Bug#906796: [Debian-science-sagemath] Bug#906796: sagemath: Sage crashes at startup (segfault in pari modules)
On 08/23/2018 12:57 AM, Julian Rüth wrote: > * Tobias Hansen [2018-08-21 10:13:26 +0200]: >> - fix at least the 24 failing sagemath doctests in >> sage/repl/ipython_kernel/install.py [1] > This is already fixed upstream. I created > https://salsa.debian.org/science-team/sagemath/merge_requests/7 for the > necessary changes. > > julian > Thanks everyone for helping out! I uploaded the fixed fpylll and gfan versions and merged this fix. Julian, you mentioned that the sagemath build was failing. That was because I changed the package to use eclib 20180815 which led to problems. I reverted that commit, going back to eclib 20171002 and it should build now. With your patch, there are still 16 failing doctests in sage/repl/ipython_kernel/install.py. The next problem is the FTBFS of flint-arb 2.14. Best, Tobias
Bug#906796: [Debian-science-sagemath] Bug#906796: sagemath: Sage crashes at startup (segfault in pari modules)
* Tobias Hansen [2018-08-21 10:13:26 +0200]: > - fix at least the 24 failing sagemath doctests in > sage/repl/ipython_kernel/install.py [1] This is already fixed upstream. I created https://salsa.debian.org/science-team/sagemath/merge_requests/7 for the necessary changes. julian
Bug#906796: [Debian-science-sagemath] Bug#906796: sagemath: Sage crashes at startup (segfault in pari modules)
On 08/21/2018 05:41 AM, Doug Torrance wrote: On 08/21/2018 04:13 AM, Tobias Hansen wrote: Control: block -1 by 905434 905300 This is expected after a major pari update. sagemath 8.3 is almost ready to be uploaded, major things we have to do: - fix build failures in fpylll and gfan - fix at least the 24 failing sagemath doctests in sage/repl/ipython_kernel/install.py [1] If gfan 0.6.2 can't be fixed we could still use version 0.5... I forwarded the gfan build failure upstream a few weeks ago but haven't gotten a response yet. I've tried debugging it on my own but haven't figured anything out yet. The build failure is from a test failing on 32-bit architectures. We could always just skip that test on those architectures for a short-term fix. I can work on that later. I've pushed some commits to git doing the above [1]. Would anyone be able to take a look and sponsor? A quick rundown of what I did: (Perhaps there's a better way?) gfan gets the list of all the tests to run from the subdirectories in the testsuites directory. Using dpkg-architecture, we remove the directories of the two failing tests only on 32-bit. We were already skipping a test which failed on 32-bit, but removed the directory using quilt. That wouldn't work with the new test because one of the files in the directory was empty and quilt wouldn't deal with it. Plus it would be nice to run these tests on 64-bit anyway. So I just got rid of that patch and now we remove both directories in d/rules. Doug [1] https://salsa.debian.org/science-team/gfan
Bug#906796: [Debian-science-sagemath] Bug#906796: sagemath: Sage crashes at startup (segfault in pari modules)
