Update of /cvsroot/fink/dists/10.4/stable/main/finkinfo/sci
In directory vz-cvs-3.sog:/tmp/cvs-serv3980

Modified Files:
        pymol-py.info coot.info 
Added Files:
        pymol-scipy.patch pdb2pqr.info apbs.info apbs.patch 
Log Message:
added UseMaxBuildJobs: false to prevent compile failure and sync with 10.7 
stable tree

Index: pymol-py.info
===================================================================
RCS file: /cvsroot/fink/dists/10.4/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       4 Sep 2011 11:57:57 -0000       1.11
+++ pymol-py.info       2 Oct 2011 14:59:58 -0000       1.12
@@ -1,10 +1,11 @@
 Info2: <<
 Package: pymol-py%type_pkg[python]
 Version: 1.4
-Revision: 7
+Revision: 8
+UseMaxBuildJobs: false
 Maintainer: W. G. Scott <wgsc...@users.sourceforge.net>
-Type: python (2.5 2.6 2.7)
-# r3959
+Type: python (2.6 2.7)
+# 3962.
 #Source: mirror:sourceforge:fink/pymol-%v-src.tar.bz2
 Source: http://diablo.ucsc.edu/~wgscott/pymol/pymol-%v-src.tar.bz2
 Source-MD5: c520de57b1b3ad7fbc891057a4e32c3e
@@ -83,7 +84,7 @@
 DescPackaging: <<
 The tarball used for this version was created in accordance to the BSD
 license of pymol using the following instructions...
-   svn -r3959 co https://pymol.svn.sourceforge.net/svnroot/pymol/trunk/pymol 
pymol-1.4
+   svn -r3962 co https://pymol.svn.sourceforge.net/svnroot/pymol/trunk/pymol 
pymol-1.4
    tar --exclude=.svn -jcvf pymol-1.4-src.tar.bz2 pymol-1.4
 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 

--- NEW FILE: pdb2pqr.info ---
Package: pdb2pqr
Version: 1.7
Revision: 1
UseMaxBuildJobs: false
Source: mirror:sourceforge:%n/%n-%v.tar.gz
Source-MD5: 058622cb2ca6ca12af04d4f11b272951
SourceDirectory: %n-%v
Depends: python27, gcc46-shlibs
BuildDepends: python, python27, gcc46
BuildConflicts: g77, g95, fort77
Description: Converts pdb files to pqr
NoSetCPPFLAGS: true
NoSetLDFLAGS: true
CompileScript: <<
#!/bin/bash -efv
#PATH=%p/bin:%p/sbin:${PATH} ; export PATH
#source %p/bin/init.sh
#
if [[ "%m" != "x86_64" ]]; then
    export CCPFLAGS="-m32"
    export LDFLAGS="-m32"
        perl -pi -e 's|-Wl,-framework -Wl,Python 
-bundle|%p/lib/python2.7/config/libpython2.7.dylib -m32 -bundle|g' ./configure
        perl -pi -e 's|-Wl,-framework -Wl,Python 
-bundle|%p/lib/python2.7/config/libpython2.7.dylib  -m32 -bundle|g' 
./propka/configure
else
        perl -pi -e 's|-Wl,-framework -Wl,Python 
-bundle|%p/lib/python2.7/config/libpython2.7.dylib  -bundle|g' ./configure
        perl -pi -e 's|-Wl,-framework -Wl,Python 
-bundle|%p/lib/python2.7/config/libpython2.7.dylib  -bundle|g' 
./propka/configure
fi
perl -pi -e 's|fort xlf95 lf95 g95|gfortran|g' ./propka/configure
perl -pi -e 's|/usr/bin/python|%p/bin/python2.7|g' ./pdb2pka/pka.py
perl -pi -e 's|/usr/bin/python|%p/bin/python2.7|g' ./src/psize.py
rm -fr contrib
./configure --with-max-atoms="1000000"    --without-url  
--with-python=%p/bin/python2.7 --with-f77=gfortran 
if [[ "%m" != "x86_64" ]]; then
    perl -pi -e 's|-DPACKAGE|-m32 -DPACKAGE|g' Makefile 
pdb2pka/substruct/Makefile tests/Makefile tests/test/Makefile pdb2pka/Makefile 
propka/Makefile tests/adv-test/Makefile
fi
make
rm -f  pdb2pka/pMC_mult.o  pdb2pka/substruct/Algorithms.o  propka/propkac.o  
tests/adv-test/test.o
rm -r  pdb2pka/pMC_mult_wrap.o   propka/propka.o  propka/propkalib.o   
tests/test/test.o
<<
InstallScript: <<
#!/bin/zsh -efv
source %p/bin/init.sh
PATH=%p/bin:%p/sbin:${PATH} ; export PATH

