Add CCP4, a popular protein X-ray crystallography toolkit. Relies on portage auto-fixing RPATHs for now, because its build system consists of a bunch of stuff thrown together into the same tarball.

(Portage version: 2.1.1_pre1)

13 files changed, 309 insertions, 0 deletions

diff --git a/sci-chemistry/ccp4/files/6.0.1-dont-make-dirs-in-configure.patch b/sci-chemistry/ccp4/files/6.0.1-dont-make-dirs-in-configure.patch
new file mode 100644
index 000000000000..1420419ffab0
--- /dev/null
+++ b/sci-chemistry/ccp4/files/6.0.1-dont-make-dirs-in-configure.patch
@@ -0,0 +1,87 @@
+--- ccp4-6.0.1.orig/configure	2006-06-10 17:30:02.000000000 -0700
++++ ccp4-6.0.1/configure	2006-06-10 17:45:43.000000000 -0700
+@@ -623,45 +623,45 @@
+ #     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 $i."
+-       badvar=1
+-     fi
+-   done
+-
+-   for i in libdir bindir; do
+-     if ( eval test -d \$$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 ./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 $i."
++#       badvar=1
++#     fi
++#   done
++#
++#   for i in libdir bindir; do
++#     if ( eval test -d \$$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 ./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/files/6.0.1-ppc-double-define-gerror.patch b/sci-chemistry/ccp4/files/6.0.1-ppc-double-define-gerror.patch
new file mode 100644
index 000000000000..a77d9494a05c
--- /dev/null
+++ b/sci-chemistry/ccp4/files/6.0.1-ppc-double-define-gerror.patch
@@ -0,0 +1,11 @@
+--- ccp4-6.0.1.orig/lib/src/library_f.c	2006-06-12 07:06:22.000000000 -0700
++++ ccp4-6.0.1/lib/src/library_f.c	2006-06-12 07:21:56.000000000 -0700
+@@ -716,7 +716,7 @@
+ 
+ #endif /* end of apple xlf support */
+ 
+-#if ( defined (__linux__) && defined (_CALL_SYSV) )
++#if ( defined (__linux__) && defined (_CALL_SYSV) && ! defined(G95) && ! defined (GFORTRAN) )
+ /* linuxppc xlf support */
+ void gerror_ (str, Lstr)
+ char *str;
diff --git a/sci-chemistry/ccp4/files/ccp4i-default-to-firefox.patch b/sci-chemistry/ccp4/files/ccp4i-default-to-firefox.patch
new file mode 100644
index 000000000000..106db895b775
--- /dev/null
+++ b/sci-chemistry/ccp4/files/ccp4i-default-to-firefox.patch
@@ -0,0 +1,13 @@
+--- ccp4-5.99.5.orig/ccp4i/etc/configure.def.dist	2006-01-06 17:54:17.000000000 -0800
++++ ccp4-5.99.5/ccp4i/etc/configure.def.dist	2006-01-06 17:54:47.000000000 -0800
+@@ -54,8 +54,8 @@
+ MESSAGE                   _text				""
+ BLT_LIBRARY               _text                     ""
+ MENU_LENGTH               _positiveint              25
+-HYPERTEXT_VIEWER          _text                     netscape
+-START_NETSCAPE	          _text			    netscape
++HYPERTEXT_VIEWER          _text                     firefox
++START_NETSCAPE	          _text			    firefox
+ O_MAPMAN                  _text                     mapman
+ MAPMAN_MAXSIZE		  _positiveint		    4194304
+ QUANTA_MBKALL             _text                     mbkall
diff --git a/sci-chemistry/ccp4/files/check-blas-lapack-pthread.patch b/sci-chemistry/ccp4/files/check-blas-lapack-pthread.patch
new file mode 100644
index 000000000000..02a2aa6d8877
--- /dev/null
+++ b/sci-chemistry/ccp4/files/check-blas-lapack-pthread.patch
@@ -0,0 +1,103 @@
+--- ccp4-5.99.5.orig/configure	2006-01-17 00:35:36.000000000 -0800
++++ ccp4-5.99.5/configure	2006-01-17 10:44:39.000000000 -0800
+@@ -2410,12 +2410,12 @@
+       end
+ EOF
+           #firslty test without -lblas
+-          test_compile="$FC $FOPTIM $XFFLAGS -o testlink testlink.f -llapack"
++          test_compile="$FC $FOPTIM $XFFLAGS -o testlink testlink.f -llapack -lpthread"
+           echo $test_compile
+           if { (eval $test_compile >& /dev/null ) 2>&1; } && test -s testlink ; then
+             # Compilation was okay
+-            echo "... only -llapack needed"
+-            XLAPACK_LIB="-llapack"
++            echo "... only -llapack -lpthread needed"
++            XLAPACK_LIB="-llapack -lpthread"
+             # Set the next two variables so that configure
+             # doesn't try to build netlib libraries
+             LAPACKLIB="lapack"
+@@ -2424,12 +2424,12 @@
+             tryblas=
+           else
+ 	    echo "more than just -llapack needed...."
