Update of /cvsroot/fink/dists/10.4/unstable/main/finkinfo/sci In directory sc8-pr-cvs17:/tmp/cvs-serv12559
Modified Files: ccp4-onlylibs-dev.info ccp4-onlylibs-dev.patch coot.info Added Files: coot.patch Log Message: fixes for 10.5 compatibility while maintaining 10.4 compatibility Index: ccp4-onlylibs-dev.patch =================================================================== RCS file: /cvsroot/fink/dists/10.4/unstable/main/finkinfo/sci/ccp4-onlylibs-dev.patch,v retrieving revision 1.1 retrieving revision 1.2 diff -u -d -r1.1 -r1.2 --- ccp4-onlylibs-dev.patch 23 Mar 2006 06:23:07 -0000 1.1 +++ ccp4-onlylibs-dev.patch 31 Oct 2007 22:03:21 -0000 1.2 @@ -1,278 +1,2400 @@ -diff -ruN ccp4-onlylibs-dev-orig/lib/clipper/clipper/core/derivs.h ccp4-onlylibs-dev/lib/clipper/clipper/core/derivs.h ---- ccp4-onlylibs-dev-orig/lib/clipper/clipper/core/derivs.h 2005-09-08 13:07:42.000000000 -0700 -+++ ccp4-onlylibs-dev/lib/clipper/clipper/core/derivs.h 2006-03-22 21:17:07.000000000 -0800 -@@ -169,7 +169,7 @@ - template<class T> Curv_orth<T> Curv_frac<T>::curv_orth( const Cell& cell ) const - { - Mat33<T> m( cell.matrix_frac() ); -- return Curv_frac<T>( m.transpose() * (*this) * m ); -+ return Curv_orth<T>( m.transpose() * (*this) * m ); +diff -ruN ccp4-onlylibs-dev-orig/lib/src/mmdb/Makefile.am ccp4-onlylibs-dev/lib/src/mmdb/Makefile.am +--- ccp4-onlylibs-dev-orig/lib/src/mmdb/Makefile.am 1969-12-31 16:00:00.000000000 -0800 [...2604 lines suppressed...] + // + // CCP4 Coordinate Library: support of coordinate-related +diff -ruN ccp4-onlylibs-dev-orig/lib/src/mmdb/stream_.cpp ccp4-onlylibs-dev/lib/src/mmdb/stream_.cpp +--- ccp4-onlylibs-dev-orig/lib/src/mmdb/stream_.cpp 2006-08-16 03:55:23.000000000 -0700 ++++ ccp4-onlylibs-dev/lib/src/mmdb/stream_.cpp 2007-10-21 22:33:35.000000000 -0700 +@@ -1,4 +1,4 @@ +-// $Id$ ++// $Id$ + // ================================================================= + // + // CCP4 Coordinate Library: support of coordinate-related +diff -ruN ccp4-onlylibs-dev-orig/lib/src/mmdb/stream_.h ccp4-onlylibs-dev/lib/src/mmdb/stream_.h +--- ccp4-onlylibs-dev-orig/lib/src/mmdb/stream_.h 2006-08-16 03:55:23.000000000 -0700 ++++ ccp4-onlylibs-dev/lib/src/mmdb/stream_.h 2007-10-21 22:33:35.000000000 -0700 +@@ -1,4 +1,4 @@ +-// $Id$ ++// $Id$ + // ================================================================= + // + // CCP4 Coordinate Library: support of coordinate-related --- NEW FILE: coot.patch --- diff -ruN coot-0.4-pre-1-orig/coot-utils/coot-fffear.cc coot-0.4-pre-1/coot-utils/coot-fffear.cc --- coot-0.4-pre-1-orig/coot-utils/coot-fffear.cc 2007-04-16 15:42:06.000000000 -0700 +++ coot-0.4-pre-1/coot-utils/coot-fffear.cc 2007-10-31 10:28:44.000000000 -0700 @@ -160,30 +160,7 @@ } - for (unsigned int iop=0; iop<ops.size(); iop++) { - - clipper::Xmap<float> r1; - r1.init(clipper::Spacegroup::p1(), xmap.cell(), xmap.grid_sampling()); // fixed to be consistent with above results init. - clipper::FFFear_fft<float> search(xmap); - clipper::NX_operator