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-rw-r--r--sci-chemistry/ccp4-apps/files/6.1.3-clipper-template.patch70
-rw-r--r--sci-chemistry/ccp4-apps/files/6.1.3-dont-build-balbes.patch14
-rw-r--r--sci-chemistry/ccp4-apps/files/6.1.3-dont-build-double-and-make-bindir.patch24
-rw-r--r--sci-chemistry/ccp4-apps/files/6.1.3-dont-build-imosflm.patch11
-rw-r--r--sci-chemistry/ccp4-apps/files/6.1.3-dont-build-libs.patch35
-rw-r--r--sci-chemistry/ccp4-apps/files/6.1.3-dont-build-molref.patch19
-rw-r--r--sci-chemistry/ccp4-apps/files/6.1.3-dont-build-scala.patch42
-rw-r--r--sci-chemistry/ccp4-apps/files/6.1.3-dont-build-xia.patch14
-rw-r--r--sci-chemistry/ccp4-apps/files/6.1.3-dont-configure.patch111
-rw-r--r--sci-chemistry/ccp4-apps/files/6.1.3-dont-make-dirs-in-configure.patch87
-rw-r--r--sci-chemistry/ccp4-apps/files/6.1.3-impl-dec.patch152
-rw-r--r--sci-chemistry/ccp4-apps/files/6.1.3-lapack.patch597
-rw-r--r--sci-chemistry/ccp4-apps/files/6.1.3-pisa.patch23
-rw-r--r--sci-chemistry/ccp4-apps/files/6.1.3-pythonpath.patch65
-rw-r--r--sci-chemistry/ccp4-apps/files/6.1.3-rename-rapper-ng.patch60
-rw-r--r--sci-chemistry/ccp4-apps/files/6.1.3-unbundle.patch131
-rw-r--r--sci-chemistry/ccp4-apps/files/ccp4-apps-6.1.3-tcl8.6.patch130
17 files changed, 0 insertions, 1585 deletions
diff --git a/sci-chemistry/ccp4-apps/files/6.1.3-clipper-template.patch b/sci-chemistry/ccp4-apps/files/6.1.3-clipper-template.patch
deleted file mode 100644
index 433a78dbd23b..000000000000
--- a/sci-chemistry/ccp4-apps/files/6.1.3-clipper-template.patch
+++ /dev/null
@@ -1,70 +0,0 @@
---- 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
diff --git a/sci-chemistry/ccp4-apps/files/6.1.3-dont-build-balbes.patch b/sci-chemistry/ccp4-apps/files/6.1.3-dont-build-balbes.patch
deleted file mode 100644
index f1df3e5e19f9..000000000000
--- a/sci-chemistry/ccp4-apps/files/6.1.3-dont-build-balbes.patch
+++ /dev/null
@@ -1,14 +0,0 @@
-diff --git a/share/Makefile.in b/share/Makefile.in
-index 2d4f20b..4500993 100755
---- a/share/Makefile.in
-+++ b/share/Makefile.in
-@@ -18,9 +18,6 @@ install :
- for i in $(MRBUMP_TARGETS); do \
- test -s $(MRBUMP_BINDIR)/$$i && $(INSTALL_PROGRAM) $(MRBUMP_BINDIR)/$$i $(bindir)/$$i || true ;\
- done
-- for i in $(BALBES_TARGETS); do \
-- test -s $(BALBES_BINDIR)/$$i && $(INSTALL_PROGRAM) $(BALBES_BINDIR)/$$i $(bindir)/$$i || true ;\
-- done
-
- clean : ; -rm -f core *.o *~ a.out
-
diff --git a/sci-chemistry/ccp4-apps/files/6.1.3-dont-build-double-and-make-bindir.patch b/sci-chemistry/ccp4-apps/files/6.1.3-dont-build-double-and-make-bindir.patch
deleted file mode 100644
index e62ae12adfbe..000000000000
--- a/sci-chemistry/ccp4-apps/files/6.1.3-dont-build-double-and-make-bindir.patch
+++ /dev/null
@@ -1,24 +0,0 @@
---- 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
- #
diff --git a/sci-chemistry/ccp4-apps/files/6.1.3-dont-build-imosflm.patch b/sci-chemistry/ccp4-apps/files/6.1.3-dont-build-imosflm.patch
deleted file mode 100644
index f645643e1c67..000000000000
--- a/sci-chemistry/ccp4-apps/files/6.1.3-dont-build-imosflm.patch
+++ /dev/null
@@ -1,11 +0,0 @@
---- 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 \
diff --git a/sci-chemistry/ccp4-apps/files/6.1.3-dont-build-libs.patch b/sci-chemistry/ccp4-apps/files/6.1.3-dont-build-libs.patch
deleted file mode 100644
index 1d1323005540..000000000000
--- a/sci-chemistry/ccp4-apps/files/6.1.3-dont-build-libs.patch
+++ /dev/null
@@ -1,35 +0,0 @@
---- 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 @@
- # $Id$
-
- 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
-
diff --git a/sci-chemistry/ccp4-apps/files/6.1.3-dont-build-molref.patch b/sci-chemistry/ccp4-apps/files/6.1.3-dont-build-molref.patch
deleted file mode 100644
index f16b0ecb938c..000000000000
--- a/sci-chemistry/ccp4-apps/files/6.1.3-dont-build-molref.patch
+++ /dev/null
@@ -1,19 +0,0 @@
---- 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
-
diff --git a/sci-chemistry/ccp4-apps/files/6.1.3-dont-build-scala.patch b/sci-chemistry/ccp4-apps/files/6.1.3-dont-build-scala.patch
deleted file mode 100644
index af4fd8219c4f..000000000000
--- a/sci-chemistry/ccp4-apps/files/6.1.3-dont-build-scala.patch
+++ /dev/null
@@ -1,42 +0,0 @@
---- ./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
diff --git a/sci-chemistry/ccp4-apps/files/6.1.3-dont-build-xia.patch b/sci-chemistry/ccp4-apps/files/6.1.3-dont-build-xia.patch
deleted file mode 100644
index 3af4af503fa6..000000000000
--- a/sci-chemistry/ccp4-apps/files/6.1.3-dont-build-xia.patch
+++ /dev/null
@@ -1,14 +0,0 @@
---- 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 $(REFMACTARGETS) dtrek2scala crunch2 pmf
-
- # targets built from .c sources:
- CSIMPLE = pltdev binsort
diff --git a/sci-chemistry/ccp4-apps/files/6.1.3-dont-configure.patch b/sci-chemistry/ccp4-apps/files/6.1.3-dont-configure.patch
deleted file mode 100644
index 1e59578473ff..000000000000
--- a/sci-chemistry/ccp4-apps/files/6.1.3-dont-configure.patch
+++ /dev/null
@@ -1,111 +0,0 @@
---- configure 2009-08-07 12:11:28.000000000 +0200
-+++ configure.new.nolib 2009-08-17 22:30:39.000000000 +0200
-@@ -3113,41 +3113,6 @@
- RX_L="$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
diff --git a/sci-chemistry/ccp4-apps/files/6.1.3-dont-make-dirs-in-configure.patch b/sci-chemistry/ccp4-apps/files/6.1.3-dont-make-dirs-in-configure.patch
deleted file mode 100644
index 583697cea0a1..000000000000
--- a/sci-chemistry/ccp4-apps/files/6.1.3-dont-make-dirs-in-configure.patch
+++ /dev/null
@@ -1,87 +0,0 @@
---- 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
-
diff --git a/sci-chemistry/ccp4-apps/files/6.1.3-impl-dec.patch b/sci-chemistry/ccp4-apps/files/6.1.3-impl-dec.patch
deleted file mode 100644
index db8236063043..000000000000
--- a/sci-chemistry/ccp4-apps/files/6.1.3-impl-dec.patch
+++ /dev/null
@@ -1,152 +0,0 @@
-diff --git a/lib/DiffractionImage/Bruker/FRM_LIB.c b/lib/DiffractionImage/Bruker/FRM_LIB.c
-index bfda882..f821e04 100755
---- a/lib/DiffractionImage/Bruker/FRM_LIB.c
-+++ b/lib/DiffractionImage/Bruker/FRM_LIB.c
-@@ -38,6 +38,8 @@ FRM_LIB: Routines for reading, writing, and handling frame files.
