Update of /cvsroot/fink/dists/10.4/unstable/main/finkinfo/sci
In directory vz-cvs-3.sog:/tmp/cvs-serv5442
Modified Files:
ccp4.info
Log Message:
update to official 6.2.0 release, critical pointless bug-fix, updated for 10.7
Index: ccp4.info
===================================================================
RCS file: /cvsroot/fink/dists/10.4/unstable/main/finkinfo/sci/ccp4.info,v
retrieving revision 1.64
retrieving revision 1.65
diff -u -d -r1.64 -r1.65
--- ccp4.info 25 Jul 2011 15:06:16 -0000 1.64
+++ ccp4.info 30 Jul 2011 17:21:16 -0000 1.65
@@ -1,6 +1,6 @@
Package: ccp4
Version: 6.2.0
-Revision: 3
+Revision: 101
GCC: 1
#
Source: ftp://ftp.%n.ac.uk/%n/%v/%n-%v-core-src.tar.gz
@@ -13,6 +13,10 @@
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
#
@@ -33,12 +37,11 @@
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 in $CCP4/include.
-
- If needed, please install the phaser, pointless and cctbx fink packages.
+ need to do so manually. The actual files are located (not my choice)
+ in $CCP4/include.
The ccp4i mail utility by default will only work on machines that run
- a mail server. As a workaround, a public domain perl script called
+ a unix mail server. As a workaround, a public domain perl script called
osx_ccp4_mail is installed that glues the ccp4i mail button to the
Apple OS X Mail.app.
@@ -47,18 +50,20 @@
are issued by CCP4 are now downloaded and applied individually, helping
to keep the ccp4.patch file from growing metastatically and also to
permit the user to verify that the latest patches have been applied.
- These start with Source2 (above) and are applied individually at the
- end of the PatchScript field.
+ These start, when present, with Source2 (above) and are applied
+ individually at the end of the PatchScript field.
Clipper libraries are not behaving properly when linked to fink fftw
so we return to the option of having ccp4 build its own private fftw.
Yes, I hate it too, but now all the examples pass the run-all test.
- 64-bit version appears to require ccp4\'s own blas/lapak to avoid
- run-time errors.
+ 64-bit version prior to OS X 10.7 appears to require ccp4\'s own
+ blas/lapak to avoid run-time errors. I use that in all versions now,
+ but plan to get rid of this as soon as possible.
<<
Depends: x11, tcltk, blt, gcc46-shlibs, %N-shlibs (= %v-%r)
-BuildDepends: gcc46, f2c, fort77, tcltk-dev, x11-dev, xmkmf (>= 1.0.2-3), fink
(>= 0.24.12)
+BuildDepends: gcc46, tcltk-dev, x11-dev, xmkmf (>= 1.0.2-3), fink (>= 0.24.12)
+BuildDependsOnly: False
BuildConflicts: gpp4-dev, gpp4, ssm, ssm-dev, mmdb, mmdb-dev, clipper,
clipper-bin, clipper-dev, ccp4-onlylibs-dev, python
Replaces: phaser (<= 2.3.0-1), pointless (<= 1.2.18-1), mosflm (<= 7.0.3-3),
mosflm-small (<= 7.0.3-3), imosflm (<= 1:1.0.4-4), imosflm-aqua (<= 1:1.0.4-4),
refmac (<= 5.5.0070-1), bundle-ccp4-intel, clipper-bin, ccp4-gfortran,
ccp4-gfortran-dev, bundle-ccp4-powerpc
Conflicts: <<
@@ -151,21 +156,21 @@
export PATH=%p/lib/xmkmf/bin:$PATH
export IMAKEINCLUDE=-I%p/lib/X11/config
export FC="gfortran"
-## if [[ -x /usr/llvm-gcc-4.2/bin/llvm-gcc-4.2 ]];then
-## export CC=/usr/llvm-gcc-4.2/bin/llvm-gcc-4.2
-## export CXX=/usr/llvm-gcc-4.2/bin/llvm-g++-4.2
-## export CPP=/usr/llvm-gcc-4.2/bin/llvm-cpp-4.2
-## fi
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
+# touch .agree2ccp4v6
#
#
-F_LIBS="-L%p/lib/gcc4.6/lib -lgfortran " \
-./configure --with-netlib-lapack --with-shared-libs --with-x Darwin
+#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
@@ -182,10 +187,11 @@
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 to prevent linking to gcc4.6 libraries as this creates a
run-time error
+# 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
@@ -193,12 +199,16 @@
perl -pi.bak -e 's|LD_LIBRARY_PATH|DYLD_LIBRARY_PATH|g' lib/ccif/Makefile
+
#################
+#################
+cd $CCP4
make
-make install
+make install
+#################
#################
-# xloggraph will fail, but we will link it with fort77 below
+# 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
@@ -218,10 +228,10 @@
make xdlmapman xdldataman
cp xdlmapman $CBIN/.
cp xdldataman $CBIN/.
-# Manually link xloggraph with fort77 (fails in make)
+# Manually link xloggraph with gfortran (fails in make)
echo ""
echo "**********************************************************************"
-echo "Re-linking xloggraph with fort77. Ignore previous error messages."
+echo "Re-linking xloggraph with gfortran. Ignore previous error messages."
echo "**********************************************************************"
echo ""
#
@@ -230,7 +240,7 @@
if [[ -x $CBIN/xloggraph ]];then
true
else
- fort77 -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
+ 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
@@ -302,6 +312,28 @@
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:
#
------------------------------------------------------------------------------
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