Update of /cvsroot/fink/dists/10.4/unstable/main/finkinfo/sci In directory sc8-pr-cvs17.sourceforge.net:/tmp/cvs-serv12584
Modified Files: coot.info mmdb.info Added Files: clipper.info ssm.info gpp4.info Log Message: upgrade coot and add streamlined dependencies --- NEW FILE: gpp4.info --- Package: gpp4 Version: 1.0.4 Revision: 5 Maintainer: W. G. Scott <[EMAIL PROTECTED]> # Maintainer: Morten Kjeldgaard <[EMAIL PROTECTED]> DescPackaging: << Based on package created by Morten Kjeldgaard <[EMAIL PROTECTED]> with minor edits to conform to standard Fink packaging requirements. << Description: Library providing CCP4 functionality License: LGPL Source: ftp://ftp.bioxray.au.dk/pub/mok/src/gpp4-%v.tar.gz Source-MD5: 48931781425a5b79a8255ebefaed24b3 NoSourceDirectory: false Depends: %N-shlibs (= %v-%r) BuildDependsOnly: true HomePage: http://www.bioxray.dk/~mok/gpp4 DocFiles: README AUTHORS NEWS 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: << ./configure --prefix=%p make << InstallScript: << make install DESTDIR=%d << SplitOff: << Package: %N-shlibs Files: << lib/libgpp4.0.dylib lib/libgpp4.0.0.0.dylib << Shlibs: << %p/lib/libgpp4.0.dylib 1.0.0 %n (>= 1.0.4-2) << << SplitOff2: << Package: %N-dev BuildDependsOnly: True Conflicts: ccp4-onlylibs-dev Replaces: ccp4-onlylibs-dev Files: << lib/*.a lib/*.la include/gpp4/ccp4/*.h share/gpp4/default.def share/gpp4/environ.def share/gpp4/syminfo.lib << << Index: mmdb.info =================================================================== RCS file: /cvsroot/fink/dists/10.4/unstable/main/finkinfo/sci/mmdb.info,v retrieving revision 1.1 retrieving revision 1.2 diff -u -d -r1.1 -r1.2 --- mmdb.info 26 Aug 2008 23:46:08 -0000 1.1 +++ mmdb.info 10 Sep 2008 08:14:02 -0000 1.2 @@ -1,6 +1,6 @@ Package: mmdb Version: 1.12 -Revision: 1 +Revision: 5 # Maintainer: Morten Kjeldgaard <[EMAIL PROTECTED]> Maintainer: W. G. Scott <[EMAIL PROTECTED]> DescPackaging: << @@ -43,12 +43,14 @@ SplitOff: << Package: %N-shlibs Files: lib/libmmdb.0.dylib lib/libmmdb.0.0.0.dylib - Shlibs: %p/lib/libmmdb.0.dylib 1.0.0 %n (>= 1.12-1) + Shlibs: %p/lib/libmmdb.0.dylib 1.0.0 %n (>= 1.12-2) << SplitOff2: << Package: %N-dev Depends: %N (= %v-%r) BuildDependsOnly: True +Conflicts: ccp4-onlylibs-dev +Replaces: ccp4-onlylibs-dev Files: << include/mmdb/*.h lib/*.a --- NEW FILE: clipper.info --- Package: clipper Epoch: 1 Version: 2.0.3 Revision: 5 BuildDepends: fftw (>= 2.1.5-1010) | fftw-mpi (>= 2.1.5-1010), mmdb-dev (>= 1.12-5), ssm-dev (>= 0.1-5), gpp4-dev (>= 1.0.4-5) Depends: %n-shlibs (>= 1:%v-%r), fftw-shlibs (>= 2.1.5-1010) | fftw-mpi-shlibs (>= 2.1.5-1010), mmdb-shlibs (>= 1.0.10-5), ssm-shlibs (>= 0.1-5), gpp4-shlibs (>= 1.0.4-5) Maintainer: W. G. Scott <[EMAIL PROTECTED]> Homepage: http://www.ysbl.york.ac.uk/~cowtan/clipper/clipper.html Source: http://www.ysbl.york.ac.uk/~cowtan/%n/%n20ac.latest.tar.gz Source-MD5: cf5746cd7e040180c1e4cb429c7b2ac1 NoSourceDirectory: true DocFiles: README AUTHORS NEWS COPYING Description: Object-oriented crystallographic libraries DescDetail: << The aim of the project is to