On 08/21/2018 04:13 AM, Tobias Hansen wrote: Control: block -1 by 905434 905300 This is expected after a major pari update. sagemath 8.3 is almost ready to be uploaded, major things we have to do: - fix build failures in fpylll and gfan - fix at least the 24 failing sagemath doctests in sage/repl/ipython_kernel/install.py [1] If gfan 0.6.2 can't be fixed we could still use version 0.5... I forwarded the gfan build failure upstream a few weeks ago but haven't gotten a response yet. I've tried debugging it on my own but haven't figured anything out yet. The build failure is from a test failing on 32-bit architectures. We could always just skip that test on those architectures for a short-term fix. I can work on that later. Doug
Bug#906796: sagemath: Sage crashes at startup (segfault in pari modules)
Control: block -1 by 905434 905300 This is expected after a major pari update. sagemath 8.3 is almost ready to be uploaded, major things we have to do: - fix build failures in fpylll and gfan - fix at least the 24 failing sagemath doctests in sage/repl/ipython_kernel/install.py [1] If gfan 0.6.2 can't be fixed we could still use version 0.5... [1] https://people.debian.org/~thansen/sage-test-status-experimental.html On 08/21/2018 09:00 AM, Giovanni Mascellani wrote: > Package: sagemath > Version: 8.2-5 > Severity: important > > Dear Maintainer, > > when I start sage, it immediately crashes with the attached crash > report. Before running sage I removed the directories .ipython, .sage > and .local/lib/python* (which I discovered contained some Python modules > that were executed by sage upon startup). > > The end of the crash report seems to mention a segmentation fault in > some pari module, but I am not able to extract more information from it. > > Thanks, Giovanni. > > > -- System Information: > Debian Release: buster/sid > APT prefers unstable-debug > APT policy: (500, 'unstable-debug'), (500, 'unstable'), (500, 'testing'), > (1, 'experimental') > Architecture: amd64 (x86_64) > Foreign Architectures: i386 > > Kernel: Linux 4.17.0-1-amd64 (SMP w/8 CPU cores) > Locale: LANG=it_IT.utf8, LC_CTYPE=it_IT.utf8 (charmap=UTF-8), > LANGUAGE=it_IT.utf8 (charmap=UTF-8) > Shell: /bin/sh linked to /bin/dash > Init: systemd (via /run/systemd/system) > LSM: AppArmor: enabled > > Versions of packages sagemath depends on: > ii cysignals-tools 1.6.7+ds-4 > ii cython 0.28.4-1 > ii ecl 16.1.2-4+b1 > ii eclib-tools 20171002-1+b3 > ii f2c 20160102-1 > ii fflas-ffpack 2.3.2-2 > ii flintqs 1:1.0-3 > ii gap-core 4r8p8-3 > ii gfan 0.5+dfsg-6 > ii gmp-ecm 7.0.4+ds-3 > ii ipython 5.5.0-1 > ii iso-codes3.79-1 > ii jmol 14.6.4+2016.11.05+dfsg1-3.1 > ii lcalc1.23+dfsg-7 > ii less 487-0.1+b1 > ii libatlas3-base [liblapack.so.3] 3.10.3-7+b1 > ii libblas3 [libblas.so.3] 3.8.0-1+b1 > ii libbrial-groebner3 1.2.0-2 > ii libbrial31.2.0-2 > ii libc62.27-5 > ii libcdd-tools 094h-1+b1 > ii libcliquer1 1.21-2 > ii libec3 20171002-1+b3 > ii libecm1 7.0.4+ds-3 > ii libflint-2.5.2 2.5.2-18 > ii libflint-arb21:2.12.0-3 > ii libgap-sage-4 > 4.8.8+3+20160327g69a66f0+dsx-1 > ii libgcc1 1:8.2.0-4 > ii libgd3 2.2.5-4 > ii libgivaro9 4.0.4-2 > ii libglpk404.65-2 > ii libgmp10 2:6.1.2+dfsg-3 > ii libgmpxx4ldbl2:6.1.2+dfsg-3 > ii libgsl23 2.5+dfsg-4 > ii libgslcblas0 2.5+dfsg-4 > ii libiml0 1.0.4-1+b2 > ii libjs-mathjax2.7.4+dfsg-1 > ii libjs-three 80+dfsg2-2 > ii liblapack3 [liblapack.so.3] 3.8.0-1+b1 > ii liblfunction01.23+dfsg-7 > ii liblinbox-1.5.2-01.5.2-2 > ii liblinboxsage-1.5.2-01.5.2-2 > ii liblrcalc1 1.2-2+b1 > ii libm4ri-0.0.20140914 20140914-2+b1 > ii libm4rie-0.0.2015090820150908-2 > ii libmpc3 1.1.0-1 > ii libmpfi0 1.5.3+ds-2 > ii libmpfr6 4.0.1-1 > ii libntl35 10.5.0-2 > ii libopenblas-base [liblapack.so.3]0.3.2+ds-1 > ii libpari-gmp-tls5 2.9.5-1 > ii libplanarity03.0.0.5-3 > ii libpng16-16 1.6.34-2 > ii libppl14 1:1.2-3 > ii libpynac17 0.7.19-2 > ii libratpoints-2.1.3