+-            test_compile="$FC $FOPTIM $XFFLAGS -o testlink testlink.f -llapack -lblas"
++            test_compile="$FC $FOPTIM $XFFLAGS -o testlink testlink.f -llapack -lblas -lpthread"
+             echo $test_compile
+             if { (eval $test_compile ) 2>&1; } && test -s testlink ; then
+               # Compilation was okay
+-              echo "...-llapack and -lblas were needed"
+-              XLAPACK_LIB="-llapack -lblas"
++              echo "...-llapack, -lpthread and -lblas were needed"
++              XLAPACK_LIB="-llapack -lpthread -lblas"
+               # Set the next two variables so that configure
+               # doesn't try to build netlib libraries
+               LAPACKLIB="lapack blas"
+@@ -2720,8 +2720,8 @@
+       STOP
+       END
+ EOF
+-                test_compile="$FC $FOPTIM $XFFLAGS -o testlink testlink.f -L$testdir -l$testlib"
+-                test_ccompile="$FC $FOPTIM $XFFLAGS -o testlink testlink.f -L$testdir -l$testlib $XLDFLAGS"
++                test_compile="$FC $FOPTIM $XFFLAGS -o testlink testlink.f -L$testdir -l$testlib -lpthread"
++                test_ccompile="$FC $FOPTIM $XFFLAGS -o testlink testlink.f -L$testdir -l$testlib $XLDFLAGS -lpthread"
+                 echo $test_compile
+                 if { (eval $test_compile ) 2>&1; } && test -s testlink ; then
+                   have_lapack=yes
+@@ -2738,7 +2738,7 @@
+                   LAPACKDIR="$testdir"
+                   echo "Link ok - using lib$LAPACKLIB from $LAPACKDIR"
+ 		  #
+-		  XLAPACK_LIB="-L$LAPACKDIR -l$LAPACKLIB"
++		  XLAPACK_LIB="-L$LAPACKDIR -l$LAPACKLIB -lpthread"
+                   #
+                   # Test to see if we need BLAS too
+                   # Do this by trying to compile a test program
+@@ -2750,8 +2750,8 @@
+                   if test -f testlsame ; then
+                     rm -f testsame testlsame.o
+                   fi
+-                  test_compile="$FC $FOPTIM $XFFLAGS -o testlsame lsametst.f -L$LAPACKDIR -l$LAPACKLIB"
+-                  test_ccompile="$FC $FOPTIM $XFFLAGS -o testlsame lsametst.f -L$LAPACKDIR -l$LAPACKLIB $XLDFLAGS"
++                  test_compile="$FC $FOPTIM $XFFLAGS -o testlsame lsametst.f -L$LAPACKDIR -l$LAPACKLIB -lpthread"
++                  test_ccompile="$FC $FOPTIM $XFFLAGS -o testlsame lsametst.f -L$LAPACKDIR -l$LAPACKLIB $XLDFLAGS -lpthread"
+                   echo $test_compile
+                   if { ( eval $test_compile) 2>&1;} && test -s testlsame ; then
+                     have_blas=yes
+@@ -2830,8 +2830,8 @@
+       STOP
+       END
+ EOF
+-                  test_compile="$FC $FOPTIM $XFFLAGS -o testlink testlink.f -L$testdir -l$testlib"
