10 files changed, 262 insertions, 0 deletions
diff --git a/sci-chemistry/coot/files/0.6.2-clipper-config.patch b/sci-chemistry/coot/files/0.6.2-clipper-config.patch
new file mode 100644
index 000000000000..311b5e88d84e
--- /dev/null
+++ b/sci-chemistry/coot/files/0.6.2-clipper-config.patch
@@ -0,0 +1,17 @@
+ macros/clipper.m4 |    3 +++
+ 1 files changed, 3 insertions(+), 0 deletions(-)
+
+diff --git a/macros/clipper.m4 b/macros/clipper.m4
+index 0bf087a..d0e8b6b 100644
+--- a/macros/clipper.m4
++++ b/macros/clipper.m4
+@@ -98,6 +98,9 @@ case $ac_cv_build_alias in
+         ;;
+ esac
+ 
++CLIPPER_CXXFLAGS=`clipper-config --cflags`
++CLIPPER_LDOPTS=`clipper-config --libs`
++
+ AC_MSG_CHECKING([for Clipper])
+ 
+ 	LIBS="$save_LIBS $CLIPPER_LDOPTS"
diff --git a/sci-chemistry/coot/files/0.6.2-gl.patch b/sci-chemistry/coot/files/0.6.2-gl.patch
new file mode 100644
index 000000000000..bbd858c646df
--- /dev/null
+++ b/sci-chemistry/coot/files/0.6.2-gl.patch
@@ -0,0 +1,10 @@
+Index: coot-surface/Makefile.am
+===================================================================
+--- coot-surface/Makefile.am	(revision 3478)
++++ coot-surface/Makefile.am	(working copy)
+@@ -29,4 +29,4 @@
+ 
+ libcoot_surface_la_LIBADD = \
+ 	$(top_builddir)/surface/libccp4mg-surface.la \
+-	$(GLUT_LIBS) $(CLIPPER_LIBS) $(MMDB_LIBS) 
++	$(GLUT_LIBS) $(CLIPPER_LIBS) $(MMDB_LIBS) -lGL
diff --git a/sci-chemistry/coot/files/0.6.2-libpng15.patch b/sci-chemistry/coot/files/0.6.2-libpng15.patch
new file mode 100644
index 000000000000..bddd251698de
--- /dev/null
+++ b/sci-chemistry/coot/files/0.6.2-libpng15.patch
@@ -0,0 +1,29 @@
+--- ccp4mg-utils/ppmutil.cc
++++ ccp4mg-utils/ppmutil.cc
+@@ -2494,15 +2494,21 @@
+ 
+   pixels = new unsigned char[width*height*colourspace];
+ 
++  png_colorp palette;
++  int num_trans;
++#if PNG_LIBPNG_VER_MAJOR >= 1 && PNG_LIBPNG_VER_MINOR >=4
++  png_bytep trans_alpha;
++#endif
++
+   for (int i=0; i<height; i++){
+     if(color_type==PNG_COLOR_TYPE_PALETTE){
+       for (int j=0; j<width; j++){
+-        pixels[i*width*colourspace+j*colourspace] = png_ptr->palette[row_pointers[i][j]].red;
+-        pixels[i*width*colourspace+j*colourspace+1] = png_ptr->palette[row_pointers[i][j]].green;
+-        pixels[i*width*colourspace+j*colourspace+2] = png_ptr->palette[row_pointers[i][j]].blue;
+-        if(row_pointers[i][j]<png_ptr->num_trans){
