[gentoo-commits] gentoo-x86 commit in sci-chemistry/ccp4-apps/files: 6.1.3-dont-build-imosflm.patch 6.1.3-dont-build-double-and-make-bindir.patch 6.1.3-dont-build-libs.patch 6.1.3-dont-build-molref.patch 6.1.3-rename-truncate.patch 6.1.3-clipper-mmdbold-ggc-4.3.patch 6.1.3-dont-configure.patch 6.1.3-dont-build-xia.patch 6.1.3-rename-rapper.patch 6.1.3-clipper-template.patch 6.1.3-pythonpath.patch 6.1.3-setup.patch 6.1.3-dont-make-dirs-in-configure.patch 6.1.3-pisa.patch 6.1.3-fix-setup-bash-incompatibility.patch 6.1.3-dont-build-scala.patch

[Justin Lecher (jlec)]

jlec        10/02/06 00:37:42

  Added:                6.1.3-dont-build-imosflm.patch
                        6.1.3-dont-build-double-and-make-bindir.patch
                        6.1.3-dont-build-libs.patch
                        6.1.3-dont-build-molref.patch
                        6.1.3-rename-truncate.patch
                        6.1.3-clipper-mmdbold-ggc-4.3.patch
                        6.1.3-dont-configure.patch
                        6.1.3-dont-build-xia.patch
                        6.1.3-rename-rapper.patch
                        6.1.3-clipper-template.patch 6.1.3-pythonpath.patch
                        6.1.3-setup.patch
                        6.1.3-dont-make-dirs-in-configure.patch
                        6.1.3-pisa.patch
                        6.1.3-fix-setup-bash-incompatibility.patch
                        6.1.3-dont-build-scala.patch
  Log:
  splitted apps from ccp4
  (Portage version: 2.2_rc62/cvs/Linux x86_64)

Revision  Changes    Path
1.1                  sci-chemistry/ccp4-apps/files/6.1.3-dont-build-imosflm.patch

file : http://sources.gentoo.org/viewcvs.py/gentoo-x86/sci-chemistry/ccp4-apps/files/6.1.3-dont-build-imosflm.patch?rev=1.1&view=markup
plain: http://sources.gentoo.org/viewcvs.py/gentoo-x86/sci-chemistry/ccp4-apps/files/6.1.3-dont-build-imosflm.patch?rev=1.1&content-type=text/plain

Index: 6.1.3-dont-build-imosflm.patch
===================================================================
--- ccp4i/Makefile.in	2009-06-19 15:08:53.000000000 +0200
+++ ccp4i/Makefile.in.new	2009-08-04 21:10:14.000000000 +0200
@@ -9,7 +9,7 @@
 SHELL = /bin/sh
 DESTDIR = $(prefix)
 CCP4I_BINDIR = $(top_srcdir)/ccp4i/bin
-CCP4I_TARGETS = ccp4i imosflm loggraph crank mapslicer
+CCP4I_TARGETS = ccp4i loggraph crank mapslicer
 
 install :
 	for i in $(CCP4I_TARGETS); do \



1.1                  sci-chemistry/ccp4-apps/files/6.1.3-dont-build-double-and-make-bindir.patch

file : http://sources.gentoo.org/viewcvs.py/gentoo-x86/sci-chemistry/ccp4-apps/files/6.1.3-dont-build-double-and-make-bindir.patch?rev=1.1&view=markup
plain: http://sources.gentoo.org/viewcvs.py/gentoo-x86/sci-chemistry/ccp4-apps/files/6.1.3-dont-build-double-and-make-bindir.patch?rev=1.1&content-type=text/plain

Index: 6.1.3-dont-build-double-and-make-bindir.patch
===================================================================
--- ccp4-6.1.1/x-windows/Makefile.in	2008-08-11 19:20:01.000000000 +0200
+++ ccp4-6.1.1/x-windows/Makefile.in.new	2009-02-27 14:32:25.000000000 +0100
@@ -35,7 +35,7 @@
 #
 # all
 #
-all : xdlview libjwc_c libjwc_f rotgen_ hklview xjiffy rasmol2 ipmosflm
+all : rotgen_ hklview xjiffy
 #
 # xdl_view
 #
@@ -157,11 +157,10 @@
 #
 install_obj = hklview rotgen ipmosflm
 install: all
+	mkdir -p $(bindir)
 	$(INSTALL_PROGRAM) $(srcdir)/hklview $(bindir)
 	cd $(srcdir)/XCCPJIFFY ; $(MAKE) bindir=$(bindir) libdir=$(libdir) install
-	$(INSTALL_PROGRAM) $(rasmol_dir)/rasmol $(bindir)
 	cd $(rotgen_dir); $(MAKE) install
-	$(INSTALL_PROGRAM) $(mosflm_dir)/bin/ipmosflm $(bindir)
 #
 # clean
 #



1.1                  sci-chemistry/ccp4-apps/files/6.1.3-dont-build-libs.patch

file : http://sources.gentoo.org/viewcvs.py/gentoo-x86/sci-chemistry/ccp4-apps/files/6.1.3-dont-build-libs.patch?rev=1.1&view=markup
plain: http://sources.gentoo.org/viewcvs.py/gentoo-x86/sci-chemistry/ccp4-apps/files/6.1.3-dont-build-libs.patch?rev=1.1&content-type=text/plain

Index: 6.1.3-dont-build-libs.patch
===================================================================
--- Makefile.in	2009-06-19 15:13:29.000000000 +0200
+++ Makefile.in.new	2009-08-02 23:06:41.000000000 +0200
@@ -2,7 +2,7 @@
 # $Header: /var/cvsroot/gentoo-x86/sci-chemistry/ccp4-apps/files/6.1.3-dont-build-libs.patch,v 1.1 2010/02/06 00:37:40 jlec Exp $
 
 SHELL = /bin/sh
-DIRS = $(fftwdir) $(clipperdir) $(diffimdir) $(lapackdir) $(ccifdir) lib/src $(ssmdir) src lib/data unsupported/src x-windows share ccp4i $(prereleasedir)
+DIRS = src lib/data unsupported/src x-windows share ccp4i $(prereleasedir)
 # this is for the benefit of makes that don't pass variable values in
 # recursive invocations, so that you can override these values on the
 # command line at the top level
@@ -69,19 +69,19 @@
 	$(MAKE) -i $(MFLAGS) $(MVARS) install; else true; fi ; \
 	$(MAKE) install
 
-srcdir :  FORCE libdir
+srcdir :  FORCE 
 	if test -d src; then cd src; $(MAKE) $(MFLAGS) $(MVARS); else true; fi
 
 supported : srcdir
 
-unsupported :  FORCE libdir
+unsupported :  FORCE
 	if test -d unsupported/src; then cd unsupported/src;  \
 	   $(MAKE) $(MFLAGS) $(MVARS); else true; fi
 
-datadir : FORCE libdir
+datadir : FORCE
 	cd lib/data; $(MAKE) $(MFLAGS) $(MVARS)
 
-xwindir : FORCE libdir
+xwindir : FORCE
 	if test -f x-windows/Makefile; then cd x-windows; \
 	   $(MAKE) -i $(MFLAGS) ; else true; fi
 



1.1                  sci-chemistry/ccp4-apps/files/6.1.3-dont-build-molref.patch

file : http://sources.gentoo.org/viewcvs.py/gentoo-x86/sci-chemistry/ccp4-apps/files/6.1.3-dont-build-molref.patch?rev=1.1&view=markup
plain: http://sources.gentoo.org/viewcvs.py/gentoo-x86/sci-chemistry/ccp4-apps/files/6.1.3-dont-build-molref.patch?rev=1.1&content-type=text/plain

