Bug#932367: sagemath: Sage does not start because of a missing symbol in GAP wrapper

Amaury Pouly amaury.pouly at gmail.com
Thu Jul 18 14:04:51 BST 2019


Package: sagemath
Version: 8.6-6
Severity: important

Dear Maintainer,

running sagemath (either directly with 'sage' or running a notebook with jupyter)
does not work because the kernel crashes. The final error reported by Python is

ImportError: /usr/lib/python2.7/dist-packages/sage/libs/gap/element.x86_64-linux-gnu.so: undefined symbol: _GAP_SetEnterStackCount

This renders sage unusable because the kernel will not start. Let me know how if I can help
by providing more information. I copy the full backtrace below:

Traceback (most recent call last):
  File "/usr/lib/python2.7/runpy.py", line 174, in _run_module_as_main
    "__main__", fname, loader, pkg_name)
  File "/usr/lib/python2.7/runpy.py", line 72, in _run_code
    exec code in run_globals
  File "/usr/lib/python2.7/dist-packages/sage/repl/ipython_kernel/__main__.py", line 3, in <module>
    IPKernelApp.launch_instance(kernel_class=SageKernel)
  File "/usr/lib/python2.7/dist-packages/traitlets/config/application.py", line 657, in launch_instance
    app.initialize(argv)
  File "<decorator-gen-121>", line 2, in initialize
  File "/usr/lib/python2.7/dist-packages/traitlets/config/application.py", line 87, in catch_config_error
    return method(app, *args, **kwargs)
  File "/usr/lib/python2.7/dist-packages/ipykernel/kernelapp.py", line 476, in initialize
    self.init_kernel()
  File "/usr/lib/python2.7/dist-packages/ipykernel/kernelapp.py", line 387, in init_kernel
    user_ns=self.user_ns,
  File "/usr/lib/python2.7/dist-packages/traitlets/config/configurable.py", line 412, in instance
    inst = cls(*args, **kwargs)
  File "/usr/lib/python2.7/dist-packages/sage/repl/ipython_kernel/kernel.py", line 52, in __init__
    SageJupyterCustomizations(self.shell)
  File "/usr/lib/python2.7/dist-packages/sage/repl/ipython_extension.py", line 433, in __init__
    import sage.all # until sage's import hell is fixed
  File "/usr/lib/python2.7/dist-packages/sage/all.py", line 102, in <module>
    from sage.modular.all    import *
  File "/usr/lib/python2.7/dist-packages/sage/modular/all.py", line 4, in <module>
    from .quatalg.all import *
  File "/usr/lib/python2.7/dist-packages/sage/modular/quatalg/__init__.py", line 4, in <module>
    from . import all
  File "/usr/lib/python2.7/dist-packages/sage/modular/quatalg/all.py", line 3, in <module>
    from .brandt import BrandtModule
  File "/usr/lib/python2.7/dist-packages/sage/modular/quatalg/brandt.py", line 206, in <module>
    from sage.modular.hecke.all import (AmbientHeckeModule, HeckeSubmodule, HeckeModuleElement)
  File "/usr/lib/python2.7/dist-packages/sage/modular/hecke/all.py", line 20, in <module>
    from .ambient_module import AmbientHeckeModule, is_AmbientHeckeModule
  File "/usr/lib/python2.7/dist-packages/sage/modular/hecke/ambient_module.py", line 38, in <module>
    from sage.modular.arithgroup.all import Gamma0 # for Sturm bound
  File "/usr/lib/python2.7/dist-packages/sage/modular/arithgroup/__init__.py", line 4, in <module>
    from . import all
  File "/usr/lib/python2.7/dist-packages/sage/modular/arithgroup/all.py", line 6, in <module>
    from .congroup_generic import is_CongruenceSubgroup, CongruenceSubgroup_constructor as CongruenceSubgroup
  File "/usr/lib/python2.7/dist-packages/sage/modular/arithgroup/congroup_generic.py", line 28, in <module>
    from sage.groups.matrix_gps.all import MatrixGroup
  File "/usr/lib/python2.7/dist-packages/sage/groups/matrix_gps/all.py", line 13, in <module>
    import sage.groups.matrix_gps.pickling_overrides
  File "/usr/lib/python2.7/dist-packages/sage/groups/matrix_gps/pickling_overrides.py", line 7, in <module>
    from sage.groups.matrix_gps.finitely_generated import FinitelyGeneratedMatrixGroup_gap
  File "/usr/lib/python2.7/dist-packages/sage/groups/matrix_gps/finitely_generated.py", line 81, in <module>
    from sage.groups.matrix_gps.matrix_group import (
  File "/usr/lib/python2.7/dist-packages/sage/groups/matrix_gps/matrix_group.py", line 61, in <module>
    from sage.groups.libgap_wrapper import ParentLibGAP
  File "sage/libs/gap/element.pxd", line 32, in init sage.groups.libgap_wrapper (build/cythonized/sage/groups/libgap_wrapper.c:9846)
    cdef class GapElement(RingElement):
ImportError: /usr/lib/python2.7/dist-packages/sage/libs/gap/element.x86_64-linux-gnu.so: undefined symbol: _GAP_SetEnterStackCount