- #include "sys/types.h" /* _open, etc. */
- #include "sys/stat.h" /* _open, etc. */
-
-+#include <unistd.h>
-+
- #ifndef _MSC_VER
- int min(int a, int b)
- {
-diff --git a/lib/DiffractionImage/MAR/mar300_header.c b/lib/DiffractionImage/MAR/mar300_header.c
-index 1a933de..1c40c32 100755
---- a/lib/DiffractionImage/MAR/mar300_header.c
-+++ b/lib/DiffractionImage/MAR/mar300_header.c
-@@ -23,6 +23,9 @@
- */
- #include "mar300_header.h"
-
-+#include <sys/types.h>
-+#include <unistd.h>
-+
- /*
- * Local functions
- */
-diff --git a/lib/DiffractionImage/MAR/mar345_header.c b/lib/DiffractionImage/MAR/mar345_header.c
-index a8351ea..16d0f7b 100755
---- a/lib/DiffractionImage/MAR/mar345_header.c
-+++ b/lib/DiffractionImage/MAR/mar345_header.c
-@@ -32,6 +32,9 @@
- */
- #include "mar345_header.h"
-
-+#include <sys/types.h>
-+#include <unistd.h>
-+
- /*
- * Definitions
- */
-diff --git a/lib/DiffractionImage/MAR/nb_header.c b/lib/DiffractionImage/MAR/nb_header.c
-index 07f2741..6364ca4 100755
---- a/lib/DiffractionImage/MAR/nb_header.c
-+++ b/lib/DiffractionImage/MAR/nb_header.c
-@@ -20,6 +20,8 @@
- #include <io.h>
- #endif
-
-+#include <sys/types.h>
-+#include <unistd.h>
- /*
- * mar software include files
- */
-diff --git a/lib/DiffractionImage/MAR/swap.c b/lib/DiffractionImage/MAR/swap.c
-index 443bb8c..0d96b3f 100755
---- a/lib/DiffractionImage/MAR/swap.c
-+++ b/lib/DiffractionImage/MAR/swap.c
-@@ -10,6 +10,9 @@
- *
- **********************************************************************/
-
-+#define _XOPEN_SOURCE
-+#include <unistd.h>
-+
- void swaplong();
- void swapshort();
-
-diff --git a/lib/ccif/f_interface.c b/lib/ccif/f_interface.c
-index 0f6a6b7..a09dc48 100755
---- a/lib/ccif/f_interface.c
-+++ b/lib/ccif/f_interface.c
-@@ -25,6 +25,7 @@
- ********************************************************************/
-
- #include "stdpccts.h"
-+#include <sys/mman.h>
-
- /* This file is terribly organised, and badly needs re-doing. There is probably
- * scope for splitting this into three modules:
-diff --git a/lib/src/ccp4_general_f.c b/lib/src/ccp4_general_f.c
-index 8b5d04f..74ee3f7 100755
---- a/lib/src/ccp4_general_f.c
-+++ b/lib/src/ccp4_general_f.c
-@@ -26,6 +26,7 @@
- #include <string.h>
- #include <stdlib.h>
- #include <math.h>
-+#include <time.h>
- #include "ccp4_errno.h"
- #include "ccp4_fortran.h"
- #include "ccp4_parser.h"
-diff --git a/lib/src/ccp4_program.c b/lib/src/ccp4_program.c
-index 3e83d4d..bb3e975 100755
---- a/lib/src/ccp4_program.c
-+++ b/lib/src/ccp4_program.c
-@@ -25,6 +25,7 @@
- #include <stdio.h>
- #include <stdlib.h>
- #include <string.h>
-+#include <time.h>
- #include "ccp4_program.h"
- #include "ccp4_parser.h"
- #include "ccp4_utils.h"
-diff --git a/lib/src/fsplit.c b/lib/src/fsplit.c
-index ee8af24..c6fb3cd 100755
---- a/lib/src/fsplit.c
-+++ b/lib/src/fsplit.c
-@@ -50,6 +50,7 @@ static char sccsid[] = "@(#)fsplit.c 5.5 (Berkeley) 3/12/91";
- #include <string.h>
- #include <sys/types.h>
- #include <sys/stat.h>
-+#include <unistd.h>
-
- /*
- * usage: fsplit [-e efile] ... [file]
-diff --git a/src/clipper_progs/src/pirate/compress42.c b/src/clipper_progs/src/pirate/compress42.c
-index ea52e96..30dbd56 100755
---- a/src/clipper_progs/src/pirate/compress42.c
-+++ b/src/clipper_progs/src/pirate/compress42.c
-@@ -142,6 +142,7 @@
- #include <sys/types.h>
- #include <sys/stat.h>
- #include <errno.h>
-+#include <unistd.h>
-
- #ifdef DIRENT
- # include <dirent.h>
-diff --git a/src/mtz2cif_/mtz2cif.c b/src/mtz2cif_/mtz2cif.c
-index e224430..c7b82f4 100755
---- a/src/mtz2cif_/mtz2cif.c
-+++ b/src/mtz2cif_/mtz2cif.c
-@@ -28,6 +28,7 @@
- #include "cmtzlib.h"
- #include "ccp4_parser.h"
- #include "ccp4_general.h"
-+#include "ccp4_program.h"
- #include "csymlib.h"
- #include "mtz2cif_lib.h"
-
-diff --git a/x-windows/XCCPJIFFY/xplot84driver.c b/x-windows/XCCPJIFFY/xplot84driver.c
-index 67e0bf1..76526ab 100755
---- a/x-windows/XCCPJIFFY/xplot84driver.c
-+++ b/x-windows/XCCPJIFFY/xplot84driver.c
-@@ -11,6 +11,7 @@
-
- #include <stdio.h>
- #include <sys/types.h>
-+#include <stdlib.h>
-
- #include <X11/StringDefs.h>
- #include <X11/Intrinsic.h>
diff --git a/sci-chemistry/ccp4-apps/files/6.1.3-lapack.patch b/sci-chemistry/ccp4-apps/files/6.1.3-lapack.patch
deleted file mode 100644
index 62892db01147..000000000000
--- a/sci-chemistry/ccp4-apps/files/6.1.3-lapack.patch
+++ /dev/null
@@ -1,597 +0,0 @@
-diff --git a/configure b/configure
-index 833f483..bcfa62d 100755
---- a/configure
-+++ b/configure
-@@ -3226,574 +3226,14 @@ else
- echo
- echo "Warning: this option has not been extensively tested!"
