Update of /cvsroot/fink/dists/10.7/stable/main/finkinfo/sci In directory vz-cvs-3.sog:/tmp/cvs-serv3719
Added Files: ccp4.info ccp4.patch Log Message: update to official 6.2.0 release, critical pointless bug-fix, updated for 10.7 --- NEW FILE: ccp4.info --- Package: ccp4 Version: 6.2.0 Revision: 101 GCC: 1 # Source: ftp://ftp.%n.ac.uk/%n/%v/%n-%v-core-src.tar.gz Source-MD5: dabedd4b7f08074bb6716312e236fa2d SourceDirectory: %n-%v # Source2: http://chemistry.ucsc.edu/~wgscott/xtal/xtalfink/XCCPJiffy-custom.gz Source2-MD5: 21568dd2475505929573a3fd452c538f # Source3: ftp://ftp.%n.ac.uk/%n/%v/%n-%v-phaser-cctbx-src.tar.gz Source3-MD5: 15ef58deb26eaacc2bacf7f4ae38d391 # 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. 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. 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 libraries is hard-coded, per fink policy. This obviates the need to set the DYLD_LIBRARY_PATH environment variable, which should remain unset. The appropriate shell startup files are automatically sourced when %p/bin/init.(c)sh is invoked upon shell startup; there is no 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 to keep the ccp4.patch file from growing metastatically and also to permit the user to verify that the latest patches have been applied. These start, when present, with Source2 (above) and are applied individually at the end of the PatchScript field. Clipper libraries are not behaving properly when linked to fink fftw so we return to the option of having ccp4 build its own private fftw. Yes, I hate it too, but now all the examples pass the run-all test. 64-bit version prior to OS X 10.7 appears to require ccp4\'s own 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) 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), bundle-ccp4-intel, bundle-ccp4-powerpc, ccp4-gfortran, ccp4-gfortran-dev, phaser (<= 2.3.0-1), pointless (<= 1.2.18-1) << NoSetCPPFLAGS: true NoSetLDFLAGS: true # ################################################################################ PatchScript: << #!/bin/zsh -efv # umask 0022 # Now apply the primary patch 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 stacksize 65536|limit stacksize unlimited|g' include/ccp4.setup* # same perl -pi.bak -e 's|ccp4_first_in_path=1|ccp4_first_in_path=0|g' include/ccp4.setup* 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 if [[ $(sw_vers -productVersion) < 10.6 ]]; then true else /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 /bin/cp x-windows/Mosflm/src/dps/index/ind_gen_direct.tmp x-windows/Mosflm/src/dps/index/ind_gen_direct.c /bin/rm -f x-windows/Mosflm/src/dps/index/ind_gen_direct.tmp fi # /bin/cp include/ccp4.setup-dist include/ccp4.setup rm -f include/ccp4.setup-sh # # Set up XCCPJiffy wrapper scripts in $CCP4/etc # These are small wrapper scripts for xplot84driver and xloggraph generated by the patch chmod a+x etc/x* # Fix the dylib install path in configure perl -pi.bak -e 's|\$rpath|%p/lib/ccp4-%v|g' **/configure # perl -pi.bak -e 's|import sys|import sys\nsys.path.append(\"%p/share/xtal/%n-%v/share/python\")|g' src/buccaneer_pipeline.py # /bin/rm -f *.bak **/configure*.bak src/buccaneer_pipeline*.bak include/*.bak << ################################################################################ CompileScript: << #!