Attachment 256757 Details for Bug 348291 – /var/tmp/portage/sci-chemistry/pymol-1.3.1_pre3925-r1/temp/build.log

/var/tmp/portage/sci-chemistry/pymol-1.3.1_pre3925-r1/temp/build.log

build.log (text/plain), 39.74 KB, created by Alexey Shvetsov on 2010-12-09 18:10:06 UTC

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Description:

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Creator: Alexey Shvetsov

Created: 2010-12-09 18:10:06 UTC

Size: 39.74 KB

patch

obsolete

>[32;01m * [39;49;00mPackage:    sci-chemistry/pymol-1.3.1_pre3925-r1
>[32;01m * [39;49;00mRepository: gentoo
>[32;01m * [39;49;00mMaintainer: jlec@gentoo.org sci-chemistry@gentoo.org
>[32;01m * [39;49;00mUSE:  amd64 apbs elibc_glibc kernel_linux multilib numpy shaders userland_GNU vmd
>>>> Unpacking source...
>>>> Unpacking pymol-1.3.1_pre3925-r1.tar.gz to /var/tmp/portage/sci-chemistry/pymol-1.3.1_pre3925-r1/work
>>>> Source unpacked in /var/tmp/portage/sci-chemistry/pymol-1.3.1_pre3925-r1/work
>>>> Preparing source in /var/tmp/portage/sci-chemistry/pymol-1.3.1_pre3925-r1/work/pymol ...
> [32;01m*[0m Applying 1.2.2-data-path.patch ...
>[A[172C [34;01m[ [32;01mok[34;01m ][0m
> [32;01m*[0m Applying 1.2.2-prefix.patch ...
>[A[172C [34;01m[ [32;01mok[34;01m ][0m
> [32;01m*[0m Adjusting to prefix /
> [32;01m*[0m   setup.py ...
>[A[172C [34;01m[ [32;01mok[34;01m ][0m
> [32;01m*[0m Applying nosplash-gentoo.patch ...
>[A[172C [34;01m[ [32;01mok[34;01m ][0m
> [32;01m*[0m Applying pymol-1.2.2-shaders.patch ...
>[A[172C [34;01m[ [32;01mok[34;01m ][0m
> [32;01m*[0m Applying 1.3.0-vmd.patch ...
>[A[172C [34;01m[ [32;01mok[34;01m ][0m
>>>> Source prepared.
>>>> Configuring source in /var/tmp/portage/sci-chemistry/pymol-1.3.1_pre3925-r1/work/pymol ...
>>>> Source configured.
>>>> Compiling source in /var/tmp/portage/sci-chemistry/pymol-1.3.1_pre3925-r1/work/pymol ...
> * Building of sci-chemistry/pymol-1.3.1_pre3925-r1 with CPython 2.6...
>python2.6 setup.py build -b build-2.6
>running build
>running build_py
>creating build-2.6
>creating build-2.6/lib.linux-x86_64-2.6
>creating build-2.6/lib.linux-x86_64-2.6/chempy
>copying modules/chempy/protein.py -> build-2.6/lib.linux-x86_64-2.6/chempy
>copying modules/chempy/io.py -> build-2.6/lib.linux-x86_64-2.6/chempy
>copying modules/chempy/brick.py -> build-2.6/lib.linux-x86_64-2.6/chempy
>copying modules/chempy/protein_amber99.py -> build-2.6/lib.linux-x86_64-2.6/chempy
>copying modules/chempy/charge.py -> build-2.6/lib.linux-x86_64-2.6/chempy
>copying modules/chempy/mass.py -> build-2.6/lib.linux-x86_64-2.6/chempy
>copying modules/chempy/protein_residues.py -> build-2.6/lib.linux-x86_64-2.6/chempy
>copying modules/chempy/arc.py -> build-2.6/lib.linux-x86_64-2.6/chempy
>copying modules/chempy/cc1.py -> build-2.6/lib.linux-x86_64-2.6/chempy
>copying modules/chempy/water_residues.py -> build-2.6/lib.linux-x86_64-2.6/chempy
>copying modules/chempy/models.py -> build-2.6/lib.linux-x86_64-2.6/chempy
>copying modules/chempy/cex.py -> build-2.6/lib.linux-x86_64-2.6/chempy
>copying modules/chempy/cif.py -> build-2.6/lib.linux-x86_64-2.6/chempy
>copying modules/chempy/cpv.py -> build-2.6/lib.linux-x86_64-2.6/chempy
>copying modules/chempy/water_amber.py -> build-2.6/lib.linux-x86_64-2.6/chempy
>copying modules/chempy/gms.py -> build-2.6/lib.linux-x86_64-2.6/chempy
>copying modules/chempy/solvate.py -> build-2.6/lib.linux-x86_64-2.6/chempy
>copying modules/chempy/mae.py -> build-2.6/lib.linux-x86_64-2.6/chempy
>copying modules/chempy/map.py -> build-2.6/lib.linux-x86_64-2.6/chempy
>copying modules/chempy/lst.py -> build-2.6/lib.linux-x86_64-2.6/chempy
>copying modules/chempy/mmd.py -> build-2.6/lib.linux-x86_64-2.6/chempy
>copying modules/chempy/mol.py -> build-2.6/lib.linux-x86_64-2.6/chempy
>copying modules/chempy/pdb.py -> build-2.6/lib.linux-x86_64-2.6/chempy
>copying modules/chempy/pkl.py -> build-2.6/lib.linux-x86_64-2.6/chempy
>copying modules/chempy/protein_mmff.py -> build-2.6/lib.linux-x86_64-2.6/chempy
>copying modules/chempy/sdf.py -> build-2.6/lib.linux-x86_64-2.6/chempy
>copying modules/chempy/place.py -> build-2.6/lib.linux-x86_64-2.6/chempy
>copying modules/chempy/bond_mmff.py -> build-2.6/lib.linux-x86_64-2.6/chempy
>copying modules/chempy/xyz.py -> build-2.6/lib.linux-x86_64-2.6/chempy
>copying modules/chempy/protein_amber.py -> build-2.6/lib.linux-x86_64-2.6/chempy
>copying modules/chempy/dictdb.py -> build-2.6/lib.linux-x86_64-2.6/chempy
>copying modules/chempy/neighbor.py -> build-2.6/lib.linux-x86_64-2.6/chempy
>copying modules/chempy/gamess1.py -> build-2.6/lib.linux-x86_64-2.6/chempy
>copying modules/chempy/bonds.py -> build-2.6/lib.linux-x86_64-2.6/chempy
>copying modules/chempy/__init__.py -> build-2.6/lib.linux-x86_64-2.6/chempy
>copying modules/chempy/hetatm.py -> build-2.6/lib.linux-x86_64-2.6/chempy
>copying modules/chempy/bond_amber.py -> build-2.6/lib.linux-x86_64-2.6/chempy
>creating build-2.6/lib.linux-x86_64-2.6/chempy/bmin