produce a set of object-oriented libraries for the organisation of crystallographic data and the performance of crystallographic computation. The libraries are designed as a framework for new crystallographic software, which will allow the full power of modern programming techniques to be exploited by the developer. << SetCFLAGS: -fno-strict-aliasing -I%p/include -I%p/include/mmdb -I%p/include/ssm -I%p/include/gpp4/ccp4 -I/usr/include -I/usr/include/sys SetLDFLAGS: -L/usr/lib License: LGPL CompileScript: << LDFLAGS="-L%p/lib" ./configure --prefix=%p --enable-shared --with-gpp4=%p --with-mmdb=%p --with-fftw=%p --enable-mmdb --enable-minimol --enable-cif --enable-cns --enable-gpp4 perl -pi -e 's|examples||g' Makefile make << InstallScript: << make install DESTDIR=%d << SplitOff: << Package: %N-shlibs Files: << lib/libclipper-ccp4.2.*dylib lib/libclipper-cif.2.*dylib lib/libclipper-cns.2.*dylib lib/libclipper-contrib.2.*dylib lib/libclipper-core.2.*dylib lib/libclipper-minimol.2.*dylib lib/libclipper-mmdb.2.*dylib lib/libclipper-phs.2.*dylib << Shlibs: << %p/lib/libclipper-ccp4.2.dylib 3.0.0 %n (>= 1:2.0.3-4) %p/lib/libclipper-cif.2.dylib 3.0.0 %n (>= 1:2.0.3-4) %p/lib/libclipper-cns.2.dylib 3.0.0 %n (>= 1:2.0.3-4) %p/lib/libclipper-contrib.2.dylib 3.0.0 %n (>= 1:2.0.3-4) %p/lib/libclipper-core.2.dylib 3.0.0 %n (>= 1:2.0.3-4) %p/lib/libclipper-minimol.2.dylib 3.0.0 %n (>= 1:2.0.3-4) %p/lib/libclipper-mmdb.2.dylib 3.0.0 %n (>= 1:2.0.3-4) %p/lib/libclipper-phs.2.dylib 3.0.0 %n (>= 1:2.0.3-4) << << SplitOff2: << Package: %N-dev BuildDependsOnly: True Conflicts: ccp4-onlylibs-dev Replaces: ccp4-onlylibs-dev Files: << lib/*.a lib/*.la include/* << << Index: coot.info =================================================================== RCS file: /cvsroot/fink/dists/10.4/unstable/main/finkinfo/sci/coot.info,v retrieving revision 1.85 retrieving revision 1.86 diff -u -d -r1.85 -r1.86 --- coot.info 8 Sep 2008 17:03:09 -0000 1.85 +++ coot.info 10 Sep 2008 08:14:02 -0000 1.86 @@ -1,10 +1,10 @@ Package: coot -Version: 0.5-pre-1-1377 -Revision: 1 +Version: 0.5-pre-1-1382 +Revision: 2 GCC: 4.0 -Source: http://www.ysbl.york.ac.uk/~emsley/software/pre-release/coot-0.5-pre-1-revision-1377.tar.gz +Source: http://www.ysbl.york.ac.uk/~emsley/software/pre-release/coot-0.5-pre-1-revision-1382.tar.gz # Source: http://www.ysbl.york.ac.uk/~emsley/software/%n-%v.tar.gz -Source-MD5: f857261f25fe719ea5b309ddbd260078 +Source-MD5: bf54db93380c1e2d23515fa4ea46cf4f SourceDirectory: %n-0.5-pre-1 Source2: http://www.ysbl.york.ac.uk/refmac/data/refmac5.4_dictionary.tar.gz Source2-MD5: 14b965dc5ab9762c819f632c133998b9 @@ -34,9 +34,16 @@ ############################################################################### Recommends: povray, ccp4, raster3d BuildDepends: << + clipper-dev (>= 1:2.0.3-5) , + clipper (>= 1:2.0.3-5) , + gpp4-dev (>= 1.0.4-5) , + gpp4 (>= 1.0.4-5) , + mmdb-dev (>= 1.12-5) , + mmdb (>= 1.12-5) , + ssm-dev (>= 0.1-5) , + ssm (>= 0.1-5) , atk1 (>= 1.20.0-1) , cairo (>= 1.6-1) , - ccp4-onlylibs-dev (>= 6.0.99-2), expat1 , fontconfig2-dev (>= 2.4.1-1) , freetype219 (>= 2.3.5-1) , @@ -76,6 +83,10 @@ # # Note: gtkglext1 IS required at runtime for stereo functionality Depends: << + clipper-shlibs (>= 1:2.0.3-5) , + gpp4-shlibs (>= 1.0.4-5) , + mmdb-shlibs (>= 1.12-5) , + ssm-shlibs (>= 0.1-5) , atk1-shlibs (>= 1.20.0-1) , coot-shlibs (= %v-%r) , freeglut-shlibs , @@ -122,7 +133,8 @@ if [[ $(sw_vers -productVersion) < 10.5 ]]; then : else - patch -p1 < %a/%n-10.5.patch + : + # patch -p1 < %a/%n-10.5.