[69427] trunk/dports/science/pymol

macsforever2000 at macports.org macsforever2000 at macports.org
Mon Jul 5 12:51:11 PDT 2010 

Revision: 69427
          http://trac.macports.org/changeset/69427
Author:   macsforever2000 at macports.org
Date:     2010-07-05 12:51:09 -0700 (Mon, 05 Jul 2010)
Log Message:
-----------
Maintainer Update to version 1.3. Added gcc45 variant. (#25498)

Modified Paths:
--------------
    trunk/dports/science/pymol/Portfile

Added Paths:
-----------
    trunk/dports/science/pymol/files/pymol-build.patch2

Modified: trunk/dports/science/pymol/Portfile
===================================================================
--- trunk/dports/science/pymol/Portfile	2010-07-05 19:12:16 UTC (rev 69426)
+++ trunk/dports/science/pymol/Portfile	2010-07-05 19:51:09 UTC (rev 69427)
@@ -4,8 +4,7 @@
 PortSystem          1.0
 
 name                pymol
-version             1.2r2
-revision            2
+version             1.3
 categories          science
 maintainers         bromo.med.uc.edu:howarth
 description         Molecular graphics system
@@ -20,13 +19,13 @@
 master_sites        sourceforge
 fetch.type          svn
 svn.url             https://pymol.svn.sourceforge.net/svnroot/pymol/trunk/pymol
-svn.revision        3866
+svn.revision        3911
 worksrcdir          pymol
 
 depends_lib         port:glut port:freetype port:libpng port:python26 port:py26-pmw port:py26-numeric port:mesa
 depends_run         port:xdpyinfo
 
-patchfiles          pymol-build.patch
+patchfiles          pymol-build.patch pymol-build.patch2
 use_configure       no
 
 post-patch {
@@ -40,7 +39,7 @@
 
 post-configure {
     copy ${worksrcpath}/setup/Rules.osx-fink ${worksrcpath}/Rules.delsci
-    if { [variant_isset gcc43] || [variant_isset gcc44] } {
+    if { [variant_isset gcc43] || [variant_isset gcc44] || [variant_isset gcc45] } {
         reinplace  "s| -no-cpp-precomp||g"          ${worksrcpath}/Rules.delsci
         reinplace  "s|^BUILD = |BUILD = -lstdc++ |" ${worksrcpath}/Rules.delsci
     }
@@ -52,7 +51,7 @@
                 CC="${configure.cc}" CXX="${configure.cxx}"
 }
 
-variant gcc43 description conflicts gcc44 description {build using macports-gcc-4.3} {
+variant gcc43 description conflicts gcc44 gcc45 description {build using macports-gcc-4.3} {
     depends_lib-append  port:gcc43
     # the current pymol makefile does not honour CC and CXX environment variables
     build.args-delete   CC="${configure.cc}" CXX="${configure.cxx}"
@@ -60,7 +59,7 @@
     configure.compiler  macports-gcc-4.3
 }
 
-variant gcc44 description conflicts gcc43 description {build using macports-gcc-4.4} {
+variant gcc44 description conflicts gcc43 gcc45 description {build using macports-gcc-4.4} {
     depends_lib-append  port:gcc44
     # the current pymol makefile does not honour CC and CXX environment variables
     build.args-delete   CC="${configure.cc}" CXX="${configure.cxx}"
@@ -68,6 +67,14 @@
     configure.compiler  macports-gcc-4.4
 }
 
+variant gcc45 description conflicts gcc43 gcc44 description {build using macports-gcc-4.5} {
+    depends_lib-append  port:gcc45
+    # the current pymol makefile does not honour CC and CXX environment variables
+    build.args-delete   CC="${configure.cc}" CXX="${configure.cxx}"
+    build.args-append   CC="${prefix}/bin/gcc-mp-4.5" CXX="${prefix}/bin/g++-mp-4.5"
+    configure.compiler  macports-gcc-4.5
+}
+
 destroot {
     file mkdir ${destroot}${prefix}/lib/pymol/bin
     copy  ${worksrcpath}/setup/pymol.com.osx-fink ${destroot}${prefix}/lib/pymol/bin/pymol