mkdir -p %i/share/pdb2pqr
cp -R * %i/share/pdb2pqr
#
mkdir -p %i/bin
echo "#!/bin/zsh -f"           >|   %i/bin/pdb2pqr
echo "%p/share/pdb2pqr/pdb2pqr.py \"\$@\" " >>|   %i/bin/pdb2pqr
chmod a+x                            %i/bin/pdb2pqr
#
echo "#!/bin/zsh -f"           >|   %i/bin/propka
echo "%p/share/pdb2pqr/propka/propka \"\$@\" "  >>|   %i/bin/propka
chmod a+x                            %i/bin/propka
<<
Homepage: http://pdb2pqr.sourceforge.net/
DescDetail: <<
PDB2PQR is a Python software package that automates many of the common tasks
of preparing structures for continuum electrostatics calculations, providing
a platform-independent utility for converting protein files in PDB format to
PQR format. These tasks include: Adding a limited number of missing heavy
atoms to biomolecular structures Determining side-chain pKas Placing missing
hydrogens Optimizing the protein for favorable hydrogen bonding Assigning
charge and radius parameters from a variety of force fields PDB2PQR was
ported to Python by Todd Dolinsky while working with Nathan Baker at
Washington University in St. Louis. The PDB2PQR code is based on C++ design
and algorithms by Jens Erik Nielsen. PDB2PQR was originally designed to
facilitate structure preparation for APBS.  PDB2PQR uses PropKa to determine
protein pKa values. PropKa is developed by the Jensen Research Group at the
University of Iowa. More information about PropKa can be found at
http://propka.chem.uiowa.edu.  
<<
License: GPL          
Maintainer: W. G. Scott <wgsc...@users.sourceforge.net>

--- NEW FILE: apbs.info ---
Package: apbs
Version: 1.3.0
Revision: 2
UseMaxBuildJobs: false
Source: 
http://downloads.sourceforge.net/project/%n/%n/%n-%v/%n-1.3-source.tar.gz
Source-MD5: f99a505365f07f6853979cfe2ef23365
Depends: readline5-shlibs, gcc46-shlibs, python27
BuildDepends: gcc46, 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 
Description: Adaptive Poisson-Boltzmann Solver
PatchFile: %n.patch
PatchFile-MD5: 2662144e3e3508a944902c0a5e29eaf1 
PatchScript: <<
sed 's|@INSTALL_DIR@|%d|g' < %{PatchFile} | patch -p1
<<
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
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
<<
PostInstScript: <<
%p/bin/python2.7 -O %p/lib/python2.7/compileall.py -q 
%p/lib/python2.7/site-packages/ZSI
<<
################################################################################
SplitOff: <<
        Package: %N-dev
        BuildDependsOnly: true
        Description: apbs headers, static libraries and libtool files
        Files:<<
                include/apbs
                lib/*.a
        lib/*.la
        <<
<<
################################################################################
Homepage: http://apbs.sourceforge.net/
RunTimeVars: <<
  APBS_PSIZE:%p/share/%n/tools/manip
<<
DescDetail: <<
APBS is a software package for the numerical solution of the 
Poisson-Boltzmann equation, a popular continuum model for describing 
electrostatic interactions between molecular solutes over a wide range 
of length scales. The Fink pymol package is pre-configured to permit
apbs to be used as a plug-in.
.
The software is released under the GPL, but the author requests that you
register your use with him to aid him in obtaining funding to continue to
develop the code.  Most electrostatics software is payware, so please help
him continue to support this free software. You can do so at this URL:
http://agave.wustl.edu/apbs/download/
<<
License: GPL          
Maintainer: W. G. Scott <wgsc...@users.sourceforge.net>

--- NEW FILE: apbs.patch ---
diff -ruN apbs-1.3-source/configure apbs-1.3-source-orig/configure
--- apbs-1.3-source/configure   2010-10-21 08:17:07.000000000 -0700
+++ apbs-1.3-source-orig/configure      2010-11-23 20:07:40.000000000 -0800
@@ -22371,7 +22371,7 @@
 
 SERVICEURL='http://kryptonite.nbcr.net/opal2/services/apbs_1.3'
 
PARALLELSERVICEURL='http://oolite.calit2.optiputer.net/opal2/services/apbs-parallel-1.3'
-SITEPKGS=${prefix}/lib/python${PY_VERSION}/site-packages
+SITEPKGS=@INSTALL_DIR@${prefix}/lib/python${PY_VERSION}/site-packages
 