- echo "Please report problems to ccp4@ccp4.ac.uk"
-- # Search for vendor LAPACK/BLAS first
-- if test ! "$with_netlib_lapack" ; then
-- # Initialise variables to blank
-- lapackdir=
-- XLAPACK_LIB=
-- # Possible directories to check for vendor or pre-existing LAPACK or
-- # BLAS - add to these if you want to test others
-- trydirs="`echo $LD_LIBRARY_PATH |sed -e s/:/\ /g` /lib /usr/lib /usr/local/lib"
-- # Possible library names
-- # These are the names like xxxx where the library will be libxxxx.a
-- # or libxxxx.so
-- echo
-- echo "Guessing names for native/vendor LAPACK and/or BLAS libraries"
-- echo "on this system"
-- case $system in
-- linux | linux64 | linux32 )
-- # linux users will usually have them in /usr/lib but don't call it
-- trylapack="lapack"
-- tryblas="blas"
-- # if code is non_shared then this can lead to problems. both blas and lapack
-- # need to be resolved even if they are not called!
-- if test "$non_shared" = yes; then
-- echo "You are compiling linux non_shared. This sometimes causes problems "
-- echo " so checking for requirements."
-- echo "Checking: try to link library against test program"
-- if test -f testlink.f || test -f testlink ; then
-- rm -f testlink*
-- fi
-- cat > testlink.f <<EOF
-- PROGRAM TESTLINK
--C A bit of scala code to test the linking
-- real bf(3), bnorm
--c
-- integer maxbmt
-- parameter (maxbmt = 2)
-- double precision B(maxbmt,maxbmt), eigval(maxbmt),
-- $ eigvec(maxbmt,maxbmt), w(5*maxbmt)
-- integer m, ia, ix, istat
--c
-- B(1,1) = 1.00
-- B(1,2) = 1.00
-- B(2,1) = 1.00
-- B(2,2) = 1.00
--c
-- m = maxbmt
-- ia = maxbmt
-- ix = maxbmt
-- call dsyev('N', 'L', m, B, ia, eigval, w, 5*maxbmt, istat)
-- end
--EOF
-- #firstly test without -lblas
-- test_compile="$FC $FOPTIM $XFFLAGS -o testlink testlink.f -llapack"
-- echo $test_compile
-- if { (eval $test_compile >& /dev/null ) 2>&1; } && test -s testlink ; then
-- # Compilation was okay
-- echo "... only -llapack needed"
-- XLAPACK_LIB="-llapack"
-- # Set the next two variables so that configure
-- # doesn't try to build netlib libraries
-- LAPACKLIB="lapack"
-- noblas=yes
-- trylapack=
-- tryblas=
-- else
-- echo "more than just -llapack needed...."
-- test_compile="$FC $FOPTIM $XFFLAGS -o testlink testlink.f -llapack -lblas"
-- echo $test_compile
-- if { (eval $test_compile ) 2>&1; } && test -s testlink ; then
-- # Compilation was okay
-- echo "...-llapack and -lblas were needed"
-- XLAPACK_LIB="-llapack -lblas"
-- # Set the next two variables so that configure
-- # doesn't try to build netlib libraries
-- LAPACKLIB="lapack blas"
-- noblas=no
-- trylapack=
-- tryblas=
-- else
-- echo "....could not find either lapack or blas."
-- fi
-- fi
-- fi
-- # add 64 bit libs
-- case $system in
-- linux64 ) trydirs="/usr/lib64 ${trydirs}" ;;
-- esac
--
-- ;;
-- osf1)
-- # OSF1 has dxml (old version) and cxml
-- # which should have both lapack and blas
-- trylapack="dxml cxml"
-- tryblas=
-- trydirs="${trydirs} /usr/shlib"
-- ;;
-- irix)
-- # Additional search paths for IRIX
-- trydirs="${trydirs} /usr/lib32"
-- # SCSL should have both LAPACK and BLAS
-- trylapack="scs"
-- tryblas="blas"
-- ;;
-- irix64)
-- # Additional search paths for IRIX64
-- trydirs="${trydirs} /usr/lib64"
-- # SCSL should have both LAPACK and BLAS
-- trylapack="scs"
-- tryblas="blas"
-- # Extra compiler flags?
-- #XLAPACKFLAGS="-OPT:IEEE_NaN_inf=ON"
-- ;;
-- aix)
-- # Additional search paths for AIX
-- trydirs="${trydirs}"
-- # AIX might have ESSL library - blas only I think
-- trylapack=
-- tryblas="essl"
-- ;;
-- hpux)
-- # Additional search paths for HPUX
-- trydirs="${trydirs} /opt/fortran/lib /opt/fortran/lib/pa2.0 /opt/mlib/lib/pa2.0"
-- # HPUX should have both LAPACK (part of mlib) and BLAS
-- trylapack="lapack"
-- tryblas="blas"
-- # Extra compiler flags?
-- # +U77 required for ETIME function - this is already in XFFLAGS
-- #XLAPACKFLAGS="+U77"
-- ;;
--
-- sunos | sunos64)
-- # Sun has libraries with BLAS and LAPACK invoked using
-- # -xlic_lib=sunperf
-- trylapack=
-- tryblas=
-- echo "SunOs can use the Sun Performance Library (if installed)"
-- echo "which has both BLAS and LAPACK 3.0"
-- echo
-- echo "Looking for a valid library to use..."
-- echo
-- # Loop over the possible library names
-- try_libs="sunperf"
-- for testlib in $try_libs
-- do
-- if test ! "$XLAPACK_LIB" ; then
-- # Try running a test compile to see if this a valid library
-- if test -f testlink.f || test -f testlink ; then
-- rm -f testlink*
-- fi
-- cat > testlink.f <<EOF
--c Test fortran program to link against library
-- PROGRAM TESTLINK
-- IMPLICIT NONE
-- INTEGER A
-- A = 1
-- STOP
-- END
--EOF
-- test_compile="$FC $FOPTIM $XFFLAGS -o testlink testlink.f -dalign -xlic_lib=$testlib"
-- echo $test_compile
-- if { (eval $test_compile ) 2>&1; } && test -s testlink ; then
-- # Compilation was okay
-- echo "... -xlic_lib=$testlib is okay"
-- XLAPACK_LIB="-dalign -xlic_lib=$testlib"
-- # Set the next two variables so that configure
-- # doesn't try to build netlib libraries
-- LAPACKLIB="$testlib"
-- noblas=yes
-- else
-- # Compilation failed
-- echo "... cannot use -xlic_lib=$testlib"
-- fi
-- # End of test for testlib
-- fi
-- # End of loop over possible lib names
-- done
-- # Report if no suitable library was found
-- if test ! "$XLAPACK_LIB" ; then
-- echo
-- echo "No suitable LAPACK library was found."