Added: trunk/dports/science/pymol/files/pymol-build.patch2
===================================================================
--- trunk/dports/science/pymol/files/pymol-build.patch2	                        (rev 0)
+++ trunk/dports/science/pymol/files/pymol-build.patch2	2010-07-05 19:51:09 UTC (rev 69427)
@@ -0,0 +1,56 @@
+--- Makefile.delsci.orig	2010-07-02 17:29:57.000000000 -0400
++++ Makefile.delsci	2010-07-02 17:35:04.000000000 -0400
+@@ -61,15 +61,15 @@
+ 	/bin/rm -f .update .includes
+ 	cd contrib;$(MAKE) -f Makefile.delsci
+ 	cd contrib/uiuc/plugins/molfile_plugin/src;$(MAKE) -f Makefile.delsci
+-	cd modules/cealign/src; g++ -c ccealignmodule.cpp -o ccealignmodule.o -Itnt -I. $(PYTHON_INC_DIR) -I$(PYMOL_PATH)/layer0 -I$(PYMOL_PATH)/ov/src 
+-	$(CC) $(BUILD) $(DEST) */*.o ov/src/*.o contrib/uiuc/plugins/molfile_plugin/src/*.o $(CFLAGS)  $(LIB_DIRS) $(LIBS)	
++	cd modules/cealign/src; $(CXX) -c ccealignmodule.cpp -o ccealignmodule.o -Itnt -I. $(PYTHON_INC_DIR) -I../../../layer0 -I../../../ov/src 
++	$(CC) $(BUILD) $(DEST) */*.o ov/src/*.o contrib/uiuc/plugins/molfile_plugin/src/*.o modules/cealign/src/*.o $(CFLAGS)  $(LIB_DIRS) $(LIBS)	
+ 
+ semistatic: .includes .depends .update
+ 	/bin/rm -f .update .includes
+ 	cd contrib;$(MAKE) -f Makefile.delsci static
+ 	cd contrib/uiuc/plugins/molfile_plugin/src;$(MAKE) -f Makefile.delsci
+-	cd modules/cealign/src; g++ -c ccealignmodule.cpp -o ccealignmodule.o -Itnt -I. $(PYTHON_INC_DIR) -I$(PYMOL_PATH)/layer0 -I$(PYMOL_PATH)/ov/src 
+-	g++ $(BUILD) $(DEST) */*.o ov/src/*.o contrib/uiuc/plugins/molfile_plugin/src/*.o $(CFLAGS) $(LIB_DIRS) $(LIBS)	
++	cd modules/cealign/src; $(CXX) -c ccealignmodule.cpp -o ccealignmodule.o -Itnt -I. $(PYTHON_INC_DIR) -I../../../layer0 -I../../../ov/src 
++	$(CXX) $(BUILD) $(DEST) */*.o ov/src/*.o contrib/uiuc/plugins/molfile_plugin/src/*.o modules/cealign/src/*.o $(CFLAGS) $(LIB_DIRS) $(LIBS)	
+ 
+ free:
+ 	/bin/rm -rf freemol
+--- layer4/Makefile.delsci.orig	2010-07-02 17:37:56.000000000 -0400
++++ layer4/Makefile.delsci	2010-07-02 17:38:17.000000000 -0400
+@@ -3,7 +3,7 @@
+ 
+ include ../Rules.delsci
+ 
+-CFLAGS = $(PYMOL_INC_DIRS) $(C_FLAGS) -I../ov/src
++CFLAGS = $(PYMOL_INC_DIRS) $(C_FLAGS) -I../ov/src -I../modules/cealign/src
+ 
+ all: layer
+ 
+--- modules/pmg_tk/startup/apbs_tools.py.orig	2010-07-02 18:40:05.000000000 -0400
++++ modules/pmg_tk/startup/apbs_tools.py	2010-07-02 18:41:40.000000000 -0400
+@@ -183,6 +183,11 @@
+         searchDirs.append("/tmp")
+         searchDirs.append(".")
+ 
++    # This must come before /opt/local/bin (which may also be in PATH) in
++    # order for our pdb2pqr importing to work
++    # correctly. /opt/local/bin/pdb2pqr just calls through to this.
++    searchDirs.append(os.path.join("/opt", "local", "share", "pdb2pqr"))
++
+     searchDirs.extend(string.split(os.environ["PATH"], ":"))
+     searchDirs.append(os.path.join("/usr", "local", "bin"))
+     searchDirs.append(os.path.join("/opt", "local", "bin"))
+@@ -787,7 +792,7 @@
+                                      label_pyclass = FileDialogButtonClassFactory.get(self.setPsizeLocation),
+                                      validate = {'validator':quickFileValidation,},
+                                      #value = '/usr/local/apbs-0.3.1/tools/manip/psize.py',
+-                                     value = get_default_location('psize.py'),
++                                     value = get_default_location('apbs-psize.py'),
+                                      label_text = 'APBS psize.py location:',
+                                      )
+         self.psize.pack(fill = 'x', padx = 20, pady = 10)
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