Index: 6.1.3-dont-build-molref.patch
===================================================================
--- src/pisa/Makefile.am	2007-07-10 10:56:05.000000000 +0200
+++ src/pisa/Makefile.am.new	2009-06-11 21:16:51.000000000 +0200
@@ -1,4 +1,4 @@
-SUBDIRS = molref pisastore sbase
+SUBDIRS = pisastore sbase
 
 pkgdatadir = $(datadir)/pisa
 
--- src/pisa/Makefile.in	2009-06-12 21:12:08.000000000 +0200
+++ src/pisa/Makefile.in.new	2009-06-12 21:41:52.000000000 +0200
@@ -82,7 +82,7 @@
 am__quote = @am__quote@
 install_sh = @install_sh@
 pisa_LDFLAGS = @pisa_LDFLAGS@
-SUBDIRS = molref pisastore sbase
+SUBDIRS = pisastore sbase
 
 dist_pkgdata_DATA = pisa.cfg
 



1.1                  sci-chemistry/ccp4-apps/files/6.1.3-rename-truncate.patch

file : http://sources.gentoo.org/viewcvs.py/gentoo-x86/sci-chemistry/ccp4-apps/files/6.1.3-rename-truncate.patch?rev=1.1&view=markup
plain: http://sources.gentoo.org/viewcvs.py/gentoo-x86/sci-chemistry/ccp4-apps/files/6.1.3-rename-truncate.patch?rev=1.1&content-type=text/plain

Index: 6.1.3-rename-truncate.patch
===================================================================
coreutils now installs a binary called truncate.

--- src/Makefile.in.orig	2009-03-02 23:25:45.000000000 -0800
+++ src/Makefile.in	2009-03-02 23:25:53.000000000 -0800
@@ -41,7 +41,7 @@
 professs r500 rantan rebatch reindex revise rfcorr rotamer rotmat \
 rstats rwcontents sapi scaleit scalepack2mtz seqwt sfall sigmaa sortmtz sortwater \
 stgrid stnet surface tffc tracer \
-truncate unique vecref vectors volume watertidy watncs watpeak \
+ftruncate unique vecref vectors volume watertidy watncs watpeak \
 wilson $(CIFTARGETS)
 
 BALBESTARGETS = search_DB get_structure_DB f2cif check_file_DB check_cell_sg \
@@ -982,7 +982,7 @@
 surface:	$(srcdir)/surface.f
 tffc:		$(srcdir)/tffc.f
 tracer:		$(srcdir)/tracer.f
-truncate:	$(srcdir)/truncate.f
+ftruncate:	$(srcdir)/truncate.f
 unique:		$(srcdir)/unique.f
 vecref:		$(srcdir)/vecref.f
 vectors:	$(srcdir)/vectors.f
--- examples/unix/runnable/truncate.exam.orig	2009-03-02 23:35:04.000000000 -0800
+++ examples/unix/runnable/truncate.exam	2009-03-02 23:35:11.000000000 -0800
@@ -15,7 +15,7 @@
   exit 1
 fi
 #
-truncate hklin $CCP4_SCR/aucn_mrg.mtz \
+ftruncate hklin $CCP4_SCR/aucn_mrg.mtz \
    hklout $CCP4_SCR/aucn_trn.mtz <<EOF-trunc
 title DMSO red aucn2 Data - mosflm
 truncate yes
@@ -28,7 +28,7 @@
 # do this if you already have Fs but want to look at the
 # output graphs of TRUNCATE
 
-truncate hklin $CEXAM/rnase/rnase18.mtz <<EOF
+ftruncate hklin $CEXAM/rnase/rnase18.mtz <<EOF
 title Analysis of rnase data
 labin F=FNAT SIGF=SIGFNAT
 nresidue 192



1.1                  sci-chemistry/ccp4-apps/files/6.1.3-clipper-mmdbold-ggc-4.3.patch

file : http://sources.gentoo.org/viewcvs.py/gentoo-x86/sci-chemistry/ccp4-apps/files/6.1.3-clipper-mmdbold-ggc-4.3.patch?rev=1.1&view=markup
plain: http://sources.gentoo.org/viewcvs.py/gentoo-x86/sci-chemistry/ccp4-apps/files/6.1.3-clipper-mmdbold-ggc-4.3.patch?rev=1.1&content-type=text/plain

Index: 6.1.3-clipper-mmdbold-ggc-4.3.patch
===================================================================
--- ccp4-6.0.99e.orig/lib/clipper/clipper/mmdbold/clipper_mmdb.cpp	2008-07-31 13:23:13.000000000 -0700
+++ ccp4-6.0.99e/lib/clipper/clipper/mmdbold/clipper_mmdb.cpp	2008-07-31 13:47:35.000000000 -0700
@@ -43,7 +43,7 @@
 
 #include <set>
 #include <algorithm>
-
+#include <string.h>
 
 namespace clipper {
 
--- ccp4-6.0.99e.orig/lib/clipper/clipper/mmdbold/clipper_mmdb_wrapper.cpp.orig	2008-07-31 13:49:53.000000000 -0700
+++ ccp4-6.0.99e/lib/clipper/clipper/mmdbold/clipper_mmdb_wrapper.cpp	2008-07-31 13:50:25.000000000 -0700
@@ -40,7 +40,7 @@
 //L  MA 02111-1307 USA
 
 #include "clipper_mmdb_wrapper.h"
-
+#include <string.h>
 
 namespace clipper {
 



1.1                  sci-chemistry/ccp4-apps/files/6.1.3-dont-configure.patch

file : http://sources.gentoo.org/viewcvs.py/gentoo-x86/sci-chemistry/ccp4-apps/files/6.1.3-dont-configure.patch?rev=1.1&view=markup
plain: http://sources.gentoo.org/viewcvs.py/gentoo-x86/sci-chemistry/ccp4-apps/files/6.1.3-dont-configure.patch?rev=1.1&content-type=text/plain