-- echo "This may be because the Sun Performance Library is not"
-- echo "installed on your system"
-- echo "Contact your system administrator or Sun vendor"
-- fi
-- ;;
-- Darwin | Darwin32 | Darwin64 )
-- # Darwin has libraries with BLAS and LAPACK invoked using
-- # -framework vecLib
-- echo "Darwin can use the vecLib Library (if installed)"
-- echo "which has both BLAS and LAPACK 3.0"
-- echo
-- # This is a special case so try running a test compile
-- echo "Checking: try to link library against test program"
-- if test -f testlink.f || test -f testlink ; then
-- rm -f testlink*
-- fi
-- cat > testlink.f <<EOF
--c Test fortran program to link against library
-- PROGRAM TESTLINK
-- IMPLICIT NONE
-- INTEGER A
-- A = 1
-- STOP
-- END
--EOF
-- test_compile="$FC $FOPTIM $XFFLAGS -o testlink testlink.f -framework vecLib"
-- echo $test_compile
-- if { (eval $test_compile ) 2>&1; } && test -s testlink ; then
-- # Compilation was okay
-- echo "... -framework vecLib is okay"
-- XLAPACK_LIB="-framework vecLib"
-- # Set the next two variables so that configure
-- # doesn't try to build netlib libraries
-- LAPACKLIB="vecLib"
-- noblas=yes
-- else
--#alternative linking for vecLib libraries
-- case `uname -sr` in
-- *Darwin\ 7.* ) test_compile="$FC $FOPTIM $XFFLAGS -o testlink testlink.f -lcc_dynamic -Wl,-framework -Wl,vecLib" ;;
-- * ) test_compile="$FC $FOPTIM $XFFLAGS -o testlink testlink.f -Wl,-framework -Wl,vecLib" ;;
-- esac
--
-- echo $test_compile
-- if { (eval $test_compile ) 2>&1; } && test -s testlink ; then
-- # Compilation was okay
-- echo "... -framework vecLib is okay"
-- XLAPACK_LIB="-Wl,-framework -Wl,vecLib"
-- # Set the next two variables so that configure
-- # doesn't try to build netlib libraries
-- LAPACKLIB="-Wl,-framework -Wl,vecLib"
-- noblas=yes
-- else
-- # Compilation failed
-- echo "... cannot use -framework vecLib"
-- echo
-- fi
-- fi
-- trylapack=
-- tryblas=
--# try the fink installation
-- trydirs="${trydirs} /sw"
-- ;;
-- Darwin_ibm_compilers )
-- # Darwin has libraries with BLAS and LAPACK invoked using
-- # -framework vecLib
-- echo "Darwin can use the vecLib Library (if installed)"
-- echo "which has both BLAS and LAPACK 3.0"
-- echo
-- # This is a special case so try running a test compile
-- echo "Checking: try to link library against test program"
-- if test -f testlink.f || test -f testlink ; then
-- rm -f testlink*
-- fi
-- cat > testlink.f <<EOF
--c Test fortran program to link against library
-- PROGRAM TESTLINK
-- IMPLICIT NONE
-- INTEGER A
-- A = 1
-- STOP
-- END
--EOF
-- case `uname -sr` in
-- Darwin\ 8* )
-- XLAPACK_LIB="-L/System/Library/Frameworks/Accelerate.framework/Versions/A/Frameworks/vecLib.framework/Versions/A -lLAPACK -lBLAS"
-- test_compile="$FC $FOPTIM $XFFLAGS -o testlink testlink.f $XLAPACK_LIB"
-- ;;
-- Darwin\ 7* )
-- XLAPACK_LIB="-L/System/Library/Frameworks/Accelerate.framework/Versions/A/Frameworks/vecLib.framework/Versions/A -lLAPACK -lBLAS"
-- test_compile="$FC $FOPTIM $XFFLAGS -o testlink testlink.f -lcc_dynamic $XLAPACK_LIB"
-- ;;
-- *)
-- XLAPACK_LIB="/System/Library/Frameworks/vecLib.Framework/Versions/Current/VecLib"
-- test_compile="$FC $FOPTIM $XFFLAGS -o testlink testlink.f $XLAPACK_LIB"
-- esac
-- echo $test_compile
-- if { (eval $test_compile ) 2>&1; } && test -s testlink ; then
-- # Compilation was okay
-- echo "... -framework vecLib is okay"
-- # Set the next two variables so that configure
-- # doesn't try to build netlib libraries
-- LAPACKLIB="vecLib"
-- noblas=yes
-- else
-- # Compilation failed
-- XLAPACK_LIB=""
-- echo "... cannot use -framework vecLib"
-- echo
-- fi
-- trylapack=
-- tryblas=
--# try the fink installation
-- trydirs="${trydirs} /sw"
-- ;;
--
-- Darwin_intel_compilers)
-- # Darwin has libraries with BLAS and LAPACK invoked using
-- # -F vecLib
-- echo "Darwin can use the vecLib Library (if installed)"
-- echo "which has both BLAS and LAPACK 3.0"
-- echo
-- # This is a special case so try running a test compile
-- echo "Checking: try to link library against test program"
-- if test -f testlink.f || test -f testlink ; then
-- rm -f testlink*
-- fi
-- cat > testlink.f <<EOF
--c Test fortran program to link against library
-- PROGRAM TESTLINK
-- IMPLICIT NONE
-- INTEGER A
-- A = 1
-- STOP
-- END
--EOF
-- test_compile="$FC $FOPTIM $XFFLAGS -o testlink testlink.f -Wl,-framework -Wl,vecLib"
-- echo $test_compile
-- if { (eval $test_compile ) 2>&1; } && test -s testlink ; then
-- # Compilation was okay
-- # doesn't try to build netlib libraries
-- XLAPACK_LIB="-F /System/Library/Frameworks -Qoption,ld,-framework -Qoption,ld,vecLib"
-- LAPACKLIB="vecLib"
-- noblas=yes
-- else
-- # Compilation failed
-- echo "... cannot use -framework vecLib"
-- echo
-- fi
-- trylapack=
-- tryblas=
--# try the fink installation
-- trydirs="${trydirs} /sw"
-- ;;
--
--# linux_ia64_sgi_altix)
--# SGI Japan
-- ia64_linux_intel)
-- # Additional search paths for Linux/IA64
-- trydirs="${trydirs} /opt/scsl/lib /usr/lib /usr/local/lib"
-- # SCSL and MKL should have both LAPACK and BLAS
-- trylapack="mkl_lapack scs lapack"
-- tryblas="mkl scs blas"
-- ;;
-- linux_ibm_compilers )
-- trylapack="lapack"
-- tryblas="blas"
-- ;;
-- linux64_ibm_compilers )
-- trydirs="/usr/lib64 ${trydirs}"
-- trylapack="lapack"
-- tryblas="blas"
-- ;;
-- linux_intel_compilers )
-- trydirs="/usr/lib64 ${trydirs}"
-- trylapack="mkl_lapack lapack"
-- tryblas="mkl blas"
-- ;;
-- *)
-- echo "The guesses for this system may not be correct - please"
-- echo "e-mail ccp4@ccp4.ac.uk if you have any extra information"
-- echo
-- # Default guess is just libblas
-- trylapack="lapack"
-- tryblas="blas"
-- ;;
-- esac
-- #
-- # Search for LAPACK libraries
-- #
-- # Write out what the guesses are
-- if test "$trylapack" ; then
-- echo "Possible LAPACK library names for this system:"
-- for libname in $trylapack
-- do
-- echo " lib$libname"
-- done
-- # Possible library name extensions
-- tryexts="a so dylib"
-- # Now loop over all the possibilities and see if anything
-- # turns up
-- echo
-- echo "Searching for libraries with LAPACK and BLAS:"
-- for testdir in $trydirs
-- do
-- for testlib in $trylapack
-- do
-- for ext in $tryexts
-- do
-- if test ! "$LAPACKLIB"; then
-- if test -s "$testdir/lib$testlib.$ext" ; then
-- echo "...found LAPACK library: $testdir/lib$testlib.$ext"
-- # Now try and link to a test program
-- # This is really for IRIX where libraries can be
-- # o32 or n32
-- echo " Testing: try to link library against test program"
-- if test -f testlink.f || test -f testlink ; then
-- rm -f testlink*
-- fi
-- cat > testlink.f <<EOF
--c Test fortran program to link against library
-- PROGRAM TESTLINK
-- IMPLICIT NONE
-- INTEGER A
-- A = 1
-- STOP
-- END
--EOF
-- test_compile="$FC $FOPTIM $XFFLAGS -o testlink testlink.f -L$testdir -l$testlib"
-- test_ccompile="$FC $FOPTIM $XFFLAGS -o testlink testlink.f -L$testdir -l$testlib $XLDFLAGS"
-- echo $test_compile
-- if { (eval $test_compile ) 2>&1; } && test -s testlink ; then
-- have_lapack=yes
-- else
--# cover clapack option
-- echo $test_ccompile
-- if { (eval $test_ccompile ) 2>&1; } && test -s testlink ; then
-- have_lapack=yes
-- fi
-- fi
-- if test x$have_lapack = xyes ; then
-- # This one is okay
-- LAPACKLIB="$testlib"
-- LAPACKDIR="$testdir"
-- echo "Link ok - using lib$LAPACKLIB from $LAPACKDIR"
-- #
-- XLAPACK_LIB="-L$LAPACKDIR -l$LAPACKLIB"
-- #
-- # Test to see if we need BLAS too
-- # Do this by trying to compile a test program
-- # Use the LSAME test for now
-- echo
-- echo " * Checking whether we need a separate BLAS library *"
-- echo " Testing: try linking library against test program"
-- cd lib/lapack/test
-- if test -f testlsame ; then
-- rm -f testsame testlsame.o
-- fi
-- test_compile="$FC $FOPTIM $XFFLAGS -o testlsame lsametst.f -L$LAPACKDIR -l$LAPACKLIB"
-- test_ccompile="$FC $FOPTIM $XFFLAGS -o testlsame lsametst.f -L$LAPACKDIR -l$LAPACKLIB $XLDFLAGS"
-- echo $test_compile
-- if { ( eval $test_compile) 2>&1;} && test -s testlsame ; then
-- have_blas=yes
-- else
--#cblas route
-- echo $test_ccompile
-- if { ( eval $test_ccompile) 2>&1;} && test -s testlsame ; then
-- have_blas=yes
-- fi
-- fi
-- if test x$have_blas = xyes ; then
-- echo "Test program okay - additional separate BLAS not required"
-- noblas=yes
-- else
-- echo "Test program failed - need a separate BLAS library"
-- fi
-- cd ../../..
