Update of /cvsroot/fink/dists/10.7/stable/main/finkinfo/sci
In directory vz-cvs-3.sog:/tmp/cvs-serv25974
Modified Files:
ccp4.info ccp4.patch
Log Message:
new version compatible with 10.8 and gcc47
Index: ccp4.info
===================================================================
RCS file: /cvsroot/fink/dists/10.7/stable/main/finkinfo/sci/ccp4.info,v
retrieving revision 1.7
retrieving revision 1.8
diff -u -d -r1.7 -r1.8
--- ccp4.info 1 Oct 2011 03:43:05 -0000 1.7
+++ ccp4.info 12 Sep 2012 06:31:56 -0000 1.8
@@ -1,25 +1,23 @@
Package: ccp4
-Version: 6.2.0
-Revision: 102
+Version: 6.3.0
+Revision: 1
GCC: 4.0
UseMaxBuildJobs: false
#
Source: ftp://ftp.%n.ac.uk/%n/%v/%n-%v-core-src.tar.gz
-Source-MD5: 1a087d3310d70501ac370804a11f341d
+Source-MD5: 5558ed62767ca0b8fbd31742b130eb61
SourceDirectory: %n-%v
#
-Source2: http://www.chem.ucsc.edu/~wgscott/xtal/xtalfink/XCCPJiffy-custom.gz
-Source2-MD5: 21568dd2475505929573a3fd452c538f
+Source2: ftp://ftp.%n.ac.uk/%n/%v/%n-%v-phaser-cctbx-src.tar.gz
+Source2-MD5: 018765c258b70726b281de506e9139c4
+#
+Source3: http://www.chem.ucsc.edu/~wgscott/xtal/xtalfink/XCCPJiffy-custom.gz
+Source3-MD5: 21568dd2475505929573a3fd452c538f
#
-Source3: ftp://ftp.%n.ac.uk/%n/%v/%n-%v-phaser-cctbx-src.tar.gz
-Source3-MD5: 15ef58deb26eaacc2bacf7f4ae38d391
+PatchFile: ccp4.patch
+PatchFile-MD5: 14418f959400df7232a5c9f1edfa5284
#
-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.
@@ -62,8 +60,8 @@
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)
+Depends: x11, tcltk, blt, gcc47-shlibs, %N-shlibs (= %v-%r)
+BuildDepends: gcc47, 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
@@ -84,6 +82,7 @@
NoSetLDFLAGS: true
#
################################################################################
+#################################################################################
PatchScript: <<
#!/bin/zsh -efv
#
@@ -104,7 +103,9 @@
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
+ perl -pi -e 's|Please get the person who installed CCP4i to run
it|Please issue the command \\\"sudo -E ccp4i\\\"|g' share/ccp4i/src/system.tcl
+ perl -pi -e 's|CCP4/ccp4i|CCP4/share/ccp4i|g' include/ccp4.setup*
+ perl -pi -e 's|\{CCP4\}/ccp4i|\{CCP4\}/share/ccp4i|g' include/ccp4.setup*
if [[ $(sw_vers -productVersion) < 10.6 ]]; then
true
else
@@ -114,7 +115,7 @@
fi
#
/bin/cp include/ccp4.setup-dist include/ccp4.setup
- rm -f include/ccp4.setup-sh
+ # rm -f include/ccp4.setup-sh
#
# Set up XCCPJiffy wrapper scripts in $CCP4/etc
# These are small wrapper scripts for xplot84driver and xloggraph
generated by the patch
@@ -125,8 +126,18 @@
perl -pi.bak -e 's|import sys|import
sys\nsys.path.append(\"%p/share/xtal/%n-%v/share/python\")|g'
src/buccaneer_pipeline.py
#
/bin/rm -f *.bak **/configure*.bak src/buccaneer_pipeline*.bak
include/*.bak
+ #
+ perl -pi -e 's,\| grep crt1,,g' configure
+ #