nxop( xmap, nxmap, ops[iop]); - search(r1, nxmap, nxmap_mask, nxop); // fill r1 with fffear search values at this orientation - - clipper::Xmap<float>::Map_reference_index ix; - for ( ix = r1.first(); !ix.last(); ix.next() ) - if ( r1[ix] < results[ix].first) { - results[ix].first = r1[ix]; - results[ix].second = iop; - } - - icount++; - // std::cout << ops.size() - iop << " "; - std::cout.flush(); - if (icount == 50) { - std::cout << " " <<100*(float(iop)/float(ops.size())) << "%"; - std::cout.flush(); - icount = 0; - } - } + std::cout << "\n"; } } diff -ruN coot-0.4-pre-1-orig/cootaneer/buccaneer-lib.cpp coot-0.4-pre-1/cootaneer/buccaneer-lib.cpp --- coot-0.4-pre-1-orig/cootaneer/buccaneer-lib.cpp 2007-07-01 07:12:02.000000000 -0700 +++ coot-0.4-pre-1/cootaneer/buccaneer-lib.cpp 2007-10-31 11:08:12.000000000 -0700 @@ -193,46 +193,7 @@ \param resulttrn The best translations. \param xmap The map to search. \param rtops The oprientations to search. */ -void LLK_map_target::search( clipper::Xmap<float>& resultscr, clipper::Xmap<int>& resultrot, clipper::Xmap<int>& resulttrn, const clipper::Xmap<float>& xmap, const std::vector<clipper::RTop_orth>& rtops ) const -{ - // set up results - const clipper::Spacegroup& spgr = xmap.spacegroup(); - const clipper::Cell& cell = xmap.cell(); - const clipper::Grid_sampling& grid = xmap.grid_sampling(); - resultscr.init( spgr, cell, grid ); - resultrot.init( spgr, cell, grid ); - resulttrn.init( spgr, cell, grid ); - resultscr = 1.0e20; - - // now search for ML target in each orientation in turn - clipper::Xmap<float> resultp1( clipper::Spacegroup::p1(), cell, grid ); - clipper::Xmap<float>::Map_reference_index i1(resultp1); - clipper::Xmap<float>::Map_reference_coord ix(resultscr); - - // set up z scoring - clipper::FFFear_fft<float> srch( xmap ); - clipper::NX_operator nxop( xmap, target, rtops[0] ); - srch( resultp1, target, weight, nxop ); - clipper::Map_stats zstats( resultp1 ); - - // loop over orientations - for ( int op = 0; op < rtops.size(); op++ ) { - // do the fffear search - clipper::NX_operator nxop( xmap, target, rtops[op].inverse() ); - srch( resultp1, target, weight, nxop ); - - // store best scores - for ( i1 = resultp1.first(); !i1.last(); i1.next() ) { - ix.set_coord( i1.coord() ); - float score = ( resultp1[i1] - zstats.mean() ) / zstats.std_dev(); - if ( score < resultscr[ix] ) { - resultscr[ix] = score; - resultrot[ix] = op; - resulttrn[ix] = grid.index( i1.coord() ); - } - } - } -} + clipper::String LLK_map_target::format() const Index: ccp4-onlylibs-dev.info =================================================================== RCS file: /cvsroot/fink/dists/10.4/unstable/main/finkinfo/sci/ccp4-onlylibs-dev.info,v retrieving revision 1.14 retrieving revision 1.15 diff -u -d -r1.14 -r1.15 --- ccp4-onlylibs-dev.info 29 Jan 2007 01:30:13 -0000 1.14 +++ ccp4-onlylibs-dev.info 31 Oct 2007 22:03:21 -0000 1.15 @@ -1,15 +1,17 @@ Package: ccp4-onlylibs-dev # Use version numbering to sync with the current CCP4 release: Version: 6.0.2 -Revision: 2 +Revision: 8 GCC: 4.0 -Source: http://xanana.ucsc.edu/xtal/%n/%n-%v.tar.gz -#Source: ftp://ftp.ccp4.ac.uk/prerelease/%n.tar.gz -Source-MD5: edb1034b0a2699bcb43abb6463f7b9e9 -#SourceRename: %n-%v.tar.gz +#Source: http://xanana.ucsc.edu/xtal/%n/%n-%v.tar.gz +Source: ftp://ftp.ccp4.ac.uk/prerelease/ccp4-onlylibs-dev.tar.gz +# Source-MD5: 67de45f1d718627ab96939f5443937ae +Source-MD5: e778478de628c75792d2401248c63350 +# SourceDirectory: %n Source2: http://chemistry.ucsc.edu/~wgscott/xtal/%n/%n-extras-0.1.tgz Source2-MD5: ea307964e3786bef0868ea56aaaa0471 +# Depends: gcc42-shlibs BuildDepends: gcc42 # BuildDepends: fort77 @@ -17,7 +19,7 @@ NoSetCPPFLAGS: true NoSetLDFLAGS: true ############################################################################### -#Patch: %n.patch +Patch: %n.patch PatchScript: << #!/bin/zsh -efv umask 0022 @@ -50,6 +52,7 @@ # clean up: rm -f include/*.bak lib/clipper/*.bak + << ############################################################################### CompileScript: << @@ -60,7 +63,7 @@ source include/ccp4.setup-zsh export DYLD_LIBRARY_PATH=$CLIB # -FC="gfortran" ./configure --onlylibs Darwin +FC="gfortran" ./configure --with-ssm --with-mmdb --onlylibs Darwin #FC="fort77" ./configure --onlylibs Darwin ln -s $CCP4/lib/src $CCP4/lib/clipper/ccp4 # @@ -74,7 +77,7 @@ command ls -1 lib/*.a sleep 10 # -rm $CCP4/lib/clipper/ccp4 +# rm $CCP4/lib/clipper/ccp4 make realclean << ############################################################################### @@ -96,6 +99,11 @@ perl -pi.bak -e 's|%b|%p/share/xtal/%n-%v|g' lib/*.la rm -f lib/*.la.bak # +# Temp fix for coot (needed in 10.4 but not 10.5) +if [[ $(sw_vers -productVersion) < 10.5 ]]; then + cp include/ssm/ssm_superpose.h include/ssm/ssm_superpose.h-orig + perl -pi -e 's|ivector FF1,FF2;||g' include/ssm/ssm_superpose.h +fi # Now install: mkdir -p %i/bin mkdir -p %i/share/xtal/%n-%v Index: coot.info =================================================================== RCS file: /cvsroot/fink/dists/10.4/unstable/main/finkinfo/sci/coot.info,v retrieving revision 1.43 retrieving revision 1.44 diff -u -d -r1.43 -r1.44 --- coot.info 12 Sep 2007 16:38:29 -0000 1.43 +++ coot.info 31 Oct 2007 22:03:21 -0000 1.44 @@ -1,10 +1,10 @@ Package:coot -Version: 0.4-pre-1-revision-375 -Revision: 1 +Version: 0.4-pre-1-revision-449 +Revision: 4 GCC: 4.0 #Source: http://www.ysbl.york.ac.uk/~emsley/software/%n-%v.tar.gz Source: http://www.ysbl.york.ac.uk/~emsley/software/pre-release/%n-%v.tar.gz -Source-MD5: a43cc7d3f4e32b85d55d5748359c18aa +Source-MD5: da881ab7c09592fe4b766d4cac419d8c #SourceDirectory: %n-%v SourceDirectory: %n-0.4-pre-1 Source2: http://www.ysbl.york.ac.uk/~emsley/software/extras/refmac-lib-data-monomers.tar.gz @@ -29,14 +29,14 @@ include \"/sw/share/themes/Glossy_P/gtk-2.0/gtkrc\" << ############################################################################### -Recommends: povray, ccp4 +Recommends: povray, ccp4, raster3d BuildDepends: << - atk1 , - ccp4-onlylibs-dev (>= 6.0.2-1) , + ccp4-onlylibs-dev (>= 6.0.2-8), + atk1 , freeglut , giflib , glib2-dev , - gmp , + gmp , gnome-libs-dev , gsl , gtk+2 , @@ -55,11 +55,11 @@ libjpeg , libpng3 , librsvg2-gtk , - libtool14 , - pango1-xft2-dev , + libtool14 , + pango1-xft2-dev , swig << -# Note: gtkglext1 required at runtime for stereo functionality +# Note: gtkglext1 IS required at runtime for stereo functionality Depends: << atk1-shlibs , coot-shlibs (= %v-%r) , @@ -93,15 +93,20 @@ libtool14-shlibs , librsvg2-gtk , pango1-xft2-shlibs , - raster3d << # +# raster3d ############################################################################### BuildDependsOnly: false NoSetLDFLAGS: true # Patch: %n.patch PatchScript: << #!/bin/zsh -exf +if [[ $(sw_vers -productVersion) < 10.5 ]]; then + : +else + patch -p1 < %a/%n.patch +fi perl -pi.bak -e 's|use-modules \(goosh\)|use-modules \(goosh goosh\)|g' scheme/coot-utils.scm #perl -pi.bak -e 's/include <malloc.h>//g' **/*.c # Use the correct povray directory @@ -110,31 +115,48 @@ perl -pi.bak -e 's|coot-png-display-program \"display\"|coot-png-display-program \"open\"|g' scheme/raster3d.scm # This is required to get the map displayed on both sides of side-by-side stereo echo "(set-display-lists-for-maps 0)" >>| scheme/group-settings.scm +# Fix configure to work with gpp4 library instead of ccp4c +# perl -pi -e 's|ccp4c|gpp4|g' configure << ############################################################################### ConfigureParams: << ---with-mmdb-prefix=$CCP4 --with-clipper-prefix=$CCP4 --with-fftw=$CCP4 \ +--with-mmdb-prefix=%p/share/xtal/ccp4-onlylibs-dev-6.0.2 --with-clipper-prefix=%p/share/xtal/ccp4-onlylibs-dev-6.0.2 --with-fftw=%p/share/xtal/ccp4-onlylibs-dev-6.0.2 \ --with-glut-prefix=%p --with-gl-prefix=/usr/X11R6 --with-gtk2 \ ---with-gnomecanvas-prefix=%p --with-ssmlib-prefix=$CCP4 \ +--with-gnomecanvas-prefix=%p --with-ssmlib-prefix=%p/share/xtal/ccp4-onlylibs-dev-6.0.2 \ --with-imlib-prefix=%p --with-gtkgl-prefix=%p --with-glib-prefix=%p \ --with-guile-gtk --with-guile-gtk-prefix=%p \ ---with-gsl-prefix=%p --with-guile --with-python - << +--with-gsl-prefix=%p --with-guile --with-python +<< ############################################################################### CompileScript: << -#!/bin/zsh -efv -alias python="/System/Library/Frameworks/Python.framework/Versions/Current/lib/python2.3" -source %p/share/xtal/ccp4-onlylibs-dev-6.0.2/include/ccp4.setup-zsh +#!