-- else
-- # Keep looking
-- echo " link failed - cannot use lib$testlib"
-- fi
-- fi
-- fi
-- done
-- done
-- if test ! "$LAPACKLIB"; then
-- echo "...nothing in $testdir"
-- fi
-- done
-- fi
--
-- # If LAPACKLIB hasn't been set at this point then no LAPACK library
-- # was found
-- if test ! "$LAPACKLIB" ; then
-- echo
-- echo "No pre-existing LAPACK library found - NetLib LAPACK will be built instead"
-- make_lapack=lapacklib
-- fi
-- # Look for possible BLAS
-- if test ! "$noblas" ; then
-- if test "$tryblas" ; then
-- echo
-- echo "Possible BLAS library names for this system:"
-- for libname in $tryblas
-- do
-- echo " lib$libname"
-- done
-- # Possible library name extensions
-- tryexts="a so"
-- # Now loop over all the possibilities and see if anything
-- # turns up
-- echo
-- echo "Searching for libraries with BLAS:"
-- for testdir in $trydirs
-- do
-- for testlib in $tryblas
-- do
-- for ext in $tryexts
-- do
-- if test ! "$BLASLIB"; then
-- if test -s "$testdir/lib$testlib.$ext" ; then
-- echo "...found BLAS library: $testdir/lib$testlib.$ext"
-- # Now try and link to a test program
-- # This is really for IRIX where libraries can be
-- # o32 or n32
-- echo " Testing: try to link library against test program"
-- if test -f testlink.f || test -f testlink ; then
-- rm -f testlink*
-- fi
-- cat > testlink.f <<EOF
--c Test fortran program to link against library
-- PROGRAM TESTLINK
-- IMPLICIT NONE
-- INTEGER A
-- A = 1
-- STOP
-- END
--EOF
-- test_compile="$FC $FOPTIM $XFFLAGS -o testlink testlink.f -L$testdir -l$testlib"
-- test_ccompile="$FC $FOPTIM $XFFLAGS -o testlink testlink.f -L$testdir -l$testlib $XLDFLAGS"
-- echo $test_compile
-- if { ( eval $test_compile) 2>&1;} && test -s testlink ; then
-- have_blas=yes
-- else
-- echo $test_ccompile
-- if { ( eval $test_compile) 2>&1;} && test -s testlink ; then
-- have_blas=yes
-- fi
-- fi
-- if test x$have_blas = xyes ; then
-- # This one is okay
-- BLASLIB="$testlib"
-- BLASDIR="$testdir"
-- BLASEXT="$ext"
-- echo "Link ok - using lib$BLASLIB from $BLASDIR"
-- XLAPACK_LIB="$XLAPACK_LIB -L$BLASDIR -l$BLASLIB"
-- else
-- # Keep looking
-- echo " link failed - cannot use lib$testlib"
-- fi
-- fi
-- fi
-- done
-- done
-- if test ! "$BLASLIB"; then
-- echo "...nothing in $testdir"
-- fi
-- done
-- fi
-- # Do we need to build BLAS too?
-- if test ! "$BLASLIB" ; then
-- echo
-- echo "No pre-existing BLAS library was found - NetLib BLAS will be built instead"
-- echo "This may result in poorer performance of the LAPACK routines"
-- make_blas=blaslib
-- BLASLIB=blas
-- BLASDIR="$srcdir/lib/lapack"
-- BLASEXT="a"
-- fi
-- fi
-+ # gentoo is clever
-+ make_blas=
-+ make_lapack=
-+ BLASLIB=$(${PKG_CONFIG} --libs blas)
-+ LAPACKLIB=$(${PKG_CONFIG} --libs lapack)
-+ XLAPACK_LIB="${BLASLIB} ${LAPACKLIB}"
-+ XFFLAGS_LAPACK="$(${PKG_CONFIG} --cflags lapack blas)"
- # Otherwise force building of NetLib BLAS and LAPACK libs
-- else
-- echo
-- echo "! Force building of NetLib BLAS and LAPACK..."