Index: 6.1.3-dont-configure.patch
===================================================================
--- configure	2009-08-07 12:11:28.000000000 +0200
+++ configure.new.nolib	2009-08-17 22:30:39.000000000 +0200
@@ -3113,41 +3113,6 @@
     RX_L="$configdir/lib/rxdispencer/rx"
     export RX_H RX_L
   fi
-  echo 
-  echo "Running separate configure for CCIF library."
-  echo
-  cd lib/ccif
-  echo "Updating modification times for configuration files"
-  echo "Please wait..."
-  for i in configure.in aclocal.m4 configure Makefile.in; do
-    touch $i && sleep 1   
-  done
-  echo "...done."      
-
-  if [ "X$LIBFOPTIM" != "X" ]; then
-    FOPTIM_save=$FOPTIM
-    FOPTIM=$LIBFOPTIM
-    FFLAGS="${FOPTIM} ${XFFLAGS}"
-  fi
-  if [ "X$LIBCOPTIM" != "X" ]; then
-    COPTIM_save=$COPTIM
-    COPTIM=$LIBCOPTIM
-    CFLAGS="${COPTIM} ${XCFLAGS}"
-  fi
-  ( touch /tmp/$$.cache_file 2>/dev/null && \
-    cat /dev/null > /tmp/$$.cache_file && \
-    ./configure $xopts --libdir=${libdir} --srcdir=${srcdir}/lib/ccif --cache-file=/tmp/$$.cache_file ) || \
-    ./configure $xopts --libdir=${libdir} --srcdir=${srcdir}/lib/ccif
-  rm -f /tmp/$$.cache_file
-  if [ "X$LIBFOPTIM" != "X" ]; then
-    FOPTIM=$FOPTIM_save
-    FFLAGS="${FOPTIM} ${XFFLAGS}"
-  fi
-  if [ "X$LIBCOPTIM" != "X" ]; then
-    COPTIM=$COPTIM_save
-    CFLAGS="${COPTIM} ${XCFLAGS}"
-  fi
-  cd ../..
   echo
   echo "Returning to main configure."
   echo
@@ -5094,53 +5059,6 @@
   echo "configure $xopts --exec_prefix=${prefix} --prefix=${prefix} --bindir=${bindir} --libdir=${libdir}"
   ./configure $xopts --exec_prefix=${prefix} --prefix=${prefix} --bindir=${bindir} --libdir=${libdir} 
   echo
-  echo "CCP4 configure: Running separate configure for libjwc_c library."
-  echo
-  cd ${srcdir}/${xwindir}/libjwc/libjwc_c
-  echo "Updating modification times for configuration files in libjwc_c"
-  echo "Please wait..."
-  for i in configure.in Makefile.am aclocal.m4 configure Makefile.in ltconfig ltmain.sh; do
-    touch $i && sleep 1
-  done
-  echo "...done."
-  echo
-  echo "configure $xopts --exec_prefix=${prefix} --prefix=${prefix} --bindir=${bindir} --libdir=${libdir}"
-  ( touch /tmp/$$.cache_file 2>/dev/null && \
-    cat /dev/null > /tmp/$$.cache_file && \
-    ./configure $xopts --exec_prefix=${prefix} --prefix=${prefix} --bindir=${bindir} --libdir=${libdir} --cache-file=/tmp/$$.cache_file ) || \
-    ./configure $xopts --exec_prefix=${prefix} --prefix=${prefix} --bindir=${bindir} --libdir=${libdir}
-  rm -f /tmp/$$.cache_file
-  echo
-  echo "CCP4 configure: Running separate configure for libjwc_f library."
-  echo
-  cd ${srcdir}/${xwindir}/libjwc/libjwc_f
-  # for g77 3.1 some builds do not have no-common for system libs,
-  # so disable for now
-  echo "Updating modification times for configuration files in libjwc_f"
-  echo "Please wait..."
-  for i in configure.in Makefile.am aclocal.m4 configure Makefile.in ltconfig ltmain.sh; do
-    touch $i && sleep 1
-  done
-  echo "...done."
-  echo
-  # for g77 3.1 some builds do not have no-common for system libs,
-  # so disable for now
-  case $system in
-  Darwin* )
-    echo "configure --disable-shared --exec_prefix=${prefix} --prefix=${prefix} --bindir=${bindir} --libdir=${libdir}"
-    ( touch /tmp/$$.cache_file 2>/dev/null && \
-      cat /dev/null > /tmp/$$.cache_file && \
-      ./configure --disable-shared --exec_prefix=${prefix} --prefix=${prefix} --bindir=${bindir} --libdir=${libdir} --cache-file=/tmp/$$.cache_file ) || \
-      ./configure --disable-shared --exec_prefix=${prefix} --prefix=${prefix} --bindir=${bindir} --libdir=${libdir}
-    ;;
-  * )
-    echo "configure $xopts --exec_prefix=${prefix} --prefix=${prefix} --bindir=${bindir} --libdir=${libdir}"
-    ( touch /tmp/$$.cache_file 2>/dev/null && \
-      cat /dev/null > /tmp/$$.cache_file && \
-      ./configure $xopts --exec_prefix=${prefix} --prefix=${prefix} --bindir=${bindir} --libdir=${libdir} --cache-file=/tmp/$$.cache_file ) || \
-      ./configure $xopts --exec_prefix=${prefix} --prefix=${prefix} --bindir=${bindir} --libdir=${libdir}
-  esac
-  rm -f /tmp/$$.cache_file
 
   if test "$non_shared" = yes; then
 #this is a bit of a cheat/fudge but that's life!
@@ -5210,12 +5128,6 @@
   fi
 
   echo
-  echo "CCP4 configure: Running separate configure for Mosflm"
-  echo
-  cd ${srcdir}/${mosflmdir}
-  echo "configure $xopts --with-ccp4-prefix=${prefix} --exec_prefix=${prefix} --prefix=${prefix} --bindir=${bindir} --libdir=${libdir}"
-  ./configure $xopts --with-ccp4-prefix=${prefix} --exec_prefix=${prefix} --prefix=${prefix} --bindir=${bindir} --libdir=${libdir}
-  echo
   cd ../..
   echo "Returning to main configure."
   echo



1.1                  sci-chemistry/ccp4-apps/files/6.1.3-dont-build-xia.patch

file : http://sources.gentoo.org/viewcvs.py/gentoo-x86/sci-chemistry/ccp4-apps/files/6.1.3-dont-build-xia.patch?rev=1.1&view=markup
plain: http://sources.gentoo.org/viewcvs.py/gentoo-x86/sci-chemistry/ccp4-apps/files/6.1.3-dont-build-xia.patch?rev=1.1&content-type=text/plain

Index: 6.1.3-dont-build-xia.patch
===================================================================
--- src/Makefile.in	2009-07-05 16:50:25.000000000 +0200
+++ src/Makefile.in.new	2009-07-05 19:38:06.000000000 +0200
@@ -50,9 +50,9 @@
 
 # these live in subdirectories and have more than one dependency:
 OTHERS = rsps anglen secstr proclean pplot gfac2pdb tplot mplot probplot rmsdev nb \
-         scala dm dmmulti stereo mapmask maprot ncsmask chef \
+         scala dm dmmulti stereo mapmask maprot ncsmask \
          sftools tlsanl tlsextract topp toplist dyndom sc combat mlphare fffear ffjoin \
-         anisoanl $(REFMACTARGETS) dtrek2scala crunch2 pmf doser mat2symop symop2mat 
+         anisoanl $(REFMACTARGETS) dtrek2scala crunch2 pmf 
 
 # targets built from .c sources:
 CSIMPLE = pltdev binsort



1.1                  sci-chemistry/ccp4-apps/files/6.1.3-rename-rapper.patch

file : http://sources.gentoo.org/viewcvs.py/gentoo-x86/sci-chemistry/ccp4-apps/files/6.1.3-rename-rapper.patch?rev=1.1&view=markup
plain: http://sources.gentoo.org/viewcvs.py/gentoo-x86/sci-chemistry/ccp4-apps/files/6.1.3-rename-rapper.patch?rev=1.1&content-type=text/plain

Index: 6.1.3-rename-rapper.patch
===================================================================
--- src/rapper/LOOP/Makefile.in	2008-05-29 16:39:40.000000000 +0200
+++ src/rapper/LOOP/Makefile.in.new	2009-03-12 20:40:03.157602172 +0100
@@ -111,9 +111,9 @@
 pyexecdir = @pyexecdir@
 pythondir = @pythondir@
 rapper_LDFLAGS = @rapper_LDFLAGS@
-bin_PROGRAMS = rapper
+bin_PROGRAMS = rappermc
 
-rapper_SOURCES = \
+rappermc_SOURCES = \
 kip.h aaconv.cpp atomconv.cpp kip_snake.cpp \
 kip_pdb.cpp measure.cpp lib_frags.cpp ran2.cpp \
 heap.cpp queue.cpp 3Dgeom.cpp space_grid.cpp list.cpp search_residue.cpp bitfield.cpp \
@@ -129,7 +129,7 @@
 residue_range.cpp pop_search_frags.cpp saxs.cpp lib_choral.cpp pdf.cpp WeightedDistribMean.cpp
 
 
-rapper_LDADD = ../gc7.0/libgc.la ../libxml2/libxml2.la
+rappermc_LDADD = ../gc7.0/libgc.la ../libxml2/libxml2.la
 dist_pkgdata_DATA = params.xml
 
 INCLUDES = -I. -I../gc7.0/include -I../libxml2/include
@@ -139,7 +139,7 @@
 bin_PROGRAMS = rapper$(EXEEXT)
 PROGRAMS = $(bin_PROGRAMS)
 
-am_rapper_OBJECTS = aaconv.$(OBJEXT) atomconv.$(OBJEXT) \
+am_rappermc_OBJECTS = aaconv.$(OBJEXT) atomconv.$(OBJEXT) \
 	kip_snake.$(OBJEXT) kip_pdb.$(OBJEXT) measure.$(OBJEXT) \
 	lib_frags.$(OBJEXT) ran2.$(OBJEXT) heap.$(OBJEXT) \
 	queue.$(OBJEXT) 3Dgeom.$(OBJEXT) space_grid.$(OBJEXT) \
@@ -164,8 +164,8 @@
 	iterator.$(OBJEXT) residue_range.$(OBJEXT) \
 	pop_search_frags.$(OBJEXT) saxs.$(OBJEXT) lib_choral.$(OBJEXT) \
 	pdf.$(OBJEXT) WeightedDistribMean.$(OBJEXT)
-rapper_OBJECTS = $(am_rapper_OBJECTS)
-rapper_DEPENDENCIES = ../gc7.0/libgc.la ../libxml2/libxml2.la
+rappermc_OBJECTS = $(am_rapper_OBJECTS)
+rappermc_DEPENDENCIES = ../gc7.0/libgc.la ../libxml2/libxml2.la
 