/bin/bash -efv umask 0022 # These are required for the build environment TEMPXTAL=$(dirname $PWD) export TEMPXTAL export CCP4_VERSION="" export CCP4_MASTER="" export BLTWISHPREFIX="" export CCP4="" # Fix for problem reported with 10.4 if [[ $(sw_vers -productVersion) < 10.5 ]]; then cp $PWD/include/ccp4.setup-bash $PWD/include/ccp4.setup-bash-10.4 export CURRENT_MASTER=$( dirname $PWD ) perl -pi -e "s|export CCP4_MASTER|export CCP4_MASTER=$CURRENT_MASTER|g" $PWD/include/ccp4.setup-bash-10.4 source $PWD/include/ccp4.setup-bash-10.4 else source $PWD/include/ccp4.setup-bash fi # echo $PWD should be the same as $CCP4 [[ $CCP4 == $PWD ]] || exit 1 set +x export DYLD_LIBRARY_PATH=$CLIB export GFORTRAN_UNBUFFERED_ALL="Y" export rpath=%p/lib/ccp4-%v export RPATH=%p/lib/ccp4-%v export PATH=%p/lib/xmkmf/bin:$PATH export IMAKEINCLUDE=-I%p/lib/X11/config export FC="gfortran" export libdir="$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 # # #if [[ $(sw_vers -productVersion) < 10.7 ]]; then F_LIBS="-L%p/lib/gcc4.6/lib -lgfortran " \ ./configure --with-netlib-lapack --with-shared-libs --with-x Darwin #else # F_LIBS="-L%p/lib/gcc4.6/lib -lgfortran " \ # ./configure --with-shared-libs --with-x Darwin #fi # # 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/gcc4.6/lib |g' *akefile* ) || exit 1 if [[ $(sw_vers -productVersion) < 10.5 ]]; then perl -pi.bak -e 's| -flat_namespace -undefined suppress| -twolevel_namespace -undefined dynamic_lookup|g' lib/src/Makefile fi perl -pi.bak -e "s|-lcrt1.10.6.o||g" Makefile ccp4i/Makefile deprecated/src/Makefile lib/data/Makefile lib/src/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 perl -pi.bak -e "s|-lcrt1.10.5.o||g" Makefile ccp4i/Makefile deprecated/src/Makefile lib/data/Makefile lib/src/Makefile share/Makefile src/Makefile perl -pi.bak -e "s|-lcrt1.10.5.o||g" src/ccp4mapwish_/Makefile unsupported/src/Makefile x-windows/Makefile x-windows/Mosflm/mosflm/Makefile x-windows/Rotgen/Makefile perl -pi.bak -e "s|-lcrt1.o||g" Makefile ccp4i/Makefile deprecated/src/Makefile lib/data/Makefile lib/src/Makefile share/Makefile src/Makefile perl -pi.bak -e "s|-lcrt1.o||g" src/ccp4mapwish_/Makefile unsupported/src/Makefile x-windows/Makefile x-windows/Mosflm/mosflm/Makefile x-windows/Rotgen/Makefile # Fix for pointless, bp3 etc to prevent linking to gcc4.6 libraries as this creates a run-time error perl -pi.mod -e 's|-O2|-O3|g' src/pointless/Makefile grep -v "gcc4.6" src/pointless/Makefile.mod > src/pointless/Makefile # Fix newly indtroduced X11 library error perl -pi.bak -e 's|/usr/X11R6/lib64|/usr/X11R6/lib|g' Makefile ccp4i/Makefile deprecated/src/Makefile lib/data/Makefile lib/src/Makefile share/Makefile src/Makefile src/ccp4mapwish_/Makefile unsupported/src/Makefile x-windows/Makefile # Fix newly intdroduced ccif error perl -pi.bak -e 's|LD_LIBRARY_PATH|DYLD_LIBRARY_PATH|g' lib/ccif/Makefile ################# ################# cd $CCP4 make make install ################# ################# # xloggraph may fail, but we will link it with gfortran below # # Make wrappers for xplot84driver and xloggraph, so rename the executables cd x-windows/XCCPJIFFY if [[ "%m" != "x86_64" ]]; then make msg_box.o ZDr2d.o EditString.o hardcopy_ctrl.o xloggraph.o log_file.o