+ perl -pi -e 's|python
../cctbx_sources/cctbx_project/libtbx/configure.py|python
../cctbx_sources/cctbx_project/libtbx/configure.py --compiler=gcc |g'
lib/cctbx/ccp4_build
+ #
+ perl -pi -e 's|phaseropts="\$phaseropts \$1"|phaseropts="\$phaseropts
--compiler=gcc \$1"|g' src/phaser/ccp4_build
+ #
+ NUMPROC="$(sysctl -n hw.ncpu)"
+ perl -pi -e "s|libtbx.scons|libtbx.scons -j $NUMPROC |g"
lib/cctbx/ccp4_build
<<
################################################################################
+#################################################################################
CompileScript: <<
#!/bin/bash -efv
umask 0022
@@ -149,7 +160,9 @@
#
echo $PWD should be the same as $CCP4
[[ $CCP4 == $PWD ]] || exit 1
-set +x
+
+CLIB="%p/lib/ccp4-6.3.0"
+export CLIB
export DYLD_LIBRARY_PATH=$CLIB
export GFORTRAN_UNBUFFERED_ALL="Y"
export rpath=%p/lib/ccp4-%v
@@ -157,6 +170,8 @@
export PATH=%p/lib/xmkmf/bin:$PATH
export IMAKEINCLUDE=-I%p/lib/X11/config
export FC="gfortran"
+export CC="/usr/bin/gcc"
+export CXX="/usr/bin/g++"
export libdir="$PWD/lib"
#
# Uncomment the following line only for testing purposes. The ccp4
restrictive/commercial
@@ -164,110 +179,123 @@
#
# 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
+
+ F_LIBS="-L%p/lib/gcc4.7/lib -lgfortran " \
+ ./configure --disable-cctbx --disable-phaser --with-netlib-lapack
--with-shared-libs --with-x Darwin
#
# 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
+( cd x-windows/XCCPJIFFY; perl -pi.bak -e 's|-lgfortran|-lgfortran
-L%p/lib/gcc4.7/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" Makefile share/ccp4i/Makefile
deprecated/src/Makefile lib/data/Makefile lib/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" Makefile share/ccp4i/Makefile
deprecated/src/Makefile lib/data/Makefile lib/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" Makefile share/ccp4i/Makefile
deprecated/src/Makefile lib/data/Makefile lib/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
+# Fix for pointless, bp3 etc to prevent linking to gcc4.7 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
+#grep -v "gcc4.7" 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
+perl -pi.bak -e 's|R/usr|L/usr|g' x-windows/Mosflm/mosflm/Makefile
+
+
# Fix newly intdroduced ccif error
perl -pi.bak -e 's|LD_LIBRARY_PATH|DYLD_LIBRARY_PATH|g' lib/ccif/Makefile
+#### Try rapper fix here
+
+cd $CCP4/src/rapper
+./configure --prefix=$PWD CC=/usr/bin/clang CXX=/usr/bin/clang++ CFLAGS="-O3"
#################
#################
+NUMPROC="$(sysctl -n hw.ncpu)"
cd $CCP4
-make
-make install
+make -i -j $NUMPROC
+make -i -j $NUMPROC 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:
+ cd x-windows/XCCPJIFFY
+ perl -pi -e 's|\-lgfortran| |g' Makefile
+ make
+ make xccpjiffy2idraw
+ cp xccpjiffy2idraw $CBIN/.
+ cd ..
+ make xdlmapman xdldataman
+ cp xdlmapman $CBIN/.
+ cp xdldataman $CBIN/.
