff -u -d -r1.2 -r1.3
--- libccp4.info15 Aug 2013 01:34:54 -  1.2
+++ libccp4.info27 Aug 2013 16:43:41 -  1.3
@@ -1,6 +1,6 @@
 Package: libccp4
 Version: 6.3.1
-Revision: 2
+Revision: 3
 Maintainer: W. G. Scott wgsc...@users.sourceforge.net 
 DescPackaging: 
  Based on package created by Morten Kjeldgaard m...@bioxray.dk with minor
@@ -13,6 +13,8 @@
 Source-MD5: 82d662032893329fd4ccf32186c649a1
 Source2: ftp://ftp.ccp4.ac.uk/ccp4/6.3.0/ccp4-6.3.0/src/Prodrg/prodrg.param
 Source2-MD5: 807f5df3c33e8dda9b49eab939c6fd69
+Source3: ftp://ftp.ccp4.ac.uk/opensource/ccp4srs-data-20120621.tar.gz
+Source3-MD5: f8b62642f313ae1342cd13ea8699eca7
 NoSourceDirectory: false
 Depends: %N-shlibs (= %v-%r), gcc48-shlibs 
 BuildDepends: mmdb-dev (= 1.25.3-1), ssm-dev (= 1.3-1), gcc48, pkgconfig
@@ -58,7 +60,10 @@
 InstallScript: 
   make install DESTDIR=%d
   mkdir -p %i/share/ccp4
-  cp ../prodrg.param %i/share/ccp4/.
+  cp ../prodrg.param%i/share/ccp4/.
+  cp ../ccp4srs-data-20120621/index.srs %i/share/ccp4/.
+  cp ../ccp4srs-data-20120621/graph.srs %i/share/ccp4/.
+  cp ../ccp4srs-data-20120621/struct.srs%i/share/ccp4/.
 
 SplitOff: 
   Package: %N-shlibs
@@ -98,6 +103,9 @@
share/ccp4/syminfo.lib
share/ccp4/symop.lib
share/ccp4/prodrg.param
+   share/ccp4/index.srs 
+   share/ccp4/graph.srs 
+   share/ccp4/struct.srs
  
 
  

Index: coot.info
===
RCS file: /cvsroot/fink/dists/10.7/stable/main/finkinfo/sci/coot.info,v
retrieving revision 1.26
retrieving revision 1.27
diff -u -d -r1.26 -r1.27
--- coot.info   15 Aug 2013 02:38:14 -  1.26
+++ coot.info   27 Aug 2013 16:43:41 -  1.27
@@ -1,6 +1,6 @@
 Package: coot
 Version: 0.7.1.0  
-Revision: 5
+Revision: 6
 SourceDirectory: %n-0.7.1
 Distribution: 10.6, 10.7, 10.8
 GCC: 4.0 
@@ -33,12 +33,14 @@
 stereo on OS X.
 
 ###
-Recommends:  povray, ccp4, raster3d
+Recommends:  povray, ccp4, raster3d  
+Conflicts: coot-pre
+Replaces: coot-pre  
 BuildDepends: 
  fink (= 0.24.12)   ,
  boost1.53.python27 (= 1.53.0-1),
  clipper-dev (= 1:2.1.20130601-1),
- libccp4-dev (= 6.3.1-2),
+ libccp4-dev (= 6.3.1-3),
  mmdb-dev (= 1.25.3-1)  ,
  ssm-dev (= 1.3-1)  ,
  atk1 (= 1.28.0-1)  ,
@@ -87,8 +89,8 @@
  coot-shlibs (= 0.7.1.0-%r)   ,
  boost1.53.python27-shlibs (= 1.53.0-1),
  clipper-shlibs (= 1:2.1.20130601-1),
- libccp4-shlibs (= 6.3.1-2)  ,
- libccp4-lib (= 6.3.1-2) ,
+ libccp4-shlibs (= 6.3.1-3)  ,
+ libccp4-lib (= 6.3.1-3) ,
  mmdb-shlibs (= 1.25.3-1),
  ssm-shlibs (= 1.3-1),
  atk1-shlibs (= 1.28.0-1),
@@ -241,7 +243,7 @@
 echo export LC_NUMERIC=C%i/bin/coot
 echo export COOT_REFMAC_LIB_DIR=%p/share/coot/lib   %i/bin/coot
 echo export COOT_PYTHON_DIR=%p/share/coot/python%i/bin/coot
-echo 'export COOT_SBASE_DIR=$CCP4/share/sbase'  %i/bin/coot
+echo 'export COOT_SBASE_DIR=%p/share/ccp4'  %i/bin/coot
 echo 'export CLIBD=%p/share/ccp4'   %i/bin/coot
  
 echo export 
PYTHONPATH=%p/lib/python2.7/site-packages:%p/lib/python2.7/site-packages/gtk-2.0:%p/share/coot/python
%i/bin/coot
 echo %p/bin/coot-real \\$@\   %i/bin/coot
@@ -253,11 +255,13 @@
 DocFiles: README AUTHORS NEWS COPYING ABOUT-NLS BUGS TODO
 License: GPL
 Maintainer: W. G. Scott wgsc...@users.sourceforge.net 
-Homepage: http://lmb.bioch.ox.ac.uk/coot
+Homepage: http://www2.mrc-lmb.cam.ac.uk/Personal/pemsley/coot/
 ###
 #
 SplitOff: 
 Package: %N-shlibs
+Conflicts: coot-pre-shlibs
+Replaces: coot-pre-shlibs
 Files: 
 lib/libccp4mg-*.0*.dylib  
 lib/libcoot-*.0*.dylib  
@@ -305,6 +309,8 @@
 Package: %N-dev
 Depends: %N (= 0.7.1.0-%r)
 BuildDependsOnly: True
+Conflicts: coot-pre-dev
+Replaces: coot-pre-dev
 Files:
 lib/*.a
 


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[cvs] dists/10.7/stable/main/finkinfo/sci coot-pre.info, NONE, 1.1 coot-pre.patch, NONE, 1.1

[William Scott]

Update of /cvsroot/fink/dists/10.7/stable/main/finkinfo/sci
In directory sfp-cvs-1.v30.ch3.sourceforge.com:/tmp/cvs-serv14733

Added Files:
coot-pre.info coot-pre.patch 
Log Message:
coot variant to placate those demanding access to the latest features

--- NEW FILE: coot-pre.patch ---
diff -ruN coot-0.6.2-pre-1-orig/scheme/group-settings.scm 
coot-0.6.2-pre-1/scheme/group-settings.scm
--- coot-0.6.2-pre-1-orig/scheme/group-settings.scm 2009-07-04 
05:57:36.0 -0700
+++ coot-0.6.2-pre-1/scheme/group-settings.scm  2010-03-31 09:52:42.0 
-0700
@@ -28,6 +28,7 @@
   (set-browser-interface firefox))
 
   (if (string=? os-type Darwin)
+ (set-display-lists-for-maps 0)
   (set-browser-interface open)))
 
 ;; York setting for molprobity. 
diff -ruN coot-0.6.2-pre-1-orig/scheme/povray.scm 
coot-0.6.2-pre-1/scheme/povray.scm
--- coot-0.6.2-pre-1-orig/scheme/povray.scm 2009-07-04 05:57:34.0 
-0700
+++ coot-0.6.2-pre-1/scheme/povray.scm  2010-03-31 09:54:43.0 -0700
@@ -14,7 +14,7 @@
   (lambda ()
 
 ; this is directory that contains colors.inc
-(list (string-append +L/sw/share/povray- povray-version /include)
+(list (string-append +L@PREFIX@/share/povray- povray-version /include)
  +FN16)))
 
 ;; Run provray using current displayed image and write .pov file to
diff -ruN coot-0.6.2-pre-1-orig/scheme/raster3d.scm 
coot-0.6.2-pre-1/scheme/raster3d.scm
--- coot-0.6.2-pre-1-orig/scheme/raster3d.scm   2009-07-04 05:57:34.0 
-0700
+++ coot-0.6.2-pre-1/scheme/raster3d.scm2010-03-31 09:55:54.0 
-0700
@@ -1,7 +1,7 @@
 
 (define coot-r3d-file-name coot.r3d)
 (define coot-png-file-name coot.png)
-(define coot-png-display-program display)
+(define coot-png-display-program open)
 
 ;; run raster3d
 (define render-image

--- NEW FILE: coot-pre.info ---
Package: coot-pre
Version: 0.8-pre
Revision: 4747
SourceDirectory: coot-%v
Distribution: 10.6, 10.7, 10.8
GCC: 4.0 
Source: 
http://www2.mrc-lmb.cam.ac.uk/Personal/pemsley/coot/source/pre-releases/coot-%v-revision-%r.tar.gz
Source-MD5: 049a0af2bbeda5d4a9761c682f74c8a0
Source2: 
http://www.ysbl.york.ac.uk/~emsley/software/extras/reference-structures.tar.gz
Source2-MD5: 257ab90d44f1c877ada96720dbb87c13
###
Description: Crystallographic molecular graphics
DescDetail: 
This version contains pre-release features and will be updated upon request.
.
Coot stands for Crystallograhic Object Oriented Toolkit. It is a toolkit and
interactive molecular graphical display and manipulation program designed for
macromolecular crystallography. Coot uses professional (and free) widgets (with
the gui builder glade), mmdb, clipper, and OpenGL, together with a new approach
to map contouring and importing/creation and other (modelling) operations. The
mmdb, clipper, ssm and mccp4 libraries are provided in individual fink packages
that replace the now obsolete ccp4-onlylibs-dev fink package. On-line
documentation is available from the coot website accessed via the help menu,
or manually, via the web-site, (see below) and is updated regularly.
.
To have an Aqua-like Coot gtk+2 environment, issue the following command:
 echo include \%p/share/themes/Glossy_P/gtk-2.0/gtkrc\~/.gtkrc-2.0
or simply create a file called ~/.gtkrc-2.0 and put this line in it:
 include \%p/share/themes/Glossy_P/gtk-2.0/gtkrc\
.
Install povray and raster3d fink packages to use the F8 key for producing 
ray-traced images. You may have to re-map the Spaces.app keybinding.
.
Coot now works with Zalman LCD hardware stereo and old-fashioned CRT hardware
stereo on OS X.

###
Recommends:  povray, ccp4, raster3d
Conflicts: coot
Replaces: coot
BuildDepends: 
 fink (= 0.24.12)   ,
 boost1.53.python27 (= 1.53.0-1),
 clipper-dev (= 1:2.1.20130601-1),
 libccp4-dev (= 6.3.1-3),
 mmdb-dev (= 1.25.3-1)  ,
 ssm-dev (= 1.3-1)  ,
 atk1 (= 1.28.0-1)  ,
 cairo (= 1.8.8-3)  ,
 expat1  ,
 fftw | fftw-mpi ,
 fontconfig2-dev (= 2.8.0-4),
 freetype219 (= 2.3.12-1)   ,
 freeglut,
 giflib  ,
 glib2-dev (= 2.22.0-1) ,
 glitz   ,
 goocanvas  (= 0.15-2)  ,
 gmp5,
 gsl ,
 gtk+2  (= 2.18.0-1),
 gtk+2-dev (= 2.18.0-1) ,
 gtkglext1   ,
 guile18 ,
 guile18-dev ,
 guile18-lib ,
 guile18-gtk-dev (= 2.0-10) ,
 libart2 (= 2.3.16-2)   ,
 libcurl4,
 libgettext8-dev ,
 libglade2 (= 2.6.2-1)  ,
 libgnomecanvas2-dev (= 2.20.0) ,
 libjpeg8,
 libpng15   

[cvs] dists/10.7/stable/main/finkinfo/sci tinker.patch, NONE, 1.1 tinker.info, 1.4, 1.5

[William Scott]

Update of /cvsroot/fink/dists/10.7/stable/main/finkinfo/sci
In directory sfp-cvs-1.v30.ch3.sourceforge.com:/tmp/cvs-serv23783

Modified Files:
tinker.info 
Added Files:
tinker.patch 
Log Message:
tinker updates via Jack Howarth

--- NEW FILE: tinker.patch ---
--- tinker/source/initial.f.orig2013-06-07 09:19:19.0 -0400
+++ tinker/source/initial.f 2013-06-07 09:21:08.0 -0400
@@ -60,8 +60,8 @@
 c
 c Intel compiler extensions to OpenMP standard
 c
-!$call kmp_set_stacksize (2**28)
-!$call kmp_set_blocktime (0)
+c !$call kmp_set_stacksize (2**28)
+c !$call kmp_set_blocktime (0)
 c
 c default unit numbers for input and output
 c

Index: tinker.info
===
RCS file: /cvsroot/fink/dists/10.7/stable/main/finkinfo/sci/tinker.info,v
retrieving revision 1.4
retrieving revision 1.5
diff -u -d -r1.4 -r1.5
--- tinker.info 3 Jul 2013 21:13:06 -   1.4
+++ tinker.info 27 Aug 2013 19:31:09 -  1.5
@@ -1,15 +1,20 @@
 Package: tinker
-Version: 6.2.05
+Version: 6.2.06
 Revision: 1
 Source: http://dasher.wustl.edu/%n/downloads/%n-%v.tar.gz
 SourceRename: %n-%v.tar.gz 
 SourceDirectory: %n
-Source-MD5: 5a2be7b669e49636f9d602f76534c6e9
-BuildDepends: gcc48
-Depends: gcc48-shlibs
+Source-MD5: 5b26971634f65f13e16011d1cd781aac
+PatchFile: %n.patch
+PatchFile-MD5: 962d75c0f3eecdccde5c0b6b2e6e8839
+BuildDepends: gcc48-compiler, fftw3
+Depends: gcc48-shlibs, fftw3-shlibs
 PatchScript: 
 #!/bin/zsh -efv
-perl -pi -e 's|gfortran -c -O3|gfortran -c -O3 -fno-align-commons|g' 
macosx/**/*.make
+%{default_script}
+perl -pi -e 's|gfortran -c -O3|gfortran-fsf-4.8 -c -O3 -fno-align-commons 
-fopenmp|g' macosx/**/*.make
+perl -pi -e 's|gfortran |gfortran-fsf-4.8 -fopenmp |g' macosx/**/link*.make
+perl -pi -e 's|libtinker.a|libtinker.a -L%p/lib -lfftw3 -lfftw3_omp 
-L%p/lib/gcc4.8/lib -lgomp|g' macosx/**/link*.make
 
 CompileScript:  
 #!/bin/bash -ev


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[cvs] dists/10.7/stable/main/finkinfo/sci pointless.info, NONE, 1.1 pointless.patch, NONE, 1.1

[William Scott]

Update of /cvsroot/fink/dists/10.7/stable/main/finkinfo/sci
In directory sfp-cvs-1.v30.ch3.sourceforge.com:/tmp/cvs-serv18193

Added Files:
pointless.info pointless.patch 
Log Message:
another pointless update

--- NEW FILE: pointless.patch ---
diff -ruN pointless-orig/Makefile pointless/Makefile
--- pointless-orig/Makefile 2013-08-13 23:20:31.0 -0700
+++ pointless/Makefile  2013-08-13 23:20:06.0 -0700
@@ -4,14 +4,14 @@
 #  -static doesn't work on hex
 
 # Compilers
-CC = cc
-CXX= g++
+CC = /usr/bin/llvm-gcc-4.2
+CXX= /usr/bin/llvm-g++-4.2
 
 # Compiler flags
 #OPT = -g -m32
 #OPT = -g -Wreturn-type
 #OPT = -O -m32 -Wall
-OPT = -O -static
+OPT = -O3 
 #OPT = -O0 -g3
 
 CXXFLAGS=  ${OPT}
@@ -20,27 +20,26 @@
 # Link flags
 LFLAGS= ${OPT}
 STATIC=
-#STATIC=  -static-libgcc  -static-libstdc++
+ 
 
 #  CCP4 stuff: point to the latest version compiled from source
-CCP4SRC=${CCP4}/../CurrentSource
-CLIB=${CCP4SRC}/lib
-CLIBS=${CLIB}/libccp4
+CCP4SRC=
+CLIB=@prefix@/lib
+CLIBS=@prefix@/lib
 
 
 # CCTBX locations
-CCTBX=${CLIB}/cctbx
+CCTBX=@prefix@/lib/cctbx
 #CCTBX=/usr/local/CCTBX
 CCTBX_sources=${CCTBX}/cctbx_sources
 
 #  Version 1 = 2006
 #CCTBX_VERSION=2006
 #  Version 2 = 2007
-CCTBX_VERSION=2007
+CCTBX_VERSION=2013
 
 XCPPFLAGS=  -DCCTBX_VERSION=${CCTBX_VERSION}
-#XCPPFLAGS= -ftemplate-depth-120  -Wno-long-double
-#XCPPFLAGS= -ftemplate-depth-120 -fcoalesce-templates -Wno-long-double
+ 
 
 # Clipper location
 CLPLIB=${CLIB}
@@ -57,12 +56,15 @@
 # cctbx
 ITBX=\
 -I${CCTBX_sources}/boost \
--I${CCP4}/include \
--I${CCTBX_sources}/cctbx_project
+-I@prefix@/include -I@prefix@/include/ccp4  \
+-I${CCTBX_sources}/cctbx_project \
+-I${CCTBX}/cctbx_sources \
+-I${CCTBX}/cctbx_sources/include \
+-I${CCTBX}/cctbx_build/include
 
 ##-I${CCTBX_sources}/cctbx_project/scitbx/include
 
-INCLUDE=-I. ${ITBX} ${ICLPR} ${ICCP4}
+INCLUDE=-I. -I@prefix@/include ${ITBX} ${ICLPR} ${ICCP4} 
 
 # Libraries
 # CCP4
@@ -72,10 +74,10 @@
 LCLPR=-L${CLPLIB} -lclipper-ccp4 -lclipper-contrib -lclipper-minimol 
-lclipper-mmdb -lclipper-core 
 
 # cctbx
-LTBX= ${CLIB}/libcctbx.a
+LTBX= ${CCTBX}/cctbx_build/lib/libcctbx.a
 
-SLIB = -Wl,--whole-archive -lpthread -Wl,--no-whole-archive
-#SLIB=
+#SLIB = -Wl,--whole-archive -lpthread -Wl,--no-whole-archive
+SLIB=
 
 LDLIBS=${LTBX} ${LCLPR} ${LCCP4} ${SLIB} ${STATIC}
 

--- NEW FILE: pointless.info ---
Package: pointless
Version: 1.8.7
Revision: 1
Source: ftp://ftp.mrc-lmb.cam.ac.uk/pub/pre/%n-%v.tar.gz
Source-MD5: 512b203d31800b7546455ad41f4ffbf8
NoSourceDirectory: yes
Depends:  
libccp4-shlibs, 
fftw-shlibs,
clipper-shlibs,
mmdb-shlibs,
cctbx

BuildDepends: 
fftw, 
libccp4-dev,  
clipper-dev,
mmdb-dev,
cctbx

NoSetCPPFLAGS: true
NoSetLDFLAGS: true
PatchFile: %n.patch
PatchFile-MD5: 94e2db982e380d456c3b5ed7ad98bc8b
PatchScript: 
 cp Makefile.make Makefile
 sed 's|@prefix@|%p|g'  %{PatchFile} | patch -p1

CompileScript:  
#!/bin/bash -efv
source %p/bin/init.sh
make

InstallScript: 
#!/bin/bash -efv
source %p/bin/init.sh
mkdir -p %i/bin
cp pointless othercell  %i/bin/.

Description: CCP4 point and space group and index tests
DescDetail: 
Pointless has several possible functions:
1. Determination of Laue group and space group (LAUEGROUP mode).
2. Testing of alternative indexing schemes
3. Checking the centre of the diffraction pattern
4. Reindexing

License: Restrictive 
Homepage: http://www.ccp4.ac.uk/html/pointless.html
Maintainer: W. G. Scott wgsc...@users.sourceforge.net


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[cvs] dists/10.7/stable/main/finkinfo/sci libccp4.info,1.1,1.2

[William Scott]

Update of /cvsroot/fink/dists/10.7/stable/main/finkinfo/sci
In directory sfp-cvs-1.v30.ch3.sourceforge.com:/tmp/cvs-serv4412

Modified Files:
libccp4.info 
Log Message:
added missing parameter file

Index: libccp4.info
===
RCS file: /cvsroot/fink/dists/10.7/stable/main/finkinfo/sci/libccp4.info,v
retrieving revision 1.1
retrieving revision 1.2
diff -u -d -r1.1 -r1.2
--- libccp4.info7 Aug 2013 01:14:42 -   1.1
+++ libccp4.info15 Aug 2013 01:34:54 -  1.2
@@ -1,6 +1,6 @@
 Package: libccp4
 Version: 6.3.1
-Revision: 1
+Revision: 2
 Maintainer: W. G. Scott wgsc...@users.sourceforge.net 
 DescPackaging: 
  Based on package created by Morten Kjeldgaard m...@bioxray.dk with minor
@@ -11,6 +11,8 @@
 GCC:4.0
 Source: ftp://ftp.ccp4.ac.uk/opensource/%n-%v.tar.gz
 Source-MD5: 82d662032893329fd4ccf32186c649a1
+Source2: ftp://ftp.ccp4.ac.uk/ccp4/6.3.0/ccp4-6.3.0/src/Prodrg/prodrg.param
+Source2-MD5: 807f5df3c33e8dda9b49eab939c6fd69
 NoSourceDirectory: false
 Depends: %N-shlibs (= %v-%r), gcc48-shlibs 
 BuildDepends: mmdb-dev (= 1.25.3-1), ssm-dev (= 1.3-1), gcc48, pkgconfig
@@ -55,6 +57,8 @@
 
 InstallScript: 
   make install DESTDIR=%d
+  mkdir -p %i/share/ccp4
+  cp ../prodrg.param %i/share/ccp4/.
 
 SplitOff: 
   Package: %N-shlibs
@@ -93,6 +97,7 @@
share/ccp4/atomsf_neutron.lib
share/ccp4/syminfo.lib
share/ccp4/symop.lib
+   share/ccp4/prodrg.param
  
 
  


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[cvs] dists/10.7/stable/main/finkinfo/sci refmac.info, NONE, 1.1 refmac.patch, NONE, 1.1

[William Scott]

Update of /cvsroot/fink/dists/10.7/stable/main/finkinfo/sci
In directory sfp-cvs-1.v30.ch3.sourceforge.com:/tmp/cvs-serv4482

Added Files:
refmac.info refmac.patch 
Log Message:
reintroduce stand-alone refmac package to augment coot

--- NEW FILE: refmac.patch ---
diff -ruN refmac-orig/covmat.h refmac/covmat.h
--- refmac-orig/covmat.h2011-11-30 17:03:44.0 -0800
+++ refmac/covmat.h 2013-08-14 15:13:23.0 -0700
@@ -44,7 +44,7 @@
~covar_matrix();
 void Make_matrix();// 
computes re and im from sigmas and D's
void Print();
-   void SetZeroRows(int,int,int,int,int,int);  // specifies the order 
numbers of rows(=columns) for which the covariances should be 0.
+   void SetZeroRows(int = -1,int = -1,int = -1,int = -1,int = -1,int = 
-1);// specifies the order numbers of rows(=columns) for which the 
covariances should be 0.
int CheckZeroRow(int row);  // returns 1 if 
row has been set to be covariance zeroed, 0 otherwise
int GetNumZeroRows();   // returns the 
number of rows with covariaces zeroed
 
@@ -2106,7 +2106,7 @@
 
 // defines zero rows. If the first argument is negative, resets all no 
non-zero.
 template typename realnum
-void covar_matrixrealnum::SetZeroRows( int r1=-1, int r2=-1, int r3=-1, int 
r4=-1, int r5=-1, int r6=-1 )
+void covar_matrixrealnum::SetZeroRows( int r1, int r2, int r3, int r4, int 
r5, int r6 )
 {
   int r[6] = {r1,r2,r3,r4,r5,r6};
   int i=0;
diff -ruN refmac-orig/makefile refmac/makefile
--- refmac-orig/makefile2011-07-19 03:41:56.0 -0700
+++ refmac/makefile 2013-08-14 15:15:22.0 -0700
@@ -1,19 +1,29 @@
-VERSION = gfortran
-FC  = gfortran
-CC  = gcc
-CPP = g++
-FOPTIM  = -O2 
-COPTIM  = -O2 
-XFFLAGS = -fno-second-underscore -static
-
-XCFLAGS = -DGFORTRAN -DPROTOTYPE
-FFLAGS = $(FOPTIM) $(XFFLAGS) 
-CFLAGS = $(COPTIM) $(XCFLAGS)
+VERSION = 5 
+FC  = ${PREFIX_SW}/lib/gcc4.8/bin/gfortran
+CC  = llvm-gcc-4.2
+CXX = llvm-g++-4.2
+FOPTIM  = -O3 
+COPTIM  = -O 
+XFFLAGS = -m64 -fno-second-underscore 
+ 
+
+XCFLAGS = -DGFORTRAN -DPROTOTYPE 
+FFLAGS = $(FOPTIM) $(XFFLAGS)  
+ 
+
+CFLAGS = $(COPTIM) $(XCFLAGS) 
 CPPFLAGS = $(CFLAGS)
 
+CLIB = ${PREFIX_SW}/lib
+
 LLIBCIF = 
-LLIBCCP = $(CLIB)/libccp4f.a $(CLIB)/libccp4c.a 
-LLIBLAPACK = $(CLIB)/liblapack.a $(CLIB)/libblas.a
-LLIBOTHERS =  -lgfortran -lgfortranbegin -lstdc++ 
 
+BLAS_DIR = 
/System/Library/Frameworks/Accelerate.framework/Versions/A/Frameworks/vecLib.framework/Versions/A
+
+LLIBCCP = /usr/lib/libSystem.B.dylib  ${BLAS_DIR}/libBLAS.dylib  
${BLAS_DIR}/libLAPACK.dylib  
+
+LLIBLAPACK =  
+
+LLIBOTHERS =  -L/usr/lib -L${CLIB} -L${PREFIX_SW}/lib/gcc4.8/lib -lgfortran  
${CLIB}/libccp4c.dylib ${CLIB}/libccp4f.dylib  -lstdc++  
/usr/lib/libSystem.B.dylib  -lSystem -lm
 include makefile_refmac.inc1
+

--- NEW FILE: refmac.info ---
Package: refmac
Version: 5.7.0032
Revision: 1
Source: 
http://www2.mrc-lmb.cam.ac.uk/groups/murshudov/content/%n/SourceEtal/%n5.7_source_v%v.tar.gz
Source-MD5: 6bde74d6fc1c7f32026ced6fd8741c99 
Source2: 
http://www2.mrc-lmb.cam.ac.uk/groups/murshudov/content/%n/Dictionary/%n_dictionary_v5.41.tar.gz
Source2-MD5: e7acb760fcbbe663147f5245b6c523c4
NoSourceDirectory: yes
Depends: gcc48-shlibs (= 4.8.1-1000), libccp4-shlibs (= 6.3.1-2),  
libccp4-lib (= 6.3.1-2)
BuildDepends: gcc48 (= 4.8.1-1000), gcc48-compiler (= 4.8.1-1000), 
libccp4-dev (= 6.3.1-2)
NoSetCPPFLAGS: true
NoSetLDFLAGS: true
PatchFile: refmac.patch
PatchFile-MD5: e15a5cbe31c50217a5c907c6e2c1cc80
CompileScript:  
#!/bin/bash -efv
export PREFIX_SW=%p
make -j 1 refmac

InstallScript: 
#!/bin/bash -efv
mkdir -p %i/bin
mkdir -p   %i/share/%n
mkdir -p   %i/etc/profile.d
cp refmac5 %i/bin/.
cp refmac5 %i/bin/%n
touch   %i/share/%n/environ.def   %i/share/%n/default.def   
cp -R monomers  %i/share/%n/.
#
echo 'if [[ ! -f  ${CINCL}/environ.def ]];then'   
%i/etc/profile.d/refmac.sh
echo 'export CINCL=%p/share/%n'  
%i/etc/profile.d/refmac.sh
echo 'export CCP4_SCR=/tmp/$USER; mkdir -p $CCP4_SCR'
%i/etc/profile.d/refmac.sh
echo 'fi'
%i/etc/profile.d/refmac.sh
#
echo 'if ( ! -d  ${CINCL} ) then' 
%i/etc/profile.d/refmac.csh
echo 'setenv CINCL %p/share/%n'  
%i/etc/profile.d/refmac.csh
echo 'setenv CCP4_SCR /tmp/$USER; mkdir -p $CCP4_SCR'
%i/etc/profile.d/refmac.csh
echo 'endif' 
%i/etc/profile.d/refmac.csh

RunTimeVars: 
CLIBD_MON: %p/share/%n/monomers/
SYMINFO: %p/share/ccp4/syminfo.lib
ATOMSF: %p/share/ccp4/atomsf.lib

Description: CCP4 refmac5 standalone update
DescDetail: 
This is a drop-in update replacement for refmac5. As long as you have

[cvs] dists/10.7/stable/main/finkinfo/sci coot.info,1.25,1.26

[William Scott]

Update of /cvsroot/fink/dists/10.7/stable/main/finkinfo/sci
In directory sfp-cvs-1.v30.ch3.sourceforge.com:/tmp/cvs-serv6921

Modified Files:
coot.info 
Log Message:
fixed url and integrated standalone refmac and consolidated monomer library 
with refmac

Index: coot.info
===
RCS file: /cvsroot/fink/dists/10.7/stable/main/finkinfo/sci/coot.info,v
retrieving revision 1.25
retrieving revision 1.26
diff -u -d -r1.25 -r1.26
--- coot.info   9 Aug 2013 04:09:02 -   1.25
+++ coot.info   15 Aug 2013 02:38:14 -  1.26
@@ -1,15 +1,13 @@
 Package: coot
 Version: 0.7.1.0  
-Revision: 4
+Revision: 5
 SourceDirectory: %n-0.7.1
 Distribution: 10.6, 10.7, 10.8
 GCC: 4.0 
-Source: 
http://www2.mrc-lmb.cam.ac.uk/groups/murshudov/coot/source/releases/%n-0.7.1.tar.gz
+Source: 
http://www2.mrc-lmb.cam.ac.uk/Personal/pemsley/%n/source/releases/%n-0.7.1.tar.gz
 Source-MD5: 94557d40bb2d1643b613c34fea10300b 
-Source2: 
http://www2.mrc-lmb.cam.ac.uk/groups/murshudov/content/refmac/Dictionary/refmac_dictionary_v5.41.tar.gz
-Source2-MD5: e7acb760fcbbe663147f5245b6c523c4
-Source3: 
http://www.ysbl.york.ac.uk/~emsley/software/extras/reference-structures.tar.gz
-Source3-MD5: 257ab90d44f1c877ada96720dbb87c13 
+Source2: 
http://www.ysbl.york.ac.uk/~emsley/software/extras/reference-structures.tar.gz
+Source2-MD5: 257ab90d44f1c877ada96720dbb87c13 
 ###
 Description: Crystallographic molecular graphics
 DescDetail: 
@@ -40,7 +38,7 @@
  fink (= 0.24.12)   ,
  boost1.53.python27 (= 1.53.0-1),
  clipper-dev (= 1:2.1.20130601-1),
- libccp4-dev (= 6.3.1-1),
+ libccp4-dev (= 6.3.1-2),
  mmdb-dev (= 1.25.3-1)  ,
  ssm-dev (= 1.3-1)  ,
  atk1 (= 1.28.0-1)  ,
@@ -89,8 +87,8 @@
  coot-shlibs (= 0.7.1.0-%r)   ,
  boost1.53.python27-shlibs (= 1.53.0-1),
  clipper-shlibs (= 1:2.1.20130601-1),
- libccp4-shlibs (= 6.3.1-1)  ,
- libccp4-lib (= 6.3.1-1)  | ccp4  (= 6.3.0-1),
+ libccp4-shlibs (= 6.3.1-2)  ,
+ libccp4-lib (= 6.3.1-2) ,
  mmdb-shlibs (= 1.25.3-1),
  ssm-shlibs (= 1.3-1),
  atk1-shlibs (= 1.28.0-1),
@@ -126,8 +124,10 @@
  pango1-xft2-ft219-shlibs (= 1.24.5-4) ,
  pygtk2-gtk-py27  ,
  python27 ,
+ raster3d (= 3.0-2-3),
  rdkit-shlibs (= 2013.03.2-4),
  rdkit (= 2013.03.2-4)   ,
+ refmac (=5.7.0032-1),
  x11
 
 #
@@ -225,10 +225,10 @@
 install_name_tool -change 
/System/Library/Frameworks/Python.framework/Versions/2.6/Python  
%p/lib/python2.6/config/libpython2.6.dylib %i/bin/coot-real
fi
 
-# This installs the refmac monomer library
+# This consolidates the refmac monomer library
 mkdir -p %i/share/coot/lib/data
-cp -R ../monomers %i/share/coot/lib/data/monomers
-cp%i/share/coot/lib/data/monomers/ener_lib.cif%i/share/coot/lib/.
+ln -s %p/share/refmac/monomers/ener_lib.cif%i/share/coot/lib/.
+ln -s %p/share/refmac/monomers %i/share/coot/lib/data/.
 # Reference structures should be in %i/share/coot/reference-structures
 cp -R ../reference-structures %i/share/coot/.
 cp -R * %i/share/coot/etc/.
@@ -242,12 +242,7 @@
 echo export COOT_REFMAC_LIB_DIR=%p/share/coot/lib   %i/bin/coot
 echo export COOT_PYTHON_DIR=%p/share/coot/python%i/bin/coot
 echo 'export COOT_SBASE_DIR=$CCP4/share/sbase'  %i/bin/coot
-echo 'export CLIBD=$CCP4/lib/data'  %i/bin/coot
-echo 'if [[ -f  $CCP4/lib/data/symop.lib ]];then' %i/bin/coot
-echo 'export SYMINFO=$CCP4/lib/data/syminfo.lib'%i/bin/coot
-echo 'else'   %i/bin/coot
-echo export SYMINFO=\%p/share/ccp4/syminfo.lib\   %i/bin/coot
-echo 'fi' %i/bin/coot
+echo 'export CLIBD=%p/share/ccp4'   %i/bin/coot
  
 echo export 
PYTHONPATH=%p/lib/python2.7/site-packages:%p/lib/python2.7/site-packages/gtk-2.0:%p/share/coot/python
%i/bin/coot
 echo %p/bin/coot-real \\$@\   %i/bin/coot
 chmod a+x %i/bin/coot


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[cvs] dists/10.7/stable/main/finkinfo/sci coot.info, 1.24, 1.25 coot.patch, 1.1, 1.2 clipper.info, 1.5, 1.6 mmdb.info, 1.6, 1.7 ssm.info, 1.5, 1.6

[William Scott]

Update of /cvsroot/fink/dists/10.7/stable/main/finkinfo/sci
In directory sfp-cvs-1.v30.ch3.sourceforge.com:/tmp/cvs-serv4957

Modified Files:
coot.info coot.patch clipper.info mmdb.info ssm.info 
Log Message:
updates for coot dependencies

Index: coot.patch
===
RCS file: /cvsroot/fink/dists/10.7/stable/main/finkinfo/sci/coot.patch,v
retrieving revision 1.1
retrieving revision 1.2
diff -u -d -r1.1 -r1.2
--- coot.patch  4 Aug 2011 14:10:11 -   1.1
+++ coot.patch  9 Aug 2013 04:09:02 -   1.2
@@ -33,3 +33,327 @@
  
  ;; run raster3d
  (define render-image
+
+
+diff -crB ./src/graphics-info.h ../coot-patched/src/graphics-info.h
+*** ./src/graphics-info.h  2013-04-27 16:04:58.0 +0200
+--- ../coot-patched/src/graphics-info.h2013-07-25 04:09:17.861265837 
+0200
+***
+*** 3307,3313 
+ short int move_copy_of_imol2_flag);
+
+  #ifdef HAVE_SSMLIB
+!void print_ssm_sequence_alignment(CSSMAlign *SSMAlign,
+atom_selection_container_t asc_ref,
+atom_selection_container_t asc_mov,
+PCAtom *atom_selection1, 
+--- 3307,3313 
+ short int move_copy_of_imol2_flag);
+
+  #ifdef HAVE_SSMLIB
+!void print_ssm_sequence_alignment(ssm::Align *SSMAlign,
+atom_selection_container_t asc_ref,
+atom_selection_container_t asc_mov,
+PCAtom *atom_selection1, 
+***
+*** 3315,3321 
+int n_selected_atoms_1, int 
n_selected_atoms_2, 
+short int move_copy_of_imol2_flag);
+
+!void make_and_print_horizontal_ssm_sequence_alignment(CSSMAlign *SSMAlign,
+
atom_selection_container_t asc_ref,
+
atom_selection_container_t asc_mov,
+PCAtom 
*atom_selection1, 
+--- 3315,3321 
+int n_selected_atoms_1, int 
n_selected_atoms_2, 
+short int move_copy_of_imol2_flag);
+
+!void make_and_print_horizontal_ssm_sequence_alignment(ssm::Align 
*SSMAlign,
+
atom_selection_container_t asc_ref,
+
atom_selection_container_t asc_mov,
+PCAtom 
*atom_selection1, 
+***
+*** 3325,3331 
+ void print_horizontal_ssm_sequence_alignment(std::pairstd::string, 
std::string aligned_sequences) const;
+
+ std::pairstd::string, std::string
+!  get_horizontal_ssm_sequence_alignment(CSSMAlign *SSMAlign,
+  atom_selection_container_t asc_ref,
+  atom_selection_container_t asc_mov,
+  PCAtom *atom_selection1, PCAtom 
*atom_selection2,
+--- 3325,3331 
+ void print_horizontal_ssm_sequence_alignment(std::pairstd::string, 
std::string aligned_sequences) const;
+
+ std::pairstd::string, std::string
+!  get_horizontal_ssm_sequence_alignment(ssm::Align *SSMAlign,
+  atom_selection_container_t asc_ref,
+  atom_selection_container_t asc_mov,
+  PCAtom *atom_selection1, PCAtom 
*atom_selection2,
+diff -crB ./src/graphics-info-superpose.cc 
../coot-patched/src/graphics-info-superpose.cc
+*** ./src/graphics-info-superpose.cc   2013-01-16 17:40:31.0 +0100
+--- ../coot-patched/src/graphics-info-superpose.cc 2013-07-25 
04:42:47.876256551 +0200
+***
+*** 22,27 
+--- 22,31 
+  #include Python.h  // before system includes to stop POSIX_C_SOURCE 
redefined problems
+  #endif
+
++ #ifdef HAVE_SSMLIB
++ #include ssm_defs.h
++ #endif 
++ 
+  #if defined _MSC_VER
+  #include windows.h
+  #endif
+***
+*** 168,179 
+
+  #ifdef HAVE_SSMLIB
+
+!int precision = SSMP_Normal;
+!int connectivity = CSSC_Flexible;
+
+ // probably not necessary, not sure:
+!SetSSConnectivityCheck ( CSSC_Flexible );
+!SetSSMatchPrecision( SSMP_Normal );
+
+ if (asc_ref.n_selected_atoms  0) { 
+if (asc_mov.n_selected_atoms  0) {
+--- 172,183 
+
+  #ifdef HAVE_SSMLIB
+
+!ssm::PRECISION precision = ssm::PREC_Normal;
+!ssm::CONNECTIVITY connectivity = ssm::CONNECT_Flexible;
+
+ // probably not necessary, not sure:
+!ssm::SetConnectivityCheck ( ssm::CONNECT_Flexible );
+!ssm::SetMatchPrecision( ssm::PREC_Normal );
+
+ if 

[cvs] dists/10.7/stable/main/finkinfo/sci xia2.info, NONE, 1.1 cctbx.info, NONE, 1.1

[William Scott]

Update of /cvsroot/fink/dists/10.7/stable/main/finkinfo/sci
In directory sfp-cvs-1.v30.ch3.sourceforge.com:/tmp/cvs-serv864

Added Files:
xia2.info cctbx.info 
Log Message:
cctbx reintroduced as dependency for new xia2 package

--- NEW FILE: cctbx.info ---
Package: cctbx
Version: 2013.07.05
Revision: 1
Distribution: 10.6, 10.7, 10.8
GCC: 4.0
BuildDependsOnly: false
NoSourceDirectory: true
UseMaxBuildJobs: false
Source: 
http://cci.lbl.gov/cctbx_build/results/last_published/cctbx_bundle.tar.gz
Source-MD5: 335110c462f6d919ec38e4c04faa2dde
SourceRename: cctbx-%v.tar.gz
Depends: %n-shlibs (= %v-%r) 
Description: Computational Crystallography Toolbox
DescDetail: 
The Computational Crystallography Toolbox (cctbx) is being developed as the
open source component of the PHENIX system. The goal of the PHENIX project is
to advance automation of macromolecular structure determination. PHENIX
depends on the cctbx, but not vice versa. This hierarchical approach enforces
a clean design as a reusable library. The cctbx is therefore also useful for
small-molecule crystallography and even general scientific applications.

The cctbx code base is available without restrictions and free of charge to
all interested developers, both academic and commercial. The entire community
is invited to actively participate in the development of the code base. A
sophisticated technical infrastructure that enables community based software
development is provided by SourceForge. This service is also free of charge
and open to the entire world.

The cctbx is designed with an open and flexible architecture to promote
extendability and easy incorporation into other software environments. The
package is organized as a set of ISO C++ classes with Python bindings. This
organization combines the computational efficiency of a strongly typed
compiled language with the convenience and flexibility of a dynamically typed
scripting language in a strikingly uniform and very maintainable way.

Use of the Python interfaces is highly recommended, but optional. The cctbx
can also be used purely as a C++ class library. The SourceForge cctbx project
currently contains these modules:

libtbx: The build system common to all other modules. This is a very thin
wrapper around the SCons software construction tool.

boost_adaptbx: A very small adaptor toolbox with platform-independent
instructions for building the Boost.Python library.

scitbx: Libraries for general scientific computing (i.e.  libraries that are
not specific to crystallographic applications): a family of high-level C++
array types, a fast Fourier transform library, and a C++ port of the popular
LBFGS conjugate gradient minimizer, all including Python bindings. These
libraries are separated from the crystallographic code base to make them
easily accessible for non-crystallographic application developers.

cctbx: Libraries for general crystallographic applications, useful for both
small-molecule and macro-molecular crystallography. The libraries in the cctbx
module cover everything from algorithms for the handling of unit cells to
high-level building blocks for refinement algorithms. Note the distinction
between the cctbx project and the cctbx module. In retrospect we should have
chosen a different name for the project, but the current naming reflects how
the modules have evolved and it would be too disruptive to start a grand
renaming.

iotbx: The youngest member in the family: evolving libraries for reading and
writing established file formats.

#PatchScript: 
#perl -pi.orig -e \
#s|cxx \= cc.replace\('gcc', 'g\+\+'\)|cxx \= cc.replace\('gcc', 
'%p/bin/g\+\+-4'\)|g cctbx_sources/libtbx/SConscript
#
CompileScript: 
#!/bin/sh -efv
true

InstallScript: 
#!/bin/sh -efv
mkdir cctbx_build
cd cctbx_build
# requires a Framwork python build
/System/Library/Frameworks/Python.framework/Versions/Current/bin/python \
../cctbx_sources/libtbx/configure.py \
--clear-scons-memory --compiler=gcc mmtbx --enable-openmp-if-possible=True  
# The last command initializes the cctbx_build directory and creates 
# a file setpaths.csh (among others). This file must be used to initialize
# a new shell or process with the cctbx settings:

source setpaths.sh

# Find the number of cpus:
num_cpu=$( sysctl hw.logicalcpu | awk '{print $NF}' )
# On a machine with multiple CPUs enter:

libtbx.scons -j $num_cpu .
perl -pi -e 's|prepend|append|g'  setpaths.csh
perl -pi -e 's|prepend|append|g'  setpaths.sh

cd ..

# clean up
find . -type f -name *.pyc -exec rm -f {} \;


install_name_tool -id %p/lib/cctbx/cctbx_build/lib/libboost_python.dylib   
cctbx_build/lib/libboost_python.dylib
  

mkdir -p %i/lib/cctbx
cp -R cctbx_build  %i/lib/cctbx/. 
cp -R cctbx_sources  %i/lib/cctbx/.
#
# Set up startup scripts
mkdir -p %i/etc/profile.d
echo source %p/lib/cctbx/cctbx_build/setpaths.sh  %i/etc/profile.d/cctbx.sh
echo source %p/lib/cctbx/cctbx_build/setpaths.csh  %i/etc/profile.d/cctbx.csh
chmod a+x %i/etc/profile.d/cctbx.sh 

[cvs] dists/10.7/stable/main/finkinfo/sci libccp4.info,NONE,1.1

[William Scott]

Update of /cvsroot/fink/dists/10.7/stable/main/finkinfo/sci
In directory sfp-cvs-1.v30.ch3.sourceforge.com:/tmp/cvs-serv932

Added Files:
libccp4.info 
Log Message:
LGPL ccp4 libs to replace older gpp4 and add in symmetry libs

--- NEW FILE: libccp4.info ---
Package: libccp4
Version: 6.3.1
Revision: 1
Maintainer: W. G. Scott wgsc...@users.sourceforge.net 
DescPackaging: 
 Based on package created by Morten Kjeldgaard m...@bioxray.dk with minor
 edits to conform to standard Fink packaging requirements.

