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