-- System Information:
Debian Release: bullseye/sid
  APT prefers unstable
  APT policy: (500, 'unstable')
Architecture: amd64 (x86_64)
Foreign Architectures: i386

Kernel: Linux 4.19.0-5-amd64 (SMP w/4 CPU cores)
Locale: LANG=fr_FR.UTF-8, LC_CTYPE=fr_FR.UTF-8 (charmap=UTF-8), LANGUAGE=fr (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                                   1.8.1+ds-2
ii  cython                                            0.29.2-2
ii  ecl                                               16.1.3+ds-2
ii  eclib-tools                                       20190226-2
ii  fflas-ffpack                                      2.3.2-3
ii  flintqs                                           1:1.0-3
ii  gap-atlasrep                                      1.5.1-2
ii  gap-core                                          4r10p2-1
ii  gap-dev                                           4r10p2-1
ii  gap-online-help                                   4r10p2-1
ii  gap-primgrp                                       3.3.2-1
ii  gap-smallgrp                                      1.3-1
ii  gap-table-of-marks                                1.2.7-2
ii  gap-transgrp                                      2.0.4-1
ii  gfan                                              0.6.2-2
ii  gmp-ecm                                           7.0.4+ds-5
ii  ipython                                           5.8.0-1
ii  iso-codes                                         4.3-1
ii  jmol                                              14.6.4+2016.11.05+dfsg1-4
ii  lcalc                                             1.23+dfsg-11
ii  less                                              487-0.1+b1
ii  libatlas3-base [liblapack.so.3]                   3.10.3-8
ii  libblas3 [libblas.so.3]                           3.8.0-2
ii  libbraiding0                                      1.0-1
ii  libbrial-groebner3                                1.2.4-2
ii  libbrial3                                         1.2.4-2
ii  libc6                                             2.28-10
ii  libcdd-tools                                      094j-2
ii  libcliquer1                                       1.21-2
ii  libec4                                            20180815-2
ii  libecm1                                           7.0.4+ds-5
ii  libflint-2.5.2                                    2.5.2-19
ii  libflint-arb2                                     1:2.16.0-2
ii  libgc1c2                                          1:7.6.4-0.4
ii  libgcc1                                           1:9.1.0-8
ii  libgd3                                            2.2.5-5.2
ii  libgivaro9                                        4.0.4-2
ii  libglpk40                                         4.65-2
ii  libgmp10                                          2:6.1.2+dfsg-4
ii  libgmpxx4ldbl                                     2:6.1.2+dfsg-4
ii  libgomp1                                          9.1.0-8
ii  libgsl23                                          2.5+dfsg-6
ii  libgslcblas0                                      2.5+dfsg-6
ii  libhomfly0                                        1.02r5-1
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]                       3.8.0-2
ii  liblfunction0                                     1.23+dfsg-11
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                                          4.0.2-1
ii  libntl35                                          10.5.0-2
ii  libpari-gmp-tls6                                  2.11.2-2
ii  libplanarity0                                     3.0.0.5-3
ii  libpng16-16                                       1.6.37-1
ii  libppl14                                          1:1.2-7
ii  libpynac18                                        0.7.23-2
ii  libratpoints-2.1.3                                1:2.1.3-1+b2
ii  libreadline7                                      7.0-5
ii  librw0                                            0.8+ds-1
ii  libsingular4m1                                    1:4.1.1-p2+ds-3
ii  libstdc++6                                        9.1.0-8
ii  libsymmetrica2                                    2.0+ds-6
ii  libzn-poly-0.9                                    0.9.1-1
ii  maxima-sage                                       5.41.0+ds-4
ii  maxima-sage-share                                 5.41.0+ds-4
ii  nauty                                             2.6r10+ds-1
ii  palp                                              2.1-5
ii  pari-galdata                                      0.20080411-2
ii  pari-gp                                           2.11.2-2
ii  pari-seadata                                      0.20090618-1
ii  python                                            2.7.16-1
ii  python-alabaster                                  0.7.8-1
ii  python-babel                                      2.6.0+dfsg.1-1
ii  python-backports-abc                              0.5-2
ii  python-backports-shutil-get-terminal-size         1.0.0-5