Description: LGPL Library providing CCP4 functionality 
License: LGPL
GCC:4.0
Source: ftp://ftp.ccp4.ac.uk/opensource/%n-%v.tar.gz
Source-MD5: 82d662032893329fd4ccf32186c649a1
NoSourceDirectory: false
Depends: %N-shlibs (= %v-%r), gcc48-shlibs 
BuildDepends: mmdb-dev (= 1.25.3-1), ssm-dev (= 1.3-1), gcc48, pkgconfig
BuildConflicts: g77, fort77, g95
Conflicts: gpp4 
Replaces: gpp4 
BuildDependsOnly: true
HomePage:  
DocFiles: COPYING.LESSER COPYING
DescDetail:  
The CCP4 software suite is based around a library of routines that
cover common tasks, such as file opening, parsing keyworded input,
reading and writing of standard data formats, applying symmetry
operations, etc. Programs in the suite call these routines which, as
well as saving the programmer some effort, ensure that the varied
programs in the suite have a similar look-and-feel.

The library contains several subcomponents: 
  * CMTZ library -- Contains a variety of functions for manipulating 
the data structure, for example adding crystals, datasets or columns. 
The data structure can be dumped to an output MTZ data file.
  * CMAP library -- Functions defining the C-level API for accessing 
CCP4 map files.
  * CSYM library -- a collection of functions centred around a data file 
syminfo.lib which is auto-generated from sgtbx (the Space Group Toolbox 
of cctbx).
  * CCP4 utility library -- many utility functions which either give 
specific CCP4 or platform independent functionality.
  * CCP4 Parser library -- provides CCP4-style parsing, as used for 
processing keywords of CCP4 programs, MTZ header records, etc.
  * CCP4 resizable arrays -- defines an object and methods which looks 
just like a simple C array, but can be resized at will without 
incurring excessive overheads.

CompileScript: 
#!/bin/bash -evf
LDFLAGS=-L%p/lib/gcc4.8/lib -L%p/lib -L/usr/lib \
MMDB_CFLAGS=-I%p/include/mmdb MMDB_LIBS=-L%p/lib  \
FC=%p/bin/gfortran-fsf-4.8 \
  ./configure --enable-shared F77=%p/bin/gfortran-fsf-4.8 
FFLAGS=-L%p/lib/gcc4.8/lib -lgfortran  --prefix=%p 
  make

InstallScript: 
  make install DESTDIR=%d

SplitOff: 
  Package: %N-shlibs
  Files: 
lib/libccp4c.0.dylib
lib/libccp4f.0.dylib
  
  Shlibs: 
%p/lib/libccp4c.0.dylib 1.0.0 %n (= 6.3.1-1)
%p/lib/libccp4f.0.dylib 1.0.0 %n (= 6.3.1-1)
  
Depends: gcc48-shlibs 

SplitOff2: 
Package: %N-dev
BuildDependsOnly: True
Conflicts: ccp4-onlylibs-dev, ccp4-dev, gpp4-dev
Replaces: ccp4-onlylibs-dev, ccp4-dev, gpp4-dev
 Files:
  lib/*.a
  lib/*.la
  include/ccp4/*.h
  lib/libccp4c.dylib
  lib/libccp4f.dylib
  lib/pkgconfig/libccp4c.pc
  lib/pkgconfig/libccp4f.pc
  share/ccp4/ccp4-config.cmake
 

SplitOff3: 
Package: %N-lib
BuildDependsOnly: False
Description: CCP4 ascii text library files 
Files:
share/ccp4/atomsf.lib
share/ccp4/atomsf_neutron.lib
share/ccp4/syminfo.lib
share/ccp4/symop.lib
 

 


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[cvs] dists/10.7/stable/main/finkinfo/sci rdkit.info,1.5,1.6

[William Scott]

Update of /cvsroot/fink/dists/10.7/stable/main/finkinfo/sci
In directory sfp-cvs-1.v30.ch3.sourceforge.com:/tmp/cvs-serv13833

Modified Files:
rdkit.info 
Log Message:
update and fix Conflicts

Index: rdkit.info
===
RCS file: /cvsroot/fink/dists/10.7/stable/main/finkinfo/sci/rdkit.info,v
retrieving revision 1.5
retrieving revision 1.6
diff -u -d -r1.5 -r1.6
--- rdkit.info  30 Jul 2013 06:55:48 -  1.5
+++ rdkit.info  31 Jul 2013 15:43:30 -  1.6
@@ -1,11 +1,11 @@
 Package: rdkit
-Version: 2013.03.2
-Revision: 4
+Version: 2013.06.1
+Revision: 1
 Distribution: 10.6, 10.7, 10.8
 GCC: 4.0
 BuildDependsOnly: false
-Source: mirror:sourceforge:rdkit/RDKit_2013_03_2.tgz
-Source-MD5: b5cff9fb70124e544d2e26ea16c92d95
+Source: mirror:sourceforge:rdkit/RDKit_2013_06_1.tgz
+Source-MD5: 13b9ea2c4c03e04dcea055c79b3173a9
 Description: Cheminformatics and machine-learning software 
 DescDetail: 
 A collection of cheminformatics and machine-learning software written in C++ 
@@ -15,7 +15,7 @@
 to be stored in a relational database and retrieved via substructure and 
 similarity searches.
 
-BuildConflicts:  boost1.35.nopython, boost1.35.python26, boost1.35.python27, 
boost1.35.systempython, boost1.46.cmake, boost-jam, boost1.46.1.cmake, 
boost1.52.0.cmake, boost1.52.0.cmake-shlibs
+BuildConflicts:  boost1.35.nopython, boost1.35.python26, boost1.35.python27, 
boost1.35.systempython, boost1.46.cmake, boost-jam, boost1.46.1.cmake, 
boost1.52.0.cmake
 Depends: %N-shlibs (= %v-%r), python27-shlibs, numpy-py27, sqlite3-shlibs, 
pil-py27, boost1.53.python27-shlibs
 BuildDepends:  python27, numpy-py27, sqlite3-dev, cmake, boost1.53.python27
 CompileScript: 
@@ -47,38 +47,38 @@
 lib/%N/*.1.dylib   
  
 
 Shlibs: 
-%p/lib/%N/libAlignment.1.dylib1.0.0 %n  (= 
2013.03.2-1)   
-%p/lib/%N/libCatalogs.1.dylib 1.0.0 %n  (= 
2013.03.2-1)
-%p/lib/%N/libChemReactions.1.dylib1.0.0 %n  (= 
2013.03.2-1)
-%p/lib/%N/libChemTransforms.1.dylib   1.0.0 %n  (= 
2013.03.2-1)
-%p/lib/%N/libChemicalFeatures.1.dylib 1.0.0 %n  (= 
2013.03.2-1)
-%p/lib/%N/libDataStructs.1.dylib  1.0.0 %n  (= 
2013.03.2-1)
-%p/lib/%N/libDepictor.1.dylib 1.0.0 %n  (= 
2013.03.2-1)
-%p/lib/%N/libDescriptors.1.dylib  1.0.0 %n  (= 
2013.03.2-1)
-%p/lib/%N/libDistGeomHelpers.1.dylib  1.0.0 %n  (= 
2013.03.2-1)
-%p/lib/%N/libDistGeometry.1.dylib 1.0.0 %n  (= 
2013.03.2-1)
-%p/lib/%N/libEigenSolvers.1.dylib 1.0.0 %n  (= 
2013.03.2-1)
-%p/lib/%N/libFileParsers.1.dylib  1.0.0 %n  (= 
2013.03.2-1)
-%p/lib/%N/libFingerprints.1.dylib 1.0.0 %n  (= 
2013.03.2-1)
-%p/lib/%N/libForceField.1.dylib   1.0.0 %n  (= 
2013.03.2-1)
-%p/lib/%N/libForceFieldHelpers.1.dylib1.0.0 %n  (= 
2013.03.2-1)
-%p/lib/%N/libFragCatalog.1.dylib  1.0.0 %n  (= 
2013.03.2-1)
-%p/lib/%N/libGraphMol.1.dylib 1.0.0 %n  (= 
2013.03.2-1)
-%p/lib/%N/libMolAlign.1.dylib 1.0.0 %n  (= 
2013.03.2-1)
-%p/lib/%N/libMolCatalog.1.dylib   1.0.0 %n  (= 
2013.03.2-1)
-%p/lib/%N/libMolChemicalFeatures.1.dylib  1.0.0 %n  (= 
2013.03.2-1)
-%p/lib/%N/libMolTransforms.1.dylib1.0.0 %n  (= 
2013.03.2-1)
-%p/lib/%N/libOptimizer.1.dylib1.0.0 %n  (= 
2013.03.2-1)
-%p/lib/%N/libPartialCharges.1.dylib   1.0.0 %n  (= 
2013.03.2-1)
-%p/lib/%N/libRDBoost.1.dylib  1.0.0 %n  (= 
2013.03.2-1)
-%p/lib/%N/libRDGeneral.1.dylib1.0.0 %n  (= 
2013.03.2-1)
-%p/lib/%N/libRDGeometryLib.1.dylib1.0.0 %n  (= 
2013.03.2-1)
-%p/lib/%N/libShapeHelpers.1.dylib 1.0.0 %n  (= 
2013.03.2-1)
-%p/lib/%N/libSimDivPickers.1.dylib1.0.0 %n  (= 
2013.03.2-1)
-%p/lib/%N/libSmilesParse.1.dylib  1.0.0 %n  (= 
2013.03.2-1)
-%p/lib/%N/libSubgraphs.1.dylib1.0.0 %n  (= 
2013.03.2-1)
-%p/lib/%N/libSubstructMatch.1.dylib   1.0.0 %n  (= 
2013.03.2-1)
-%p/lib/%N/libhc.1.dylib   1.0.0 %n  (= 
2013.03.2-1)
+%p/lib/%N/libAlignment.1.dylib1.0.0 %n  (= 
2013.06.1-1)   
+%p/lib/%N/libCatalogs.1.dylib 1.0.0 %n  (= 

[cvs] dists/10.4/stable/main/finkinfo/sci rdkit.info,1.1,1.2

[William Scott]

Update of /cvsroot/fink/dists/10.4/stable/main/finkinfo/sci
In directory sfp-cvs-1.v30.ch3.sourceforge.com:/tmp/cvs-serv25633

Modified Files:
rdkit.info 
Log Message:
version updated to current

Index: rdkit.info
===
RCS file: /cvsroot/fink/dists/10.4/stable/main/finkinfo/sci/rdkit.info,v
retrieving revision 1.1
retrieving revision 1.2
diff -u -d -r1.1 -r1.2
--- rdkit.info  11 Feb 2013 22:09:36 -  1.1
+++ rdkit.info  31 Jul 2013 23:33:19 -  1.2
@@ -1,11 +1,11 @@
 Package: rdkit
-Version: 2012.12.1
+Version: 2013.06.1
 Revision: 1
 Distribution: 10.6, 10.7, 10.8
 GCC: 4.0
 BuildDependsOnly: false
-Source: mirror:sourceforge:rdkit/RDKit_2012_12_1.tgz
-Source-MD5: 36596b18ff71c70b04d25c43810c2b01
+Source: mirror:sourceforge:rdkit/RDKit_2013_06_1.tgz
+Source-MD5: 13b9ea2c4c03e04dcea055c79b3173a9
 Source2: mirror:sourceforge:boost/boost_1_53_0.tar.bz2
 Source2-MD5: a00d22605d5dbcfb4c9936a9b35bc4c2
 Description: Cheminformatics and machine-learning software 


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[cvs] dists/10.7/stable/main/finkinfo/sci rdkit.info,1.6,1.7

[William Scott]

Update of /cvsroot/fink/dists/10.7/stable/main/finkinfo/sci
In directory sfp-cvs-1.v30.ch3.sourceforge.com:/tmp/cvs-serv421

Modified Files:
rdkit.info 
Log Message:
added DFLEX_EXECUTABLE:FILEPATH=/usr/bin/flex

Index: rdkit.info
===
RCS file: /cvsroot/fink/dists/10.7/stable/main/finkinfo/sci/rdkit.info,v
retrieving revision 1.6
retrieving revision 1.7
diff -u -d -r1.6 -r1.7
--- rdkit.info  31 Jul 2013 15:43:30 -  1.6
+++ rdkit.info  1 Aug 2013 01:12:55 -   1.7
@@ -1,6 +1,6 @@
 Package: rdkit
 Version: 2013.06.1
-Revision: 1
+Revision: 2
 Distribution: 10.6, 10.7, 10.8
 GCC: 4.0
 BuildDependsOnly: false
@@ -22,7 +22,7 @@
 #!/bin/sh -efv
 mkdir build
 cd build
-cmake -DCMAKE_OSX_SYSROOT:PATH=/ -DCMAKE_OSX_DEPLOYMENT_TARGET:STRING= 
-DCMAKE_INSTALL_PREFIX=%p -DCMAKE_INSTALL_NAME_DIR=%p/lib/%n   
-DCMAKE_PREFIX_PATH=%p  -DBOOST_LIBRARYDIR=%p/lib/python2.7/site-packages 
-DBOOST_ROOT=%p/lib/boost-1_53 -DBoost_NO_SYSTEM_PATHS=ON 
-DPYTHON_LIBRARY=%p/lib/python2.7/config/libpython2.7.dylib  
-DPYTHON_INCLUDE_DIR=%p/include/python2.7 -DPYTHON_EXECUTABLE=%p/bin/python2.7 
..  
+cmake -DFLEX_EXECUTABLE:FILEPATH=/usr/bin/flex -DCMAKE_OSX_SYSROOT:PATH=/ 
-DCMAKE_OSX_DEPLOYMENT_TARGET:STRING= -DCMAKE_INSTALL_PREFIX=%p 
-DCMAKE_INSTALL_NAME_DIR=%p/lib/%n   -DCMAKE_PREFIX_PATH=%p  
-DBOOST_LIBRARYDIR=%p/lib/python2.7/site-packages 
-DBOOST_ROOT=%p/lib/boost-1_53 -DBoost_NO_SYSTEM_PATHS=ON 
-DPYTHON_LIBRARY=%p/lib/python2.7/config/libpython2.7.dylib  
-DPYTHON_INCLUDE_DIR=%p/include/python2.7 -DPYTHON_EXECUTABLE=%p/bin/python2.7 
..  
 make install
 
 InstallScript: 


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[cvs] dists/10.7/stable/main/finkinfo/sci coot.info, 1.22, 1.23 rdkit.info, 1.4, 1.5

[William Scott]

Update of /cvsroot/fink/dists/10.7/stable/main/finkinfo/sci
In directory sfp-cvs-1.v30.ch3.sourceforge.com:/tmp/cvs-serv13666

Modified Files:
coot.info rdkit.info 
Log Message:
fix rdkit and coot to work with new boost1.53

Index: rdkit.info
===
RCS file: /cvsroot/fink/dists/10.7/stable/main/finkinfo/sci/rdkit.info,v
retrieving revision 1.4
retrieving revision 1.5
diff -u -d -r1.4 -r1.5
--- rdkit.info  29 Jul 2013 01:55:32 -  1.4
+++ rdkit.info  30 Jul 2013 06:55:48 -  1.5
@@ -1,6 +1,6 @@
 Package: rdkit
 Version: 2013.03.2
-Revision: 3
+Revision: 4
 Distribution: 10.6, 10.7, 10.8
 GCC: 4.0
 BuildDependsOnly: false
@@ -16,7 +16,7 @@
 similarity searches.
 
 BuildConflicts:  boost1.35.nopython, boost1.35.python26, boost1.35.python27, 
boost1.35.systempython, boost1.46.cmake, boost-jam, boost1.46.1.cmake, 
boost1.52.0.cmake, boost1.52.0.cmake-shlibs
-Depends: %N-shlibs, python27-shlibs, numpy-py27, sqlite3-shlibs, pil-py27, 
boost1.53.python27-shlibs
+Depends: %N-shlibs (= %v-%r), python27-shlibs, numpy-py27, sqlite3-shlibs, 
pil-py27, boost1.53.python27-shlibs
 BuildDepends:  python27, numpy-py27, sqlite3-dev, cmake, boost1.53.python27
 CompileScript: 
 #!/bin/sh -efv
@@ -32,6 +32,12 @@
 cp -R rdkit %i/lib/python2.7/site-packages/.
 mkdir -p %i/lib
 cp -R lib %i/lib/%n
+mkdir -p %i/include
+cp -R Code %i/include/%n
+cp -R Contrib/PBF  %i/include/%n/.
+cp -R External/AvalonTools  %i/include/%n/.
+cp -R External/INCHI-API  %i/include/%n/.
+cp -R External/cmim-1.0  %i/include/%n/.
 
 SplitOff: 
 Package: %N-shlibs
@@ -83,6 +89,7 @@
 Description: rdkit static libraries and headers
 Files:
 lib/%N/*.a  
+include/%N/*
 
 DocFiles:  license.txt README
 License: BSD

Index: coot.info
===
RCS file: /cvsroot/fink/dists/10.7/stable/main/finkinfo/sci/coot.info,v
retrieving revision 1.22
retrieving revision 1.23
diff -u -d -r1.22 -r1.23
--- coot.info   6 Jul 2013 18:55:56 -   1.22
+++ coot.info   30 Jul 2013 06:55:48 -  1.23
@@ -1,6 +1,6 @@
 Package: coot
 Version: 0.7.1.0  
-Revision: 1
+Revision: 2
 SourceDirectory: %n-0.7.1
 Distribution: 10.6, 10.7, 10.8
 GCC: 4.0 
@@ -38,6 +38,7 @@
 Recommends:  povray, ccp4, raster3d
 BuildDepends: 
  fink (= 0.24.12)   ,
+ boost1.53.python27 (= 1.53.0-1),
  clipper-dev (= 1:2.1-32)   ,
  gpp4-dev (= 1.2.0-32)  ,
  mmdb-dev (= 1.25.0-32) ,
@@ -78,14 +79,15 @@
  pygtk2-gtk-py27-dev ,
  pygobject2-py27-dev ,
  python27,
- rdkit-dev   ,
- rdkit   ,
+ rdkit-dev (= 2013.03.2-4)  ,
+ rdkit (= 2013.03.2-4)  ,
  swig,
  x11-dev
 
 #   
 Depends: 
  coot-shlibs (= 0.7.1.0-%r)   ,
+ boost1.53.python27-shlibs (= 1.53.0-1),
  clipper-shlibs (= 1:2.1-32) ,
  gpp4-shlibs (= 1.2.0-32),
  mmdb-shlibs (= 1.25.0-32)   ,
@@ -123,7 +125,7 @@
  pango1-xft2-ft219-shlibs (= 1.24.5-4) ,
  pygtk2-gtk-py27  ,
  python27 ,
- rdkit,
+ rdkit-shlibs (= 2013.03.2-4),
  x11
 
 #
@@ -167,7 +169,7 @@
   rdkit_prefix=%p \
   FLIBS=-L%p/lib -L%p/lib/rdkit \
   CPPFLAGS=-I%p/include/rdkit -I%b/lidia-core -I%p/include/libglade-2.0/glade 
-I%p/include/libglade-2.0 -I%p/include/python2.7  -I%p/include/mmdb 
-I%p/include/ssm -I%p/include/gpp4/ccp4 -I%p/include/clipper -I%p/include 
-I/usr/X11R6/include \
-  
LDFLAGS=-Wl,-dylib_file,%p/lib/python2.7/config/libpython2.7.dylib:%p/lib/libsfftw.2.0.7.dylib:%p/lib/libsrfftw.2.0.7.dylib:%p/lib/pango-ft219/lib/libpango-1.0.dylib:%p/lib/pango-ft219/lib/libpangocairo-1.0.dylib:%p/lib/pango-ft219/lib/libpangoft2-1.0.dylib:%p/lib/pango-ft219/lib/libpangox-1.0.dylib:%p/lib/pango-ft219/lib/libpangoxft-1.0.dylib
 -L%p/lib  -L/usr/lib  -flat_namespace 
-L/System/Library/Frameworks/OpenGL.framework/Versions/A/Libraries \
+  
LDFLAGS=-Wl,-dylib_file,%p/lib/libboost_python.dylib:%p/lib/python2.7/site-packages/libboost_python-1_53.dylib:%p/lib/python2.7/config/libpython2.7.dylib:%p/lib/libsfftw.2.0.7.dylib:%p/lib/libsrfftw.2.0.7.dylib:%p/lib/pango-ft219/lib/libpango-1.0.dylib:%p/lib/pango-ft219/lib/libpangocairo-1.0.dylib:%p/lib/pango-ft219/lib/libpangoft2-1.0.dylib:%p/lib/pango-ft219/lib/libpangox-1.0.dylib:%p/lib/pango-ft219/lib/libpangoxft-1.0.dylib
 -L%p/lib  -L/usr/lib  -flat_namespace 
-L/System/Library/Frameworks/OpenGL.framework/Versions/A/Libraries \
   DYLD_LIBRARY_PATH= \
   RDKIT_CXXFLAGS=-I$rdkit_prefix/include/rdkit \
   RDKIT_LIBS=\-L%p/lib/rdkit $rdkit_libs\ \


--
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[cvs] dists/10.7/stable/main/finkinfo/sci coot.info,1.23,1.24

[William Scott]

Update of /cvsroot/fink/dists/10.7/stable/main/finkinfo/sci
In directory sfp-cvs-1.v30.ch3.sourceforge.com:/tmp/cvs-serv6368

Modified Files:
coot.info 
Log Message:
added rdkit Depends

Index: coot.info
===
RCS file: /cvsroot/fink/dists/10.7/stable/main/finkinfo/sci/coot.info,v
retrieving revision 1.23
retrieving revision 1.24
diff -u -d -r1.23 -r1.24
--- coot.info   30 Jul 2013 06:55:48 -  1.23
+++ coot.info   30 Jul 2013 16:33:10 -  1.24
@@ -1,6 +1,6 @@
 Package: coot
 Version: 0.7.1.0  
-Revision: 2
+Revision: 3
 SourceDirectory: %n-0.7.1
 Distribution: 10.6, 10.7, 10.8
 GCC: 4.0 
@@ -126,6 +126,7 @@
  pygtk2-gtk-py27  ,
  python27 ,
  rdkit-shlibs (= 2013.03.2-4),
+ rdkit (= 2013.03.2-4)   ,
  x11
 
 #


--
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caught up. So what steps can you take to put your SQL databases under 
version control? Why should you start doing it? Read more to find out.
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[cvs] dists/10.7/stable/main/finkinfo/sci rdkit.info,1.3,1.4

[William Scott]

Update of /cvsroot/fink/dists/10.7/stable/main/finkinfo/sci
In directory sfp-cvs-1.v30.ch3.sourceforge.com:/tmp/cvs-serv5958

Modified Files:
rdkit.info 
Log Message:
updated to use boot1.53

Index: rdkit.info
===
RCS file: /cvsroot/fink/dists/10.7/stable/main/finkinfo/sci/rdkit.info,v
retrieving revision 1.3
retrieving revision 1.4
diff -u -d -r1.3 -r1.4
--- rdkit.info  27 Jul 2013 17:02:47 -  1.3
+++ rdkit.info  29 Jul 2013 01:55:32 -  1.4
@@ -1,13 +1,11 @@
 Package: rdkit
 Version: 2013.03.2
-Revision: 1
+Revision: 3
 Distribution: 10.6, 10.7, 10.8
 GCC: 4.0
 BuildDependsOnly: false
 Source: mirror:sourceforge:rdkit/RDKit_2013_03_2.tgz
 Source-MD5: b5cff9fb70124e544d2e26ea16c92d95
-Source2: mirror:sourceforge:boost/boost_1_53_0.tar.bz2
-Source2-MD5: a00d22605d5dbcfb4c9936a9b35bc4c2
 Description: Cheminformatics and machine-learning software 
 DescDetail: 
 A collection of cheminformatics and machine-learning software written in C++ 
@@ -18,44 +16,14 @@
 similarity searches.
 
 BuildConflicts:  boost1.35.nopython, boost1.35.python26, boost1.35.python27, 
boost1.35.systempython, boost1.46.cmake, boost-jam, boost1.46.1.cmake, 
boost1.52.0.cmake, boost1.52.0.cmake-shlibs
-Depends: %N-shlibs, python27-shlibs, numpy-py27, sqlite3-shlibs, pil-py27
-BuildDepends:  python27, numpy-py27, sqlite3-dev, cmake
+Depends: %N-shlibs, python27-shlibs, numpy-py27, sqlite3-shlibs, pil-py27, 
boost1.53.python27-shlibs
+BuildDepends:  python27, numpy-py27, sqlite3-dev, cmake, boost1.53.python27
 CompileScript: 
 #!/bin/sh -efv
-#
-# First build a more current boost libboost_python library and we will put it 
in the rdkit 
-# library subdirectory to avoid confusion
-#
-RDKIT_ROOT=$PWD
-cd ../boost_1_53_0
-BOOSTROOT=$PWD
-./bootstrap.sh --with-libraries=python,regex --with-python-root=%p 
--with-python=%p/bin/python2.7  --prefix=$PWD  
-# 
-./b2 install --prefix=$BOOSTROOT  
-cd lib
-# Despite the above it links to the system python, so fix that and give it a 
proper instal name id
-install_name_tool -change 
/System/Library/Frameworks/Python.framework/Versions/2.7/Python 
%p/lib/python2.7/config/libpython2.7.dylib libboost_python.dylib
-install_name_tool -id %p/lib/rdkit/libboost_python.dylib   
libboost_python.dylib
-#
-#
-install_name_tool -change 
/System/Library/Frameworks/Python.framework/Versions/2.7/Python 
%p/lib/python2.7/config/libpython2.7.dylib  libboost_regex.dylib
-install_name_tool -id %p/lib/rdkit/libboost_regex.dylib  libboost_regex.dylib
-#
-#
-# Now for rdkit itself
-#
-cd $RDKIT_ROOT 
 mkdir build
 cd build
-cmake -DCMAKE_OSX_SYSROOT:PATH=/ -DCMAKE_OSX_DEPLOYMENT_TARGET:STRING= 
-DCMAKE_INSTALL_PREFIX=%p -DCMAKE_INSTALL_NAME_DIR=%p/lib/%n   
-DCMAKE_PREFIX_PATH=%p   -DBOOST_ROOT=$BOOSTROOT -DBoost_NO_SYSTEM_PATHS=ON 
-DPYTHON_LIBRARY=%p/lib/python2.7/config/libpython2.7.dylib  
-DPYTHON_INCLUDE_DIR=%p/include/python2.7 -DPYTHON_EXECUTABLE=%p/bin/python2.7 
..  
-# NUMPROC=$(sysctl -n hw.ncpu)
-# make -j $NUMPROC install
- make install
-#
-# We only require the boost_python library and boost_regex library
-cp $BOOSTROOT/lib/libboost_python.dylib  
$RDKIT_ROOT/lib/libboost_python.dylib
-cp $BOOSTROOT/lib/libboost_regex.dylib   
$RDKIT_ROOT/lib/libboost_regex.dylib
-cp -R $BOOSTROOT/boost  $RDKIT_ROOT/Code/.
+cmake -DCMAKE_OSX_SYSROOT:PATH=/ -DCMAKE_OSX_DEPLOYMENT_TARGET:STRING= 
-DCMAKE_INSTALL_PREFIX=%p -DCMAKE_INSTALL_NAME_DIR=%p/lib/%n   
-DCMAKE_PREFIX_PATH=%p  -DBOOST_LIBRARYDIR=%p/lib/python2.7/site-packages 
-DBOOST_ROOT=%p/lib/boost-1_53 -DBoost_NO_SYSTEM_PATHS=ON 
-DPYTHON_LIBRARY=%p/lib/python2.7/config/libpython2.7.dylib  
-DPYTHON_INCLUDE_DIR=%p/include/python2.7 -DPYTHON_EXECUTABLE=%p/bin/python2.7 
..  
+make install
 
 InstallScript: 
 #!/bin/sh -efv
@@ -64,21 +32,15 @@
 cp -R rdkit %i/lib/python2.7/site-packages/.
 mkdir -p %i/lib
 cp -R lib %i/lib/%n
-mkdir -p %i/include
-cp -R Code %i/include/%n
 
 SplitOff: 
 Package: %N-shlibs
 Description: rdkit dynamic libraries
 Files:  
 lib/%N/*.%v.dylib 
-lib/%N/*.1.dylib 
-lib/%N/libboost_python.dylib   
   
-lib/%N/libboost_regex.dylib
  
+lib/%N/*.1.dylib   
  
 
 Shlibs: 
-%p/lib/%N/libboost_python.dylib0.0.0 %n  (= 
0.0.0-1) 
-%p/lib/%N/libboost_regex.dylib 0.0.0 %n  (= 
0.0.0-1) 
 %p/lib/%N/libAlignment.1.dylib1.0.0 %n  (= 
2013.03.2-1)   
 %p/lib/%N/libCatalogs.1.dylib 1.0.0 %n  (= 
2013.03.2-1)
 %p/lib/%N/libChemReactions.1.dylib1.0.0 %n  (= 
2013.03.2-1)
@@ -121,7 +83,6 @@
 

[cvs] dists/10.7/stable/main/finkinfo/sci rdkit.info,1.2,1.3

[William Scott]

Update of /cvsroot/fink/dists/10.7/stable/main/finkinfo/sci
In directory sfp-cvs-1.v30.ch3.sourceforge.com:/tmp/cvs-serv3876

Modified Files:
rdkit.info 
Log Message:
corrected for compile error when only Xcode compilers are available

Index: rdkit.info
===
RCS file: /cvsroot/fink/dists/10.7/stable/main/finkinfo/sci/rdkit.info,v
retrieving revision 1.2
retrieving revision 1.3
diff -u -d -r1.2 -r1.3
--- rdkit.info  12 Jun 2013 20:59:38 -  1.2
+++ rdkit.info  27 Jul 2013 17:02:47 -  1.3
@@ -47,7 +47,7 @@
 cd $RDKIT_ROOT 
 mkdir build
 cd build
-cmake -DCMAKE_INSTALL_PREFIX=%p -DCMAKE_INSTALL_NAME_DIR=%p/lib/%n   
-DCMAKE_PREFIX_PATH=%p   -DBOOST_ROOT=$BOOSTROOT -DBoost_NO_SYSTEM_PATHS=ON 
-DPYTHON_LIBRARY=%p/lib/python2.7/config/libpython2.7.dylib  
-DPYTHON_INCLUDE_DIR=%p/include/python2.7 -DPYTHON_EXECUTABLE=%p/bin/python2.7 
..  
+cmake -DCMAKE_OSX_SYSROOT:PATH=/ -DCMAKE_OSX_DEPLOYMENT_TARGET:STRING= 
-DCMAKE_INSTALL_PREFIX=%p -DCMAKE_INSTALL_NAME_DIR=%p/lib/%n   
-DCMAKE_PREFIX_PATH=%p   -DBOOST_ROOT=$BOOSTROOT -DBoost_NO_SYSTEM_PATHS=ON 
-DPYTHON_LIBRARY=%p/lib/python2.7/config/libpython2.7.dylib  
-DPYTHON_INCLUDE_DIR=%p/include/python2.7 -DPYTHON_EXECUTABLE=%p/bin/python2.7 
..  
 # NUMPROC=$(sysctl -n hw.ncpu)
 # make -j $NUMPROC install
  make install


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[cvs] dists/10.7/stable/main/finkinfo/sci coot.info,1.21,1.22

[William Scott]

Update of /cvsroot/fink/dists/10.7/stable/main/finkinfo/sci
In directory sfp-cvs-1.v30.ch3.sourceforge.com:/tmp/cvs-serv4762

Modified Files:
coot.info 
Log Message:
corrected md5sum for refmac_dictionary_v5.41.tar.gz

Index: coot.info
===
RCS file: /cvsroot/fink/dists/10.7/stable/main/finkinfo/sci/coot.info,v
retrieving revision 1.21
retrieving revision 1.22
diff -u -d -r1.21 -r1.22
--- coot.info   3 Jul 2013 00:31:19 -   1.21
+++ coot.info   6 Jul 2013 18:55:56 -   1.22
@@ -7,7 +7,7 @@
 Source: 
http://www2.mrc-lmb.cam.ac.uk/groups/murshudov/coot/source/releases/%n-0.7.1.tar.gz
 Source-MD5: 94557d40bb2d1643b613c34fea10300b 
 Source2: 
http://www2.mrc-lmb.cam.ac.uk/groups/murshudov/content/refmac/Dictionary/refmac_dictionary_v5.41.tar.gz
-Source2-MD5: 7dc4af3a32a3e030ae79e6f67aaf7e79
+Source2-MD5: e7acb760fcbbe663147f5245b6c523c4
 Source3: 
http://www.ysbl.york.ac.uk/~emsley/software/extras/reference-structures.tar.gz
 Source3-MD5: 257ab90d44f1c877ada96720dbb87c13 
 ###


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[cvs] dists/10.4/stable/main/finkinfo/sci coot.info,1.40,1.41

[William Scott]

Update of /cvsroot/fink/dists/10.4/stable/main/finkinfo/sci
In directory sfp-cvs-1.v30.ch3.sourceforge.com:/tmp/cvs-serv4812

Modified Files:
coot.info 
Log Message:
corrected md5sum for refmac_dictionary_v5.41.tar.gz

Index: coot.info
===
RCS file: /cvsroot/fink/dists/10.4/stable/main/finkinfo/sci/coot.info,v
retrieving revision 1.40
retrieving revision 1.41
diff -u -d -r1.40 -r1.41
--- coot.info   5 Jul 2013 01:07:39 -   1.40
+++ coot.info   6 Jul 2013 18:57:05 -   1.41
@@ -7,7 +7,7 @@
 Source: 
http://www2.mrc-lmb.cam.ac.uk/groups/murshudov/coot/source/releases/%n-0.7.1.tar.gz
 Source-MD5: 94557d40bb2d1643b613c34fea10300b 
 Source2: 
http://www2.mrc-lmb.cam.ac.uk/groups/murshudov/content/refmac/Dictionary/refmac_dictionary_v5.41.tar.gz
-Source2-MD5: 7dc4af3a32a3e030ae79e6f67aaf7e79
+Source2-MD5: e7acb760fcbbe663147f5245b6c523c4
 Source3: 
http://www.ysbl.york.ac.uk/~emsley/software/extras/reference-structures.tar.gz
 Source3-MD5: 257ab90d44f1c877ada96720dbb87c13 
 ###


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[cvs] dists/10.4/stable/main/finkinfo/sci clipper.info, 1.10, 1.11 coot.info, 1.39, 1.40 gpp4.info, 1.8, 1.9 ssm.info, 1.7, 1.8

[William Scott]

Update of /cvsroot/fink/dists/10.4/stable/main/finkinfo/sci
In directory sfp-cvs-1.v30.ch3.sourceforge.com:/tmp/cvs-serv17344

Modified Files:
clipper.info coot.info gpp4.info ssm.info 
Log Message:
update to coot and its dependencies to latest version and gcc4.8

Index: gpp4.info
===
RCS file: /cvsroot/fink/dists/10.4/stable/main/finkinfo/sci/gpp4.info,v
retrieving revision 1.8
retrieving revision 1.9
diff -u -d -r1.8 -r1.9
--- gpp4.info   29 Jul 2012 15:27:53 -  1.8
+++ gpp4.info   5 Jul 2013 01:07:39 -   1.9
@@ -1,6 +1,6 @@
 Package: gpp4
 Version: 1.2.0
-Revision: 31
+Revision: 32
 Maintainer: W. G. Scott wgsc...@users.sourceforge.net 
 DescPackaging: 
  Based on package created by Morten Kjeldgaard m...@bioxray.dk with minor
@@ -13,8 +13,8 @@
 Source: http://diablo.ucsc.edu/~wgscott/%n/%n-%v.tar.gz
 Source-MD5: bb443de0b3385847ea9987f1220e56f1
 NoSourceDirectory: false
-Depends: %N-shlibs (= %v-%r), gcc47-shlibs 
-BuildDepends: mmdb-dev (= 1.23.2-30), ssm-dev (= 0.1-30), gcc47, pkgconfig
+Depends: %N-shlibs (= %v-%r), gcc48-shlibs 
+BuildDepends: mmdb-dev (= 1.25.0-32), ssm-dev (= 0.1-32), gcc48, pkgconfig
 BuildConflicts: g77, fort77, g95
 BuildDependsOnly: true
 HomePage: http://www.bioxray.dk/~mok/gpp4
@@ -46,7 +46,7 @@
 
 CompileScript: 
 #!/bin/bash -evf
-LDFLAGS=-L%p/lib/gcc4.7/lib -L%p/lib -L/usr/lib \
+LDFLAGS=-L%p/lib/gcc4.8/lib -L%p/lib -L/usr/lib \
 MMDB_CFLAGS=-I%p/include/mmdb MMDB_LIBS=-L%p/lib  \
 FC=gfortran \
   ./configure --prefix=%p 
@@ -65,7 +65,7 @@
%p/lib/libgpp4.0.dylib 1.0.0 %n (= 1.2.0-1)
 %p/lib/libgpp4f.0.dylib 1.0.0 %n (=1.2.0-1)
   
-   Depends: gcc47-shlibs 
+   Depends: gcc48-shlibs 
 
 SplitOff2: 
 Package: %N-dev

Index: clipper.info
===
RCS file: /cvsroot/fink/dists/10.4/stable/main/finkinfo/sci/clipper.info,v
retrieving revision 1.10
retrieving revision 1.11
diff -u -d -r1.10 -r1.11
--- clipper.info29 Jul 2012 15:27:53 -  1.10
+++ clipper.info5 Jul 2013 01:07:39 -   1.11
@@ -1,14 +1,14 @@
 Package: clipper
 Epoch: 1
 Version: 2.1
-Revision: 31
+Revision: 32
 GCC:4.0
 BuildDepends: 
 fftw (= 2.1.5-1010) | fftw-mpi (= 2.1.5-1010), 
 mmdb-dev (= 1.23.2-31), 
 ssm-dev (= 0.1-31), 
 gpp4-dev (= 1.2.0-31), 
-gcc47
+gcc48
 
 Depends: 
 %n-shlibs (= %e:%v-%r)
@@ -52,7 +52,7 @@
mmdb-shlibs (= 1.23.2-1),
ssm-shlibs (= 0.1-26), 
gpp4-shlibs (= 1.2.0-26),
-   gcc47-shlibs 
+   gcc48-shlibs 
   
   Files: 
lib/libclipper-ccp4.2.*dylib

Index: coot.info
===
RCS file: /cvsroot/fink/dists/10.4/stable/main/finkinfo/sci/coot.info,v
retrieving revision 1.39
retrieving revision 1.40
diff -u -d -r1.39 -r1.40
--- coot.info   11 Feb 2013 22:09:36 -  1.39
+++ coot.info   5 Jul 2013 01:07:39 -   1.40
@@ -1,17 +1,15 @@
 Package: coot
-Version: 0.7.1-pre
-Revision: 4562
-SourceDirectory: %n-%v
+Version: 0.7.1.0  
+Revision: 1
+SourceDirectory: %n-0.7.1
 Distribution: 10.6, 10.7, 10.8
 GCC: 4.0 
-Source: 
http://www2.mrc-lmb.cam.ac.uk/groups/murshudov/coot/source/pre-releases/%n-%v-revision-%r.tar.gz
-Source-MD5: 82d653d6e97bb940b024833314a3ccfc
-Source2: 
http://www2.mrc-lmb.cam.ac.uk/groups/murshudov/content/refmac/Dictionary/refmac_dictionary_v5.38.tar.gz
-Source2-MD5: 174a5fc5e5be03cb432c61e8da4283df
+Source: 
http://www2.mrc-lmb.cam.ac.uk/groups/murshudov/coot/source/releases/%n-0.7.1.tar.gz
+Source-MD5: 94557d40bb2d1643b613c34fea10300b 
+Source2: 
http://www2.mrc-lmb.cam.ac.uk/groups/murshudov/content/refmac/Dictionary/refmac_dictionary_v5.41.tar.gz
+Source2-MD5: 7dc4af3a32a3e030ae79e6f67aaf7e79
 Source3: 
http://www.ysbl.york.ac.uk/~emsley/software/extras/reference-structures.tar.gz
 Source3-MD5: 257ab90d44f1c877ada96720dbb87c13 
-#Source4: 
http://coot.googlecode.com/svn-history/r4544/trunk/lidia-core/cod-types.hh
-#Source4-MD5: 333ee49b341b9ee534b3e6f72cff7064
 ###
 Description: Crystallographic molecular graphics
 DescDetail: 
@@ -40,9 +38,9 @@
 Recommends:  povray, ccp4, raster3d
 BuildDepends: 
  fink (= 0.24.12)   ,
- clipper-dev (= 1:2.1-31)   ,
- gpp4-dev (= 1.2.0-31)  ,
- mmdb-dev (= 1.23.2-31) ,
+ clipper-dev (= 1:2.1-32)   ,
+ gpp4-dev (= 1.2.0-32)  ,
+ mmdb-dev (= 1.25.0-32) ,
  ssm-dev (= 0.1-31) ,
  atk1 (= 1.28.0-1)  ,
  cairo (= 1.8.8-3)  ,
@@ -87,15 +85,15 @@
 
 #   
 Depends: 
- clipper-shlibs (= 1:2.1-31) ,
- gpp4-shlibs (= 1.2.0-31),
- mmdb-shlibs (= 1.23.2-31)   ,
- ssm-shlibs (= 0.1-31)   ,
+ coot-shlibs (= 0.7.1.0-%r)   ,
+ clipper-shlibs (= 1:2.1-32) ,
+ gpp4-shlibs (= 1.2.0-32),
+ mmdb-shlibs (= 1.25.0-32)   

[cvs] dists/10.4/stable/main/finkinfo/sci mmdb.info,1.8,1.9

[William Scott]

Update of /cvsroot/fink/dists/10.4/stable/main/finkinfo/sci
In directory sfp-cvs-1.v30.ch3.sourceforge.com:/tmp/cvs-serv17490

Modified Files:
mmdb.info 
Log Message:
update to coot and its dependencies to latest version and gcc4.8

Index: mmdb.info
===
RCS file: /cvsroot/fink/dists/10.4/stable/main/finkinfo/sci/mmdb.info,v
retrieving revision 1.8
retrieving revision 1.9
diff -u -d -r1.8 -r1.9
--- mmdb.info   4 Jul 2013 19:48:21 -   1.8
+++ mmdb.info   5 Jul 2013 01:09:54 -   1.9
@@ -1,6 +1,6 @@
 Package: mmdb
-Version: 1.23.2
-Revision: 31
+Version: 1.25.0
+Revision: 32
 Maintainer: W. G. Scott wgsc...@users.sourceforge.net 
 DescPackaging: 
  Based on package created by Morten Kjeldgaard m...@bioxray.dk with minor
@@ -10,11 +10,11 @@
 License: LGPL
 GCC:4.0
 HomePage: http://www.ebi.ac.uk/pdbe/docs/cldoc/
-Source: http://lmb.bioch.ox.ac.uk/coot/software/dependencies/%n-%v.tar.gz
-Source-MD5: c92ef26d6b12ba0930e1d7c20a263987
+Source: 
http://www2.mrc-lmb.cam.ac.uk/groups/murshudov/coot/dependencies/%n-%v.tar.gz
+Source-MD5: 8d20c3b752b7b604d3ef2b3f01a04f70
 # build-time stuff in %N-dev, runtime stuff in %N-shlibs, nothing in %N
-RuntimeDepends: fink-obsolete-packages, %n-shlibs (= %v-%r)
-BuildDepends: libtool2, automake1.11, autoconf2.6, fink (= 0.32)
+Depends: fink-obsolete-packages, %n-shlibs (= %v-%r)
+BuildDepends: libtool2, automake1.11, autoconf2.6
 DescDetail:  
 MMDB is CCP4\'s macromolecular coordinate library, written by Eugene
 Krissinel of the EBI.  The Coordinate Library is designed to assist


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[cvs] dists/10.4/stable/main/finkinfo/sci pdb2pqr.info,1.3,1.4

[William Scott]

Update of /cvsroot/fink/dists/10.4/stable/main/finkinfo/sci
In directory sfp-cvs-1.v30.ch3.sourceforge.com:/tmp/cvs-serv17571