-- make_blas=blaslib
-- make_lapack=lapacklib
-- BLASLIB=blas
-- BLASDIR="$srcdir/lib/lapack"
-- BLASEXT="a"
-- fi
- # need to know if we the lapack library was linked using the C or
- # fortran linker
- if test -f testlink.f || test -f testlink || test -f testlink.c ; then
-@@ -3916,8 +3356,8 @@ RANLIB = ${RANLIB}
- INSTALL_DATA = ${INSTALL_DATA}
- libdir = $libdir
- #
--BLASLIB = lib${BLASLIB}.${BLASEXT}
--LAPACKLIB = liblapack.a
-+BLASLIB = ${BLASLIB}
-+LAPACKLIB = ${LAPACKLIB}
- #
- # These variables define targets in the main Makefile
- blaslib = ${make_blas}
diff --git a/sci-chemistry/ccp4-apps/files/6.1.3-pisa.patch b/sci-chemistry/ccp4-apps/files/6.1.3-pisa.patch
deleted file mode 100644
index 9d8fefe965e5..000000000000
--- a/sci-chemistry/ccp4-apps/files/6.1.3-pisa.patch
+++ /dev/null
@@ -1,23 +0,0 @@
-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@
diff --git a/sci-chemistry/ccp4-apps/files/6.1.3-pythonpath.patch b/sci-chemistry/ccp4-apps/files/6.1.3-pythonpath.patch
deleted file mode 100644
index 7a012be6ef02..000000000000
--- a/sci-chemistry/ccp4-apps/files/6.1.3-pythonpath.patch
+++ /dev/null
@@ -1,65 +0,0 @@
-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
-
diff --git a/sci-chemistry/ccp4-apps/files/6.1.3-rename-rapper-ng.patch b/sci-chemistry/ccp4-apps/files/6.1.3-rename-rapper-ng.patch
deleted file mode 100644
index a5144cfa5d33..000000000000
--- a/sci-chemistry/ccp4-apps/files/6.1.3-rename-rapper-ng.patch
+++ /dev/null
@@ -1,60 +0,0 @@
-diff --git a/src/Makefile.in b/src/Makefile.in
-index 70781f3..b2dcc25 100755
---- a/src/Makefile.in
-+++ b/src/Makefile.in
-@@ -760,7 +760,7 @@ chainsawobjs = chainsaw.o
- pdbcur : $(pdbcurobjs)
- @$(SETFLAGS) ; rm -f pdbcur; eval $(CXX) $${mmdb_app_FLAGS-"$(CXXFLAGS)"} -o pdbcur $(pdbcurobjs) $(LDCXXFLAGS)
- ncont : $(ncontobjs)
-- @$(SETFLAGS) ; rm -f ncont; eval $(CXX) $${mmdb_app_FLAGS-"$(CXXFLAGS)"} -o ncont $(ncontobjs) $(LDCXXFLAGS)
-+ @$(SETFLAGS) ; rm -f ncont; eval $(CXX) $${mmdb_app_FLAGS-"$(CXXFLAGS)"} -o ncont $(ncontobjs) $(LDCXXFLAGS) -lmmdb
- coord_format : $(coord_formatobjs)
- @$(SETFLAGS) xxx=1 ; \
- rm -f coord_format; \
-diff --git a/src/rapper/LOOP/Makefile.am b/src/rapper/LOOP/Makefile.am
-index 85f212e..2608c6d 100755
---- a/src/rapper/LOOP/Makefile.am
-+++ b/src/rapper/LOOP/Makefile.am
-@@ -15,12 +15,12 @@ params.cpp typed_value.cpp misc.cpp residue.cpp atom.cpp psa.cpp edm_sidechains.
- 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
-+rapper_LDADD = @GC_LIBS@ @LIBXML_LIBS@
-
- pkgdatadir = $(datadir)/rapper
- dist_pkgdata_DATA = params.xml
-
--INCLUDES = -I. -I../gc7.0/include -I../libxml2/include
-+INCLUDES = -I. @LIBXML_CFLAGS@ @GC_CFLAGS@
- #SUBDIRS = \
- #@PYTHON_USE_TRUE@ python
-
-diff --git a/src/rapper/Makefile.am b/src/rapper/Makefile.am
-index e78b10d..486b931 100755
---- a/src/rapper/Makefile.am
-+++ b/src/rapper/Makefile.am
-@@ -1,3 +1,3 @@
--SUBDIRS = libxml2 gc7.0 LOOP data
-+SUBDIRS = LOOP data
-
- EXTRA_DIST =
-diff --git a/src/rapper/configure.ac b/src/rapper/configure.ac
-index 5e4ef69..268a579 100755
---- a/src/rapper/configure.ac
-+++ b/src/rapper/configure.ac
-@@ -48,6 +48,13 @@ AM_CONDITIONAL(AMDEP, test "x$enable_dependency_tracking" != xno)
-
- AC_SUBST(rapper_LDFLAGS)
-
--AC_CONFIG_SUBDIRS([gc7.0 libxml2])
-+PKG_CHECK_MODULES([LIBXML],[libxml-2.0])
-+AC_SUBST([LIBXML_CFLAGS])
-+AC_SUBST([LIBXML_LIBS])
-+
-+PKG_CHECK_MODULES([GC],[bdw-gc])
-+AC_SUBST([GC_CFLAGS])
-+AC_SUBST([GC_LIBS])
-+
- #AC_OUTPUT(Makefile LOOP/Makefile LOOP/python/Makefile data/Makefile)
- AC_OUTPUT(Makefile LOOP/Makefile data/Makefile)
diff --git a/sci-chemistry/ccp4-apps/files/6.1.3-unbundle.patch b/sci-chemistry/ccp4-apps/files/6.1.3-unbundle.patch
deleted file mode 100644
index 107cfd740238..000000000000
--- a/sci-chemistry/ccp4-apps/files/6.1.3-unbundle.patch
+++ /dev/null
@@ -1,131 +0,0 @@
- src/Makefile.in | 14 +++++-----
- src/pisa/configure.ac | 67 +++++++++----------------------------------------
- 2 files changed, 19 insertions(+), 62 deletions(-)
-
-diff --git a/src/Makefile.in b/src/Makefile.in
-index 70781f3..b11db04 100755
---- a/src/Makefile.in
-+++ b/src/Makefile.in
-@@ -778,8 +778,8 @@ chainsaw : $(chainsawobjs)
- eval $(CXX) $${mmdb_app_FLAGS-"$(CXXFLAGS)"} -o chainsaw $(chainsawobjs) $(LDCXXFLAGS)
- pdbcur.o pcur_funcs.o ncont.o coord_format.o pdb_merge.o chainsaw.o: # dependencies at end
- @$(SETFLAGS) xxx=1 ; \
-- echo $(CXX) -I$(mmdb_appdir) -I$(incdir) -I$(incdir)/mmdb $${mmdb_app_FLAGS-"$(CXXFLAGS)"} -c -o $@ $(mmdb_appdir)/`basename $@ .o`.cpp ;
-- eval $(CXX) -I$(mmdb_appdir) -I$(incdir) -I$(incdir)/mmdb $${mmdb_app_FLAGS-"$(CXXFLAGS)"} -c -o $@ $(mmdb_appdir)/`basename $@ .o`.cpp