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 @@ -140,15 +152,16 @@ # perl -pi.bak -e 's|have_guile_gui=no|have_guile_gui=yes|g' configure perl -pi -e "s|guile-config|guile-1.8-config|g" configure perl -pi -e 's|\(goosh\)|\(goosh goosh\)|g' configure +perl -pi -e 's|lccp4c|lgpp4|g' configure ### << ############################################################################### ConfigureParams: << ---with-mmdb-prefix=%p/share/xtal/ccp4-onlylibs-dev-6.0.99 \ ---with-clipper-prefix=%p/share/xtal/ccp4-onlylibs-dev-6.0.99 \ ---with-fftw=%p/share/xtal/ccp4-onlylibs-dev-6.0.99 \ +--with-gpp4=%p --with-mmdb=%p \ +--with-clipper-prefix=%p \ +--with-fftw=%p \ --with-glut-prefix=%p --with-gl-prefix=/usr/X11R6 --with-gtk2 \ ---with-gnomecanvas-prefix=%p --with-ssmlib-prefix=%p/share/xtal/ccp4-onlylibs-dev-6.0.99 \ +--with-gnomecanvas-prefix=%p --with-ssmlib-prefix=%p \ --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 @@ -163,13 +176,18 @@ export COOT_REFMAC_LIB_DIR=%p/share/coot/lib export PKG_CONFIG_PATH=%p/lib/pango-ft219/lib/pkgconfig:%p/lib/fontconfig2/lib/pkgconfig:%p/lib/freetype219/lib/pkgconfig:${PKG_CONFIG_PATH} FLIBS="-L%p/lib" \ -CPPFLAGS="-I%p/share/xtal/ccp4-onlylibs-dev-6.0.99/include -I%p/share/xtal/ccp4-onlylibs-dev-6.0.99/lib -I%p/share/xtal/ccp4-onlylibs-dev-6.0.99/lib/ssm -I%p/include -I/usr/X11R6/include" \ -LDFLAGS="-Wl,-dylib_file,%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/pango-ft219/lib -L%p/share/xtal/ccp4-onlylibs-dev-6.0.99/lib -L%p/lib -L/usr/lib -lSystemStubs -flat_namespace -L/System/Library/Frameworks/OpenGL.framework/Versions/A/Libraries" \ +CPPFLAGS="-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/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/pango-ft219/lib -L%p/lib -L/usr/lib -lSystemStubs -flat_namespace -L/System/Library/Frameworks/OpenGL.framework/Versions/A/Libraries" \ CXX="/usr/bin/g++" \ CC="/usr/bin/gcc" \ PYTHON=%p/bin/python2.5 \ DYLD_LIBRARY_PATH="" \ ./configure %c +# +perl -pi -e 's|lrfftw |lsrfftw |g' **/Makefile +perl -pi -e 's|lfftw |lsfftw |g' **/Makefile +perl -pi -e 's|include <rfftw.h>|include <srfftw.h>|g' surface/CXXFFTSolventMap.h +# # py_path="%p/bin/python2.5" \ # #remake the src/coot_wrap_python.cc and src/coot_wrap_guile.cc files @@ -233,40 +251,39 @@ SplitOff: << Package: %N-shlibs Files: << -lib/libccp4mg-*.dylib -lib/libcoot-*.dylib -lib/libcootaneer*.dylib +lib/libccp4mg-*.0*.dylib +lib/libcoot-*.0*.dylib +lib/libcootaneer.0*.dylib << Shlibs: << - %p/lib/libccp4mg-surface.0.dylib 1.0.0 %n (>= 0.5-pre-1-1377-1) - %p/lib/libccp4mg-utils.0.dylib 1.0.0 %n (>= 