Modified Files:
pdb2pqr.info 
Log Message:
update for gcc48

Index: pdb2pqr.info
===
RCS file: /cvsroot/fink/dists/10.4/stable/main/finkinfo/sci/pdb2pqr.info,v
retrieving revision 1.3
retrieving revision 1.4
diff -u -d -r1.3 -r1.4
--- pdb2pqr.info22 Jan 2012 22:34:39 -  1.3
+++ pdb2pqr.info5 Jul 2013 01:11:55 -   1.4
@@ -1,12 +1,12 @@
 Package: pdb2pqr
 Version: 1.7
-Revision: 1
+Revision: 3
 UseMaxBuildJobs: false
 Source: mirror:sourceforge:%n/%n-%v.tar.gz
 Source-MD5: 058622cb2ca6ca12af04d4f11b272951
 SourceDirectory: %n-%v
-Depends: python27, gcc46-shlibs
-BuildDepends: python, python27, gcc46
+Depends: python27, gcc48-shlibs
+BuildDepends: python, python27, gcc48
 BuildConflicts: g77, g95, fort77
 Description: Converts pdb files to pqr
 NoSetCPPFLAGS: true


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[cvs] dists/10.7/stable/main/finkinfo/sci phaser-mpi.info,1.1,1.2

[William Scott]

Update of /cvsroot/fink/dists/10.7/stable/main/finkinfo/sci
In directory sfp-cvs-1.v30.ch3.sourceforge.com:/tmp/cvs-serv9317

Modified Files:
phaser-mpi.info 
Log Message:
phaser update for gcc48

Index: phaser-mpi.info
===
RCS file: /cvsroot/fink/dists/10.7/stable/main/finkinfo/sci/phaser-mpi.info,v
retrieving revision 1.1
retrieving revision 1.2
diff -u -d -r1.1 -r1.2
--- phaser-mpi.info 18 Sep 2012 01:28:00 -  1.1
+++ phaser-mpi.info 3 Jul 2013 20:51:16 -   1.2
@@ -1,21 +1,21 @@
 Package: phaser-mpi
 Version: 2.5.1
-Revision: 1
+Revision: 2
 Distribution: 10.6, 10.7, 10.8
 Source: ftp://ftp.ccp4.ac.uk/ccp4/6.3.0/ccp4-6.3.0-phaser-cctbx-src.tar.gz
 Source-MD5: 018765c258b70726b281de506e9139c4  
 SourceDirectory: ccp4-6.3.0
 NoSetCPPFLAGS: true
 NoSetLDFLAGS: true
-Depends: gcc47-shlibs
-BuildDepends: gcc47-compiler
+Depends: gcc48-shlibs
+BuildDepends: gcc48-compiler
 BuildDependsOnly: false
 PatchScript:  perl -pi.orig -e s|cxx \= cc.replace\('gcc', 'g\+\+'\)|cxx \= 
cc.replace\('gcc', '%p/bin/g\+\+-4'\)|g 
lib/cctbx/cctbx_sources/cctbx_project/libtbx/SConscript
 CompileScript:  
 #!/bin/bash -efv
 CCP4=
-export CXXFLAGS=-L%p/lib/gcc4.7/lib
-export CFLAGS=-I%p/lib/gcc4.7/include
+export CXXFLAGS=-L%p/lib/gcc4.8/lib
+export CFLAGS=-I%p/lib/gcc4.8/include
 export CPPFLAGS=$CFLAGS
 NUMPROC=$(sysctl -n hw.ncpu)
 cd src/phaser
@@ -33,7 +33,7 @@
 #!/bin/bash -efv
  mkdir -p %i/bin
  cd src/phaser
- install_name_tool -change /usr/lib/libstdc++.6.dylib   
%p/lib/gcc4.7/lib/libstdc++.6.dylib   exe/phaser
+ install_name_tool -change /usr/lib/libstdc++.6.dylib   
%p/lib/gcc4.8/lib/libstdc++.6.dylib   exe/phaser
  cp exe/phaser  %i/bin/phaser_omp
 
 Description: CCP4 automated molecular replacement program


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[cvs] dists/10.7/stable/main/finkinfo/sci pdb2pqr.info,1.3,1.4

[William Scott]

Update of /cvsroot/fink/dists/10.7/stable/main/finkinfo/sci
In directory sfp-cvs-1.v30.ch3.sourceforge.com:/tmp/cvs-serv10334

Modified Files:
pdb2pqr.info 
Log Message:
pdb2pqr update for gcc48

Index: pdb2pqr.info
===
RCS file: /cvsroot/fink/dists/10.7/stable/main/finkinfo/sci/pdb2pqr.info,v
retrieving revision 1.3
retrieving revision 1.4
diff -u -d -r1.3 -r1.4
--- pdb2pqr.info23 Jul 2012 00:45:57 -  1.3
+++ pdb2pqr.info3 Jul 2013 20:59:53 -   1.4
@@ -1,12 +1,12 @@
 Package: pdb2pqr
 Version: 1.7
-Revision: 2
+Revision: 3
 UseMaxBuildJobs: false
 Source: mirror:sourceforge:%n/%n-%v.tar.gz
 Source-MD5: 058622cb2ca6ca12af04d4f11b272951
 SourceDirectory: %n-%v
-Depends: python27, gcc47-shlibs
-BuildDepends: python, python27, gcc47
+Depends: python27, gcc48-shlibs
+BuildDepends: python, python27, gcc48
 BuildConflicts: g77, g95, fort77
 Description: Converts pdb files to pqr
 NoSetCPPFLAGS: true


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[cvs] dists/10.7/stable/main/finkinfo/sci tinker.info,1.3,1.4

[William Scott]

Update of /cvsroot/fink/dists/10.7/stable/main/finkinfo/sci
In directory sfp-cvs-1.v30.ch3.sourceforge.com:/tmp/cvs-serv11776

Modified Files:
tinker.info 
Log Message:
tinker update for gcc48

Index: tinker.info
===
RCS file: /cvsroot/fink/dists/10.7/stable/main/finkinfo/sci/tinker.info,v
retrieving revision 1.3
retrieving revision 1.4
diff -u -d -r1.3 -r1.4
--- tinker.info 14 Nov 2012 17:17:25 -  1.3
+++ tinker.info 3 Jul 2013 21:13:06 -   1.4
@@ -1,12 +1,12 @@
 Package: tinker
-Version: 6.1.01
+Version: 6.2.05
 Revision: 1
 Source: http://dasher.wustl.edu/%n/downloads/%n-%v.tar.gz
 SourceRename: %n-%v.tar.gz 
 SourceDirectory: %n
-Source-MD5: 202a4b3138a53715d409382ac443e4c0
-BuildDepends: gcc47
-Depends: gcc47-shlibs
+Source-MD5: 5a2be7b669e49636f9d602f76534c6e9
+BuildDepends: gcc48
+Depends: gcc48-shlibs
 PatchScript: 
 #!/bin/zsh -efv
 perl -pi -e 's|gfortran -c -O3|gfortran -c -O3 -fno-align-commons|g' 
macosx/**/*.make


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[cvs] dists/10.7/stable/main/finkinfo/sci clipper.info, 1.4, 1.5 coot.info, 1.20, 1.21 gpp4.info, 1.4, 1.5 mmdb.info, 1.4, 1.5 ssm.info, 1.4, 1.5

[William Scott]

Update of /cvsroot/fink/dists/10.7/stable/main/finkinfo/sci
In directory sfp-cvs-1.v30.ch3.sourceforge.com:/tmp/cvs-serv13354

Modified Files:
clipper.info coot.info gpp4.info mmdb.info ssm.info 
Log Message:
update to coot and its dependencies to latest version and gcc4.8

Index: gpp4.info
===
RCS file: /cvsroot/fink/dists/10.7/stable/main/finkinfo/sci/gpp4.info,v
retrieving revision 1.4
retrieving revision 1.5
diff -u -d -r1.4 -r1.5
--- gpp4.info   29 Jul 2012 15:12:24 -  1.4
+++ gpp4.info   3 Jul 2013 00:31:19 -   1.5
@@ -1,6 +1,6 @@
 Package: gpp4
 Version: 1.2.0
-Revision: 31
+Revision: 32
 Maintainer: W. G. Scott wgsc...@users.sourceforge.net 
 DescPackaging: 
  Based on package created by Morten Kjeldgaard m...@bioxray.dk with minor
@@ -13,8 +13,8 @@
 Source: http://diablo.ucsc.edu/~wgscott/%n/%n-%v.tar.gz
 Source-MD5: bb443de0b3385847ea9987f1220e56f1
 NoSourceDirectory: false
-Depends: %N-shlibs (= %v-%r), gcc47-shlibs 
-BuildDepends: mmdb-dev (= 1.23.2-30), ssm-dev (= 0.1-30), gcc47, pkgconfig
+Depends: %N-shlibs (= %v-%r), gcc48-shlibs 
+BuildDepends: mmdb-dev (= 1.25.0-32), ssm-dev (= 0.1-32), gcc48, pkgconfig
 BuildConflicts: g77, fort77, g95
 BuildDependsOnly: true
 HomePage: http://www.bioxray.dk/~mok/gpp4
@@ -46,7 +46,7 @@
 
 CompileScript: 
 #!/bin/bash -evf
-LDFLAGS=-L%p/lib/gcc4.7/lib -L%p/lib -L/usr/lib \
+LDFLAGS=-L%p/lib/gcc4.8/lib -L%p/lib -L/usr/lib \
 MMDB_CFLAGS=-I%p/include/mmdb MMDB_LIBS=-L%p/lib  \
 FC=gfortran \
   ./configure --prefix=%p 
@@ -65,7 +65,7 @@
%p/lib/libgpp4.0.dylib 1.0.0 %n (= 1.2.0-1)
 %p/lib/libgpp4f.0.dylib 1.0.0 %n (=1.2.0-1)
   
-   Depends: gcc47-shlibs 
+   Depends: gcc48-shlibs 
 
 SplitOff2: 
 Package: %N-dev

Index: mmdb.info
===
RCS file: /cvsroot/fink/dists/10.7/stable/main/finkinfo/sci/mmdb.info,v
retrieving revision 1.4
retrieving revision 1.5
diff -u -d -r1.4 -r1.5
--- mmdb.info   24 Apr 2013 01:05:05 -  1.4
+++ mmdb.info   3 Jul 2013 00:31:19 -   1.5
@@ -1,6 +1,6 @@
 Package: mmdb
 Version: 1.25.0
-Revision: 1
+Revision: 32
 Maintainer: W. G. Scott wgsc...@users.sourceforge.net 
 DescPackaging: 
  Based on package created by Morten Kjeldgaard m...@bioxray.dk with minor

Index: clipper.info
===
RCS file: /cvsroot/fink/dists/10.7/stable/main/finkinfo/sci/clipper.info,v
retrieving revision 1.4
retrieving revision 1.5
diff -u -d -r1.4 -r1.5
--- clipper.info29 Jul 2012 15:12:24 -  1.4
+++ clipper.info3 Jul 2013 00:31:19 -   1.5
@@ -1,14 +1,14 @@
 Package: clipper
 Epoch: 1
 Version: 2.1
-Revision: 31
+Revision: 32
 GCC:4.0
 BuildDepends: 
 fftw (= 2.1.5-1010) | fftw-mpi (= 2.1.5-1010), 
 mmdb-dev (= 1.23.2-31), 
 ssm-dev (= 0.1-31), 
 gpp4-dev (= 1.2.0-31), 
-gcc47
+gcc48
 
 Depends: 
 %n-shlibs (= %e:%v-%r)
@@ -52,7 +52,7 @@
mmdb-shlibs (= 1.23.2-1),
ssm-shlibs (= 0.1-26), 
gpp4-shlibs (= 1.2.0-26),
-   gcc47-shlibs 
+   gcc48-shlibs 
   
   Files: 
lib/libclipper-ccp4.2.*dylib

Index: coot.info
===
RCS file: /cvsroot/fink/dists/10.7/stable/main/finkinfo/sci/coot.info,v
retrieving revision 1.20
retrieving revision 1.21
diff -u -d -r1.20 -r1.21
--- coot.info   16 May 2013 16:47:12 -  1.20
+++ coot.info   3 Jul 2013 00:31:19 -   1.21
@@ -1,17 +1,15 @@
 Package: coot
-Version: 0.7.1-pre
-Revision: 4630
-SourceDirectory: %n-%v
+Version: 0.7.1.0  
+Revision: 1
+SourceDirectory: %n-0.7.1
 Distribution: 10.6, 10.7, 10.8
 GCC: 4.0 
-Source: 
http://www2.mrc-lmb.cam.ac.uk/groups/murshudov/coot/source/pre-releases/%n-%v-revision-%r.tar.gz
-Source-MD5: d67065eb5eb8152f320ba2b7ba33434e 
-Source2: 
http://www2.mrc-lmb.cam.ac.uk/groups/murshudov/content/refmac/Dictionary/refmac_dictionary_v5.38.tar.gz
-Source2-MD5: 174a5fc5e5be03cb432c61e8da4283df
+Source: 
http://www2.mrc-lmb.cam.ac.uk/groups/murshudov/coot/source/releases/%n-0.7.1.tar.gz
+Source-MD5: 94557d40bb2d1643b613c34fea10300b 
+Source2: 
http://www2.mrc-lmb.cam.ac.uk/groups/murshudov/content/refmac/Dictionary/refmac_dictionary_v5.41.tar.gz
+Source2-MD5: 7dc4af3a32a3e030ae79e6f67aaf7e79
 Source3: 
http://www.ysbl.york.ac.uk/~emsley/software/extras/reference-structures.tar.gz
 Source3-MD5: 257ab90d44f1c877ada96720dbb87c13 
-#Source4: 
http://coot.googlecode.com/svn-history/r4544/trunk/lidia-core/cod-types.hh
-#Source4-MD5: 333ee49b341b9ee534b3e6f72cff7064
 ###
 Description: Crystallographic molecular graphics
 DescDetail: 
@@ -40,9 +38,9 @@
 Recommends:  povray, ccp4, raster3d
 BuildDepends: 
  fink (= 0.24.12)   ,
- clipper-dev (= 1:2.1-31)   ,
- gpp4-dev (= 1.2.0-31)  ,
- mmdb-dev (= 

[cvs] dists/10.7/stable/main/finkinfo/utils a2ps.info,1.2,1.3

[William Scott]

Update of /cvsroot/fink/dists/10.7/stable/main/finkinfo/utils
In directory sfp-cvs-1.v30.ch3.sourceforge.com:/tmp/cvs-serv17079

Modified Files:
a2ps.info 
Log Message:
BuildDepends fix and elimination of precompiled emacs files

Index: a2ps.info
===
RCS file: /cvsroot/fink/dists/10.7/stable/main/finkinfo/utils/a2ps.info,v
retrieving revision 1.2
retrieving revision 1.3
diff -u -d -r1.2 -r1.3
--- a2ps.info   20 Jun 2013 22:29:58 -  1.2
+++ a2ps.info   24 Jun 2013 18:22:58 -  1.3
@@ -1,13 +1,13 @@
 Package: a2ps
 Version: 4.14
-Revision: 2
+Revision: 3
 Source: http://ftp.gnu.org/gnu/%n/%n-%v.tar.gz
 Source-MD5: 781ac3d9b213fa3e1ed0d79f986dc8c7
 UpdateConfigGuessInDirs: auxdir
 Depends: libgettext8-shlibs, libpaper1-shlibs, psutils, ghostscript
-BuildDepends: libgettext8-dev, gettext-bin, gettext-tools, libpaper1-dev
+BuildDepends: libgettext8-dev, gettext-bin, gettext-tools, libpaper1-dev, 
emacsen | xemacs-base-pkg
 PatchScript: 
-#perl -ni -e 'print unless /^ELCFILES =/' contrib/emacs/Makefile.in
+perl -ni -e 'print unless /^ELCFILES =/' contrib/emacs/Makefile.in
 #perl -ni -e 'print unless /extern char \* stpcpy/'   lib/xstrrpl.c   
 perl -pi -e 's|extern char \* stpcpy\(\)\;||g' lib/xstrrpl.c
 


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[cvs] dists/10.4/stable/main/finkinfo/utils a2ps.info,1.5,1.6

[William Scott]

Update of /cvsroot/fink/dists/10.4/stable/main/finkinfo/utils
In directory sfp-cvs-1.v30.ch3.sourceforge.com:/tmp/cvs-serv17702

Modified Files:
a2ps.info 
Log Message:
BuildDepends fix and elimination of precompiled emacs files

Index: a2ps.info
===
RCS file: /cvsroot/fink/dists/10.4/stable/main/finkinfo/utils/a2ps.info,v
retrieving revision 1.5
retrieving revision 1.6
diff -u -d -r1.5 -r1.6
--- a2ps.info   15 Nov 2009 06:40:08 -  1.5
+++ a2ps.info   24 Jun 2013 18:36:27 -  1.6
@@ -1,15 +1,15 @@
 Package: a2ps
-Version: 4.13
+Version: 4.14
 Revision: 3
-Source: ftp://ftp.enst.fr/pub/unix/%n/%n-%v.tar.gz
-Source-MD5: c4361045913b27dbb6b6315874f6b196
+Source: http://ftp.gnu.org/gnu/%n/%n-%v.tar.gz
+Source-MD5: 781ac3d9b213fa3e1ed0d79f986dc8c7
 UpdateConfigGuessInDirs: auxdir
-UpdateLibtoolInDirs: auxdir
-Depends: libpaper1-shlibs, psutils, ghostscript
-BuildDepends: libgettext3-dev, gettext-bin, gettext-tools, libpaper1-dev
+Depends: libgettext8-shlibs, libpaper1-shlibs, psutils, ghostscript
+BuildDepends: libgettext8-dev, gettext-bin, gettext-tools, libpaper1-dev, 
emacsen | xemacs-base-pkg
 PatchScript: 
 perl -ni -e 'print unless /^ELCFILES =/' contrib/emacs/Makefile.in
-perl -ni -e 'print unless /extern char \* stpcpy/'   lib/xstrrpl.c   
+#perl -ni -e 'print unless /extern char \* stpcpy/'   lib/xstrrpl.c   
+perl -pi -e 's|extern char \* stpcpy\(\)\;||g' lib/xstrrpl.c
 
 ConfigureParams: --mandir='${prefix}/share/man' 
--infodir='${prefix}/share/info' ac_cv_exeext=''
 ConfFiles: 
@@ -21,7 +21,7 @@
 #
 # Maintainer: Jeremy Higgs f...@higgs-family.net
 Maintainer: W. G. Scott wgsc...@users.sourceforge.net
-Homepage: http://www.gnu.org/software/a2ps/a2ps.es.html
+Homepage: http://www.gnu.org/software/a2ps/a2ps.html
 License: GPL
 Description: Any to PostScript filter
 DescDetail: 


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[cvs] dists/10.7/stable/main/finkinfo/sci rdkit.info,1.1,1.2

[William Scott]

Update of /cvsroot/fink/dists/10.7/stable/main/finkinfo/sci
In directory sfp-cvs-1.v30.ch3.sourceforge.com:/tmp/cvs-serv22802

Modified Files:
rdkit.info 
Log Message:
rdkit update

Index: rdkit.info
===
RCS file: /cvsroot/fink/dists/10.7/stable/main/finkinfo/sci/rdkit.info,v
retrieving revision 1.1
retrieving revision 1.2
diff -u -d -r1.1 -r1.2
--- rdkit.info  11 Feb 2013 22:08:48 -  1.1
+++ rdkit.info  12 Jun 2013 20:59:38 -  1.2
@@ -1,11 +1,11 @@
 Package: rdkit
-Version: 2012.12.1
+Version: 2013.03.2
 Revision: 1
 Distribution: 10.6, 10.7, 10.8
 GCC: 4.0
 BuildDependsOnly: false
-Source: mirror:sourceforge:rdkit/RDKit_2012_12_1.tgz
-Source-MD5: 36596b18ff71c70b04d25c43810c2b01
+Source: mirror:sourceforge:rdkit/RDKit_2013_03_2.tgz
+Source-MD5: b5cff9fb70124e544d2e26ea16c92d95
 Source2: mirror:sourceforge:boost/boost_1_53_0.tar.bz2
 Source2-MD5: a00d22605d5dbcfb4c9936a9b35bc4c2
 Description: Cheminformatics and machine-learning software 
@@ -17,8 +17,8 @@
 to be stored in a relational database and retrieved via substructure and 
 similarity searches.
 
-BuildConflicts:  boost1.35.nopython, boost1.35.python26, boost1.35.python27, 
boost1.35.systempython, boost1.46.cmake, boost-jam, boost1.46.1.cmake
-Depends: %N-shlibs, python27-shlibs, numpy-py27, sqlite3-shlibs
+BuildConflicts:  boost1.35.nopython, boost1.35.python26, boost1.35.python27, 
boost1.35.systempython, boost1.46.cmake, boost-jam, boost1.46.1.cmake, 
boost1.52.0.cmake, boost1.52.0.cmake-shlibs
+Depends: %N-shlibs, python27-shlibs, numpy-py27, sqlite3-shlibs, pil-py27
 BuildDepends:  python27, numpy-py27, sqlite3-dev, cmake
 CompileScript: 
 #!/bin/sh -efv
@@ -60,6 +60,7 @@
 InstallScript: 
 #!/bin/sh -efv
 mkdir -p %i/lib/python2.7/site-packages
+perl -pi -e 's|import Image|from PIL import Image|g' rdkit/sping/PIL/pidPIL.py
 cp -R rdkit %i/lib/python2.7/site-packages/.
 mkdir -p %i/lib
 cp -R lib %i/lib/%n
@@ -70,45 +71,46 @@
 Package: %N-shlibs
 Description: rdkit dynamic libraries
 Files:  
+lib/%N/*.%v.dylib 
 lib/%N/*.1.dylib 
 lib/%N/libboost_python.dylib   
   
 lib/%N/libboost_regex.dylib
  
 
 Shlibs: 
-%p/lib/%N/libboost_python.dylib   0.0.0 %n  (= 
2012.12.1-1) 
-%p/lib/%N/libboost_regex.dylib0.0.0 %n  (= 
2012.12.1-1) 
-%p/lib/%N/libAlignment.1.dylib1.0.0 %n  (= 
2012.12.1-1)   
-%p/lib/%N/libCatalogs.1.dylib 1.0.0 %n  (= 
2012.12.1-1)
-%p/lib/%N/libChemReactions.1.dylib1.0.0 %n  (= 
2012.12.1-1)
-%p/lib/%N/libChemTransforms.1.dylib   1.0.0 %n  (= 
2012.12.1-1)
-%p/lib/%N/libChemicalFeatures.1.dylib 1.0.0 %n  (= 
2012.12.1-1)
-%p/lib/%N/libDataStructs.1.dylib  1.0.0 %n  (= 
2012.12.1-1)
-%p/lib/%N/libDepictor.1.dylib 1.0.0 %n  (= 
2012.12.1-1)
-%p/lib/%N/libDescriptors.1.dylib  1.0.0 %n  (= 
2012.12.1-1)
-%p/lib/%N/libDistGeomHelpers.1.dylib  1.0.0 %n  (= 
2012.12.1-1)
-%p/lib/%N/libDistGeometry.1.dylib 1.0.0 %n  (= 
2012.12.1-1)
-%p/lib/%N/libEigenSolvers.1.dylib 1.0.0 %n  (= 
2012.12.1-1)
-%p/lib/%N/libFileParsers.1.dylib  1.0.0 %n  (= 
2012.12.1-1)
-%p/lib/%N/libFingerprints.1.dylib 1.0.0 %n  (= 
2012.12.1-1)
-%p/lib/%N/libForceField.1.dylib   1.0.0 %n  (= 
2012.12.1-1)
-%p/lib/%N/libForceFieldHelpers.1.dylib1.0.0 %n  (= 
2012.12.1-1)
-%p/lib/%N/libFragCatalog.1.dylib  1.0.0 %n  (= 
2012.12.1-1)
-%p/lib/%N/libGraphMol.1.dylib 1.0.0 %n  (= 
2012.12.1-1)
-%p/lib/%N/libMolAlign.1.dylib 1.0.0 %n  (= 
2012.12.1-1)
-%p/lib/%N/libMolCatalog.1.dylib   1.0.0 %n  (= 
2012.12.1-1)
-%p/lib/%N/libMolChemicalFeatures.1.dylib  1.0.0 %n  (= 
2012.12.1-1)
-%p/lib/%N/libMolTransforms.1.dylib1.0.0 %n  (= 
2012.12.1-1)
-%p/lib/%N/libOptimizer.1.dylib1.0.0 %n  (= 
2012.12.1-1)
-%p/lib/%N/libPartialCharges.1.dylib   1.0.0 %n  (= 
2012.12.1-1)
-%p/lib/%N/libRDBoost.1.dylib  1.0.0 %n  (= 
2012.12.1-1)
-%p/lib/%N/libRDGeneral.1.dylib1.0.0 %n  (= 
2012.12.1-1)
-%p/lib/%N/libRDGeometryLib.1.dylib1.0.0 %n  (= 
2012.12.1-1)
-

[cvs] dists/10.7/stable/main/finkinfo/sci coot.info,1.19,1.20

[William Scott]

Update of /cvsroot/fink/dists/10.7/stable/main/finkinfo/sci
In directory sfp-cvs-1.v30.ch3.sourceforge.com:/tmp/cvs-serv9755

Modified Files:
coot.info 
Log Message:
fixed two env var in wrapper script and updated to latest revision

Index: coot.info
===
RCS file: /cvsroot/fink/dists/10.7/stable/main/finkinfo/sci/coot.info,v
retrieving revision 1.19
retrieving revision 1.20
diff -u -d -r1.19 -r1.20
--- coot.info   11 Feb 2013 22:08:49 -  1.19
+++ coot.info   16 May 2013 16:47:12 -  1.20
@@ -1,11 +1,11 @@
 Package: coot
 Version: 0.7.1-pre
-Revision: 4562
+Revision: 4630
 SourceDirectory: %n-%v
 Distribution: 10.6, 10.7, 10.8
 GCC: 4.0 
 Source: 
http://www2.mrc-lmb.cam.ac.uk/groups/murshudov/coot/source/pre-releases/%n-%v-revision-%r.tar.gz
-Source-MD5: 82d653d6e97bb940b024833314a3ccfc
+Source-MD5: d67065eb5eb8152f320ba2b7ba33434e 
 Source2: 
http://www2.mrc-lmb.cam.ac.uk/groups/murshudov/content/refmac/Dictionary/refmac_dictionary_v5.38.tar.gz
 Source2-MD5: 174a5fc5e5be03cb432c61e8da4283df
 Source3: 
http://www.ysbl.york.ac.uk/~emsley/software/extras/reference-structures.tar.gz
@@ -236,9 +236,11 @@
 # and a few others as follows:
 /bin/rm -f %i/bin/coot
 echo '#!/bin/sh -f '   %i/bin/coot
+echo export LC_NUMERIC=C   %i/bin/coot
 echo export COOT_REFMAC_LIB_DIR=%p/share/coot/lib%i/bin/coot
 echo export COOT_PYTHON_DIR=%p/share/coot/python %i/bin/coot
 echo 'export COOT_SBASE_DIR=$CCP4/share/sbase'   %i/bin/coot
+echo 'export CLIBD=$CCP4/lib/data'   %i/bin/coot
 echo export 
PYTHONPATH=%p/lib/python2.7/site-packages:%p/lib/python2.7/site-packages/gtk-2.0:%p/share/coot/python
%i/bin/coot
 echo %p/bin/coot-real \\$@\ %i/bin/coot
 chmod a+x %i/bin/coot


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from a single console and one unified framework. Download a free trial.
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[cvs] dists/10.7/stable/main/finkinfo/sci mmdb.info,1.3,1.4

[William Scott]

Update of /cvsroot/fink/dists/10.7/stable/main/finkinfo/sci
In directory sfp-cvs-1.v30.ch3.sourceforge.com:/tmp/cvs-serv28227

Modified Files:
mmdb.info 
Log Message:
version update


Index: mmdb.info
===
RCS file: /cvsroot/fink/dists/10.7/stable/main/finkinfo/sci/mmdb.info,v
retrieving revision 1.3
retrieving revision 1.4
diff -u -d -r1.3 -r1.4
--- mmdb.info   29 Jul 2012 15:12:24 -  1.3
+++ mmdb.info   24 Apr 2013 01:05:05 -  1.4
@@ -1,6 +1,6 @@
 Package: mmdb
-Version: 1.23.2
-Revision: 31
+Version: 1.25.0
+Revision: 1
 Maintainer: W. G. Scott wgsc...@users.sourceforge.net 
 DescPackaging: 
  Based on package created by Morten Kjeldgaard m...@bioxray.dk with minor
@@ -10,8 +10,8 @@
 License: LGPL
 GCC:4.0
 HomePage: http://www.ebi.ac.uk/pdbe/docs/cldoc/
-Source: http://lmb.bioch.ox.ac.uk/coot/software/dependencies/%n-%v.tar.gz
-Source-MD5: c92ef26d6b12ba0930e1d7c20a263987
+Source: 
http://www2.mrc-lmb.cam.ac.uk/groups/murshudov/coot/dependencies/%n-%v.tar.gz
+Source-MD5: 8d20c3b752b7b604d3ef2b3f01a04f70
 # build-time stuff in %N-dev, runtime stuff in %N-shlibs, nothing in %N
 Depends: fink-obsolete-packages, %n-shlibs (= %v-%r)
 BuildDepends: libtool2, automake1.11, autoconf2.6


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[cvs] dists/10.7/stable/main/finkinfo/sci pymol-py.info, 1.11, 1.12 pymol-py.patch, 1.6, 1.7

[William Scott]

Update of /cvsroot/fink/dists/10.7/stable/main/finkinfo/sci
In directory sfp-cvs-1.v30.ch3.sourceforge.com:/tmp/cvs-serv6926

Modified Files:
pymol-py.info pymol-py.patch 
Log Message:
fixes for startup problem reported by some users

Index: pymol-py.info
===
RCS file: /cvsroot/fink/dists/10.7/stable/main/finkinfo/sci/pymol-py.info,v
retrieving revision 1.11
retrieving revision 1.12
diff -u -d -r1.11 -r1.12
--- pymol-py.info   26 Feb 2013 03:29:05 -  1.11
+++ pymol-py.info   8 Mar 2013 17:04:03 -   1.12
@@ -1,9 +1,10 @@
 Info2: 
 Package: pymol-py%type_pkg[python]
 Version: 1.5
-Revision: 8
+Revision: 9
 UseMaxBuildJobs: false
-Maintainer: W. G. Scott wgsc...@users.sourceforge.net
+# Maintainer: W. G. Scott wgsc...@users.sourceforge.net
+Maintainer: Jack Howarth howa...@bromo.med.uc.edu
 Type: python (2.6 2.7)
 # r4023
 #Source: mirror:sourceforge:fink/pymol-%v-src.tar.bz2
@@ -16,7 +17,7 @@
 Source4: http://diablo.ucsc.edu/~wgscott/pymol/pynmr_0.37f_src.tar.bz2
 Source4-MD5: cb4a3906766681ce9230ef5515e1aa1c
 PatchFile: pymol-py.patch
-PatchFile-MD5: 2e287d04ecb51af13767e658ef5d
+PatchFile-MD5: 8048eb990477ee8a404324c864baed57
 PatchFile2: pymol-py-rest.patch
 PatchFile2-MD5: 2df10a5a2d66b16082317a823878bde0
 SourceDirectory: pymol-%v
@@ -48,7 +49,7 @@
 # setup2.py currently mishandles the creation of the pymol_path symlink
 # and the placement of the associated subdirectories.
 #%p/bin/python%type_raw[python] setup2.py install --root %d
-ln -s %p/lib/python%type_raw[python]/site-packages/pymol 
%i/lib/python%type_raw[python]/site-packages/pymol/pymol_path
+#ln -s %p/lib/python%type_raw[python]/site-packages/pymol 
%i/lib/python%type_raw[python]/site-packages/pymol/pymol_path
 cp -r data modules examples test scripts 
%i/lib/python%type_raw[python]/site-packages/pymol
 mkdir -p %i/lib/pymol-py%type_pkg[python]/bin
 cp pymol.cmd %i/lib/pymol-py%type_pkg[python]/bin/pymol

Index: pymol-py.patch
===
RCS file: /cvsroot/fink/dists/10.7/stable/main/finkinfo/sci/pymol-py.patch,v
retrieving revision 1.6
retrieving revision 1.7
diff -u -d -r1.6 -r1.7
--- pymol-py.patch  26 Feb 2013 03:29:05 -  1.6
+++ pymol-py.patch  8 Mar 2013 17:04:03 -   1.7
@@ -1,6 +1,6 @@
 diff -uNr pymol-1.5/modules/pmg_tk/PMGApp.py 
pymol-1.5.fink/modules/pmg_tk/PMGApp.py
 pymol-1.5/modules/pmg_tk/PMGApp.py 2012-05-16 21:39:13.0 -0400
-+++ pymol-1.5.fink/modules/pmg_tk/PMGApp.py2013-02-25 21:01:06.0 
-0500
+--- pymol-1.5/modules/pmg_tk/PMGApp.py 2013-02-25 22:21:17.0 -0500
 pymol-1.5.fink/modules/pmg_tk/PMGApp.py2013-03-08 10:29:35.0 
-0500
 @@ -184,7 +184,7 @@
  self.fifo.put(cmmd)
  
@@ -20,8 +20,8 @@
  else: 
  win.destroy()
 diff -uNr pymol-1.5/modules/pmg_tk/skins/normal/__init__.py 
pymol-1.5.fink/modules/pmg_tk/skins/normal/__init__.py
 pymol-1.5/modules/pmg_tk/skins/normal/__init__.py  2013-02-25 
20:51:28.0 -0500
-+++ pymol-1.5.fink/modules/pmg_tk/skins/normal/__init__.py 2013-02-25 
21:01:06.0 -0500
+--- pymol-1.5/modules/pmg_tk/skins/normal/__init__.py  2013-02-25 
22:21:17.0 -0500
 pymol-1.5.fink/modules/pmg_tk/skins/normal/__init__.py 2013-03-08 
10:29:35.0 -0500
 @@ -250,7 +250,7 @@
  self.buttonArea.destroy()
  
@@ -57,8 +57,8 @@
  else: # autocenter, deiconify, and run mainloop
  win.destroy()
 diff -uNr pymol-1.5/modules/pmg_tk/startup/apbs_tools.py 
pymol-1.5.fink/modules/pmg_tk/startup/apbs_tools.py
 pymol-1.5/modules/pmg_tk/startup/apbs_tools.py 2012-04-28 
12:45:52.0 -0400
-+++ pymol-1.5.fink/modules/pmg_tk/startup/apbs_tools.py2013-02-25 
21:01:06.0 -0500
+--- pymol-1.5/modules/pmg_tk/startup/apbs_tools.py 2013-02-25 
22:21:16.0 -0500
 pymol-1.5.fink/modules/pmg_tk/startup/apbs_tools.py2013-03-08 
10:29:35.0 -0500
 @@ -141,7 +141,7 @@
  # APBS_BINARY_LOCATION = '/opt/bin/apbs'
  #
@@ -68,9 +68,21 @@
  APBS_PDB2PQR_LOCATION = None
  TEMPORARY_FILE_DIR = None
  
+diff -uNr pymol-1.5/modules/pymol/__init__.py 
pymol-1.5.fink/modules/pymol/__init__.py
+--- pymol-1.5/modules/pymol/__init__.py2013-02-25 22:21:15.0 
-0500
 pymol-1.5.fink/modules/pymol/__init__.py   2013-03-08 10:31:16.0 
-0500
+@@ -142,7 +142,7 @@
+ if (pymol_file[0:1] not in [ '\\', '/' ]) and 
pymol_file[1:2]!=':': 
+ pymol_file = os.getcwd()+/+pymol_file # make path 
absolute
+ 
+-pymol_path = 
re.sub(r[\/\\][^\/\\]*$,/pymol_path,pymol_file)
++pymol_path = re.sub(r[\/\\][^\/\\]*$,,pymol_file)
+ 
+ if os.path.isdir(pymol_path):
+ os.environ['PYMOL_PATH'] = pymol_path
 diff -uNr pymol-1.5/pymol.cmd pymol-1.5.fink/pymol.cmd
 --- 

[cvs] dists/10.7/stable/main/finkinfo/sci apbs.info,1.3,1.4

[William Scott]

Update of /cvsroot/fink/dists/10.7/stable/main/finkinfo/sci
In directory sfp-cvs-1.v30.ch3.sourceforge.com:/tmp/cvs-serv6961

Modified Files:
apbs.info 
Log Message:
update to work with latest pymol

Index: apbs.info
===
RCS file: /cvsroot/fink/dists/10.7/stable/main/finkinfo/sci/apbs.info,v
retrieving revision 1.3
retrieving revision 1.4
diff -u -d -r1.3 -r1.4
--- apbs.info   23 Jul 2012 00:45:57 -  1.3
+++ apbs.info   8 Mar 2013 17:04:32 -   1.4
@@ -1,89 +1,52 @@
 Package: apbs
-Version: 1.3.0
-Revision: 3
-UseMaxBuildJobs: false
-Source: 
http://downloads.sourceforge.net/project/%n/%n/%n-%v/%n-1.3-source.tar.gz
-Source-MD5: f99a505365f07f6853979cfe2ef23365
-Depends: readline5-shlibs, gcc47-shlibs, python27
-BuildDepends: gcc47, python27, fink (= 0.24.12)
-BuildConflicts: g77, g95, fort77
-Conflicts: maloc, maloc-mpi-lammpi,  maloc-mpi-openmpi
-Replaces:  maloc, maloc-mpi-lammpi,  maloc-mpi-openmpi
-ConfigureParams: --disable-openmp --build=%m-apple-darwin`uname -r|cut -f1 
-d.` --host=%m-apple-darwin`uname -r|cut -f1 -d.`
-SetCFLAGS: -O3 
+Version: 1.4.0
+Revision: 1
+Source: 
http://downloads.sourceforge.net/project/%n/%n/%n-%v/APBS-1.4-source.tar.gz
+Source-MD5: e0281bd44ffecb651e40687cdaa26361
+Depends: readline6-shlibs, maloc-shlibs, python27
+BuildDepends: readline6, maloc, fink (= 0.28)
+BuildDependsOnly: true
 Description: Adaptive Poisson-Boltzmann Solver
-PatchFile: %n.patch
-PatchFile-MD5: 2662144e3e3508a944902c0a5e29eaf1 
-PatchScript: 
-sed 's|@INSTALL_DIR@|%d|g'  %{PatchFile} | patch -p1
-
+SourceDirectory: %n
 CompileScript: 
 #!/bin/bash -efv
-PATH=%p/bin:%p/sbin:${PATH} ; export PATH
-source %p/bin/init.sh
-perl -pi -e 's|PY_SHARED=-shared|PY_SHARED=-bundle|g' configure
-BLAS_DIR='/System/Library/Frameworks/Accelerate.framework/Versions/A/Frameworks/vecLib.framework/Versions/A'
-py_path=%p/bin/python2.7 F77=gfortran ./configure %c --enable-python 
--with-python=%p/bin/python2.7 \
---disable-openmp --with-blas=-L${BLAS_DIR} -lblas -Wl,-framework -Wl,vecLib 
-Wl,-undefined -Wl,dynamic_lookup FFLAGS=-O3
-perl -pi -e 's|\${prefix}/share|%i/share/%n|g' Makefile
-perl -pi -e 's|\$\(DESTDIR\)\$\(libdir\)|share/apbs/lib|g'  
contrib/blas/Makefile
+cd build
+CMAKE_OPTIONS=-DCMAKE_INSTALL_PREFIX=%p \
+   -DCMAKE_VERBOSE_MAKEFILE=ON \
+   -DCMAKE_COLOR_MAKEFILE=ON \
+   -DCMAKE_BUILD_TYPE=Release \
+   -DCMAKE_BUILD_WITH_INSTALL_RPATH=ON \
+   -DCMAKE_INSTALL_NAME_DIR=%p/lib \
+   -DCMAKE_SYSTEM_PREFIX_PATH=\%p;\/usr\ \
+   -DCMAKE_FIND_FRAMEWORK=LAST \
+   -DENABLE_OPENMP:BOOL=OFF \
+   -DENABLE_MPI:BOOL=OFF
+cmake $CMAKE_OPTIONS -DCMAKE_C_FLAGS=-I%p/include -O3 -ffast-math -g ..
 make
 
 InstallScript: 
 #!/bin/zsh -efv
-rm -Rf **/CVS # fink validate complains if this junk is left behind.
-perl -pi -e 's|/usr/bin/env python|%p/bin/python|g' examples/**/*.py
-perl -pi -e 's|/usr/bin/env python|%p/bin/python|g' tools/**/*.py
-rm -f **/*.o
-# 
-#   make install DESTDIR=%d
-# install it ourselves:
-   mkdir -p %i/bin
-   /bin/cp bin/apbs bin/ApbsClient.py %i/bin/.
-   echo '#!%p/bin/python2.7'  |  %i/bin/wsdl2py
-   echo from ZSI.generate.commands import wsdl2py %i/bin/wsdl2py
-   echo wsdl2py() %i/bin/wsdl2py
-   chmod a+x  %i/bin/wsdl2py   
-   #
-   mkdir -p %i/share/%n
-   /bin/cp -r   examples %i/share/%n/.
-   /bin/cp -r   tools %i/share/%n/.
-   /bin/cp -r   doc %i/share/%n/.
-   #
-   mkdir -p %i/share/doc
-   ln -s   %p/share/%n/doc %i/share/doc/%n
-   #
-   mkdir -p %i/lib/python2.7/site-packages/ZSI
-   /bin/cp -r   contrib/opal/ZSI/ZSI/*  
%i/lib/python2.7/site-packages/ZSI/.
-   #
-   mkdir -p %i/include/apbs
-   /bin/cp  **/*.h  %i/include/apbs/.
-   #
-   mkdir -p %i/lib
-/bin/rm -rf contrib
-   /bin/cp **/.*/*.a  %i/lib/.
-   /bin/cp **/*.la%i/lib/.
-   ranlib %i/lib/*.a
-#
-
-PreRmScript: 
-/usr/bin/find %p/lib/python2.7/site-packages/ZSI -name '*.pyo' -delete
+cd build
+make install DESTDIR=%d
+perl -pi -e s|env python|env %p/bin/python2.7|g 
%i/share/%n/tools/manip/psize.py
+perl -pi -e s|env python|env %p/bin/python2.7|g 
%i/share/apbs/examples/protein-rna/fit.py
+for f in apbs_check_forces apbs_check_results apbs_logger apbs_tester; do
+perl -pi -e s|env python|env %p/bin/python2.7|g %i/share/apbs/tests/$f.py
+done
 
-PostInstScript: 
-%p/bin/python2.7 -O %p/lib/python2.7/compileall.py -q 
%p/lib/python2.7/site-packages/ZSI
+Shlibs: 
+   !%p/lib/libapbs_generic.dylib
+   !%p/lib/libapbs_mg.dylib 
+   !%p/lib/libapbs_pmgc.dylib 
 
-
-SplitOff: 
-   Package: %N-dev
-   

[cvs] dists/10.4/stable/main/finkinfo/sci pymol-py.info, 1.20, 1.21 pymol-py.patch, 1.8, 1.9 apbs.info, 1.2, 1.3

[William Scott]

Update of /cvsroot/fink/dists/10.4/stable/main/finkinfo/sci
In directory sfp-cvs-1.v30.ch3.sourceforge.com:/tmp/cvs-serv8691

Modified Files:
pymol-py.info pymol-py.patch apbs.info 
Log Message:
fix for startup problem

Index: pymol-py.info
===
RCS file: /cvsroot/fink/dists/10.4/stable/main/finkinfo/sci/pymol-py.info,v
retrieving revision 1.20
retrieving revision 1.21
diff -u -d -r1.20 -r1.21
--- pymol-py.info   26 Feb 2013 03:30:52 -  1.20
+++ pymol-py.info   8 Mar 2013 17:43:03 -   1.21
@@ -1,9 +1,10 @@
 Info2: 
 Package: pymol-py%type_pkg[python]
 Version: 1.5
-Revision: 8
+Revision: 9
 UseMaxBuildJobs: false
-Maintainer: W. G. Scott wgsc...@users.sourceforge.net
+# Maintainer: W. G. Scott wgsc...@users.sourceforge.net
+Maintainer: Jack Howarth howa...@bromo.med.uc.edu
 Type: python (2.6 2.7)
 # r4023
 #Source: mirror:sourceforge:fink/pymol-%v-src.tar.bz2
@@ -16,7 +17,7 @@
 Source4: http://diablo.ucsc.edu/~wgscott/pymol/pynmr_0.37f_src.tar.bz2
 Source4-MD5: cb4a3906766681ce9230ef5515e1aa1c
 PatchFile: pymol-py.patch
-PatchFile-MD5: 2e287d04ecb51af13767e658ef5d
+PatchFile-MD5: 8048eb990477ee8a404324c864baed57
 PatchFile2: pymol-py-rest.patch
 PatchFile2-MD5: 2df10a5a2d66b16082317a823878bde0
 SourceDirectory: pymol-%v
@@ -48,7 +49,7 @@
 # setup2.py currently mishandles the creation of the pymol_path symlink
 # and the placement of the associated subdirectories.
 #%p/bin/python%type_raw[python] setup2.py install --root %d
-ln -s %p/lib/python%type_raw[python]/site-packages/pymol 
%i/lib/python%type_raw[python]/site-packages/pymol/pymol_path
+#ln -s %p/lib/python%type_raw[python]/site-packages/pymol 
%i/lib/python%type_raw[python]/site-packages/pymol/pymol_path
 cp -r data modules examples test scripts 
%i/lib/python%type_raw[python]/site-packages/pymol
 mkdir -p %i/lib/pymol-py%type_pkg[python]/bin
 cp pymol.cmd %i/lib/pymol-py%type_pkg[python]/bin/pymol

