[Debichem-devel] Bug#1013010: openmm: ftbfs with GCC-12

[Matthias Klose]

Package: src:openmm
Version: 7.7.0+dfsg-5
Severity: normal
Tags: sid bookworm
User: debian-gcc at lists.debian.org
Usertags: ftbfs-gcc-12

[This bug is targeted to the upcoming bookworm release]

Please keep this issue open in the bug tracker for the package it
was filed for.  If a fix in another package is required, please
file a bug for the other package (or clone), and add a block in this
package. Please keep the issue open until the package can be built in
a follow-up test rebuild.

The package fails to build in a test rebuild on at least amd64 with
gcc-12/g++-12, but succeeds to build with gcc-11/g++-11. The
severity of this report will be raised before the bookworm release.

The full build log can be found at:
http://qa-logs.debian.net/2022/06/09/gcc12/openmm_7.7.0+dfsg-5_unstable_gcc12.log
The last lines of the build log are at the end of this report.

To build with GCC 11, either set CC=gcc-11 CXX=g++-11 explicitly,
or install the gcc, g++, gfortran, ... packages from experimental.

  apt-get -t=experimental install g++ 

Common build failures are new warnings resulting in build failures with
-Werror turned on, or new/dropped symbols in Debian symbols files.
For other C/C++ related build failures see the porting guide at
http://gcc.gnu.org/gcc-11/porting_to.html

GCC 11 defaults to the GNU++17 standard.  If your package installs
header files in /usr/include, please don't work around C++17 issues
by choosing a lower C++ standard for the package build, but fix these
issues to build with the C++17 standard.

[...]

110: Test command: /<<PKGBUILDDIR>>/obj-x86_64-linux-gnu/TestSplineFitter
110: Test timeout computed to be: 1500
110: Done
103/115 Test #110: TestSplineFitter ..............................   Passed    0.01 sec
test 111
        Start 111: TestSystem

111: Test command: /<<PKGBUILDDIR>>/obj-x86_64-linux-gnu/TestSystem
111: Test timeout computed to be: 1500
111: Done
104/115 Test #111: TestSystem ....................................   Passed    0.00 sec
test 112
        Start 112: TestVectorExpression

112: Test command: /<<PKGBUILDDIR>>/obj-x86_64-linux-gnu/TestVectorExpression
112: Test timeout computed to be: 1500
112: Done
105/115 Test #112: TestVectorExpression ..........................   Passed    0.00 sec
test 113
        Start 113: TestVectorize

113: Test command: /<<PKGBUILDDIR>>/obj-x86_64-linux-gnu/TestVectorize
113: Test timeout computed to be: 1500
113: Done
106/115 Test #113: TestVectorize .................................   Passed    0.00 sec
test 114
        Start 114: TestVectorizeAvx

114: Test command: /<<PKGBUILDDIR>>/obj-x86_64-linux-gnu/TestVectorizeAvx
114: Test timeout computed to be: 1500
114: Done
107/115 Test #114: TestVectorizeAvx ..............................   Passed    0.00 sec
test 115
        Start 115: TestVectorizeAvx2

115: Test command: /<<PKGBUILDDIR>>/obj-x86_64-linux-gnu/TestVectorizeAvx2
115: Test timeout computed to be: 1500
115: Done
108/115 Test #115: TestVectorizeAvx2 .............................   Passed    0.00 sec
41: Done
109/115 Test  #41: TestReferenceVariableLangevinIntegrator .......   Passed   33.21 sec
16: Done
110/115 Test  #16: TestReferenceCustomManyParticleForce ..........   Passed   39.66 sec
72: Done
111/115 Test  #72: TestReferenceDrudeNoseHoover ..................   Passed    8.76 sec
71: Done
112/115 Test  #71: TestReferenceDrudeLangevinIntegrator ..........   Passed   18.51 sec
73: Done
113/115 Test  #73: TestReferenceDrudeSCFIntegrator ...............   Passed   17.15 sec
69: Done
114/115 Test  #69: TestReferenceRpmd .............................   Passed   32.94 sec
17: Done
115/115 Test  #17: TestReferenceCustomNonbondedForce .............   Passed   56.50 sec

98% tests passed, 2 tests failed out of 115

Total Test time (real) =  56.63 sec

The following tests FAILED:
	 99 - TestSerializeNoseHooverIntegrator (SEGFAULT)
	103 - TestSerializeState (SEGFAULT)
Errors while running CTest
make[2]: *** [Makefile:74: test] Error 8
make[2]: Leaving directory '/<<PKGBUILDDIR>>/obj-x86_64-linux-gnu'
dh_auto_test: error: cd obj-x86_64-linux-gnu && make -j8 test ARGS\+=--verbose ARGS\+=-j8 returned exit code 2
make[1]: *** [debian/rules:40: override_dh_auto_test] Error 25
make[1]: Leaving directory '/<<PKGBUILDDIR>>'
make: *** [debian/rules:29: binary] Error 2
dpkg-buildpackage: error: debian/rules binary subprocess returned exit status 2