Bug#906796: sagemath: Sage crashes at startup (segfault in pari modules)
Package: sagemath Version: 8.2-5 Severity: important Dear Maintainer, when I start sage, it immediately crashes with the attached crash report. Before running sage I removed the directories .ipython, .sage and .local/lib/python* (which I discovered contained some Python modules that were executed by sage upon startup). The end of the crash report seems to mention a segmentation fault in some pari module, but I am not able to extract more information from it. Thanks, Giovanni. -- System Information: Debian Release: buster/sid APT prefers unstable-debug APT policy: (500, 'unstable-debug'), (500, 'unstable'), (500, 'testing'), (1, 'experimental') Architecture: amd64 (x86_64) Foreign Architectures: i386 Kernel: Linux 4.17.0-1-amd64 (SMP w/8 CPU cores) Locale: LANG=it_IT.utf8, LC_CTYPE=it_IT.utf8 (charmap=UTF-8), LANGUAGE=it_IT.utf8 (charmap=UTF-8) Shell: /bin/sh linked to /bin/dash Init: systemd (via /run/systemd/system) LSM: AppArmor: enabled Versions of packages sagemath depends on: ii cysignals-tools 1.6.7+ds-4 ii cython 0.28.4-1 ii ecl 16.1.2-4+b1 ii eclib-tools 20171002-1+b3 ii f2c 20160102-1 ii fflas-ffpack 2.3.2-2 ii flintqs 1:1.0-3 ii gap-core 4r8p8-3 ii gfan 0.5+dfsg-6 ii gmp-ecm 7.0.4+ds-3 ii ipython 5.5.0-1 ii iso-codes3.79-1 ii jmol 14.6.4+2016.11.05+dfsg1-3.1 ii lcalc1.23+dfsg-7 ii less 487-0.1+b1 ii libatlas3-base [liblapack.so.3] 3.10.3-7+b1 ii libblas3 [libblas.so.3] 3.8.0-1+b1 ii libbrial-groebner3 1.2.0-2 ii libbrial31.2.0-2 ii libc62.27-5 ii libcdd-tools 094h-1+b1 ii libcliquer1 1.21-2 ii libec3 20171002-1+b3 ii libecm1 7.0.4+ds-3 ii libflint-2.5.2 2.5.2-18 ii libflint-arb21:2.12.0-3 ii libgap-sage-44.8.8+3+20160327g69a66f0+dsx-1 ii libgcc1 1:8.2.0-4 ii libgd3 2.2.5-4 ii libgivaro9 4.0.4-2 ii libglpk404.65-2 ii libgmp10 2:6.1.2+dfsg-3 ii libgmpxx4ldbl2:6.1.2+dfsg-3 ii libgsl23 2.5+dfsg-4 ii libgslcblas0 2.5+dfsg-4 ii libiml0 1.0.4-1+b2 ii libjs-mathjax2.7.4+dfsg-1 ii libjs-three 80+dfsg2-2 ii liblapack3 [liblapack.so.3] 3.8.0-1+b1 ii liblfunction01.23+dfsg-7 ii liblinbox-1.5.2-01.5.2-2 ii liblinboxsage-1.5.2-01.5.2-2 ii liblrcalc1 1.2-2+b1 ii libm4ri-0.0.20140914 20140914-2+b1 ii libm4rie-0.0.2015090820150908-2 ii libmpc3 1.1.0-1 ii libmpfi0 1.5.3+ds-2 ii libmpfr6 4.0.1-1 ii libntl35 10.5.0-2 ii libopenblas-base [liblapack.so.3]0.3.2+ds-1 ii libpari-gmp-tls5 2.9.5-1 ii libplanarity03.0.0.5-3 ii libpng16-16 1.6.34-2 ii libppl14 1:1.2-3 ii libpynac17 0.7.19-2 ii libratpoints-2.1.3 1:2.1.3-1+b2 ii libreadline7 7.0-5 ii librw0 0.8+ds-1 ii libsingular4 1:4.1.0-p3+ds-2+b3 ii libstdc++6 8.2.0-4 ii libsymmetrica2 2.0+ds-5 ii libzn-poly-0.9 0.9-3+b2 ii maxima-sage 5.39.0+ds-3 ii maxima-sage-doc 5.39.0+ds-3 ii maxima-sage-share5.39.0+ds-3 ii nauty2.6r10+ds-1 ii octave