Index: pymol-py.patch
===
RCS file: /cvsroot/fink/dists/10.4/stable/main/finkinfo/sci/pymol-py.patch,v
retrieving revision 1.8
retrieving revision 1.9
diff -u -d -r1.8 -r1.9
--- pymol-py.patch  26 Feb 2013 03:30:52 -  1.8
+++ pymol-py.patch  8 Mar 2013 17:43:03 -   1.9
@@ -1,6 +1,6 @@
 diff -uNr pymol-1.5/modules/pmg_tk/PMGApp.py 
pymol-1.5.fink/modules/pmg_tk/PMGApp.py
 pymol-1.5/modules/pmg_tk/PMGApp.py 2012-05-16 21:39:13.0 -0400
-+++ pymol-1.5.fink/modules/pmg_tk/PMGApp.py2013-02-25 21:01:06.0 
-0500
+--- pymol-1.5/modules/pmg_tk/PMGApp.py 2013-02-25 22:21:17.0 -0500
 pymol-1.5.fink/modules/pmg_tk/PMGApp.py2013-03-08 10:29:35.0 
-0500
 @@ -184,7 +184,7 @@
  self.fifo.put(cmmd)
  
@@ -20,8 +20,8 @@
  else: 
  win.destroy()
 diff -uNr pymol-1.5/modules/pmg_tk/skins/normal/__init__.py 
pymol-1.5.fink/modules/pmg_tk/skins/normal/__init__.py
 pymol-1.5/modules/pmg_tk/skins/normal/__init__.py  2013-02-25 
20:51:28.0 -0500
-+++ pymol-1.5.fink/modules/pmg_tk/skins/normal/__init__.py 2013-02-25 
21:01:06.0 -0500
+--- pymol-1.5/modules/pmg_tk/skins/normal/__init__.py  2013-02-25 
22:21:17.0 -0500
 pymol-1.5.fink/modules/pmg_tk/skins/normal/__init__.py 2013-03-08 
10:29:35.0 -0500
 @@ -250,7 +250,7 @@
  self.buttonArea.destroy()
  
@@ -57,8 +57,8 @@
  else: # autocenter, deiconify, and run mainloop
  win.destroy()
 diff -uNr pymol-1.5/modules/pmg_tk/startup/apbs_tools.py 
pymol-1.5.fink/modules/pmg_tk/startup/apbs_tools.py
 pymol-1.5/modules/pmg_tk/startup/apbs_tools.py 2012-04-28 
12:45:52.0 -0400
-+++ pymol-1.5.fink/modules/pmg_tk/startup/apbs_tools.py2013-02-25 
21:01:06.0 -0500
+--- pymol-1.5/modules/pmg_tk/startup/apbs_tools.py 2013-02-25 
22:21:16.0 -0500
 pymol-1.5.fink/modules/pmg_tk/startup/apbs_tools.py2013-03-08 
10:29:35.0 -0500
 @@ -141,7 +141,7 @@
  # APBS_BINARY_LOCATION = '/opt/bin/apbs'
  #
@@ -68,9 +68,21 @@
  APBS_PDB2PQR_LOCATION = None
  TEMPORARY_FILE_DIR = None
  
+diff -uNr pymol-1.5/modules/pymol/__init__.py 
pymol-1.5.fink/modules/pymol/__init__.py
+--- pymol-1.5/modules/pymol/__init__.py2013-02-25 22:21:15.0 
-0500
 pymol-1.5.fink/modules/pymol/__init__.py   2013-03-08 10:31:16.0 
-0500
+@@ -142,7 +142,7 @@
+ if (pymol_file[0:1] not in [ '\\', '/' ]) and 
pymol_file[1:2]!=':': 
+ pymol_file = os.getcwd()+/+pymol_file # make path 
absolute
+ 
+-pymol_path = 
re.sub(r[\/\\][^\/\\]*$,/pymol_path,pymol_file)
++pymol_path = re.sub(r[\/\\][^\/\\]*$,,pymol_file)
+ 
+ if os.path.isdir(pymol_path):
+ os.environ['PYMOL_PATH'] = pymol_path
 diff -uNr pymol-1.5/pymol.cmd pymol-1.5.fink/pymol.cmd
 --- pymol-1.5/pymol.cmd  

[cvs] dists/10.7/stable/main/finkinfo/sci viennarna-10.8.info, NONE, 1.1

[William Scott]

Update of /cvsroot/fink/dists/10.7/stable/main/finkinfo/sci
In directory sfp-cvs-1.v30.ch3.sourceforge.com:/tmp/cvs-serv28278

Added Files:
viennarna-10.8.info 
Log Message:
didn't know it was missing until I needed it

--- NEW FILE: viennarna-10.8.info ---
Package: viennarna
Version: 1.8.5
Revision: 205
Distribution: 10.8
Source: http://www.tbi.univie.ac.at/~ivo/RNA/ViennaRNA-%v.tar.gz   
Source-MD5: cd70d63cc1be928a5f0973bd6c211e96
SourceDirectory: ViennaRNA-%v
InfoDocs: RNAlib.info
ConfigureParams: --mandir=%p/share/man --infodir=%p/share/info   CC=/usr/bin/gcc
Depends: system-perl5124
UpdatePOD: true
Description: RNA structural prediction
DescDetail: 
The Vienna RNA Package consists of a C code library 
and several stand-alone programs for the
prediction and comparison of RNA secondary structures. 
The package allows you to
- predict minimum free energy secondary structures
- calculate the partition function for the ensemble of structures
- calculate suboptimal structures in a given energy range
- predict consensus secondary structures from a multiple sequence alignment
- predict melting curves
- search for sequences folding into a given structure
- compare two secondary structures 
-
The package includes a Perl5 module that gives access to almost all
functions of the C library from Perl. 
-
The following executables are provided in /sw/bin:
RNAfold -- predict minimum energy secondary structures and pair probabilities
RNAeval -- evaluate energy of RNA secondary structures
RNAheat -- calculate the specific heat (melting curve) of an RNA sequence
RNAinverse -- inverse fold (design) sequences with predefined structure
RNAdistance -- compare secondary structures
RNApdist -- compare base pair probabilities
RNAsubopt -- complete suboptimal folding
RNAplot -- RNA structure drawings in PostScript, SVG, or GML
RNAcofold -- predict hybrid structure of two sequences
RNAduplex -- predict possible hybridization sites between two sequences
RNAalifold -- predict the consensus structure of several aligned sequences
RNALfold -- predict locally stable structure of long sequences
RNAplfold -- compute average pair probabilities for local base pairs  
RNApaln -- fast structural alignment of RNA sequences using string alignments
Kinfold -- explores the folding kinetics of RNA
RNAforester -- computes tree-alignments of RNA structures
Several small but helpful Perl Utilities are in /sw/share/ViennaRNA/bin
which is not added to your PATH by default.
--
For more detailed information on these please enter the command
info RNA .

PatchScript: 
#!/bin/zsh -efv
perl -pi -e 's|Version 1.6|Version 1.8|g' README
perl -pi -e 's|Version 1.6|Version 1.8|g' man/RNAlib.texinfo

ConfigureParams:
SetCFLAGS: -I%p/include
CompileScript: 
#!/bin/zsh -efv
export ARCHFLAGS=''
./configure %c PerlCmd=/usr/bin/perl5.12
make

InstallScript: 
#!/bin/zsh -efv
perl -pi.bak -e 's|/usr/local|%p/share|g' Perl/Makefile.perl
perl -pi.bak -e 's;/usr/share/man;%p/share/man;g' Perl/Makefile.perl
mkdir -p %i/share/man/man3/
mkdir -p %i/lib
mkdir -p %i/include
perl -pi.bak -e 's|%p/|%i/|g' RNAforester/g2-0.70/Makefile
if [[ $(sw_vers -productVersion)  10.6 ]]; then
make -j1 install DESTDIR=%d INSTALLPRIVLIB=%p/lib/perl5/5.8.8/ 
INSTALLARCHLIB=%p/lib/perl5/5.8.8/darwin-thread-multi-2level/ 
INSTALLSITELIB=%p/lib/perl5/5.8.8/ 
INSTALLSITEARCH=%p/lib/perl5/5.8.8/darwin-thread-multi-2level 
INSTALLSCRIPT=%p/share/viennarna/scripts
elif [[ $(sw_vers -productVersion)  10.7 ]]; then
make -j1 install DESTDIR=%d INSTALLPRIVLIB=%p/lib/perl5/5.10.0/ 
INSTALLARCHLIB=%p/lib/perl5/5.10.0/darwin-thread-multi-2level/ 
INSTALLSITELIB=%p/lib/perl5/5.10.0/ 
INSTALLSITEARCH=%p/lib/perl5/5.10.0/darwin-thread-multi-2level 
INSTALLSCRIPT=%p/share/viennarna/scripts
else
make -j1 install DESTDIR=%d INSTALLPRIVLIB=%p/lib/perl5/5.12.3/ 
INSTALLARCHLIB=%p/lib/perl5/5.12.3/darwin-thread-multi-2level/ 
INSTALLSITELIB=%p/lib/perl5/5.12.3/ 
INSTALLSITEARCH=%p/lib/perl5/5.12.3/darwin-thread-multi-2level 
INSTALLSCRIPT=%p/share/viennarna/scripts
fi


#
###
#
SplitOff: 
Package: %N-dev
BuildDependsOnly: True
Files: 
include/*.h
include/ViennaRNA/*.h
lib/*.a


###
DocFiles: AUTHORS ChangeLog COPYING INSTALL INSTALL.configure NEWS README THANKS
License: GPL
Homepage: http://www.tbi.univie.ac.at/~ivo/RNA/
Maintainer: W. G. Scott wgsc...@users.sourceforge.net


--
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[cvs] dists/10.7/stable/main/finkinfo/sci pymol-py.info, 1.10, 1.11 pymol-py.patch, 1.5, 1.6

[William Scott]

Update of /cvsroot/fink/dists/10.7/stable/main/finkinfo/sci
In directory sfp-cvs-1.v30.ch3.sourceforge.com:/tmp/cvs-serv20804

Modified Files:
pymol-py.info pymol-py.patch 
Log Message:
pymol update from upstream svn changes

Index: pymol-py.info
===
RCS file: /cvsroot/fink/dists/10.7/stable/main/finkinfo/sci/pymol-py.info,v
retrieving revision 1.10
retrieving revision 1.11
diff -u -d -r1.10 -r1.11
--- pymol-py.info   6 Oct 2012 17:51:51 -   1.10
+++ pymol-py.info   26 Feb 2013 03:29:05 -  1.11
@@ -1,14 +1,14 @@
 Info2: 
 Package: pymol-py%type_pkg[python]
 Version: 1.5
-Revision: 7
+Revision: 8
 UseMaxBuildJobs: false
 Maintainer: W. G. Scott wgsc...@users.sourceforge.net
 Type: python (2.6 2.7)
-# r3983
-Source: mirror:sourceforge:fink/pymol-%v-src.tar.bz2
-#Source: http://diablo.ucsc.edu/~wgscott/pymol/pymol-%v-src.tar.bz2
-Source-MD5: 7ec7f1eb4302672d65bbe4de9ffc01e5
+# r4023
+#Source: mirror:sourceforge:fink/pymol-%v-src.tar.bz2
+Source: http://scottlab.ucsc.edu/~wgscott/pymol/pymol-%v-src.tar.bz2
+Source-MD5: 7f7c377c4f6e04dfba4a842543144a35  
 Source2: http://www.weizmann.ac.il/ISPC/eMovie.py
 Source2-MD5: 832252d4cee1ba88d50a35681b5ecd4b
 Source3: http://www.weizmann.ac.il/ISPC/eMovie_rigimol.inp
@@ -16,7 +16,7 @@
 Source4: http://diablo.ucsc.edu/~wgscott/pymol/pynmr_0.37f_src.tar.bz2
 Source4-MD5: cb4a3906766681ce9230ef5515e1aa1c
 PatchFile: pymol-py.patch
-PatchFile-MD5: f812def4c13c0542e3830f187ac00523
+PatchFile-MD5: 2e287d04ecb51af13767e658ef5d
 PatchFile2: pymol-py-rest.patch
 PatchFile2-MD5: 2df10a5a2d66b16082317a823878bde0
 SourceDirectory: pymol-%v
@@ -61,6 +61,7 @@
 cd pynmr
 cp -r Crmsd.so *.py BIOPYTHON_LICENSE LICENSE README help images test_data 
%i/lib/python%type_raw[python]/site-packages/pmg_tk/startup/pynmr
 rm 
%i/lib/python%type_raw[python]/site-packages/pmg_tk/startup/pynmr/test_data/.noe.tbl.swp
+rm -f %i/bin/pymol
 
 DocFiles: DEVELOPERS LICENSE README
 PostInstScript: 
@@ -88,7 +89,7 @@
 DescPackaging: 
 The tarball used for this version was created in accordance to the BSD
 license of pymol using the following instructions...
-   svn -r3983 co https://pymol.svn.sourceforge.net/svnroot/pymol/trunk/pymol 
pymol-1.5
+   svn -r4023 co https://pymol.svn.sourceforge.net/svnroot/pymol/trunk/pymol 
pymol-1.5
tar --exclude=.svn -jcvf pymol-1.5-src.tar.bz2 pymol-1.5
 Added eMovie.py plug-in manually.  Commented out line that opens the window 
for eMovie by
 default every time pymol is started as this is annoying behavior. eMovie is 
activated via 

Index: pymol-py.patch
===
RCS file: /cvsroot/fink/dists/10.7/stable/main/finkinfo/sci/pymol-py.patch,v
retrieving revision 1.5
retrieving revision 1.6
diff -u -d -r1.5 -r1.6
--- pymol-py.patch  6 Oct 2012 17:51:51 -   1.5
+++ pymol-py.patch  26 Feb 2013 03:29:05 -  1.6
@@ -1,76 +1,8 @@
 pymol-1.5/setup.py.orig2012-02-18 13:25:51.0 -0500
-+++ pymol-1.5/setup.py 2012-02-18 13:29:45.0 -0500
-@@ -43,7 +43,7 @@
- ext_link_args=[]
- #
- elif sys.platform=='darwin':
--using_fink = '/sw/ in str(sys.path)
-+using_fink = '@FINKPREFIX@/ in str(sys.path)
- if using_fink:
- # under Fink, with the following packages installed:
- #
-@@ -84,9 +84,9 @@
- inc_dirs=[ov/src,
-   layer0,layer1,layer2,
-   layer3,layer4,layer5, 
--  /sw/include/freetype2/freetype,
--  /sw/include/freetype2,
--  /sw/include,
-+  @FINKPREFIX@/include/freetype2/freetype,
-+  @FINKPREFIX@/include/freetype2,
-+  @FINKPREFIX@/include,
-   /usr/X11/include,
- modules/cealign/src,
- modules/cealign/src/tnt,
-@@ -113,12 +113,12 @@
- ]
- ext_comp_args=[]
- ext_link_args=[
--   -L/sw/lib, -lpng,
-+   -L@FINKPREFIX@/lib, -lpng,
-/usr/X11/lib/libGL.dylib,
-/usr/X11/lib/libGLU.dylib,
--lfreeglut,
--lglew,
--   -L/sw/lib/freetype219/lib, -lfreetype
-+   -L@FINKPREFIX@/lib/freetype219/lib, -lfreetype
- ]
- else:
- # Not using Fink -- building as if we are on Linux/X11 with
 /dev/null  2012-02-14 20:24:44.0 -0500
-+++ pymol-1.5.0.1/pymol.cmd2012-02-14 19:31:08.0 -0500
-@@ -0,0 +1,16 @@
-+#!/bin/sh
-+#
-+# PyMOL startup script
-+#
-+# ==
-+# Set PYMOL_PATH to point at the correct location on your system
-+#
-+PYMOL_PATH=@FINKPREFIX@/lib/python2.X/site-packages/pymol

[cvs] dists/10.4/stable/main/finkinfo/sci pymol-py.info, 1.19, 1.20 pymol-py.patch, 1.7, 1.8

[William Scott]

Update of /cvsroot/fink/dists/10.4/stable/main/finkinfo/sci
In directory sfp-cvs-1.v30.ch3.sourceforge.com:/tmp/cvs-serv21022

Modified Files:
pymol-py.info pymol-py.patch 
Log Message:
pymol update from upstream svn changes

Index: pymol-py.info
===
RCS file: /cvsroot/fink/dists/10.4/stable/main/finkinfo/sci/pymol-py.info,v
retrieving revision 1.19
retrieving revision 1.20
diff -u -d -r1.19 -r1.20
--- pymol-py.info   6 Oct 2012 17:54:26 -   1.19
+++ pymol-py.info   26 Feb 2013 03:30:52 -  1.20
@@ -1,14 +1,14 @@
 Info2: 
 Package: pymol-py%type_pkg[python]
 Version: 1.5
-Revision: 7
+Revision: 8
 UseMaxBuildJobs: false
 Maintainer: W. G. Scott wgsc...@users.sourceforge.net
 Type: python (2.6 2.7)
-# r3983
-Source: mirror:sourceforge:fink/pymol-%v-src.tar.bz2
-#Source: http://diablo.ucsc.edu/~wgscott/pymol/pymol-%v-src.tar.bz2
-Source-MD5: 7ec7f1eb4302672d65bbe4de9ffc01e5
+# r4023
+#Source: mirror:sourceforge:fink/pymol-%v-src.tar.bz2
+Source: http://scottlab.ucsc.edu/~wgscott/pymol/pymol-%v-src.tar.bz2
+Source-MD5: 7f7c377c4f6e04dfba4a842543144a35  
 Source2: http://www.weizmann.ac.il/ISPC/eMovie.py
 Source2-MD5: 832252d4cee1ba88d50a35681b5ecd4b
 Source3: http://www.weizmann.ac.il/ISPC/eMovie_rigimol.inp
@@ -16,7 +16,7 @@
 Source4: http://diablo.ucsc.edu/~wgscott/pymol/pynmr_0.37f_src.tar.bz2
 Source4-MD5: cb4a3906766681ce9230ef5515e1aa1c
 PatchFile: pymol-py.patch
-PatchFile-MD5: f812def4c13c0542e3830f187ac00523
+PatchFile-MD5: 2e287d04ecb51af13767e658ef5d
 PatchFile2: pymol-py-rest.patch
 PatchFile2-MD5: 2df10a5a2d66b16082317a823878bde0
 SourceDirectory: pymol-%v
@@ -61,6 +61,7 @@
 cd pynmr
 cp -r Crmsd.so *.py BIOPYTHON_LICENSE LICENSE README help images test_data 
%i/lib/python%type_raw[python]/site-packages/pmg_tk/startup/pynmr
 rm 
%i/lib/python%type_raw[python]/site-packages/pmg_tk/startup/pynmr/test_data/.noe.tbl.swp
+rm -f %i/bin/pymol
 
 DocFiles: DEVELOPERS LICENSE README
 PostInstScript: 
@@ -88,7 +89,7 @@
 DescPackaging: 
 The tarball used for this version was created in accordance to the BSD
 license of pymol using the following instructions...
-   svn -r3983 co https://pymol.svn.sourceforge.net/svnroot/pymol/trunk/pymol 
pymol-1.5
+   svn -r4023 co https://pymol.svn.sourceforge.net/svnroot/pymol/trunk/pymol 
pymol-1.5
tar --exclude=.svn -jcvf pymol-1.5-src.tar.bz2 pymol-1.5
 Added eMovie.py plug-in manually.  Commented out line that opens the window 
for eMovie by
 default every time pymol is started as this is annoying behavior. eMovie is 
activated via 

Index: pymol-py.patch
===
RCS file: /cvsroot/fink/dists/10.4/stable/main/finkinfo/sci/pymol-py.patch,v
retrieving revision 1.7
retrieving revision 1.8
diff -u -d -r1.7 -r1.8
--- pymol-py.patch  6 Oct 2012 17:54:26 -   1.7
+++ pymol-py.patch  26 Feb 2013 03:30:52 -  1.8
@@ -1,76 +1,8 @@
 pymol-1.5/setup.py.orig2012-02-18 13:25:51.0 -0500
-+++ pymol-1.5/setup.py 2012-02-18 13:29:45.0 -0500
-@@ -43,7 +43,7 @@
- ext_link_args=[]
- #
- elif sys.platform=='darwin':
--using_fink = '/sw/ in str(sys.path)
-+using_fink = '@FINKPREFIX@/ in str(sys.path)
- if using_fink:
- # under Fink, with the following packages installed:
- #
-@@ -84,9 +84,9 @@
- inc_dirs=[ov/src,
-   layer0,layer1,layer2,
-   layer3,layer4,layer5, 
--  /sw/include/freetype2/freetype,
--  /sw/include/freetype2,
--  /sw/include,
-+  @FINKPREFIX@/include/freetype2/freetype,
-+  @FINKPREFIX@/include/freetype2,
-+  @FINKPREFIX@/include,
-   /usr/X11/include,
- modules/cealign/src,
- modules/cealign/src/tnt,
-@@ -113,12 +113,12 @@
- ]
- ext_comp_args=[]
- ext_link_args=[
--   -L/sw/lib, -lpng,
-+   -L@FINKPREFIX@/lib, -lpng,
-/usr/X11/lib/libGL.dylib,
-/usr/X11/lib/libGLU.dylib,
--lfreeglut,
--lglew,
--   -L/sw/lib/freetype219/lib, -lfreetype
-+   -L@FINKPREFIX@/lib/freetype219/lib, -lfreetype
- ]
- else:
- # Not using Fink -- building as if we are on Linux/X11 with
 /dev/null  2012-02-14 20:24:44.0 -0500
-+++ pymol-1.5.0.1/pymol.cmd2012-02-14 19:31:08.0 -0500
-@@ -0,0 +1,16 @@
-+#!/bin/sh
-+#
-+# PyMOL startup script
-+#
-+# ==
-+# Set PYMOL_PATH to point at the correct location on your system
-+#
-+PYMOL_PATH=@FINKPREFIX@/lib/python2.X/site-packages/pymol

[cvs] dists/10.7/stable/main/finkinfo/sci gromacs-mpi.info, NONE, 1.1 gromacs.patch, NONE, 1.1 gromacs.info, 1.2, 1.3

[William Scott]

Update of /cvsroot/fink/dists/10.7/stable/main/finkinfo/sci
In directory sfp-cvs-1.v30.ch3.sourceforge.com:/tmp/cvs-serv32393

Modified Files:
gromacs.info 
Added Files:
gromacs-mpi.info gromacs.patch 
Log Message:
update of gromacs package

Index: gromacs.info
===
RCS file: /cvsroot/fink/dists/10.7/stable/main/finkinfo/sci/gromacs.info,v
retrieving revision 1.2
retrieving revision 1.3
diff -u -d -r1.2 -r1.3
--- gromacs.info9 Sep 2012 11:43:57 -   1.2
+++ gromacs.info13 Feb 2013 18:57:16 -  1.3
@@ -1,108 +1,70 @@
 Package: gromacs
-Version: 4.5.4
-Revision: 2
+Version: 4.6
+Revision: 1
 Depends: %N-shlibs (= %v-%r), fftw3-shlibs, gcc47-shlibs, gsl-shlibs, 
openmotif4-shlibs, x11
-BuildDepends: fftw3, gcc47-compiler, gsl, openmotif4, x11-dev
-BuildConflicts: gromacs-dev ( %v-%r), gromacs-mpi-dev, gromacs-mpi, 
gromacs-mpi-openmpi-dev, gromacs-mpi-openmpi, gromacs-mpi-lammpi-dev, 
gromacs-mpi-lammpi-dev
-Conflicts: gromacs-mpi-dev, gromacs-mpi, gromacs-mpi-openmpi-dev, 
gromacs-mpi-openmpi, gromacs-mpi-lammpi-dev, gromacs-mpi-lammpi-dev
-Replaces:  gromacs-mpi-dev, gromacs-mpi, gromacs-mpi-openmpi-dev, 
gromacs-mpi-openmpi, gromacs-mpi-lammpi-dev, gromacs-mpi-lammpi-dev
-BuildDependsOnly: false
+BuildDepends: fftw3, gcc47-compiler, gsl, openmotif4, x11-dev, cmake
+BuildConflicts: gromacs-dev, gromacs-mpi-dev
+Conflicts: gromacs-mpi, gromacs-bin ( 4.6-1), gromacs-mpi-bin ( 4.6-1), 
gromacs-dev ( 4.6-1), gromacs-mpi-dev ( 4.6-1)
+Replaces: gromacs-mpi, gromacs-bin ( 4.6-1), gromacs-mpi-bin ( 4.6-1), 
gromacs-dev ( 4.6-1), gromacs-mpi-dev ( 4.6-1)
+BuildDependsOnly: False
 UseMaxBuildJobs: True
-SetCC: gcc
-SetCXX: g++
+Distribution: 10.7, 10.8
+SetCC: gcc-fsf-4.7
+SetCXX: g++-fsf-4.7
 Source: mirror:custom:%n-%v.tar.gz
+PatchFile: %n.patch
 CustomMirror: 
 Primary: ftp://ftp.gromacs.org/pub/gromacs/
 
-Source-MD5: 5013de941017e014b92d41f82c7e86d6
-ConfigureParams: --enable-shared --prefix=%p --exec-prefix=%p 
--mandir=%p/share --with-x --with-gsl --x-includes=/usr/X11/include 
--x-libraries=/usr/X11/lib
+Source-MD5: d920a57884961a9fcbdcd9953ade469b
+PatchFile-MD5: 38fa52bb30693b1a9fd970b21e3e7531  
 DocFiles: AUTHORS COPYING README
 PatchScript: 
 #!/bin/zsh -efv
+%{default_script}
 perl -pi.bak -e 's|512|4096|g'  src/gmxlib/futil.c
 perl -pi.bak -e 's|/bin/csh|/bin/csh -f|g' share/**/* 2/dev/null
 perl -pi.bak -e 's|/lib/cpp|/usr/bin/cpp|g' share/**/* 2/dev/null
 
 CompileScript: 
 #!/bin/bash -efv
-./configure %c --build=%m-apple-darwin`uname -r|cut -f1 -d.` 
--host=%m-apple-darwin`uname -r|cut -f1 -d.`
+mkdir build
+cd build
+cmake -DGMX_GSL=ON -DCMAKE_INSTALL_NAME_DIR=%p/lib -DCMAKE_INSTALL_PREFIX=%p 
..
 make
 
 InstallScript: 
 #!/bin/bash -efv
 mkdir -p %i/include/%n
-make -j 1 install DESTDIR=%d
+cd build
+make install DESTDIR=%d
 make clean
-./configure %c --build=%m-apple-darwin`uname -r|cut -f1 -d.` 
--host=%m-apple-darwin`uname -r|cut -f1 -d.` --disable-float 
--program-suffix=_d 
-make
-make -j 1 install DESTDIR=%d
+cmake -DGMX_DOUBLE=ON -DGMX_GSL=ON -DCMAKE_INSTALL_NAME_DIR=%p/lib 
-DCMAKE_INSTALL_PREFIX=%p ..
+make install DESTDIR=%d
 
 SplitOff: 
 Package: %N-shlibs
 Depends: fftw3-shlibs, gcc47-shlibs, gsl-shlibs, openmotif4-shlibs, x11
 Files: 
-lib/libgmx.6.dylib
-lib/libgmxana.6.0.0.dylib
-lib/libgmxana.6.dylib
-lib/libmd.6.0.0.dylib
-lib/libmd.6.dylib
-lib/libgmx_d.6.0.0.dylib
-lib/libgmx_d.6.dylib
-lib/libgmxana_d.6.0.0.dylib
-lib/libgmxana_d.6.dylib
-lib/libmd_d.6.0.0.dylib
-lib/libmd_d.6.dylib
-   lib/libgmxpreprocess.6.dylib
-   lib/libgmxpreprocess.6.0.0.dylib
-   lib/libgmxpreprocess_d.6.dylib
-   lib/libgmxpreprocess_d.6.0.0.dylib
+lib/libgmx.6*.dylib
+lib/libgmxana.6*.dylib
+lib/libmd.6*.dylib
+   lib/libgmxpreprocess.6*.dylib
+lib/libgmx_d.6*.dylib
+lib/libgmxana_d.6*.dylib
+lib/libmd_d.6*.dylib
+lib/libgmxpreprocess_d.6*.dylib
 
 Shlibs: 
-%p/lib/libgmx.6.dylib 7.0.0 %n (= 4.5.3-1)
-%p/lib/libgmxana.6.dylib 7.0.0 %n (= 4.5.3-1)
-%p/lib/libmd.6.dylib 7.0.0 %n (= 4.5.3-1)
-%p/lib/libgmx_d.6.dylib 7.0.0 %n (= 4.5.3-1)
-%p/lib/libgmxana_d.6.dylib 7.0.0 %n (= 4.5.3-1)
-%p/lib/libmd_d.6.dylib 7.0.0 %n (= 4.5.3-1)
-%p/lib/libgmxpreprocess.6.dylib 7.0.0 %n  (= 4.5.4-1)
-%p/lib/libgmxpreprocess_d.6.dylib 7.0.0 %n  (= 4.5.4-1)
-
-DocFiles: AUTHORS COPYING README
-
-SplitOff2: 
-Package: %N-dev
-Depends: %N-shlibs (= %v-%r)
-Conflicts: gromacs-mpi-shlibs, gromacs-mpi-lammpi-shlibs, 
gromacs-mpi-openmpi-shlibs
-Replaces: gromacs-mpi-shlibs, gromacs-mpi-lammpi-shlibs, 
gromacs-mpi-openmpi-shlibs
-Files: 
-   lib/*.a
-   lib/*.la
-   include/gromacs
-   lib/libgmx.dylib
-   lib/libgmxana.dylib
-   lib/libmd_d.dylib
-   lib/libgmx_d.dylib
-   lib/libgmxana_d.dylib
-
-BuildDependsOnly: True

[cvs] dists/10.4/stable/main/finkinfo/sci gromacs.patch, NONE, 1.1 gromacs.info, 1.5, 1.6 gromacs-mpi.info, 1.4, 1.5

[William Scott]

Update of /cvsroot/fink/dists/10.4/stable/main/finkinfo/sci
In directory sfp-cvs-1.v30.ch3.sourceforge.com:/tmp/cvs-serv4349

Modified Files:
gromacs.info gromacs-mpi.info 
Added Files:
gromacs.patch 
Log Message:
update of gromacs package

Index: gromacs.info
===
RCS file: /cvsroot/fink/dists/10.4/stable/main/finkinfo/sci/gromacs.info,v
retrieving revision 1.5
retrieving revision 1.6
diff -u -d -r1.5 -r1.6
--- gromacs.info18 Jun 2012 06:41:03 -  1.5
+++ gromacs.info13 Feb 2013 19:30:04 -  1.6
@@ -1,128 +1,70 @@
 Package: gromacs
-Version: 4.5.4
+Version: 4.6
 Revision: 1
-Depends: %N-shlibs (= %v-%r), fftw3-shlibs, gcc46-shlibs, gsl-shlibs, 
openmotif4-shlibs, x11
-BuildDepends: fftw3, gcc46-compiler, gsl, openmotif4, x11-dev
-BuildConflicts: gromacs-dev ( %v-%r), gromacs-mpi-dev, gromacs-mpi, 
gromacs-mpi-openmpi-dev, gromacs-mpi-openmpi, gromacs-mpi-lammpi-dev, 
gromacs-mpi-lammpi-dev
-Conflicts: gromacs-mpi-dev, gromacs-mpi, gromacs-mpi-openmpi-dev, 
gromacs-mpi-openmpi, gromacs-mpi-lammpi-dev, gromacs-mpi-lammpi-dev
-Replaces:  gromacs-mpi-dev, gromacs-mpi, gromacs-mpi-openmpi-dev, 
gromacs-mpi-openmpi, gromacs-mpi-lammpi-dev, gromacs-mpi-lammpi-dev
-BuildDependsOnly: false
+Depends: %N-shlibs (= %v-%r), fftw3-shlibs, gcc47-shlibs, gsl-shlibs, 
openmotif4-shlibs, x11
+BuildDepends: fftw3, gcc47-compiler, gsl, openmotif4, x11-dev, cmake
+BuildConflicts: gromacs-dev, gromacs-mpi-dev, gromacs-mpi-openmpi-dev, 
gromacs-mpi-lammpi-dev
+Conflicts: gromacs-mpi-openmpi, gromacs-mpi-lammpi, gromacs-bin ( 4.6-1), 
gromacs-mpi-openmpi-bin ( 4.6-1), gromacs-mpi-lammpi-bin ( 4.6-1), 
gromacs-dev ( 4.6-1), gromacs-mpi-dev ( 4.6-1)
+Replaces:  gromacs-mpi-openmpi, gromacs-mpi-lammpi, gromacs-bin ( 4.6-1), 
gromacs-mpi-openmpi-bin ( 4.6-1), gromacs-mpi-lammpi-bin ( 4.6-1), 
gromacs-dev ( 4.6-1), gromacs-mpi-dev ( 4.6-1)
+BuildDependsOnly: False
 UseMaxBuildJobs: True
-SetCC: gcc-fsf-4.6
-SetCXX: g++-fsf-4.6
+Distribution: 10.4, 10.5, 10.6
+SetCC: gcc-fsf-4.7
+SetCXX: g++-fsf-4.7
 Source: mirror:custom:%n-%v.tar.gz
+PatchFile: %n.patch
 CustomMirror: 
 Primary: ftp://ftp.gromacs.org/pub/gromacs/
 
-Source-MD5: 5013de941017e014b92d41f82c7e86d6
-ConfigureParams: --enable-shared --prefix=%p --exec-prefix=%p 
--mandir=%p/share --with-x --with-gsl --x-includes=/usr/X11/include 
--x-libraries=/usr/X11/lib
+Source-MD5: d920a57884961a9fcbdcd9953ade469b
+PatchFile-MD5: 38fa52bb30693b1a9fd970b21e3e7531  
 DocFiles: AUTHORS COPYING README
 PatchScript: 
 #!/bin/zsh -efv
+%{default_script}
 perl -pi.bak -e 's|512|4096|g'  src/gmxlib/futil.c
 perl -pi.bak -e 's|/bin/csh|/bin/csh -f|g' share/**/* 2/dev/null
 perl -pi.bak -e 's|/lib/cpp|/usr/bin/cpp|g' share/**/* 2/dev/null
 
 CompileScript: 
 #!/bin/bash -efv
-
-flag64=
-if [[ %m == x86_64 ]]; then
-flag64=--enable-apple-64bit
-fi
-
-if [[ $(uname -p) == powerpc ]]; then
-./configure %c --enable-ppc-altivec 
-else
-./configure %c --build=%m-apple-darwin`uname -r|cut -f1 -d.` 
--host=%m-apple-darwin`uname -r|cut -f1 -d.` $flag64
-fi
+mkdir build
+cd build
+cmake -DGMX_GSL=ON -DCMAKE_INSTALL_NAME_DIR=%p/lib -DCMAKE_INSTALL_PREFIX=%p 
..
 make
 
 InstallScript: 
 #!/bin/bash -efv
-
-flag64=
-if [[ %m == x86_64 ]]; then
-flag64=--enable-apple-64bit
-fi
-
 mkdir -p %i/include/%n
-make -j 1 install DESTDIR=%d
+cd build
+make install DESTDIR=%d
 make clean
-if [[ $(uname -p) == powerpc ]]; then
-./configure %c --enable-ppc-altivec --disable-float --program-suffix=_d
-else
-./configure %c --build=%m-apple-darwin`uname -r|cut -f1 -d.` 
--host=%m-apple-darwin`uname -r|cut -f1 -d.` --disable-float 
--program-suffix=_d  $flag64
-fi
-make
-make -j 1 install DESTDIR=%d
+cmake -DGMX_DOUBLE=ON -DGMX_GSL=ON -DCMAKE_INSTALL_NAME_DIR=%p/lib 
-DCMAKE_INSTALL_PREFIX=%p ..
+make install DESTDIR=%d
 
 SplitOff: 
 Package: %N-shlibs
-Depends: fftw3-shlibs, gcc46-shlibs, gsl-shlibs, openmotif4-shlibs, x11
+Depends: fftw3-shlibs, gcc47-shlibs, gsl-shlibs, openmotif4-shlibs, x11
 Files: 
-lib/libgmx.6.dylib
-lib/libgmxana.6.0.0.dylib
-lib/libgmxana.6.dylib
-lib/libmd.6.0.0.dylib
-lib/libmd.6.dylib
-lib/libgmx_d.6.0.0.dylib
-lib/libgmx_d.6.dylib
-lib/libgmxana_d.6.0.0.dylib
-lib/libgmxana_d.6.dylib
-lib/libmd_d.6.0.0.dylib
-lib/libmd_d.6.dylib
-   lib/libgmxpreprocess.6.dylib
-   lib/libgmxpreprocess.6.0.0.dylib
-   lib/libgmxpreprocess_d.6.dylib
-   lib/libgmxpreprocess_d.6.0.0.dylib
+lib/libgmx.6*.dylib
+lib/libgmxana.6*.dylib
+lib/libmd.6*.dylib
+   lib/libgmxpreprocess.6*.dylib
+lib/libgmx_d.6*.dylib
+lib/libgmxana_d.6*.dylib
+lib/libmd_d.6*.dylib
+lib/libgmxpreprocess_d.6*.dylib
 
 Shlibs: 
-%p/lib/libgmx.6.dylib 7.0.0 %n (= 4.5.3-1)
-%p/lib/libgmxana.6.dylib 7.0.0 %n (= 4.5.3-1)
-%p/lib/libmd.6.dylib 7.0.0 %n (= 

[cvs] dists/10.7/stable/main/finkinfo/sci rdkit.info, NONE, 1.1 coot.info, 1.18, 1.19

[William Scott]

Update of /cvsroot/fink/dists/10.7/stable/main/finkinfo/sci
In directory sfp-cvs-1.v30.ch3.sourceforge.com:/tmp/cvs-serv31318

Modified Files:
coot.info 
Added Files:
rdkit.info 
Log Message:
rdkit added as new dependency for coot

--- NEW FILE: rdkit.info ---
Package: rdkit
Version: 2012.12.1
Revision: 1
Distribution: 10.6, 10.7, 10.8
GCC: 4.0
BuildDependsOnly: false
Source: mirror:sourceforge:rdkit/RDKit_2012_12_1.tgz
Source-MD5: 36596b18ff71c70b04d25c43810c2b01
Source2: mirror:sourceforge:boost/boost_1_53_0.tar.bz2
Source2-MD5: a00d22605d5dbcfb4c9936a9b35bc4c2
Description: Cheminformatics and machine-learning software 
DescDetail: 
A collection of cheminformatics and machine-learning software written in C++ 
and Python. Core algorithms and data structures are written in C++. Wrappers
are provided to use the toolkit from either Python or Java. Additionally, the
RDKit distribution includes a PostgreSQL-based cartridge that allows molecules 
to be stored in a relational database and retrieved via substructure and 
similarity searches.

BuildConflicts:  boost1.35.nopython, boost1.35.python26, boost1.35.python27, 
boost1.35.systempython, boost1.46.cmake, boost-jam, boost1.46.1.cmake
Depends: %N-shlibs, python27-shlibs, numpy-py27, sqlite3-shlibs
BuildDepends:  python27, numpy-py27, sqlite3-dev, cmake
CompileScript: 
#!/bin/sh -efv
#
# First build a more current boost libboost_python library and we will put it 
in the rdkit 
# library subdirectory to avoid confusion
#
RDKIT_ROOT=$PWD
cd ../boost_1_53_0
BOOSTROOT=$PWD
./bootstrap.sh --with-libraries=python,regex --with-python-root=%p 
--with-python=%p/bin/python2.7  --prefix=$PWD  
# 
./b2 install --prefix=$BOOSTROOT  
cd lib
# Despite the above it links to the system python, so fix that and give it a 
proper instal name id
install_name_tool -change 
/System/Library/Frameworks/Python.framework/Versions/2.7/Python 
%p/lib/python2.7/config/libpython2.7.dylib libboost_python.dylib
install_name_tool -id %p/lib/rdkit/libboost_python.dylib   libboost_python.dylib
#
#
install_name_tool -change 
/System/Library/Frameworks/Python.framework/Versions/2.7/Python 
%p/lib/python2.7/config/libpython2.7.dylib  libboost_regex.dylib
install_name_tool -id %p/lib/rdkit/libboost_regex.dylib  libboost_regex.dylib
#
#
# Now for rdkit itself
#
cd $RDKIT_ROOT 
mkdir build
cd build
cmake -DCMAKE_INSTALL_PREFIX=%p -DCMAKE_INSTALL_NAME_DIR=%p/lib/%n   
-DCMAKE_PREFIX_PATH=%p   -DBOOST_ROOT=$BOOSTROOT -DBoost_NO_SYSTEM_PATHS=ON 
-DPYTHON_LIBRARY=%p/lib/python2.7/config/libpython2.7.dylib  
-DPYTHON_INCLUDE_DIR=%p/include/python2.7 -DPYTHON_EXECUTABLE=%p/bin/python2.7 
..  
# NUMPROC=$(sysctl -n hw.ncpu)
# make -j $NUMPROC install
 make install
#
# We only require the boost_python library and boost_regex library
cp $BOOSTROOT/lib/libboost_python.dylib  
$RDKIT_ROOT/lib/libboost_python.dylib
cp $BOOSTROOT/lib/libboost_regex.dylib   
$RDKIT_ROOT/lib/libboost_regex.dylib
cp -R $BOOSTROOT/boost  $RDKIT_ROOT/Code/.

InstallScript: 
#!/bin/sh -efv
mkdir -p %i/lib/python2.7/site-packages
cp -R rdkit %i/lib/python2.7/site-packages/.
mkdir -p %i/lib
cp -R lib %i/lib/%n
mkdir -p %i/include
cp -R Code %i/include/%n

SplitOff: 
Package: %N-shlibs
Description: rdkit dynamic libraries
Files:  
lib/%N/*.1.dylib 
lib/%N/libboost_python.dylib
  
lib/%N/libboost_regex.dylib 
 

Shlibs: 
%p/lib/%N/libboost_python.dylib   0.0.0 %n  (= 
2012.12.1-1) 
%p/lib/%N/libboost_regex.dylib0.0.0 %n  (= 
2012.12.1-1) 
%p/lib/%N/libAlignment.1.dylib1.0.0 %n  (= 
2012.12.1-1)   
%p/lib/%N/libCatalogs.1.dylib 1.0.0 %n  (= 
2012.12.1-1)
%p/lib/%N/libChemReactions.1.dylib1.0.0 %n  (= 
2012.12.1-1)
%p/lib/%N/libChemTransforms.1.dylib   1.0.0 %n  (= 
2012.12.1-1)
%p/lib/%N/libChemicalFeatures.1.dylib 1.0.0 %n  (= 
2012.12.1-1)
%p/lib/%N/libDataStructs.1.dylib  1.0.0 %n  (= 
2012.12.1-1)
%p/lib/%N/libDepictor.1.dylib 1.0.0 %n  (= 
2012.12.1-1)
%p/lib/%N/libDescriptors.1.dylib  1.0.0 %n  (= 
2012.12.1-1)
%p/lib/%N/libDistGeomHelpers.1.dylib  1.0.0 %n  (= 
2012.12.1-1)
%p/lib/%N/libDistGeometry.1.dylib 1.0.0 %n  (= 
2012.12.1-1)
%p/lib/%N/libEigenSolvers.1.dylib 1.0.0 %n  (= 
2012.12.1-1)
%p/lib/%N/libFileParsers.1.dylib  1.0.0 %n  (= 
2012.12.1-1)
%p/lib/%N/libFingerprints.1.dylib 1.0.0 %n  (= 
2012.12.1-1)
%p/lib/%N/libForceField.1.dylib 

[cvs] dists/10.4/stable/main/finkinfo/sci rdkit.info, NONE, 1.1 coot.info, 1.38, 1.39

[William Scott]

Update of /cvsroot/fink/dists/10.4/stable/main/finkinfo/sci
In directory sfp-cvs-1.v30.ch3.sourceforge.com:/tmp/cvs-serv31467

Modified Files:
coot.info 
Added Files:
rdkit.info 
Log Message:
rdkit added as new dependency for coot

--- NEW FILE: rdkit.info ---
Package: rdkit
Version: 2012.12.1
Revision: 1
Distribution: 10.6, 10.7, 10.8
GCC: 4.0
BuildDependsOnly: false
Source: mirror:sourceforge:rdkit/RDKit_2012_12_1.tgz
Source-MD5: 36596b18ff71c70b04d25c43810c2b01
Source2: mirror:sourceforge:boost/boost_1_53_0.tar.bz2
Source2-MD5: a00d22605d5dbcfb4c9936a9b35bc4c2
Description: Cheminformatics and machine-learning software 
DescDetail: 
A collection of cheminformatics and machine-learning software written in C++ 
and Python. Core algorithms and data structures are written in C++. Wrappers
are provided to use the toolkit from either Python or Java. Additionally, the
RDKit distribution includes a PostgreSQL-based cartridge that allows molecules 
to be stored in a relational database and retrieved via substructure and 
similarity searches.

