Bug#994474: altree bug fixed but autopkgtest causes Segmentation fault (Was: Bug#994474: please update recommends on openblas)
On Fri, Sep 17, 2021 at 03:40:33PM +0200, Vincent Danjean wrote: > > > altree recommends libopenblas-base, which is a transitional dummy package. > > > Please replace it by libopenblas0. > > > > this is fixed in Git but when rebuilding (with more recent gcc) I get > > I built the package locally, installed it and executed the > debian/tests/run-unit-test manually. > No errors occurred (with gcc from up-to-date unstable, ie > gcc=4:10.2.1-1 and gcc-10=10.3.0-10). > > Did you try with gcc from experimental ? No, I was building in unstable chroot and was executing autopkgtest in the same chroot. I admit salsa-ci did not reproduced my local problem here. Kind regards Andreas. > > > > autopkgtest [12:08:54]: test run-unit-test: [--- > > Analyzing file number 1 > > read done > > Starting tree analysis > > Starting permutations > > /tmp/autopkgtest.BGTBdL/tree/debian/tests/run-unit-test: line 26: 150 > > Segmentation fault altree -i test.res.log -j nb_cas_control.txt -a -t > > SNP -p paup -r 1 --tree-to-analyse 1 -o 1_caco.asso -q qualitative > > autopkgtest [12:08:55]: test run-unit-test: ---] > > autopkgtest [12:08:55]: test run-unit-test: - - - - - - - - - - results - > > - - - - - - - - - > > run-unit-testFAIL non-zero exit status 139 > > > > > > I'd love if someone could have a look > > > > Andreas. > > > > -- http://fam-tille.de
Bug#994474: altree bug fixed but autopkgtest causes Segmentation fault (Was: Bug#994474: please update recommends on openblas)
On 17/09/2021 19:45, Nilesh Patra wrote: On Fri, 17 Sept 2021 at 22:48, Vincent Danjean mailto:vdanj...@debian.org>> wrote: I cannot push to salsa (yet) because I'm not in the Debian-Med groups nor in the members of the altree project. I just requested the Debian-Med group membership on salsa. I'm waiting for approval. Granted access, welcome. Thanks. PS: I made two MR (for master and pristine-tar) if someone wants to see/merge before I gain write access. I think it is much more cleaner if you push directly. Done. Regards, Vincent
Bug#994474: altree bug fixed but autopkgtest causes Segmentation fault (Was: Bug#994474: please update recommends on openblas)
On Fri, 17 Sept 2021 at 22:48, Vincent Danjean wrote: > On 17/09/2021 15:40, Vincent Danjean wrote: > >I built the package locally, installed it and executed the > > debian/tests/run-unit-test manually. > >No errors occurred (with gcc from up-to-date unstable, ie > > gcc=4:10.2.1-1 and gcc-10=10.3.0-10). > > > >Did you try with gcc from experimental ? > >I applied debian patches to upstream where I also fixed a missing > include. Then, I generated a new (upstream) version, updated the Debian > package (fixing the watch file) and upload it. >I cannot push to salsa (yet) because I'm not in the Debian-Med groups > nor in the members of the altree project. I just requested the Debian-Med > group membership on salsa. I'm waiting for approval. > Granted access, welcome. > PS: I made two MR (for master and pristine-tar) if someone wants to > see/merge > before I gain write access. > I think it is much more cleaner if you push directly. Cheers,
Bug#994474: altree bug fixed but autopkgtest causes Segmentation fault (Was: Bug#994474: please update recommends on openblas)
On 17/09/2021 15:40, Vincent Danjean wrote: I built the package locally, installed it and executed the debian/tests/run-unit-test manually. No errors occurred (with gcc from up-to-date unstable, ie gcc=4:10.2.1-1 and gcc-10=10.3.0-10). Did you try with gcc from experimental ? I applied debian patches to upstream where I also fixed a missing include. Then, I generated a new (upstream) version, updated the Debian package (fixing the watch file) and upload it. I cannot push to salsa (yet) because I'm not in the Debian-Med groups nor in the members of the altree project. I just requested the Debian-Med group membership on salsa. I'm waiting for approval. Andreas: can you check if the missing header fix makes autopkg tests to succeed? Regards, Vincent PS: I made two MR (for master and pristine-tar) if someone wants to see/merge before I gain write access. Regards, Vincent autopkgtest [12:08:54]: test run-unit-test: [--- Analyzing file number 1 read done Starting tree analysis Starting permutations /tmp/autopkgtest.BGTBdL/tree/debian/tests/run-unit-test: line 26: 150 Segmentation fault altree -i test.res.log -j nb_cas_control.txt -a -t SNP -p paup -r 1 --tree-to-analyse 1 -o 1_caco.asso -q qualitative autopkgtest [12:08:55]: test run-unit-test: ---] autopkgtest [12:08:55]: test run-unit-test: - - - - - - - - - - results - - - - - - - - - - run-unit-test FAIL non-zero exit status 139 I'd love if someone could have a look Andreas.