tom_fortran_interface.o bits_and_pieces.o graphics.o CFLAGS="-m32" FFLAGS="-m32" else make msg_box.o ZDr2d.o EditString.o hardcopy_ctrl.o xloggraph.o log_file.o tom_fortran_interface.o bits_and_pieces.o graphics.o CFLAGS="-m64" FFLAGS="-m64" fi gcc -o xplot84driver xplot84driver.o plot84_file.o msg_box.o ZDr2d.o EditString.o hardcopy_ctrl.o -Os -I/usr/include/X11R6 -L/usr/X11R6/lib -lXaw -lXmu -lXt -lSM -lICE -lXpm -lXp -lXext -lX11 -lm -L%p/lib/gcc4.6/lib -lgfortran cp xplot84driver $CBIN/xplot84driver.exe if [[ -x $CBIN/xplot84driver ]];then /bin/rm -f $CBIN/xplot84driver fi make xccpjiffy2idraw cp xccpjiffy2idraw $CBIN/. cd .. make xdlmapman xdldataman cp xdlmapman $CBIN/. cp xdldataman $CBIN/. # Manually link xloggraph with gfortran (fails in make) echo "" echo "**********************************************************************" echo "Re-linking xloggraph with gfortran. Ignore previous error messages." echo "**********************************************************************" echo "" # cd XCCPJIFFY # Check to see if it really did fail before we try again. if [[ -x $CBIN/xloggraph ]];then true else gfortran -o xloggraph msg_box.o ZDr2d.o EditString.o hardcopy_ctrl.o xloggraph.o log_file.o tom_fortran_interface.o bits_and_pieces.o graphics.o -g -Os -I/usr/include/X11R6 -L/usr/X11R6/lib -lXaw -lXmu -lXt -lSM -lICE -lXpm -lXext -lX11 -lm -lgfortran -L%p/lib/gcc4.6/lib fi # sleep 10 # cp xloggraph $CBIN/xloggraph.exe if [[ -x $CBIN/xloggraph ]];then /bin/rm -f $CBIN/xloggraph fi cd ../.. # # Cleanup: # Get rid of the corrupting influence of ccp4's own xml2-config: if [[ -x $CBIN/xml2-config ]];then /bin/rm -f $CBIN/xml2-config fi # Do the rest in the InstallScript to take advantage of zsh. << ################################################################################ InstallScript: << #!/bin/zsh -efv umask 0022 export TEMPXTAL=$PWD:h source $PWD/include/ccp4.setup-zsh export DYLD_LIBRARY_PATH=$CLIB ORIGDIR=$(dirname $PWD) export PATH=%p/lib/xmkmf/bin:$PATH 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 /bin/rm -Rf lib/cctbx /bin/rm -Rf lib/**/.libs /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* # Change environment scripts to match final installation perl -pi -e 's|\$TEMPXTAL|%p/share/xtal|g' include/ccp4.setup* # install prefix # # Bugzilla number : #3593 perl -pi -e "s|$PWD|%p/share/xtal/%n-%v|g" share/pisa/pisa.cfg # # cp ../XCCPJiffy-custom.gz XCCPJiffy.gz ; gunzip XCCPJiffy.gz; chmod a+x XCCPJiffy perl -pi -e 's|5.0.1|%v|g' XCCPJiffy mv -f XCCPJiffy lib/X11/app-defaults/XCCPJiffy # perl -pi.bak -e 's|/src/fink.build/ccp4-%v-%r|/share/xtal|g' bin/clipper-config rm -f bin/clipper-config.bak perl -pi.bak -e 's|lclipper |lclipper-core |g' bin/clipper-config rm -f bin/clipper-config.bak perl -pi.bak -e 's|lib/lib -lrfftw -lfftw |lib/ccp4-%v -lsrfftw -lsfftw |g' bin/clipper-config rm -f bin/clipper-config.bak # # Fix path in libfoo.la libtool files: # 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 ####### # make and install the leiden stuff. It has to go here. cd $CCP4/src/leiden make clean perl -pi -e 's|LAPACK_LIBS = -framework vecLib -L%p/lib/gcc4.6/lib -lgfortran|LAPACK_LIBS = -L$CLIB/lapack|g' **/Makefile perl -pi -e 's|FCLIBS = -L%p/lib/gcc4.6/lib/gcc/x86_64-apple-darwin11.0.0/4.6.1 -L%p/lib/gcc4.6/lib/gcc/x86_64-apple-darwin11.0.0/4.6.1/../../.. -lgfortran -lquadmath -lm||g' **/Makefile perl -pi -e 's|-L%p/lib/gcc4.6/lib -lgfortran||g' **/Makefile make -i make -i install cd $CCP4 ################# # More cleanup: /bin/rm -Rf src/leiden/bp3lib/src/.libs /bin/rm -f **/*.o 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 ###### # # Now install: # mkdir -p %i/lib cp -R lib %i/lib/ccp4-%v mkdir -p %i/bin # mkdir -p %i/share/xtal/ccp4-%v/help mkdir -p %i/share/man/man1 # set up man pages in a fink-compliant manner cd $PWD/doc mv rasmol.doc eightbit_rasmol.doc foreach docfilepage ( *.doc ) cp ${docfilepage} %i/share/man/man1/${docfilepage:r}.1 cp ${docfilepage} %i/share/xtal/ccp4-%v/help/${docfilepage:r} end # back to build directory cd .. # /bin/rm -rf lib cp -R * %i/share/xtal/ccp4-%v/. ln -s %p/lib/ccp4-%v %i/share/xtal/ccp4-%v/lib # # making scripts for %p/etc/profile.d mkdir -p %i/etc/profile.d # echo "source %p/share/xtal/ccp4-%v/include/ccp4.setup" > %i/etc/profile.d/ccp4.csh echo "setenv CLIB %p/lib/ccp4-%v " >> %i/etc/profile.d/ccp4.csh # echo "if [ -z \$ZSH_NAME ];then " > %i/etc/profile.d/ccp4.sh echo " source %p/share/xtal/ccp4-%v/include/ccp4.setup-bash " >> %i/etc/profile.d/ccp4.sh echo "else " >> %i/etc/profile.d/ccp4.sh echo " source %p/share/xtal/ccp4-%v/include/ccp4.setup-zsh" >> %i/etc/profile.d/ccp4.sh echo "fi " >> %i/etc/profile.d/ccp4.sh echo "export CLIB=%p/lib/ccp4-%v " >> %i/etc/profile.d/ccp4.sh # chmod a+x %i/etc/profile.d/ccp4.* # chmod a+x %i/share/xtal/ccp4-%v/ccp4i/etc/osx_ccp4_mail # chmod a+r,a+x %i/share/xtal/ccp4-%v/etc/* chmod a+r,a+x %i/share/xtal/ccp4-%v/bin/* chmod a+r,a+x %i/share/xtal/ccp4-%v/ccp4i/bin/* chmod a+r,a+x %i/share/xtal/ccp4-%v/share/dbccp4i/bin/* chmod a+r,a+x %i/share/xtal/ccp4-6.2.0/ccp4i/imosflm/src/* # # chmod a+x %i/share/xtal/ccp4-%v/etc/ccp4help # ranlib %i/lib/ccp4-%v/*.a ranlib %i/lib/ccp4-%v/**/*.a # perl -pi -e 's|%p/share/%p/share|%p/share|g' %i/share/xtal/ccp4-%v/include/ccp4.setup* # fix # remove build path from .la files # perl -pi -e "s, \-L[^ ']*/%n-%v-%r/%n-%v/src/rapper/libxml2/.libs, \-L %p/lib,g" %i/lib/%n-%v/python*/site-packages/**/*.la # don't package these .la files /usr/bin/find %i/share/xtal/%n-%v/src/rapper -name '*.la' -delete /usr/bin/find %i/share/xtal/%n-%v/x-windows -name '*.la' -delete /usr/bin/find %i/share/xtal/%n-%v/src/leiden/bp3lib/src -name '*.la' -delete /usr/bin/find %i/share/xtal/%n-%v/src/Prodrg -name '*.la' -delete # hand install these shared libraries for now mv %i/share/xtal/ccp4-%v/src/phaser/phaser-2.3.0/build/mac-osx/lib/libboost_python.dylib %i/lib/ccp4-%v install_name_tool -id %p/lib/ccp4-%v/libboost_python.dylib %i/lib/ccp4-%v/libboost_python.dylib mv %i/share/xtal/ccp4-%v/x-windows/libjwc/libjwc_c/.libs/libjwc_c.0.1.1.dylib %i/lib/ccp4-%v install_name_tool -id %p/lib/ccp4-6.2.0/libjwc_c.0.dylib %i/lib/ccp4-%v/libjwc_c.0.1.1.dylib mv %i/share/xtal/ccp4-%v/x-windows/xdl_view/src/.libs/libxdl_view.2.0.0.dylib %i/lib/ccp4-%v install_name_tool -id %p/lib/ccp4-%v/libxdl_view.2.dylib %i/lib/ccp4-%v/libxdl_view.2.0.0.dylib mv %i/share/xtal/ccp4-%v/x-windows/xdl_view/src/.libs/libxdl_viewextra.0.0.0.dylib %i/lib/ccp4-%v install_name_tool -id %p/lib/ccp4-%v/libxdl_viewextra.0.dylib %i/lib/ccp4-%v/libxdl_viewextra.0.0.0.dylib # don't package .pyc files generated in the buildroot /usr/bin/find %i/share/xtal/%n-%v/src/phaser/phaser-2.3.0 -name '*.pyc' -delete << ################################################################################ PreRmScript: << [[ -d %p/share/xtal/%n-%v/src/phaser/phaser-2.3.0 ]] && /usr/bin/find %p/share/xtal/%n-%v/src/phaser/phaser-2.3.0 -name '*.pyo' -delete << ################################################################################ PostInstScript: << PyVers=$( /usr/bin/python --version 2>&1 | awk '{print $NF}' ) if [[ $PyVers:r == 2.6 ]]; then /usr/bin/python -O /usr/lib/python2.6/compileall.py -q %p/share/xtal/%n-%v/src/phaser/phaser-2.3.0 elif [[ $PyVers:r == 2.5 ]]; then /usr/bin/python -O /usr/lib/python2.5/compileall.py -q %p/share/xtal/%n-%v/src/phaser/phaser-2.3.0 elif [[ $PyVers:r == 2.4 ]]; then /usr/bin/python -O /usr/lib/python2.4/compileall.py -q %p/share/xtal/%n-%v/src/phaser/phaser-2.3.0 fi # Make the user read the license conditions more %p/share/xtal/ccp4-%v/conditions.txt << ################################################################################ ################################################################################ SplitOff: << Package: %N-shlibs Description: CCP4 dynamic libraries Files:<< lib/ccp4-%v/*.*.dylib lib/ccp4-%v/libccif.dylib lib/ccp4-%v/libccp4c.dylib lib/ccp4-%v/libmmdb.dylib lib/ccp4-%v/libboost_python.dylib << Shlibs: << %p/lib/ccp4-%v/libDiffractionImage.0.dylib 1.0.0 %n (>= 6.2.0-1) %p/lib/ccp4-%v/lib_DiffractionImage.0.dylib 1.0.0 %n (>= 6.2.0-1) %p/lib/ccp4-%v/libccif.dylib 0.0.0 %n (>= 6.2.0-1) %p/lib/ccp4-%v/libccp4c.dylib 0.0.0 %n (>= 6.2.0-1) %p/lib/ccp4-%v/libclipper-ccp4.2.dylib 3.0.0 %n (>= 6.2.0-1) %p/lib/ccp4-%v/libclipper-cif.2.dylib 3.0.0 %n (>= 6.2.0-1) %p/lib/ccp4-%v/libclipper-cns.0.dylib 1.0.0 %n (>= 6.2.0-1) %p/lib/ccp4-%v/libclipper-contrib.2.dylib 3.0.0 %n (>= 6.2.0-1) %p/lib/ccp4-%v/libclipper-core.2.dylib 3.0.0 %n (>= 6.2.0-1) %p/lib/ccp4-%v/libclipper-minimol.2.dylib 3.0.0 %n (>= 6.2.0-1) %p/lib/ccp4-%v/libclipper-mmdb.2.dylib 3.0.0 %n (>= 6.2.0-1) %p/lib/ccp4-%v/libclipper-phs.2.dylib 3.0.0 %n (>= 6.2.0-1) %p/lib/ccp4-%v/libjwc_c.0.dylib 2.0.0 %n (>= 6.2.0-1) %p/lib/ccp4-%v/libmmdb.dylib 0.0.0 %n (>= 6.2.0-1) %p/lib/ccp4-%v/libssm.0.dylib 1.0.0 %n (>= 6.2.0-1) %p/lib/ccp4-%v/libxdl_view.2.dylib 3.0.0 %n (>= 6.2.0-1) %p/lib/ccp4-%v/libxdl_viewextra.0.dylib 1.0.0 %n (>= 6.2.0-1) %p/lib/ccp4-%v/libfftw.2.dylib 3.0.0 %n (>= 6.2.0-1) %p/lib/ccp4-%v/librfftw.2.dylib 3.0.0 %n (>= 6.2.0-1) %p/lib/ccp4-%v/libboost_python.dylib 0.0.0 %n (>= 6.2.0-1) %p/lib/ccp4-%v/libbp3.1.dylib 2.0.0 %n (>= 6.2.0-1) %p/lib/ccp4-%v/libprodrg.0.dylib 1.0.0 %n (>= 6.2.0-1) << DocFiles: CHANGES COPYING INSTALL INSTALL.html INSTALL.ps README PROBLEMS academic_software_licence.pdf << ################################################################################ ################################################################################ SplitOff2: << Package: %N-dev BuildDependsOnly: true Conflicts: gpp4-dev, ssm-dev, mmdb-dev, clipper-dev, ccp4-onlylibs-dev Replaces: gpp4-dev, ssm-dev, mmdb-dev, clipper-dev, ccp4-onlylibs-dev Description: CCP4 static libraries and libtool files Files:<< lib/ccp4-%v/*.a lib/ccp4-%v/*.la << DocFiles: CHANGES