BuildConflicts:  boost1.35.nopython, boost1.35.python26, boost1.35.python27, 
boost1.35.systempython, boost1.46.cmake, boost-jam, boost1.46.1.cmake
Depends: %N-shlibs, python27-shlibs, numpy-py27, sqlite3-shlibs
BuildDepends:  python27, numpy-py27, sqlite3-dev, cmake
CompileScript: 
#!/bin/sh -efv
#
# First build a more current boost libboost_python library and we will put it 
in the rdkit 
# library subdirectory to avoid confusion
#
RDKIT_ROOT=$PWD
cd ../boost_1_53_0
BOOSTROOT=$PWD
./bootstrap.sh --with-libraries=python,regex --with-python-root=%p 
--with-python=%p/bin/python2.7  --prefix=$PWD  
# 
./b2 install --prefix=$BOOSTROOT  
cd lib
# Despite the above it links to the system python, so fix that and give it a 
proper instal name id
install_name_tool -change 
/System/Library/Frameworks/Python.framework/Versions/2.7/Python 
%p/lib/python2.7/config/libpython2.7.dylib libboost_python.dylib
install_name_tool -id %p/lib/rdkit/libboost_python.dylib   libboost_python.dylib
#
#
install_name_tool -change 
/System/Library/Frameworks/Python.framework/Versions/2.7/Python 
%p/lib/python2.7/config/libpython2.7.dylib  libboost_regex.dylib
install_name_tool -id %p/lib/rdkit/libboost_regex.dylib  libboost_regex.dylib
#
#
# Now for rdkit itself
#
cd $RDKIT_ROOT 
mkdir build
cd build
cmake -DCMAKE_INSTALL_PREFIX=%p -DCMAKE_INSTALL_NAME_DIR=%p/lib/%n   
-DCMAKE_PREFIX_PATH=%p   -DBOOST_ROOT=$BOOSTROOT -DBoost_NO_SYSTEM_PATHS=ON 
-DPYTHON_LIBRARY=%p/lib/python2.7/config/libpython2.7.dylib  
-DPYTHON_INCLUDE_DIR=%p/include/python2.7 -DPYTHON_EXECUTABLE=%p/bin/python2.7 
..  
# NUMPROC=$(sysctl -n hw.ncpu)
# make -j $NUMPROC install
 make install
#
# We only require the boost_python library and boost_regex library
cp $BOOSTROOT/lib/libboost_python.dylib  
$RDKIT_ROOT/lib/libboost_python.dylib
cp $BOOSTROOT/lib/libboost_regex.dylib   
$RDKIT_ROOT/lib/libboost_regex.dylib
cp -R $BOOSTROOT/boost  $RDKIT_ROOT/Code/.

InstallScript: 
#!/bin/sh -efv
mkdir -p %i/lib/python2.7/site-packages
cp -R rdkit %i/lib/python2.7/site-packages/.
mkdir -p %i/lib
cp -R lib %i/lib/%n
mkdir -p %i/include
cp -R Code %i/include/%n

SplitOff: 
Package: %N-shlibs
Description: rdkit dynamic libraries
Files:  
lib/%N/*.1.dylib 
lib/%N/libboost_python.dylib
  
lib/%N/libboost_regex.dylib 
 

Shlibs: 
%p/lib/%N/libboost_python.dylib   0.0.0 %n  (= 
2012.12.1-1) 
%p/lib/%N/libboost_regex.dylib0.0.0 %n  (= 
2012.12.1-1) 
%p/lib/%N/liboost_regex.dylib0.0.0 %n  (= 
2012.12.1-1)   ost_NO_SYSTEM_PATHS=ON 
-DPYTHON_LIBRARY=%p/lib/python2.7/config/libpython2.7.dylib  
-DPYTHON_INCLUDE_DIR=%p/include/python2.7 -DPYTHON_EXECUTABLE=%p/bin/python2.7 
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[cvs] dists/10.4/stable/main/finkinfo/sci ccp4.info, 1.21, 1.22 ccp4.patch, 1.6, 1.7

[William Scott]

Update of /cvsroot/fink/dists/10.4/stable/main/finkinfo/sci
In directory sfp-cvs-1.v30.ch3.sourceforge.com:/tmp/cvs-serv20575

Modified Files:
ccp4.info ccp4.patch 
Log Message:
fixes for 32 bit thanks to Hanspeter

Index: ccp4.info
===
RCS file: /cvsroot/fink/dists/10.4/stable/main/finkinfo/sci/ccp4.info,v
retrieving revision 1.21
retrieving revision 1.22
diff -u -d -r1.21 -r1.22
--- ccp4.info   23 Sep 2012 05:20:28 -  1.21
+++ ccp4.info   12 Feb 2013 03:28:48 -  1.22
@@ -1,6 +1,6 @@
 Package: ccp4
 Version: 6.3.0
-Revision: 5
+Revision: 6
 GCC: 4.0
 Distribution: 10.6, 10.7, 10.8
 UseMaxBuildJobs: false
@@ -16,7 +16,7 @@
 Source3-MD5: 21568dd2475505929573a3fd452c538f
 #  
 PatchFile: %n.patch
-PatchFile-MD5: b170eaad8f6926d7be9fee5abe017bd3 
+PatchFile-MD5: 0b5099178f6388ae065903ab67de61a4
 #
 #
 #
@@ -99,6 +99,11 @@
 # Now apply the primary patch
   sed 's|@PREFIX@|%p|g' %{PatchFile} | patch -p1
 
+# make sure we're building stuff under our %m and not the system default
+perl -pi -e 's|python ../cctbx_sources|arch -arch %m /usr/bin/python2.6 
../cctbx_sources|g; \
+s|libtbx.scons|arch -arch %m $|g' lib/cctbx/ccp4_build
+[ %m = i386 ]  perl -pi -e 's|cctbxopts ccp4io|cctbxopts 
--force_32bit ccp4io|g' lib/cctbx/ccp4_build
+
 # setup script for tcsh, zsh and bash users
 export TEMPXTAL=$PWD:h
 /usr/bin/grep -v char \*strcat( char \*, const char \*); 
x-windows/Mosflm/src/dps/index/ind_gen_direct.c | 
x-windows/Mosflm/src/dps/index/ind_gen_direct.tmp
@@ -141,14 +146,14 @@
 export PATH=%p/lib/xmkmf/bin:$PATH 
 export IMAKEINCLUDE=-I%p/lib/X11/config
 export FC=gfortran
-export CC=/usr/bin/gcc
-export CXX=/usr/bin/g++
+export CC=gcc
+export CXX=g++
 export libdir=$PWD/lib
 #
 # Uncomment the following line only for testing purposes.  The ccp4 
restrictive/commercial
 # license forbid disabling the interactive check in this way for the end-user
 #
-#  touch .agree2ccp4v6
+  touch .agree2ccp4v6
 #
 
 F_LIBS=-L%p/lib/gcc4.7/lib -lgfortran  \
@@ -157,7 +162,7 @@
 #  fix some post-configure bugs by getting rid of -lg2c
 /usr/bin/perl -pi.bak -e s|-lg2c||g deprecated/src/beast_/beast_MPI/Makefile 
 x-windows/XCCPJIFFY/Imakefile
 ( cd x-windows/XCCPJIFFY; perl -pi.bak -e 's|-lgfortran|-lgfortran 
-L%p/lib/gcc4.7/lib |g' *akefile* ) || exit 1
- 
+
 perl -pi.bak -e s|-lcrt1.10.6.o||g  Makefile share/ccp4i/Makefile 
deprecated/src/Makefile  lib/data/Makefile  lib/Makefile  share/Makefile  
src/Makefile
 perl -pi.bak -e s|-lcrt1.10.6.o||g  src/ccp4mapwish_/Makefile  
unsupported/src/Makefile  x-windows/Makefile  x-windows/Mosflm/mosflm/Makefile  
x-windows/Rotgen/Makefile
 
@@ -185,21 +190,22 @@
 
 #
 #
-NUMPROC=$(sysctl -n hw.ncpu)
+# NUMPROC=$(sysctl -n hw.ncpu)
+NUMPROC=1
 cd $CCP4
-make -i -j $NUMPROC
-make -i -j $NUMPROC  install
+make -w -i -j $NUMPROC
+make -w -i -j $NUMPROC  install
 #
 #
 #  
 
   cd  x-windows/XCCPJIFFY
   perl -pi -e 's|\-lgfortran| |g' Makefile
-  make 
-  make xccpjiffy2idraw
+  make -w
+  make -w xccpjiffy2idraw
   cp  xccpjiffy2idraw $CBIN/.
   cd ..
-  make xdlmapman xdldataman
+  make -w xdlmapman xdldataman
   cp  xdlmapman   $CBIN/.
   cp  xdldataman  $CBIN/.
 
@@ -213,28 +219,34 @@
   umask 0022
   export TEMPXTAL=$PWD:h
   source $PWD/include/%n.setup-zsh
-  NUMPROC=$(sysctl -n hw.ncpu)
+  #NUMPROC=$(sysctl -n hw.ncpu)
+  NUMPROC=1
+
+  export FC=gfortran
+  export CC=gcc
+  export CXX=g++
 
   cd lib/cctbx
-  ./ccp4_build
+  arch -arch %m ./ccp4_build
 
   cd $CCP4
   
   cd src/pointless
-  ./configure --with-clipper=$CCP4 --with-fftw=$CCP4 
FFTW_LIBS=-L$CCP4/lib -lrfftw -lfftw FFTW_CXXFLAGS=-I$CCP4/lib/fftw/fftw 
-I$CCP4/lib/fftw/rfftw -I$CCP4/include -I$CCP4/lib/libccp4 -I$CCP4/lib/mmdb 
--with-ccp4=$CCP4 CXXFLAGS=-O2   --with-cctbx=$CCP4/lib/cctbx/cctbx_sources 
--with-cctbx-build=$CCP4/lib/cctbx/cctbx_build CXXFLAGS=-O2   CXXFLAGS=-O2  
 --prefix=$CCP4 --bindir=$CCP4/bin LDFLAGS=-L$CCP4/lib CXX=/usr/bin/g++ 
CC=/usr/bin/gcc  
-  make -j $NUMPROC install
+  ./configure --with-clipper=$CCP4 --with-fftw=$CCP4 
FFTW_LIBS=-L$CCP4/lib -lrfftw -lfftw FFTW_CXXFLAGS=-I$CCP4/lib/fftw/fftw 
-I$CCP4/lib/fftw/rfftw -I$CCP4/include -I$CCP4/lib/libccp4 -I$CCP4/lib/mmdb 
--with-ccp4=$CCP4 CXXFLAGS=-O2   --with-cctbx=$CCP4/lib/cctbx/cctbx_sources 
--with-cctbx-build=$CCP4/lib/cctbx/cctbx_build CXXFLAGS=-O2   CXXFLAGS=-O2  
 --prefix=$CCP4 --bindir=$CCP4/bin LDFLAGS=-L$CCP4/lib CXX=g++ -arch %m 
CC=gcc -arch %m  
+  make -w -j $NUMPROC install
 
   cd $CCP4
   cd src/aimless
-  ./configure --with-clipper=$CCP4 --with-fftw=$CCP4 
FFTW_LIBS=-L$CCP4/lib -lrfftw -lfftw FFTW_CXXFLAGS=-I$CCP4/lib/fftw/fftw 
-I$CCP4/lib/fftw/rfftw -I$CCP4/include -I$CCP4/lib/libccp4 -I$CCP4/lib/mmdb 
--with-ccp4=$CCP4 

[cvs] dists/10.7/stable/main/finkinfo/sci coot.info,1.17,1.18

[William Scott]

Update of /cvsroot/fink/dists/10.7/stable/main/finkinfo/sci
In directory sfp-cvs-1.v30.ch3.sourceforge.com:/tmp/cvs-serv5845

Modified Files:
coot.info 
Log Message:
updates upstream

Index: coot.info
===
RCS file: /cvsroot/fink/dists/10.7/stable/main/finkinfo/sci/coot.info,v
retrieving revision 1.17
retrieving revision 1.18
diff -u -d -r1.17 -r1.18
--- coot.info   28 Sep 2012 13:51:42 -  1.17
+++ coot.info   29 Jan 2013 07:24:53 -  1.18
@@ -1,12 +1,10 @@
 Package: coot
-Version: 0.7.0
-Revision: 1
-#SourceDirectory: %n-%v
-SourceDirectory: %n-0.7
+Version: 0.7.1-pre
+Revision: 4552
+SourceDirectory: %n-%v
 GCC: 4.0 
-Source: http://lmb.bioch.ox.ac.uk/%n/software/source/releases/%n-0.7.tar.gz
-#Source: 
http://lmb.bioch.ox.ac.uk/%n/software/source/pre-releases/%n-%v-revision-%r.tar.gz
-Source-MD5: 29e10cb3b77d882c1d5480983e9b1218
+Source: 
http://www2.mrc-lmb.cam.ac.uk/groups/murshudov/coot/source/pre-releases/%n-%v-revision-%r.tar.gz
+Source-MD5: dc42bb2504ff3281f14f1dc7694c5107
 Source2: 
http://www2.mrc-lmb.cam.ac.uk/groups/murshudov/content/refmac/Dictionary/refmac_dictionary_v5.38.tar.gz
 Source2-MD5: 174a5fc5e5be03cb432c61e8da4283df
 Source3: 
http://www.ysbl.york.ac.uk/~emsley/software/extras/reference-structures.tar.gz
@@ -159,7 +157,7 @@
 export COOT_REFMAC_LIB_DIR=%p/share/coot/lib
 export 
PKG_CONFIG_PATH=%p/lib/glib-2.0/pkgconfig-strict:%p/lib/fontconfig2/lib/pkgconfig:${PKG_CONFIG_PATH}
   FLIBS=-L%p/lib \
-  CPPFLAGS=-I%p/include/libglade-2.0/glade -I%p/include/libglade-2.0 
-I%p/include/python2.7  -I%p/include/mmdb -I%p/include/ssm 
-I%p/include/gpp4/ccp4 -I%p/include/clipper -I%p/include -I/usr/X11R6/include \
+  CPPFLAGS=-I%b/lidia-core -I%p/include/libglade-2.0/glade 
-I%p/include/libglade-2.0 -I%p/include/python2.7  -I%p/include/mmdb 
-I%p/include/ssm -I%p/include/gpp4/ccp4 -I%p/include/clipper -I%p/include 
-I/usr/X11R6/include \
   
LDFLAGS=-Wl,-dylib_file,%p/lib/python2.7/config/libpython2.7.dylib:%p/lib/libsfftw.2.0.7.dylib:%p/lib/libsrfftw.2.0.7.dylib:%p/lib/pango-ft219/lib/libpango-1.0.dylib:%p/lib/pango-ft219/lib/libpangocairo-1.0.dylib:%p/lib/pango-ft219/lib/libpangoft2-1.0.dylib:%p/lib/pango-ft219/lib/libpangox-1.0.dylib:%p/lib/pango-ft219/lib/libpangoxft-1.0.dylib
 -L%p/lib  -L/usr/lib  -flat_namespace 
-L/System/Library/Frameworks/OpenGL.framework/Versions/A/Libraries \
   DYLD_LIBRARY_PATH= \
   ./configure %c
@@ -249,37 +247,36 @@
 lib/libcootilus.0*.dylib
 
 Shlibs: 
-%p/lib/libccp4mg-surface.0.dylib1.0.0 %n (= 0.6-1)
-%p/lib/libccp4mg-utils.0.dylib  1.0.0 %n (= 0.6-1)
-%p/lib/libcoot-analysis.0.dylib 1.0.0 %n (= 0.6-1)
-%p/lib/libcoot-AngleInfo.0.dylib1.0.0 %n (= 0.6-1)
-%p/lib/libcoot-cabuild.0.dylib  1.0.0 %n (= 0.6-1)
-%p/lib/libcoot-compat.0.dylib   1.0.0 %n (= 0.6-1)
-%p/lib/libcoot-coord-extras.0.dylib 1.0.0 %n (= 0.6-1)
-%p/lib/libcoot-coord-utils.0.dylib  1.0.0 %n (= 0.6-1)
-%p/lib/libcoot-coords.0.dylib   1.0.0 %n (= 0.6-1)
-%p/lib/libcoot-db-main.0.dylib  1.0.0 %n (= 0.6-1)
-%p/lib/libcoot-geometry.0.dylib 1.0.0 %n (= 0.6-1)
-%p/lib/libcoot-goograph.0.dylib 1.0.0 %n (= 0.6-1)
-%p/lib/libcoot-gtkgraph.0.dylib 1.0.0 %n (= 0.6-1)
-%p/lib/libcoot-high-res.0.dylib 1.0.0 %n (= 0.6-1)
-%p/lib/libcoot-ideal.0.dylib1.0.0 %n (= 0.6-1)
-%p/lib/libcoot-isosurface.0.dylib   1.0.0 %n (= 0.6-1)
-%p/lib/libcoot-lidia-core.0.dylib   1.0.0 %n (= 0.6-1)
-%p/lib/libcoot-lidia.0.dylib1.0.0 %n (= 0.6-1)
-%p/lib/libcoot-ligand.0.dylib   1.0.0 %n (= 0.6-1)
-%p/lib/libcoot-map-heavy.0.dylib1.0.0 %n (= 0.6-1)
-%p/lib/libcoot-map-utils.0.dylib1.0.0 %n (= 0.6-1)
-%p/lib/libcoot-mini-mol.0.dylib 1.0.0 %n (= 0.6-1)
-%p/lib/libcoot-protein-db.0.dylib   1.0.0 %n (= 0.6-1)
-%p/lib/libcoot-shelx.0.dylib1.0.0 %n (= 0.6-1)
-%p/lib/libcoot-skeleton.0.dylib 1.0.0 %n (= 0.6-1)
-%p/lib/libcoot-surface.0.dylib  1.0.0 %n (= 0.6-1)
-%p/lib/libcoot-tw.0.dylib   1.0.0 %n (= 0.6-1)
-%p/lib/libcoot-utils.0.dylib1.0.0 %n (= 0.6-1)
-%p/lib/libcootaneer.0.dylib 1.0.0 %n (= 0.6-1)
-%p/lib/libcootilus.0.dylib  1.0.0 %n (= 0.6-1)
-%p/lib/libcootilus.0.dylib  1.0.0 %n (= 
0.7-pre-1-4305)
+%p/lib/libccp4mg-surface.0.dylib1.0.0 %n (= 0.7-1)
+%p/lib/libccp4mg-utils.0.dylib  1.0.0 %n (= 0.7-1)
+%p/lib/libcoot-analysis.0.dylib 1.0.0 %n (= 0.7-1)
+ 

[cvs] dists/10.7/stable/main/finkinfo/languages guile18-gtk.info, 1.4, 1.5

[William Scott]

Update of /cvsroot/fink/dists/10.7/stable/main/finkinfo/languages
In directory sfp-cvs-1.v30.ch3.sourceforge.com:/tmp/cvs-serv27991

Modified Files:
guile18-gtk.info 
Log Message:
undo fix that breaks everything. Note to self: never commit to cvs while under 
influence of pain-killers.

Index: guile18-gtk.info
===
RCS file: 
/cvsroot/fink/dists/10.7/stable/main/finkinfo/languages/guile18-gtk.info,v
retrieving revision 1.4
retrieving revision 1.5
diff -u -d -r1.4 -r1.5
--- guile18-gtk.info9 Jan 2013 18:52:54 -   1.4
+++ guile18-gtk.info13 Jan 2013 19:46:41 -  1.5
@@ -1,6 +1,6 @@
 Package: guile18-gtk
 Version: 2.1
-Revision: 14
+Revision: 15
 #PatchFile: %n.patch
 #PatchFile-MD5: cd2e62770b704f00043ae4b073647935
 BuildDepends: 
@@ -78,8 +78,7 @@
 CompileScript:
 #!/bin/bash -efv
 source %p/bin/init.sh
-export CFLAGS=/usr/X11/include 
- export 
PKG_CONFIG_PATH=%p/lib/pango-ft219/lib/pkgconfig:%p/lib/fontconfig2/lib/pkgconfig:%p/lib/freetype219/lib/pkgconfig:%p/lib/pkgconfig:${PKG_CONFIG_PATH}
 FREETYPE_CONFIG=%p/lib/freetype219/bin/freetype-config 
PATH=%p/share/guile/1.8/scripts/binoverride:${PATH}
+export 
PKG_CONFIG_PATH=%p/lib/pango-ft219/lib/pkgconfig:%p/lib/fontconfig2/lib/pkgconfig:%p/lib/freetype219/lib/pkgconfig:%p/lib/pkgconfig:${PKG_CONFIG_PATH}
 FREETYPE_CONFIG=%p/lib/freetype219/bin/freetype-config 
PATH=%p/share/guile/1.8/scripts/binoverride:${PATH}
  ./configure --prefix=%i  --with-gtk-prefix=%p  --infodir=%i/share/info 
--with-gdk-pixbuf=yes --with-glade=yes --with-gtkgl=yes
  export GUILE_LOAD_PATH=%p/share/guile/1.8
  make


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[cvs] dists/10.7/stable/main/finkinfo/languages guile18-gtk.info, 1.3, 1.4

[William Scott]

Update of /cvsroot/fink/dists/10.7/stable/main/finkinfo/languages
In directory sfp-cvs-1.v30.ch3.sourceforge.com:/tmp/cvs-serv28496

Modified Files:
guile18-gtk.info 
Log Message:
user reports export 'CFLAGS=/usr/X11/include' needed to compile on 10.8

Index: guile18-gtk.info
===
RCS file: 
/cvsroot/fink/dists/10.7/stable/main/finkinfo/languages/guile18-gtk.info,v
retrieving revision 1.3
retrieving revision 1.4
diff -u -d -r1.3 -r1.4
--- guile18-gtk.info20 Aug 2012 18:44:50 -  1.3
+++ guile18-gtk.info9 Jan 2013 18:52:54 -   1.4
@@ -1,6 +1,6 @@
 Package: guile18-gtk
 Version: 2.1
-Revision: 13
+Revision: 14
 #PatchFile: %n.patch
 #PatchFile-MD5: cd2e62770b704f00043ae4b073647935
 BuildDepends: 
@@ -78,6 +78,7 @@
 CompileScript:
 #!/bin/bash -efv
 source %p/bin/init.sh
+export CFLAGS=/usr/X11/include 
  export 
PKG_CONFIG_PATH=%p/lib/pango-ft219/lib/pkgconfig:%p/lib/fontconfig2/lib/pkgconfig:%p/lib/freetype219/lib/pkgconfig:%p/lib/pkgconfig:${PKG_CONFIG_PATH}
 FREETYPE_CONFIG=%p/lib/freetype219/bin/freetype-config 
PATH=%p/share/guile/1.8/scripts/binoverride:${PATH}
  ./configure --prefix=%i  --with-gtk-prefix=%p  --infodir=%i/share/info 
--with-gdk-pixbuf=yes --with-glade=yes --with-gtkgl=yes
  export GUILE_LOAD_PATH=%p/share/guile/1.8


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[cvs] dists/10.7/stable/main/finkinfo/shells zsh.info, 1.1, 1.2 zsh-helpfiles.info, 1.1, 1.2

[William Scott]

Update of /cvsroot/fink/dists/10.7/stable/main/finkinfo/shells
In directory sfp-cvs-1.v30.ch3.sourceforge.com:/tmp/cvs-serv25695

Modified Files:
zsh.info zsh-helpfiles.info 
Log Message:
updates upstream

Index: zsh-helpfiles.info
===
RCS file: 
/cvsroot/fink/dists/10.7/stable/main/finkinfo/shells/zsh-helpfiles.info,v
retrieving revision 1.1
retrieving revision 1.2
diff -u -d -r1.1 -r1.2
--- zsh-helpfiles.info  2 Aug 2011 03:06:07 -   1.1
+++ zsh-helpfiles.info  22 Dec 2012 17:30:11 -  1.2
@@ -1,10 +1,10 @@
 Package: zsh-helpfiles
-Version: 4.3.12
+Version: 5.0.2
 Revision: 1
 Depends: zsh (= %v) | zsh-multibyte (= %v) 
 BuildDepends: zsh (= %v) | zsh-multibyte (= %v)
-Source: http://sourceforge.net/projects/zsh/files/zsh-dev/%v/zsh-%v.tar.bz2
-Source-MD5: 7a82c0bf0635e046ca4e9ec1bdef3811
+Source: mirror:sourceforge:zsh/zsh/%v/zsh-%v.tar.bz2
+Source-MD5: b8f2ad691acf58b3252225746480dcad
 Source2: 
http://code.google.com/p/zsh-templates-osx/source/browse/trunk/Library/init/zsh/local-functions/general/run-help
 Source2-MD5: 371638ce4c255993ea9c528981b3d113 
 CompileScript:

Index: zsh.info
===
RCS file: /cvsroot/fink/dists/10.7/stable/main/finkinfo/shells/zsh.info,v
retrieving revision 1.1
retrieving revision 1.2
diff -u -d -r1.1 -r1.2
--- zsh.info2 Aug 2011 02:48:27 -   1.1
+++ zsh.info22 Dec 2012 17:30:11 -  1.2
@@ -1,21 +1,19 @@
 Package: zsh 
-Version: 4.3.12
+Version: 5.0.2
 Revision: 1
 Conflicts: zsh-multibyte
 Replaces: zsh-multibyte
 Depends: libiconv, pcre-shlibs, libncurses5-shlibs (= 5.4-20041023-1006)
 BuildDepends: libiconv-dev, pcre, pcre-bin, libncurses5 (= 5.4-20041023-1006)
-# Source: mirror:sourceforge:%n/%n-%v.tar.bz2
-Source: http://sourceforge.net/projects/%n/files/%n-dev/%v/%n-%v.tar.bz2
-Source-MD5: 7a82c0bf0635e046ca4e9ec1bdef3811
-#Source2: mirror:sourceforge:%n/%n-%v-doc.tar.bz2
-Source2: 
http://sourceforge.net/projects/%n/files/%n-doc-dev/%v/%n-%v-doc.tar.bz2
-Source2-MD5: d1bcb1e1716ac5726444dee2a3dca98d
+Source: mirror:sourceforge:%n/%n/%v/%n-%v.tar.bz2
+Source-MD5: b8f2ad691acf58b3252225746480dcad
+Source2: mirror:sourceforge:%n/%n-doc/%v/%n-%v-doc.tar.bz2
+Source2-MD5: b6818cbbea635b2f70883bb913d0a04a
 ConfigureParams:
 --mandir=%p/share/man --infodir=%p/share/info --enable-etcdir=%p/etc/%n   \
 --enable-maildir-support --enable-pcre --enable-zsh-secure-free   \
 --enable-fndir=%p/share/%n --enable-function-subdirs  \
---with-curses-terminfo --with-tcsetpgrp AWK=/usr/bin/awk 
+--with-curses-terminfo --with-tcsetpgrp --enable-multibyte 
AWK=/usr/bin/awk 
 
 NoSetMAKEFLAGS: true
 SetMAKEFLAGS: -j1
@@ -31,8 +29,8 @@
 make install DESTDIR=%d
 
 
-DocFiles: Doc/zsh.dvi Doc/*.html StartupFiles/* ChangeLog* INSTALL LICENCE 
META-FAQ README 
-Description: The Z Shell
+DocFiles: Doc/zsh.dvi Doc/*.html StartupFiles/* ChangeLog* INSTALL LICENCE 
META-FAQ README
+Description: The Z Shell with multibyte support
 DescDetail: 
 To make the Fink zsh your default user shell, do the following:
   1. Add the line /sw/bin/zsh to the file /etc/shells


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[cvs] dists/10.7/stable/main/finkinfo/sci xmakemol.info, NONE, 1.1 xmakemol.patch, NONE, 1.1

[William Scott]

Update of /cvsroot/fink/dists/10.7/stable/main/finkinfo/sci
In directory sfp-cvs-1.v30.ch3.sourceforge.com:/tmp/cvs-serv11564

Added Files:
xmakemol.info xmakemol.patch 
Log Message:
unmodified.  Package is up to date

--- NEW FILE: xmakemol.info ---
Package: xmakemol
Version: 5.16
Revision: 1
Maintainer: None fink-de...@lists.sourceforge.net
Source: http://savannah.nongnu.org/download/%n/%n-%v.tar.gz
Source-MD5: e466a81bf407be6e7476f279af1968dc
Depends: lesstif-shlibs, mesa-libglw-lesstif-shlibs, imagemagick (= 5.5.1-13), 
gifsicle | ungifsicle, libgl, x11, freeglut-shlibs
BuildDepends: lesstif, mesa-libglw-lesstif, x11-dev, freeglut, fink (= 
0.24.12-1)
PatchFile: %n.patch
PatchFile-MD5: 578fa5a786ee87348302bca1fbec401e
PatchScript: sed 's|@FINKPREFIX@|%p|g' %{PatchFile} | patch -p1
ConfigureParams: --mandir=%p/share/man
InstallScript: 
  make install DESTDIR=%d
  mkdir -p %i/share/doc/%n
  cp -r examples %i/share/doc/%n

DocFiles: AUTHORS COPYING NEWS PROBLEMS README ToDo.txt xmakemol.html
Description: View atomic and molecular systems
DescDetail: 
XMakemol is a program used to view and manipulate atomic and molecular
data given in xyz form. XMakemol can produce output in PostScript (black
and white or colour) and in xpm format. XMakemol can also produce a series
of xpm files which can be translated into an animated gif file using the
bundled utility xmake_anim.pl

DescPackaging: 
 Originally packaged by Matt Stephenson.

License: GPL
Homepage: http://savannah.nongnu.org/projects/xmakemol

--- NEW FILE: xmakemol.patch ---
diff -Nurd -x'*~' xmakemol-5.16.orig/configure xmakemol-5.16/configure
--- xmakemol-5.16.orig/configure2007-08-30 13:45:18.0 -0400
+++ xmakemol-5.16/configure 2007-10-15 00:18:43.0 -0400
@@ -6209,9 +6209,9 @@
   echo $ECHO_N (cached) $ECHO_C 6
 else
 
-   XWIDGETLIBS=$X_LIBS $X11_LIBS $XT_LIBS $X_LIBS $X_PRE_LIBS $XM_LIBS
+   XWIDGETLIBS=$X_LIBS $X11_LIBS $XM_LIBS $XT_LIBS $X_LIBS $X_PRE_LIBS
sim_cv_motif_glwidget=UNKNOWN
-   for lib in GLwM GLw MesaGLwM MesaGLw; do
+   for lib in GLw; do
  if test x$sim_cv_motif_glwidget = xUNKNOWN; then
LIBS=-l$lib $SAVELIBS $XWIDGETLIBS $GL_LIBS -lm
cat conftest.$ac_ext _ACEOF
diff -Nurd -x'*~' xmakemol-5.15.orig/file.c xmakemol-5.15/file.c
--- xmakemol-5.15.orig/file.c   2005-03-06 12:04:32.0 -0500
+++ xmakemol-5.15/file.c2005-12-16 01:38:10.0 -0500
@@ -29,6 +29,7 @@
 #include alloca.h
 #endif
 #include ctype.h /* aro - needed for isalnum() */
+#include sys/types.h
 #include dirent.h
 #include locale.h
 #include math.h
@@ -96,6 +97,15 @@
 /* directory that was accessed in any of the file selection dialogs */
 static XmString current_directory = NULL;
 
+  void export_type_cb(Widget, XtPointer, XtPointer);
+  void file_type_cb(Widget, XtPointer, XtPointer);
+  void load_file_cb(Widget, XtPointer, XtPointer);
+  void save_file_cb(Widget, XtPointer, XtPointer);
+  void merge_file_cb(Widget, XtPointer, XtPointer);
+  void export_file_cb(Widget, XtPointer, XtPointer);
+  void print_file_cb(Widget, XtPointer, XtPointer);/* aro */
+  void print_file_select_cb(Widget, XtPointer, XtPointer);/* aro */
+  void cleanup_cb(Widget, XtPointer, XtPointer);/* aro */
 
 void
 file_cb(Widget widget, XtPointer client_data, XtPointer call_data)
@@ -112,15 +122,6 @@
  Widgets p_dialog, print_printer, temp_widget; 
  XmStringTable printer_xmstrings. */
  
-  void export_type_cb(Widget, XtPointer, XtPointer);
-  void file_type_cb(Widget, XtPointer, XtPointer);
-  void load_file_cb(Widget, XtPointer, XtPointer);
-  void save_file_cb(Widget, XtPointer, XtPointer);
-  void merge_file_cb(Widget, XtPointer, XtPointer);
-  void export_file_cb(Widget, XtPointer, XtPointer);
-  void print_file_cb(Widget, XtPointer, XtPointer);/* aro */
-  void print_file_select_cb(Widget, XtPointer, XtPointer);/* aro */
-  void cleanup_cb(Widget, XtPointer, XtPointer);/* aro */
   int item_no=(int) client_data, i, j;/* aro */
   char *printer_name, *line_ptr, line[1024], 
printer_strings[MAX_PRINTERS+1][80],
print_command_string[1024];/* aro */
diff -Nurd -x'*~' xmakemol-5.15.orig/xmake_anim.pl xmakemol-5.15/xmake_anim.pl
--- xmakemol-5.15.orig/xmake_anim.pl2005-03-07 05:10:41.0 -0500
+++ xmakemol-5.15/xmake_anim.pl 2005-12-16 01:38:39.0 -0500
@@ -27,13 +27,13 @@
 
 # Configure: specify where the binaries are
 
-$convert = /usr/bin/convert;
+$convert = @FINKPREFIX@/bin/convert;
 if (! -e $convert)
   {
 die (Cannot find convert program (part of ImageMagick). Please install 
it.\n);
   }
 
-$gifsicle = /usr/bin/gifsicle;
+$gifsicle = @FINKPREFIX@/bin/gifsicle;
 if (! -e $gifsicle)
   {
 print (Cannot find gifsicle program, install it for better 
performance.\n);
diff -Nurd -x'*~' xmakemol-5.15.orig/xmakemol.1 xmakemol-5.15/xmakemol.1
--- xmakemol-5.15.orig/xmakemol.1   2005-01-28 09:34:54.0 -0500
+++ 

[cvs] dists/10.7/stable/main/finkinfo/sci pymol-py.patch, 1.4, 1.5 pymol-py.info, 1.9, 1.10

[William Scott]

Update of /cvsroot/fink/dists/10.7/stable/main/finkinfo/sci
In directory vz-cvs-3.sog:/tmp/cvs-serv17857

Modified Files:
pymol-py.patch pymol-py.info 
Log Message:
work-around for Radeon graphics card incompatibility

Index: pymol-py.info
===
RCS file: /cvsroot/fink/dists/10.7/stable/main/finkinfo/sci/pymol-py.info,v
retrieving revision 1.9
retrieving revision 1.10
diff -u -d -r1.9 -r1.10
--- pymol-py.info   29 Apr 2012 17:18:37 -  1.9
+++ pymol-py.info   6 Oct 2012 17:51:51 -   1.10
@@ -1,13 +1,13 @@
 Info2: 
 Package: pymol-py%type_pkg[python]
 Version: 1.5
-Revision: 6
+Revision: 7
 UseMaxBuildJobs: false
 Maintainer: W. G. Scott wgsc...@users.sourceforge.net
 Type: python (2.6 2.7)
 # r3983
-#Source: mirror:sourceforge:fink/pymol-%v-src.tar.bz2
-Source: http://diablo.ucsc.edu/~wgscott/pymol/pymol-%v-src.tar.bz2
+Source: mirror:sourceforge:fink/pymol-%v-src.tar.bz2
+#Source: http://diablo.ucsc.edu/~wgscott/pymol/pymol-%v-src.tar.bz2
 Source-MD5: 7ec7f1eb4302672d65bbe4de9ffc01e5
 Source2: http://www.weizmann.ac.il/ISPC/eMovie.py
 Source2-MD5: 832252d4cee1ba88d50a35681b5ecd4b
@@ -16,7 +16,7 @@
 Source4: http://diablo.ucsc.edu/~wgscott/pymol/pynmr_0.37f_src.tar.bz2
 Source4-MD5: cb4a3906766681ce9230ef5515e1aa1c
 PatchFile: pymol-py.patch
-PatchFile-MD5: 04fd2893af1db8924f6da71cd3afc03e
+PatchFile-MD5: f812def4c13c0542e3830f187ac00523
 PatchFile2: pymol-py-rest.patch
 PatchFile2-MD5: 2df10a5a2d66b16082317a823878bde0
 SourceDirectory: pymol-%v

Index: pymol-py.patch
===
RCS file: /cvsroot/fink/dists/10.7/stable/main/finkinfo/sci/pymol-py.patch,v
retrieving revision 1.4
retrieving revision 1.5
diff -u -d -r1.4 -r1.5
--- pymol-py.patch  12 Apr 2012 20:01:53 -  1.4
+++ pymol-py.patch  6 Oct 2012 17:51:51 -   1.5
@@ -49,13 +49,13 @@
 +#
 +PYMOL_PATH=@FINKPREFIX@/lib/python2.X/site-packages/pymol
 +export PYMOL_PATH
-+#
++HasRadeon=($(system_profiler SPDisplaysDataType | grep Radeon ))
 +# ==
-+# (no changes usually required below here)
-+#
-+# python modules
-+#
-+exec @FINKPREFIX@/bin/python2.X  
@FINKPREFIX@/lib/python2.X/site-packages/pymol/__init__.py -d _ set 
stereo_double_pump_mono,quiet=1 $@
++if [[ -z $HasRadeon  ]];then
++exec @FINKPREFIX@/bin/python2.X  
@FINKPREFIX@/lib/python2.X/site-packages/pymol/__init__.py -d _ set 
stereo_double_pump_mono,quiet=1 $@
++else
++exec @FINKPREFIX@/bin/python2.X  
@FINKPREFIX@/lib/python2.X/site-packages/pymol/__init__.py -d _ set 
stereo_double_pump_mono,quiet=1 -M $@
++fi
 --- pymol-1.5/modules/pmg_tk/startup/apbs_tools.py.orig2012-02-18 
14:50:35.0 -0500
 +++ pymol-1.5/modules/pmg_tk/startup/apbs_tools.py 2012-02-18 
14:51:33.0 -0500
 @@ -141,7 +141,7 @@


--
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[cvs] dists/10.4/stable/main/finkinfo/sci pymol-py.patch, 1.6, 1.7 pymol-py.info, 1.18, 1.19

[William Scott]

Update of /cvsroot/fink/dists/10.4/stable/main/finkinfo/sci
In directory vz-cvs-3.sog:/tmp/cvs-serv17957

Modified Files:
pymol-py.patch pymol-py.info 
Log Message:
work-around for Radeon graphics card incompatibility

Index: pymol-py.info
===
RCS file: /cvsroot/fink/dists/10.4/stable/main/finkinfo/sci/pymol-py.info,v
retrieving revision 1.18
retrieving revision 1.19
diff -u -d -r1.18 -r1.19
--- pymol-py.info   29 Apr 2012 17:19:26 -  1.18
+++ pymol-py.info   6 Oct 2012 17:54:26 -   1.19
@@ -1,13 +1,13 @@
 Info2: 
 Package: pymol-py%type_pkg[python]
 Version: 1.5
-Revision: 6
+Revision: 7
 UseMaxBuildJobs: false
 Maintainer: W. G. Scott wgsc...@users.sourceforge.net
 Type: python (2.6 2.7)
 # r3983
-#Source: mirror:sourceforge:fink/pymol-%v-src.tar.bz2
-Source: http://diablo.ucsc.edu/~wgscott/pymol/pymol-%v-src.tar.bz2
+Source: mirror:sourceforge:fink/pymol-%v-src.tar.bz2
+#Source: http://diablo.ucsc.edu/~wgscott/pymol/pymol-%v-src.tar.bz2
 Source-MD5: 7ec7f1eb4302672d65bbe4de9ffc01e5
 Source2: http://www.weizmann.ac.il/ISPC/eMovie.py
 Source2-MD5: 832252d4cee1ba88d50a35681b5ecd4b
@@ -16,7 +16,7 @@
 Source4: http://diablo.ucsc.edu/~wgscott/pymol/pynmr_0.37f_src.tar.bz2
 Source4-MD5: cb4a3906766681ce9230ef5515e1aa1c
 PatchFile: pymol-py.patch
-PatchFile-MD5: 04fd2893af1db8924f6da71cd3afc03e
+PatchFile-MD5: f812def4c13c0542e3830f187ac00523
 PatchFile2: pymol-py-rest.patch
 PatchFile2-MD5: 2df10a5a2d66b16082317a823878bde0
 SourceDirectory: pymol-%v

Index: pymol-py.patch
===
RCS file: /cvsroot/fink/dists/10.4/stable/main/finkinfo/sci/pymol-py.patch,v
retrieving revision 1.6
retrieving revision 1.7
diff -u -d -r1.6 -r1.7
--- pymol-py.patch  12 Apr 2012 20:03:41 -  1.6
+++ pymol-py.patch  6 Oct 2012 17:54:26 -   1.7
@@ -49,13 +49,13 @@
 +#
 +PYMOL_PATH=@FINKPREFIX@/lib/python2.X/site-packages/pymol
 +export PYMOL_PATH
-+#
++HasRadeon=($(system_profiler SPDisplaysDataType | grep Radeon ))
 +# ==
-+# (no changes usually required below here)
-+#
-+# python modules
-+#
-+exec @FINKPREFIX@/bin/python2.X  
@FINKPREFIX@/lib/python2.X/site-packages/pymol/__init__.py -d _ set 
stereo_double_pump_mono,quiet=1 $@
++if [[ -z $HasRadeon  ]];then
++exec @FINKPREFIX@/bin/python2.X  
@FINKPREFIX@/lib/python2.X/site-packages/pymol/__init__.py -d _ set 
stereo_double_pump_mono,quiet=1 $@
++else
++exec @FINKPREFIX@/bin/python2.X  
@FINKPREFIX@/lib/python2.X/site-packages/pymol/__init__.py -d _ set 
stereo_double_pump_mono,quiet=1 -M $@
++fi
 --- pymol-1.5/modules/pmg_tk/startup/apbs_tools.py.orig2012-02-18 
14:50:35.0 -0500
 +++ pymol-1.5/modules/pmg_tk/startup/apbs_tools.py 2012-02-18 
14:51:33.0 -0500
 @@ -141,7 +141,7 @@


--
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what is happening inside your Ruby, Python, PHP, Java, and .NET app
Try New Relic at no cost today and get our sweet Data Nerd shirt too!
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[cvs] dists/10.4/stable/main/finkinfo/sci coot.info,1.37,1.38

[William Scott]

Update of /cvsroot/fink/dists/10.4/stable/main/finkinfo/sci
In directory vz-cvs-3.sog:/tmp/cvs-serv24518

Modified Files:
coot.info 
Log Message:
stable 0.7 release for coot

Index: coot.info
===
RCS file: /cvsroot/fink/dists/10.4/stable/main/finkinfo/sci/coot.info,v
retrieving revision 1.37
retrieving revision 1.38
diff -u -d -r1.37 -r1.38
--- coot.info   20 Aug 2012 02:54:28 -  1.37
+++ coot.info   29 Sep 2012 16:25:47 -  1.38
@@ -1,14 +1,14 @@
 Package: coot
-Version: 0.7-pre-1
-Revision: 4305
-SourceDirectory: %n-%v
+Version: 0.7.0
+Revision: 1
+#SourceDirectory: %n-%v
+SourceDirectory: %n-0.7
 GCC: 4.0 
-#Source: http://lmb.bioch.ox.ac.uk/%n/software/source/releases/%n-0.6.2.tar.gz
+Source: http://lmb.bioch.ox.ac.uk/%n/software/source/releases/%n-0.7.tar.gz
 #Source: 
http://lmb.bioch.ox.ac.uk/%n/software/source/pre-releases/%n-%v-revision-%r.tar.gz
-Source: 
http://lmb.bioch.ox.ac.uk/%n/software/source/pre-releases/%n-%v-revision-4303.tar.gz
-Source-MD5: 2abfb42fe0cc52ae114b44468c6b404d
-Source2: 
http://www.ysbl.york.ac.uk/~garib/refmac/data/refmac_experimental/refmac_dictionary_v5.33.tar.gz
 