>copying modules/chempy/bmin/commands.py -> build-2.6/lib.linux-x86_64-2.6/chempy/bmin
>copying modules/chempy/bmin/state.py -> build-2.6/lib.linux-x86_64-2.6/chempy/bmin
>copying modules/chempy/bmin/util.py -> build-2.6/lib.linux-x86_64-2.6/chempy/bmin
>copying modules/chempy/bmin/__init__.py -> build-2.6/lib.linux-x86_64-2.6/chempy/bmin
>copying modules/chempy/bmin/realtime.py -> build-2.6/lib.linux-x86_64-2.6/chempy/bmin
>creating build-2.6/lib.linux-x86_64-2.6/chempy/champ
>copying modules/chempy/champ/assign.py -> build-2.6/lib.linux-x86_64-2.6/chempy/champ
>copying modules/chempy/champ/amber99.py -> build-2.6/lib.linux-x86_64-2.6/chempy/champ
>copying modules/chempy/champ/formal_charges.py -> build-2.6/lib.linux-x86_64-2.6/chempy/champ
>copying modules/chempy/champ/__init__.py -> build-2.6/lib.linux-x86_64-2.6/chempy/champ
>creating build-2.6/lib.linux-x86_64-2.6/chempy/fast
>copying modules/chempy/fast/__init__.py -> build-2.6/lib.linux-x86_64-2.6/chempy/fast
>creating build-2.6/lib.linux-x86_64-2.6/chempy/fragments
>copying modules/chempy/fragments/__init__.py -> build-2.6/lib.linux-x86_64-2.6/chempy/fragments
>creating build-2.6/lib.linux-x86_64-2.6/chempy/tinker
>copying modules/chempy/tinker/state.py -> build-2.6/lib.linux-x86_64-2.6/chempy/tinker
>copying modules/chempy/tinker/amber.py -> build-2.6/lib.linux-x86_64-2.6/chempy/tinker
>copying modules/chempy/tinker/__init__.py -> build-2.6/lib.linux-x86_64-2.6/chempy/tinker
>copying modules/chempy/tinker/realtime.py -> build-2.6/lib.linux-x86_64-2.6/chempy/tinker
>copying modules/chempy/tinker/keyword.py -> build-2.6/lib.linux-x86_64-2.6/chempy/tinker
>creating build-2.6/lib.linux-x86_64-2.6/pmg_tk
>copying modules/pmg_tk/Demo.py -> build-2.6/lib.linux-x86_64-2.6/pmg_tk
>copying modules/pmg_tk/Setting.py -> build-2.6/lib.linux-x86_64-2.6/pmg_tk
>copying modules/pmg_tk/SetEditor.py -> build-2.6/lib.linux-x86_64-2.6/pmg_tk
>copying modules/pmg_tk/ColorEditor.py -> build-2.6/lib.linux-x86_64-2.6/pmg_tk
>copying modules/pmg_tk/PMGApp.py -> build-2.6/lib.linux-x86_64-2.6/pmg_tk
>copying modules/pmg_tk/__init__.py -> build-2.6/lib.linux-x86_64-2.6/pmg_tk
>creating build-2.6/lib.linux-x86_64-2.6/pmg_tk/startup
>copying modules/pmg_tk/startup/remote_pdb_load.py -> build-2.6/lib.linux-x86_64-2.6/pmg_tk/startup
>copying modules/pmg_tk/startup/__init__.py -> build-2.6/lib.linux-x86_64-2.6/pmg_tk/startup
>creating build-2.6/lib.linux-x86_64-2.6/pmg_tk/skins
>copying modules/pmg_tk/skins/__init__.py -> build-2.6/lib.linux-x86_64-2.6/pmg_tk/skins
>creating build-2.6/lib.linux-x86_64-2.6/pmg_tk/skins/normal
>copying modules/pmg_tk/skins/normal/builder.py -> build-2.6/lib.linux-x86_64-2.6/pmg_tk/skins/normal
>copying modules/pmg_tk/skins/normal/__init__.py -> build-2.6/lib.linux-x86_64-2.6/pmg_tk/skins/normal
>creating build-2.6/lib.linux-x86_64-2.6/pmg_wx
>copying modules/pmg_wx/__init__.py -> build-2.6/lib.linux-x86_64-2.6/pmg_wx
>creating build-2.6/lib.linux-x86_64-2.6/pymol
>copying modules/pymol/creating.py -> build-2.6/lib.linux-x86_64-2.6/pymol
>copying modules/pymol/povray.py -> build-2.6/lib.linux-x86_64-2.6/pymol
>copying modules/pymol/experimenting.py -> build-2.6/lib.linux-x86_64-2.6/pymol
>copying modules/pymol/parser.py -> build-2.6/lib.linux-x86_64-2.6/pymol
>copying modules/pymol/moving.py -> build-2.6/lib.linux-x86_64-2.6/pymol
>copying modules/pymol/xray.py -> build-2.6/lib.linux-x86_64-2.6/pymol
>copying modules/pymol/internal.py -> build-2.6/lib.linux-x86_64-2.6/pymol
>copying modules/pymol/parsing.py -> build-2.6/lib.linux-x86_64-2.6/pymol
>copying modules/pymol/xwin.py -> build-2.6/lib.linux-x86_64-2.6/pymol
>copying modules/pymol/editor.py -> build-2.6/lib.linux-x86_64-2.6/pymol
>copying modules/pymol/helping.py -> build-2.6/lib.linux-x86_64-2.6/pymol
>copying modules/pymol/monitoring.py -> build-2.6/lib.linux-x86_64-2.6/pymol
>copying modules/pymol/selecting.py -> build-2.6/lib.linux-x86_64-2.6/pymol
>copying modules/pymol/checking.py -> build-2.6/lib.linux-x86_64-2.6/pymol
>copying modules/pymol/menu.py -> build-2.6/lib.linux-x86_64-2.6/pymol
>copying modules/pymol/externing.py -> build-2.6/lib.linux-x86_64-2.6/pymol
>copying modules/pymol/selector.py -> build-2.6/lib.linux-x86_64-2.6/pymol
>copying modules/pymol/importing.py -> build-2.6/lib.linux-x86_64-2.6/pymol
>copying modules/pymol/api.py -> build-2.6/lib.linux-x86_64-2.6/pymol
>copying modules/pymol/cgo.py -> build-2.6/lib.linux-x86_64-2.6/pymol
>copying modules/pymol/cmd.py -> build-2.6/lib.linux-x86_64-2.6/pymol
>copying modules/pymol/preset.py -> build-2.6/lib.linux-x86_64-2.6/pymol
>copying modules/pymol/feedingback.py -> build-2.6/lib.linux-x86_64-2.6/pymol
>copying modules/pymol/fitting.py -> build-2.6/lib.linux-x86_64-2.6/pymol
>copying modules/pymol/constants.py -> build-2.6/lib.linux-x86_64-2.6/pymol
>copying modules/pymol/callback.py -> build-2.6/lib.linux-x86_64-2.6/pymol
