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
--
Andreas Förster
Crystallization and Xray Facility Manager
Centre for Structural Biology
Imperial College London
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