-Source2-MD5: 9d71dc2cc3985c77c6d1412dbf31d6fd
+Source-MD5: 29e10cb3b77d882c1d5480983e9b1218
+Source2: 
http://www2.mrc-lmb.cam.ac.uk/groups/murshudov/content/refmac/Dictionary/refmac_dictionary_v5.38.tar.gz
+Source2-MD5: 174a5fc5e5be03cb432c61e8da4283df
 Source3: 
http://www.ysbl.york.ac.uk/~emsley/software/extras/reference-structures.tar.gz
 Source3-MD5: 257ab90d44f1c877ada96720dbb87c13 
 ###
@@ -116,6 +116,7 @@
  libtool2-shlibs  ,
  librsvg2-gtk  (= 2.20.0-1)  ,
  libxml2-shlibs   ,
+ openldap24-shlibs,
  pango1-xft2-ft219-shlibs (= 1.24.5-4) ,
  pygtk2-gtk-py27  ,
  python27 ,
@@ -147,6 +148,8 @@
 alias python=%p/bin/python2.7
 export PYTHON=%p/bin/python2.7
 export python=%p/bin/python2.7
+export PYTHON_LIBS=%p/lib/python2.7/config
+export PYTHON_CFLAGS=%p/include/python2.7
 export GUILE=%p/bin/guile-1.8
 if [[ $(sw_vers -productVersion)  10.6 ]]; then
 export PATH=%p/share/guile/1.8/scripts/binoverride:%p/bin:$PWD/bin:$PATH
@@ -157,9 +160,9 @@
 export GDK_USE_XFT='1'
 export COOT_REFMAC_LIB_DIR=%p/share/coot/lib
 export 
PKG_CONFIG_PATH=%p/lib/glib-2.0/pkgconfig-strict:%p/lib/fontconfig2/lib/pkgconfig:${PKG_CONFIG_PATH}
-  FLIBS=-L%p/lib \
-  CPPFLAGS=-I%p/include/libglade-2.0/glade -I%p/include/libglade-2.0 
-I%p/include/python2.7  -I%p/include/mmdb -I%p/include/ssm 
-I%p/include/gpp4/ccp4 -I%p/include/clipper -I%p/include -I/usr/X11R6/include \
-  
LDFLAGS=-Wl,-dylib_file,%p/lib/python2.7/config/libpython2.7.dylib:%p/lib/libsfftw.2.0.7.dylib:%p/lib/libsrfftw.2.0.7.dylib:%p/lib/pango-ft219/lib/libpango-1.0.dylib:%p/lib/pango-ft219/lib/libpangocairo-1.0.dylib:%p/lib/pango-ft219/lib/libpangoft2-1.0.dylib:%p/lib/pango-ft219/lib/libpangox-1.0.dylib:%p/lib/pango-ft219/lib/libpangoxft-1.0.dylib
 -L%p/lib  -L/usr/lib  -flat_namespace 
-L/System/Library/Frameworks/OpenGL.framework/Versions/A/Libraries \
+  FLIBS=-L%p/lib/python2.7/config -L%p/lib \
+  CPPFLAGS=-I%p/include/python2.7 -I%p/include/libglade-2.0/glade 
-I%p/include/libglade-2.0 -I%p/include/python2.7  -I%p/include/mmdb 
-I%p/include/ssm -I%p/include/gpp4/ccp4 -I%p/include/clipper -I%p/include 
-I/usr/X11R6/include \
+  
LDFLAGS=-Wl,-dylib_file,%p/lib/python2.7/config/libpython2.7.dylib:%p/lib/libsfftw.2.0.7.dylib:%p/lib/libsrfftw.2.0.7.dylib:%p/lib/pango-ft219/lib/libpango-1.0.dylib:%p/lib/pango-ft219/lib/libpangocairo-1.0.dylib:%p/lib/pango-ft219/lib/libpangoft2-1.0.dylib:%p/lib/pango-ft219/lib/libpangox-1.0.dylib:%p/lib/pango-ft219/lib/libpangoxft-1.0.dylib
 -L%p/lib-L%p/lib/python2.7/config -flat_namespace 
-L/System/Library/Frameworks/OpenGL.framework/Versions/A/Libraries \
   DYLD_LIBRARY_PATH= \
   ./configure %c
 #
@@ -168,27 +171,36 @@
 find . -name Makefile -exec perl -pi -e 's|lrfftw |lsrfftw |g' '{}' \;
 find . -name Makefile -exec perl -pi -e 's|lfftw |lsfftw |g' '{}' \;
 perl -pi -e 's|include rfftw.h|include srfftw.h|g'   
surface/CXXFFTSolventMap.h
+
+find . -name Makefile -exec  perl -pi -e 
's|/System/Library/Frameworks/Python.framework/Versions/2.6/lib/python2.6/config|/sw/lib/python2.7/config|g'
  '{}' \;
+find . -name Makefile -exec  perl -pi -e 
's|/System/Library/Frameworks/Python.framework/Versions/2.6/include/python2.6|/sw/include/python2.7|g'
  '{}' \;
+find . -name Makefile -exec  perl -pi -e 's|lpython2.6|lpython2.7|g' '{}' \;
+
 #
 if [[ $(sw_vers -productVersion)  10.5 ]]; then
 # Fix libtool compatibility issues
 sed -e '/verstring=/s/\${wl}//g'  libtool  libtool.fixed
 mv libtool.fixed libtool
 fi
+perl -pi -e 's|lidia_LDFLAGS = -Wl,--export-dynamic||g' lbg/Makefile
 #
-NUMPROC=$(sysctl -n hw.ncpu)
-make -j $NUMPROC
+/bin/rm -f  

[cvs] dists/10.7/stable/main/finkinfo/sci coot.info,1.16,1.17

[William Scott]

Update of /cvsroot/fink/dists/10.7/stable/main/finkinfo/sci
In directory vz-cvs-3.sog:/tmp/cvs-serv8074

Modified Files:
coot.info 
Log Message:
new version of coot, finally

Index: coot.info
===
RCS file: /cvsroot/fink/dists/10.7/stable/main/finkinfo/sci/coot.info,v
retrieving revision 1.16
retrieving revision 1.17
diff -u -d -r1.16 -r1.17
--- coot.info   18 Sep 2012 21:02:33 -  1.16
+++ coot.info   28 Sep 2012 13:51:42 -  1.17
@@ -1,11 +1,12 @@
 Package: coot
-Version: 0.7-pre-1
-Revision: 4424
-SourceDirectory: %n-%v
+Version: 0.7.0
+Revision: 1
+#SourceDirectory: %n-%v
+SourceDirectory: %n-0.7
 GCC: 4.0 
-#Source: http://lmb.bioch.ox.ac.uk/%n/software/source/releases/%n-0.6.2.tar.gz
-Source: 
http://lmb.bioch.ox.ac.uk/%n/software/source/pre-releases/%n-%v-revision-%r.tar.gz
-Source-MD5: 3f72f5a46691d17602122d3af2f10c40
+Source: http://lmb.bioch.ox.ac.uk/%n/software/source/releases/%n-0.7.tar.gz
+#Source: 
http://lmb.bioch.ox.ac.uk/%n/software/source/pre-releases/%n-%v-revision-%r.tar.gz
+Source-MD5: 29e10cb3b77d882c1d5480983e9b1218
 Source2: 
http://www2.mrc-lmb.cam.ac.uk/groups/murshudov/content/refmac/Dictionary/refmac_dictionary_v5.38.tar.gz
 Source2-MD5: 174a5fc5e5be03cb432c61e8da4283df
 Source3: 
http://www.ysbl.york.ac.uk/~emsley/software/extras/reference-structures.tar.gz


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[cvs] dists/10.7/stable/main/finkinfo/sci ccp4.info,1.10,1.11

[William Scott]

Update of /cvsroot/fink/dists/10.7/stable/main/finkinfo/sci
In directory vz-cvs-3.sog:/tmp/cvs-serv15616

Modified Files:
ccp4.info 
Log Message:
fixed another couple of instances of linking the wrong dylib

Index: ccp4.info
===
RCS file: /cvsroot/fink/dists/10.7/stable/main/finkinfo/sci/ccp4.info,v
retrieving revision 1.10
retrieving revision 1.11
diff -u -d -r1.10 -r1.11
--- ccp4.info   18 Sep 2012 18:14:03 -  1.10
+++ ccp4.info   23 Sep 2012 05:19:11 -  1.11
@@ -1,6 +1,6 @@
 Package: ccp4
 Version: 6.3.0
-Revision: 4
+Revision: 5
 GCC: 4.0
 Distribution: 10.6, 10.7, 10.8
 UseMaxBuildJobs: false
@@ -61,30 +61,30 @@
 BuildDependsOnly: False
 BuildConflicts: gpp4-dev, gpp4, ssm, ssm-dev, mmdb, mmdb-dev, clipper, 
clipper-bin, clipper-dev, ccp4-onlylibs-dev, python
 Conflicts: 
-   mosflm (=7.0.5-2), 
-   mosflm-small (=7.0.5-2), 
-   imosflm,
-   imosflm-aqua,
-   refmac (=5.7.0),
+mosflm (=7.0.5-2), 
+mosflm-small (=7.0.5-2), 
+imosflm,
+imosflm-aqua,
+refmac (=5.7.0),
 bundle-ccp4-intel, 
 bundle-ccp4-powerpc, 
 ccp4-gfortran, 
 ccp4-gfortran-dev,
-   phaser (= 2.5.0-1),
-   pointless (= 1.6.18-1)
+phaser (= 2.5.0-1),
+pointless (= 1.6.18-1)
 
 Replaces: 
-   mosflm (=7.0.5-2), 
-   mosflm-small (=7.0.5-2), 
-   imosflm,
-   imosflm-aqua,
-   refmac (=5.7.0),
+mosflm (=7.0.5-2), 
+mosflm-small (=7.0.5-2), 
+imosflm,
+imosflm-aqua,
+refmac (=5.7.0),
 bundle-ccp4-intel, 
 bundle-ccp4-powerpc, 
 ccp4-gfortran, 
 ccp4-gfortran-dev,
-   phaser (= 2.5.0-1),
-   pointless (= 1.6.18-1)
+phaser (= 2.5.0-1),
+pointless (= 1.6.18-1)
 
 NoSetCPPFLAGS: true
 NoSetLDFLAGS: true
@@ -112,6 +112,7 @@
   perl -pi.orig -e 's|import sys|import 
sys\nsys.path.append(\%p/opt/%n-%v/share/python\)|g'  
src/buccaneer_pipeline.py  
   NUMPROC=$(sysctl -n hw.ncpu)
   perl -pi -e s|libtbx.scons|libtbx.scons -j $NUMPROC |g  
lib/cctbx/ccp4_build
+  perl -pi -e 's|enable-mmdb|enable-mmdb --enable-cns|g' configure
 
 

 
#
@@ -269,18 +270,18 @@
   export IMAKEINCLUDE=-I%p/lib/X11/config
 
 # Cleanup is much easier with zsh recursive globbing
-   # several requests made from users to leave
-   # source code in place
-   /bin/rm -f **/*.o
-   /bin/rm -f **/*.bak
-   # remove redundant library junk
+# several requests made from users to leave
+# source code in place
+/bin/rm -f **/*.o
+/bin/rm -f **/*.bak
+# remove redundant library junk
 /bin/rm -Rf src/leiden/bp3lib/src/.libs   
 /bin/rm -Rf src/Prodrg/.libs
-   /bin/rm -f lib/ccif/libccif.dylib
-   /bin/rm -f lib/src/libccp4c.dylib
-   /bin/rm -f lib/src/libmmdb.dylib
-   /bin/rm -R testcomp* 
-   /bin/rm -R BINARY*
+/bin/rm -f lib/ccif/libccif.dylib
+/bin/rm -f lib/src/libccp4c.dylib
+/bin/rm -f lib/src/libmmdb.dylib
+/bin/rm -R testcomp* 
+/bin/rm -R BINARY*
 
 
 # Change environment scripts to match final installation
@@ -306,14 +307,14 @@
   perl -pi.bak -e 
's|/src/fink.build/ccp4-%v-%r/ccp4-%v/lib|/lib/ccp4-%v|g' lib/**/*.la
   #/bin/rm -f lib/python*/site-packages/libxml2mod.la
   /bin/rm -f lib/**/*.la.bak
-   ###
+###
 
-   cd $CCP4
-   #
-   # More cleanup:
-   perl -pi.bak -e 
's|/src/fink.build/ccp4-%v-%r/ccp4-%v/lib|/lib/ccp4-%v|g' lib/**/*.la
-   # Remove duplicate header files
-   /bin/rm -f  include/**/*.h
+cd $CCP4
+#
+# More cleanup:
+perl -pi.bak -e 's|/src/fink.build/ccp4-%v-%r/ccp4-%v/lib|/lib/ccp4-%v|g' 
lib/**/*.la
+# Remove duplicate header files
+/bin/rm -f  include/**/*.h
 
 ##
 #
@@ -327,6 +328,10 @@
 install_name_tool -change   %p/lib/gcc4.7/lib/libstdc++.6.dylib  
/usr/lib/libstdc++.6.dylibbin/bp3 
 install_name_tool -change   %p/lib/gcc4.7/lib/libstdc++.6.dylib  
/usr/lib/libstdc++.6.dylibbin/gcx
 install_name_tool -change   %p/lib/gcc4.7/lib/libstdc++.6.dylib  
/usr/lib/libstdc++.6.dylibbin/mapro
+# Fix linking to wrong library for pointless and aimless
+install_name_tool -change   %p/lib/gcc4.7/lib/libstdc++.6.dylib  
/usr/lib/libstdc++.6.dylibbin/pointless
+install_name_tool -change   %p/lib/gcc4.7/lib/libstdc++.6.dylib  
/usr/lib/libstdc++.6.dylibbin/aimless
+install_name_tool -change   %p/lib/gcc4.7/lib/libstdc++.6.dylib  
/usr/lib/libstdc++.6.dylibbin/othercell
 # Fix for linking problem with rapper
 install_name_tool -change   %p/lib/%n-%v/libgc.1.dylib   
%p/lib/libgc.1.dylib  bin/rapper
 

[cvs] dists/10.4/stable/main/finkinfo/sci ccp4.info,1.19,1.20

[William Scott]

Update of /cvsroot/fink/dists/10.4/stable/main/finkinfo/sci
In directory vz-cvs-3.sog:/tmp/cvs-serv15655

Modified Files:
ccp4.info 
Log Message:
fixed another couple of instances of linking the wrong dylib

Index: ccp4.info
===
RCS file: /cvsroot/fink/dists/10.4/stable/main/finkinfo/sci/ccp4.info,v
retrieving revision 1.19
retrieving revision 1.20
diff -u -d -r1.19 -r1.20
--- ccp4.info   21 Sep 2012 01:08:36 -  1.19
+++ ccp4.info   23 Sep 2012 05:19:36 -  1.20
@@ -1,6 +1,6 @@
 Package: ccp4
 Version: 6.3.0
-Revision: 4
+Revision: 5
 GCC: 4.0
 Distribution: 10.6, 10.7, 10.8
 UseMaxBuildJobs: false
@@ -61,30 +61,30 @@
 BuildDependsOnly: False
 BuildConflicts: gpp4-dev, gpp4, ssm, ssm-dev, mmdb, mmdb-dev, clipper, 
clipper-bin, clipper-dev, ccp4-onlylibs-dev, python
 Conflicts: 
-   mosflm (=7.0.5-2), 
-   mosflm-small (=7.0.5-2), 
-   imosflm,
-   imosflm-aqua,
-   refmac (=5.7.0),
+mosflm (=7.0.5-2), 
+mosflm-small (=7.0.5-2), 
+imosflm,
+imosflm-aqua,
+refmac (=5.7.0),
 bundle-ccp4-intel, 
 bundle-ccp4-powerpc, 
 ccp4-gfortran, 
 ccp4-gfortran-dev,
-   phaser (= 2.5.0-1),
-   pointless (= 1.6.18-1)
+phaser (= 2.5.0-1),
+pointless (= 1.6.18-1)
 
 Replaces: 
-   mosflm (=7.0.5-2), 
-   mosflm-small (=7.0.5-2), 
-   imosflm,
-   imosflm-aqua,
-   refmac (=5.7.0),
+mosflm (=7.0.5-2), 
+mosflm-small (=7.0.5-2), 
+imosflm,
+imosflm-aqua,
+refmac (=5.7.0),
 bundle-ccp4-intel, 
 bundle-ccp4-powerpc, 
 ccp4-gfortran, 
 ccp4-gfortran-dev,
-   phaser (= 2.5.0-1),
-   pointless (= 1.6.18-1)
+phaser (= 2.5.0-1),
+pointless (= 1.6.18-1)
 
 NoSetCPPFLAGS: true
 NoSetLDFLAGS: true
@@ -112,6 +112,7 @@
   perl -pi.orig -e 's|import sys|import 
sys\nsys.path.append(\%p/opt/%n-%v/share/python\)|g'  
src/buccaneer_pipeline.py  
   NUMPROC=$(sysctl -n hw.ncpu)
   perl -pi -e s|libtbx.scons|libtbx.scons -j $NUMPROC |g  
lib/cctbx/ccp4_build
+  perl -pi -e 's|enable-mmdb|enable-mmdb --enable-cns|g' configure
 
 

 
#
@@ -147,7 +148,7 @@
 # Uncomment the following line only for testing purposes.  The ccp4 
restrictive/commercial
 # license forbid disabling the interactive check in this way for the end-user
 #
-#  touch .agree2ccp4v6
+  touch .agree2ccp4v6
 #
 
 F_LIBS=-L%p/lib/gcc4.7/lib -lgfortran  \
@@ -269,18 +270,18 @@
   export IMAKEINCLUDE=-I%p/lib/X11/config
 
 # Cleanup is much easier with zsh recursive globbing
-   # several requests made from users to leave
-   # source code in place
-   /bin/rm -f **/*.o
-   /bin/rm -f **/*.bak
-   # remove redundant library junk
+# several requests made from users to leave
+# source code in place
+/bin/rm -f **/*.o
+/bin/rm -f **/*.bak
+# remove redundant library junk
 /bin/rm -Rf src/leiden/bp3lib/src/.libs   
 /bin/rm -Rf src/Prodrg/.libs
-   /bin/rm -f lib/ccif/libccif.dylib
-   /bin/rm -f lib/src/libccp4c.dylib
-   /bin/rm -f lib/src/libmmdb.dylib
-   /bin/rm -R testcomp* 
-   /bin/rm -R BINARY*
+/bin/rm -f lib/ccif/libccif.dylib
+/bin/rm -f lib/src/libccp4c.dylib
+/bin/rm -f lib/src/libmmdb.dylib
+/bin/rm -R testcomp* 
+/bin/rm -R BINARY*
 
 
 # Change environment scripts to match final installation
@@ -306,14 +307,14 @@
   perl -pi.bak -e 
's|/src/fink.build/ccp4-%v-%r/ccp4-%v/lib|/lib/ccp4-%v|g' lib/**/*.la
   #/bin/rm -f lib/python*/site-packages/libxml2mod.la
   /bin/rm -f lib/**/*.la.bak
-   ###
+###
 
-   cd $CCP4
-   #
-   # More cleanup:
-   perl -pi.bak -e 
's|/src/fink.build/ccp4-%v-%r/ccp4-%v/lib|/lib/ccp4-%v|g' lib/**/*.la
-   # Remove duplicate header files
-   /bin/rm -f  include/**/*.h
+cd $CCP4
+#
+# More cleanup:
+perl -pi.bak -e 's|/src/fink.build/ccp4-%v-%r/ccp4-%v/lib|/lib/ccp4-%v|g' 
lib/**/*.la
+# Remove duplicate header files
+/bin/rm -f  include/**/*.h
 
 ##
 #
@@ -327,6 +328,10 @@
 install_name_tool -change   %p/lib/gcc4.7/lib/libstdc++.6.dylib  
/usr/lib/libstdc++.6.dylibbin/bp3 
 install_name_tool -change   %p/lib/gcc4.7/lib/libstdc++.6.dylib  
/usr/lib/libstdc++.6.dylibbin/gcx
 install_name_tool -change   %p/lib/gcc4.7/lib/libstdc++.6.dylib  
/usr/lib/libstdc++.6.dylibbin/mapro
+# Fix linking to wrong library for pointless and aimless
+install_name_tool -change   %p/lib/gcc4.7/lib/libstdc++.6.dylib  
/usr/lib/libstdc++.6.dylibbin/pointless
+install_name_tool -change   %p/lib/gcc4.7/lib/libstdc++.6.dylib  
/usr/lib/libstdc++.6.dylibbin/aimless
+

[cvs] dists/10.4/stable/main/finkinfo/sci ccp4.info,1.20,1.21

[William Scott]

Update of /cvsroot/fink/dists/10.4/stable/main/finkinfo/sci
In directory vz-cvs-3.sog:/tmp/cvs-serv15705

Modified Files:
ccp4.info 
Log Message:
fixed another couple of instances of linking the wrong dylib

Index: ccp4.info
===
RCS file: /cvsroot/fink/dists/10.4/stable/main/finkinfo/sci/ccp4.info,v
retrieving revision 1.20
retrieving revision 1.21
diff -u -d -r1.20 -r1.21
--- ccp4.info   23 Sep 2012 05:19:36 -  1.20
+++ ccp4.info   23 Sep 2012 05:20:28 -  1.21
@@ -148,7 +148,7 @@
 # Uncomment the following line only for testing purposes.  The ccp4 
restrictive/commercial
 # license forbid disabling the interactive check in this way for the end-user
 #
-  touch .agree2ccp4v6
+#  touch .agree2ccp4v6
 #
 
 F_LIBS=-L%p/lib/gcc4.7/lib -lgfortran  \


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[cvs] dists/10.4/stable/main/finkinfo/sci ccp4.info, 1.18, 1.19 ccp4.patch, 1.5, 1.6

[William Scott]

Update of /cvsroot/fink/dists/10.4/stable/main/finkinfo/sci
In directory vz-cvs-3.sog:/tmp/cvs-serv27691

Modified Files:
ccp4.info ccp4.patch 
Log Message:
sync with 10.7 branch, moves files to /sw/opt to conform to fink policy after 
10 years of doing it wrong

Index: ccp4.info
===
RCS file: /cvsroot/fink/dists/10.4/stable/main/finkinfo/sci/ccp4.info,v
retrieving revision 1.18
retrieving revision 1.19
diff -u -d -r1.18 -r1.19
--- ccp4.info   16 Sep 2012 19:27:13 -  1.18
+++ ccp4.info   21 Sep 2012 01:08:36 -  1.19
@@ -1,6 +1,6 @@
 Package: ccp4
 Version: 6.3.0
-Revision: 2
+Revision: 4
 GCC: 4.0
 Distribution: 10.6, 10.7, 10.8
 UseMaxBuildJobs: false
@@ -15,8 +15,8 @@
 Source3: http://www.chem.ucsc.edu/~wgscott/xtal/xtalfink/XCCPJiffy-custom.gz
 Source3-MD5: 21568dd2475505929573a3fd452c538f
 #  
-PatchFile: ccp4.patch
-PatchFile-MD5: 14418f959400df7232a5c9f1edfa5284
+PatchFile: %n.patch
+PatchFile-MD5: b170eaad8f6926d7be9fee5abe017bd3 
 #
 #
 #
@@ -25,11 +25,11 @@
 Jack Howarth has provided multiple improvements in the patch file to
 address several bugs and to permit optimization with gfortran at -O3.
 
-Users typically install all of the ccp4 files into /xtal/ccp4-%v or
-into /usr/local/xtal/ccp4-%v.  In the present case, these files are
-installed into %p/share/xtal/ccp4-%v.  The library files are installed 
-into the directory %p/lib/ccp4-%v and this directory is symbolically 
-linked to %p/share/xtal/ccp4-%v/lib which is the canonical location.
+Users typically install all of the ccp4 files into /xtal/%n-%v or
+into /usr/local/xtal/%n-%v.  In the present case, these files are
+installed into %p/opt/%n-%v.  The library files are installed 
+into the directory %p/lib/%n-%v and this directory is symbolically 
+linked to %p/opt/%n-%v/lib which is the canonical ccp4 location.
 Dynamic libraries are provided in the ccp4-shlibs splitoff package, and
 static libraries are provided in the ccp4-dev splitoff package. The 
 configure files are patched so that the full path to the dynamic 
@@ -40,11 +40,6 @@
 need to do so manually. The actual files are located (not my choice)
 in $CCP4/include.
 
-The ccp4i mail utility by default will only work on machines that run
-a unix mail server.  As a workaround, a public domain perl script called
-osx_ccp4_mail is installed that glues the ccp4i mail button to the
-Apple OS X Mail.app.
-
 Further adaptations are commented in place in the patch, configure and
 install scripts below. Relevant patches specific to this version that
 are issued by CCP4 are now downloaded and applied individually, helping
@@ -61,23 +56,35 @@
 blas/lapak to avoid run-time errors.   I use that in all versions now, 
 but plan to get rid of this as soon as possible.
 
-Depends:  x11, tcltk, blt, gcc47-shlibs, %N-shlibs (= %v-%r)
+Depends:  x11, tcltk, blt, gcc47-shlibs, gc-shlibs, %N-shlibs (= %v-%r)
 BuildDepends: gcc47, tcltk-dev, x11-dev, xmkmf (= 1.0.2-3), fink (= 0.24.12)
 BuildDependsOnly: False
 BuildConflicts: gpp4-dev, gpp4, ssm, ssm-dev, mmdb, mmdb-dev, clipper, 
clipper-bin, clipper-dev, ccp4-onlylibs-dev, python
-Replaces: phaser (= 2.3.0-1), pointless (= 1.2.18-1), mosflm (= 7.0.3-3), 
mosflm-small (= 7.0.3-3), imosflm (= 1:1.0.4-4), imosflm-aqua (= 1:1.0.4-4), 
refmac (= 5.5.0070-1), bundle-ccp4-intel, clipper-bin, ccp4-gfortran, 
ccp4-gfortran-dev, bundle-ccp4-powerpc
 Conflicts: 
-   mosflm (= 7.0.3-3), 
-   mosflm-small (= 7.0.3-3), 
-   imosflm (= 1:1.0.4-4),
-   imosflm-aqua (= 1:1.0.4-4),
-   refmac (= 5.5.0070-1),
+   mosflm (=7.0.5-2), 
+   mosflm-small (=7.0.5-2), 
+   imosflm,
+   imosflm-aqua,
+   refmac (=5.7.0),
 bundle-ccp4-intel, 
 bundle-ccp4-powerpc, 
 ccp4-gfortran, 
 ccp4-gfortran-dev,
-   phaser (= 2.3.0-1),
-   pointless (= 1.2.18-1)
+   phaser (= 2.5.0-1),
+   pointless (= 1.6.18-1)
+
+Replaces: 
+   mosflm (=7.0.5-2), 
+   mosflm-small (=7.0.5-2), 
+   imosflm,
+   imosflm-aqua,
+   refmac (=5.7.0),
+bundle-ccp4-intel, 
+bundle-ccp4-powerpc, 
+ccp4-gfortran, 
+ccp4-gfortran-dev,
+   phaser (= 2.5.0-1),
+   pointless (= 1.6.18-1)
 
 NoSetCPPFLAGS: true
 NoSetLDFLAGS: true
@@ -93,48 +100,16 @@
   sed 's|@PREFIX@|%p|g' %{PatchFile} | patch -p1
 
 # setup script for tcsh, zsh and bash users
-  export TEMPXTAL=$PWD:h
-#
-  perl -pi.bak -e 's|-traditional-cpp||g' 
src/harvest_app_/pdb_extract/etc/*.platform*
-  perl -pi.bak -e 's|/xtal|\$TEMPXTAL|g' include/ccp4.setup-csh # 
build prefix (changed in install)
-  perl -pi.bak -e 's|/prefix|%p|g' include/ccp4.setup*   # 
location of tcktk, blt
-  perl -pi.bak -e 's|/usr/local/bin|%p/bin|g' include/ccp4.setup*# same
-  perl -pi.bak -e 's|limit 

[cvs] dists/10.7/stable/main/finkinfo/sci ccp4.info, 1.9, 1.10 ccp4.patch, 1.2, 1.3

[William Scott]

Update of /cvsroot/fink/dists/10.7/stable/main/finkinfo/sci
In directory vz-cvs-3.sog:/tmp/cvs-serv22082

Modified Files:
ccp4.info ccp4.patch 
Log Message:
further fixes and cleanup, moved from /sw/share/xtal to /sw/opt for consistency 
with fink packaging policy

Index: ccp4.info
===
RCS file: /cvsroot/fink/dists/10.7/stable/main/finkinfo/sci/ccp4.info,v
retrieving revision 1.9
retrieving revision 1.10
diff -u -d -r1.9 -r1.10
--- ccp4.info   16 Sep 2012 19:16:51 -  1.9
+++ ccp4.info   18 Sep 2012 18:14:03 -  1.10
@@ -1,6 +1,6 @@
 Package: ccp4
 Version: 6.3.0
-Revision: 2
+Revision: 4
 GCC: 4.0
 Distribution: 10.6, 10.7, 10.8
 UseMaxBuildJobs: false
@@ -15,8 +15,8 @@
 Source3: http://www.chem.ucsc.edu/~wgscott/xtal/xtalfink/XCCPJiffy-custom.gz
 Source3-MD5: 21568dd2475505929573a3fd452c538f
 #  
-PatchFile: ccp4.patch
-PatchFile-MD5: 14418f959400df7232a5c9f1edfa5284
+PatchFile: %n.patch
+PatchFile-MD5: b170eaad8f6926d7be9fee5abe017bd3 
 #
 #
 #
@@ -25,11 +25,11 @@
 Jack Howarth has provided multiple improvements in the patch file to
 address several bugs and to permit optimization with gfortran at -O3.
 
-Users typically install all of the ccp4 files into /xtal/ccp4-%v or
-into /usr/local/xtal/ccp4-%v.  In the present case, these files are
-installed into %p/share/xtal/ccp4-%v.  The library files are installed 
-into the directory %p/lib/ccp4-%v and this directory is symbolically 
-linked to %p/share/xtal/ccp4-%v/lib which is the canonical location.
+Users typically install all of the ccp4 files into /xtal/%n-%v or
+into /usr/local/xtal/%n-%v.  In the present case, these files are
+installed into %p/opt/%n-%v.  The library files are installed 
+into the directory %p/lib/%n-%v and this directory is symbolically 
+linked to %p/opt/%n-%v/lib which is the canonical ccp4 location.
 Dynamic libraries are provided in the ccp4-shlibs splitoff package, and
 static libraries are provided in the ccp4-dev splitoff package. The 
 configure files are patched so that the full path to the dynamic 
@@ -40,11 +40,6 @@
 need to do so manually. The actual files are located (not my choice)
 in $CCP4/include.
 
-The ccp4i mail utility by default will only work on machines that run
-a unix mail server.  As a workaround, a public domain perl script called
-osx_ccp4_mail is installed that glues the ccp4i mail button to the
-Apple OS X Mail.app.
-
 Further adaptations are commented in place in the patch, configure and
 install scripts below. Relevant patches specific to this version that
 are issued by CCP4 are now downloaded and applied individually, helping
@@ -61,23 +56,35 @@
 blas/lapak to avoid run-time errors.   I use that in all versions now, 
 but plan to get rid of this as soon as possible.
 
-Depends:  x11, tcltk, blt, gcc47-shlibs, %N-shlibs (= %v-%r)
+Depends:  x11, tcltk, blt, gcc47-shlibs, gc-shlibs, %N-shlibs (= %v-%r)
 BuildDepends: gcc47, tcltk-dev, x11-dev, xmkmf (= 1.0.2-3), fink (= 0.24.12)
 BuildDependsOnly: False
 BuildConflicts: gpp4-dev, gpp4, ssm, ssm-dev, mmdb, mmdb-dev, clipper, 
clipper-bin, clipper-dev, ccp4-onlylibs-dev, python
-Replaces: phaser (= 2.3.0-1), pointless (= 1.2.18-1), mosflm (= 7.0.3-3), 
mosflm-small (= 7.0.3-3), imosflm (= 1:1.0.4-4), imosflm-aqua (= 1:1.0.4-4), 
refmac (= 5.5.0070-1), bundle-ccp4-intel, clipper-bin, ccp4-gfortran, 
ccp4-gfortran-dev, bundle-ccp4-powerpc
 Conflicts: 
-   mosflm (= 7.0.3-3), 
-   mosflm-small (= 7.0.3-3), 
-   imosflm (= 1:1.0.4-4),
-   imosflm-aqua (= 1:1.0.4-4),
-   refmac (= 5.5.0070-1),
+   mosflm (=7.0.5-2), 
+   mosflm-small (=7.0.5-2), 
+   imosflm,
+   imosflm-aqua,
+   refmac (=5.7.0),
 bundle-ccp4-intel, 
 bundle-ccp4-powerpc, 
 ccp4-gfortran, 
 ccp4-gfortran-dev,
-   phaser (= 2.3.0-1),
-   pointless (= 1.2.18-1)
+   phaser (= 2.5.0-1),
+   pointless (= 1.6.18-1)
+
+Replaces: 
+   mosflm (=7.0.5-2), 
+   mosflm-small (=7.0.5-2), 
+   imosflm,
+   imosflm-aqua,
+   refmac (=5.7.0),
+bundle-ccp4-intel, 
+bundle-ccp4-powerpc, 
+ccp4-gfortran, 
+ccp4-gfortran-dev,
+   phaser (= 2.5.0-1),
+   pointless (= 1.6.18-1)
 
 NoSetCPPFLAGS: true
 NoSetLDFLAGS: true
@@ -93,48 +100,16 @@
   sed 's|@PREFIX@|%p|g' %{PatchFile} | patch -p1
 
 # setup script for tcsh, zsh and bash users
-  export TEMPXTAL=$PWD:h
-#
-  perl -pi.bak -e 's|-traditional-cpp||g' 
src/harvest_app_/pdb_extract/etc/*.platform*
-  perl -pi.bak -e 's|/xtal|\$TEMPXTAL|g' include/ccp4.setup-csh # 
build prefix (changed in install)
-  perl -pi.bak -e 's|/prefix|%p|g' include/ccp4.setup*   # 
location of tcktk, blt
-  perl -pi.bak -e 's|/usr/local/bin|%p/bin|g' include/ccp4.setup*# same
-  perl -pi.bak -e 's|limit 

[cvs] dists/10.7/stable/main/finkinfo/sci eden.info,1.1,1.2

[William Scott]

Update of /cvsroot/fink/dists/10.7/stable/main/finkinfo/sci
In directory vz-cvs-3.sog:/tmp/cvs-serv22277

Modified Files:
eden.info 
Log Message:
cleanup and moved supporting ascii text files from /sw/share/xtal/eden to 
/sw/share/eden

Index: eden.info
===
RCS file: /cvsroot/fink/dists/10.7/stable/main/finkinfo/sci/eden.info,v
retrieving revision 1.1
retrieving revision 1.2
diff -u -d -r1.1 -r1.2
--- eden.info   2 Aug 2011 03:54:51 -   1.1
+++ eden.info   18 Sep 2012 18:15:44 -  1.2
@@ -1,6 +1,6 @@
 Package: eden
 Version: 5.3
-Revision: 9
+Revision: 10
 Source: http://edencrystallography.googlecode.com/files/%n-%v.tar.gz
 Source-MD5: 17f4908db1944d788bac44e59c8a5cb5 
 SourceDirectory: eden
@@ -43,16 +43,16 @@
  make install
  make clean
 cd ..
-mkdir -p %i/share/xtal/%n
-cp -R * %i/share/xtal/%n/.
+mkdir -p %i/share/%n
+cp -R * %i/share/%n/.
 mkdir -p %i/share/doc/%n
 cp manual/UserManual.pdf %i/share/doc/%n/EdenUserManual.pdf
 rm -f %i/bin/eden
 rm -f %i/bin/ieden
-ln -s %p/share/xtal/%n/python/%n.py %i/bin/ieden
+ln -s %p/share/%n/python/%n.py %i/bin/ieden
 cp %i/bin/seden %i/bin/eden
 
-RunTimeVars: EDENHOME: %p/share/xtal/%n
+RunTimeVars: EDENHOME: %p/share/%n
 Description: Electron density holographic refinement
 DescDetail: 
 Improve electron density maps in a maximally unbiased manner.


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[cvs] dists/10.7/stable/main/finkinfo/sci coot.info,1.15,1.16

[William Scott]

Update of /cvsroot/fink/dists/10.7/stable/main/finkinfo/sci
In directory vz-cvs-3.sog:/tmp/cvs-serv25600

Modified Files:
coot.info 
Log Message:
added dependency missing further down chain

Index: coot.info
===
RCS file: /cvsroot/fink/dists/10.7/stable/main/finkinfo/sci/coot.info,v
retrieving revision 1.15
retrieving revision 1.16
diff -u -d -r1.15 -r1.16
--- coot.info   13 Sep 2012 03:03:09 -  1.15
+++ coot.info   18 Sep 2012 21:02:33 -  1.16
@@ -1,11 +1,11 @@
 Package: coot
 Version: 0.7-pre-1
-Revision: 4408
+Revision: 4424
 SourceDirectory: %n-%v
 GCC: 4.0 
 #Source: http://lmb.bioch.ox.ac.uk/%n/software/source/releases/%n-0.6.2.tar.gz
 Source: 
http://lmb.bioch.ox.ac.uk/%n/software/source/pre-releases/%n-%v-revision-%r.tar.gz
-Source-MD5: 364c215360159a2a5e3e12de583e5fba
+Source-MD5: 3f72f5a46691d17602122d3af2f10c40
 Source2: 
http://www2.mrc-lmb.cam.ac.uk/groups/murshudov/content/refmac/Dictionary/refmac_dictionary_v5.38.tar.gz
 Source2-MD5: 174a5fc5e5be03cb432c61e8da4283df
 Source3: 
http://www.ysbl.york.ac.uk/~emsley/software/extras/reference-structures.tar.gz
@@ -115,6 +115,7 @@
  libtool2-shlibs  ,
  librsvg2-gtk  (= 2.20.0-1)  ,
  libxml2-shlibs   ,
+ openldap24-shlibs,
  pango1-xft2-ft219-shlibs (= 1.24.5-4) ,
  pygtk2-gtk-py27  ,
  python27 ,


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[cvs] dists/10.4/stable/main/finkinfo/sci phaser-mpi.info,NONE,1.1

[William Scott]

Update of /cvsroot/fink/dists/10.4/stable/main/finkinfo/sci
In directory vz-cvs-3.sog:/tmp/cvs-serv29802

Added Files:
phaser-mpi.info 
Log Message:
standalone version of phaser capable of using mp

--- NEW FILE: phaser-mpi.info ---
Package: phaser-mpi
Version: 2.5.1
Revision: 1
Distribution: 10.6, 10.7, 10.8
Source: ftp://ftp.ccp4.ac.uk/ccp4/6.3.0/ccp4-6.3.0-phaser-cctbx-src.tar.gz
Source-MD5: 018765c258b70726b281de506e9139c4  
SourceDirectory: ccp4-6.3.0
NoSetCPPFLAGS: true
NoSetLDFLAGS: true
Depends: gcc47-shlibs
BuildDepends: gcc47-compiler
BuildDependsOnly: false
PatchScript:  perl -pi.orig -e s|cxx \= cc.replace\('gcc', 'g\+\+'\)|cxx \= 
cc.replace\('gcc', '%p/bin/g\+\+-4'\)|g 
lib/cctbx/cctbx_sources/cctbx_project/libtbx/SConscript
CompileScript:  
#!/bin/bash -efv
CCP4=
export CXXFLAGS=-L%p/lib/gcc4.7/lib
export CFLAGS=-I%p/lib/gcc4.7/include
export CPPFLAGS=$CFLAGS
NUMPROC=$(sysctl -n hw.ncpu)
cd src/phaser
mv bin bin.orig

/usr/bin/python \
../../lib/cctbx/cctbx_sources/cctbx_project/libtbx/configure.py 
--repository=source phaser --build-boost-python-extensions=False 
--enable-openmp-if-possible=True --static-exe --use-environment-flags 
--compiler=gcc  

source setpaths.sh  

libtbx.scons -j $NUMPROC .


InstallScript: 
#!/bin/bash -efv
 mkdir -p %i/bin
 cd src/phaser
 install_name_tool -change /usr/lib/libstdc++.6.dylib   
%p/lib/gcc4.7/lib/libstdc++.6.dylib   exe/phaser
 cp exe/phaser  %i/bin/phaser_omp

Description: CCP4 automated molecular replacement program
DescDetail: 
Stand-alone version of the cctbx/ccp4 affiliated automatic
molecular replacement program, built with OpenMP enabled.  To use
with multiple processors, invoke with  phaser_omp  
and use the keyword JOBS  N, where N is the number of processors
to be used (up to the vaule returned with the command sysctl -n hw.ncpu.
If you use this software please cite:
Phaser Crystallographic Software A.J. McCoy, R.W. Grosse-Kunstleve, 
P.D. Adams, M.D. Winn, L.C. Storoni  R.J. Read
J. Appl. Cryst. (2007). 40, 658-674

License: Restrictive 
Homepage: http://www.phaser.cimr.cam.ac.uk
Maintainer: W. G. Scott wgsc...@users.sourceforge.net


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[cvs] dists/10.7/stable/main/finkinfo/sci phaser-mpi.info,NONE,1.1

[William Scott]

Update of /cvsroot/fink/dists/10.7/stable/main/finkinfo/sci
In directory vz-cvs-3.sog:/tmp/cvs-serv29845

Added Files:
phaser-mpi.info 
Log Message:
standalone version of phaser capable of using mp

--- NEW FILE: phaser-mpi.info ---
Package: phaser-mpi
Version: 2.5.1
Revision: 1
Distribution: 10.6, 10.7, 10.8
Source: ftp://ftp.ccp4.ac.uk/ccp4/6.3.0/ccp4-6.3.0-phaser-cctbx-src.tar.gz
Source-MD5: 018765c258b70726b281de506e9139c4  
SourceDirectory: ccp4-6.3.0
NoSetCPPFLAGS: true
NoSetLDFLAGS: true
Depends: gcc47-shlibs
BuildDepends: gcc47-compiler
BuildDependsOnly: false
PatchScript:  perl -pi.orig -e s|cxx \= cc.replace\('gcc', 'g\+\+'\)|cxx \= 
cc.replace\('gcc', '%p/bin/g\+\+-4'\)|g 
lib/cctbx/cctbx_sources/cctbx_project/libtbx/SConscript
CompileScript:  
#!/bin/bash -efv
CCP4=
export CXXFLAGS=-L%p/lib/gcc4.7/lib
export CFLAGS=-I%p/lib/gcc4.7/include
export CPPFLAGS=$CFLAGS
NUMPROC=$(sysctl -n hw.ncpu)
cd src/phaser
mv bin bin.orig

/usr/bin/python \
../../lib/cctbx/cctbx_sources/cctbx_project/libtbx/configure.py 
--repository=source phaser --build-boost-python-extensions=False 
--enable-openmp-if-possible=True --static-exe --use-environment-flags 
--compiler=gcc  

source setpaths.sh  

libtbx.scons -j $NUMPROC .


