Update of /cvsroot/fink/dists/10.4/unstable/main/finkinfo/sci
In directory sfp-cvsdas-3.v30.ch3.sourceforge.com:/tmp/cvs-serv8328
Modified Files:
ccp4.info ccp4.patch
Log Message:
new upstream version of ccp4
Index: ccp4.info
===================================================================
RCS file: /cvsroot/fink/dists/10.4/unstable/main/finkinfo/sci/ccp4.info,v
retrieving revision 1.55
retrieving revision 1.56
diff -u -d -r1.55 -r1.56
--- ccp4.info 26 Feb 2010 18:59:11 -0000 1.55
+++ ccp4.info 28 Feb 2010 03:36:20 -0000 1.56
@@ -1,20 +1,20 @@
Package: ccp4
-Version: 6.1.2
-Revision: 4
+Version: 6.1.3
+Revision: 1
GCC: 1
#
Source: ftp://ftp.%n.ac.uk/%n/%v/%n-%v-core-src.tar.gz
-Source-MD5: bbc72fc9375f1ac3454fa8e81c673ec8
+Source-MD5: bf974554e0f727d0307240d1e5d3e6f0
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/phaser-2.1.4-cctbx-src.tar.gz
-Source3-MD5: 4467bb6a0647304c33dd14843959e15d
+Source3: ftp://ftp.%n.ac.uk/%n/%v/phaser-2.1.4-cctbx-src.tar.gz
+Source3-MD5: 0164d674defd7db75b6bbe465950f4c5
#
PatchFile: ccp4.patch
-PatchFile-MD5: 962729882cec050176df631ff02feccd
+PatchFile-MD5: 49dfd7f5400bc48dc55580b6c3109cfc
#
DescPort: <<
CCP4 is designed to compile with gfortran on OS X >= 10.4 by default.
@@ -95,6 +95,7 @@
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
@@ -137,6 +138,7 @@
#
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
@@ -145,7 +147,12 @@
export IMAKEINCLUDE=-I%p/lib/X11/config
export FC="gfortran"
#
-#touch .agree2ccp4v6
+# Uncomment the following line only for testing purposes. The ccp4
restrictive/commercial
+# license forbind disabling the interactive check in this way for the end-user
+#
+# touch .agree2ccp4v6
+#
+#
F_LIBS="-L%p/lib/gcc4.4/lib " \
./configure --with-netlib-lapack --with-shared-libs --with-x Darwin
#
@@ -168,6 +175,9 @@
perl -pi.mod -e 's|-O2|-O3|g' src/pointless/Makefile
grep -v "gcc4.4" 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
+
#################
make
make install
@@ -334,7 +344,7 @@
mv
%i/share/xtal/ccp4-%v/src/phaser/phaser-2.1.4/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/ccp4-6.1.2/libjwc_c.0.dylib
%i/lib/ccp4-%v/libjwc_c.0.1.1.dylib
+ install_name_tool -id %p/lib/ccp4-6.1.3/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
@@ -377,26 +387,26 @@
lib/ccp4-%v/libboost_python.dylib
<<
Shlibs: <<
- %p/lib/ccp4-%v/libDiffractionImage.0.dylib 1.0.0 %n
(>= 6.1.2-1)
- %p/lib/ccp4-%v/lib_DiffractionImage.0.dylib 1.0.0 %n
(>= 6.1.2-1)
- %p/lib/ccp4-%v/libccif.dylib 0.0.0 %n
(>= 6.1.2-1)
- %p/lib/ccp4-%v/libccp4c.dylib 0.0.0 %n
(>= 6.1.2-1)
- %p/lib/ccp4-%v/libclipper-ccp4.2.dylib 3.0.0 %n
(>= 6.1.2-1)
- %p/lib/ccp4-%v/libclipper-cif.2.dylib 3.0.0 %n
(>= 6.1.2-1)
- %p/lib/ccp4-%v/libclipper-cns.0.dylib 1.0.0 %n
(>= 6.1.2-1)
- %p/lib/ccp4-%v/libclipper-contrib.2.dylib 3.0.0 %n
(>= 6.1.2-1)
- %p/lib/ccp4-%v/libclipper-core.2.dylib 3.0.0 %n
(>= 6.1.2-1)
- %p/lib/ccp4-%v/libclipper-minimol.2.dylib 3.0.0 %n
(>= 6.1.2-1)
- %p/lib/ccp4-%v/libclipper-mmdb.2.dylib 3.0.0 %n
(>= 6.1.2-1)
- %p/lib/ccp4-%v/libclipper-phs.2.dylib 3.0.0 %n
(>= 6.1.2-1)
- %p/lib/ccp4-%v/libjwc_c.0.dylib 2.0.0 %n
(>= 6.1.2-1)
- %p/lib/ccp4-%v/libmmdb.dylib 0.0.0 %n
(>= 6.1.2-1)
- %p/lib/ccp4-%v/libssm.0.dylib 1.0.0 %n
(>= 6.1.2-1)
- %p/lib/ccp4-%v/libxdl_view.2.dylib 3.0.0 %n
(>= 6.1.2-1)
- %p/lib/ccp4-%v/libxdl_viewextra.0.dylib 1.0.0 %n
(>= 6.1.2-1)
- %p/lib/ccp4-%v/libfftw.2.dylib 3.0.0 %n
(>= 6.1.2-1)
- %p/lib/ccp4-%v/librfftw.2.dylib 3.0.0 %n
(>= 6.1.2-1)
- %p/lib/ccp4-%v/libboost_python.dylib 0.0.0 %n
(>= 6.1.2-6)
+ %p/lib/ccp4-%v/libDiffractionImage.0.dylib 1.0.0 %n
(>= 6.1.3-1)