>copying modules/pymol/gui.py -> build-2.6/lib.linux-x86_64-2.6/pymol
>copying modules/pymol/commanding.py -> build-2.6/lib.linux-x86_64-2.6/pymol
>copying modules/pymol/m4x.py -> build-2.6/lib.linux-x86_64-2.6/pymol
>copying modules/pymol/setting.py -> build-2.6/lib.linux-x86_64-2.6/pymol
>copying modules/pymol/completing.py -> build-2.6/lib.linux-x86_64-2.6/pymol
>copying modules/pymol/movie.py -> build-2.6/lib.linux-x86_64-2.6/pymol
>copying modules/pymol/invocation.py -> build-2.6/lib.linux-x86_64-2.6/pymol
>copying modules/pymol/vfont.py -> build-2.6/lib.linux-x86_64-2.6/pymol
>copying modules/pymol/rpc.py -> build-2.6/lib.linux-x86_64-2.6/pymol
>copying modules/pymol/keywords.py -> build-2.6/lib.linux-x86_64-2.6/pymol
>copying modules/pymol/wizarding.py -> build-2.6/lib.linux-x86_64-2.6/pymol
>copying modules/pymol/util.py -> build-2.6/lib.linux-x86_64-2.6/pymol
>copying modules/pymol/editing.py -> build-2.6/lib.linux-x86_64-2.6/pymol
>copying modules/pymol/keyboard.py -> build-2.6/lib.linux-x86_64-2.6/pymol
>copying modules/pymol/locking.py -> build-2.6/lib.linux-x86_64-2.6/pymol
>copying modules/pymol/computing.py -> build-2.6/lib.linux-x86_64-2.6/pymol
>copying modules/pymol/controlling.py -> build-2.6/lib.linux-x86_64-2.6/pymol
>copying modules/pymol/__init__.py -> build-2.6/lib.linux-x86_64-2.6/pymol
>copying modules/pymol/querying.py -> build-2.6/lib.linux-x86_64-2.6/pymol
>copying modules/pymol/viewing.py -> build-2.6/lib.linux-x86_64-2.6/pymol
>copying modules/pymol/exporting.py -> build-2.6/lib.linux-x86_64-2.6/pymol
>copying modules/pymol/shortcut.py -> build-2.6/lib.linux-x86_64-2.6/pymol
>creating build-2.6/lib.linux-x86_64-2.6/pymol/contrib
>copying modules/pymol/contrib/__init__.py -> build-2.6/lib.linux-x86_64-2.6/pymol/contrib
>creating build-2.6/lib.linux-x86_64-2.6/pymol/opengl
>copying modules/pymol/opengl/__init__.py -> build-2.6/lib.linux-x86_64-2.6/pymol/opengl
>creating build-2.6/lib.linux-x86_64-2.6/pymol/opengl/gl
>copying modules/pymol/opengl/gl/glconst.py -> build-2.6/lib.linux-x86_64-2.6/pymol/opengl/gl
>copying modules/pymol/opengl/gl/__init__.py -> build-2.6/lib.linux-x86_64-2.6/pymol/opengl/gl
>creating build-2.6/lib.linux-x86_64-2.6/pymol/opengl/glu
>copying modules/pymol/opengl/glu/gluconst.py -> build-2.6/lib.linux-x86_64-2.6/pymol/opengl/glu
>copying modules/pymol/opengl/glu/__init__.py -> build-2.6/lib.linux-x86_64-2.6/pymol/opengl/glu
>creating build-2.6/lib.linux-x86_64-2.6/pymol/opengl/glut
>copying modules/pymol/opengl/glut/__init__.py -> build-2.6/lib.linux-x86_64-2.6/pymol/opengl/glut
>copying modules/pymol/opengl/glut/glutconst.py -> build-2.6/lib.linux-x86_64-2.6/pymol/opengl/glut
>creating build-2.6/lib.linux-x86_64-2.6/pymol/wizard
>copying modules/pymol/wizard/measurement.py -> build-2.6/lib.linux-x86_64-2.6/pymol/wizard
>copying modules/pymol/wizard/demo.py -> build-2.6/lib.linux-x86_64-2.6/pymol/wizard
>copying modules/pymol/wizard/message.py -> build-2.6/lib.linux-x86_64-2.6/pymol/wizard
>copying modules/pymol/wizard/benchmark.py -> build-2.6/lib.linux-x86_64-2.6/pymol/wizard
>copying modules/pymol/wizard/dragging.py -> build-2.6/lib.linux-x86_64-2.6/pymol/wizard
>copying modules/pymol/wizard/distance.py -> build-2.6/lib.linux-x86_64-2.6/pymol/wizard
>copying modules/pymol/wizard/filter.py -> build-2.6/lib.linux-x86_64-2.6/pymol/wizard
>copying modules/pymol/wizard/charge.py -> build-2.6/lib.linux-x86_64-2.6/pymol/wizard
>copying modules/pymol/wizard/box.py -> build-2.6/lib.linux-x86_64-2.6/pymol/wizard
>copying modules/pymol/wizard/pair_fit.py -> build-2.6/lib.linux-x86_64-2.6/pymol/wizard
>copying modules/pymol/wizard/annotation.py -> build-2.6/lib.linux-x86_64-2.6/pymol/wizard
>copying modules/pymol/wizard/fedora.py -> build-2.6/lib.linux-x86_64-2.6/pymol/wizard
>copying modules/pymol/wizard/stereodemo.py -> build-2.6/lib.linux-x86_64-2.6/pymol/wizard
>copying modules/pymol/wizard/label.py -> build-2.6/lib.linux-x86_64-2.6/pymol/wizard
>copying modules/pymol/wizard/cleanup.py -> build-2.6/lib.linux-x86_64-2.6/pymol/wizard
>copying modules/pymol/wizard/renaming.py -> build-2.6/lib.linux-x86_64-2.6/pymol/wizard
>copying modules/pymol/wizard/pseudoatom.py -> build-2.6/lib.linux-x86_64-2.6/pymol/wizard
>copying modules/pymol/wizard/mutagenesis.py -> build-2.6/lib.linux-x86_64-2.6/pymol/wizard
>copying modules/pymol/wizard/appearance.py -> build-2.6/lib.linux-x86_64-2.6/pymol/wizard
>copying modules/pymol/wizard/__init__.py -> build-2.6/lib.linux-x86_64-2.6/pymol/wizard
>copying modules/pymol/wizard/density.py -> build-2.6/lib.linux-x86_64-2.6/pymol/wizard
>copying modules/pymol/wizard/sculpting.py -> build-2.6/lib.linux-x86_64-2.6/pymol/wizard
>copying modules/pymol/wizard/toggle.py -> build-2.6/lib.linux-x86_64-2.6/pymol/wizard
>copying modules/pymol/wizard/security.py -> build-2.6/lib.linux-x86_64-2.6/pymol/wizard
>warning: build_py: byte-compiling is disabled, skipping.