-# 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 $PWD/include/ccp4.setup-zsh
+ NUMPROC="$(sysctl -n hw.ncpu)"
+
+ cd lib/cctbx
+ ./ccp4_build
+
+ cd $CCP4
+
+ cd src/pointless
+ ./configure --with-clipper=$CCP4 --with-fftw=$CCP4
FFTW_LIBS="-L$CCP4/lib -lrfftw -lfftw" FFTW_CXXFLAGS="-I$CCP4/lib/fftw/fftw
-I$CCP4/lib/fftw/rfftw -I$CCP4/include -I$CCP4/lib/libccp4 -I$CCP4/lib/mmdb"
--with-ccp4=$CCP4 CXXFLAGS="-O2 " --with-cctbx=$CCP4/lib/cctbx/cctbx_sources
--with-cctbx-build=$CCP4/lib/cctbx/cctbx_build CXXFLAGS="-O2 " CXXFLAGS="-O2
" --prefix=$CCP4 --bindir=$CCP4/bin LDFLAGS=-L$CCP4/lib CXX="/usr/bin/g++"
CC="/usr/bin/gcc"
+ make -j $NUMPROC install
+
+ cd $CCP4
+ cd src/aimless
+ ./configure --with-clipper=$CCP4 --with-fftw=$CCP4
FFTW_LIBS="-L$CCP4/lib -lrfftw -lfftw" FFTW_CXXFLAGS="-I$CCP4/lib/fftw/fftw
-I$CCP4/lib/fftw/rfftw -I$CCP4/include -I$CCP4/lib/libccp4 -I$CCP4/lib/mmdb"
--with-ccp4=$CCP4 CXXFLAGS="-O2 " --with-cctbx=$CCP4/lib/cctbx/cctbx_sources
--with-cctbx-build=$CCP4/lib/cctbx/cctbx_build CXXFLAGS="-O2 " CXXFLAGS="-O2
" --prefix=$CCP4 --bindir=$CCP4/bin LDFLAGS=-L$CCP4/lib CXX="/usr/bin/g++"
CC="/usr/bin/gcc"
+ make -j $NUMPROC install
+
+ cd $CCP4
+ cd src/phaser
+ mv bin bin.sav
+ /usr/bin/python
$CCP4/lib/cctbx/cctbx_sources/cctbx_project/libtbx/configure.py
--clear-scons-memory --repository=source --compiler=gcc phaser
--build-boost-python-extensions=false
+ source setpaths.sh
+ libtbx.scons -j $NUMPROC .
+ cd exe
+ cp phaser $CCP4/bin/.
+
+ cd $CCP4
+
+ # rapper manual install
+ if [[ -x src/rapper/bin/rapper ]]; then
+ cp src/rapper/bin/rapper $CCP4/bin/.
+ cp src/rapper/lib/libcord.1.0.3.dylib $CCP4/lib/libcord.1.dylib
+ cp src/rapper/lib/libgc.1.0.3.dylib $CCP4/lib/libgc.1.dylib
+ cp src/rapper/lib/libxml2.2.dylib $CCP4/lib/libxml2.2.dylib
+ /bin/rm -rf src/rapper/lib/*.dylib
+ fi
+
+
export DYLD_LIBRARY_PATH=$CLIB
+ cd $CLIB/libccp4
+ gfortran -m64 -fno-second-underscore -O2 -fno-second-underscore -L$CLIB
-o data/fontpack data/fontpack.o -lccp4f -lccp4c
+ cd data
+ ./fontpack
+ cp font84.dat $CLIB/.
+ cd $CCP4
+
+ cp lib/ccif/data/*.lib lib/.
+
+
ORIGDIR=$(dirname $PWD)
export PATH=%p/lib/xmkmf/bin:$PATH
@@ -279,8 +307,7 @@
/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 lib/**/.libs
/bin/rm -Rf src/leiden/bp3lib/src/.libs
/bin/rm -Rf src/Prodrg/.libs
/bin/rm -f lib/ccif/libccif.dylib
@@ -311,25 +338,15 @@
# 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/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
+#/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
@@ -337,26 +354,34 @@
######
#
# Now install:
+
+ # Fix for relative path in the install_name of libboost_python.dylib
+ install_name_tool -id
%p/lib/%n-%v/cctbx/cctbx_build/lib/libboost_python.dylib
lib/cctbx/cctbx_build/lib/libboost_python.dylib
+
#
+ cd %b
mkdir -p %i/lib
- cp -R lib %i/lib/ccp4-%v
+ #
+ /bin/rm -rf lib/cctbx/cctbx_sources/**/*.pyc
+ /bin/rm -f lib/libclipper-cif.la lib/libclipper-minimol.la
lib/libclipper-mmdb.la
+ cp -R lib %i/lib/%n-%v
mkdir -p %i/bin
#
- mkdir -p %i/share/xtal/ccp4-%v/help
+ mkdir -p %i/share/xtal/%n-%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}
+ cp ${docfilepage} %i/share/xtal/%n-%v/help/${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
+ cd $CCP4
+ #
+
+ /bin/rm -rf lib
+ cp -R * %i/share/xtal/%n-%v/.