/bin/zsh -ef + export PATH=/System/Library/Frameworks/Python.framework/Versions/Current/bin:%p/bin:%p/share/guile/1.8/scripts/binoverride:$PATH export SED=/usr/bin/sed -export PYTHONPATH="/System/Library/Frameworks/Python.framework/Versions/Current/lib/python2.3" -FLIBS="-L/System/Library/Frameworks/Python.framework/Versions/Current/lib -L%p/lib" \ -CPPFLAGS="-I$CCP4/lib/clipper/clipper/mmdbold -I/System/Library/Frameworks/Python.framework/Versions/Current/include/python2.3" \ -LDFLAGS="-L$CLIB -L/usr/lib -lSystemStubs -flat_namespace -L/System/Library/Frameworks/Python.framework/Versions/Current/lib/python2.3/config" \ -CXX="g++" \ -CC="gcc" \ -py_path=/System/Library/Frameworks/Python.framework/Versions/Current/bin/python2.3 \ -./configure %c +# Use the system-supplied python, which differs for 10.4 vs. 10.5 +if [[ -d /System/Library/Frameworks/Python.framework/Versions/Current/lib/python2.5 ]];then + alias python="/System/Library/Frameworks/Python.framework/Versions/Current/lib/python2.5" + export PYTHONPATH="/System/Library/Frameworks/Python.framework/Versions/Current/lib/python2.5" + FLIBS="-L/System/Library/Frameworks/Python.framework/Versions/Current/lib -L%p/lib" \ + CPPFLAGS="-I%p/share/xtal/ccp4-onlylibs-dev-6.0.2/include -I%p/share/xtal/ccp4-onlylibs-dev-6.0.2/lib -I%p/share/xtal/ccp4-onlylibs-dev-6.0.2/lib/ssm -I%p/include -I/System/Library/Frameworks/Python.framework/Versions/Current/include/python2.5" \ + LDFLAGS="-L%p/share/xtal/ccp4-onlylibs-dev-6.0.2/lib -L%p/lib -L/usr/lib -lSystemStubs -flat_namespace -L/System/Library/Frameworks/Python.framework/Versions/Current/lib/python2.5/config -L/System/Library/Frameworks/OpenGL.framework/Versions/A/Libraries" \ + CXX="/usr/bin/g++" \ + CC="/usr/bin/gcc" \ + py_path=/System/Library/Frameworks/Python.framework/Versions/Current/bin/python2.5 \ + ./configure %c +else + alias python="/System/Library/Frameworks/Python.framework/Versions/Current/lib/python2.3" + export PYTHONPATH="/System/Library/Frameworks/Python.framework/Versions/Current/lib/python2.3" + FLIBS="-L/System/Library/Frameworks/Python.framework/Versions/Current/lib -L%p/lib" \ + CPPFLAGS="-I%p/share/xtal/ccp4-onlylibs-dev-6.0.2/include -I%p/share/xtal/ccp4-onlylibs-dev-6.0.2/lib -I%p/share/xtal/ccp4-onlylibs-dev-6.0.2/lib/ssm -I%p/include -I/System/Library/Frameworks/Python.framework/Versions/Current/include/python2.3" \ + LDFLAGS="-L%p/share/xtal/ccp4-onlylibs-dev-6.0.2/lib -L%p/lib -L/usr/lib -lSystemStubs -flat_namespace -L/System/Library/Frameworks/Python.framework/Versions/Current/lib/python2.3/config -L/System/Library/Frameworks/OpenGL.framework/Versions/A/Libraries" \ + CXX="/usr/bin/g++" \ + CC="/usr/bin/gcc" \ + py_path=/System/Library/Frameworks/Python.framework/Versions/Current/bin/python2.3 \ + ./configure %c +fi + + #remake the src/coot_wrap_python.cc and src/coot_wrap_guile.cc files /bin/rm -f **/coot_wrap_*.cc cd src @@ -146,8 +168,7 @@ << ############################################################################### InstallScript: << -#!/bin/zsh -exf -source %p/share/xtal/ccp4-onlylibs-dev-6.0.2/include/ccp4.setup-zsh +#!/bin/zsh -efv export PATH=%p/bin:%p/share/guile/1.8/scripts/binoverride:$PATH export PYTHONPATH="" export SED=/usr/bin/sed ------------------------------------------------------------------------- This SF.net email is sponsored by: Splunk Inc. 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