-+ echo $(CXX) -I$(mmdb_appdir) -I$(incdir) `pkg-config --cflags mmdb` $${mmdb_app_FLAGS-"$(CXXFLAGS)"} -c -o $@ $(mmdb_appdir)/`basename $@ .o`.cpp ;
-+ eval $(CXX) -I$(mmdb_appdir) -I$(incdir) `pkg-config --cflags mmdb` $${mmdb_app_FLAGS-"$(CXXFLAGS)"} -c -o $@ $(mmdb_appdir)/`basename $@ .o`.cpp
-
- ### bp3, afro, gcx
-
-@@ -813,8 +813,8 @@ gcx : libbp3 $(gcxobjs)
-
- $(libbp3objs) $(bp3objs) $(afroobjs) $(gcxobjs) : # dependencies at end
- @$(SETFLAGS) xxx=1 ; \
-- echo $(CXX) -I$(bp3dir) -I$(incdir) -I$(incdir)/mmdb $${bp3_FLAGS-"$(CXXFLAGS)"} -c -o $@ $(bp3dir)/`basename $@ .o`.C ; \
-- eval $(CXX) -I$(bp3dir) -I$(incdir) -I$(incdir)/mmdb $${bp3_FLAGS-"$(CXXFLAGS)"} -c -o $@ $(bp3dir)/`basename $@ .o`.C
-+ echo $(CXX) -I$(bp3dir) -I$(incdir) `pkg-config --cflags mmdb` $${bp3_FLAGS-"$(CXXFLAGS)"} -c -o $@ $(bp3dir)/`basename $@ .o`.C ; \
-+ eval $(CXX) -I$(bp3dir) -I$(incdir) `pkg-config --cflags mmdb` $${bp3_FLAGS-"$(CXXFLAGS)"} -c -o $@ $(bp3dir)/`basename $@ .o`.C
-
- ### crunch2 pmf
-
-@@ -853,7 +853,7 @@ cif2xml : $(cif2xmlobjs)
- cross_validate : $(cross_validateobjs)
- @$(SETFLAGS); rm -f cross_validate; eval $(CXX) $${harvest_app_FLAGS-"$(CXXFLAGS)"} -o cross_validate $(cross_validateobjs) $(LDCXXFLAGS)
- cif2xml.o cross_validate.o : # dependencies at end
-- @$(SETFLAGS); eval $(CXX) -I$(harvest_appdir) -I$(incdir) -I$(incdir)/mmdb $${harvest_app_FLAGS-"$(CXXFLAGS)"} -c -o $@ $(harvest_appdir)/`basename $@ .o`.cpp
-+ @$(SETFLAGS); eval $(CXX) -I$(harvest_appdir) -I$(incdir) `pkg-config --cflags mmdb` $${harvest_app_FLAGS-"$(CXXFLAGS)"} -c -o $@ $(harvest_appdir)/`basename $@ .o`.cpp
-
- pdb_extractdir = $(srcdir)/harvest_app_/pdb_extract
- pdb_extract_suite :
-@@ -873,8 +873,8 @@ $(dev_tools_ctargets) :
- $(dev_tools_cxxtargets) :
- @$(SETFLAGS) xxx=1; \
- rm -f $@; \
-- echo $(CXX) $${dev_tools_FLAGS-"$(CXXFLAGS)"} -o $@ $(dev_toolsdir)/$@.cpp -I$(incdir) -I$(incdir)/mmdb $(LDCXXFLAGS) ;\
-- eval $(CXX) $${dev_tools_FLAGS-"$(CXXFLAGS)"} -o $@ $(dev_toolsdir)/$@.cpp -I$(incdir) -I$(incdir)/mmdb $(LDCXXFLAGS)
-+ echo $(CXX) $${dev_tools_FLAGS-"$(CXXFLAGS)"} -o $@ $(dev_toolsdir)/$@.cpp -I$(incdir) `pkg-config --cflags mmdb` $(LDCXXFLAGS) ;\
-+ eval $(CXX) $${dev_tools_FLAGS-"$(CXXFLAGS)"} -o $@ $(dev_toolsdir)/$@.cpp -I$(incdir) `pkg-config --cflags mmdb` $(LDCXXFLAGS)
-
- ### mlphare
- mlphare:
-diff --git a/src/pisa/configure.ac b/src/pisa/configure.ac
-index 81afdda..044b6f8 100755
---- a/src/pisa/configure.ac
-+++ b/src/pisa/configure.ac
-@@ -31,64 +31,21 @@ AC_CHECK_FUNCS([floor pow rint sqrt])
- # test for function in m
- AC_CHECK_LIB([m], [sqrt])
-
--dnl Optional: Check for MMDB.
--AM_PATH_MMDB(,
-- [ if test "x$mmdb_prefix" != x ; then
-- if test "x$ac_MMDB_CXXFLAGS" != x && test "x$ac_MMDB_LDOPTS" = x ; then
-- case "$ac_MMDB_CXXFLAGS" in
-- *src/mmdb )
-- ac_MMDB_LDOPTS=`echo "$ac_MMDB_CXXFLAGS" | sed s#src/mmdb#src#g`
-- ;;
-- *include/mmdb )
-- ac_MMDB_LDOPTS=`echo "$ac_MMDB_CXXFLAGS" | sed s#include/mmdb#lib#g`
-- ;;
-- *)
-- esac
-- MMDB_CXXFLAGS="$ac_MMDB_CXXFLAGS"
-- MMDB_LIBS=`echo "$ac_MMDB_LDOPTS -lmmdb" | sed s#-I#-L#`
-- AC_MSG_WARN([assuming library $MMDB_LIBS headers $MMDB_CXXFLAGS])
-- else
-- MMDB_CXXFLAGS="-I$mmdb_prefix/src -I$mmdb_prefix/src/mmdb -I$mmdb_prefix/include -I$mmdb_prefix/include/mmdb"
-- MMDB_LIBS="-L$mmdb_prefix/src -L$mmdb_prefix/lib -lmmdb"
-- AC_MSG_WARN([assuming library $MMDB_LIBS headers $MMDB_CXXFLAGS])
-- fi
-- else
-- AC_MSG_ERROR([mmdb not found])
-- fi
-- ]
--)
-+PKG_CHECK_MODULES([MMDB],[mmdb])
-+PKG_CHECK_MODULES([SSM],[ssm])
-+
-+MMDB_CXXFLAGS=${MMDB_CFLAGS}
-+
-+AC_SUBST([MMDB_CFLAGS])
-+AC_SUBST([MMDB_CXXFLAGS])
-+AC_SUBST([SSM_CFLAGS])
-+
-+AC_SUBST([MMDB_LIBS])
-+AC_SUBST([SSM_LIBS])
-
--ac_saved_CXXFLAGS=$CXXFLAGS
--ac_saved_LIBS=$LIBS
- CXXFLAGS="$CXXFLAGS $MMDB_CXXFLAGS"
- LIBS="$MMDB_LIBS $LIBS"
--AM_PATH_SSM(,
-- [ if test "x$ssm_prefix" != x ; then
-- if test "x$ac_SSM_CXXFLAGS" != x && test "x$ac_SSM_LDOPTS" = x ; then
-- case "$ac_SSM_CXXFLAGS" in
-- *lib/ssm )
-- ac_SSM_LDOPTS=`echo "$ac_SSM_CXXFLAGS" | sed s#lib/ssm#lib#g`
-- ;;
-- *include/ssm )
-- ac_SSM_LDOPTS=`echo "$ac_SSM_CXXFLAGS" | sed s#include/ssm#lib#g`
-- ;;
-- *)
-- esac
-- SSM_CXXFLAGS="$ac_SSM_CXXFLAGS"
-- SSM_LIBS=`echo "$ac_SSM_LDOPTS -lssm" | sed s#-I#-L#`
-- AC_MSG_WARN([assuming library $SSM_LIBS headers $SSM_CXXFLAGS])
-- else
-- SSM_CXXFLAGS="-I$ssm_prefix/include/ssm -I$ssm_prefix/lib/ssm"
-- SSM_LIBS="-L$ssm_prefix/lib -L$ssm_prefix/lib/ssm -lssm"
-- AC_MSG_WARN([assuming library $SSM_LIBS headers $SSM_CXXFLAGS])
-- fi
-- else
-- AC_MSG_ERROR([ssm not found])
-- fi
-- ]
--)
--CXXFLAGS=$ac_saved_CXXFLAGS
--LIBS=$ac_saved_LIBS
-+
-
- # Checks for typedefs, structures, and compiler characteristics.