COPYING INSTALL INSTALL.html INSTALL.ps README PROBLEMS academic_software_licence.pdf << ################################################################################ Description: Macromolecular crystallography package DescDetail: << The CCP4 macromolecular crystallography suite has approximately 200 programs and utilities. This version includes the Clipper libraries. Current phaser and cctbx programs are available as separate fink packages. Type "ccp4help" for a summary listing of all ccp4 programs. Type "ccp4help foo" for a detailed description of program "foo." Invoke optional ccp4i gui for the first run using "sudo ccp4i" on 10.4, or "sudo -E ccp4i" on 10.5 and above to permit global configuration. Thereafter, you can invoke ccp4i without sudo. This version compiles with the Apple Lapack/Blas framework. License agreement is part of configure file -- print out form and mail in, additional comments at http://sage.ucsc.edu/xtal/ccp4.html CCP4 files will be installed under /sw/share/xtal/ccp4-6.2.0 This revision includes all available CCP4 patches, and new bash and zsh command completions specific to ccp4. The ccp4-associated molecular graphics display program coot is also available as a fink package. It builds against the GPL gpp4 libraries rather than those of this package. Thanks to Jack Howarth for many helpful improvements. << DocFiles: << README CHANGES COPYING PROBLEMS INSTALL INSTALL.html INSTALL.ps ccp4i_installation.html academic_software_licence.pdf academic_software_licence.ps.gz academic_software_licence.rtf << Homepage: http://www.ccp4.ac.uk License: Commercial Maintainer: W. G. Scott <wgsc...@users.sourceforge.net> --- NEW FILE: ccp4.patch --- diff -ruN ccp4-6.2.0-dist/ccp4i/bin/imosflm ccp4-6.2.0/ccp4i/bin/imosflm --- ccp4-6.2.0-dist/ccp4i/bin/imosflm 2009-04-21 05:46:23.000000000 -0700 +++ ccp4-6.2.0/ccp4i/bin/imosflm 2010-12-17 20:33:01.000000000 -0800 @@ -1,3 +1,14 @@ #!/bin/sh # Start iMosflm interface +if [[ $(uname) == Darwin ]];then + + CCP4_BROWSER="" + export CCP4_BROWSER="Safari" + + if [[ $(sw_vers -productVersion) < 10.6 ]]; then + true + else + export MOSFLM_WISH=/usr/bin/wish8.4 + fi +fi exec $CCP4I_TOP/imosflm/src/imosflm diff -ruN ccp4-6.2.0-dist/ccp4i/etc/configure.def.dist ccp4-6.2.0/ccp4i/etc/configure.def.dist [...1876 lines suppressed...] --- ccp4-6.2.0.orig/src/refmac5_/covmat.h 2011-07-19 12:47:52.000000000 -0400 +++ ccp4-6.2.0/src/refmac5_/covmat.h 2011-07-19 12:50:33.000000000 -0400 @@ -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 @@ -2036,7 +2036,7 @@ // defines zero rows. If the first argument is negative, resets all no non-zero. template <typename realnum> -void covar_matrix<realnum>::SetZeroRows( int r1=-1, int r2=-1, int r3=-1, int r4=-1, int r5=-1, int r6=-1 ) +void covar_matrix<realnum>::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; ------------------------------------------------------------------------------ Got Input? Slashdot Needs You. Take our quick survey online. Come on, we don't ask for help often. Plus, you'll get a chance to win $100 to spend on ThinkGeek. http://p.sf.net/sfu/slashdot-survey _______________________________________________ Fink-commits mailing list Fink-commits@lists.sourceforge.net http://news.gmane.org/gmane.os.apple.fink.cvs