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;
------------------------------------------------------------------------------
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