 DEFS = @DEFS@
 DEFAULT_INCLUDES =  -I. -I$(srcdir)
@@ -233,11 +233,11 @@
 CCLD = $(CC)
 LINK = $(LIBTOOL) --mode=link $(CCLD) $(AM_CFLAGS) $(CFLAGS) \
 	$(AM_LDFLAGS) $(LDFLAGS) -o $@
-DIST_SOURCES = $(rapper_SOURCES)
+DIST_SOURCES = $(rappermc_SOURCES)
 DATA = $(dist_pkgdata_DATA)
 
 DIST_COMMON = $(dist_pkgdata_DATA) Makefile.am Makefile.in
-SOURCES = $(rapper_SOURCES)
+SOURCES = $(rappermc_SOURCES)
 
 all: all-am
 
--- src/rapper/LOOP/Makefile.am 2008-01-24 15:08:17.000000000 +0100
+++ src/rapper/LOOP/Makefile.am.new     2009-03-12 23:01:56.697533874 +0100
@@ -1,6 +1,6 @@
-bin_PROGRAMS = rapper
+bin_PROGRAMS = rappermc
 
-rapper_SOURCES = \
+rappermc_SOURCES = \
 kip.h aaconv.cpp atomconv.cpp kip_snake.cpp \
 kip_pdb.cpp measure.cpp lib_frags.cpp ran2.cpp \
 heap.cpp queue.cpp 3Dgeom.cpp space_grid.cpp list.cpp search_residue.cpp bitfield.cpp \
@@ -15,7 +15,7 @@
 hash_table.cpp surface.cpp parse.cpp band.cpp edensity.cpp read_map.cpp iterator.cpp \
 residue_range.cpp pop_search_frags.cpp saxs.cpp lib_choral.cpp pdf.cpp WeightedDistribMean.cpp
 
-rapper_LDADD = ../gc7.0/libgc.la ../libxml2/libxml2.la
+rappermc_LDADD = ../gc7.0/libgc.la ../libxml2/libxml2.la
 
 pkgdatadir = $(datadir)/rapper
 dist_pkgdata_DATA = params.xml



1.1                  sci-chemistry/ccp4-apps/files/6.1.3-clipper-template.patch

file : http://sources.gentoo.org/viewcvs.py/gentoo-x86/sci-chemistry/ccp4-apps/files/6.1.3-clipper-template.patch?rev=1.1&view=markup
plain: http://sources.gentoo.org/viewcvs.py/gentoo-x86/sci-chemistry/ccp4-apps/files/6.1.3-clipper-template.patch?rev=1.1&content-type=text/plain

Index: 6.1.3-clipper-template.patch
===================================================================
--- src/clipper_progs/src/intensity_target.h.orig	2010-01-21 11:27:13.236795886 -0600
+++ src/clipper_progs/src/intensity_target.h	2010-01-21 11:31:33.450686927 -0600
@@ -70,9 +70,31 @@
   {
   public:
     //! constructor: takes the datalist against which to calc target
-    TargetFn_scaleLogI1I2( const HKL_data<T1>& hkl_data1_, const HKL_data<T2>& hkl_data2_ );
+    TargetFn_scaleLogI1I2( const HKL_data<T1>& hkl_data1_, const HKL_data<T2>& hkl_data2_ )
+    {
+      hkl_data1 = &hkl_data1_;
+      hkl_data2 = &hkl_data2_;
+    }
     //! return the value and derivatives of the target function
-    Rderiv rderiv( const HKL_info::HKL_reference_index& ih, const ftype& intensityh ) const;
+    Rderiv rderiv( const HKL_info::HKL_reference_index& ih, const ftype& intensityh ) const
+    {
+      Rderiv result;
+      result.r = result.dr = result.dr2 = 0.0;
+      const T1& it1 = (*hkl_data1)[ih];
+      const T2& it2 = (*hkl_data2)[ih];
+      if ( !it1.missing() && !it2.missing() )
+        if ( it1.I() > 1.0e-6 && it2.I() > 1.0e-6 ) {
+          const ftype eps = ih.hkl_class().epsilon();
+          const ftype i1 = it1.I() / eps;
+          const ftype i2 = it2.I() / eps;
+          const ftype w = sqrt( i1 * i2 );    
+          const ftype d = intensityh + log(i1) - log(i2);
+          result.r   =       w * d * d;
+          result.dr  = 2.0 * w * d;
+          result.dr2 = 2.0 * w;
+      }
+      return result;
+    }
     //! the type of the function: optionally used to improve convergence
     FNtype type() const { return QUADRATIC; }
   private:
@@ -109,33 +131,4 @@
     return result;
   }
 
-  // Log I1-I2 scaling
-
-  template<class T1, class T2> TargetFn_scaleLogI1I2<T1,T2>::TargetFn_scaleLogI1I2( const HKL_data<T1>& hkl_data1_, const HKL_data<T2>& hkl_data2_ )
-  {
-    hkl_data1 = &hkl_data1_;
-    hkl_data2 = &hkl_data2_;
-  }
-
-  template<class T1, class T2> TargetFn_base::Rderiv TargetFn_scaleLogI1I2<T1,T2>::rderiv( const HKL_info::HKL_reference_index& ih, const ftype& intensityh ) const
-  {
-    Rderiv result;
-    result.r = result.dr = result.dr2 = 0.0;
-    const T1& it1 = (*hkl_data1)[ih];
-    const T2& it2 = (*hkl_data2)[ih];
-    if ( !it1.missing() && !it2.missing() )
-      if ( it1.I() > 1.0e-6 && it2.I() > 1.0e-6 ) {
-	const ftype eps = ih.hkl_class().epsilon();
-	const ftype i1 = it1.I() / eps;
-	const ftype i2 = it2.I() / eps;
-	const ftype w = sqrt( i1 * i2 );    
-	const ftype d = intensityh + log(i1) - log(i2);
-	result.r   =       w * d * d;
-	result.dr  = 2.0 * w * d;
-	result.dr2 = 2.0 * w;
-    }
-    return result;
-  }
-
-
 #endif



1.1                  sci-chemistry/ccp4-apps/files/6.1.3-pythonpath.patch

file : http://sources.gentoo.org/viewcvs.py/gentoo-x86/sci-chemistry/ccp4-apps/files/6.1.3-pythonpath.patch?rev=1.1&view=markup
plain: http://sources.gentoo.org/viewcvs.py/gentoo-x86/sci-chemistry/ccp4-apps/files/6.1.3-pythonpath.patch?rev=1.1&content-type=text/plain

Index: 6.1.3-pythonpath.patch
===================================================================
diff --git a/ccp4-6.1.2/include/ccp4.setup-bash b/ccp4-6.1.2/include/ccp4.setup-bash
index 9848101..cea8ae6 100755
--- a/ccp4-6.1.2/include/ccp4.setup-bash
+++ b/ccp4-6.1.2/include/ccp4.setup-bash
@@ -188,9 +188,9 @@ fi
 #Python path for the subprocess fixed module
 
 if [ $ccp4_first_in_path -eq 1 ]; then
-    setenv PYTHONPATH ${CCP4}/share/python:${PYTHONPATH}
+    setenv PYTHONPATH ${CCP4}/share/ccp4/smartie:${CCP4I_TOP}/python:${PYTHONPATH}
 else
-    setenv PYTHONPATH ${PYTHONPATH}:${CCP4}/share/python
+    setenv PYTHONPATH ${PYTHONPATH}:${CCP4}/share/ccp4/smartie:${CCP4I_TOP}/python
 fi
 
