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.dylib 0.0.0 %n (>= 2012.12.1-1) %p/lib/%N/libAlignment.1.dylib 1.0.0 %n (>= 2012.12.1-1) %p/lib/%N/libCatalogs.1.dylib 1.0.0 %n (>= 2012.12.1-1) %p/lib/%N/libChemReactions.1.dylib 1.0.0 %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.dylib 1.0.0 %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.dylib 1.0.0 %n (>= 2012.12.1-1) %p/lib/%N/libOptimizer.1.dylib 1.0.0 %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.dylib 1.0.0 %n (>= 2012.12.1-1) %p/lib/%N/libRDGeometryLib.1.dylib 1.0.0 %n (>= 2012.12.1-1) %p/lib/%N/libShapeHelpers.1.dylib 1.0.0 %n (>= 2012.12.1-1) %p/lib/%N/libSimDivPickers.1.dylib 1.0.0 %n (>= 2012.12.1-1) %p/lib/%N/libSmilesParse.1.dylib 1.0.0 %n (>= 2012.12.1-1) %p/lib/%N/libSubgraphs.1.dylib 1.0.0 %n (>= 2012.12.1-1) %p/lib/%N/libSubstructMatch.1.dylib 1.0.0 %n (>= 2012.12.1-1) %p/lib/%N/libhc.1.dylib 1.0.0 %n (>= 2012.12.1-1) << DocFiles: license.txt README License: BSD << SplitOff2: << Package: %N-dev BuildDependsOnly: true Description: rdkit static libraries and headers Files:<< lib/%N/*.a include/%N/* << DocFiles: license.txt README License: BSD << License: BSD Maintainer: W. G. Scott <wgsc...@users.sourceforge.net> Homepage: http://www.rdkit.org Index: coot.info =================================================================== RCS file: /cvsroot/fink/dists/10.7/stable/main/finkinfo/sci/coot.info,v retrieving revision 1.18 retrieving revision 1.19 diff -u -d -r1.18 -r1.19 --- coot.info 29 Jan 2013 07:24:53 -0000 1.18 +++ coot.info 11 Feb 2013 22:08:49 -0000 1.19 @@ -1,14 +1,17 @@ Package: coot Version: 0.7.1-pre -Revision: 4552 +Revision: 4562 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: dc42bb2504ff3281f14f1dc7694c5107 +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 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: << @@ -39,14 +42,14 @@ fink (>= 0.24.12) , clipper-dev (>= 1:2.1-31) , gpp4-dev (>= 1.2.0-31) , - mmdb-dev (>= 1.23.2-31) , + mmdb-dev (>= 1.23.2-31) , ssm-dev (>= 0.1-31) , 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) , + freetype219 (>= 2.3.12-1) , freeglut , giflib , glib2-dev (>= 2.22.0-1) , @@ -63,6 +66,7 @@ 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 , @@ -76,6 +80,8 @@ pygtk2-gtk-py27-dev , pygobject2-py27-dev , python27 , + rdkit-dev , + rdkit , swig , x11-dev << @@ -83,7 +89,7 @@ Depends: << clipper-shlibs (>= 1:2.1-31) , gpp4-shlibs (>= 1.2.0-31) , - mmdb-shlibs (>= 1.23.2-31) , + mmdb-shlibs (>= 1.23.2-31) , ssm-shlibs (>= 0.1-31) , atk1-shlibs (>= 1.28.0-1) , coot-shlibs (= %v-%r) , @@ -106,6 +112,7 @@ guile18-shlibs , libart2-shlibs , libcurl4-shlibs , + libgettext8-shlibs , libgnomecanvas2-shlibs (>= 2.20.0), libjpeg8-shlibs , libpng15-shlibs , @@ -118,6 +125,7 @@ pango1-xft2-ft219-shlibs (>= 1.24.5-4) , pygtk2-gtk-py27 , python27 , + rdkit , x11 << # @@ -131,6 +139,7 @@ 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 +#cp ../cod-types.hh lidia-core/cod-types.hh << ############################################################################### ConfigureParams: << @@ -138,7 +147,7 @@ --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-gsl-prefix=%p --with-guile --with-python=%p --with-pygtk=%p --with-enterprise-tools << ############################################################################### CompileScript: << @@ -156,11 +165,15 @@ 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%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" \ +rdkit_libs='-lMolChemicalFeatures -lDescriptors -lSubgraphs -lPartialCharges -lForceFieldHelpers -lForceField -lSubstructMatch -lOptimizer -lDistGeomHelpers -lDistGeometry -lAlignment -lEigenSolvers -lDepictor -lFileParsers -lRDGeometryLib -lGraphMol -lSmilesParse -lDataStructs -lRDGeneral -lboost_python ' \ + 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" \ DYLD_LIBRARY_PATH="" \ - ./configure %c + RDKIT_CXXFLAGS=-I$rdkit_prefix/include/rdkit \ + RDKIT_LIBS="\"-L%p/lib/rdkit $rdkit_libs\"" \ + PYTHON=%p/bin/python2.7 ./configure %c # # Force coot to link to single-precision fftw libraries. The double-precision libraries # cause coot to crash. @@ -175,8 +188,9 @@ fi perl -pi -e 's|lidia_LDFLAGS = -Wl,--export-dynamic||g' lbg/Makefile # -NUMPROC="$(sysctl -n hw.ncpu)" -make -j $NUMPROC +# NUMPROC="$(sysctl -n hw.ncpu)" + NUMPROC="1" + PYTHON=%p/bin/python2.7 make -j $NUMPROC << ############################################################################### InstallScript: << @@ -202,14 +216,14 @@ mkdir -p %i/bin # -if [[ $(sw_vers -productVersion) < 10.8 ]]; then - true -else -# Fix a new bug that appears with 10.8. +# Fix a bug with system python linking + 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 + elif [[ -f /System/Library/Frameworks/Python.framework/Versions/2.6/Python ]];then + 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 -fi + # This installs the refmac monomer library mkdir -p %i/share/coot/lib/data cp -R ../monomers %i/share/coot/lib/data/monomers ------------------------------------------------------------------------------ Free Next-Gen Firewall Hardware Offer Buy your Sophos next-gen firewall before the end March 2013 and get the hardware for free! Learn more. http://p.sf.net/sfu/sophos-d2d-feb _______________________________________________ Fink-commits mailing list Fink-commits@lists.sourceforge.net http://news.gmane.org/gmane.os.apple.fink.cvs