 
 # Check whether --with-maxmem was given.
diff -ruN apbs-1.3-source/contrib/opal/ZSI/Makefile.in 
apbs-1.3-source-orig/contrib/opal/ZSI/Makefile.in
--- apbs-1.3-source/contrib/opal/ZSI/Makefile.in        2010-05-19 
10:24:24.000000000 -0700
+++ apbs-1.3-source-orig/contrib/opal/ZSI/Makefile.in   2010-11-23 
20:09:12.000000000 -0800
@@ -542,7 +542,7 @@
 
 install-data-local:
        -mkdir -p ${SITEPKGS}
-       ${py_path} setup.py install --prefix=${prefix}
+       ${py_path} setup.py install --prefix=@INSTALL_DIR@${prefix}
 # Tell versions [3.59,3.63) of GNU make to not export all variables.
 # Otherwise a system limit (for SysV at least) may be exceeded.
 .NOEXPORT:
diff -ruN apbs-1.3-source/tools/python/Makefile.in 
apbs-1.3-source-orig/tools/python/Makefile.in
--- apbs-1.3-source/tools/python/Makefile.in    2010-05-19 10:24:24.000000000 
-0700
+++ apbs-1.3-source-orig/tools/python/Makefile.in       2010-11-23 
20:11:08.000000000 -0800
@@ -52,7 +52,6 @@
        ${top_builddir}/bin/.libs/libapbsmainroutines.a \
        ${top_builddir}/src/aaa_lib/.libs/libapbs.a \
        ${top_builddir}/contrib/lib/libmaloc.a \
-       ${top_builddir}/contrib/blas/.libs/libapbsblas.a \
        $(am__DEPENDENCIES_1) $(am__DEPENDENCIES_1)
 DEFAULT_INCLUDES = -I. -I$(top_builddir)/src/aaa_inc@am__isrc@
 depcomp =
@@ -248,7 +247,7 @@
 SUBDIRS = vgrid 
 _apbslib_so_SOURCES = apbslib.c
 _apbslib_so_LINK = $(PY_CC) $(PY_LINKFLAGS) -o $@ $(PY_SHARED)
-_apbslib_so_LDADD = ${top_builddir}/bin/.libs/libapbsmainroutines.a 
${top_builddir}/src/aaa_lib/.libs/libapbs.a 
${top_builddir}/contrib/lib/libmaloc.a 
${top_builddir}/contrib/blas/.libs/libapbsblas.a $(PY_LDFLAGS) ${z_lib} 
+_apbslib_so_LDADD = ${top_builddir}/bin/.libs/libapbsmainroutines.a 
${top_builddir}/src/aaa_lib/.libs/libapbs.a 
${top_builddir}/contrib/lib/libmaloc.a  $(PY_LDFLAGS) ${z_lib} 
 all: all-recursive
 
 .SUFFIXES:

--- NEW FILE: pymol-scipy.patch ---
diff -uNr pymol-1.4/contrib/pyopengl/_glumodule.c 
pymol-1.4.scipy/contrib/pyopengl/_glumodule.c
--- pymol-1.4/contrib/pyopengl/_glumodule.c     2009-02-24 22:30:40.000000000 
-0500
+++ pymol-1.4.scipy/contrib/pyopengl/_glumodule.c       2011-07-22 
22:02:17.000000000 -0400
@@ -652,7 +652,7 @@
 #elif defined(HAVE_EXTENSIONS_ARRAYOBJECT_H)
 #include "Extensions/arrayobject.h"
 #elif defined(HAVE_NUMERIC_ARRAYOBJECT_H)
-#include "Numeric/arrayobject.h"
+#include "numpy/oldnumeric.h"
 #elif defined(HAVE_NUMERICAL_ARRAYOBJECT_H)
 #include "numerical/arrayobject.h"
 #else
diff -uNr pymol-1.4/contrib/pyopengl/_openglmodule.c 
pymol-1.4.scipy/contrib/pyopengl/_openglmodule.c
--- pymol-1.4/contrib/pyopengl/_openglmodule.c  2009-02-24 22:30:40.000000000 
-0500
+++ pymol-1.4.scipy/contrib/pyopengl/_openglmodule.c    2011-07-22 
22:02:17.000000000 -0400
@@ -93,7 +93,7 @@
 #elif defined(HAVE_EXTENSIONS_ARRAYOBJECT_H)
 #include "Extensions/arrayobject.h"
 #elif defined(HAVE_NUMERIC_ARRAYOBJECT_H)
-#include "Numeric/arrayobject.h"
+#include "numpy/oldnumeric.h"
 #elif defined(HAVE_NUMERICAL_ARRAYOBJECT_H)
 #include "numerical/arrayobject.h"
 #else
diff -uNr pymol-1.4/contrib/pyopengl/openglutil.h 
pymol-1.4.scipy/contrib/pyopengl/openglutil.h
--- pymol-1.4/contrib/pyopengl/openglutil.h     2009-02-24 22:30:40.000000000 
-0500
+++ pymol-1.4.scipy/contrib/pyopengl/openglutil.h       2011-07-22 
22:02:17.000000000 -0400
@@ -14,7 +14,7 @@
 #elif defined(HAVE_EXTENSIONS_ARRAYOBJECT_H)
 #include "Extensions/arrayobject.h"
 #elif defined(HAVE_NUMERIC_ARRAYOBJECT_H)
-#include "Numeric/arrayobject.h"
+#include "numpy/oldnumeric.h"
 #elif defined(HAVE_NUMERICAL_ARRAYOBJECT_H)
 #include "numerical/arrayobject.h"
 #else
diff -uNr pymol-1.4/modules/pymol/opengl/__init__.py 
pymol-1.4.scipy/modules/pymol/opengl/__init__.py
--- pymol-1.4/modules/pymol/opengl/__init__.py  2009-02-24 22:29:21.000000000 
-0500
+++ pymol-1.4.scipy/modules/pymol/opengl/__init__.py    2011-07-22 
22:02:17.000000000 -0400
@@ -1,7 +1,9 @@
+## Automatically adapted for numpy.oldnumeric Jul 09, 2010 by -c
+
 # PyOpenGL: modified for usage inside of PyMOL
 