>running build_ext
>building 'pymol._cmd' extension
>creating build-2.6/temp.linux-x86_64-2.6
>creating build-2.6/temp.linux-x86_64-2.6/modules
>creating build-2.6/temp.linux-x86_64-2.6/modules/cealign
>creating build-2.6/temp.linux-x86_64-2.6/modules/cealign/src
>creating build-2.6/temp.linux-x86_64-2.6/ov
>creating build-2.6/temp.linux-x86_64-2.6/ov/src
>creating build-2.6/temp.linux-x86_64-2.6/layer0
>creating build-2.6/temp.linux-x86_64-2.6/layer1
>creating build-2.6/temp.linux-x86_64-2.6/layer2
>creating build-2.6/temp.linux-x86_64-2.6/layer3
>creating build-2.6/temp.linux-x86_64-2.6/layer4
>creating build-2.6/temp.linux-x86_64-2.6/layer5
>creating build-2.6/temp.linux-x86_64-2.6/contrib
>creating build-2.6/temp.linux-x86_64-2.6/contrib/uiuc
>creating build-2.6/temp.linux-x86_64-2.6/contrib/uiuc/plugins
>creating build-2.6/temp.linux-x86_64-2.6/contrib/uiuc/plugins/molfile_plugin
>creating build-2.6/temp.linux-x86_64-2.6/contrib/uiuc/plugins/molfile_plugin/src
>x86_64-pc-linux-gnu-g++ -pthread -O2 -ggdb -pipe -march=native -mtune=native -mfpmath=sse -msse4 -floop-interchange -floop-strip-mine -floop-block -fPIC -D_PYMOL_MODULE -D_PYMOL_INLINE -D_PYMOL_FREETYPE -D_PYMOL_LIBPNG -D_PYMOL_OPENGL_SHADERS -D_PYMOL_NUMPY -D_PYMOL_VMD_PLUGINS -Iov/src -Ilayer0 -Ilayer1 -Ilayer2 -Ilayer3 -Ilayer4 -Ilayer5 -I/usr/include/freetype2 -Icontrib/uiuc/plugins/include -Icontrib/uiuc/plugins/molfile_plugin/src -Imodules/cealign/src -Imodules/cealign/src/tnt -I/usr/include/python2.6 -c modules/cealign/src/ccealignmodule.cpp -o build-2.6/temp.linux-x86_64-2.6/modules/cealign/src/ccealignmodule.o
>In file included from /usr/include/python2.6/Python.h:8:0,
>                 from layer0/os_python.h:30,
>                 from modules/cealign/src/ccealignmodule.H:57,
>                 from modules/cealign/src/ccealignmodule.cpp:32:
>/usr/include/python2.6/pyconfig.h:1067:0: warning: "_POSIX_C_SOURCE" redefined
>/usr/include/features.h:162:0: note: this is the location of the previous definition
>/usr/include/python2.6/pyconfig.h:1079:0: warning: "_XOPEN_SOURCE" redefined
>/usr/include/features.h:164:0: note: this is the location of the previous definition
>x86_64-pc-linux-gnu-gcc -pthread -O2 -ggdb -pipe -march=native -mtune=native -mfpmath=sse -msse4 -floop-interchange -floop-strip-mine -floop-block -fPIC -D_PYMOL_MODULE -D_PYMOL_INLINE -D_PYMOL_FREETYPE -D_PYMOL_LIBPNG -D_PYMOL_OPENGL_SHADERS -D_PYMOL_NUMPY -D_PYMOL_VMD_PLUGINS -Iov/src -Ilayer0 -Ilayer1 -Ilayer2 -Ilayer3 -Ilayer4 -Ilayer5 -I/usr/include/freetype2 -Icontrib/uiuc/plugins/include -Icontrib/uiuc/plugins/molfile_plugin/src -Imodules/cealign/src -Imodules/cealign/src/tnt -I/usr/include/python2.6 -c ov/src/OVContext.c -o build-2.6/temp.linux-x86_64-2.6/ov/src/OVContext.o
>x86_64-pc-linux-gnu-gcc -pthread -O2 -ggdb -pipe -march=native -mtune=native -mfpmath=sse -msse4 -floop-interchange -floop-strip-mine -floop-block -fPIC -D_PYMOL_MODULE -D_PYMOL_INLINE -D_PYMOL_FREETYPE -D_PYMOL_LIBPNG -D_PYMOL_OPENGL_SHADERS -D_PYMOL_NUMPY -D_PYMOL_VMD_PLUGINS -Iov/src -Ilayer0 -Ilayer1 -Ilayer2 -Ilayer3 -Ilayer4 -Ilayer5 -I/usr/include/freetype2 -Icontrib/uiuc/plugins/include -Icontrib/uiuc/plugins/molfile_plugin/src -Imodules/cealign/src -Imodules/cealign/src/tnt -I/usr/include/python2.6 -c ov/src/OVHeapArray.c -o build-2.6/temp.linux-x86_64-2.6/ov/src/OVHeapArray.o
>x86_64-pc-linux-gnu-gcc -pthread -O2 -ggdb -pipe -march=native -mtune=native -mfpmath=sse -msse4 -floop-interchange -floop-strip-mine -floop-block -fPIC -D_PYMOL_MODULE -D_PYMOL_INLINE -D_PYMOL_FREETYPE -D_PYMOL_LIBPNG -D_PYMOL_OPENGL_SHADERS -D_PYMOL_NUMPY -D_PYMOL_VMD_PLUGINS -Iov/src -Ilayer0 -Ilayer1 -Ilayer2 -Ilayer3 -Ilayer4 -Ilayer5 -I/usr/include/freetype2 -Icontrib/uiuc/plugins/include -Icontrib/uiuc/plugins/molfile_plugin/src -Imodules/cealign/src -Imodules/cealign/src/tnt -I/usr/include/python2.6 -c ov/src/OVHeap.c -o build-2.6/temp.linux-x86_64-2.6/ov/src/OVHeap.o
>x86_64-pc-linux-gnu-gcc -pthread -O2 -ggdb -pipe -march=native -mtune=native -mfpmath=sse -msse4 -floop-interchange -floop-strip-mine -floop-block -fPIC -D_PYMOL_MODULE -D_PYMOL_INLINE -D_PYMOL_FREETYPE -D_PYMOL_LIBPNG -D_PYMOL_OPENGL_SHADERS -D_PYMOL_NUMPY -D_PYMOL_VMD_PLUGINS -Iov/src -Ilayer0 -Ilayer1 -Ilayer2 -Ilayer3 -Ilayer4 -Ilayer5 -I/usr/include/freetype2 -Icontrib/uiuc/plugins/include -Icontrib/uiuc/plugins/molfile_plugin/src -Imodules/cealign/src -Imodules/cealign/src/tnt -I/usr/include/python2.6 -c ov/src/OVLexicon.c -o build-2.6/temp.linux-x86_64-2.6/ov/src/OVLexicon.o
>x86_64-pc-linux-gnu-gcc -pthread -O2 -ggdb -pipe -march=native -mtune=native -mfpmath=sse -msse4 -floop-interchange -floop-strip-mine -floop-block -fPIC -D_PYMOL_MODULE -D_PYMOL_INLINE -D_PYMOL_FREETYPE -D_PYMOL_LIBPNG -D_PYMOL_OPENGL_SHADERS -D_PYMOL_NUMPY -D_PYMOL_VMD_PLUGINS -Iov/src -Ilayer0 -Ilayer1 -Ilayer2 -Ilayer3 -Ilayer4 -Ilayer5 -I/usr/include/freetype2 -Icontrib/uiuc/plugins/include -Icontrib/uiuc/plugins/molfile_plugin/src -Imodules/cealign/src -Imodules/cealign/src/tnt -I/usr/include/python2.6 -c ov/src/OVOneToOne.c -o build-2.6/temp.linux-x86_64-2.6/ov/src/OVOneToOne.o
>ov/src/OVOneToOne.c: In function âOVOneToOne_Dumpâ:
>ov/src/OVOneToOne.c:87:17: warning: format â%dâ expects type âintâ, but argument 4 has type âov_wordâ
>ov/src/OVOneToOne.c:87:17: warning: format â%dâ expects type âintâ, but argument 6 has type âov_wordâ