ii  python-backports.functools-lru-cache              1.5-3
ii  python-brial                                      1.2.4-2
ii  python-configparser                               3.5.0b2-1
ii  python-cvxopt                                     1.1.9+dfsg-3+b1
ii  python-cycler                                     0.10.0-1
ii  python-cypari2                                    1.3.1-2
ii  python-cysignals-pari                             1.8.1+ds-2
ii  python-decorator                                  4.3.0-1.1
ii  python-docutils                                   0.14+dfsg-4
ii  python-enum34                                     1.1.6-2
ii  python-fpylll                                     0.4.1+ds1-5
ii  python-functools32                                3.2.3.2-3
ii  python-future                                     0.16.0-1
ii  python-imagesize                                  1.0.0-1
ii  python-ipython-genutils                           0.2.0-1
ii  python-itsdangerous                               0.24+dfsg1-2
ii  python-matplotlib                                 2.2.3-6
ii  python-mistune                                    0.8.4-1
ii  python-mpmath                                     1.1.0-1
ii  python-networkx                                   2.2-1
ii  python-numpy [python-numpy-abi9]                  1:1.16.2-1
ii  python-openid                                     2.2.5-7
ii  python-packaging                                  19.0-1
ii  python-path                                       11.5.0-3
ii  python-pathlib2                                   2.3.4-1
ii  python-pexpect                                    4.6.0-1
ii  python-pickleshare                                0.7.5-1
ii  python-pil                                        6.1.0-1
ii  python-pip                                        18.1-5
ii  python-pkgconfig                                  1.5.1-2
ii  python-prompt-toolkit                             1.0.15-1
ii  python-psutil                                     5.5.1-1
ii  python-ptyprocess                                 0.6.0-1
ii  python-pygments                                   2.3.1+dfsg-1
ii  python-rpy2                                       2.8.6-3
ii  python-sagenb                                     1.1.2+ds1-1
ii  python-scipy                                      1.1.0-7
ii  python-setuptools                                 41.0.1-1
ii  python-setuptools-scm                             3.3.3-1
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                                     1.8.5-2
ii  python-stemmer                                    1.3.0+dfsg-1+b9
ii  python-subprocess32                               3.5.3-1
ii  python-sympy                                      1.3-2
ii  python-terminado                                  0.8.2-1
ii  python-tornado                                    5.1.1-4
ii  python-traitlets                                  4.3.2-1
ii  python-twisted                                    18.9.0-3
ii  python-typing                                     3.6.6-1
ii  python-tz                                         2019.1-1
ii  python-vcversioner                                2.16.0.0-1
ii  python-wcwidth                                    0.1.7+dfsg1-3
ii  python-werkzeug                                   0.14.1+dfsg1-4
ii  python-zmq                                        17.1.2-2
ii  python-zope.interface                             4.3.2-1+b2
ii  r-base-core                                       3.6.1-2
ii  rubiks                                            20070912-4
ii  sagemath-common                                   8.6-6
ii  sagemath-database-conway-polynomials              0.5-5
ii  sagemath-database-elliptic-curves                 0.8.1-2
ii  sagemath-database-graphs                          20161026+dfsg-3
ii  sagemath-database-mutually-combinatorial-designs  20140630-4
ii  sagemath-database-polytopes                       20170220-3
ii  singular                                          1:4.1.1-p2+ds-3
ii  sqlite3                                           3.29.0-1
ii  sympow                                            2.023.5-2
ii  tachyon                                           0.99~b6+dsx-9
ii  xcas                                              1.4.9.69+dfsg1-2
ii  zlib1g                                            1:1.2.11.dfsg-1

Versions of packages sagemath recommends:
ii  maxima-sage-doc       5.41.0+ds-4
ii  pari-doc              2.11.2-2
ii  python-sagenb-export  3.2-3
ii  r-cran-lattice        0.20-38-1
ii  sagemath-doc-en       8.6-6
ii  sagemath-jupyter      8.6-6
ii  sagetex               3.2+ds-2
ii  singular-doc          1:4.1.1-p2+ds-3
ii  texlive-latex-base    2019.20190710-1

Versions of packages sagemath suggests:
pn  dot2tex      <none>
pn  gap-design   <none>
ii  gap-factint  1.6.2+ds-1
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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