 try:
-    import multiarray
+    import numpy.oldnumeric as multiarray
     _numeric = 1
 except ImportError:
     _numeric = 0
diff -uNr pymol-1.4/modules/pymol/opengl/gl/__init__.py 
pymol-1.4.scipy/modules/pymol/opengl/gl/__init__.py
--- pymol-1.4/modules/pymol/opengl/gl/__init__.py       2009-02-24 
22:29:21.000000000 -0500
+++ pymol-1.4.scipy/modules/pymol/opengl/gl/__init__.py 2011-07-22 
22:02:17.000000000 -0400
@@ -1,3 +1,5 @@
+## Automatically adapted for numpy.oldnumeric Jul 09, 2010 by -c
+
 import sys
 from pymol import opengl
 
@@ -13,7 +15,7 @@
 """
 
 if opengl._numeric:
-    from Numeric import ArrayType
+    from numpy.oldnumeric import ArrayType
     try:
         import _opengl_num
         _opengl = _opengl_num
diff -uNr pymol-1.4/modules/pymol/opengl/glu/__init__.py 
pymol-1.4.scipy/modules/pymol/opengl/glu/__init__.py
--- pymol-1.4/modules/pymol/opengl/glu/__init__.py      2009-02-24 
22:29:21.000000000 -0500
+++ pymol-1.4.scipy/modules/pymol/opengl/glu/__init__.py        2011-07-22 
22:02:17.000000000 -0400
@@ -1,9 +1,11 @@
+## Automatically adapted for numpy.oldnumeric Jul 09, 2010 by -c
+
 # $Id: __init__.py 336 2001-02-24 12:11:45Z wdelano $
 import sys
 from pymol import opengl
 
 if opengl._numeric:
-    from Numeric import ArrayType
+    from numpy.oldnumeric import ArrayType
     try:
         import _glu_num
         _glu = _glu_num

Index: coot.info
===================================================================
RCS file: /cvsroot/fink/dists/10.4/stable/main/finkinfo/sci/coot.info,v
retrieving revision 1.27
retrieving revision 1.28
diff -u -d -r1.27 -r1.28
--- coot.info   18 Aug 2011 16:07:19 -0000      1.27
+++ coot.info   2 Oct 2011 14:59:58 -0000       1.28
@@ -1,11 +1,12 @@
 Package: coot
 Version: 0.7-pre-1
-Revision: 628
+Revision: 632
 SourceDirectory: %n-%v
 GCC: 4.0 
+UseMaxBuildJobs: false
 #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-3%r.tar.gz
-Source-MD5: d9188ef3c9251f1930912392502d0caa 
+Source-MD5: 78ce1007c6f2633378be10c96b487820 
 Source2: 
http://www.ysbl.york.ac.uk/~garib/refmac/data/refmac_experimental/refmac_dictionary_v5.29.tar.gz
 
 Source2-MD5: bc3469d0c1ac4104a683b5dcf397edae
 Source3: 
http://www.ysbl.york.ac.uk/~emsley/software/extras/reference-structures.tar.gz


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