>x86_64-pc-linux-gnu-gcc -pthread -O2 -ggdb -pipe -march=native -mtune=native -mfpmath=sse -msse4 -floop-interchange -floop-strip-mine -floop-block -fPIC -D_PYMOL_MODULE -D_PYMOL_INLINE -D_PYMOL_FREETYPE -D_PYMOL_LIBPNG -D_PYMOL_OPENGL_SHADERS -D_PYMOL_NUMPY -D_PYMOL_VMD_PLUGINS -Iov/src -Ilayer0 -Ilayer1 -Ilayer2 -Ilayer3 -Ilayer4 -Ilayer5 -I/usr/include/freetype2 -Icontrib/uiuc/plugins/include -Icontrib/uiuc/plugins/molfile_plugin/src -Imodules/cealign/src -Imodules/cealign/src/tnt -I/usr/include/python2.6 -c ov/src/OVOneToAny.c -o build-2.6/temp.linux-x86_64-2.6/ov/src/OVOneToAny.o
>x86_64-pc-linux-gnu-gcc -pthread -O2 -ggdb -pipe -march=native -mtune=native -mfpmath=sse -msse4 -floop-interchange -floop-strip-mine -floop-block -fPIC -D_PYMOL_MODULE -D_PYMOL_INLINE -D_PYMOL_FREETYPE -D_PYMOL_LIBPNG -D_PYMOL_OPENGL_SHADERS -D_PYMOL_NUMPY -D_PYMOL_VMD_PLUGINS -Iov/src -Ilayer0 -Ilayer1 -Ilayer2 -Ilayer3 -Ilayer4 -Ilayer5 -I/usr/include/freetype2 -Icontrib/uiuc/plugins/include -Icontrib/uiuc/plugins/molfile_plugin/src -Imodules/cealign/src -Imodules/cealign/src/tnt -I/usr/include/python2.6 -c ov/src/OVRandom.c -o build-2.6/temp.linux-x86_64-2.6/ov/src/OVRandom.o
>x86_64-pc-linux-gnu-gcc -pthread -O2 -ggdb -pipe -march=native -mtune=native -mfpmath=sse -msse4 -floop-interchange -floop-strip-mine -floop-block -fPIC -D_PYMOL_MODULE -D_PYMOL_INLINE -D_PYMOL_FREETYPE -D_PYMOL_LIBPNG -D_PYMOL_OPENGL_SHADERS -D_PYMOL_NUMPY -D_PYMOL_VMD_PLUGINS -Iov/src -Ilayer0 -Ilayer1 -Ilayer2 -Ilayer3 -Ilayer4 -Ilayer5 -I/usr/include/freetype2 -Icontrib/uiuc/plugins/include -Icontrib/uiuc/plugins/molfile_plugin/src -Imodules/cealign/src -Imodules/cealign/src/tnt -I/usr/include/python2.6 -c ov/src/ov_utility.c -o build-2.6/temp.linux-x86_64-2.6/ov/src/ov_utility.o
>x86_64-pc-linux-gnu-gcc -pthread -O2 -ggdb -pipe -march=native -mtune=native -mfpmath=sse -msse4 -floop-interchange -floop-strip-mine -floop-block -fPIC -D_PYMOL_MODULE -D_PYMOL_INLINE -D_PYMOL_FREETYPE -D_PYMOL_LIBPNG -D_PYMOL_OPENGL_SHADERS -D_PYMOL_NUMPY -D_PYMOL_VMD_PLUGINS -Iov/src -Ilayer0 -Ilayer1 -Ilayer2 -Ilayer3 -Ilayer4 -Ilayer5 -I/usr/include/freetype2 -Icontrib/uiuc/plugins/include -Icontrib/uiuc/plugins/molfile_plugin/src -Imodules/cealign/src -Imodules/cealign/src/tnt -I/usr/include/python2.6 -c layer0/Block.c -o build-2.6/temp.linux-x86_64-2.6/layer0/Block.o
>In file included from /usr/include/python2.6/Python.h:8:0,
>                 from layer0/os_python.h:30,
>                 from layer5/main.h:36,
>                 from layer0/Block.c:22:
>/usr/include/python2.6/pyconfig.h:1067:0: warning: "_POSIX_C_SOURCE" redefined
>/usr/include/features.h:213:0: note: this is the location of the previous definition
>x86_64-pc-linux-gnu-gcc -pthread -O2 -ggdb -pipe -march=native -mtune=native -mfpmath=sse -msse4 -floop-interchange -floop-strip-mine -floop-block -fPIC -D_PYMOL_MODULE -D_PYMOL_INLINE -D_PYMOL_FREETYPE -D_PYMOL_LIBPNG -D_PYMOL_OPENGL_SHADERS -D_PYMOL_NUMPY -D_PYMOL_VMD_PLUGINS -Iov/src -Ilayer0 -Ilayer1 -Ilayer2 -Ilayer3 -Ilayer4 -Ilayer5 -I/usr/include/freetype2 -Icontrib/uiuc/plugins/include -Icontrib/uiuc/plugins/molfile_plugin/src -Imodules/cealign/src -Imodules/cealign/src/tnt -I/usr/include/python2.6 -c layer0/Crystal.c -o build-2.6/temp.linux-x86_64-2.6/layer0/Crystal.o
>In file included from /usr/include/python2.6/Python.h:8:0,
>                 from layer0/os_python.h:30,
>                 from layer1/Setting.h:20,
>                 from layer1/CGO.h:22,
>                 from layer0/Crystal.c:23:
>/usr/include/python2.6/pyconfig.h:1067:0: warning: "_POSIX_C_SOURCE" redefined
>/usr/include/features.h:213:0: note: this is the location of the previous definition
>x86_64-pc-linux-gnu-gcc -pthread -O2 -ggdb -pipe -march=native -mtune=native -mfpmath=sse -msse4 -floop-interchange -floop-strip-mine -floop-block -fPIC -D_PYMOL_MODULE -D_PYMOL_INLINE -D_PYMOL_FREETYPE -D_PYMOL_LIBPNG -D_PYMOL_OPENGL_SHADERS -D_PYMOL_NUMPY -D_PYMOL_VMD_PLUGINS -Iov/src -Ilayer0 -Ilayer1 -Ilayer2 -Ilayer3 -Ilayer4 -Ilayer5 -I/usr/include/freetype2 -Icontrib/uiuc/plugins/include -Icontrib/uiuc/plugins/molfile_plugin/src -Imodules/cealign/src -Imodules/cealign/src/tnt -I/usr/include/python2.6 -c layer0/Debug.c -o build-2.6/temp.linux-x86_64-2.6/layer0/Debug.o
>x86_64-pc-linux-gnu-gcc -pthread -O2 -ggdb -pipe -march=native -mtune=native -mfpmath=sse -msse4 -floop-interchange -floop-strip-mine -floop-block -fPIC -D_PYMOL_MODULE -D_PYMOL_INLINE -D_PYMOL_FREETYPE -D_PYMOL_LIBPNG -D_PYMOL_OPENGL_SHADERS -D_PYMOL_NUMPY -D_PYMOL_VMD_PLUGINS -Iov/src -Ilayer0 -Ilayer1 -Ilayer2 -Ilayer3 -Ilayer4 -Ilayer5 -I/usr/include/freetype2 -Icontrib/uiuc/plugins/include -Icontrib/uiuc/plugins/molfile_plugin/src -Imodules/cealign/src -Imodules/cealign/src/tnt -I/usr/include/python2.6 -c layer0/Deferred.c -o build-2.6/temp.linux-x86_64-2.6/layer0/Deferred.o
>x86_64-pc-linux-gnu-gcc -pthread -O2 -ggdb -pipe -march=native -mtune=native -mfpmath=sse -msse4 -floop-interchange -floop-strip-mine -floop-block -fPIC -D_PYMOL_MODULE -D_PYMOL_INLINE -D_PYMOL_FREETYPE -D_PYMOL_LIBPNG -D_PYMOL_OPENGL_SHADERS -D_PYMOL_NUMPY -D_PYMOL_VMD_PLUGINS -Iov/src -Ilayer0 -Ilayer1 -Ilayer2 -Ilayer3 -Ilayer4 -Ilayer5 -I/usr/include/freetype2 -Icontrib/uiuc/plugins/include -Icontrib/uiuc/plugins/molfile_plugin/src -Imodules/cealign/src -Imodules/cealign/src/tnt -I/usr/include/python2.6 -c layer0/Err.c -o build-2.6/temp.linux-x86_64-2.6/layer0/Err.o