++        pixels[i*width*colourspace+j*colourspace] = palette[row_pointers[i][j]].red;
++        pixels[i*width*colourspace+j*colourspace+1] = palette[row_pointers[i][j]].green;
++        pixels[i*width*colourspace+j*colourspace+2] = palette[row_pointers[i][j]].blue;
++        if(row_pointers[i][j]<num_trans){
+ #if PNG_LIBPNG_VER_MAJOR >= 1 && PNG_LIBPNG_VER_MINOR >=4
+-         pixels[i*width*colourspace+j*colourspace+3] = png_ptr->trans_alpha[row_pointers[i][j]];
++         pixels[i*width*colourspace+j*colourspace+3] = trans_alpha[row_pointers[i][j]];
+ #else
+          pixels[i*width*colourspace+j*colourspace+3] = png_ptr->trans[row_pointers[i][j]];
+ #endif
diff --git a/sci-chemistry/coot/files/0.6.2-mmdb-config.patch b/sci-chemistry/coot/files/0.6.2-mmdb-config.patch
new file mode 100644
index 000000000000..1d7cbd452f7b
--- /dev/null
+++ b/sci-chemistry/coot/files/0.6.2-mmdb-config.patch
@@ -0,0 +1,18 @@
+ macros/mmdb.m4 |    4 ++++
+ 1 files changed, 4 insertions(+), 0 deletions(-)
+
+diff --git a/macros/mmdb.m4 b/macros/mmdb.m4
+index b477597..d05cf66 100644
+--- a/macros/mmdb.m4
++++ b/macros/mmdb.m4
+@@ -86,6 +86,10 @@ else
+  ac_MMDB_LDOPTS="-lmmdb -lm"
+ fi
+ 
++PKG_CHECK_MODULES([MMDB],[mmdb >= 1.2])
++ac_MMDB_LDOPTS="${MMDB_LIBS}"
++ac_MMDB_CXXFLAGS="${MMDB_CFLAGS}"
++
+ AC_MSG_CHECKING([for MMDB])
+ 
+ 	LIBS="$save_LIBS $ac_MMDB_LDOPTS"
diff --git a/sci-chemistry/coot/files/0.6.2-ssm.patch b/sci-chemistry/coot/files/0.6.2-ssm.patch
new file mode 100644
index 000000000000..c801da72410a
--- /dev/null
+++ b/sci-chemistry/coot/files/0.6.2-ssm.patch
@@ -0,0 +1,56 @@
+ macros/mmdb-ssm.m4 |   42 +-----------------------------------------
+ 1 files changed, 1 insertions(+), 41 deletions(-)
+
+diff --git a/macros/mmdb-ssm.m4 b/macros/mmdb-ssm.m4
+index 1937a16..6ef547c 100644
+--- a/macros/mmdb-ssm.m4
++++ b/macros/mmdb-ssm.m4
+@@ -22,47 +22,7 @@
+ AC_DEFUN([AM_WITH_MMDBSSM],
+ [AC_PROVIDE([AM_USE_MMDBSSM])
+ 
+-
+-AC_ARG_WITH(ssmlib-prefix, 
+-	AC_HELP_STRING( [--with-ssmlib-prefix=PFX], [Prefix where SSMLib has been installed] ),
+-	[ with_ssmlib_prefix="$withval" ],
+- with_ssmlib_prefix="")
+-
+-AC_MSG_CHECKING([for SSMLib])
+-
+-if test x$with_ssmlib_prefix != x; then
+-
+-   MMDBSSM_CXXFLAGS="-DHAVE_SSMLIB"
+-   MMDBSSM_LIBS="-L$with_ssmlib_prefix/$acl_libdirstem -lssm"
+-
+-ac_mmdb_dirs='
+-.