+-                  test_ccompile="$FC $FOPTIM $XFFLAGS -o testlink testlink.f -L$testdir -l$testlib $XLDFLAGS"
++                  test_compile="$FC $FOPTIM $XFFLAGS -o testlink testlink.f -L$testdir -l$testlib -lpthread"
++                  test_ccompile="$FC $FOPTIM $XFFLAGS -o testlink testlink.f -L$testdir -l$testlib $XLDFLAGS -lpthread"
+                   echo $test_compile
+                   if { ( eval $test_compile) 2>&1;} && test -s testlink ; then
+                     have_blas=yes
+@@ -3033,7 +3033,7 @@
+         if test -f testlsame ; then
+           rm -f testsame testlsame.o
+         fi
+-        test_compile="$FC $FOPTIM $XFFLAGS -o testlsame lsametst.f -L$BLASDIR -l$BLASLIB"
++        test_compile="$FC $FOPTIM $XFFLAGS -o testlsame lsametst.f -L$BLASDIR -l$BLASLIB -lpthread"
+         echo $test_compile
+         if { ( eval $test_compile) 2>&1;} && test -s testlsame ; then
+           echo "Found LSAME in lib$BLASLIB"
+@@ -3046,7 +3046,7 @@
+         if test -f testxerbla ; then
+           rm -f testxerbla testxerbla.o
+         fi
+-        test_compile="$FC $FOPTIM $XFFLAGS -o testxerbla xerblatst.f -L$BLASDIR -l$BLASLIB"
++        test_compile="$FC $FOPTIM $XFFLAGS -o testxerbla xerblatst.f -L$BLASDIR -l$BLASLIB -lpthread"
+         echo $test_compile
+         if { ( eval $test_compile) 2>&1;} && test -s testxerbla ; then
+           # Found lsame
+@@ -3080,7 +3080,7 @@
+     cd ../..
+     #
+     lapackdir=lib/lapack
+-    XLAPACK_LIB="-L$srcdir/lib/lapack -llapack -L$BLASDIR -l$BLASLIB"
++    XLAPACK_LIB="-L$srcdir/lib/lapack -llapack -L$BLASDIR -l$BLASLIB -lpthread"
+ # netlib lapack is in fortran, so we may need the fortran libraries when
+ # we are linking using the C or C++ compilers
+     case $system in 
diff --git a/sci-chemistry/ccp4/files/clipper-find-mccp4-includes.patch b/sci-chemistry/ccp4/files/clipper-find-mccp4-includes.patch
new file mode 100644
index 000000000000..3bf5a0652247
--- /dev/null
+++ b/sci-chemistry/ccp4/files/clipper-find-mccp4-includes.patch
@@ -0,0 +1,11 @@
+--- ccp4-5.99.5/lib/clipper/configure.orig	2006-01-07 16:54:13.000000000 -0800
++++ ccp4-5.99.5/lib/clipper/configure	2006-01-07 16:54:31.000000000 -0800
+@@ -21751,7 +21751,7 @@
+ 
+ if test "x$mccp4_prefix" != x; then
+  # ie. mccp4=thing was given (thing is what we're checking for)
+- ac_MCCP4_CXXFLAGS="-I$mccp4_prefix/include"
++ ac_MCCP4_CXXFLAGS="-I$mccp4_prefix/include -I$mccp4_prefix/include/mccp4"
+  ac_MCCP4_LDOPTS="-L$mccp4_prefix/lib -lmccp4"
+ else
+  # treat as standard lib/include
diff --git a/sci-chemistry/ccp4/files/create-mosflm-bindir.patch b/sci-chemistry/ccp4/files/create-mosflm-bindir.patch
new file mode 100644
index 000000000000..34d6197572fc
--- /dev/null