0.5-pre-1-1377-1) - %p/lib/libcoot-analysis.0.dylib 1.0.0 %n (>= 0.5-pre-1-1377-1) - %p/lib/libcoot-AngleInfo.0.dylib 1.0.0 %n (>= 0.5-pre-1-1377-1) - %p/lib/libcoot-atomutils.0.dylib 1.0.0 %n (>= 0.5-pre-1-1377-1) - %p/lib/libcoot-cabuild.0.dylib 1.0.0 %n (>= 0.5-pre-1-1377-1) - %p/lib/libcoot-compat.0.dylib 1.0.0 %n (>= 0.5-pre-1-1377-1) - %p/lib/libcoot-coord-extras.0.dylib 1.0.0 %n (>= 0.5-pre-1-1377-1) - %p/lib/libcoot-coord-utils.0.dylib 1.0.0 %n (>= 0.5-pre-1-1377-1) - %p/lib/libcoot-coords.0.dylib 1.0.0 %n (>= 0.5-pre-1-1377-1) - %p/lib/libcoot-db-main.0.dylib 1.0.0 %n (>= 0.5-pre-1-1377-1) - %p/lib/libcoot-geometry.0.dylib 1.0.0 %n (>= 0.5-pre-1-1377-1) - %p/lib/libcoot-high-res.0.dylib 1.0.0 %n (>= 0.5-pre-1-1377-1) - %p/lib/libcoot-ideal.0.dylib 1.0.0 %n (>= 0.5-pre-1-1377-1) - %p/lib/libcoot-isosurface.0.dylib 1.0.0 %n (>= 0.5-pre-1-1377-1) - %p/lib/libcoot-ligand.0.dylib 1.0.0 %n (>= 0.5-pre-1-1377-1) - %p/lib/libcoot-map-heavy.0.dylib 1.0.0 %n (>= 0.5-pre-1-1377-1) - %p/lib/libcoot-map-utils.0.dylib 1.0.0 %n (>= 0.5-pre-1-1377-1) - %p/lib/libcoot-mini-mol.0.dylib 1.0.0 %n (>= 0.5-pre-1-1377-1) - %p/lib/libcoot-mmtz-extras.0.dylib 1.0.0 %n (>= 0.5-pre-1-1377-1) - %p/lib/libcoot-sequence-view.0.dylib 1.0.0 %n (>= 0.5-pre-1-1377-1) - %p/lib/libcoot-shelx.0.dylib 1.0.0 %n (>= 0.5-pre-1-1377-1) - %p/lib/libcoot-skeleton.0.dylib 1.0.0 %n (>= 0.5-pre-1-1377-1) - %p/lib/libcoot-surface.0.dylib 1.0.0 %n (>= 0.5-pre-1-1377-1) - %p/lib/libcoot-tw.0.dylib 1.0.0 %n (>= 0.5-pre-1-1377-1) - %p/lib/libcoot-utils.0.dylib 1.0.0 %n (>= 0.5-pre-1-1377-1) - %p/lib/libcoot-wrap-guile.0.dylib 1.0.0 %n (>= 0.5-pre-1-1377-1) - %p/lib/libcoot-wrap-python.0.dylib 1.0.0 %n (>= 0.5-pre-1-1377-1) - %p/lib/libcootaneer.0.dylib 1.0.0 %n (>= 0.5-pre-1-1377-1) + %p/lib/libccp4mg-surface.0.dylib 1.0.0 %n (>= 0.5-pre-1-1382-1) + %p/lib/libccp4mg-utils.0.dylib 1.0.0 %n (>= 0.5-pre-1-1382-1) + %p/lib/libcoot-analysis.0.dylib 1.0.0 %n (>= 0.5-pre-1-1382-1) + %p/lib/libcoot-AngleInfo.0.dylib 1.0.0 %n (>= 0.5-pre-1-1382-1) + %p/lib/libcoot-atomutils.0.dylib 1.0.0 %n (>= 0.5-pre-1-1382-1) + %p/lib/libcoot-cabuild.0.dylib 1.0.0 %n (>= 0.5-pre-1-1382-1) + %p/lib/libcoot-compat.0.dylib 1.0.0 %n (>= 0.5-pre-1-1382-1) + %p/lib/libcoot-coord-extras.0.dylib 1.0.0 %n (>= 0.5-pre-1-1382-1) + %p/lib/libcoot-coord-utils.0.dylib 1.0.0 %n (>= 0.5-pre-1-1382-1) + %p/lib/libcoot-coords.0.dylib 1.0.0 %n (>= 0.5-pre-1-1382-1) + %p/lib/libcoot-db-main.0.dylib 1.0.0 %n (>= 0.5-pre-1-1382-1) + %p/lib/libcoot-geometry.0.dylib 1.0.0 %n (>= 0.5-pre-1-1382-1) + %p/lib/libcoot-high-res.0.dylib 1.0.0 %n (>= 0.5-pre-1-1382-1) + %p/lib/libcoot-ideal.0.dylib 1.0.0 %n (>= 0.5-pre-1-1382-1) + %p/lib/libcoot-isosurface.0.dylib 1.0.0 %n (>= 0.5-pre-1-1382-1) + %p/lib/libcoot-ligand.0.dylib 1.0.0 %n (>= 0.5-pre-1-1382-1) + %p/lib/libcoot-map-heavy.0.dylib 1.0.0 %n (>= 0.5-pre-1-1382-1) + %p/lib/libcoot-map-utils.0.dylib 1.0.0 %n (>= 0.5-pre-1-1382-1) + %p/lib/libcoot-mini-mol.0.dylib 1.0.0 %n (>= 0.5-pre-1-1382-1) + %p/lib/libcoot-sequence-view.0.dylib 1.0.0 %n (>= 0.5-pre-1-1382-1) + %p/lib/libcoot-shelx.0.dylib 