 ### PLOT_COMMAND PRINT_COMMAND for the XCCPJIFFY programs to compile ###
diff --git a/ccp4-6.1.2/include/ccp4.setup-csh b/ccp4-6.1.2/include/ccp4.setup-csh
index 42f0820..93c2cf3 100755
--- a/ccp4-6.1.2/include/ccp4.setup-csh
+++ b/ccp4-6.1.2/include/ccp4.setup-csh
@@ -180,9 +180,9 @@ endif
 #Python path for the subprocess fixed module
 if (${?PYTHONPATH}) then
   if ($ccp4_first_in_path) then
-      setenv PYTHONPATH ${CCP4}/share/python:${PYTHONPATH}
+      setenv PYTHONPATH ${CCP4}/share/ccp4/smartie:${CCP4I_TOP}/python:${PYTHONPATH}
   else
-      setenv PYTHONPATH ${PYTHONPATH}:${CCP4}/share/python
+      setenv PYTHONPATH ${PYTHONPATH}:${CCP4}/share/ccp4/smartie:${CCP4I_TOP}/python
   endif
 else
     setenv PYTHONPATH ${CCP4}/share/python
diff --git a/ccp4-6.1.2/include/ccp4.setup-sh b/ccp4-6.1.2/include/ccp4.setup-sh
index 4396ebf..a0455bd 100755
--- a/ccp4-6.1.2/include/ccp4.setup-sh
+++ b/ccp4-6.1.2/include/ccp4.setup-sh
@@ -228,9 +228,9 @@ test -r $CCP4/include/ccp4.msg && cat $CCP4/include/ccp4.msg
 #Python path for the subprocess fixed module
 
 if test $ccp4_first_in_path -eq 1; then
-    export PYTHONPATH=${CCP4}/share/python:${PYTHONPATH}
+    export PYTHONPATH=${CCP4}/share/ccp4/smartie:${CCP4I_TOP}/python:${PYTHONPATH}
 else
-    export PYTHONPATH=${PYTHONPATH}:${CCP4}/share/python
+    export PYTHONPATH=${PYTHONPATH}:${CCP4}/share/ccp4/smartie:${CCP4I_TOP}/python
 fi
 
 ################### THE REST SHOULDN'T NEED EDITING #####################
diff --git a/ccp4-6.1.2/include/ccp4.setup-zsh b/ccp4-6.1.2/include/ccp4.setup-zsh
index 0e5c2ce..53523f3 100755
--- a/ccp4-6.1.2/include/ccp4.setup-zsh
+++ b/ccp4-6.1.2/include/ccp4.setup-zsh
@@ -157,10 +157,10 @@ export CLASSPATH
 #Python path for the subprocess fixed module
 
 if ($ccp4_first_in_path) then
-    PYTHONPATH=${CCP4}/share/python:${PYTHONPATH}
+    PYTHONPATH=${CCP4}/share/ccp4/smartie:${CCP4I_TOP}/python:${PYTHONPATH}
     export PYTHONPATH
 else
-    PYTHONPATH=${PYTHONPATH}:${CCP4}/share/python
+    PYTHONPATH=${PYTHONPATH}:${CCP4}/share/ccp4/smartie:${CCP4I_TOP}/python
     export PYTHONPATH
 fi
 



1.1                  sci-chemistry/ccp4-apps/files/6.1.3-setup.patch

file : http://sources.gentoo.org/viewcvs.py/gentoo-x86/sci-chemistry/ccp4-apps/files/6.1.3-setup.patch?rev=1.1&view=markup
plain: http://sources.gentoo.org/viewcvs.py/gentoo-x86/sci-chemistry/ccp4-apps/files/6.1.3-setup.patch?rev=1.1&content-type=text/plain

Index: 6.1.3-setup.patch
===================================================================
diff --git a/include/ccp4.setup-bash b/include/ccp4.setup-bash
index 9848101..d76fe3b 100755
--- a/include/ccp4.setup-bash
+++ b/include/ccp4.setup-bash
@@ -37,8 +37,8 @@ fi
 # This is usually the directory in which you ran the tar command to unpack the
 # code, and is assumed to be shared between machines at a multi-machine site.
 
-setenv CCP4_MASTER	/xtal                    
-setenv CCP4		$CCP4_MASTER/ccp4-6.1.2
+setenv CCP4_MASTER /usr
+setenv CCP4	$CCP4_MASTER
 
 # Check for existence of CCP4_MASTER
 if (! test -d $CCP4_MASTER) ; then
@@ -54,7 +54,7 @@ fi
 # files. A dedicated scratch filesystem is probably better than (/usr)/tmp
 # BINSORT_SCR: a scratch directory for binsort's use; normally same as CCP4_SCR
 
-setenv CCP4_SCR      /tmp/$USER	
+setenv CCP4_SCR     /tmp/$USER	
 # check to see if this exists and if not try to make it
 test -d $CCP4_SCR || mkdir $CCP4_SCR
 test -d $CCP4_SCR || \
@@ -70,7 +70,7 @@ setenv CCP4I_TOP ${CCP4}/ccp4i
 #               For 'standard' installations this is /usr/local/bin
 #               but note the SGI distributed version of Tcl/Tk is not 
 #               appropriate version
-setenv CCP4I_TCLTK /usr/local/bin        
+setenv CCP4I_TCLTK /usr/bin        
 # CCP4I_HELP - directory contain ccp4i help - default is $CCP4I_TOP/help
 setenv CCP4I_HELP ${CCP4I_TOP}/help
 
@@ -128,7 +128,7 @@ setenv GFORTRAN_UNBUFFERED_ALL Y
 #                                       # for multiple systems
 #   foo)
     setenv CBIN      $CCP4/bin		
-    setenv CLIB      $CCP4/lib	
+    setenv CLIB      $CCP4/GENTOOLIBDIR
 
     setenv CCP4_BROWSER  firefox             
 
@@ -188,9 +188,9 @@ fi
 #Python path for the subprocess fixed module
 
 if [ $ccp4_first_in_path -eq 1 ]; then
-    setenv PYTHONPATH ${CCP4}/share/python:${PYTHONPATH}
+    setenv PYTHONPATH ${CCP4}/share/ccp4/smartie:${CCP4I_TOP}/python:${PYTHONPATH}
 else
-    setenv PYTHONPATH ${PYTHONPATH}:${CCP4}/share/python
+    setenv PYTHONPATH ${PYTHONPATH}:${CCP4}/share/ccp4/smartie:${CCP4I_TOP}/python
 fi
 
 ### PLOT_COMMAND PRINT_COMMAND for the XCCPJIFFY programs to compile ###
@@ -292,14 +292,12 @@ test -r $CCP4/include/ccp4.msg && cat $CCP4/include/ccp4.msg
 
 ### dbCCP4i database handler setup ###
 
-setenv DBCCP4I_TOP ${CCP4}/share/dbccp4i
+setenv DBCCP4I_TOP ${CCP4}/share/ccp4/dbccp4i
 
 ### IMOSFLM environment is now defined here
 
 setenv MOSFLM_EXEC ${CBIN}/ipmosflm
 setenv MOSFLM_WISH ${CCP4I_TCLTK}/wish
-setenv IMOSFLM_VERSION "1.0.0"
-
 
 ### MMCIFDIC is now defined here. cif_mmdic.lib is a binary file ===
 # so on multiple installs it need to be unique and not in $CLIBD
@@ -309,21 +307,13 @@ setenv MMCIFDIC $CLIB/cif_mmdic.lib
 ### MOLREPLIB Point to the location of the files bs-zeros.dat  ps.resource  symlib.blc
 # They are distributed with CCP4 in $CLIBD. This env must have the trailing \ or /
 
-setenv MOLREPLIB $CCP4/lib/data/monomers/
+setenv MOLREPLIB $CCP4/share/ccp4/data/monomers/
 
 ### CRANK points to location of Crank automation suite within ccp4i
 
-setenv CRANK $CCP4/ccp4i/crank
+setenv CRANK $CCP4I_TOP/bin/crank
 setenv CCP4_CRANK 1
 
-### XIA2 setup
-# XIAROOT directory (default is under the share folder)
-
-if test -e $CCP4/share/XIAROOT/setup.sh
-then
-. $CCP4/share/XIAROOT/setup.sh
-fi
-
 # Note: The PATH is updated with the xia2 Applications directory in the 
 # construct below.
 
