Bug#906796: sagemath: Sage crashes at startup (segfault in pari modules)
Tobias Hansen
thansen at posteo.de
Tue Aug 21 09:13:26 BST 2018
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-codes 3.79-1
> ii jmol 14.6.4+2016.11.05+dfsg1-3.1
> ii lcalc 1.23+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 libbrial3 1.2.0-2
> ii libc6 2.27-5
> 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-arb2 1:2.12.0-3
> 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 libglpk40 4.65-2
> ii libgmp10 2:6.1.2+dfsg-3
> ii libgmpxx4ldbl 2:6.1.2+dfsg-3
> ii libgsl23 2.5+dfsg-4
> ii libgslcblas0 2.5+dfsg-4
> ii libiml0 1.0.4-1+b2
> ii libjs-mathjax 2.7.4+dfsg-1
> ii libjs-three 80+dfsg2-2
> ii liblapack3 [liblapack.so.3] 3.8.0-1+b1
> ii liblfunction0 1.23+dfsg-7
> ii liblinbox-1.5.2-0 1.5.2-2
> ii liblinboxsage-1.5.2-0 1.5.2-2
> ii liblrcalc1 1.2-2+b1
> ii libm4ri-0.0.20140914 20140914-2+b1
> ii libm4rie-0.0.20150908 20150908-2
> 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 libplanarity0 3.0.0.5-3
> 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-share 5.39.0+ds-3
> ii nauty 2.6r10+ds-1
> ii octave 4.4.1~rc2-3
> ii palp 2.1-5
> ii pari-doc 2.11.0-1
> ii pari-galdata 0.20080411-2
> ii pari-gp 2.11.0-1
> ii pari-seadata 0.20090618-1
> ii python 2.7.15-3
> ii python-alabaster 0.7.8-1
> ii python-babel 2.4.0+dfsg.1-2
> ii python-backports-abc 0.5-2
> ii python-backports-shutil-get-terminal-size 1.0.0-5
> ii python-backports.functools-lru-cache 1.5-1
> ii python-backports.ssl-match-hostname 3.5.0.1-1
> ii python-brial 1.2.0-2
> ii python-configparser 3.5.0b2-1
> ii python-crypto 2.6.1-9+b1
> ii python-cvxopt 1.1.9+dfsg-3+b1
> ii python-cycler 0.10.0-1
> ii python-cypari2 1.2.1-1
> ii python-cysignals-pari 1.6.7+ds-4
> ii python-decorator 4.3.0-1
> ii python-docutils 0.14+dfsg-3
> ii python-enum34 1.1.6-2
> ii python-flask 1.0.2-1
> ii python-flask-autoindex 0.6.1-1
> ii python-flask-babel 0.11.2-2
> ii python-flask-oldsessions 0.10+git20121007-2
> ii python-flask-openid 1.2.5+dfsg-2
> ii python-flask-silk 0.2-13
> ii python-fpylll 0.3.0+ds-3+b1
> ii python-functools32 3.2.3.2-3
> ii python-future 0.15.2-4
> ii python-gd 0.59-1
> ii python-gnutls 3.0.0-1
> ii python-imagesize 1.0.0-1
> ii python-ipython-genutils 0.2.0-1
> ii python-itsdangerous 0.24+dfsg1-2
> ii python-jsonschema 2.6.0-2
> ii python-matplotlib 2.2.2-4+b1
> ii python-mistune 0.8.3-2
> ii python-moinmoin 1.9.9-1
> ii python-mpmath 1.0.0-1
> ii python-networkx 2.1-1
> ii python-numpy [python-numpy-abi9] 1:1.14.5-1+b1
> ii python-openid 2.2.5-6
> ii python-path 11.0.1-2
> ii python-pathlib2 2.3.2-1
> ii python-pexpect 4.6.0-1
> ii python-pickleshare 0.7.4-4
> ii python-pil 5.2.0-2
> ii python-pip 9.0.1-2.3
> ii python-pkgconfig 1.3.1-1
> ii python-ply 3.11-3
> ii python-prompt-toolkit 1.0.15-1
> ii python-psutil 5.4.6-1+b1
> ii python-ptyprocess 0.6.0-1
> ii python-pygments 2.2.0+dfsg-1
> ii python-rpy2 2.8.6-2+b1
> ii python-sagenb 1.0.1+ds1-5
> ii python-sagenb-export 3.2-3
> ii python-scipy 1.1.0-1+b1
> ii python-setuptools 39.2.0-1
> ii python-setuptools-scm 3.0.6-1
> ii python-simplegeneric 0.8.1-2
> ii python-singledispatch 3.4.0.3-2
> ii python-snowballstemmer 1.2.1-1
> ii python-sphinx 1.7.6-1
> ii python-subprocess32 3.5.2-1
> ii python-sympy 1.2-1
> ii python-terminado 0.8.1-3
> ii python-tk 2.7.15-1
> ii python-tornado 5.0.2-1+b1
> ii python-traitlets 4.3.2-1
> ii python-twisted 18.7.0-2
> ii python-typing 3.6.4-1
> ii python-tz 2018.5-1
> ii python-vcversioner 2.16.0.0-1
> ii python-wcwidth 0.1.7+dfsg1-2
> ii python-werkzeug 0.14.1+dfsg1-1
> ii python-zmq 17.1.0-1
> ii python-zope.interface 4.3.2-1+b2
> ii python2.7 2.7.15-3
> ii python3 3.6.6-1
> ii r-base-core 3.5.1-1+b1
> ii r-cran-lattice 0.20-35-1+b2
> ii rubiks 20070912-3
> ii sagemath-common 8.2-5
> ii sagemath-database-conway-polynomials 0.5-4
> ii sagemath-database-elliptic-curves 0.8-2
> ii sagemath-database-graphs 20161026+dfsg-2
> ii sagemath-database-mutually-combinatorial-de 20140630-3
> ii sagemath-database-polytopes 20170220-2
> ii singular 1:4.1.0-p3+ds-2+b3
> ii singular-doc 1:4.1.0-p3+ds-2
> ii sqlite3 3.24.0-1
> ii sympow 2.023.3-1
> ii tachyon 0.99~b6+dsx-8
> ii xcas 1.2.3.57+dfsg1-2+b5
> ii zlib1g 1:1.2.11.dfsg-1
>
> Versions of packages sagemath recommends:
> ii sagemath-doc-en 8.2-5
> ii sagemath-jupyter 8.2-5
> ii sagetex 3.0+ds-6
> ii texlive-latex-base 2018.20180725-1
>
> Versions of packages sagemath suggests:
> pn dot2tex <none>
> pn gap-design <none>
> pn gap-factint <none>
> pn gap-grape <none>
> pn gap-guava <none>
> pn gap-laguna <none>
> pn gap-sonata <none>
> pn gap-toric <none>
>
> -- no debconf information
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