+++ b/sci-chemistry/ccp4/files/create-mosflm-bindir.patch
@@ -0,0 +1,10 @@
+--- ccp4-5.99.5.orig/x-windows/Makefile.in	2006-01-06 12:31:02.000000000 -0800
++++ ccp4-5.99.5/x-windows/Makefile.in	2006-01-06 12:31:30.000000000 -0800
+@@ -158,6 +158,7 @@
+ install_obj = ipdisp.exe hklview xdldataman xdlmapman \
+ rotgen ipmosflm
+ install: all
++	mkdir -p $(bindir)
+ 	$(INSTALL_PROGRAM) $(srcdir)/ipdisp.exe $(bindir)
+ 	$(INSTALL_PROGRAM) $(srcdir)/ipdisp/ipdisp $(bindir)
+ 	$(INSTALL_PROGRAM) $(srcdir)/hklview $(bindir)
diff --git a/sci-chemistry/ccp4/files/digest-ccp4-6.0.1 b/sci-chemistry/ccp4/files/digest-ccp4-6.0.1
new file mode 100644
index 000000000000..acc5dc94a96a
--- /dev/null
+++ b/sci-chemistry/ccp4/files/digest-ccp4-6.0.1
@@ -0,0 +1,3 @@
+MD5 bd3ff43388b58841de79bcc23ebf81e3 ccp4-6.0.1-core-src.tar.gz 59311291
+RMD160 0f514fe30f22a4f6eb2e05c8bab567d2132e8fae ccp4-6.0.1-core-src.tar.gz 59311291
+SHA256 26a5704d707c3bc2fbe4c1d0804abccc1c50255005d26a8ec3a03fcba63335f2 ccp4-6.0.1-core-src.tar.gz 59311291
diff --git a/sci-chemistry/ccp4/files/dont-build-rasmol.patch b/sci-chemistry/ccp4/files/dont-build-rasmol.patch
new file mode 100644
index 000000000000..8da54fd26de8
--- /dev/null
+++ b/sci-chemistry/ccp4/files/dont-build-rasmol.patch
@@ -0,0 +1,19 @@
+--- ccp4-5.99.5.orig/x-windows/Makefile.in	2005-12-05 03:06:57.000000000 -0800
++++ ccp4-5.99.5/x-windows/Makefile.in	2005-12-05 03:07:23.000000000 -0800
+@@ -35,7 +35,7 @@
+ #
+ # all
+ #
+-all : xdlview libjwc_c libjwc_f rotgen_ hklview ipdisp.exe xdlgjk xjiffy rasmol2 ipmosflm
++all : xdlview libjwc_c libjwc_f rotgen_ hklview ipdisp.exe xdlgjk xjiffy ipmosflm
+ #
+ # xdl_view
+ #
+@@ -161,7 +161,6 @@
+ 	$(INSTALL_PROGRAM) $(srcdir)/xdldataman $(bindir)
+ 	$(INSTALL_PROGRAM) $(srcdir)/xdlmapman $(bindir)
+ 	cd $(srcdir)/XCCPJIFFY ; $(MAKE) install
+-	$(INSTALL_PROGRAM) $(rasmol_dir)/rasmol $(bindir)
+ 	cd $(rotgen_dir); $(MAKE) install
+ 	$(INSTALL_PROGRAM) $(mosflm_dir)/bin/ipmosflm $(bindir)
+ 	cd $(xdlview_dir); $(MAKE) install
diff --git a/sci-chemistry/ccp4/files/make-ipmosflm-dir.patch b/sci-chemistry/ccp4/files/make-ipmosflm-dir.patch
new file mode 100644
index 000000000000..7813141b2ec2
--- /dev/null
+++ b/sci-chemistry/ccp4/files/make-ipmosflm-dir.patch
@@ -0,0 +1,10 @@
+--- ccp4-5.99.5.orig/x-windows/Mosflm/mosflm/Makefile.in	2006-01-06 00:04:12.000000000 -0800
++++ ccp4-5.99.5/x-windows/Mosflm/mosflm/Makefile.in	2006-01-06 00:04:41.000000000 -0800
+@@ -37,6 +37,7 @@
+ 	${F77} ${FFLAGS} -o $@ $<
+ 
+ ipmosflm:	${OBJS}
++		mkdir -p ${DPSBIN}
+ 		${FLINK} ${FFLAGS} ${OBJS} ${LOCALLIBS} ${LIBS} \
+                 -o ${DPSBIN}/ipmosflm ${LDFLAGS}
+ 