@@ -339,7 +329,7 @@ fi
 # They are distributed with CCP4 in $CLIBD/monomers. This env must have 
 # the trailing \ or /
 
-setenv CLIBD_MON $CCP4/lib/data/monomers/
+setenv CLIBD_MON $CCP4/share/ccp4/data/monomers/
 
 ### PUBLIC_FONT84, CCP4_HELPDIR, HELPDIR, MOSHELPFILE ###
 # (essential for the relevant programs)
@@ -347,10 +337,10 @@ setenv PUBLIC_FONT84   $CLIB/font84.dat  # plot84 fonts [used by plot84lib]
 
 # location of VMS-style help files required for mosflm [used by hlplib, chelp,
 #   chlp, (ip)mosflm]:
-setenv CCP4_HELPDIR    $CCP4/help/            # NB trailing /
+setenv CCP4_HELPDIR    $CCP4I_TOP/help/            # NB trailing /
 
 # Rasmol path. Needed for prog. to find rasmol.hlp
-setenv RASMOLPATH $CCP4/x-windows/RasMol/src
+setenv RASMOLPATH $CCP4/GENTOOLIBDIR/rasmol
 
 # CCP4 executables and scripts live in $CBIN and $CETC respectively; put them
 # on the path in an appropriate order for scripts to be used as wrappers for
@@ -373,32 +363,14 @@ done
 
 # Optional (useful) additional environment variables
   setenv CCP4             $CCP4
-  setenv CDOC             $CCP4/doc
-  setenv CHTML            $CCP4/html
-  setenv CETC             $CCP4/etc
-  setenv CEXAM            $CCP4/examples
+  setenv CDOC             $DBCCP4I_TOP/doc
+  setenv CHTML            $CCP4I_TOP/html
+  setenv CETC             $CCP4I_TOP/etc
+  setenv CEXAM            $CLIB/ccp4/examples
   setenv CINCL            $CCP4/include
-  setenv CLIBD            $CCP4/lib/data
-  setenv CLIBS            $CCP4/lib/src
-  setenv CPROG            $CCP4/src
+  setenv CLIBD            $CCP4/share/ccp4/data
 
 if [ "`basename $SHELL`" != "ksh" ]; then
-# useful aliases, at least for developers
-  alias ccp4   'pushd $CCP4>/dev/null'
-  alias xtal   'pushd $CCP4_MASTER>/dev/null'
-  alias cbin   'pushd $CBIN>/dev/null'
-  alias cetc   'pushd $CETC>/dev/null'
-  alias cprog  'pushd $CPROG>/dev/null'
-  alias cincl  'pushd $CINCL>/dev/null'
-  alias clib   'pushd $CLIB>/dev/null'
-  alias clibd  'pushd $CLIBD>/dev/null'
-  alias clibs  'pushd $CLIBS>/dev/null'
-  alias cbin   'pushd $CBIN>/dev/null'
-  alias cexam  'pushd $CEXAM>/dev/null'
-  alias cdoc   'pushd $CDOC>/dev/null'
-  alias chtml  'pushd $CHTML>/dev/null'
-  alias ccp4help '$CCP4_BROWSER $CHTML/INDEX.html \&'
-
 ### laue, lget, linkimages ###
 
 ### only if we have the Laue software suite...
@@ -430,23 +402,6 @@ if [ "`basename $SHELL`" != "ksh" ]; then
     alias lbin   'pushd $CBIN>/dev/null'
 
   fi
-
+else
   unset alias  # clean up
 fi             # ksh test
-
-# Set-up cctbx environment
-test -r $CCP4/lib/cctbx/cctbx_build/setpaths.sh && . $CCP4/lib/cctbx/cctbx_build/setpaths.sh
-
-# Set-up phaser environment
-if ( test -d $CCP4/src/phaser) ; then
-  phaser_mtype=`$CCP4/src/phaser/bin/machine_type`
-  phaser_version=`grep PHASER_VERSION $CCP4/src/phaser/conf/version.sh | awk '{print $3}'`
-  phaser_setup_file="${CCP4}/src/phaser/phaser-${phaser_version}/build/${phaser_mtype}/setpaths.sh"
-  test -r $phaser_setup_file && . $phaser_setup_file
-fi
-
-#BALBES root configuration
-if ( test -d $CCP4/share/balbes/BALBES_0.0.1)
-then
-  setenv BALBES_ROOT $CCP4/share/balbes/BALBES_0.0.1
-fi
diff --git a/include/ccp4.setup-csh b/include/ccp4.setup-csh
index 42f0820..ed3c671 100755
--- a/include/ccp4.setup-csh
+++ b/include/ccp4.setup-csh
@@ -24,8 +24,8 @@
 # This is usually the directory in which you ran the tar command to unpack the
 # code, and is assumed to be shared between machines at a multi-machine site.
 
-setenv CCP4_MASTER	/xtal                  
-setenv CCP4		$CCP4_MASTER/ccp4-6.1.2
+setenv CCP4_MASTER	/usr
+setenv CCP4		$CCP4_MASTER
 
 # Check for existence of CCP4_MASTER
 if (! -e $CCP4_MASTER) then
@@ -57,7 +57,7 @@ setenv CCP4I_TOP ${CCP4}/ccp4i
 #               For 'standard' installations this is /usr/local/bin
 #               but note the SGI distributed version of Tcl/Tk is not 
 #               appropriate version
-setenv CCP4I_TCLTK /usr/local/bin        
+setenv CCP4I_TCLTK /usr/bin        
 # CCP4I_HELP - directory contain ccp4i help - default is $CCP4I_TOP/help
 setenv CCP4I_HELP ${CCP4I_TOP}/help
 
@@ -115,7 +115,7 @@ setenv GFORTRAN_UNBUFFERED_ALL Y
 #                                       # for multiple systems
 #   case 'foo':
     setenv CBIN      $CCP4/bin		
-    setenv CLIB      $CCP4/lib	
+    setenv CLIB      $CCP4/GENTOOLIBDIR	
 
     setenv CCP4_BROWSER  firefox          
 
@@ -180,9 +180,9 @@ endif
 #Python path for the subprocess fixed module
 if (${?PYTHONPATH}) then
   if ($ccp4_first_in_path) then
-      setenv PYTHONPATH ${CCP4}/share/python:${PYTHONPATH}
+      setenv PYTHONPATH ${CCP4}/share/ccp4/smartie:${CCP4I_TOP}/python:${PYTHONPATH}
   else
-      setenv PYTHONPATH ${PYTHONPATH}:${CCP4}/share/python
+      setenv PYTHONPATH ${PYTHONPATH}:${CCP4}/share/ccp4/smartie:${CCP4I_TOP}/python
   endif
 else
     setenv PYTHONPATH ${CCP4}/share/python
@@ -284,13 +284,12 @@ if (-e $CCP4/include/ccp4.msg) cat $CCP4/include/ccp4.msg
 
 ### dbCCP4i database handler setup ###
 
-setenv DBCCP4I_TOP ${CCP4}/share/dbccp4i
+setenv DBCCP4I_TOP ${CCP4}/share/ccp4/dbccp4i
 
 ### IMOSFLM environment is now defined here
 
 setenv MOSFLM_EXEC ${CBIN}/ipmosflm
 setenv MOSFLM_WISH ${CCP4I_TCLTK}/wish
-setenv IMOSFLM_VERSION "1.0.0"
 
 ### MMCIFDIC is now defined here. cif_mmdic.lib is a binary file ===
 # so on multiple installs it need to be unique and not in $CLIBD
@@ -300,20 +299,13 @@ setenv MMCIFDIC $CLIB/cif_mmdic.lib
 ### MOLREPLIB Point to the location of the files bs-zeros.dat  ps.resource  symlib.blc
 # They are distributed with CCP4 in $CLIBD. This env must have the trailing \ or /
 
-setenv MOLREPLIB $CCP4/lib/data/monomers/
+setenv MOLREPLIB $CCP4/share/ccp4/data/monomers/
 
 ### CRANK points to location of Crank automation suite within ccp4i
 
-setenv CRANK $CCP4/ccp4i/crank
+setenv CRANK $CCP4I_TOP/bin/crank
 setenv CCP4_CRANK 1
 
-### XIA2 setup
-# XIAROOT directory (default is under the share folder)
-
-if (-e $CCP4/share/XIAROOT/setup.csh) then
-   source $CCP4/share/XIAROOT/setup.csh
-endif
-
 # Note: The PATH is updated with the xia2 Applications directory in the 
 # construct below.
 