+ %p/lib/ccp4-%v/lib_DiffractionImage.0.dylib 1.0.0 %n
(>= 6.1.3-1)
+ %p/lib/ccp4-%v/libccif.dylib 0.0.0 %n
(>= 6.1.3-1)
+ %p/lib/ccp4-%v/libccp4c.dylib 0.0.0 %n
(>= 6.1.3-1)
+ %p/lib/ccp4-%v/libclipper-ccp4.2.dylib 3.0.0 %n
(>= 6.1.3-1)
+ %p/lib/ccp4-%v/libclipper-cif.2.dylib 3.0.0 %n
(>= 6.1.3-1)
+ %p/lib/ccp4-%v/libclipper-cns.0.dylib 1.0.0 %n
(>= 6.1.3-1)
+ %p/lib/ccp4-%v/libclipper-contrib.2.dylib 3.0.0 %n
(>= 6.1.3-1)
+ %p/lib/ccp4-%v/libclipper-core.2.dylib 3.0.0 %n
(>= 6.1.3-1)
+ %p/lib/ccp4-%v/libclipper-minimol.2.dylib 3.0.0 %n
(>= 6.1.3-1)
+ %p/lib/ccp4-%v/libclipper-mmdb.2.dylib 3.0.0 %n
(>= 6.1.3-1)
+ %p/lib/ccp4-%v/libclipper-phs.2.dylib 3.0.0 %n
(>= 6.1.3-1)
+ %p/lib/ccp4-%v/libjwc_c.0.dylib 2.0.0 %n
(>= 6.1.3-1)
+ %p/lib/ccp4-%v/libmmdb.dylib 0.0.0 %n
(>= 6.1.3-1)
+ %p/lib/ccp4-%v/libssm.0.dylib 1.0.0 %n
(>= 6.1.3-1)
+ %p/lib/ccp4-%v/libxdl_view.2.dylib 3.0.0 %n
(>= 6.1.3-1)
+ %p/lib/ccp4-%v/libxdl_viewextra.0.dylib 1.0.0 %n
(>= 6.1.3-1)
+ %p/lib/ccp4-%v/libfftw.2.dylib 3.0.0 %n
(>= 6.1.3-1)
+ %p/lib/ccp4-%v/librfftw.2.dylib 3.0.0 %n
(>= 6.1.3-1)
+ %p/lib/ccp4-%v/libboost_python.dylib 0.0.0 %n
(>= 6.1.3-6)
<<
DocFiles: CHANGES COPYING INSTALL INSTALL.html INSTALL.ps README PROBLEMS
academic_software_licence.pdf
<<
@@ -426,15 +436,14 @@
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 /bin/zsh" followed by "source /sw/bin/init.sh ; ccp4i"
- on 10.5 to permit global configuration. Thereafter, you can invoke
- ccp4i without sudo.
+ 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/ccp4-6.1.2
+ CCP4 files will be installed under /sw/share/xtal/ccp4-6.1.3
This revision includes all available CCP4 patches,
and new bash and zsh command completions specific to ccp4.
Index: ccp4.patch
===================================================================
RCS file: /cvsroot/fink/dists/10.4/unstable/main/finkinfo/sci/ccp4.patch,v
retrieving revision 1.21
retrieving revision 1.22
diff -u -d -r1.21 -r1.22
--- ccp4.patch 8 Sep 2009 22:02:11 -0000 1.21
+++ ccp4.patch 28 Feb 2010 03:36:21 -0000 1.22
@@ -1,6 +1,6 @@
-diff -ruN ccp4-6.1.2-dist/ccp4i/etc/configure.def.dist
ccp4-6.1.2/ccp4i/etc/configure.def.dist
---- ccp4-6.1.2-dist/ccp4i/etc/configure.def.dist 2009-06-15
02:37:22.000000000 -0700
-+++ ccp4-6.1.2/ccp4i/etc/configure.def.dist 2009-07-15 17:33:55.000000000
-0700
+diff -ruN ccp4-6.1.3-dist/ccp4i/etc/configure.def.dist
ccp4-6.1.3/ccp4i/etc/configure.def.dist
+--- ccp4-6.1.3-dist/ccp4i/etc/configure.def.dist 2009-06-15
02:37:22.000000000 -0700
++++ ccp4-6.1.3/ccp4i/etc/configure.def.dist 2009-07-15 17:33:55.000000000
-0700
@@ -61,8 +61,8 @@
MESSAGE _text ""
BLT_LIBRARY _text ""
@@ -12,9 +12,9 @@
O_MAPMAN _text mapman
[...1963 lines suppressed...]
- instr->instruction_type = instruction_type;
-
- if (ppart->current_instr)
---- ccp4-6.1.2/x-windows/XCCPJIFFY/EditString.c.org 2009-08-30
22:17:02.000000000 -0400
-+++ ccp4-6.1.2/x-windows/XCCPJIFFY/EditString.c 2009-08-30
22:19:06.000000000 -0400
-@@ -256,10 +256,10 @@
- WidgetClass editStringWidgetClass = (WidgetClass)&editStringClassRec;
-
-
--static char space_char [] = {' ',NULL};
-+static char space_char [] = {' ',(uintptr_t)NULL};
- static XawTextBlock new_input,
-- no_input = {0, 0, NULL, NULL},
-- space_input = {0, 1, space_char, NULL};
-+ no_input = {0, 0, NULL, (uintptr_t)NULL},
-+ space_input = {0, 1, space_char,
(uintptr_t)NULL};
-
- /***********************************************************/
- static void
+ if ( test -d $CCP4/share/balbes/BALBES_0.0.1)
------------------------------------------------------------------------------
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