- #
diff --git a/sci-chemistry/ccp4-apps/files/ccp4-apps-6.1.3-tcl8.6.patch b/sci-chemistry/ccp4-apps/files/ccp4-apps-6.1.3-tcl8.6.patch
deleted file mode 100644
index 4b98545eec83..000000000000
--- a/sci-chemistry/ccp4-apps/files/ccp4-apps-6.1.3-tcl8.6.patch
+++ /dev/null
@@ -1,130 +0,0 @@
- src/ccp4mapwish_/c_src/ccp4mapwish_canvas.c | 34 ++++++++++++++---------------
- 1 file changed, 17 insertions(+), 17 deletions(-)
-
-diff --git a/src/ccp4mapwish_/c_src/ccp4mapwish_canvas.c b/src/ccp4mapwish_/c_src/ccp4mapwish_canvas.c
-index 2c9f02f..98d814a 100755
---- a/src/ccp4mapwish_/c_src/ccp4mapwish_canvas.c
-+++ b/src/ccp4mapwish_/c_src/ccp4mapwish_canvas.c
-@@ -297,7 +297,7 @@ int canvas_draw_line(char *canvas, int npts, float *x, float *y, char *tags,
- puts("canvas_draw_line: about to evaluate the command...");
- }
- if (Tcl_Eval(interp,command) != TCL_OK) {
-- printf("canvas_draw_line: error from Tcl_Eval: %s",interp->result);
-+ printf("canvas_draw_line: error from Tcl_Eval: %s",Tcl_GetStringResult(interp));
- return 0;
- }
- if (CCP4MAPWISH_CANVAS_DIAG)
-@@ -432,7 +432,7 @@ int canvas_draw_rectangle(char *canvas, int npts, float *x, float *y,
- puts("canvas_draw_rectangle: about to evaluate the command...");
- }
- if (Tcl_Eval(interp,command) != TCL_OK) {
-- printf("canvas_draw_rectangle: error from Tcl_Eval: %s",interp->result);
-+ printf("canvas_draw_rectangle: error from Tcl_Eval: %s",Tcl_GetStringResult(interp));
- printf("canvas_draw_rectangle:\ncanvas = \"%s\"\ntags = \"%s\"\ncolor = \"%s\"\nunits = \"%c\"\n",canvas,tags,color,units);
- return 0;
- }
-@@ -536,7 +536,7 @@ int canvas_draw_label(char *canvas, char *text, float x, float y,
- /* Execute the command which draws the label */
- if (CCP4MAPWISH_CANVAS_DIAG) printf("canvas_draw_label: command is: %s\n",command);
- if (Tcl_Eval(interp,command) != TCL_OK) {
-- printf("canvas_draw_label: error from Tcl_Eval: %s\n",interp->result);
-+ printf("canvas_draw_label: error from Tcl_Eval: %s\n",Tcl_GetStringResult(interp));
- return 0;
- }
-
-@@ -617,7 +617,7 @@ int canvas_scale_canvas(char *canvas, char *tag, float scale)
- /* Execute the command which scales the canvas */
- if (CCP4MAPWISH_CANVAS_DIAG) printf("canvas_scale_canvas: command is: %s\n",command);
- if (Tcl_Eval(interp,command) != TCL_OK) {
-- printf("canvas_scale_canvas: error from Tcl_Eval: %s\n",interp->result);
-+ printf("canvas_scale_canvas: error from Tcl_Eval: %s\n",Tcl_GetStringResult(interp));
- return 0;
- }
-
-@@ -706,7 +706,7 @@ int canvas_shift_canvas(char *canvas)
- /* Execute the command which resizes the canvas */
- if (CCP4MAPWISH_CANVAS_DIAG) printf("canvas_shift_canvas: command is: %s\n",command);
- if (Tcl_Eval(interp,command) != TCL_OK) {
-- printf("canvas_shift_canvas: error from Tcl_Eval: %s\n",interp->result);
-+ printf("canvas_shift_canvas: error from Tcl_Eval: %s\n",Tcl_GetStringResult(interp));
- return 0;
- }
-
-@@ -789,7 +789,7 @@ int canvas_shift_element(char *canvas, char *tag, int shiftx, int shifty)
- /* Execute the command which resizes the canvas */
- if (CCP4MAPWISH_CANVAS_DIAG) printf("canvas_shift_canvas: command is: %s\n",command);
- if (Tcl_Eval(interp,command) != TCL_OK) {
-- printf("canvas_shift_element: error from Tcl_Eval: %s\n",interp->result);
-+ printf("canvas_shift_element: error from Tcl_Eval: %s\n",Tcl_GetStringResult(interp));
- return 0;
- }
-
-@@ -861,7 +861,7 @@ int canvas_delete(char *canvas, char *tag)
- /* Execute the command which deletes the tagged items */
- if (CCP4MAPWISH_CANVAS_DIAG) printf("canvas_delete: command is: %s\n",command);
- if (Tcl_Eval(interp,command) != TCL_OK) {
-- printf("canvas_scale_canvas: error from Tcl_Eval: %s\n",interp->result);
-+ printf("canvas_scale_canvas: error from Tcl_Eval: %s\n",Tcl_GetStringResult(interp));
- return 0;
- }
-
-@@ -892,15 +892,15 @@ int canvas_exists(char *canvas)
-
- sprintf(tmpstr,"winfo exists %s",canvas);
- if (Tcl_Eval(interp,tmpstr) != TCL_OK) {
-- printf("canvas_exists: error from Tcl_Eval: %s",interp->result);
-+ printf("canvas_exists: error from Tcl_Eval: %s",Tcl_GetStringResult(interp));
- return 0;
- }
- /* Extract a long int using strtol
- If no conversion takes place then "endptr" will be equal
- to "result" */
-- istatus = (int) strtol(interp->result,&endptr,10);
-- if (strcmp(interp->result,endptr) == 0) {
-- printf("canvas_exists: bad return status from winfo command \"%s\"\n",interp->result);
-+ istatus = (int) strtol(Tcl_GetStringResult(interp),&endptr,10);
-+ if (strcmp(Tcl_GetStringResult(interp),endptr) == 0) {
-+ printf("canvas_exists: bad return status from winfo command \"%s\"\n",Tcl_GetStringResult(interp));
- return 0;
- }
- if (!istatus) {
-@@ -930,13 +930,13 @@ float canvas_get_tk_scaling(char *canvas, char units)
-
- /* Execute the tk scaling command */
- if (Tcl_Eval(interp,"tk scaling") != TCL_OK) {
-- printf("canvas_get_tk_scaling: error from Tcl_Eval: %s",interp->result);
-+ printf("canvas_get_tk_scaling: error from Tcl_Eval: %s",Tcl_GetStringResult(interp));
- return (float) 0.0;
- }
-
- /* Extract a float from the result */
-- tkscale = ((float) strtod(interp->result,&endptr));
-- if (strcmp(interp->result,endptr) == 0) {
-+ tkscale = ((float) strtod(Tcl_GetStringResult(interp),&endptr));
-+ if (strcmp(Tcl_GetStringResult(interp),endptr) == 0) {
- printf("canvas_get_tk_scaling: couldn't extract scale factor\n");
- return (float) 0.0;
- }
-@@ -1021,19 +1021,19 @@ int canvas_get_limits(char *canvas, int limits[4])
-
- /* Evaluate the command */
- if (Tcl_Eval(interp,command) != TCL_OK) {
-- printf("canvas_get_limits: error from Tcl_Eval: %s\n",interp->result);
-+ printf("canvas_get_limits: error from Tcl_Eval: %s\n",Tcl_GetStringResult(interp));
- return 0;
- }
-
- /* Process the result - it should consist of 4 integers */
- /* Use strtok which can split the string based on tokens
- set by the programmer - in this case a space */
-- if (!interp->result) {
-+ if (!Tcl_GetStringResult(interp)) {
- puts("canvas_get_limits: failed to fetch canvas limits");
- return TCL_ERROR;
- }
- i = 0;
-- p = strtok(interp->result," ");
-+ p = strtok(Tcl_GetStringResult(interp)," ");
- if (p == NULL) {
- return 0;
- }