@@ -328,7 +320,7 @@ endif
 # They are distributed with CCP4 in $CLIBD/monomers. This env must have 
 # the trailing \ or /
 
-setenv CLIBD_MON $CCP4/lib/data/monomers/
+setenv CLIBD_MON $CCP4/share/ccp4/data/monomers/
 
 ### PUBLIC_FONT84, CCP4_HELPDIR, HELPDIR, MOSHELPFILE ###
 # (essential for the relevant programs)
@@ -339,7 +331,7 @@ setenv PUBLIC_FONT84   $CLIB/font84.dat  # plot84 fonts [used by plot84lib]
 setenv CCP4_HELPDIR    $CCP4/help/            # NB trailing /
 
 # Rasmol path. Needed for prog. to find rasmol.hlp
-setenv RASMOLPATH $CCP4/x-windows/RasMol/src
+setenv RASMOLPATH $CCP4/GENTOOLIBDIR/rasmol
 
 # CCP4 executables and scripts live in $CBIN and $CETC respectively; put them
 # on the path in an appropriate order for scripts to be used as wrappers for
@@ -366,30 +358,12 @@ end
 
 # Optional (useful) additional environment variables
   setenv CCP4             $CCP4
-  setenv CDOC             $CCP4/doc
-  setenv CHTML            $CCP4/html
-  setenv CETC             $CCP4/etc
-  setenv CEXAM            $CCP4/examples
+  setenv CDOC             $DBCCP4I_TOP/doc
+  setenv CHTML            $CCP4I_TOP/html
+  setenv CETC             $CCP4I_TOP/etc
+  setenv CEXAM            $CLIB/ccp4/examples
   setenv CINCL            $CCP4/include
-  setenv CLIBD            $CCP4/lib/data
-  setenv CLIBS            $CCP4/lib/src
-  setenv CPROG            $CCP4/src
-
-# useful aliases, at least for developers
-  alias ccp4   'pushd $CCP4>/dev/null'
-  alias xtal   'pushd $CCP4_MASTER>/dev/null'
-  alias cbin   'pushd $CBIN>/dev/null'
-  alias cetc   'pushd $CETC>/dev/null'
-  alias cprog  'pushd $CPROG>/dev/null'
-  alias cincl  'pushd $CINCL>/dev/null'
-  alias clib   'pushd $CLIB>/dev/null'
-  alias clibd  'pushd $CLIBD>/dev/null'
-  alias clibs  'pushd $CLIBS>/dev/null'
-  alias cbin   'pushd $CBIN>/dev/null'
-  alias cexam  'pushd $CEXAM>/dev/null'
-  alias cdoc   'pushd $CDOC>/dev/null'
-  alias chtml  'pushd $CHTML>/dev/null'
-  alias ccp4help '$CCP4_BROWSER $CHTML/INDEX.html &'
+  setenv CLIBD            $CCP4/share/ccp4/data
 
 ### laue, lget, linkimages ###
 
@@ -421,19 +395,3 @@ end
 #
 
   endif 
-
-# Set-up cctbx environment
-if (-e $CCP4/lib/cctbx/cctbx_build/setpaths.csh) source $CCP4/lib/cctbx/cctbx_build/setpaths.csh
-
-# Set-up phaser environment
-if (-d $CCP4/src/phaser) then
-  set phaser_mtype = `$CCP4/src/phaser/bin/machine_type`
-  set phaser_version = `grep PHASER_VERSION $CCP4/src/phaser/conf/version.csh | awk '{print $3}'`
-  set phaser_setup_file = "${CCP4}/src/phaser/phaser-${phaser_version}/build/${phaser_mtype}/setpaths.csh"
-  if (-e $phaser_setup_file) source $phaser_setup_file
-endif
-
-#BALBES root configuration
-if ( -d $CCP4/share/balbes/BALBES_0.0.1) then
-  setenv BALBES_ROOT $CCP4/share/balbes/BALBES_0.0.1
-endif



1.1                  sci-chemistry/ccp4-apps/files/6.1.3-dont-make-dirs-in-configure.patch

file : http://sources.gentoo.org/viewcvs.py/gentoo-x86/sci-chemistry/ccp4-apps/files/6.1.3-dont-make-dirs-in-configure.patch?rev=1.1&view=markup
plain: http://sources.gentoo.org/viewcvs.py/gentoo-x86/sci-chemistry/ccp4-apps/files/6.1.3-dont-make-dirs-in-configure.patch?rev=1.1&content-type=text/plain

Index: 6.1.3-dont-make-dirs-in-configure.patch
===================================================================
--- ccp4-6.0.99e.orig/configure	2008-07-31 10:37:22.000000000 -0700
+++ ccp4-6.0.99e/configure	2008-07-31 10:39:18.000000000 -0700
@@ -643,45 +643,45 @@
 #     echo "! Beware -- the $system installation isn't properly tested." ; }
 syswarn='echo; echo "! Beware -- the $system installation is not properly tested."'
 
-if test -z "$onlylibs" ; then 
-   for i in CCP4_SCR BINSORT_SCR; do
-     if ( eval test -d \$$i || eval mkdir -p \$$i ) ; then :
-     else
-       eval echo "! No directory \$$i and can\'t create it."
-       echo "  Check the value of $i."
-       badvar=1
-     fi
-   done
-
-   for i in libdir bindir includedir; do
-     if ( eval test -d \$$i || eval mkdir -p \$$i ) ; then :
-     else
-       eval echo "! No directory \$$i and can\'t create it."
-       echo "  Check the argument of --$i."
-       badvar=1
-     fi
-   done
-
-   for i in $dotsrc $dotunsupp $dotunsuppsrc $dotdeprec $dotdeprecsrc ./lib ./lib/src ./lib/data ./ccp4i/etc/unix $mosflmdir/lib $mosflmdir/bin $mosflmdir/cbf/lib ; do
-     if test -d $i || mkdir $i; then :
-     else
-       eval echo "! No directory $i and can\'t create it."
-       badvar=1
-     fi
-   done
-else
-   # Kludge to fool the "Makefile" target in the top-level CCP4
-   # Makefile into not trying to remake src/Makefile.in
-   for i in $srcdir/src $srcdir/lib/src ; do
-     if test -d $i || mkdir $i; then
-       if ! test -f $i/Makefile.in ; then
-         echo
-         echo "onlylibs: making dummy file $i/Makefile.in"
-	 touch $i/Makefile.in
-       fi
-     fi
-   done
-fi
+#if test -z "$onlylibs" ; then 
+#   for i in CCP4_SCR BINSORT_SCR; do
+#     if ( eval test -d \$$i || eval mkdir -p \$$i ) ; then :
+#     else
+#       eval echo "! No directory \$$i and can\'t create it."
+#       echo "  Check the value of $i."
+#       badvar=1
+#     fi
+#   done
+#
+#   for i in libdir bindir includedir; do
+#     if ( eval test -d \$$i || eval mkdir -p \$$i ) ; then :
+#     else
+#       eval echo "! No directory \$$i and can\'t create it."
+#       echo "  Check the argument of --$i."
+#       badvar=1
+#     fi
+#   done
+#
+#   for i in $dotsrc $dotunsupp $dotunsuppsrc $dotdeprec $dotdeprecsrc ./lib ./lib/src ./lib/data ./ccp4i/etc/unix $mosflmdir/lib $mosflmdir/bin $mosflmdir/cbf/lib ; do
+#     if test -d $i || mkdir $i; then :
+#     else
+#       eval echo "! No directory $i and can\'t create it."
+#       badvar=1
+#     fi
+#   done
+#else
+#   # Kludge to fool the "Makefile" target in the top-level CCP4
+#   # Makefile into not trying to remake src/Makefile.in
+#   for i in $srcdir/src $srcdir/lib/src ; do
+#     if test -d $i || mkdir $i; then
+#       if ! test -f $i/Makefile.in ; then
+#         echo
+#         echo "onlylibs: making dummy file $i/Makefile.in"
+#	 touch $i/Makefile.in
+#       fi
+#     fi
+#   done
+#fi
 