InstallScript: 
#!/bin/bash -efv
 mkdir -p %i/bin
 cd src/phaser
 install_name_tool -change /usr/lib/libstdc++.6.dylib   
%p/lib/gcc4.7/lib/libstdc++.6.dylib   exe/phaser
 cp exe/phaser  %i/bin/phaser_omp

Description: CCP4 automated molecular replacement program
DescDetail: 
Stand-alone version of the cctbx/ccp4 affiliated automatic
molecular replacement program, built with OpenMP enabled.  To use
with multiple processors, invoke with  phaser_omp  
and use the keyword JOBS  N, where N is the number of processors
to be used (up to the vaule returned with the command sysctl -n hw.ncpu.
If you use this software please cite:
Phaser Crystallographic Software A.J. McCoy, R.W. Grosse-Kunstleve, 
P.D. Adams, M.D. Winn, L.C. Storoni  R.J. Read
J. Appl. Cryst. (2007). 40, 658-674

License: Restrictive 
Homepage: http://www.phaser.cimr.cam.ac.uk
Maintainer: W. G. Scott wgsc...@users.sourceforge.net


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[cvs] dists/10.7/stable/main/finkinfo/sci ccp4.info,1.8,1.9

[William Scott]

Update of /cvsroot/fink/dists/10.7/stable/main/finkinfo/sci
In directory vz-cvs-3.sog:/tmp/cvs-serv1031

Modified Files:
ccp4.info 
Log Message:
fix for bp3 seg fault and correct ENV var for BALBES_ROOT

Index: ccp4.info
===
RCS file: /cvsroot/fink/dists/10.7/stable/main/finkinfo/sci/ccp4.info,v
retrieving revision 1.8
retrieving revision 1.9
diff -u -d -r1.8 -r1.9
--- ccp4.info   12 Sep 2012 06:31:56 -  1.8
+++ ccp4.info   16 Sep 2012 19:16:51 -  1.9
@@ -1,7 +1,8 @@
 Package: ccp4
 Version: 6.3.0
-Revision: 1
+Revision: 2
 GCC: 4.0
+Distribution: 10.6, 10.7, 10.8
 UseMaxBuildJobs: false
 #
 Source: ftp://ftp.%n.ac.uk/%n/%v/%n-%v-core-src.tar.gz
@@ -103,9 +104,10 @@
   perl -pi.bak -e 's|ccp4_first_in_path\ =\ 1|ccp4_first_in_path\ =\ 0|g'  
include/ccp4.setup*
   perl -pi.bak -e 's|setenv GFORTRAN_UNBUFFERED_ALL Y|# setenv 
GFORTRAN_UNBUFFERED_ALL Y|g'   include/ccp4.setup*
   perl -pi.bak -e 's|export GFORTRAN_UNBUFFERED_ALL|# export 
GFORTRAN_UNBUFFERED_ALL|g'   include/ccp4.setup*
-  perl -pi -e 's|Please get the person who installed CCP4i to run 
it|Please issue the command \\\sudo -E ccp4i\\\|g' share/ccp4i/src/system.tcl
-  perl -pi -e 's|CCP4/ccp4i|CCP4/share/ccp4i|g' include/ccp4.setup*
-  perl -pi -e 's|\{CCP4\}/ccp4i|\{CCP4\}/share/ccp4i|g' include/ccp4.setup*
+  perl -pi.bak -e 's|share/balbes/BALBES_0.0.1|share/BALBES/Package|g' 
include/ccp4.setup*
+  perl -pi.bak -e 's|Please get the person who installed CCP4i to run 
it|Please issue the command \\\sudo -E ccp4i\\\|g' share/ccp4i/src/system.tcl
+  perl -pi.bak -e 's|CCP4/ccp4i|CCP4/share/ccp4i|g' include/ccp4.setup*
+  perl -pi.bak -e 's|\{CCP4\}/ccp4i|\{CCP4\}/share/ccp4i|g' 
include/ccp4.setup*
   if [[ $(sw_vers -productVersion)  10.6 ]]; then
   true
   else
@@ -216,7 +218,7 @@
  Try rapper fix here
 
 cd $CCP4/src/rapper
-./configure --prefix=$PWD CC=/usr/bin/clang CXX=/usr/bin/clang++ CFLAGS=-O3 
+./configure --prefix=$PWD CC=%p/bin/gcc-4 CXX=%p/bin/g++-4 
 
 #
 #
@@ -357,7 +359,12 @@
 
 # Fix for relative path in the install_name of libboost_python.dylib
 install_name_tool -id 
%p/lib/%n-%v/cctbx/cctbx_build/lib/libboost_python.dylib   
lib/cctbx/cctbx_build/lib/libboost_python.dylib
-
+#
+# Fix linking to wrong library for afro and bp3
+install_name_tool -change %p/lib/gcc4.7/lib/libstdc++.6.dylib 
/usr/lib/libstdc++.6.dylib bin/afro
+install_name_tool -change %p/lib/gcc4.7/lib/libstdc++.6.dylib 
/usr/lib/libstdc++.6.dylib bin/bp3 
+install_name_tool -change %p/lib/gcc4.7/lib/libstdc++.6.dylib 
/usr/lib/libstdc++.6.dylib bin/gcx
+install_name_tool -change %p/lib/gcc4.7/lib/libstdc++.6.dylib 
/usr/lib/libstdc++.6.dylib bin/mapro
 #
   cd %b
   mkdir -p %i/lib


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[cvs] dists/10.4/stable/main/finkinfo/sci ccp4.info, 1.17, 1.18 ccp4.patch, 1.4, 1.5

[William Scott]

Update of /cvsroot/fink/dists/10.4/stable/main/finkinfo/sci
In directory vz-cvs-3.sog:/tmp/cvs-serv1584

Modified Files:
ccp4.info ccp4.patch 
Log Message:
new version compatible with 10.6 to 10.8  and gcc47

Index: ccp4.info
===
RCS file: /cvsroot/fink/dists/10.4/stable/main/finkinfo/sci/ccp4.info,v
retrieving revision 1.17
retrieving revision 1.18
diff -u -d -r1.17 -r1.18
--- ccp4.info   1 Oct 2011 03:43:55 -   1.17
+++ ccp4.info   16 Sep 2012 19:27:13 -  1.18
@@ -1,25 +1,24 @@
 Package: ccp4
-Version: 6.2.0
-Revision: 102
+Version: 6.3.0
+Revision: 2
 GCC: 4.0
+Distribution: 10.6, 10.7, 10.8
 UseMaxBuildJobs: false
 #
 Source: ftp://ftp.%n.ac.uk/%n/%v/%n-%v-core-src.tar.gz
-Source-MD5: 1a087d3310d70501ac370804a11f341d
+Source-MD5: 5558ed62767ca0b8fbd31742b130eb61
 SourceDirectory: %n-%v
 #
-Source2: http://www.chem.ucsc.edu/~wgscott/xtal/xtalfink/XCCPJiffy-custom.gz
-Source2-MD5: 21568dd2475505929573a3fd452c538f
+Source2: ftp://ftp.%n.ac.uk/%n/%v/%n-%v-phaser-cctbx-src.tar.gz
+Source2-MD5: 018765c258b70726b281de506e9139c4
+#
+Source3: http://www.chem.ucsc.edu/~wgscott/xtal/xtalfink/XCCPJiffy-custom.gz
+Source3-MD5: 21568dd2475505929573a3fd452c538f
 #  
-Source3: ftp://ftp.%n.ac.uk/%n/%v/%n-%v-phaser-cctbx-src.tar.gz
-Source3-MD5: 15ef58deb26eaacc2bacf7f4ae38d391
+PatchFile: ccp4.patch
+PatchFile-MD5: 14418f959400df7232a5c9f1edfa5284
 #
-Source4: ftp://ftp.mrc-lmb.cam.ac.uk/pub/pre/pointless-1.6.1.tar.gz
-Source4-MD5: 6a2cc719e4e5a018e336375aac47288c
-Source4ExtractDir: %n-%v/src/pointless
 #
-PatchFile: ccp4.patch
-PatchFile-MD5: 30a2ecc69f0030fe33cf7c9e76d83878
 #
 DescPort: 
 CCP4 is designed to compile with gfortran on OS X = 10.4 by default. 
@@ -62,8 +61,8 @@
 blas/lapak to avoid run-time errors.   I use that in all versions now, 
 but plan to get rid of this as soon as possible.
 
-Depends:  x11, tcltk, blt, gcc46-shlibs, %N-shlibs (= %v-%r)
-BuildDepends: gcc46, tcltk-dev, x11-dev, xmkmf (= 1.0.2-3), fink (= 0.24.12)
+Depends:  x11, tcltk, blt, gcc47-shlibs, %N-shlibs (= %v-%r)
+BuildDepends: gcc47, tcltk-dev, x11-dev, xmkmf (= 1.0.2-3), fink (= 0.24.12)
 BuildDependsOnly: False
 BuildConflicts: gpp4-dev, gpp4, ssm, ssm-dev, mmdb, mmdb-dev, clipper, 
clipper-bin, clipper-dev, ccp4-onlylibs-dev, python
 Replaces: phaser (= 2.3.0-1), pointless (= 1.2.18-1), mosflm (= 7.0.3-3), 
mosflm-small (= 7.0.3-3), imosflm (= 1:1.0.4-4), imosflm-aqua (= 1:1.0.4-4), 
refmac (= 5.5.0070-1), bundle-ccp4-intel, clipper-bin, ccp4-gfortran, 
ccp4-gfortran-dev, bundle-ccp4-powerpc
@@ -84,6 +83,7 @@
 NoSetLDFLAGS: true
 #
 

+#
 PatchScript: 
 #!/bin/zsh -efv
 #
@@ -104,7 +104,10 @@
   perl -pi.bak -e 's|ccp4_first_in_path\ =\ 1|ccp4_first_in_path\ =\ 0|g'  
include/ccp4.setup*
   perl -pi.bak -e 's|setenv GFORTRAN_UNBUFFERED_ALL Y|# setenv 
GFORTRAN_UNBUFFERED_ALL Y|g'   include/ccp4.setup*
   perl -pi.bak -e 's|export GFORTRAN_UNBUFFERED_ALL|# export 
GFORTRAN_UNBUFFERED_ALL|g'   include/ccp4.setup*
-  perl -pi -e 's|Please get the person who installed CCP4i to run 
it|Please issue the command \\\sudo -E ccp4i\\\|g' ccp4i/src/system.tcl
+  perl -pi.bak -e 's|share/balbes/BALBES_0.0.1|share/BALBES/Package|g' 
include/ccp4.setup*
+  perl -pi.bak -e 's|Please get the person who installed CCP4i to run 
it|Please issue the command \\\sudo -E ccp4i\\\|g' share/ccp4i/src/system.tcl
+  perl -pi.bak -e 's|CCP4/ccp4i|CCP4/share/ccp4i|g' include/ccp4.setup*
+  perl -pi.bak -e 's|\{CCP4\}/ccp4i|\{CCP4\}/share/ccp4i|g' 
include/ccp4.setup*
   if [[ $(sw_vers -productVersion)  10.6 ]]; then
   true
   else
@@ -114,7 +117,7 @@
   fi
 #
   /bin/cp include/ccp4.setup-dist include/ccp4.setup
-  rm -f include/ccp4.setup-sh
+  # rm -f include/ccp4.setup-sh
 #
 # Set up XCCPJiffy wrapper scripts in $CCP4/etc
 # These are small wrapper scripts for xplot84driver and xloggraph 
generated by the patch
@@ -125,8 +128,18 @@
   perl -pi.bak -e 's|import sys|import 
sys\nsys.path.append(\%p/share/xtal/%n-%v/share/python\)|g'  
src/buccaneer_pipeline.py  
 #
   /bin/rm -f  *.bak **/configure*.bak  src/buccaneer_pipeline*.bak 
include/*.bak
+#
+  perl -pi -e 's,\| grep crt1,,g' configure
+#
+  perl -pi -e 's|python 
../cctbx_sources/cctbx_project/libtbx/configure.py|python 
../cctbx_sources/cctbx_project/libtbx/configure.py --compiler=gcc |g' 
lib/cctbx/ccp4_build
+#
+  perl -pi -e 's|phaseropts=\$phaseropts \$1|phaseropts=\$phaseropts 
--compiler=gcc \$1|g' src/phaser/ccp4_build
+#
+  NUMPROC=$(sysctl -n hw.ncpu)
+  perl -pi -e s|libtbx.scons|libtbx.scons -j $NUMPROC |g  
lib/cctbx/ccp4_build
 
 

[cvs] dists/10.7/stable/main/finkinfo/sci ccp4.info, 1.7, 1.8 ccp4.patch, 1.1, 1.2

[William Scott]

Update of /cvsroot/fink/dists/10.7/stable/main/finkinfo/sci
In directory vz-cvs-3.sog:/tmp/cvs-serv25974

Modified Files:
ccp4.info ccp4.patch 
Log Message:
new version compatible with 10.8 and gcc47

Index: ccp4.info
===
RCS file: /cvsroot/fink/dists/10.7/stable/main/finkinfo/sci/ccp4.info,v
retrieving revision 1.7
retrieving revision 1.8
diff -u -d -r1.7 -r1.8
--- ccp4.info   1 Oct 2011 03:43:05 -   1.7
+++ ccp4.info   12 Sep 2012 06:31:56 -  1.8
@@ -1,25 +1,23 @@
 Package: ccp4
-Version: 6.2.0
-Revision: 102
+Version: 6.3.0
+Revision: 1
 GCC: 4.0
 UseMaxBuildJobs: false
 #
 Source: ftp://ftp.%n.ac.uk/%n/%v/%n-%v-core-src.tar.gz
-Source-MD5: 1a087d3310d70501ac370804a11f341d
+Source-MD5: 5558ed62767ca0b8fbd31742b130eb61
 SourceDirectory: %n-%v
 #
-Source2: http://www.chem.ucsc.edu/~wgscott/xtal/xtalfink/XCCPJiffy-custom.gz
-Source2-MD5: 21568dd2475505929573a3fd452c538f
+Source2: ftp://ftp.%n.ac.uk/%n/%v/%n-%v-phaser-cctbx-src.tar.gz
+Source2-MD5: 018765c258b70726b281de506e9139c4
+#
+Source3: http://www.chem.ucsc.edu/~wgscott/xtal/xtalfink/XCCPJiffy-custom.gz
+Source3-MD5: 21568dd2475505929573a3fd452c538f
 #  
-Source3: ftp://ftp.%n.ac.uk/%n/%v/%n-%v-phaser-cctbx-src.tar.gz
-Source3-MD5: 15ef58deb26eaacc2bacf7f4ae38d391
+PatchFile: ccp4.patch
+PatchFile-MD5: 14418f959400df7232a5c9f1edfa5284
 #
-Source4: ftp://ftp.mrc-lmb.cam.ac.uk/pub/pre/pointless-1.6.1.tar.gz
-Source4-MD5: 6a2cc719e4e5a018e336375aac47288c
-Source4ExtractDir: %n-%v/src/pointless
 #
-PatchFile: ccp4.patch
-PatchFile-MD5: 30a2ecc69f0030fe33cf7c9e76d83878
 #
 DescPort: 
 CCP4 is designed to compile with gfortran on OS X = 10.4 by default. 
@@ -62,8 +60,8 @@
 blas/lapak to avoid run-time errors.   I use that in all versions now, 
 but plan to get rid of this as soon as possible.
 
-Depends:  x11, tcltk, blt, gcc46-shlibs, %N-shlibs (= %v-%r)
-BuildDepends: gcc46, tcltk-dev, x11-dev, xmkmf (= 1.0.2-3), fink (= 0.24.12)
+Depends:  x11, tcltk, blt, gcc47-shlibs, %N-shlibs (= %v-%r)
+BuildDepends: gcc47, tcltk-dev, x11-dev, xmkmf (= 1.0.2-3), fink (= 0.24.12)
 BuildDependsOnly: False
 BuildConflicts: gpp4-dev, gpp4, ssm, ssm-dev, mmdb, mmdb-dev, clipper, 
clipper-bin, clipper-dev, ccp4-onlylibs-dev, python
 Replaces: phaser (= 2.3.0-1), pointless (= 1.2.18-1), mosflm (= 7.0.3-3), 
mosflm-small (= 7.0.3-3), imosflm (= 1:1.0.4-4), imosflm-aqua (= 1:1.0.4-4), 
refmac (= 5.5.0070-1), bundle-ccp4-intel, clipper-bin, ccp4-gfortran, 
ccp4-gfortran-dev, bundle-ccp4-powerpc
@@ -84,6 +82,7 @@
 NoSetLDFLAGS: true
 #
 

+#
 PatchScript: 
 #!/bin/zsh -efv
 #
@@ -104,7 +103,9 @@
   perl -pi.bak -e 's|ccp4_first_in_path\ =\ 1|ccp4_first_in_path\ =\ 0|g'  
include/ccp4.setup*
   perl -pi.bak -e 's|setenv GFORTRAN_UNBUFFERED_ALL Y|# setenv 
GFORTRAN_UNBUFFERED_ALL Y|g'   include/ccp4.setup*
   perl -pi.bak -e 's|export GFORTRAN_UNBUFFERED_ALL|# export 
GFORTRAN_UNBUFFERED_ALL|g'   include/ccp4.setup*
-  perl -pi -e 's|Please get the person who installed CCP4i to run 
it|Please issue the command \\\sudo -E ccp4i\\\|g' ccp4i/src/system.tcl
+  perl -pi -e 's|Please get the person who installed CCP4i to run 
it|Please issue the command \\\sudo -E ccp4i\\\|g' share/ccp4i/src/system.tcl
+  perl -pi -e 's|CCP4/ccp4i|CCP4/share/ccp4i|g' include/ccp4.setup*
+  perl -pi -e 's|\{CCP4\}/ccp4i|\{CCP4\}/share/ccp4i|g' include/ccp4.setup*
   if [[ $(sw_vers -productVersion)  10.6 ]]; then
   true
   else
@@ -114,7 +115,7 @@
   fi
 #
   /bin/cp include/ccp4.setup-dist include/ccp4.setup
-  rm -f include/ccp4.setup-sh
+  # rm -f include/ccp4.setup-sh
 #
 # Set up XCCPJiffy wrapper scripts in $CCP4/etc
 # These are small wrapper scripts for xplot84driver and xloggraph 
generated by the patch
@@ -125,8 +126,18 @@
   perl -pi.bak -e 's|import sys|import 
sys\nsys.path.append(\%p/share/xtal/%n-%v/share/python\)|g'  
src/buccaneer_pipeline.py  
 #
   /bin/rm -f  *.bak **/configure*.bak  src/buccaneer_pipeline*.bak 
include/*.bak
+#
+  perl -pi -e 's,\| grep crt1,,g' configure
+#
+  perl -pi -e 's|python 
../cctbx_sources/cctbx_project/libtbx/configure.py|python 
../cctbx_sources/cctbx_project/libtbx/configure.py --compiler=gcc |g' 
lib/cctbx/ccp4_build
+#
+  perl -pi -e 's|phaseropts=\$phaseropts \$1|phaseropts=\$phaseropts 
--compiler=gcc \$1|g' src/phaser/ccp4_build
+#
+  NUMPROC=$(sysctl -n hw.ncpu)
+  perl -pi -e s|libtbx.scons|libtbx.scons -j $NUMPROC |g  
lib/cctbx/ccp4_build
 
 

+#
 CompileScript: 
 #!/bin/bash -efv
 umask 

[cvs] dists/10.7/stable/main/finkinfo/sci coot.info,1.14,1.15

[William Scott]

Update of /cvsroot/fink/dists/10.7/stable/main/finkinfo/sci
In directory vz-cvs-3.sog:/tmp/cvs-serv16064

Modified Files:
coot.info 
Log Message:
coot fix for linking to system python rather than fink python, latest version 
update

Index: coot.info
===
RCS file: /cvsroot/fink/dists/10.7/stable/main/finkinfo/sci/coot.info,v
retrieving revision 1.14
retrieving revision 1.15
diff -u -d -r1.14 -r1.15
--- coot.info   5 Sep 2012 17:19:36 -   1.14
+++ coot.info   13 Sep 2012 03:03:09 -  1.15
@@ -1,12 +1,11 @@
 Package: coot
 Version: 0.7-pre-1
-Revision: 4392
+Revision: 4408
 SourceDirectory: %n-%v
 GCC: 4.0 
 #Source: http://lmb.bioch.ox.ac.uk/%n/software/source/releases/%n-0.6.2.tar.gz
 Source: 
http://lmb.bioch.ox.ac.uk/%n/software/source/pre-releases/%n-%v-revision-%r.tar.gz
-Source-MD5: c66f602abdb93c88bfd8357d9d7bb674
-#Source2: 
http://www.ysbl.york.ac.uk/~garib/refmac/data/refmac_experimental/refmac_dictionary_v5.33.tar.gz
 
+Source-MD5: 364c215360159a2a5e3e12de583e5fba
 Source2: 
http://www2.mrc-lmb.cam.ac.uk/groups/murshudov/content/refmac/Dictionary/refmac_dictionary_v5.38.tar.gz
 Source2-MD5: 174a5fc5e5be03cb432c61e8da4283df
 Source3: 
http://www.ysbl.york.ac.uk/~emsley/software/extras/reference-structures.tar.gz
@@ -174,6 +173,7 @@
 sed -e '/verstring=/s/\${wl}//g'  libtool  libtool.fixed
 mv libtool.fixed libtool
 fi
+perl -pi -e 's|lidia_LDFLAGS = -Wl,--export-dynamic||g' lbg/Makefile
 #
 NUMPROC=$(sysctl -n hw.ncpu)
 make -j $NUMPROC
@@ -188,7 +188,6 @@
 export PATH=$PWD/bin:%p/bin:%p/share/guile/1.8/scripts/binoverride:$PATH
 export SED=/usr/bin/sed
 export COOT_REFMAC_LIB_DIR=%p/share/coot/lib
-#cp src/coot.py python/coot.py
 #
 #NUMPROC=$(sysctl -n hw.ncpu)
 NUMPROC=1
@@ -201,7 +200,16 @@
 mkdir -p %i/share/coot/etc
 mkdir -p %i/share/coot/python
 mkdir -p %i/bin
-# cp src/coot.py %i/share/coot/python/coot.py
+#
+
+if [[ $(sw_vers -productVersion)  10.8 ]]; then
+   true
+else
+# Fix a new bug that appears with 10.8.
+   if [[ -f 
/System/Library/Frameworks/Python.framework/Versions/2.7/Python ]];then
+   install_name_tool -change 
/System/Library/Frameworks/Python.framework/Versions/2.7/Python  
%p/lib/python2.7/config/libpython2.7.dylib %i/bin/coot-real 
+   fi
+fi
 # This installs the refmac monomer library
 mkdir -p %i/share/coot/lib/data
 cp -R ../monomers %i/share/coot/lib/data/monomers
@@ -214,13 +222,10 @@
 # and a few others as follows:
 /bin/rm -f %i/bin/coot
 echo '#!/bin/sh -f '   %i/bin/coot
-echo PATH=/usr/bin:\$PATH%i/bin/coot
 echo export COOT_REFMAC_LIB_DIR=%p/share/coot/lib%i/bin/coot
 echo export COOT_PYTHON_DIR=%p/share/coot/python %i/bin/coot
 echo 'export COOT_SBASE_DIR=$CCP4/share/sbase'   %i/bin/coot
 echo export 
PYTHONPATH=%p/lib/python2.7/site-packages:%p/lib/python2.7/site-packages/gtk-2.0:%p/share/coot/python
%i/bin/coot
-#echo export 
PYTHONPATH=%p/lib/python2.7/site-packages:%p/lib/python2.7/site-packages/gtk-2.0:%p/share/coot/python:\$PYTHONPATH
%i/bin/coot
-#echo export 
PYTHONPATH=/System/Library/Frameworks/Python.framework/Versions/2.6/lib/python2.6:/System/Library/Frameworks/Python.framework/Versions/2.5/lib/python2.5:%p/lib/python2.7/site-packages:%p/lib/python2.7/site-packages/gtk-2.0:%p/share/coot/python:\$PYTHONPATH
%i/bin/coot
 echo %p/bin/coot-real \\$@\ %i/bin/coot
 chmod a+x %i/bin/coot
 # Clean up the rest of the mess.


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[cvs] dists/10.7/stable/main/finkinfo/sci tinker.info,1.1,1.2

[William Scott]

Update of /cvsroot/fink/dists/10.7/stable/main/finkinfo/sci
In directory vz-cvs-3.sog:/tmp/cvs-serv12266

Modified Files:
tinker.info 
Log Message:
tinker update and gcc47 dependency

Index: tinker.info
===
RCS file: /cvsroot/fink/dists/10.7/stable/main/finkinfo/sci/tinker.info,v
retrieving revision 1.1
retrieving revision 1.2
diff -u -d -r1.1 -r1.2
--- tinker.info 2 Aug 2011 00:25:31 -   1.1
+++ tinker.info 11 Sep 2012 23:56:58 -  1.2
@@ -1,12 +1,16 @@
 Package: tinker
-Version: 6.0
+Version: 6.1.01
 Revision: 1
 Source: http://dasher.wustl.edu/%n/downloads/%n-%v.tar.gz
 SourceRename: %n-%v.tar.gz 
 SourceDirectory: %n
-Source-MD5: b8f093e8dae9b5f5c9c8035bdc6a5df2
-BuildDepends: gcc46
-Depends: gcc46-shlibs
+Source-MD5: 202a4b3138a53715d409382ac443e4c0
+BuildDepends: gcc47
+Depends: gcc47-shlibs
+PatchScript: 
+#!/bin/zsh -f
+perl -pi -e 's|gfortran -c -O3|gfortran -c -O3 -fno-align-commons|g' 
macosx/**/*.make
+
 CompileScript:  
 #!/bin/bash -ev
  cd source
@@ -14,13 +18,13 @@
  :
  : This will take a few minutes to compile everything ...
  :
- ../macosx/gfortran/compile.make
- ../macosx/gfortran/library.make
+ ../macosx/gfortran/compile.make 
+ ../macosx/gfortran/library.make 
  ranlib libtinker.a
- ../macosx/gfortran/link.make
- ../macosx/gfortran/linkgui.make
+ ../macosx/gfortran/link.make 
+ ../macosx/gfortran/linkgui.make 
  mkdir -p ../bin
- ../macosx/gfortran/rename.make
+ ../macosx/gfortran/rename.make 
 cd ..
  /bin/rm -rf linux  make  source   unix  macosx  other   windows
 


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[cvs] dists/10.7/stable/main/finkinfo/sci gromacs-mpi-10.7.info, 1.1, 1.2 gromacs.info, 1.1, 1.2

[William Scott]

Update of /cvsroot/fink/dists/10.7/stable/main/finkinfo/sci
In directory vz-cvs-3.sog:/tmp/cvs-serv7785

Modified Files:
gromacs-mpi-10.7.info gromacs.info 
Log Message:
updated for 10.8 and gcc47

Index: gromacs.info
===
RCS file: /cvsroot/fink/dists/10.7/stable/main/finkinfo/sci/gromacs.info,v
retrieving revision 1.1
retrieving revision 1.2
diff -u -d -r1.1 -r1.2
--- gromacs.info1 Aug 2011 02:59:30 -   1.1
+++ gromacs.info9 Sep 2012 11:43:57 -   1.2
@@ -1,15 +1,15 @@
 Package: gromacs
 Version: 4.5.4
-Revision: 1
-Depends: %N-shlibs (= %v-%r), fftw3-shlibs, gcc46-shlibs, gsl-shlibs, 
openmotif4-shlibs, x11
-BuildDepends: fftw3, gcc46-compiler, gsl, openmotif4, x11-dev
+Revision: 2
+Depends: %N-shlibs (= %v-%r), fftw3-shlibs, gcc47-shlibs, gsl-shlibs, 
openmotif4-shlibs, x11
+BuildDepends: fftw3, gcc47-compiler, gsl, openmotif4, x11-dev
 BuildConflicts: gromacs-dev ( %v-%r), gromacs-mpi-dev, gromacs-mpi, 
gromacs-mpi-openmpi-dev, gromacs-mpi-openmpi, gromacs-mpi-lammpi-dev, 
gromacs-mpi-lammpi-dev
 Conflicts: gromacs-mpi-dev, gromacs-mpi, gromacs-mpi-openmpi-dev, 
gromacs-mpi-openmpi, gromacs-mpi-lammpi-dev, gromacs-mpi-lammpi-dev
 Replaces:  gromacs-mpi-dev, gromacs-mpi, gromacs-mpi-openmpi-dev, 
gromacs-mpi-openmpi, gromacs-mpi-lammpi-dev, gromacs-mpi-lammpi-dev
 BuildDependsOnly: false
 UseMaxBuildJobs: True
-SetCC: gcc-fsf-4.6
-SetCXX: g++-fsf-4.6
+SetCC: gcc
+SetCXX: g++
 Source: mirror:custom:%n-%v.tar.gz
 CustomMirror: 
 Primary: ftp://ftp.gromacs.org/pub/gromacs/
@@ -39,7 +39,7 @@
 
 SplitOff: 
 Package: %N-shlibs
-Depends: fftw3-shlibs, gcc46-shlibs, gsl-shlibs, openmotif4-shlibs, x11
+Depends: fftw3-shlibs, gcc47-shlibs, gsl-shlibs, openmotif4-shlibs, x11
 Files: 
 lib/libgmx.6.dylib
 lib/libgmxana.6.0.0.dylib

Index: gromacs-mpi-10.7.info
===
RCS file: 
/cvsroot/fink/dists/10.7/stable/main/finkinfo/sci/gromacs-mpi-10.7.info,v
retrieving revision 1.1
retrieving revision 1.2
diff -u -d -r1.1 -r1.2
--- gromacs-mpi-10.7.info   1 Aug 2011 22:07:48 -   1.1
+++ gromacs-mpi-10.7.info   9 Sep 2012 11:43:57 -   1.2
@@ -1,8 +1,8 @@
 Package: gromacs-mpi
 Version: 4.5.4
-Revision: 1
-Depends: %N-shlibs (= %v-%r), gsl-shlibs, fftw3-shlibs, gcc46-shlibs, 
openmotif4-shlibs, openmpi-shlibs, x11
-BuildDepends: gsl, fftw3, gcc46-compiler, openmpi, x11-dev
+Revision: 2
+Depends: %N-shlibs (= %v-%r), gsl-shlibs, fftw3-shlibs, gcc47-shlibs, 
openmotif4-shlibs, openmpi-shlibs, x11
+BuildDepends: gsl, fftw3, gcc47-compiler, openmpi, x11-dev
 BuildDependsOnly: false
 Distribution: 10.7
 UseMaxBuildJobs: True
@@ -36,7 +36,7 @@
 
 SplitOff: 
 Package: %N-shlibs
-Depends: gsl-shlibs, fftw3-shlibs, gcc46-shlibs, openmotif4-shlibs, 
openmpi-shlibs, x11
+Depends: gsl-shlibs, fftw3-shlibs, gcc47-shlibs, openmotif4-shlibs, 
openmpi-shlibs, x11
 Files: 
lib/libgmx_mpi.6.0.0.dylib
lib/libgmx_mpi.6.dylib


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[cvs] dists/10.7/stable/main/finkinfo/sci coot.info,1.13,1.14

[William Scott]

Update of /cvsroot/fink/dists/10.7/stable/main/finkinfo/sci
In directory vz-cvs-3.sog:/tmp/cvs-serv29877

Modified Files:
coot.info 
Log Message:
fix packaging error and update for 10.8 compatibility

Index: coot.info
===
RCS file: /cvsroot/fink/dists/10.7/stable/main/finkinfo/sci/coot.info,v
retrieving revision 1.13
retrieving revision 1.14
diff -u -d -r1.13 -r1.14
--- coot.info   5 Sep 2012 00:06:53 -   1.13
+++ coot.info   5 Sep 2012 17:19:36 -   1.14
@@ -1,13 +1,14 @@
 Package: coot
 Version: 0.7-pre-1
-Revision: 4386
+Revision: 4392
 SourceDirectory: %n-%v
 GCC: 4.0 
 #Source: http://lmb.bioch.ox.ac.uk/%n/software/source/releases/%n-0.6.2.tar.gz
 Source: 
http://lmb.bioch.ox.ac.uk/%n/software/source/pre-releases/%n-%v-revision-%r.tar.gz
-Source-MD5: bbb5f5fb265b79b13847f3e23b929b04
-Source2: 
http://www.ysbl.york.ac.uk/~garib/refmac/data/refmac_experimental/refmac_dictionary_v5.33.tar.gz
 
-Source2-MD5: 9d71dc2cc3985c77c6d1412dbf31d6fd
+Source-MD5: c66f602abdb93c88bfd8357d9d7bb674
+#Source2: 
http://www.ysbl.york.ac.uk/~garib/refmac/data/refmac_experimental/refmac_dictionary_v5.33.tar.gz
 
+Source2: 
http://www2.mrc-lmb.cam.ac.uk/groups/murshudov/content/refmac/Dictionary/refmac_dictionary_v5.38.tar.gz
+Source2-MD5: 174a5fc5e5be03cb432c61e8da4283df
 Source3: 
http://www.ysbl.york.ac.uk/~emsley/software/extras/reference-structures.tar.gz
 Source3-MD5: 257ab90d44f1c877ada96720dbb87c13 
 ###
@@ -270,6 +271,7 @@
 %p/lib/libcoot-tw.0.dylib   1.0.0 %n (= 0.6-1)
 %p/lib/libcoot-utils.0.dylib1.0.0 %n (= 0.6-1)
 %p/lib/libcootaneer.0.dylib 1.0.0 %n (= 0.6-1)
+%p/lib/libcootilus.0.dylib  1.0.0 %n (= 0.6-1)
 %p/lib/libcootilus.0.dylib  1.0.0 %n (= 
0.7-pre-1-4305)
 
 DocFiles: README AUTHORS NEWS COPYING ABOUT-NLS BUGS TODO


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[cvs] dists/10.7/stable/main/finkinfo/sci coot.info,1.12,1.13

[William Scott]

Update of /cvsroot/fink/dists/10.7/stable/main/finkinfo/sci
In directory vz-cvs-3.sog:/tmp/cvs-serv8030

Modified Files:
coot.info 
Log Message:
fixes and update for 10.8 compatibility

Index: coot.info
===
RCS file: /cvsroot/fink/dists/10.7/stable/main/finkinfo/sci/coot.info,v
retrieving revision 1.12
retrieving revision 1.13
diff -u -d -r1.12 -r1.13
--- coot.info   20 Aug 2012 02:54:27 -  1.12
+++ coot.info   5 Sep 2012 00:06:53 -   1.13
@@ -1,12 +1,11 @@
 Package: coot
 Version: 0.7-pre-1
-Revision: 4305
+Revision: 4386
 SourceDirectory: %n-%v
 GCC: 4.0 
 #Source: http://lmb.bioch.ox.ac.uk/%n/software/source/releases/%n-0.6.2.tar.gz
-#Source: 
http://lmb.bioch.ox.ac.uk/%n/software/source/pre-releases/%n-%v-revision-%r.tar.gz
-Source: 
http://lmb.bioch.ox.ac.uk/%n/software/source/pre-releases/%n-%v-revision-4303.tar.gz
-Source-MD5: 2abfb42fe0cc52ae114b44468c6b404d
+Source: 
http://lmb.bioch.ox.ac.uk/%n/software/source/pre-releases/%n-%v-revision-%r.tar.gz
+Source-MD5: bbb5f5fb265b79b13847f3e23b929b04
 Source2: 
http://www.ysbl.york.ac.uk/~garib/refmac/data/refmac_experimental/refmac_dictionary_v5.33.tar.gz
 
 Source2-MD5: 9d71dc2cc3985c77c6d1412dbf31d6fd
 Source3: 
http://www.ysbl.york.ac.uk/~emsley/software/extras/reference-structures.tar.gz
@@ -181,6 +180,10 @@
 ###
 InstallScript: 
 #!/bin/zsh -efv
+alias python=%p/bin/python2.7
+export PYTHON=%p/bin/python2.7
+export python=%p/bin/python2.7
+export GUILE=%p/bin/guile-1.8
 export PATH=$PWD/bin:%p/bin:%p/share/guile/1.8/scripts/binoverride:$PATH
 export SED=/usr/bin/sed
 export COOT_REFMAC_LIB_DIR=%p/share/coot/lib
@@ -210,10 +213,12 @@
 # and a few others as follows:
 /bin/rm -f %i/bin/coot
 echo '#!/bin/sh -f '   %i/bin/coot
+echo PATH=/usr/bin:\$PATH%i/bin/coot
 echo export COOT_REFMAC_LIB_DIR=%p/share/coot/lib%i/bin/coot
 echo export COOT_PYTHON_DIR=%p/share/coot/python %i/bin/coot
 echo 'export COOT_SBASE_DIR=$CCP4/share/sbase'   %i/bin/coot
-echo export 
PYTHONPATH=%p/lib/python2.7/site-packages:%p/lib/python2.7/site-packages/gtk-2.0:%p/share/coot/python:\$PYTHONPATH
%i/bin/coot
+echo export 
PYTHONPATH=%p/lib/python2.7/site-packages:%p/lib/python2.7/site-packages/gtk-2.0:%p/share/coot/python
%i/bin/coot
+#echo export 
PYTHONPATH=%p/lib/python2.7/site-packages:%p/lib/python2.7/site-packages/gtk-2.0:%p/share/coot/python:\$PYTHONPATH
%i/bin/coot
 #echo export 
PYTHONPATH=/System/Library/Frameworks/Python.framework/Versions/2.6/lib/python2.6:/System/Library/Frameworks/Python.framework/Versions/2.5/lib/python2.5:%p/lib/python2.7/site-packages:%p/lib/python2.7/site-packages/gtk-2.0:%p/share/coot/python:\$PYTHONPATH
%i/bin/coot
 echo %p/bin/coot-real \\$@\ %i/bin/coot
 chmod a+x %i/bin/coot


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[cvs] dists/10.7/stable/main/finkinfo/sci coot.info, 1.10, 1.11 clipper.info, 1.3, 1.4 ssm.info, 1.3, 1.4 mmdb.info, 1.2, 1.3 gpp4.info, 1.3, 1.4

[William Scott]

Update of /cvsroot/fink/dists/10.7/stable/main/finkinfo/sci
In directory vz-cvs-3.sog:/tmp/cvs-serv12205

Modified Files:
coot.info clipper.info ssm.info mmdb.info gpp4.info 
Log Message:
coordinate updates and dependencies on gcc47

Index: gpp4.info
===
RCS file: /cvsroot/fink/dists/10.7/stable/main/finkinfo/sci/gpp4.info,v
retrieving revision 1.3
retrieving revision 1.4
diff -u -d -r1.3 -r1.4
--- gpp4.info   21 Dec 2011 01:47:57 -  1.3
+++ gpp4.info   29 Jul 2012 15:12:24 -  1.4
@@ -1,6 +1,6 @@
 Package: gpp4
 Version: 1.2.0
-Revision: 30
+Revision: 31
 Maintainer: W. G. Scott wgsc...@users.sourceforge.net 
 DescPackaging: 
  Based on package created by Morten Kjeldgaard m...@bioxray.dk with minor
@@ -13,8 +13,8 @@
 Source: http://diablo.ucsc.edu/~wgscott/%n/%n-%v.tar.gz
 Source-MD5: bb443de0b3385847ea9987f1220e56f1
 NoSourceDirectory: false
-Depends: %N-shlibs (= %v-%r), gcc46-shlibs 
-BuildDepends: mmdb-dev (= 1.23.2-30), ssm-dev (= 0.1-30), gcc46, pkgconfig
+Depends: %N-shlibs (= %v-%r), gcc47-shlibs 
+BuildDepends: mmdb-dev (= 1.23.2-30), ssm-dev (= 0.1-30), gcc47, pkgconfig
 BuildConflicts: g77, fort77, g95
 BuildDependsOnly: true
 HomePage: http://www.bioxray.dk/~mok/gpp4
@@ -46,7 +46,7 @@
 
 CompileScript: 
 #!/bin/bash -evf
-LDFLAGS=-L%p/lib/gcc4.6/lib -L%p/lib -L/usr/lib \
+LDFLAGS=-L%p/lib/gcc4.7/lib -L%p/lib -L/usr/lib \
 MMDB_CFLAGS=-I%p/include/mmdb MMDB_LIBS=-L%p/lib  \
 FC=gfortran \
   ./configure --prefix=%p 
@@ -65,6 +65,7 @@
%p/lib/libgpp4.0.dylib 1.0.0 %n (= 1.2.0-1)
 %p/lib/libgpp4f.0.dylib 1.0.0 %n (=1.2.0-1)
   
+   Depends: gcc47-shlibs 
 
 SplitOff2: 
 Package: %N-dev

Index: mmdb.info
===
RCS file: /cvsroot/fink/dists/10.7/stable/main/finkinfo/sci/mmdb.info,v
retrieving revision 1.2
retrieving revision 1.3
diff -u -d -r1.2 -r1.3
--- mmdb.info   21 Dec 2011 01:47:56 -  1.2
+++ mmdb.info   29 Jul 2012 15:12:24 -  1.3
@@ -1,6 +1,6 @@
 Package: mmdb
 Version: 1.23.2
-Revision: 30
+Revision: 31
 Maintainer: W. G. Scott wgsc...@users.sourceforge.net 
 DescPackaging: 
  Based on package created by Morten Kjeldgaard m...@bioxray.dk with minor

Index: clipper.info
===
RCS file: /cvsroot/fink/dists/10.7/stable/main/finkinfo/sci/clipper.info,v
retrieving revision 1.3
retrieving revision 1.4
diff -u -d -r1.3 -r1.4
--- clipper.info21 Dec 2011 01:47:57 -  1.3
+++ clipper.info29 Jul 2012 15:12:24 -  1.4
@@ -1,14 +1,14 @@
 Package: clipper
 Epoch: 1
 Version: 2.1
-Revision: 30
+Revision: 31
 GCC:4.0
 BuildDepends: 
 fftw (= 2.1.5-1010) | fftw-mpi (= 2.1.5-1010), 
-mmdb-dev (= 1.23.2-30), 
-ssm-dev (= 0.1-30), 
-gpp4-dev (= 1.2.0-30), 
-gcc46
+mmdb-dev (= 1.23.2-31), 
+ssm-dev (= 0.1-31), 
+gpp4-dev (= 1.2.0-31), 
+gcc47
 
 Depends: 
 %n-shlibs (= %e:%v-%r)
@@ -52,7 +52,7 @@
mmdb-shlibs (= 1.23.2-1),
ssm-shlibs (= 0.1-26), 
gpp4-shlibs (= 1.2.0-26),
-   gcc46-shlibs 
+   gcc47-shlibs 
   
   Files: 
lib/libclipper-ccp4.2.*dylib

Index: coot.info
===
RCS file: /cvsroot/fink/dists/10.7/stable/main/finkinfo/sci/coot.info,v
retrieving revision 1.10
retrieving revision 1.11
diff -u -d -r1.10 -r1.11
--- coot.info   28 Jul 2012 21:17:19 -  1.10
+++ coot.info   29 Jul 2012 15:12:24 -  1.11
@@ -1,10 +1,11 @@
 Package: coot
 Version: 0.7-pre-1
-Revision: 4303
+Revision: 4304
 SourceDirectory: %n-%v
 GCC: 4.0 
 #Source: http://lmb.bioch.ox.ac.uk/%n/software/source/releases/%n-0.6.2.tar.gz
-Source: 
http://lmb.bioch.ox.ac.uk/%n/software/source/pre-releases/%n-%v-revision-%r.tar.gz
+#Source: 
http://lmb.bioch.ox.ac.uk/%n/software/source/pre-releases/%n-%v-revision-%r.tar.gz
+Source: 
http://lmb.bioch.ox.ac.uk/%n/software/source/pre-releases/%n-%v-revision-4303.tar.gz
 Source-MD5: 2abfb42fe0cc52ae114b44468c6b404d
 Source2: 
http://www.ysbl.york.ac.uk/~garib/refmac/data/refmac_experimental/refmac_dictionary_v5.33.tar.gz
 
 Source2-MD5: 9d71dc2cc3985c77c6d1412dbf31d6fd
@@ -38,10 +39,10 @@
 Recommends:  povray, ccp4, raster3d
 BuildDepends: 
  fink (= 0.24.12)   ,
- clipper-dev (= 1:2.1-26)   ,
- gpp4-dev (= 1.2.0-26)  ,
- mmdb-dev (= 1.23.2-1)  ,
- ssm-dev (= 0.1-26) ,
+ clipper-dev (= 1:2.1-31)   ,
+ gpp4-dev (= 1.2.0-31)  ,
+ mmdb-dev (= 1.23.2-31)  ,
+ ssm-dev (= 0.1-31) ,
  atk1 (= 1.20.0-1)  ,
  cairo (= 1.6-1),
  expat1  ,
@@ -85,15 +86,15 @@
 
 #   
 Depends: 
- clipper-shlibs (= 1:2.1-26) ,
- gpp4-shlibs (= 1.2.0-26),
- mmdb-shlibs (= 1.23.2-1),
- ssm-shlibs (= 0.1-26)   ,
+ clipper-shlibs (= 1:2.1-31) ,
+ gpp4-shlibs (= 

[cvs] dists/10.4/stable/main/finkinfo/sci coot.info, 1.35, 1.36 clipper.info, 1.9, 1.10 ssm.info, 1.6, 1.7 mmdb.info, 1.6, 1.7 gpp4.info, 1.7, 1.8

[William Scott]

Update of /cvsroot/fink/dists/10.4/stable/main/finkinfo/sci
In directory vz-cvs-3.sog:/tmp/cvs-serv15563

Modified Files:
coot.info clipper.info ssm.info mmdb.info gpp4.info 
Log Message:
coordinate updates and dependencies on gcc47

