Hi Andreas, I recently made a small change regarding numpy support. Can you please send me the output of the following command:
ls /usr/lib64/python2.6/site-packages/numpy/core/include/numpy Meanwhile, just disable numpy support by removing the try/except block in setup.py line 221. Thanks, Thomas Andreas Förster wrote, On 07/23/13 11:05: > Dear all, > > I'm installing PyMOL from svn on a RHEL 6.2 machine. This has always > worked. Today, I get an "command 'gcc' failed with exit status 1" error > (see below). > > Any suggestions? Is there something amiss with the source? > > Thanks. > > Andreas > > gcc -pthread -fno-strict-aliasing -O2 -g -pipe -Wall > -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector > --param=ssp-buffer-size=4 -m64 -mtune=generic -D_GNU_SOURCE -fPIC > -fwrapv -DNDEBUG -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions > -fstack-protector --param=ssp-buffer-size=4 -m64 -mtune=generic > -D_GNU_SOURCE -fPIC -fwrapv -fPIC -D_PYMOL_VMD_PLUGINS -D_PYMOL_LIBPNG > -D_PYMOL_FREETYPE -D_PYMOL_INLINE -D_PYMOL_OPENGL_SHADERS -DNO_MMLIBS > -D_PYMOL_CGO_DRAWARRAYS -D_PYMOL_CGO_DRAWBUFFERS -D_CGO_DRAWARRAYS > -D_PYMOL_GL_CALLLISTS -DOPENGL_ES_2 -D_PYMOL_NUMPY -Iov/src -Ilayer0 > -Ilayer1 -Ilayer2 -Ilayer3 -Ilayer4 -Ilayer5 -Imodules/cealign/src > -Imodules/cealign/src/tnt -Ibuild/generated > -Icontrib/uiuc/plugins/include -Icontrib/uiuc/plugins/molfile_plugin/src > -I/usr/lib64/python2.6/site-packages/numpy/core/include -I/usr/include > -I/usr/include/freetype2 -I/usr/include/python2.6 -c layer3/Executive.c > -o build/temp.linux-x86_64-2.6/layer3/Executive.o -ffast-math > -funroll-loops -O3 -fcommon > layer2/ObjectMap.c:42:32: error: numpy/ndarraytypes.h: No such file or > directory > layer2/ObjectMap.c:43: error: expected ‘=’, ‘,’, ‘;’, ‘asm’ or > ‘__attribute__’ before ‘MyArrayObject’ > layer2/ObjectMap.c: In function ‘ObjectMapNumPyArrayToMapState’: > layer2/ObjectMap.c:5555: error: ‘MyArrayObject’ undeclared (first use in > this function) > layer2/ObjectMap.c:5555: error: (Each undeclared identifier is reported > only once > layer2/ObjectMap.c:5555: error: for each function it appears in.) > layer2/ObjectMap.c:5555: error: ‘pao’ undeclared (first use in this > function) > layer2/ObjectMap.c:5559: error: expected expression before ‘)’ token > error: command 'gcc' failed with exit status 1 > gcc -pthread -fno-strict-aliasing -O2 -g -pipe -Wall > -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector > --param=ssp-buffer-size=4 -m64 -mtune=generic -D_GNU_SOURCE -fPIC > -fwrapv -DNDEBUG -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions > -fstack-protector --param=ssp-buffer-size=4 -m64 -mtune=generic > -D_GNU_SOURCE -fPIC -fwrapv -fPIC -D_PYMOL_VMD_PLUGINS -D_PYMOL_LIBPNG > -D_PYMOL_FREETYPE -D_PYMOL_INLINE -D_PYMOL_OPENGL_SHADERS -DNO_MMLIBS > -D_PYMOL_CGO_DRAWARRAYS -D_PYMOL_CGO_DRAWBUFFERS -D_CGO_DRAWARRAYS > -D_PYMOL_GL_CALLLISTS -DOPENGL_ES_2 -D_PYMOL_NUMPY -Iov/src -Ilayer0 > -Ilayer1 -Ilayer2 -Ilayer3 -Ilayer4 -Ilayer5 -Imodules/cealign/src > -Imodules/cealign/src/tnt -Ibuild/generated > -Icontrib/uiuc/plugins/include -Icontrib/uiuc/plugins/molfile_plugin/src > -I/usr/lib64/python2.6/site-packages/numpy/core/include -I/usr/include > -I/usr/include/freetype2 -I/usr/include/python2.6 -c layer4/Export.c -o > build/temp.linux-x86_64-2.6/layer4/Export.o -ffast-math -funroll-loops > -O3 -fcommon > csbadmin@csb6 in pymol-src: layer2/RepSurface.c: In function > ‘SurfaceJobRun’: > layer2/RepSurface.c:4506: warning: ‘solv_map’ may be used uninitialized > in this function > layer1/CGO.c: In function ‘CGOOptimizeGLSLCylindersToVBOIndexedImpl’: > layer1/CGO.c:4344: warning: ‘org_colorVals’ may be used uninitialized in > this function > layer1/CGO.c:4337: warning: ‘col2[1]’ may be used uninitialized in this > function > layer1/CGO.c:4337: warning: ‘col2[2]’ may be used uninitialized in this > function > layer1/CGO.c: In function ‘CGOProcessCGOtoArrays’: > layer1/CGO.c:2815: warning: ‘normalValsDA’ may be used uninitialized in > this function > layer1/CGO.c:2815: warning: ‘accessibilityValsDA’ may be used > uninitialized in this function > layer1/CGO.c:2816: warning: ‘pickColorValsDA’ may be used uninitialized > in this function > layer1/CGO.c: In function ‘CGORenderGL’: > layer1/CGO.c:7954: warning: ‘normalVals_tmp’ may be used uninitialized > in this function > layer1/CGO.c: In function ‘CGOOptimizeToVBONotIndexedWithReturnedData’: > layer1/CGO.c:3371: warning: ‘normalValsDA’ may be used uninitialized in > this function > layer1/CGO.c:3372: warning: ‘pickColorValsDA’ may be used uninitialized > in this function > layer1/CGO.c: In function ‘CGORenderRay’: > layer1/CGO.c:6185: warning: ‘vertexVals’ may be used uninitialized in > this function > layer1/CGO.c: In function ‘CGOSimplify’: > layer1/CGO.c:5136: warning: ‘normalVals’ may be used uninitialized in > this function -- Thomas Holder PyMOL Developer Schrödinger Contractor ------------------------------------------------------------------------------ See everything from the browser to the database with AppDynamics Get end-to-end visibility with application monitoring from AppDynamics Isolate bottlenecks and diagnose root cause in seconds. 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