 ### sanity checks
 



1.1                  sci-chemistry/ccp4-apps/files/6.1.3-pisa.patch

file : http://sources.gentoo.org/viewcvs.py/gentoo-x86/sci-chemistry/ccp4-apps/files/6.1.3-pisa.patch?rev=1.1&view=markup
plain: http://sources.gentoo.org/viewcvs.py/gentoo-x86/sci-chemistry/ccp4-apps/files/6.1.3-pisa.patch?rev=1.1&content-type=text/plain

Index: 6.1.3-pisa.patch
===================================================================
diff --git a/src/pisa/sbase/Makefile.am b/src/pisa/sbase/Makefile.am
index 053e83a..4ff3394 100755
--- a/src/pisa/sbase/Makefile.am
+++ b/src/pisa/sbase/Makefile.am
@@ -1,4 +1,4 @@
-pkgdatadir = $(datadir)/sbase
+pkgdatadir = $(datadir)/pisa/sbase
 dist_pkgdata_DATA = \
 graph.sbase     index.sbase     struct.sbase
 
diff --git a/src/pisa/sbase/Makefile.in b/src/pisa/sbase/Makefile.in
index faa3f7f..8630bd7 100755
--- a/src/pisa/sbase/Makefile.in
+++ b/src/pisa/sbase/Makefile.in
@@ -62,7 +62,7 @@ POST_UNINSTALL = :
 EXEEXT = @EXEEXT@
 OBJEXT = @OBJEXT@
 PATH_SEPARATOR = @PATH_SEPARATOR@
-pkgdatadir = $(datadir)/sbase
+pkgdatadir = $(datadir)/pisa/sbase
 AMTAR = @AMTAR@
 AR_FLAGS = @AR_FLAGS@
 AWK = @AWK@



1.1                  sci-chemistry/ccp4-apps/files/6.1.3-fix-setup-bash-incompatibility.patch

file : http://sources.gentoo.org/viewcvs.py/gentoo-x86/sci-chemistry/ccp4-apps/files/6.1.3-fix-setup-bash-incompatibility.patch?rev=1.1&view=markup
plain: http://sources.gentoo.org/viewcvs.py/gentoo-x86/sci-chemistry/ccp4-apps/files/6.1.3-fix-setup-bash-incompatibility.patch?rev=1.1&content-type=text/plain

Index: 6.1.3-fix-setup-bash-incompatibility.patch
===================================================================
--- ccp4-6.0.99e.orig/include/ccp4.setup-bash	2008-07-31 10:37:22.000000000 -0700
+++ ccp4-6.0.99e/include/ccp4.setup-bash	2008-07-31 12:47:14.000000000 -0700
@@ -181,7 +181,7 @@
 
 #Python path for the subprocess fixed module
 
-if ($ccp4_first_in_path) then
+if [ $ccp4_first_in_path -eq 1 ]; then
     setenv PYTHONPATH ${CCP4}/share/python:${PYTHONPATH}
 else
     setenv PYTHONPATH ${PYTHONPATH}:${CCP4}/share/python



1.1                  sci-chemistry/ccp4-apps/files/6.1.3-dont-build-scala.patch

file : http://sources.gentoo.org/viewcvs.py/gentoo-x86/sci-chemistry/ccp4-apps/files/6.1.3-dont-build-scala.patch?rev=1.1&view=markup
plain: http://sources.gentoo.org/viewcvs.py/gentoo-x86/sci-chemistry/ccp4-apps/files/6.1.3-dont-build-scala.patch?rev=1.1&content-type=text/plain

Index: 6.1.3-dont-build-scala.patch
===================================================================
--- ./src/Makefile.in	2009-03-20 15:06:41.000000000 +0100
+++ ./src/Makefile.in.new	2009-07-31 23:46:13.000000000 +0200
@@ -50,7 +50,7 @@
 
 # these live in subdirectories and have more than one dependency:
 OTHERS = rsps anglen secstr proclean pplot gfac2pdb tplot mplot probplot rmsdev nb \
-         scala dm dmmulti stereo mapmask maprot ncsmask \
+         dm dmmulti stereo mapmask maprot ncsmask \
          sftools tlsanl tlsextract topp toplist dyndom sc combat mlphare fffear ffjoin \
          anisoanl $(REFMACTARGETS) dtrek2scala crunch2 pmf doser mat2symop symop2mat 
 
@@ -637,7 +637,7 @@
 
 ### scala, mapmask, maprot, ncsmask, combat
 
-scala mapmask maprot ncsmask combat sc dyndom: # dependencies below
+mapmask maprot ncsmask combat sc dyndom: # dependencies below
 	@$(SETFLAGS) pwd=`pwd` ; rm -f $@; \
 	  cd $(srcdir)/$@_; \
 	  echo $(FC) $${$@_FLAGS-"$(FFLAGS)"} -c -o $$pwd/$@.o `pwd`/$@.f ;\
@@ -1002,21 +1002,6 @@
 proclean:	$(srcdir)/procheck/clean.f $(srcdir)/procheck/brkcln.par
 rmsdev:		$(srcdir)/procheck/rmsdev.f $(srcdir)/procheck/rmsdev.inc
 
-scaladir = $(srcdir)/scala_
-scala : $(scaladir)/scala.f $(scaladir)/column.fh $(scaladir)/orient.fh \
-	$(scaladir)/params.fh $(scaladir)/rfile.fh $(scaladir)/scales.fh \
-	$(scaladir)/nbtchc.fh $(scaladir)/parameter.fh $(scaladir)/refcon.fh \
-	$(scaladir)/rundef.fh $(scaladir)/sdfacc.fh $(scaladir)/flags.fh \
-	$(scaladir)/inout.fh $(scaladir)/dump.fh $(scaladir)/tie.fh \
-	$(scaladir)/outcon.fh $(scaladir)/version.fh $(scaladir)/anomtc.fh \
-        $(scaladir)/axes.fh $(scaladir)/bigarg.fh \
-        $(scaladir)/errors.fh $(scaladir)/flow.fh $(scaladir)/glocon.fh \
-        $(scaladir)/means.fh $(scaladir)/refflg.fh $(scaladir)/stats.fh \
-        $(scaladir)/symmty.fh $(scaladir)/sharvest.fh $(scaladir)/chtml.fh \
-        $(scaladir)/htmbuf.fh $(scaladir)/sphhrm.fh $(scaladir)/crlncf.fh \
-        $(scaladir)/datasets.fh $(scaladir)/dts_storage.fh \
-        $(scaladir)/sclinimeans.fh $(scaladir)/timecor.fh
-
 freemask.o:	$(dmdir)/freemask.f $(dmdir)/crystal.fh $(dmdir)/cycl.fh \
 		$(dmdir)/dmheader.fh $(dmdir)/io.fh $(dmdir)/output.fh \
 		$(dmdir)/params.fh $(dmdir)/uvwdata.fh