>x86_64-pc-linux-gnu-gcc -pthread -O2 -ggdb -pipe -march=native -mtune=native -mfpmath=sse -msse4 -floop-interchange -floop-strip-mine -floop-block -fPIC -D_PYMOL_MODULE -D_PYMOL_INLINE -D_PYMOL_FREETYPE -D_PYMOL_LIBPNG -D_PYMOL_OPENGL_SHADERS -D_PYMOL_NUMPY -D_PYMOL_VMD_PLUGINS -Iov/src -Ilayer0 -Ilayer1 -Ilayer2 -Ilayer3 -Ilayer4 -Ilayer5 -I/usr/include/freetype2 -Icontrib/uiuc/plugins/include -Icontrib/uiuc/plugins/molfile_plugin/src -Imodules/cealign/src -Imodules/cealign/src/tnt -I/usr/include/python2.6 -c layer0/Feedback.c -o build-2.6/temp.linux-x86_64-2.6/layer0/Feedback.o
>x86_64-pc-linux-gnu-gcc -pthread -O2 -ggdb -pipe -march=native -mtune=native -mfpmath=sse -msse4 -floop-interchange -floop-strip-mine -floop-block -fPIC -D_PYMOL_MODULE -D_PYMOL_INLINE -D_PYMOL_FREETYPE -D_PYMOL_LIBPNG -D_PYMOL_OPENGL_SHADERS -D_PYMOL_NUMPY -D_PYMOL_VMD_PLUGINS -Iov/src -Ilayer0 -Ilayer1 -Ilayer2 -Ilayer3 -Ilayer4 -Ilayer5 -I/usr/include/freetype2 -Icontrib/uiuc/plugins/include -Icontrib/uiuc/plugins/molfile_plugin/src -Imodules/cealign/src -Imodules/cealign/src/tnt -I/usr/include/python2.6 -c layer0/Field.c -o build-2.6/temp.linux-x86_64-2.6/layer0/Field.o
>In file included from /usr/include/python2.6/Python.h:8:0,
>                 from layer0/os_python.h:30,
>                 from layer1/PConv.h:20,
>                 from layer0/Field.c:24:
>/usr/include/python2.6/pyconfig.h:1067:0: warning: "_POSIX_C_SOURCE" redefined
>/usr/include/features.h:213:0: note: this is the location of the previous definition
>x86_64-pc-linux-gnu-gcc -pthread -O2 -ggdb -pipe -march=native -mtune=native -mfpmath=sse -msse4 -floop-interchange -floop-strip-mine -floop-block -fPIC -D_PYMOL_MODULE -D_PYMOL_INLINE -D_PYMOL_FREETYPE -D_PYMOL_LIBPNG -D_PYMOL_OPENGL_SHADERS -D_PYMOL_NUMPY -D_PYMOL_VMD_PLUGINS -Iov/src -Ilayer0 -Ilayer1 -Ilayer2 -Ilayer3 -Ilayer4 -Ilayer5 -I/usr/include/freetype2 -Icontrib/uiuc/plugins/include -Icontrib/uiuc/plugins/molfile_plugin/src -Imodules/cealign/src -Imodules/cealign/src/tnt -I/usr/include/python2.6 -c layer0/Isosurf.c -o build-2.6/temp.linux-x86_64-2.6/layer0/Isosurf.o
>In file included from /usr/include/python2.6/Python.h:8:0,
>                 from layer0/os_python.h:30,
>                 from layer1/Setting.h:20,
>                 from layer1/CGO.h:22,
>                 from layer0/Crystal.h:22,
>                 from layer1/Symmetry.h:20,
>                 from layer0/Isosurf.h:23,
>                 from layer0/Isosurf.c:25:
>/usr/include/python2.6/pyconfig.h:1067:0: warning: "_POSIX_C_SOURCE" redefined
>/usr/include/features.h:213:0: note: this is the location of the previous definition
>x86_64-pc-linux-gnu-gcc -pthread -O2 -ggdb -pipe -march=native -mtune=native -mfpmath=sse -msse4 -floop-interchange -floop-strip-mine -floop-block -fPIC -D_PYMOL_MODULE -D_PYMOL_INLINE -D_PYMOL_FREETYPE -D_PYMOL_LIBPNG -D_PYMOL_OPENGL_SHADERS -D_PYMOL_NUMPY -D_PYMOL_VMD_PLUGINS -Iov/src -Ilayer0 -Ilayer1 -Ilayer2 -Ilayer3 -Ilayer4 -Ilayer5 -I/usr/include/freetype2 -Icontrib/uiuc/plugins/include -Icontrib/uiuc/plugins/molfile_plugin/src -Imodules/cealign/src -Imodules/cealign/src/tnt -I/usr/include/python2.6 -c layer0/Map.c -o build-2.6/temp.linux-x86_64-2.6/layer0/Map.o
>In file included from /usr/include/python2.6/Python.h:8:0,
>                 from layer0/os_python.h:30,
>                 from layer1/Setting.h:20,
>                 from layer0/Map.c:25:
>/usr/include/python2.6/pyconfig.h:1067:0: warning: "_POSIX_C_SOURCE" redefined
>/usr/include/features.h:213:0: note: this is the location of the previous definition
>x86_64-pc-linux-gnu-gcc -pthread -O2 -ggdb -pipe -march=native -mtune=native -mfpmath=sse -msse4 -floop-interchange -floop-strip-mine -floop-block -fPIC -D_PYMOL_MODULE -D_PYMOL_INLINE -D_PYMOL_FREETYPE -D_PYMOL_LIBPNG -D_PYMOL_OPENGL_SHADERS -D_PYMOL_NUMPY -D_PYMOL_VMD_PLUGINS -Iov/src -Ilayer0 -Ilayer1 -Ilayer2 -Ilayer3 -Ilayer4 -Ilayer5 -I/usr/include/freetype2 -Icontrib/uiuc/plugins/include -Icontrib/uiuc/plugins/molfile_plugin/src -Imodules/cealign/src -Imodules/cealign/src/tnt -I/usr/include/python2.6 -c layer0/Match.c -o build-2.6/temp.linux-x86_64-2.6/layer0/Match.o
>x86_64-pc-linux-gnu-gcc -pthread -O2 -ggdb -pipe -march=native -mtune=native -mfpmath=sse -msse4 -floop-interchange -floop-strip-mine -floop-block -fPIC -D_PYMOL_MODULE -D_PYMOL_INLINE -D_PYMOL_FREETYPE -D_PYMOL_LIBPNG -D_PYMOL_OPENGL_SHADERS -D_PYMOL_NUMPY -D_PYMOL_VMD_PLUGINS -Iov/src -Ilayer0 -Ilayer1 -Ilayer2 -Ilayer3 -Ilayer4 -Ilayer5 -I/usr/include/freetype2 -Icontrib/uiuc/plugins/include -Icontrib/uiuc/plugins/molfile_plugin/src -Imodules/cealign/src -Imodules/cealign/src/tnt -I/usr/include/python2.6 -c layer0/Matrix.c -o build-2.6/temp.linux-x86_64-2.6/layer0/Matrix.o
>In file included from /usr/include/python2.6/Python.h:8:0,
>                 from layer0/os_python.h:30,
>                 from layer1/Setting.h:20,
>                 from layer0/Matrix.c:28:
>/usr/include/python2.6/pyconfig.h:1067:0: warning: "_POSIX_C_SOURCE" redefined
>/usr/include/features.h:213:0: note: this is the location of the previous definition
