Your message dated Sun, 01 Sep 2019 16:34:30 +0000
with message-id <e1i4soa-000j8l...@fasolo.debian.org>
and subject line Bug#932367: fixed in sagemath 8.8-1
has caused the Debian Bug report #932367,
regarding sagemath: Sage does not start because of a missing symbol in GAP
wrapper
to be marked as done.
This means that you claim that the problem has been dealt with.
If this is not the case it is now your responsibility to reopen the
Bug report if necessary, and/or fix the problem forthwith.
(NB: If you are a system administrator and have no idea what this
message is talking about, this may indicate a serious mail system
misconfiguration somewhere. Please contact ow...@bugs.debian.org
immediately.)
--
932367: https://bugs.debian.org/cgi-bin/bugreport.cgi?bug=932367
Debian Bug Tracking System
Contact ow...@bugs.debian.org with problems
--- Begin Message ---
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
--- End Message ---
--- Begin Message ---
Source: sagemath
Source-Version: 8.8-1
We believe that the bug you reported is fixed in the latest version of
sagemath, which is due to be installed in the Debian FTP archive.
A summary of the changes between this version and the previous one is
attached.
Thank you for reporting the bug, which will now be closed. If you
have further comments please address them to 932...@bugs.debian.org,
and the maintainer will reopen the bug report if appropriate.
Debian distribution maintenance software
pp.
Tobias Hansen <than...@debian.org> (supplier of updated sagemath package)
(This message was generated automatically at their request; if you
believe that there is a problem with it please contact the archive
administrators by mailing ftpmas...@ftp-master.debian.org)
-----BEGIN PGP SIGNED MESSAGE-----
Hash: SHA256
Format: 1.8
Date: Sun, 01 Sep 2019 16:14:42 +0000
Source: sagemath
Architecture: source
Version: 8.8-1
Distribution: unstable
Urgency: medium
Maintainer: Debian Science Team
<debian-science-maintain...@lists.alioth.debian.org>
Changed-By: Tobias Hansen <than...@debian.org>
Closes: 932367 934171
Changes:
sagemath (8.8-1) unstable; urgency=medium
.
* New upstream release. (Closes: #932367, #934171)
* New (Build-)Depends:
- libbrial-dev (>= 1.2.5)
- libbrial-groebner-dev (>= 1.2.5)
- libec-dev (>= 20190226)
- maxima-sage (>= 5.42.2)
- python-cypari2 (>= 2.1)
- python-gmpy2
- python-nose
- python-ppl
- python-ppl-doc
- python-scipy (>= 1.2)
- python-sphinx (>= 1.8.5)
- sagemath-database-conway-polynomials (>= 0.5-7)
* Remove patches (applied upstream):
- u0-version-numpy-1.16-inline-fortran.patch #27061
- u0-version-sphinx-1.8.patch #26451
- u0-version-sphinx-1.8-dependency.patch #26949
- u1-sphinx-1.8-doctest-transform.patch #27528
- u2-libgap-symbol-loading.patch #26930
- d1-disable-post-install-tests.patch
* Patches with non-trivial modifications:
- u0-version-sphinx-1.8.patch #26451
- d0-singular.patch
- d0-paths.patch
- d0-libgap-path.patch
- d1-install-paths.patch
- d1-sage-cli.patch
- d1-sage-env.patch
- dt-version-ipywidgets-6-revert-23177.patch
* Allow up to 65 failed tests.
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Files:
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