[Debichem-devel] Bug#1107330: Bug#1107330: openbabel: autopkgtest uses incredible amount of memory on s390x

[Paul Gevers]

Hi

On 6/6/25 18:51, Paul Gevers wrote:
> It seems this doesn't only affect s390x, but ppc64el as well. Added a 
> block on that architecture too.


And now I ran into this on riscv64. The issue seems to be intermittent.

Paul

https://ci.debian.net/packages/o/openbabel/testing/riscv64/67437005/

216s *** Open Babel Warning  in ParseRingBond
216s   Warning: Tetrahedral stereo specified for atom with more than 4 
connections.
216s ==============================
216s *** Open Babel Warning  in ParseSmiles
216s   Failed to kekulize aromatic SMILES
216s
19979s ...terminate called after throwing an instance of 'std::bad_alloc'
19979s   what():  std::bad_alloc
20000s 
/tmp/autopkgtest-lxc.qiiewp51/downtmp/build.cyq/src/debian/tests/python3: 
line 9:  4650 Aborted                    python3 ${TEST}
20001s Ignoring test/testbindings.py on riscv64 ...
20001s Running test/testcdjsonformat.py ...
20001s 
/tmp/autopkgtest-lxc.qiiewp51/downtmp/build.cyq/src/test/testcdjsonformat.py:5: 
SyntaxWarning: invalid escape sequence '\P'
20001s   "C:\Program Files\CMake 2.6\bin\ctest.exe" -C CTestTestfile.cmake
20001s ..........
20001s 
----------------------------------------------------------------------
20001s Ran 10 tests in 0.023s
20001s
20001s OK
20002s Running test/testdistgeom.py ...
20002s 
/tmp/autopkgtest-lxc.qiiewp51/downtmp/build.cyq/src/test/testdistgeom.py:7: 
SyntaxWarning: invalid escape sequence '\P'
20002s   "C:\Program Files\CMake 2.6\bin\ctest.exe" -C CTestTestfile.cmake
20002s /usr/lib/python3.13/subprocess.py:1023: RuntimeWarning: line 
buffering (buffering=1) isn't supported in binary mode, the default 
buffer size will be used
20002s   self.stdin = io.open(p2cwrite, 'wb', bufsize)
20002s /usr/lib/python3.13/subprocess.py:1029: RuntimeWarning: line 
buffering (buffering=1) isn't supported in binary mode, the default 
buffer size will be used
20002s   self.stdout = io.open(c2pread, 'rb', bufsize)
20002s /usr/lib/python3.13/subprocess.py:1034: RuntimeWarning: line 
buffering (buffering=1) isn't supported in binary mode, the default 
buffer size will be used
20002s   self.stderr = io.open(errread, 'rb', bufsize)
20128s autopkgtest [16:24:25]: ERROR: timed out
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