+-include
+-include/ssm
+-include/mmdb
+-lib
+-src
+-lib/src
+-lib/src/mmdb'
+-
+-   for ac_dir in $ac_mmdb_dirs; do
+-      if test -r "$with_ssmlib_prefix/$ac_dir/ssm_superpose.h"; then
+-         ac_MMDBSSM_CXXFLAGS="-I$with_ssmlib_prefix/$ac_dir"
+-         break
+-      fi
+-   done
+-
+-  MMDBSSM_CXXFLAGS="$MMDBSSM_CXXFLAGS $ac_MMDBSSM_CXXFLAGS"
+-  
+-else 
+-
+-   MMDBSSM_CXXFLAGS=""
+-   MMDBSSM_LIBS=""
+-   with_ssmlib_prefix=no 
+-
+-fi
+-
+-AC_MSG_RESULT([$with_ssmlib_prefix])
++PKG_CHECK_MODULES([MMDBSSM],[ssm])
+ 
+ AC_SUBST(MMDBSSM_CXXFLAGS)
+ AC_SUBST(MMDBSSM_LIBS)
diff --git a/sci-chemistry/coot/files/0.6.2-test.patch b/sci-chemistry/coot/files/0.6.2-test.patch
new file mode 100644
index 000000000000..8cb79e65d767
--- /dev/null
+++ b/sci-chemistry/coot/files/0.6.2-test.patch
@@ -0,0 +1,16 @@
+ src/testing.cc |    4 +++-
+ 1 files changed, 3 insertions(+), 1 deletions(-)
+
+diff --git a/src/testing.cc b/src/testing.cc
+index f767bf6..097b9b9 100644
+--- a/src/testing.cc
++++ b/src/testing.cc
+@@ -86,6 +86,8 @@ std::string greg_test(const std::string &file_name) {
+    const char *c = getenv("COOT_TEST_DATA_DIR");
+    if (c) {
+       dd = c;
++      dd += "/";
++      dd += file_name;
+    } else { 
+       const char *d = getenv("HOME");
+       if (d) {
diff --git a/sci-chemistry/coot/files/coot-0.7-clipper-config.patch b/sci-chemistry/coot/files/coot-0.7-clipper-config.patch
new file mode 100644
index 000000000000..311b5e88d84e
--- /dev/null
+++ b/sci-chemistry/coot/files/coot-0.7-clipper-config.patch
@@ -0,0 +1,17 @@
+ macros/clipper.m4 |    3 +++
+ 1 files changed, 3 insertions(+), 0 deletions(-)
+
+diff --git a/macros/clipper.m4 b/macros/clipper.m4
+index 0bf087a..d0e8b6b 100644
+--- a/macros/clipper.m4
++++ b/macros/clipper.m4
+@@ -98,6 +98,9 @@ case $ac_cv_build_alias in
+         ;;
+ esac
+ 
++CLIPPER_CXXFLAGS=`clipper-config --cflags`
++CLIPPER_LDOPTS=`clipper-config --libs`
++
+ AC_MSG_CHECKING([for Clipper])
+ 
+ 	LIBS="$save_LIBS $CLIPPER_LDOPTS"
diff --git a/sci-chemistry/coot/files/coot-0.7-goocanvas.patch b/sci-chemistry/coot/files/coot-0.7-goocanvas.patch
new file mode 100644
index 000000000000..ce0d4a00abba
--- /dev/null
+++ b/sci-chemistry/coot/files/coot-0.7-goocanvas.patch
@@ -0,0 +1,25 @@
+Index: macros/goo-canvas.m4
+===================================================================
+--- macros/goo-canvas.m4	(revision 3307)
++++ macros/goo-canvas.m4	(working copy)
+@@ -56,9 +56,9 @@
+   fi
+ fi
+ 
+-AC_MSG_CHECKING([for Goocanvas])
++PKG_CHECK_MODULES(GOOCANVAS, goocanvas)
+ 
+-LIBS="$saved_LIBS $GOOCANVAS_LDOPTS $GTK_LIBS"
++LIBS="$saved_LIBS $GOOCANVAS_LIBS $GTK_LIBS"