>x86_64-pc-linux-gnu-gcc -pthread -O2 -ggdb -pipe -march=native -mtune=native -mfpmath=sse -msse4 -floop-interchange -floop-strip-mine -floop-block -fPIC -D_PYMOL_MODULE -D_PYMOL_INLINE -D_PYMOL_FREETYPE -D_PYMOL_LIBPNG -D_PYMOL_OPENGL_SHADERS -D_PYMOL_NUMPY -D_PYMOL_VMD_PLUGINS -Iov/src -Ilayer0 -Ilayer1 -Ilayer2 -Ilayer3 -Ilayer4 -Ilayer5 -I/usr/include/freetype2 -Icontrib/uiuc/plugins/include -Icontrib/uiuc/plugins/molfile_plugin/src -Imodules/cealign/src -Imodules/cealign/src/tnt -I/usr/include/python2.6 -c layer0/MemoryDebug.c -o build-2.6/temp.linux-x86_64-2.6/layer0/MemoryDebug.o
>x86_64-pc-linux-gnu-gcc -pthread -O2 -ggdb -pipe -march=native -mtune=native -mfpmath=sse -msse4 -floop-interchange -floop-strip-mine -floop-block -fPIC -D_PYMOL_MODULE -D_PYMOL_INLINE -D_PYMOL_FREETYPE -D_PYMOL_LIBPNG -D_PYMOL_OPENGL_SHADERS -D_PYMOL_NUMPY -D_PYMOL_VMD_PLUGINS -Iov/src -Ilayer0 -Ilayer1 -Ilayer2 -Ilayer3 -Ilayer4 -Ilayer5 -I/usr/include/freetype2 -Icontrib/uiuc/plugins/include -Icontrib/uiuc/plugins/molfile_plugin/src -Imodules/cealign/src -Imodules/cealign/src/tnt -I/usr/include/python2.6 -c layer0/MemoryCache.c -o build-2.6/temp.linux-x86_64-2.6/layer0/MemoryCache.o
>x86_64-pc-linux-gnu-gcc -pthread -O2 -ggdb -pipe -march=native -mtune=native -mfpmath=sse -msse4 -floop-interchange -floop-strip-mine -floop-block -fPIC -D_PYMOL_MODULE -D_PYMOL_INLINE -D_PYMOL_FREETYPE -D_PYMOL_LIBPNG -D_PYMOL_OPENGL_SHADERS -D_PYMOL_NUMPY -D_PYMOL_VMD_PLUGINS -Iov/src -Ilayer0 -Ilayer1 -Ilayer2 -Ilayer3 -Ilayer4 -Ilayer5 -I/usr/include/freetype2 -Icontrib/uiuc/plugins/include -Icontrib/uiuc/plugins/molfile_plugin/src -Imodules/cealign/src -Imodules/cealign/src/tnt -I/usr/include/python2.6 -c layer0/MyPNG.c -o build-2.6/temp.linux-x86_64-2.6/layer0/MyPNG.o
>In file included from /usr/include/python2.6/Python.h:8:0,
>                 from layer0/os_python.h:30,
>                 from layer1/Setting.h:20,
>                 from layer0/MyPNG.c:59:
>/usr/include/python2.6/pyconfig.h:1067:0: warning: "_POSIX_C_SOURCE" redefined
>/usr/include/features.h:213:0: note: this is the location of the previous definition
>x86_64-pc-linux-gnu-gcc -pthread -O2 -ggdb -pipe -march=native -mtune=native -mfpmath=sse -msse4 -floop-interchange -floop-strip-mine -floop-block -fPIC -D_PYMOL_MODULE -D_PYMOL_INLINE -D_PYMOL_FREETYPE -D_PYMOL_LIBPNG -D_PYMOL_OPENGL_SHADERS -D_PYMOL_NUMPY -D_PYMOL_VMD_PLUGINS -Iov/src -Ilayer0 -Ilayer1 -Ilayer2 -Ilayer3 -Ilayer4 -Ilayer5 -I/usr/include/freetype2 -Icontrib/uiuc/plugins/include -Icontrib/uiuc/plugins/molfile_plugin/src -Imodules/cealign/src -Imodules/cealign/src/tnt -I/usr/include/python2.6 -c layer0/Parse.c -o build-2.6/temp.linux-x86_64-2.6/layer0/Parse.o
>x86_64-pc-linux-gnu-gcc -pthread -O2 -ggdb -pipe -march=native -mtune=native -mfpmath=sse -msse4 -floop-interchange -floop-strip-mine -floop-block -fPIC -D_PYMOL_MODULE -D_PYMOL_INLINE -D_PYMOL_FREETYPE -D_PYMOL_LIBPNG -D_PYMOL_OPENGL_SHADERS -D_PYMOL_NUMPY -D_PYMOL_VMD_PLUGINS -Iov/src -Ilayer0 -Ilayer1 -Ilayer2 -Ilayer3 -Ilayer4 -Ilayer5 -I/usr/include/freetype2 -Icontrib/uiuc/plugins/include -Icontrib/uiuc/plugins/molfile_plugin/src -Imodules/cealign/src -Imodules/cealign/src/tnt -I/usr/include/python2.6 -c layer0/Pixmap.c -o build-2.6/temp.linux-x86_64-2.6/layer0/Pixmap.o
>x86_64-pc-linux-gnu-gcc -pthread -O2 -ggdb -pipe -march=native -mtune=native -mfpmath=sse -msse4 -floop-interchange -floop-strip-mine -floop-block -fPIC -D_PYMOL_MODULE -D_PYMOL_INLINE -D_PYMOL_FREETYPE -D_PYMOL_LIBPNG -D_PYMOL_OPENGL_SHADERS -D_PYMOL_NUMPY -D_PYMOL_VMD_PLUGINS -Iov/src -Ilayer0 -Ilayer1 -Ilayer2 -Ilayer3 -Ilayer4 -Ilayer5 -I/usr/include/freetype2 -Icontrib/uiuc/plugins/include -Icontrib/uiuc/plugins/molfile_plugin/src -Imodules/cealign/src -Imodules/cealign/src/tnt -I/usr/include/python2.6 -c layer0/Queue.c -o build-2.6/temp.linux-x86_64-2.6/layer0/Queue.o
>x86_64-pc-linux-gnu-gcc -pthread -O2 -ggdb -pipe -march=native -mtune=native -mfpmath=sse -msse4 -floop-interchange -floop-strip-mine -floop-block -fPIC -D_PYMOL_MODULE -D_PYMOL_INLINE -D_PYMOL_FREETYPE -D_PYMOL_LIBPNG -D_PYMOL_OPENGL_SHADERS -D_PYMOL_NUMPY -D_PYMOL_VMD_PLUGINS -Iov/src -Ilayer0 -Ilayer1 -Ilayer2 -Ilayer3 -Ilayer4 -Ilayer5 -I/usr/include/freetype2 -Icontrib/uiuc/plugins/include -Icontrib/uiuc/plugins/molfile_plugin/src -Imodules/cealign/src -Imodules/cealign/src/tnt -I/usr/include/python2.6 -c layer0/Raw.c -o build-2.6/temp.linux-x86_64-2.6/layer0/Raw.o
>x86_64-pc-linux-gnu-gcc -pthread -O2 -ggdb -pipe -march=native -mtune=native -mfpmath=sse -msse4 -floop-interchange -floop-strip-mine -floop-block -fPIC -D_PYMOL_MODULE -D_PYMOL_INLINE -D_PYMOL_FREETYPE -D_PYMOL_LIBPNG -D_PYMOL_OPENGL_SHADERS -D_PYMOL_NUMPY -D_PYMOL_VMD_PLUGINS -Iov/src -Ilayer0 -Ilayer1 -Ilayer2 -Ilayer3 -Ilayer4 -Ilayer5 -I/usr/include/freetype2 -Icontrib/uiuc/plugins/include -Icontrib/uiuc/plugins/molfile_plugin/src -Imodules/cealign/src -Imodules/cealign/src/tnt -I/usr/include/python2.6 -c layer0/Sphere.c -o build-2.6/temp.linux-x86_64-2.6/layer0/Sphere.o
>x86_64-pc-linux-gnu-gcc -pthread -O2 -ggdb -pipe -march=native -mtune=native -mfpmath=sse -msse4 -floop-interchange -floop-strip-mine -floop-block -fPIC -D_PYMOL_MODULE -D_PYMOL_INLINE -D_PYMOL_FREETYPE -D_PYMOL_LIBPNG -D_PYMOL_OPENGL_SHADERS -D_PYMOL_NUMPY -D_PYMOL_VMD_PLUGINS -Iov/src -Ilayer0 -Ilayer1 -Ilayer2 -Ilayer3 -Ilayer4 -Ilayer5 -I/usr/include/freetype2 -Icontrib/uiuc/plugins/include -Icontrib/uiuc/plugins/molfile_plugin/src -Imodules/cealign/src -Imodules/cealign/src/tnt -I/usr/include/python2.6 -c layer0/Tetsurf.c -o build-2.6/temp.linux-x86_64-2.6/layer0/Tetsurf.o
