[MacPorts] #29345: PyMOL 1.4 fails to build with gcc 4.4 error

MacPorts noreply at macports.org
Mon May 2 13:26:46 PDT 2011 

#29345: PyMOL 1.4 fails to build with gcc 4.4 error
------------------------------------------+---------------------------------
 Reporter:  michelle.lynn.gill@…          |       Owner:  macports-tickets@…                   
     Type:  defect                        |      Status:  new                                  
 Priority:  Normal                        |   Milestone:                                       
Component:  ports                         |     Version:  1.9.2                                
 Keywords:                                |        Port:  pymol                                
------------------------------------------+---------------------------------

Comment(by howarth@…):

 The partial fix solves the part of the build but it still fails with gcc45
 at...


 /opt/local/bin/gcc-mp-4.5 -fno-strict-aliasing -fno-common -dynamic -pipe
 -O2 -DNDEBUG -g -fwrapv -O3 -Wall -Wstrict-prototypes -D_PYMOL_MODULE
 -D_PYMOL_INLINE -D_PYMOL_LIBPNG -D_PYMOL_FREETYPE -D_PYMOL_NUMPY
 -D_PYMOL_OPENGL_SHADERS -DNO_MMLIBS -Iov/src -Ilayer0 -Ilayer1 -Ilayer2
 -Ilayer3 -Ilayer4 -Ilayer5 -I/opt/local/include -I/opt/local/include/GL
 -I/opt/local/include/freetype2 -Imodules/cealign/src
 -Imodules/cealign/src/tnt
 -I/opt/local/Library/Frameworks/Python.framework/Versions/2.6/include/python2.6
 -c layer5/TestPyMOL.c -o
 build/temp.macosx-10.6-x86_64-2.6/layer5/TestPyMOL.o -ffast-math -funroll-
 loops -O3
 /opt/local/bin/gcc-mp-4.5 -fno-strict-aliasing -fno-common -dynamic -pipe
 -O2 -DNDEBUG -g -fwrapv -O3 -Wall -Wstrict-prototypes -D_PYMOL_MODULE
 -D_PYMOL_INLINE -D_PYMOL_LIBPNG -D_PYMOL_FREETYPE -D_PYMOL_NUMPY
 -D_PYMOL_OPENGL_SHADERS -DNO_MMLIBS -Iov/src -Ilayer0 -Ilayer1 -Ilayer2
 -Ilayer3 -Ilayer4 -Ilayer5 -I/opt/local/include -I/opt/local/include/GL
 -I/opt/local/include/freetype2 -Imodules/cealign/src
 -Imodules/cealign/src/tnt
 -I/opt/local/Library/Frameworks/Python.framework/Versions/2.6/include/python2.6
 -c layer5/main.c -o build/temp.macosx-10.6-x86_64-2.6/layer5/main.o
 -ffast-math -funroll-loops -O3
 /opt/local/bin/g++-mp-4.5 -L/opt/local/lib -bundle -undefined
 dynamic_lookup
 build/temp.macosx-10.6-x86_64-2.6/modules/cealign/src/ccealignmodule.o
 build/temp.macosx-10.6-x86_64-2.6/ov/src/OVContext.o
 build/temp.macosx-10.6-x86_64-2.6/ov/src/OVHeapArray.o
 build/temp.macosx-10.6-x86_64-2.6/ov/src/OVHeap.o
 build/temp.macosx-10.6-x86_64-2.6/ov/src/OVLexicon.o
 build/temp.macosx-10.6-x86_64-2.6/ov/src/OVOneToOne.o
 build/temp.macosx-10.6-x86_64-2.6/ov/src/OVOneToAny.o
 build/temp.macosx-10.6-x86_64-2.6/ov/src/OVRandom.o
 build/temp.macosx-10.6-x86_64-2.6/ov/src/ov_utility.o
 build/temp.macosx-10.6-x86_64-2.6/layer0/Block.o
 build/temp.macosx-10.6-x86_64-2.6/layer0/Crystal.o
 build/temp.macosx-10.6-x86_64-2.6/layer0/Debug.o
 build/temp.macosx-10.6-x86_64-2.6/layer0/Deferred.o
 build/temp.macosx-10.6-x86_64-2.6/layer0/Err.o
 build/temp.macosx-10.6-x86_64-2.6/layer0/Feedback.o
 build/temp.macosx-10.6-x86_64-2.6/layer0/Field.o
 build/temp.macosx-10.6-x86_64-2.6/layer0/Isosurf.o
 build/temp.macosx-10.6-x86_64-2.6/layer0/Map.o