Index: gpp4.info
===
RCS file: /cvsroot/fink/dists/10.4/stable/main/finkinfo/sci/gpp4.info,v
retrieving revision 1.7
retrieving revision 1.8
diff -u -d -r1.7 -r1.8
--- gpp4.info   21 Dec 2011 01:50:08 -  1.7
+++ gpp4.info   29 Jul 2012 15:27:53 -  1.8
@@ -1,6 +1,6 @@
 Package: gpp4
 Version: 1.2.0
-Revision: 30
+Revision: 31
 Maintainer: W. G. Scott wgsc...@users.sourceforge.net 
 DescPackaging: 
  Based on package created by Morten Kjeldgaard m...@bioxray.dk with minor
@@ -13,8 +13,8 @@
 Source: http://diablo.ucsc.edu/~wgscott/%n/%n-%v.tar.gz
 Source-MD5: bb443de0b3385847ea9987f1220e56f1
 NoSourceDirectory: false
-Depends: %N-shlibs (= %v-%r), gcc46-shlibs 
-BuildDepends: mmdb-dev (= 1.23.2-30), ssm-dev (= 0.1-30), gcc46, pkgconfig
+Depends: %N-shlibs (= %v-%r), gcc47-shlibs 
+BuildDepends: mmdb-dev (= 1.23.2-30), ssm-dev (= 0.1-30), gcc47, pkgconfig
 BuildConflicts: g77, fort77, g95
 BuildDependsOnly: true
 HomePage: http://www.bioxray.dk/~mok/gpp4
@@ -46,7 +46,7 @@
 
 CompileScript: 
 #!/bin/bash -evf
-LDFLAGS=-L%p/lib/gcc4.6/lib -L%p/lib -L/usr/lib \
+LDFLAGS=-L%p/lib/gcc4.7/lib -L%p/lib -L/usr/lib \
 MMDB_CFLAGS=-I%p/include/mmdb MMDB_LIBS=-L%p/lib  \
 FC=gfortran \
   ./configure --prefix=%p 
@@ -65,6 +65,7 @@
%p/lib/libgpp4.0.dylib 1.0.0 %n (= 1.2.0-1)
 %p/lib/libgpp4f.0.dylib 1.0.0 %n (=1.2.0-1)
   
+   Depends: gcc47-shlibs 
 
 SplitOff2: 
 Package: %N-dev

Index: mmdb.info
===
RCS file: /cvsroot/fink/dists/10.4/stable/main/finkinfo/sci/mmdb.info,v
retrieving revision 1.6
retrieving revision 1.7
diff -u -d -r1.6 -r1.7
--- mmdb.info   21 Dec 2011 01:50:08 -  1.6
+++ mmdb.info   29 Jul 2012 15:27:53 -  1.7
@@ -1,6 +1,6 @@
 Package: mmdb
 Version: 1.23.2
-Revision: 30
+Revision: 31
 Maintainer: W. G. Scott wgsc...@users.sourceforge.net 
 DescPackaging: 
  Based on package created by Morten Kjeldgaard m...@bioxray.dk with minor

Index: clipper.info
===
RCS file: /cvsroot/fink/dists/10.4/stable/main/finkinfo/sci/clipper.info,v
retrieving revision 1.9
retrieving revision 1.10
diff -u -d -r1.9 -r1.10
--- clipper.info21 Dec 2011 01:50:08 -  1.9
+++ clipper.info29 Jul 2012 15:27:53 -  1.10
@@ -1,14 +1,14 @@
 Package: clipper
 Epoch: 1
 Version: 2.1
-Revision: 30
+Revision: 31
 GCC:4.0
 BuildDepends: 
 fftw (= 2.1.5-1010) | fftw-mpi (= 2.1.5-1010), 
-mmdb-dev (= 1.23.2-30), 
-ssm-dev (= 0.1-30), 
-gpp4-dev (= 1.2.0-30), 
-gcc46
+mmdb-dev (= 1.23.2-31), 
+ssm-dev (= 0.1-31), 
+gpp4-dev (= 1.2.0-31), 
+gcc47
 
 Depends: 
 %n-shlibs (= %e:%v-%r)
@@ -52,7 +52,7 @@
mmdb-shlibs (= 1.23.2-1),
ssm-shlibs (= 0.1-26), 
gpp4-shlibs (= 1.2.0-26),
-   gcc46-shlibs 
+   gcc47-shlibs 
   
   Files: 
lib/libclipper-ccp4.2.*dylib

Index: coot.info
===
RCS file: /cvsroot/fink/dists/10.4/stable/main/finkinfo/sci/coot.info,v
retrieving revision 1.35
retrieving revision 1.36
diff -u -d -r1.35 -r1.36
--- coot.info   28 Jul 2012 21:20:46 -  1.35
+++ coot.info   29 Jul 2012 15:27:53 -  1.36
@@ -1,10 +1,11 @@
 Package: coot
 Version: 0.7-pre-1
-Revision: 4303
+Revision: 4304
 SourceDirectory: %n-%v
 GCC: 4.0 
 #Source: http://lmb.bioch.ox.ac.uk/%n/software/source/releases/%n-0.6.2.tar.gz
-Source: 
http://lmb.bioch.ox.ac.uk/%n/software/source/pre-releases/%n-%v-revision-%r.tar.gz
+#Source: 
http://lmb.bioch.ox.ac.uk/%n/software/source/pre-releases/%n-%v-revision-%r.tar.gz
+Source: 
http://lmb.bioch.ox.ac.uk/%n/software/source/pre-releases/%n-%v-revision-4303.tar.gz
 Source-MD5: 2abfb42fe0cc52ae114b44468c6b404d
 Source2: 
http://www.ysbl.york.ac.uk/~garib/refmac/data/refmac_experimental/refmac_dictionary_v5.33.tar.gz
 
 Source2-MD5: 9d71dc2cc3985c77c6d1412dbf31d6fd
@@ -38,10 +39,10 @@
 Recommends:  povray, ccp4, raster3d
 BuildDepends: 
  fink (= 0.24.12)   ,
- clipper-dev (= 1:2.1-26)   ,
- gpp4-dev (= 1.2.0-26)  ,
- mmdb-dev (= 1.23.2-1)  ,
- ssm-dev (= 0.1-26) ,
+ clipper-dev (= 1:2.1-31)   ,
+ gpp4-dev (= 1.2.0-31)  ,
+ mmdb-dev (= 1.23.2-31)  ,
+ ssm-dev (= 0.1-31) ,
  atk1 (= 1.20.0-1)  ,
  cairo (= 1.6-1),
  expat1  ,
@@ -85,15 +86,15 @@
 
 #   
 Depends: 
- clipper-shlibs (= 1:2.1-26) ,
- gpp4-shlibs (= 1.2.0-26),
- mmdb-shlibs (= 1.23.2-1),
- ssm-shlibs (= 0.1-26)   ,
+ clipper-shlibs (= 1:2.1-31) ,
+ gpp4-shlibs 

[cvs] dists/10.7/stable/main/finkinfo/sci coot.info,1.9,1.10

[William Scott]

Update of /cvsroot/fink/dists/10.7/stable/main/finkinfo/sci
In directory vz-cvs-3.sog:/tmp/cvs-serv19722

Modified Files:
coot.info 
Log Message:
latest revision by request

Index: coot.info
===
RCS file: /cvsroot/fink/dists/10.7/stable/main/finkinfo/sci/coot.info,v
retrieving revision 1.9
retrieving revision 1.10
diff -u -d -r1.9 -r1.10
--- coot.info   1 May 2012 20:00:37 -   1.9
+++ coot.info   28 Jul 2012 21:17:19 -  1.10
@@ -1,11 +1,11 @@
 Package: coot
 Version: 0.7-pre-1
-Revision: 4149
+Revision: 4303
 SourceDirectory: %n-%v
 GCC: 4.0 
 #Source: http://lmb.bioch.ox.ac.uk/%n/software/source/releases/%n-0.6.2.tar.gz
 Source: 
http://lmb.bioch.ox.ac.uk/%n/software/source/pre-releases/%n-%v-revision-%r.tar.gz
-Source-MD5: 6390c6ca0e889feaeb5a6ece810872e5
+Source-MD5: 2abfb42fe0cc52ae114b44468c6b404d
 Source2: 
http://www.ysbl.york.ac.uk/~garib/refmac/data/refmac_experimental/refmac_dictionary_v5.33.tar.gz
 
 Source2-MD5: 9d71dc2cc3985c77c6d1412dbf31d6fd
 Source3: 
http://www.ysbl.york.ac.uk/~emsley/software/extras/reference-structures.tar.gz


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Exclusive live event will cover all the ways today's security and 
threat landscape has changed and how IT managers can respond. Discussions 
will include endpoint security, mobile security and the latest in malware 
threats. http://www.accelacomm.com/jaw/sfrnl04242012/114/50122263/
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[cvs] dists/10.4/stable/main/finkinfo/sci coot.info,1.34,1.35

[William Scott]

Update of /cvsroot/fink/dists/10.4/stable/main/finkinfo/sci
In directory vz-cvs-3.sog:/tmp/cvs-serv19868

Modified Files:
coot.info 
Log Message:
sync with 10.8 branch

Index: coot.info
===
RCS file: /cvsroot/fink/dists/10.4/stable/main/finkinfo/sci/coot.info,v
retrieving revision 1.34
retrieving revision 1.35
diff -u -d -r1.34 -r1.35
--- coot.info   1 May 2012 21:43:21 -   1.34
+++ coot.info   28 Jul 2012 21:20:46 -  1.35
@@ -1,11 +1,11 @@
 Package: coot
 Version: 0.7-pre-1
-Revision: 4149
+Revision: 4303
 SourceDirectory: %n-%v
 GCC: 4.0 
 #Source: http://lmb.bioch.ox.ac.uk/%n/software/source/releases/%n-0.6.2.tar.gz
 Source: 
http://lmb.bioch.ox.ac.uk/%n/software/source/pre-releases/%n-%v-revision-%r.tar.gz
-Source-MD5: 6390c6ca0e889feaeb5a6ece810872e5
+Source-MD5: 2abfb42fe0cc52ae114b44468c6b404d
 Source2: 
http://www.ysbl.york.ac.uk/~garib/refmac/data/refmac_experimental/refmac_dictionary_v5.33.tar.gz
 
 Source2-MD5: 9d71dc2cc3985c77c6d1412dbf31d6fd
 Source3: 
http://www.ysbl.york.ac.uk/~emsley/software/extras/reference-structures.tar.gz


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threat landscape has changed and how IT managers can respond. Discussions 
will include endpoint security, mobile security and the latest in malware 
threats. http://www.accelacomm.com/jaw/sfrnl04242012/114/50122263/
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[cvs] dists/10.7/stable/main/finkinfo/sci coot.info,1.8,1.9

[William Scott]

Update of /cvsroot/fink/dists/10.7/stable/main/finkinfo/sci
In directory vz-cvs-3.sog:/tmp/cvs-serv30381

Modified Files:
coot.info 
Log Message:
fix for OXT function and package errors

Index: coot.info
===
RCS file: /cvsroot/fink/dists/10.7/stable/main/finkinfo/sci/coot.info,v
retrieving revision 1.8
retrieving revision 1.9
diff -u -d -r1.8 -r1.9
--- coot.info   15 Apr 2012 06:15:55 -  1.8
+++ coot.info   1 May 2012 20:00:37 -   1.9
@@ -1,11 +1,11 @@
 Package: coot
 Version: 0.7-pre-1
-Revision: 4122
+Revision: 4149
 SourceDirectory: %n-%v
 GCC: 4.0 
 #Source: http://lmb.bioch.ox.ac.uk/%n/software/source/releases/%n-0.6.2.tar.gz
 Source: 
http://lmb.bioch.ox.ac.uk/%n/software/source/pre-releases/%n-%v-revision-%r.tar.gz
-Source-MD5: 56aaef6bd3b914245e9e746728420a12
+Source-MD5: 6390c6ca0e889feaeb5a6ece810872e5
 Source2: 
http://www.ysbl.york.ac.uk/~garib/refmac/data/refmac_experimental/refmac_dictionary_v5.33.tar.gz
 
 Source2-MD5: 9d71dc2cc3985c77c6d1412dbf31d6fd
 Source3: 
http://www.ysbl.york.ac.uk/~emsley/software/extras/reference-structures.tar.gz
@@ -251,6 +251,8 @@
 %p/lib/libcoot-coords.0.dylib   1.0.0 %n (= 0.6-1)
 %p/lib/libcoot-db-main.0.dylib  1.0.0 %n (= 0.6-1)
 %p/lib/libcoot-geometry.0.dylib 1.0.0 %n (= 0.6-1)
+%p/lib/libcoot-goograph.0.dylib 1.0.0 %n (= 0.6-1)
+%p/lib/libcoot-gtkgraph.0.dylib 1.0.0 %n (= 0.6-1)
 %p/lib/libcoot-high-res.0.dylib 1.0.0 %n (= 0.6-1)
 %p/lib/libcoot-ideal.0.dylib1.0.0 %n (= 0.6-1)
 %p/lib/libcoot-isosurface.0.dylib   1.0.0 %n (= 0.6-1)


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threat landscape has changed and how IT managers can respond. Discussions 
will include endpoint security, mobile security and the latest in malware 
threats. http://www.accelacomm.com/jaw/sfrnl04242012/114/50122263/
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[cvs] dists/10.4/stable/main/finkinfo/sci coot.info,1.33,1.34

[William Scott]

Update of /cvsroot/fink/dists/10.4/stable/main/finkinfo/sci
In directory vz-cvs-3.sog:/tmp/cvs-serv7190

Modified Files:
coot.info 
Log Message:
fixed OTX problem and packaging errors

Index: coot.info
===
RCS file: /cvsroot/fink/dists/10.4/stable/main/finkinfo/sci/coot.info,v
retrieving revision 1.33
retrieving revision 1.34
diff -u -d -r1.33 -r1.34
--- coot.info   15 Apr 2012 06:16:35 -  1.33
+++ coot.info   1 May 2012 21:43:21 -   1.34
@@ -1,11 +1,11 @@
 Package: coot
 Version: 0.7-pre-1
-Revision: 4122
+Revision: 4149
 SourceDirectory: %n-%v
 GCC: 4.0 
 #Source: http://lmb.bioch.ox.ac.uk/%n/software/source/releases/%n-0.6.2.tar.gz
 Source: 
http://lmb.bioch.ox.ac.uk/%n/software/source/pre-releases/%n-%v-revision-%r.tar.gz
-Source-MD5: 56aaef6bd3b914245e9e746728420a12
+Source-MD5: 6390c6ca0e889feaeb5a6ece810872e5
 Source2: 
http://www.ysbl.york.ac.uk/~garib/refmac/data/refmac_experimental/refmac_dictionary_v5.33.tar.gz
 
 Source2-MD5: 9d71dc2cc3985c77c6d1412dbf31d6fd
 Source3: 
http://www.ysbl.york.ac.uk/~emsley/software/extras/reference-structures.tar.gz
@@ -251,6 +251,8 @@
 %p/lib/libcoot-coords.0.dylib   1.0.0 %n (= 0.6-1)
 %p/lib/libcoot-db-main.0.dylib  1.0.0 %n (= 0.6-1)
 %p/lib/libcoot-geometry.0.dylib 1.0.0 %n (= 0.6-1)
+%p/lib/libcoot-goograph.0.dylib 1.0.0 %n (= 0.6-1)
+%p/lib/libcoot-gtkgraph.0.dylib 1.0.0 %n (= 0.6-1)
 %p/lib/libcoot-high-res.0.dylib 1.0.0 %n (= 0.6-1)
 %p/lib/libcoot-ideal.0.dylib1.0.0 %n (= 0.6-1)
 %p/lib/libcoot-isosurface.0.dylib   1.0.0 %n (= 0.6-1)


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will include endpoint security, mobile security and the latest in malware 
threats. http://www.accelacomm.com/jaw/sfrnl04242012/114/50122263/
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[cvs] dists/10.7/stable/main/finkinfo/sci pymol-py.info,1.8,1.9

[William Scott]

Update of /cvsroot/fink/dists/10.7/stable/main/finkinfo/sci
In directory vz-cvs-3.sog:/tmp/cvs-serv30239

Modified Files:
pymol-py.info 
Log Message:
keep this from looking for apbs in macports directory

Index: pymol-py.info
===
RCS file: /cvsroot/fink/dists/10.7/stable/main/finkinfo/sci/pymol-py.info,v
retrieving revision 1.8
retrieving revision 1.9
diff -u -d -r1.8 -r1.9
--- pymol-py.info   12 Apr 2012 20:01:53 -  1.8
+++ pymol-py.info   29 Apr 2012 17:18:37 -  1.9
@@ -1,7 +1,7 @@
 Info2: 
 Package: pymol-py%type_pkg[python]
 Version: 1.5
-Revision: 5
+Revision: 6
 UseMaxBuildJobs: false
 Maintainer: W. G. Scott wgsc...@users.sourceforge.net
 Type: python (2.6 2.7)
@@ -32,6 +32,7 @@
 cd pymol-%v
 perl -pi -e 's|self.dialog.activate|\#self.dialog.activate|g'  
modules/pmg_tk/startup/apbs_tools.py
 perl -pi -e 's/lglew/lGLEW/g' setup.py
+perl -pi -e 's|searchDirs.append\(os.path.join\(/opt, local, bin\)\)||g' 
modules/pmg_tk/startup/apbs_tools.py 
 
 CompileScript: 
 #! /bin/sh -ex


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[cvs] dists/10.4/stable/main/finkinfo/sci pymol-py.info,1.17,1.18

[William Scott]

Update of /cvsroot/fink/dists/10.4/stable/main/finkinfo/sci
In directory vz-cvs-3.sog:/tmp/cvs-serv30276

Modified Files:
pymol-py.info 
Log Message:
keep this from looking for apbs in macports directory

Index: pymol-py.info
===
RCS file: /cvsroot/fink/dists/10.4/stable/main/finkinfo/sci/pymol-py.info,v
retrieving revision 1.17
retrieving revision 1.18
diff -u -d -r1.17 -r1.18
--- pymol-py.info   12 Apr 2012 20:03:41 -  1.17
+++ pymol-py.info   29 Apr 2012 17:19:26 -  1.18
@@ -1,7 +1,7 @@
 Info2: 
 Package: pymol-py%type_pkg[python]
 Version: 1.5
-Revision: 5
+Revision: 6
 UseMaxBuildJobs: false
 Maintainer: W. G. Scott wgsc...@users.sourceforge.net
 Type: python (2.6 2.7)
@@ -32,6 +32,7 @@
 cd pymol-%v
 perl -pi -e 's|self.dialog.activate|\#self.dialog.activate|g'  
modules/pmg_tk/startup/apbs_tools.py
 perl -pi -e 's/lglew/lGLEW/g' setup.py
+perl -pi -e 's|searchDirs.append\(os.path.join\(/opt, local, bin\)\)||g' 
modules/pmg_tk/startup/apbs_tools.py 
 
 CompileScript: 
 #! /bin/sh -ex


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[cvs] dists/10.7/stable/main/finkinfo/utils a2ps.info,NONE,1.1

[William Scott]

Update of /cvsroot/fink/dists/10.7/stable/main/finkinfo/utils
In directory vz-cvs-3.sog:/tmp/cvs-serv32540

Added Files:
a2ps.info 
Log Message:
update version and fix for 10.7

--- NEW FILE: a2ps.info ---
Package: a2ps
Version: 4.14
Revision: 1
Source: http://ftp.gnu.org/gnu/%n/%n-%v.tar.gz
Source-MD5: 781ac3d9b213fa3e1ed0d79f986dc8c7
UpdateConfigGuessInDirs: auxdir
Depends: libpaper1-shlibs, psutils, ghostscript
BuildDepends: libgettext3-dev, gettext-bin, gettext-tools, libpaper1-dev
PatchScript: 
#perl -ni -e 'print unless /^ELCFILES =/' contrib/emacs/Makefile.in
#perl -ni -e 'print unless /extern char \* stpcpy/'   lib/xstrrpl.c   
perl -pi -e 's|extern char \* stpcpy\(\)\;||g' lib/xstrrpl.c

ConfigureParams: --mandir='${prefix}/share/man' 
--infodir='${prefix}/share/info' ac_cv_exeext=''
ConfFiles: 
%p/etc/a2ps.cfg
%p/etc/a2ps-site.cfg

DocFiles: COPYING ChangeLog FAQ NEWS README TODO
InfoDocs: a2ps.info regex.info
#
# Maintainer: Jeremy Higgs f...@higgs-family.net
Maintainer: W. G. Scott wgsc...@users.sourceforge.net
Homepage: http://www.gnu.org/software/a2ps/a2ps.html
License: GPL
Description: Any to PostScript filter
DescDetail: 
a2ps is a utilty that allows the user to do PostScript manipulations. It is 
able to pass on processing to other filters, such as gzip and dvips.
To use this with Preview, put the line
DefaultPrinter: | ps2pdf - | /usr/bin/open -f -a Preview
in ~/.a2ps/a2psrc in your home directory.

DescPackaging: 
ConfigureParams used to place manpages and info documentation in correct 
directories.
Patch to avoid installing compiled emacs packages.

DescPort: 
Libtool and config files copied to auxdir directory.
Package originally created and maintained by Jeremy Higgs 


 


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[cvs] dists/10.7/stable/main/finkinfo/sci coot.info,1.7,1.8

[William Scott]

Update of /cvsroot/fink/dists/10.7/stable/main/finkinfo/sci
In directory vz-cvs-3.sog:/tmp/cvs-serv17871

Modified Files:
coot.info 
Log Message:
coot add ldap dependencies and version bump and eliminate multithread install

Index: coot.info
===
RCS file: /cvsroot/fink/dists/10.7/stable/main/finkinfo/sci/coot.info,v
retrieving revision 1.7
retrieving revision 1.8
diff -u -d -r1.7 -r1.8
--- coot.info   8 Apr 2012 01:22:08 -   1.7
+++ coot.info   15 Apr 2012 06:15:55 -  1.8
@@ -1,11 +1,11 @@
 Package: coot
 Version: 0.7-pre-1
-Revision: 4099
+Revision: 4122
 SourceDirectory: %n-%v
 GCC: 4.0 
 #Source: http://lmb.bioch.ox.ac.uk/%n/software/source/releases/%n-0.6.2.tar.gz
 Source: 
http://lmb.bioch.ox.ac.uk/%n/software/source/pre-releases/%n-%v-revision-%r.tar.gz
-Source-MD5: af4a8138470dade13d8e0c137764fc02
+Source-MD5: 56aaef6bd3b914245e9e746728420a12
 Source2: 
http://www.ysbl.york.ac.uk/~garib/refmac/data/refmac_experimental/refmac_dictionary_v5.33.tar.gz
 
 Source2-MD5: 9d71dc2cc3985c77c6d1412dbf31d6fd
 Source3: 
http://www.ysbl.york.ac.uk/~emsley/software/extras/reference-structures.tar.gz
@@ -73,6 +73,7 @@
  librsvg2-gtk (= 2.20.0-1)  ,
  libtool2,
  libxml2 ,
+ openldap24-dev  ,
  pango1-xft2-ft219-dev (= 1.18.4-1) ,
  pixman (= 0.10.0-1),
  pygtk2-gtk-py27-dev ,
@@ -116,9 +117,10 @@
  libpng3-shlibs   ,
  librsvg2-shlibs (= 2.20.0-1),
  libtiff-shlibs   ,
- libtool2-shlibs ,
+ libtool2-shlibs  ,
  librsvg2-gtk  (= 2.20.0-1)  ,
  libxml2-shlibs   ,
+ openldap24-shlibs,
  pango1-xft2-ft219-shlibs (= 1.18.4-1) ,
  pygtk2-gtk-py27  ,
  python27 ,
@@ -189,7 +191,8 @@
 export COOT_REFMAC_LIB_DIR=%p/share/coot/lib
 #cp src/coot.py python/coot.py
 #
-NUMPROC=$(sysctl -n hw.ncpu)
+#NUMPROC=$(sysctl -n hw.ncpu)
+NUMPROC=1
 make -j $NUMPROC install prefix=%i
 #
 # Clean up the 120 MB  mess, which zsh makes so much fun:


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[cvs] dists/10.7/stable/main/finkinfo/sci pymol-py.info,1.5,1.6

[William Scott]

Update of /cvsroot/fink/dists/10.7/stable/main/finkinfo/sci
In directory vz-cvs-3.sog:/tmp/cvs-serv7791

Modified Files:
pymol-py.info 
Log Message:
fixes for linking GLEW and freetype219 dependency added

Index: pymol-py.info
===
RCS file: /cvsroot/fink/dists/10.7/stable/main/finkinfo/sci/pymol-py.info,v
retrieving revision 1.5
retrieving revision 1.6
diff -u -d -r1.5 -r1.6
--- pymol-py.info   21 Feb 2012 22:10:16 -  1.5
+++ pymol-py.info   12 Apr 2012 17:28:06 -  1.6
@@ -1,7 +1,7 @@
 Info2: 
 Package: pymol-py%type_pkg[python]
 Version: 1.5
-Revision: 3
+Revision: 4
 UseMaxBuildJobs: false
 Maintainer: W. G. Scott wgsc...@users.sourceforge.net
 Type: python (2.6 2.7)
@@ -16,12 +16,12 @@
 Source4: http://diablo.ucsc.edu/~wgscott/pymol/pynmr_0.37f_src.tar.bz2
 Source4-MD5: cb4a3906766681ce9230ef5515e1aa1c
 PatchFile: pymol-py.patch
-PatchFile-MD5: aac17897bdfc7632d3cc565e6ed9fd3f
+PatchFile-MD5: 04fd2893af1db8924f6da71cd3afc03e
 PatchFile2: pymol-py-rest.patch
 PatchFile2-MD5: 2df10a5a2d66b16082317a823878bde0
 SourceDirectory: pymol-%v
-Depends: python%type_pkg[python], libpng15-shlibs, scipy-py%type_pkg[python], 
tcltk, pmw-py%type_pkg[python] (= 1.3.2-1000), freeglut-shlibs, glew-shlibs, 
blt-shlibs, meschach-shlibs
-BuildDepends: libpng15, freeglut, glew, readline5, gdbm3, tcltk-dev, blt, 
x11-dev, swig, meschach, fink (= 0.30.0)
+Depends: freetype219-shlibs, python%type_pkg[python], libpng15-shlibs, 
scipy-py%type_pkg[python], tcltk, pmw-py%type_pkg[python] (= 1.3.2-1000), 
freeglut-shlibs, glew-shlibs, blt-shlibs, meschach-shlibs
+BuildDepends: freetype219, libpng15, freeglut, glew, readline5, gdbm3, 
tcltk-dev, blt, x11-dev, swig, meschach, fink (= 0.30.0)
 Conflicts: pymol, pymol-py22, pymol-py23, pymol-py24, pymol-py25, pymol-py26, 
pymol-py27
 Replaces: pymol, pymol-py22, pymol-py23, pymol-py24, pymol-py25, pymol-py26, 
pymol-py27
 PatchScript: 
@@ -31,6 +31,7 @@
 sed 's|@FINKPREFIX@|%p|g'  %{PatchFile2} | sed 
's|python2.X|python%type_raw[python]|g' | sed 
's|pymol-py2X|pymol-py%type_pkg[python]|g' | patch -p1
 cd pymol-%v
 perl -pi -e 's|self.dialog.activate|\#self.dialog.activate|g'  
modules/pmg_tk/startup/apbs_tools.py
+perl -pi -e 's/lglew/lGLEW/g' setup.py
 
 CompileScript: 
 #! /bin/sh -ex


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[cvs] dists/10.4/stable/main/finkinfo/sci pymol-py.info,1.14,1.15

[William Scott]

Update of /cvsroot/fink/dists/10.4/stable/main/finkinfo/sci
In directory vz-cvs-3.sog:/tmp/cvs-serv7815

Modified Files:
pymol-py.info 
Log Message:
fixes for linking GLEW and freetype219 dependency added

Index: pymol-py.info
===
RCS file: /cvsroot/fink/dists/10.4/stable/main/finkinfo/sci/pymol-py.info,v
retrieving revision 1.14
retrieving revision 1.15
diff -u -d -r1.14 -r1.15
--- pymol-py.info   21 Feb 2012 22:11:06 -  1.14
+++ pymol-py.info   12 Apr 2012 17:28:42 -  1.15
@@ -1,7 +1,7 @@
 Info2: 
 Package: pymol-py%type_pkg[python]
 Version: 1.5
-Revision: 3
+Revision: 4
 UseMaxBuildJobs: false
 Maintainer: W. G. Scott wgsc...@users.sourceforge.net
 Type: python (2.6 2.7)
@@ -16,12 +16,12 @@
 Source4: http://diablo.ucsc.edu/~wgscott/pymol/pynmr_0.37f_src.tar.bz2
 Source4-MD5: cb4a3906766681ce9230ef5515e1aa1c
 PatchFile: pymol-py.patch
-PatchFile-MD5: aac17897bdfc7632d3cc565e6ed9fd3f
+PatchFile-MD5: 04fd2893af1db8924f6da71cd3afc03e
 PatchFile2: pymol-py-rest.patch
 PatchFile2-MD5: 2df10a5a2d66b16082317a823878bde0
 SourceDirectory: pymol-%v
-Depends: python%type_pkg[python], libpng15-shlibs, scipy-py%type_pkg[python], 
tcltk, pmw-py%type_pkg[python] (= 1.3.2-1000), freeglut-shlibs, glew-shlibs, 
blt-shlibs, meschach-shlibs
-BuildDepends: libpng15, freeglut, glew, readline5, gdbm3, tcltk-dev, blt, 
x11-dev, swig, meschach, fink (= 0.30.0)
+Depends: freetype219-shlibs, python%type_pkg[python], libpng15-shlibs, 
scipy-py%type_pkg[python], tcltk, pmw-py%type_pkg[python] (= 1.3.2-1000), 
freeglut-shlibs, glew-shlibs, blt-shlibs, meschach-shlibs
+BuildDepends: freetype219, libpng15, freeglut, glew, readline5, gdbm3, 
tcltk-dev, blt, x11-dev, swig, meschach, fink (= 0.30.0)
 Conflicts: pymol, pymol-py22, pymol-py23, pymol-py24, pymol-py25, pymol-py26, 
pymol-py27
 Replaces: pymol, pymol-py22, pymol-py23, pymol-py24, pymol-py25, pymol-py26, 
pymol-py27
 PatchScript: 
@@ -31,6 +31,7 @@
 sed 's|@FINKPREFIX@|%p|g'  %{PatchFile2} | sed 
's|python2.X|python%type_raw[python]|g' | sed 
's|pymol-py2X|pymol-py%type_pkg[python]|g' | patch -p1
 cd pymol-%v
 perl -pi -e 's|self.dialog.activate|\#self.dialog.activate|g'  
modules/pmg_tk/startup/apbs_tools.py
+perl -pi -e 's/lglew/lGLEW/g' setup.py
 
 CompileScript: 
 #! /bin/sh -ex


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[cvs] dists/10.7/stable/main/finkinfo/sci pymol-py.info, 1.7, 1.8 pymol-py.patch, 1.3, 1.4

[William Scott]

Update of /cvsroot/fink/dists/10.7/stable/main/finkinfo/sci
In directory vz-cvs-3.sog:/tmp/cvs-serv26426

Modified Files:
pymol-py.info pymol-py.patch 
Log Message:
further fixes to patch file requiring version bump

Index: pymol-py.info
===
RCS file: /cvsroot/fink/dists/10.7/stable/main/finkinfo/sci/pymol-py.info,v
retrieving revision 1.7
retrieving revision 1.8
diff -u -d -r1.7 -r1.8
--- pymol-py.info   12 Apr 2012 18:31:28 -  1.7
+++ pymol-py.info   12 Apr 2012 20:01:53 -  1.8
@@ -1,7 +1,7 @@
 Info2: 
 Package: pymol-py%type_pkg[python]
 Version: 1.5
-Revision: 4
+Revision: 5
 UseMaxBuildJobs: false
 Maintainer: W. G. Scott wgsc...@users.sourceforge.net
 Type: python (2.6 2.7)
@@ -16,12 +16,12 @@
 Source4: http://diablo.ucsc.edu/~wgscott/pymol/pynmr_0.37f_src.tar.bz2
 Source4-MD5: cb4a3906766681ce9230ef5515e1aa1c
 PatchFile: pymol-py.patch
-PatchFile-MD5: aac17897bdfc7632d3cc565e6ed9fd3f
+PatchFile-MD5: 04fd2893af1db8924f6da71cd3afc03e
 PatchFile2: pymol-py-rest.patch
 PatchFile2-MD5: 2df10a5a2d66b16082317a823878bde0
 SourceDirectory: pymol-%v
-Depends: freetype219-shlibs, python%type_pkg[python], libpng15-shlibs, 
scipy-py%type_pkg[python], tcltk, pmw-py%type_pkg[python] (= 1.3.2-1000), 
freeglut-shlibs, glew-shlibs, blt-shlibs, meschach-shlibs
-BuildDepends: freetype219, libpng15, freeglut, glew, readline5, gdbm3, 
tcltk-dev, blt, x11-dev, swig, meschach, fink (= 0.30.0)
+Depends: python%type_pkg[python], libpng15-shlibs, scipy-py%type_pkg[python], 
tcltk, pmw-py%type_pkg[python] (= 1.3.2-1000), freeglut-shlibs, glew-shlibs, 
blt-shlibs, meschach-shlibs, freetype219-shlibs
+BuildDepends: libpng15, freeglut, glew, readline5, gdbm3, tcltk-dev, blt, 
x11-dev, swig, meschach, freetype219,  fink (= 0.30.0)
 Conflicts: pymol, pymol-py22, pymol-py23, pymol-py24, pymol-py25, pymol-py26, 
pymol-py27
 Replaces: pymol, pymol-py22, pymol-py23, pymol-py24, pymol-py25, pymol-py26, 
pymol-py27
 PatchScript: 

Index: pymol-py.patch
===
RCS file: /cvsroot/fink/dists/10.7/stable/main/finkinfo/sci/pymol-py.patch,v
retrieving revision 1.3
retrieving revision 1.4
diff -u -d -r1.3 -r1.4
--- pymol-py.patch  21 Feb 2012 22:10:16 -  1.3
+++ pymol-py.patch  12 Apr 2012 20:01:53 -  1.4
@@ -63,7 +63,7 @@
  #
  APBS_BINARY_LOCATION = None
 -APBS_PSIZE_LOCATION = None
-+APBS_PSIZE_LOCATION = '@FINKPREFIX@/share/apbs/tools/manip/'
++APBS_PSIZE_LOCATION = '@FINKPREFIX@/share/apbs/tools/manip'
  APBS_PDB2PQR_LOCATION = None
  TEMPORARY_FILE_DIR = None
  


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[cvs] dists/10.4/stable/main/finkinfo/sci pymol-py.info, 1.16, 1.17 pymol-py.patch, 1.5, 1.6

[William Scott]

Update of /cvsroot/fink/dists/10.4/stable/main/finkinfo/sci
In directory vz-cvs-3.sog:/tmp/cvs-serv27948

Modified Files:
pymol-py.info pymol-py.patch 
Log Message:
further fixes to patch file requiring version bump

Index: pymol-py.info
===
RCS file: /cvsroot/fink/dists/10.4/stable/main/finkinfo/sci/pymol-py.info,v
retrieving revision 1.16
retrieving revision 1.17
diff -u -d -r1.16 -r1.17
--- pymol-py.info   12 Apr 2012 18:31:28 -  1.16
+++ pymol-py.info   12 Apr 2012 20:03:41 -  1.17
@@ -1,7 +1,7 @@
 Info2: 
 Package: pymol-py%type_pkg[python]
 Version: 1.5
-Revision: 4
+Revision: 5
 UseMaxBuildJobs: false
 Maintainer: W. G. Scott wgsc...@users.sourceforge.net
 Type: python (2.6 2.7)
@@ -16,12 +16,12 @@
 Source4: http://diablo.ucsc.edu/~wgscott/pymol/pynmr_0.37f_src.tar.bz2
 Source4-MD5: cb4a3906766681ce9230ef5515e1aa1c
 PatchFile: pymol-py.patch
-PatchFile-MD5: aac17897bdfc7632d3cc565e6ed9fd3f
+PatchFile-MD5: 04fd2893af1db8924f6da71cd3afc03e
 PatchFile2: pymol-py-rest.patch
 PatchFile2-MD5: 2df10a5a2d66b16082317a823878bde0
 SourceDirectory: pymol-%v
-Depends: freetype219-shlibs, python%type_pkg[python], libpng15-shlibs, 
scipy-py%type_pkg[python], tcltk, pmw-py%type_pkg[python] (= 1.3.2-1000), 
freeglut-shlibs, glew-shlibs, blt-shlibs, meschach-shlibs
-BuildDepends: freetype219, libpng15, freeglut, glew, readline5, gdbm3, 
tcltk-dev, blt, x11-dev, swig, meschach, fink (= 0.30.0)
+Depends: python%type_pkg[python], libpng15-shlibs, scipy-py%type_pkg[python], 
tcltk, pmw-py%type_pkg[python] (= 1.3.2-1000), freeglut-shlibs, glew-shlibs, 
blt-shlibs, meschach-shlibs, freetype219-shlibs
+BuildDepends: libpng15, freeglut, glew, readline5, gdbm3, tcltk-dev, blt, 
x11-dev, swig, meschach, freetype219,  fink (= 0.30.0)
 Conflicts: pymol, pymol-py22, pymol-py23, pymol-py24, pymol-py25, pymol-py26, 
pymol-py27
 Replaces: pymol, pymol-py22, pymol-py23, pymol-py24, pymol-py25, pymol-py26, 
pymol-py27
 PatchScript: 

Index: pymol-py.patch
===
RCS file: /cvsroot/fink/dists/10.4/stable/main/finkinfo/sci/pymol-py.patch,v
retrieving revision 1.5
retrieving revision 1.6
diff -u -d -r1.5 -r1.6
--- pymol-py.patch  21 Feb 2012 22:11:06 -  1.5
+++ pymol-py.patch  12 Apr 2012 20:03:41 -  1.6
@@ -63,7 +63,7 @@
  #
  APBS_BINARY_LOCATION = None
 -APBS_PSIZE_LOCATION = None
-+APBS_PSIZE_LOCATION = '@FINKPREFIX@/share/apbs/tools/manip/'
++APBS_PSIZE_LOCATION = '@FINKPREFIX@/share/apbs/tools/manip'
  APBS_PDB2PQR_LOCATION = None
  TEMPORARY_FILE_DIR = None
  


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[cvs] dists/10.7/stable/main/finkinfo/sci coot.info,1.6,1.7

[William Scott]

Update of /cvsroot/fink/dists/10.7/stable/main/finkinfo/sci
In directory vz-cvs-3.sog:/tmp/cvs-serv12012

Modified Files:
coot.info 
Log Message:
coot update to fix LIDIA

Index: coot.info
===
RCS file: /cvsroot/fink/dists/10.7/stable/main/finkinfo/sci/coot.info,v
retrieving revision 1.6
retrieving revision 1.7
diff -u -d -r1.6 -r1.7
--- coot.info   14 Feb 2012 20:18:49 -  1.6
+++ coot.info   8 Apr 2012 01:22:08 -   1.7
@@ -1,11 +1,11 @@
 Package: coot
 Version: 0.7-pre-1
-Revision: 4002
+Revision: 4099
 SourceDirectory: %n-%v
 GCC: 4.0 
 #Source: http://lmb.bioch.ox.ac.uk/%n/software/source/releases/%n-0.6.2.tar.gz
 Source: 
http://lmb.bioch.ox.ac.uk/%n/software/source/pre-releases/%n-%v-revision-%r.tar.gz
-Source-MD5: 5aab6c0b2bb5f03c2f3dc3221fbdb51d 
+Source-MD5: af4a8138470dade13d8e0c137764fc02
 Source2: 
http://www.ysbl.york.ac.uk/~garib/refmac/data/refmac_experimental/refmac_dictionary_v5.33.tar.gz
 
 Source2-MD5: 9d71dc2cc3985c77c6d1412dbf31d6fd
 Source3: 
http://www.ysbl.york.ac.uk/~emsley/software/extras/reference-structures.tar.gz


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[cvs] dists/10.4/stable/main/finkinfo/sci coot.info,1.31,1.32

[William Scott]

Update of /cvsroot/fink/dists/10.4/stable/main/finkinfo/sci
In directory vz-cvs-3.sog:/tmp/cvs-serv12185

Modified Files:
coot.info 
Log Message:
coot update and fix for LIDIA

Index: coot.info
===
RCS file: /cvsroot/fink/dists/10.4/stable/main/finkinfo/sci/coot.info,v
retrieving revision 1.31
retrieving revision 1.32
diff -u -d -r1.31 -r1.32
--- coot.info   14 Feb 2012 21:48:17 -  1.31
+++ coot.info   8 Apr 2012 01:29:11 -   1.32
@@ -1,11 +1,11 @@
 Package: coot
 Version: 0.7-pre-1
-Revision: 4002
+Revision: 4099
 SourceDirectory: %n-%v
 GCC: 4.0 
 #Source: http://lmb.bioch.ox.ac.uk/%n/software/source/releases/%n-0.6.2.tar.gz
 Source: 
http://lmb.bioch.ox.ac.uk/%n/software/source/pre-releases/%n-%v-revision-%r.tar.gz
-Source-MD5: 5aab6c0b2bb5f03c2f3dc3221fbdb51d 
+Source-MD5: af4a8138470dade13d8e0c137764fc02
 Source2: 
http://www.ysbl.york.ac.uk/~garib/refmac/data/refmac_experimental/refmac_dictionary_v5.33.tar.gz
 
 Source2-MD5: 9d71dc2cc3985c77c6d1412dbf31d6fd
 Source3: 
http://www.ysbl.york.ac.uk/~emsley/software/extras/reference-structures.tar.gz


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[cvs] dists/10.7/stable/main/finkinfo/sci rnabob.info,NONE,1.1

[William Scott]

Update of /cvsroot/fink/dists/10.7/stable/main/finkinfo/sci
In directory vz-cvs-3.sog:/tmp/cvs-serv9876

Added Files:
rnabob.info 
Log Message:
version update and compile fix

--- NEW FILE: rnabob.info ---
Package: rnabob
Version: 2.2
Revision: 1
Source: http://selab.janelia.org/software/rnabob/%n-%v.tar.gz
Source-MD5: 6926d8097acbef99df1f55f73d53d68b
SourceDirectory: %n-%v
PatchScript: 
#!/bin/tcsh -ev
cp Makefile Makefile-dist
grep -v HOME Makefile-dist  junk1
echo 'BINDIR=%i/bin'  Makefile
echo 'MANDIR=%i/share/man'  Makefile
cat junk1  Makefile
rm -f junk1
perl -pi -e 's|getline|getline2|g' *.c

CompileScript:  
make

InstallScript: 
mkdir -p %i/bin
mkdir -p %i/share/man/man1
make install

DOCFILES: COPYING GNULICENSE README rnabob.ps
Description: Fast RNA motif/pattern searcher
DescDetail: 
RNABOB is an implementation of D. Gautheret\'s RNAMOT, but with a different
underlying algorithm using a nondeterministic finite state machine with 
node rewriting rules. Useful for finding an RNA motif that fits a hard 
consensus pattern.

License: GPL
Maintainer: W. G. Scott wgsc...@users.sourceforge.net


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[cvs] dists/10.4/stable/main/finkinfo/sci rnabob.info,NONE,1.1

[William Scott]

Update of /cvsroot/fink/dists/10.4/stable/main/finkinfo/sci
In directory vz-cvs-3.sog:/tmp/cvs-serv10074

Added Files:
rnabob.info 
Log Message:
version update and compile fix

--- NEW FILE: rnabob.info ---
Package: rnabob
Version: 2.2
Revision: 1
Source: http://selab.janelia.org/software/rnabob/%n-%v.tar.gz
Source-MD5: 6926d8097acbef99df1f55f73d53d68b
SourceDirectory: %n-%v
PatchScript: 
#!/bin/tcsh -ev
cp Makefile Makefile-dist
grep -v HOME Makefile-dist  junk1
echo 'BINDIR=%i/bin'  Makefile
echo 'MANDIR=%i/share/man'  Makefile
cat junk1  Makefile
rm -f junk1
perl -pi -e 's|getline|getline2|g' *.c

CompileScript:  
make

InstallScript: 
mkdir -p %i/bin
mkdir -p %i/share/man/man1
make install

DOCFILES: COPYING GNULICENSE README rnabob.ps
Description: Fast RNA motif/pattern searcher
DescDetail: 
RNABOB is an implementation of D. Gautheret\'s RNAMOT, but with a different
underlying algorithm using a nondeterministic finite state machine with 
node rewriting rules. Useful for finding an RNA motif that fits a hard 
consensus pattern.

License: GPL
Maintainer: W. G. Scott wgsc...@users.sourceforge.net


--
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The most comprehensive online learning library for Microsoft developers
is just $99.99! Visual Studio, SharePoint, SQL - plus HTML5, CSS3, MVC3,
Metro Style Apps, more. Free future releases when you subscribe now!
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