Your message dated Sun, 01 Sep 2019 16:34:30 +0000 with message-id <[email protected]> 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 [email protected] immediately.) -- 932367: https://bugs.debian.org/cgi-bin/bugreport.cgi?bug=932367 Debian Bug Tracking System Contact [email protected] 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
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--- 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 [email protected], and the maintainer will reopen the bug report if appropriate. Debian distribution maintenance software pp. Tobias Hansen <[email protected]> (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 [email protected]) -----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 <[email protected]> Changed-By: Tobias Hansen <[email protected]> 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. Checksums-Sha1: c86c89a7e8f0e6863a522821d25d683ea85e0e1e 6731 sagemath_8.8-1.dsc 77a39ed0e7f0c11167e338b2ee62c6233b7098b0 17534020 sagemath_8.8.orig.tar.xz be121a69421e4a2faaf2c91c2d8c96e52d71f9be 76764 sagemath_8.8-1.debian.tar.xz f884fc67a8534098eacf6b2d2fe9538ba287a6e3 24138 sagemath_8.8-1_source.buildinfo Checksums-Sha256: 5898ab9ad08dc4dc4e6c7ac96cd2aff0f4a55af24287090f26fbfe695fe71824 6731 sagemath_8.8-1.dsc 5c56a60a9abb5c2e28e5e0ca6e6f2c72b2b02331ca814875032a50ebf4234cd4 17534020 sagemath_8.8.orig.tar.xz a872af367d38501a19d774d2f0bf336a50e9de8464f7a42967d80e66e965a90e 76764 sagemath_8.8-1.debian.tar.xz b630662193d7e5a9643fea6bdb3c6d12ab618bfc9b2cdf02b51630c47813f0d2 24138 sagemath_8.8-1_source.buildinfo Files: d99d6151def0223e8aebd91940eea5e1 6731 math optional sagemath_8.8-1.dsc cf2ec705c08d5dd2a98866a7f284c8ab 17534020 math optional sagemath_8.8.orig.tar.xz c2e72cd4aca0732d1c78fc9e103541b6 76764 math optional sagemath_8.8-1.debian.tar.xz 7f1ca876e0935a38f043e1ce981d47a5 24138 math optional sagemath_8.8-1_source.buildinfo -----BEGIN PGP SIGNATURE----- iQIzBAEBCAAdFiEEoH46ol3M2u2mYo0kjIIWnY7OzSoFAl1r7wQACgkQjIIWnY7O zSq5zQ//Yl9Iey3OmybSwqPM2l1zOgvnt5cW9ThvhptF87SDiD/RuUj1t/QEFiya DDWeQsm17WBDDWfbv9ASsY4dwSMq9PWMaRnXFBZpf2FbLxueMcQVVFLh3z35oDjS nznPDVwmQkqa7G7QjYgT6Z5mOFgt/ASOGFuiap1cA/5PiCNqS+9+N0eoRZIB7HUe GFLW/pbmeO/3grUmVfFMJszei6Xgd7X1fwSjJ89s/CkMuRbFcgvrfOb3/AmG3GwN l1xoxV5vyZs3vwXz3xnwCJ7/aPkmWHltVEeuwupuJAEI4AnaMM4g6U4MIlcSOgTe CLQaNiMJPtGfnzYcpo0ow9ObMYPr8061/rwwrfSG2SuDRhCFmnLv/2Uw1oX3JFi4 sVzaJlUpO2IMWn/C3Gxsn1LQipNfnIGKUJa3KmGSzO+VEcuZ+ZuSGOlsOTzRZZaA gi5QfmTNU/im8Gb9iJxI4WjHmFwQtoePCir/zq6UApiSuj/AJH1jeejCIDBGOrF7 U6w9uNjNx9iunO7Fd0xTdTrclk3X+fdoO4FQnWyd4AXgOJIFbUOa7j+pPs2HEgpx MDmVtVmip/nm4MSvg6K/I2BaFBSkTPPt8GRByeLFyQeOWZHJGX2U44QwGx2uA0Ij r+/UnFObP33xUj4AYpGnM0wDV3KJUoXqYVD/GPVzQHatymeWVLI= =f5pq -----END PGP SIGNATURE-----
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