 build/temp.macosx-10.6-x86_64-2.6/layer0/Match.o
 build/temp.macosx-10.6-x86_64-2.6/layer0/Matrix.o
 build/temp.macosx-10.6-x86_64-2.6/layer0/MemoryDebug.o
 build/temp.macosx-10.6-x86_64-2.6/layer0/MemoryCache.o
 build/temp.macosx-10.6-x86_64-2.6/layer0/MyPNG.o
 build/temp.macosx-10.6-x86_64-2.6/layer0/Parse.o
 build/temp.macosx-10.6-x86_64-2.6/layer0/Pixmap.o
 build/temp.macosx-10.6-x86_64-2.6/layer0/Queue.o
 build/temp.macosx-10.6-x86_64-2.6/layer0/Raw.o
 build/temp.macosx-10.6-x86_64-2.6/layer0/Sphere.o
 build/temp.macosx-10.6-x86_64-2.6/layer0/ShaderMgr.o
 build/temp.macosx-10.6-x86_64-2.6/layer0/Tetsurf.o
 build/temp.macosx-10.6-x86_64-2.6/layer0/Texture.o
 build/temp.macosx-10.6-x86_64-2.6/layer0/Tracker.o
 build/temp.macosx-10.6-x86_64-2.6/layer0/Triangle.o
 build/temp.macosx-10.6-x86_64-2.6/layer0/Util.o
 build/temp.macosx-10.6-x86_64-2.6/layer0/Vector.o
 build/temp.macosx-10.6-x86_64-2.6/layer0/Word.o
 build/temp.macosx-10.6-x86_64-2.6/layer0/os_gl.o
 build/temp.macosx-10.6-x86_64-2.6/layer1/Basis.o
 build/temp.macosx-10.6-x86_64-2.6/layer1/ButMode.o
 build/temp.macosx-10.6-x86_64-2.6/layer1/Character.o
 build/temp.macosx-10.6-x86_64-2.6/layer1/CGO.o
 build/temp.macosx-10.6-x86_64-2.6/layer1/Color.o
 build/temp.macosx-10.6-x86_64-2.6/layer1/Control.o
 build/temp.macosx-10.6-x86_64-2.6/layer1/Extrude.o
 build/temp.macosx-10.6-x86_64-2.6/layer1/Font.o
 build/temp.macosx-10.6-x86_64-2.6/layer1/FontType.o
 build/temp.macosx-10.6-x86_64-2.6/layer1/FontGLUT.o
 build/temp.macosx-10.6-x86_64-2.6/layer1/FontGLUT8x13.o
 build/temp.macosx-10.6-x86_64-2.6/layer1/FontGLUT9x15.o
 build/temp.macosx-10.6-x86_64-2.6/layer1/FontGLUTHel10.o
 build/temp.macosx-10.6-x86_64-2.6/layer1/FontGLUTHel12.o
 build/temp.macosx-10.6-x86_64-2.6/layer1/FontGLUTHel18.o
 build/temp.macosx-10.6-x86_64-2.6/layer1/Movie.o
 build/temp.macosx-10.6-x86_64-2.6/layer1/Ortho.o
 build/temp.macosx-10.6-x86_64-2.6/layer1/P.o
 build/temp.macosx-10.6-x86_64-2.6/layer1/PConv.o
 build/temp.macosx-10.6-x86_64-2.6/layer1/Pop.o
 build/temp.macosx-10.6-x86_64-2.6/layer1/PyMOLObject.o
 build/temp.macosx-10.6-x86_64-2.6/layer1/Ray.o
 build/temp.macosx-10.6-x86_64-2.6/layer1/Rep.o
 build/temp.macosx-10.6-x86_64-2.6/layer1/Scene.o
 build/temp.macosx-10.6-x86_64-2.6/layer1/ScrollBar.o
 build/temp.macosx-10.6-x86_64-2.6/layer1/Seq.o
 build/temp.macosx-10.6-x86_64-2.6/layer1/Setting.o
 build/temp.macosx-10.6-x86_64-2.6/layer1/Shaker.o
 build/temp.macosx-10.6-x86_64-2.6/layer1/Symmetry.o
 build/temp.macosx-10.6-x86_64-2.6/layer1/Text.o
 build/temp.macosx-10.6-x86_64-2.6/layer1/TypeFace.o
 build/temp.macosx-10.6-x86_64-2.6/layer1/Wizard.o
 build/temp.macosx-10.6-x86_64-2.6/layer1/View.o
 build/temp.macosx-10.6-x86_64-2.6/layer2/AtomInfo.o
 build/temp.macosx-10.6-x86_64-2.6/layer2/CoordSet.o
 build/temp.macosx-10.6-x86_64-2.6/layer2/GadgetSet.o
 build/temp.macosx-10.6-x86_64-2.6/layer2/DistSet.o
 build/temp.macosx-10.6-x86_64-2.6/layer2/ObjectAlignment.o
 build/temp.macosx-10.6-x86_64-2.6/layer2/ObjectCGO.o
 build/temp.macosx-10.6-x86_64-2.6/layer2/ObjectCallback.o
 build/temp.macosx-10.6-x86_64-2.6/layer2/ObjectDist.o
 build/temp.macosx-10.6-x86_64-2.6/layer2/ObjectMap.o
 build/temp.macosx-10.6-x86_64-2.6/layer2/ObjectMesh.o