+ ln -s %p/lib/%n-%v %i/share/xtal/%n-%v/lib
#
# making scripts for %p/etc/profile.d
mkdir -p %i/etc/profile.d
@@ -374,18 +399,18 @@
#
chmod a+x %i/etc/profile.d/ccp4.*
#
- chmod a+x %i/share/xtal/ccp4-%v/ccp4i/etc/osx_ccp4_mail
+ #chmod a+x %i/share/xtal/ccp4-%v/share/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/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+r,a+x %i/share/xtal/ccp4-6.3.0/share/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
+ ranlib %i/lib/%n-%v/*.a
+ ranlib %i/lib/%n-%v/**/*.a
#
perl -pi -e 's|%p/share/%p/share|%p/share|g'
%i/share/xtal/ccp4-%v/include/ccp4.setup* # fix
@@ -393,46 +418,33 @@
# 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
+ /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
+ /usr/bin/find %i/lib/%n-%v/clipper/clipper -name '*.la' -delete
+
+ # # don't package .pyc files generated in the buildroot
+ /usr/bin/find %i/share/xtal/%n-%v/src/phaser -name '*.pyc' -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
+## Final cleanup:
+ cd $CCP4
+ echo "Final cleanup in $PWD"
+
+ /bin/rm -rf %i/**/.libs
+ /bin/rm -rf %i/**/.deps
+ /bin/rm -rf %i/**/*.pc
<<
-################################################################################
-PreRmScript: <<
- [[ -d %p/share/xtal/%n-%v/src/phaser/phaser-2.3.0 ]] && /usr/bin/find
%p/share/xtal/%n-%v/src/phaser/phaser-2.3.0 -name '*.pyo' -delete
-<<
-################################################################################
+#################################################################################
+#################################################################################
PostInstScript: <<
-
-PyVers=$( /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
+cd %p/share/xtal/%n-%v && ./src/phaser/bin/libtbx.refresh
+cd %p/lib/%n-%v/cctbx && ./cctbx_build/bin/libtbx.refresh
+# Make the user read the license conditions
+more %p/share/xtal/ccp4-%v/conditions.txt
<<
################################################################################
################################################################################
@@ -441,36 +453,38 @@
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
+ lib/ccp4-%v/cctbx/cctbx_build/lib/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)
+ %p/lib/ccp4-%v/libDiffractionImage.0.dylib 1.0.0 %n
(>= 6.3.0-1)
+ %p/lib/ccp4-%v/lib_DiffractionImage.0.dylib 1.0.0 %n
(>= 6.3.0-1)
+ %p/lib/ccp4-%v/libccif.0.dylib
1.0.0 %n (>= 6.3.0-1)
+ %p/lib/ccp4-%v/libccp4c.0.dylib
1.0.0 %n (>= 6.3.0-1)
+ %p/lib/ccp4-%v/libccp4srs.0.dylib
1.0.0 %n (>= 6.3.0-1)
+ %p/lib/ccp4-%v/libccp4f.0.dylib
1.0.0 %n (>= 6.3.0-1)
+ %p/lib/ccp4-%v/libclipper-ccp4.2.dylib 3.0.0 %n
(>= 6.3.0-1)
+ %p/lib/ccp4-%v/libclipper-cif.2.dylib 3.0.0 %n
(>= 6.3.0-1)
+ %p/lib/ccp4-%v/libclipper-cns.0.dylib 1.0.0 %n
(>= 6.3.0-1)
+ %p/lib/ccp4-%v/libclipper-contrib.2.dylib 3.0.0 %n
(>= 6.3.0-1)
+ %p/lib/ccp4-%v/libclipper-core.2.dylib 3.0.0 %n
(>= 6.3.0-1)
+ %p/lib/ccp4-%v/libclipper-minimol.2.dylib 3.0.0 %n
(>= 6.3.0-1)