>In file included from /usr/include/python2.6/Python.h:8:0,
>                 from layer0/os_python.h:30,
>                 from layer1/Setting.h:20,
>                 from layer1/CGO.h:22,
>                 from layer0/Crystal.h:22,
>                 from layer1/Symmetry.h:20,
>                 from layer0/Isosurf.h:23,
>                 from layer0/Tetsurf.c:22:
>/usr/include/python2.6/pyconfig.h:1067:0: warning: "_POSIX_C_SOURCE" redefined
>/usr/include/features.h:213:0: note: this is the location of the previous definition
>x86_64-pc-linux-gnu-gcc -pthread -O2 -ggdb -pipe -march=native -mtune=native -mfpmath=sse -msse4 -floop-interchange -floop-strip-mine -floop-block -fPIC -D_PYMOL_MODULE -D_PYMOL_INLINE -D_PYMOL_FREETYPE -D_PYMOL_LIBPNG -D_PYMOL_OPENGL_SHADERS -D_PYMOL_NUMPY -D_PYMOL_VMD_PLUGINS -Iov/src -Ilayer0 -Ilayer1 -Ilayer2 -Ilayer3 -Ilayer4 -Ilayer5 -I/usr/include/freetype2 -Icontrib/uiuc/plugins/include -Icontrib/uiuc/plugins/molfile_plugin/src -Imodules/cealign/src -Imodules/cealign/src/tnt -I/usr/include/python2.6 -c layer0/Texture.c -o build-2.6/temp.linux-x86_64-2.6/layer0/Texture.o
>In file included from /usr/include/python2.6/Python.h:8:0,
>                 from layer0/os_python.h:30,
>                 from layer1/Setting.h:20,
>                 from layer0/Texture.c:29:
>/usr/include/python2.6/pyconfig.h:1067:0: warning: "_POSIX_C_SOURCE" redefined
>/usr/include/features.h:213:0: note: this is the location of the previous definition
>x86_64-pc-linux-gnu-gcc -pthread -O2 -ggdb -pipe -march=native -mtune=native -mfpmath=sse -msse4 -floop-interchange -floop-strip-mine -floop-block -fPIC -D_PYMOL_MODULE -D_PYMOL_INLINE -D_PYMOL_FREETYPE -D_PYMOL_LIBPNG -D_PYMOL_OPENGL_SHADERS -D_PYMOL_NUMPY -D_PYMOL_VMD_PLUGINS -Iov/src -Ilayer0 -Ilayer1 -Ilayer2 -Ilayer3 -Ilayer4 -Ilayer5 -I/usr/include/freetype2 -Icontrib/uiuc/plugins/include -Icontrib/uiuc/plugins/molfile_plugin/src -Imodules/cealign/src -Imodules/cealign/src/tnt -I/usr/include/python2.6 -c layer0/Tracker.c -o build-2.6/temp.linux-x86_64-2.6/layer0/Tracker.o
>x86_64-pc-linux-gnu-gcc -pthread -O2 -ggdb -pipe -march=native -mtune=native -mfpmath=sse -msse4 -floop-interchange -floop-strip-mine -floop-block -fPIC -D_PYMOL_MODULE -D_PYMOL_INLINE -D_PYMOL_FREETYPE -D_PYMOL_LIBPNG -D_PYMOL_OPENGL_SHADERS -D_PYMOL_NUMPY -D_PYMOL_VMD_PLUGINS -Iov/src -Ilayer0 -Ilayer1 -Ilayer2 -Ilayer3 -Ilayer4 -Ilayer5 -I/usr/include/freetype2 -Icontrib/uiuc/plugins/include -Icontrib/uiuc/plugins/molfile_plugin/src -Imodules/cealign/src -Imodules/cealign/src/tnt -I/usr/include/python2.6 -c layer0/Triangle.c -o build-2.6/temp.linux-x86_64-2.6/layer0/Triangle.o
>In file included from /usr/include/python2.6/Python.h:8:0,
>                 from layer0/os_python.h:30,
>                 from layer1/Setting.h:20,
>                 from layer0/Triangle.c:38:
>/usr/include/python2.6/pyconfig.h:1067:0: warning: "_POSIX_C_SOURCE" redefined
>/usr/include/features.h:213:0: note: this is the location of the previous definition
>x86_64-pc-linux-gnu-gcc -pthread -O2 -ggdb -pipe -march=native -mtune=native -mfpmath=sse -msse4 -floop-interchange -floop-strip-mine -floop-block -fPIC -D_PYMOL_MODULE -D_PYMOL_INLINE -D_PYMOL_FREETYPE -D_PYMOL_LIBPNG -D_PYMOL_OPENGL_SHADERS -D_PYMOL_NUMPY -D_PYMOL_VMD_PLUGINS -Iov/src -Ilayer0 -Ilayer1 -Ilayer2 -Ilayer3 -Ilayer4 -Ilayer5 -I/usr/include/freetype2 -Icontrib/uiuc/plugins/include -Icontrib/uiuc/plugins/molfile_plugin/src -Imodules/cealign/src -Imodules/cealign/src/tnt -I/usr/include/python2.6 -c layer0/Util.c -o build-2.6/temp.linux-x86_64-2.6/layer0/Util.o
>layer0/Util.c: In function âUtilArrayCallocâ:
>layer0/Util.c:241:7: internal compiler error: in graphite_loop_normal_form, at graphite-sese-to-poly.c:2847
>Please submit a full bug report,
>with preprocessed source if appropriate.
>See <http://bugs.gentoo.org/> for instructions.
>error: command 'x86_64-pc-linux-gnu-gcc' failed with exit status 1
> [31;01m*[0m ERROR: sci-chemistry/pymol-1.3.1_pre3925-r1 failed:
> [31;01m*[0m   Building failed with CPython 2.6 in distutils_building() function
> [31;01m*[0m 
> [31;01m*[0m Call stack:
> [31;01m*[0m     ebuild.sh, line   56:  Called src_compile
> [31;01m*[0m   environment, line 4849:  Called distutils_src_compile
> [31;01m*[0m   environment, line 1356:  Called python_execute_function 'distutils_building'
> [31;01m*[0m   environment, line 3597:  Called die
> [31;01m*[0m The specific snippet of code:
> [31;01m*[0m                       die "${failure_message}";
> [31;01m*[0m 
> [31;01m*[0m If you need support, post the output of 'emerge --info =sci-chemistry/pymol-1.3.1_pre3925-r1',
> [31;01m*[0m the complete build log and the output of 'emerge -pqv =sci-chemistry/pymol-1.3.1_pre3925-r1'.
> [31;01m*[0m The complete build log is located at '/var/tmp/portage/sci-chemistry/pymol-1.3.1_pre3925-r1/temp/build.log'.
> [31;01m*[0m The ebuild environment file is located at '/var/tmp/portage/sci-chemistry/pymol-1.3.1_pre3925-r1/temp/environment'.
> [31;01m*[0m S: '/var/tmp/portage/sci-chemistry/pymol-1.3.1_pre3925-r1/work/pymol'

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