 build/temp.macosx-10.6-x86_64-2.6/layer2/ObjectMolecule.o
 build/temp.macosx-10.6-x86_64-2.6/layer2/ObjectMolecule2.o
 build/temp.macosx-10.6-x86_64-2.6/layer2/ObjectSurface.o
 build/temp.macosx-10.6-x86_64-2.6/layer2/ObjectSlice.o
 build/temp.macosx-10.6-x86_64-2.6/layer2/ObjectVolume.o
 build/temp.macosx-10.6-x86_64-2.6/layer2/RepCartoon.o
 build/temp.macosx-10.6-x86_64-2.6/layer2/RepCylBond.o
 build/temp.macosx-10.6-x86_64-2.6/layer2/RepDistDash.o
 build/temp.macosx-10.6-x86_64-2.6/layer2/RepDistLabel.o
 build/temp.macosx-10.6-x86_64-2.6/layer2/RepDot.o
 build/temp.macosx-10.6-x86_64-2.6/layer2/RepLabel.o
 build/temp.macosx-10.6-x86_64-2.6/layer2/RepMesh.o
 build/temp.macosx-10.6-x86_64-2.6/layer2/ObjectGadget.o
 build/temp.macosx-10.6-x86_64-2.6/layer2/ObjectGadgetRamp.o
 build/temp.macosx-10.6-x86_64-2.6/layer2/ObjectGroup.o
 build/temp.macosx-10.6-x86_64-2.6/layer2/RepAngle.o
 build/temp.macosx-10.6-x86_64-2.6/layer2/RepDihedral.o
 build/temp.macosx-10.6-x86_64-2.6/layer2/RepNonbonded.o
 build/temp.macosx-10.6-x86_64-2.6/layer2/RepNonbondedSphere.o
 build/temp.macosx-10.6-x86_64-2.6/layer2/RepRibbon.o
 build/temp.macosx-10.6-x86_64-2.6/layer2/RepSphere.o
 build/temp.macosx-10.6-x86_64-2.6/layer2/RepEllipsoid.o
 build/temp.macosx-10.6-x86_64-2.6/layer2/RepSurface.o
 build/temp.macosx-10.6-x86_64-2.6/layer2/RepWireBond.o
 build/temp.macosx-10.6-x86_64-2.6/layer2/Sculpt.o
 build/temp.macosx-10.6-x86_64-2.6/layer2/SculptCache.o
 build/temp.macosx-10.6-x86_64-2.6/layer2/VFont.o
 build/temp.macosx-10.6-x86_64-2.6/layer3/PlugIOManager.o
 build/temp.macosx-10.6-x86_64-2.6/layer3/Editor.o
 build/temp.macosx-10.6-x86_64-2.6/layer3/Executive.o
 build/temp.macosx-10.6-x86_64-2.6/layer3/Seeker.o
 build/temp.macosx-10.6-x86_64-2.6/layer3/Selector.o
 build/temp.macosx-10.6-x86_64-2.6/layer4/Cmd.o
 build/temp.macosx-10.6-x86_64-2.6/layer4/Export.o
 build/temp.macosx-10.6-x86_64-2.6/layer4/Menu.o
 build/temp.macosx-10.6-x86_64-2.6/layer4/PopUp.o
 build/temp.macosx-10.6-x86_64-2.6/layer5/PyMOL.o
 build/temp.macosx-10.6-x86_64-2.6/layer5/TestPyMOL.o
 build/temp.macosx-10.6-x86_64-2.6/layer5/main.o -o
 build/lib.macosx-10.6-x86_64-2.6/pymol/_cmd.so -L/opt/local/lib -lpng -lGL
 -lglut -lGLEW -lfreetype
 ld: duplicate symbol __CShaderMgr in
 build/temp.macosx-10.6-x86_64-2.6/layer2/ObjectVolume.o and
 build/temp.macosx-10.6-x86_64-2.6/layer0/ShaderMgr.o for architecture
 x86_64
 collect2: ld returned 1 exit status
 error: command '/opt/local/bin/g++-mp-4.5' failed with exit status 1
 shell command " cd
 "/opt/local/var/macports/build/_Users_howarth_ports_science_pymol/work/pymol"
 && CC="/opt/local/bin/gcc-mp-4.5" CXX="/opt/local/bin/g++-mp-4.5"
 /opt/local/Library/Frameworks/Python.framework/Versions/2.6/bin/python2.6
 setup.py --no-user-cfg build " returned error 1
 Error: Target org.macports.build returned: shell command failed (see log
 for details)

 Note that upstream isn't maintaining the delsci Makefiles so that the
 setup.py approach is better for normal maintenance. I was also told that
 package maintainers are not forced to support the gcc4x variants so fixing
 this is optional.

-- 
Ticket URL: <https://trac.macports.org/ticket/29345#comment:5>
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