1.0.0 %n (>= 0.5-pre-1-1382-1) + %p/lib/libcoot-skeleton.0.dylib 1.0.0 %n (>= 0.5-pre-1-1382-1) + %p/lib/libcoot-surface.0.dylib 1.0.0 %n (>= 0.5-pre-1-1382-1) + %p/lib/libcoot-tw.0.dylib 1.0.0 %n (>= 0.5-pre-1-1382-1) + %p/lib/libcoot-utils.0.dylib 1.0.0 %n (>= 0.5-pre-1-1382-1) + %p/lib/libcoot-wrap-guile.0.dylib 1.0.0 %n (>= 0.5-pre-1-1382-1) + %p/lib/libcoot-wrap-python.0.dylib 1.0.0 %n (>= 0.5-pre-1-1382-1) + %p/lib/libcootaneer.0.dylib 1.0.0 %n (>= 0.5-pre-1-1382-1) << DocFiles: README AUTHORS NEWS COPYING ABOUT-NLS BUGS TODO << --- NEW FILE: ssm.info --- Package: ssm Version: 0.1 Revision: 5 Maintainer: W. G. Scott <[EMAIL PROTECTED]> DescPackaging: << Based on package created by Morten Kjeldgaard <[EMAIL PROTECTED]> with minor edits to conform to standard Fink packaging requirements. Hack of ssm_superpose.h in the install script is required to prevent run-time error in coot. << # Maintainer: Morten Kjeldgaard <[EMAIL PROTECTED]> Description: Macromolecular coordinate library License: LGPL HomePage: http://www.bioxray.dk/~mok/%N Source: ftp://ftp.bioxray.au.dk/pub/mok/src/%N-%v.tar.gz Source-MD5: 317d9cc78a88fa5652a4a4b06f329823 NoSourceDirectory: false Depends: %n-shlibs (= %v-%r) BuildDepends: mmdb-dev (>= 1.0.10-5) BuildDependsOnly: true DocFiles: README AUTHORS NEWS COPYING DescDetail: << SSM is a macromolecular coordinate superposition library, written by Eugene Krissinel of the EBI. The library implements the SSM algorithm of protein structure comparison in three dimensions, which includes an original procedure of matching graphs built on the protein\'s secondary-structure elements, followed by an iterative three-dimensional alignment of protein backbone Calpha atoms. The algorithm implemented by the software is described in: E. Krissinel & K. Henrick (2004) Secondary-structure matching (SSM), a new tool for fast protein structure alignment in three dimensions. Acta Crystallogr D Biol Crystallogr. 60, 2256-68. << PatchScript: << # # To avoid a conflict with python # perl -pi -e 's|FF1|FF1RENAMED|g' src/ssm_superpose.* perl -pi -e 's|FF2|FF2RENAMED|g' src/ssm_superpose.* # << CompileScript: << ./configure --prefix=%p make << InstallScript: << make install DESTDIR=%d << SplitOff: << Package: %N-shlibs Files: << lib/libssm.0.dylib lib/libssm.0.0.0.dylib << Shlibs: << %p/lib/libssm.0.dylib 1.0.0 %n (>= 0.1-3) << << SplitOff2: << Package: %N-dev BuildDependsOnly: True Conflicts: ccp4-onlylibs-dev Replaces: ccp4-onlylibs-dev Files: << lib/*.a lib/*.la include/ssm/*.h lib/pkgconfig/ssm.pc << << ------------------------------------------------------------------------- This SF.Net email is sponsored by the Moblin Your Move Developer's challenge Build the coolest Linux based applications with Moblin SDK & win great prizes Grand prize is a trip for two to an Open Source event anywhere in the world http://moblin-contest.org/redirect.php?banner_id=100&url=/ _______________________________________________ Fink-commits mailing list Fink-commits@lists.sourceforge.net http://news.gmane.org/gmane.os.apple.fink.cvs