+ CXXFLAGS="$saved_CXXFLAGS $GOOCANVAS_CFLAGS $GTK_CFLAGS"
+ #
+ # AC_TRY_LINK uses the c compiler (set by AC_LANG), so we will
+@@ -76,7 +76,7 @@
+ if test x$have_goocanvas = xyes; then
+ 
+  GOOCANVAS_CFLAGS="$GOOCANVAS_CFLAGS"
+- GOOCANVAS_LIBS="$GOOCANVAS_LDOPTS"
++ GOOCANVAS_LIBS="$GOOCANVAS_LIBS"
+ 
+ ifelse([$1], , :, [$1])
+ 
diff --git a/sci-chemistry/coot/files/coot-0.7-mmdb-config.patch b/sci-chemistry/coot/files/coot-0.7-mmdb-config.patch
new file mode 100644
index 000000000000..b3b66ab65786
--- /dev/null
+++ b/sci-chemistry/coot/files/coot-0.7-mmdb-config.patch
@@ -0,0 +1,18 @@
+Index: macros/mmdb.m4
+===================================================================
+--- macros/mmdb.m4	(revision 3579)
++++ macros/mmdb.m4	(working copy)
+@@ -86,8 +86,12 @@
+  ac_MMDB_LDOPTS="-lmmdb -lm"
+ fi
+ 
+-AC_MSG_CHECKING([for MMDB])
++PKG_CHECK_MODULES([MMDB],[mmdb >= 1.2])
++ac_MMDB_LDOPTS="${MMDB_LIBS}"
++ac_MMDB_CXXFLAGS="${MMDB_CFLAGS}"
+ 
++AC_MSG_CHECKING([for CISPEP in MMDB])
++
+ 	LIBS="$save_LIBS $ac_MMDB_LDOPTS"
+ 	CXXFLAGS="$save_CXXFLAGS $ac_MMDB_CXXFLAGS"
+ 	#
diff --git a/sci-chemistry/coot/files/coot-0.7-ssm.patch b/sci-chemistry/coot/files/coot-0.7-ssm.patch
new file mode 100644
index 000000000000..c801da72410a
--- /dev/null
+++ b/sci-chemistry/coot/files/coot-0.7-ssm.patch
@@ -0,0 +1,56 @@
+ macros/mmdb-ssm.m4 |   42 +-----------------------------------------
+ 1 files changed, 1 insertions(+), 41 deletions(-)
+
+diff --git a/macros/mmdb-ssm.m4 b/macros/mmdb-ssm.m4
+index 1937a16..6ef547c 100644
+--- a/macros/mmdb-ssm.m4
++++ b/macros/mmdb-ssm.m4
+@@ -22,47 +22,7 @@
+ AC_DEFUN([AM_WITH_MMDBSSM],
+ [AC_PROVIDE([AM_USE_MMDBSSM])
+ 
+-
+-AC_ARG_WITH(ssmlib-prefix, 
+-	AC_HELP_STRING( [--with-ssmlib-prefix=PFX], [Prefix where SSMLib has been installed] ),
+-	[ with_ssmlib_prefix="$withval" ],
+- with_ssmlib_prefix="")
+-
+-AC_MSG_CHECKING([for SSMLib])
+-
+-if test x$with_ssmlib_prefix != x; then
+-
+-   MMDBSSM_CXXFLAGS="-DHAVE_SSMLIB"
+-   MMDBSSM_LIBS="-L$with_ssmlib_prefix/$acl_libdirstem -lssm"
+-
+-ac_mmdb_dirs='
+-.
+-include
+-include/ssm
+-include/mmdb
+-lib
+-src
+-lib/src
+-lib/src/mmdb'
+-
+-   for ac_dir in $ac_mmdb_dirs; do
+-      if test -r "$with_ssmlib_prefix/$ac_dir/ssm_superpose.h"; then
+-         ac_MMDBSSM_CXXFLAGS="-I$with_ssmlib_prefix/$ac_dir"
+-         break
+-      fi
+-   done
+-
+-  MMDBSSM_CXXFLAGS="$MMDBSSM_CXXFLAGS $ac_MMDBSSM_CXXFLAGS"
+-  
+-else 
+-
+-   MMDBSSM_CXXFLAGS=""
+-   MMDBSSM_LIBS=""
+-   with_ssmlib_prefix=no 
+-
+-fi
+-
+-AC_MSG_RESULT([$with_ssmlib_prefix])
++PKG_CHECK_MODULES([MMDBSSM],[ssm])
+ 
+ AC_SUBST(MMDBSSM_CXXFLAGS)
+ AC_SUBST(MMDBSSM_LIBS)