+ %p/lib/ccp4-%v/libclipper-mmdb.2.dylib 3.0.0 %n
(>= 6.3.0-1)
+ %p/lib/ccp4-%v/libclipper-phs.2.dylib 3.0.0 %n
(>= 6.3.0-1)
+ %p/lib/ccp4-%v/libjwc_c.0.dylib 2.0.0 %n
(>= 6.3.0-1)
+ %p/lib/ccp4-%v/libmmdb.0.dylib
1.0.0 %n (>= 6.3.0-1)
+ %p/lib/ccp4-%v/libssm.0.dylib 1.0.0 %n
(>= 6.3.0-1)
+ %p/lib/ccp4-%v/libxdl_view.2.dylib 3.0.0 %n
(>= 6.3.0-1)
+ %p/lib/ccp4-%v/libxdl_viewextra.0.dylib 1.0.0 %n
(>= 6.3.0-1)
+ %p/lib/ccp4-%v/libfftw.2.dylib 3.0.0 %n
(>= 6.3.0-1)
+ %p/lib/ccp4-%v/librfftw.2.dylib 3.0.0 %n
(>= 6.3.0-1)
+ %p/lib/ccp4-%v/libbp3.1.dylib
2.0.0 %n (>= 6.3.0-1)
+ %p/lib/ccp4-%v/cctbx/cctbx_build/lib/libboost_python.dylib 0.0.0
%n (>= 6.3.0-1)
+ %p/lib/ccp4-6.3.0/libxml2.2.dylib
10.0.0 %n (>= 6.3.0-1)
+ %p/lib/ccp4-6.3.0/libgc.1.dylib
2.0.0 %n (>= 6.3.0-1)
+ %p/lib/ccp4-6.3.0/libcord.1.dylib
2.0.0 %n (>= 6.3.0-1)
<<
- DocFiles: CHANGES COPYING INSTALL INSTALL.html INSTALL.ps README PROBLEMS
academic_software_licence.pdf
+ DocFiles: CHANGES COPYING INSTALL README PROBLEMS
academic_software_licence.pdf
+ License: LGPL
<<
################################################################################
################################################################################
@@ -483,8 +497,12 @@
Files:<<
lib/ccp4-%v/*.a
lib/ccp4-%v/*.la
+ lib/ccp4-%v/libccif.dylib
+ lib/ccp4-%v/libccp4c.dylib
+ lib/ccp4-%v/libmmdb.dylib
<<
- DocFiles: CHANGES COPYING INSTALL INSTALL.html INSTALL.ps README PROBLEMS
academic_software_licence.pdf
+ DocFiles: CHANGES COPYING INSTALL README PROBLEMS
academic_software_licence.pdf
+ License: LGPL
<<
################################################################################
Description: Macromolecular crystallography package
@@ -505,7 +523,7 @@
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
+ CCP4 files will be installed under /sw/share/xtal/ccp4-6.3.0
This revision includes all available CCP4 patches,
and new bash and zsh command completions specific to ccp4.
@@ -516,10 +534,8 @@
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
+ README CHANGES COPYING PROBLEMS INSTALL
<<
Homepage: http://www.ccp4.ac.uk
-License: Commercial
+License: Restrictive
Maintainer: W. G. Scott <wgsc...@users.sourceforge.net>
Index: ccp4.patch
===================================================================
RCS file: /cvsroot/fink/dists/10.7/stable/main/finkinfo/sci/ccp4.patch,v
retrieving revision 1.1
retrieving revision 1.2
diff -u -d -r1.1 -r1.2
--- ccp4.patch 30 Jul 2011 17:15:25 -0000 1.1
+++ ccp4.patch 12 Sep 2012 06:31:56 -0000 1.2
@@ -1,9 +1,70 @@
-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 @@
+diff -ruN ccp4-6.3.0-dist/lib/cctbx/ccp4_build ccp4-6.3.0/lib/cctbx/ccp4_build
+--- ccp4-6.3.0-dist/lib/cctbx/ccp4_build 2010-12-08 04:57:30.000000000
-0800
++++ ccp4-6.3.0/lib/cctbx/ccp4_build 2012-08-01 14:25:03.000000000 -0700
+@@ -8,7 +8,7 @@
+ exit 1
+ fi
+
[...965 lines suppressed...]
-@@ -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;
++
\ No newline at end of file
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