Bug#994474: altree bug fixed but autopkgtest causes Segmentation fault (Was: Bug#994474: please update recommends on openblas)
On 17/09/2021 14:15, Andreas Tille wrote: Control: tags -1 pending Hi, On Thu, Sep 16, 2021 at 12:03:44PM +0200, Sébastien Villemot wrote: altree recommends libopenblas-base, which is a transitional dummy package. Please replace it by libopenblas0. this is fixed in Git but when rebuilding (with more recent gcc) I get I built the package locally, installed it and executed the debian/tests/run-unit-test manually. No errors occurred (with gcc from up-to-date unstable, ie gcc=4:10.2.1-1 and gcc-10=10.3.0-10). Did you try with gcc from experimental ? Regards, Vincent autopkgtest [12:08:54]: test run-unit-test: [--- Analyzing file number 1 read done Starting tree analysis Starting permutations /tmp/autopkgtest.BGTBdL/tree/debian/tests/run-unit-test: line 26: 150 Segmentation fault altree -i test.res.log -j nb_cas_control.txt -a -t SNP -p paup -r 1 --tree-to-analyse 1 -o 1_caco.asso -q qualitative autopkgtest [12:08:55]: test run-unit-test: ---] autopkgtest [12:08:55]: test run-unit-test: - - - - - - - - - - results - - - - - - - - - - run-unit-testFAIL non-zero exit status 139 I'd love if someone could have a look Andreas.
Bug#994474: altree bug fixed but autopkgtest causes Segmentation fault (Was: Bug#994474: please update recommends on openblas)
Hi, On 17/09/2021 14:15, Andreas Tille wrote: Control: tags -1 pending Hi, On Thu, Sep 16, 2021 at 12:03:44PM +0200, Sébastien Villemot wrote: altree recommends libopenblas-base, which is a transitional dummy package. Please replace it by libopenblas0. this is fixed in Git but when rebuilding (with more recent gcc) I get autopkgtest [12:08:54]: test run-unit-test: [--- Analyzing file number 1 read done Starting tree analysis Starting permutations /tmp/autopkgtest.BGTBdL/tree/debian/tests/run-unit-test: line 26: 150 Segmentation fault altree -i test.res.log -j nb_cas_control.txt -a -t SNP -p paup -r 1 --tree-to-analyse 1 -o 1_caco.asso -q qualitative autopkgtest [12:08:55]: test run-unit-test: ---] autopkgtest [12:08:55]: test run-unit-test: - - - - - - - - - - results - - - - - - - - - - run-unit-testFAIL non-zero exit status 139 I'd love if someone could have a look I will handle it. Regards, Vincent Andreas.
Bug#994474: altree bug fixed but autopkgtest causes Segmentation fault (Was: Bug#994474: please update recommends on openblas)
Control: tags -1 pending Hi, On Thu, Sep 16, 2021 at 12:03:44PM +0200, Sébastien Villemot wrote: > > altree recommends libopenblas-base, which is a transitional dummy package. > Please replace it by libopenblas0. this is fixed in Git but when rebuilding (with more recent gcc) I get autopkgtest [12:08:54]: test run-unit-test: [--- Analyzing file number 1 read done Starting tree analysis Starting permutations /tmp/autopkgtest.BGTBdL/tree/debian/tests/run-unit-test: line 26: 150 Segmentation fault altree -i test.res.log -j nb_cas_control.txt -a -t SNP -p paup -r 1 --tree-to-analyse 1 -o 1_caco.asso -q qualitative autopkgtest [12:08:55]: test run-unit-test: ---] autopkgtest [12:08:55]: test run-unit-test: - - - - - - - - - - results - - - - - - - - - - run-unit-testFAIL non-zero exit status 139 I'd love if someone could have a look Andreas. -- http://fam-tille.de