diff --git a/sci-chemistry/ccp4/files/make-mosflm-cbf-libdir.patch b/sci-chemistry/ccp4/files/make-mosflm-cbf-libdir.patch
new file mode 100644
index 000000000000..ae4b7633b105
--- /dev/null
+++ b/sci-chemistry/ccp4/files/make-mosflm-cbf-libdir.patch
@@ -0,0 +1,11 @@
+--- ccp4-5.99.5.orig/x-windows/Mosflm/cbf/Makefile.in	2006-01-05 23:42:19.000000000 -0800
++++ ccp4-5.99.5/x-windows/Mosflm/cbf/Makefile.in	2006-01-05 23:43:35.000000000 -0800
+@@ -132,7 +132,7 @@
+ #
+ # CBF library
+ #
+-$(LIB)/libcbf.a: $(SOURCE) $(HEADERS) $(COMMONDEP)
++$(LIB)/libcbf.a: $(SOURCE) $(HEADERS) $(COMMONDEP) $(LIB)
+ 	$(CC) $(CFLAGS) $(INCLUDES) $(WARNINGS) -c $(SOURCE)
+ 	$(AR) cr $@ *.o
+ 	$(RANLIB) $@
diff --git a/sci-chemistry/ccp4/files/make-mosflm-index-libdir.patch b/sci-chemistry/ccp4/files/make-mosflm-index-libdir.patch
new file mode 100644
index 000000000000..97607b689672
--- /dev/null
+++ b/sci-chemistry/ccp4/files/make-mosflm-index-libdir.patch
@@ -0,0 +1,10 @@
+--- ccp4-5.99.5.orig/x-windows/Mosflm/index/Makefile.in	2006-01-05 23:15:09.000000000 -0800
++++ ccp4-5.99.5/x-windows/Mosflm/index/Makefile.in	2006-01-05 23:15:30.000000000 -0800
+@@ -76,6 +76,7 @@
+ 
+ # local version of libdps_index.a
+ ${LIB}/dps_index.a: ${IOBJS} ${HOBJS}
++	mkdir -p ${LIB}
+ 	ar ru ${LIB}/dps_index.a ${IOBJS} ${HOBJS}
+ 
+ ${LIB}/libpeak.a: 
diff --git a/sci-chemistry/ccp4/files/make-mosflm-libdir.patch b/sci-chemistry/ccp4/files/make-mosflm-libdir.patch
new file mode 100644
index 000000000000..eac1b9f1721e
--- /dev/null
+++ b/sci-chemistry/ccp4/files/make-mosflm-libdir.patch
@@ -0,0 +1,10 @@
+--- ccp4-5.99.5.orig/x-windows/Mosflm/src/dps/index/Makefile.in	2006-01-05 22:48:47.000000000 -0800
++++ ccp4-5.99.5/x-windows/Mosflm/src/dps/index/Makefile.in	2006-01-05 22:49:02.000000000 -0800
+@@ -42,6 +42,7 @@
+ 	$(LOCALLIBS) $(LIBS) 
+ 
+ index: $(IOBJS) 
++	mkdir -p $(LIBDIR)
+ 	${AR} $(AR_FLAGS) $(LIBDIR)/libdps_index.a $(IOBJS)
+ 	chmod 644 $(LIBDIR)/libdps_index.a
+ 
diff --git a/sci-chemistry/ccp4/files/pass-clipper-enablevals.patch b/sci-chemistry/ccp4/files/pass-clipper-enablevals.patch
new file mode 100644
index 000000000000..3e1a8b0e6be8
--- /dev/null
+++ b/sci-chemistry/ccp4/files/pass-clipper-enablevals.patch
@@ -0,0 +1,11 @@
+--- ccp4-5.99.5.orig/configure	2006-01-06 11:45:43.000000000 -0800
++++ ccp4-5.99.5/configure	2006-01-06 11:46:53.000000000 -0800
+@@ -3210,7 +3210,7 @@
+ #ccp4 setup
+   xopts="${xopts} --with-ccp4=${srcdir}"
+ #interface setup
+-  xopts="${xopts} --enable-mmdb --enable-cif --enable-ccp4 --enable-minimol"
++  xopts="${xopts} --enable-mmdb --enable-cif --enable-ccp4 --enable-minimol --enable-mmdbold --enable-mtz --with-mccp4=/usr"
+   echo   
+   echo "********* CLIPPER CONFIGURATION ***********"
+   echo