pymol 1.2r2-1.1build1 ftbfs (ICE in set_jump_prob, at stmt.c:2319)

[Matthias Klose]

pymol version 1.2r2-1.1build1 failed to build on i386
Link to failed build: https://launchpad.net/ubuntu/+archive/test-rebuild-20110329/+buildjob/2408152

Direct link to the build log: https://launchpad.net/ubuntu/+archive/test-rebuild-20110329/+buildjob/2408152/+files/buildlog_ubuntu-natty-i386.pymol_1.2r2-1.1build1_FAILEDTOBUILD.txt.gz

This log snippet might be of interest, since it triggered the matcher 'Purging chroot-autobuild'.
Excerpt 1680 lines into the build log:

/usr/include/features.h:214:0: note: this is the location of the previous definition
gcc -pthread -fno-strict-aliasing -DNDEBUG -g -fwrapv -O2 -Wall -Wstrict-prototypes -g -O2 -fPIC -D_PYMOL_MODULE -D_PYMOL_INLINE -D_PYMOL_FREETYPE -D_PYMOL_LIBPNG -D_PYMOL_OPENGL_SHADERS -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 -I/usr/include/python2.7 -c layer1/Scene.c -o build/temp.linux-i686-2.7/layer1/Scene.o -ffast-math -funroll-loops -O3
In file included from /usr/include/python2.7/Python.h:8:0,
                 from layer0/os_python.h:30,
                 from layer1/Scene.c:21:
/usr/include/python2.7/pyconfig.h:1155:0: warning: "_POSIX_C_SOURCE" redefined
/usr/include/features.h:214:0: note: this is the location of the previous definition
layer1/Scene.c: In function 'SceneClick':
layer1/Scene.c:4557:11: internal compiler error: in set_jump_prob, at stmt.c:2319
Please submit a full bug report,
with preprocessed source if appropriate.
See <file:///usr/share/doc/gcc-4.5/README.Bugs> for instructions.
error: command 'gcc' failed with exit status 1
make: *** [build-stamp] Error 1
dpkg-buildpackage: error: debian/rules build gave error exit status 2
******************************************************************************
Build finished at 20110408-1521
FAILED [dpkg-buildpackage died]
Purging chroot-autobuild/build/buildd/pymol-1.2r2

[Matthias Klose (doko)]

fails with both gcc-4.5 and gcc-4.6 in oneiric with -O1 or higher, builds ok with these compilers in unstable

$ gcc -c -O2 Scene.i
layer1/Scene.c: In function 'SceneClick':
layer1/Scene.c:4557:11: internal compiler error: in set_jump_prob, at stmt.c:2319
Please submit a full bug report,
with preprocessed source if appropriate.

[Matthias Klose (doko)]

build with trunk 20110424, so either an Ubuntu specific configure option, or fixed

[jocko (jomnal00)]

This problem still happens when trying to build pymol in natty (gcc-4.5 v. 4.5.2-8ubuntu4 and the pymol source from svn or from the ubuntu source package), see http://ubuntuforums.org/showthread.php?t=1756545.
I have found a temporary workaround by building with gcc-4.4, but I'm guessing from reading this bug report that there is a fix in an upstream version of gcc-4.5...

[Matthias Klose (doko)]

now builds on i386, fails on amd64:

Finished at 20110502-2128
Build needed 00:06:57, 124592k disk space
Function `findPath' implicitly converted to pointer at layer4/Cmd.c:8561

Our automated build log filter detected the problem(s) above that will
likely cause your package to segfault on architectures where the size of
a pointer is greater than the size of an integer, such as ia64 and amd64.

This is often due to a missing function prototype definition.

[Matthias Klose (doko)]

fixed at least in gcc-4.6

[Steve Langasek (vorlon)]

build failure in a universe package; canonical-foundations is not the right assignee for this.

[Matthias Klose (doko)]

the synced 1.4.1-1 did build