Sage crash report
152 views
Skip to first unread message
emanuel.c...@gmail.com
Dec 9, 2021, 3:18:02 PM12/9/21
to sage-s...@googlegroups.com
A recent upgrade of Debian testing seems to have broken Sage, which does not find libgsl.so.25 Crash report attached.
An attempt at make -b also fails (see attached install.log).
The worse is :
charpent@zen-book-flip:/usr/local/sage-9$ locate libgsl.so
/usr/lib/x86_64-linux-gnu/libgsl.so
/usr/lib/x86_64-linux-gnu/libgsl.so.25
/usr/lib/x86_64-linux-gnu/libgsl.so.25.0.0
charpent@zen-book-flip:/usr/local/sage-9$ dpkg -l "*libgsl*"
Souhait=inconnU/Installé/suppRimé/Purgé/H=à garder
| État=Non/Installé/fichier-Config/dépaqUeté/échec-conFig/H=semi-installé/W=att>
|/ Err?=(aucune)/besoin Réinstallation (État,Err: majuscule=mauvais)
||/ Nom Version Architecture Description
+++-==================-============-============-==============================>
ii libgsl-dev 2.7.1+dfsg-3 amd64 GNU Scientific Library (GSL) ->
un libgsl0 <aucune> <aucune> (aucune description n'est disp>
un libgsl0-dev <aucune> <aucune> (aucune description n'est disp>
un libgsl0ldbl <aucune> <aucune> (aucune description n'est disp>
un libgsl2 <aucune> <aucune> (aucune description n'est disp>
un libgsl23 <aucune> <aucune> (aucune description n'est disp>
ii libgsl27:amd64 2.7.1+dfsg-3 amd64 GNU Scientific Library (GSL) ->
ii libgslcblas0:amd64 2.7.1+dfsg-3 amd64 GNU Scientific Library (GSL) ->
I'm a bit at loss...
Matthias Koeppe
Dec 9, 2021, 7:04:33 PM12/9/21
to sage-support
"make sagelib-clean" will fix this
Emmanuel Charpentier
Dec 10, 2021, 5:36:15 AM12/10/21
to sage-support
Le vendredi 10 décembre 2021 à 01:04:33 UTC+1, Matthias Koeppe a écrit :
"make sagelib-clean" will fix this
Nope. `make sagelib-clean` succeeds, but the following `make` fails at documentation ; attempting `make doc-clean && make also fails, *with the very same error*... :
```
[sagemath_doc_html-none] cd /usr/local/sage-9 && ./sage --docbuild --no-pdf-links reference/libs inventory --no-prune-empty-dirs
[sagemath_doc_html-none] Warning: Could not import sage.libs.giac libgsl.so.25: cannot open shared object file: No such file or directory
[sagemath_doc_html-none] /usr/local/sage-9/local/var/lib/sage/venv-python3.9/lib/python3.9/site-packages/sage_docbuild/__init__.py:1066: DeprecationWarning: the module sage.libs.ratpoints is deprecated; use pari.ellratpoints or pari.hyperellratpoints instead
[sagemath_doc_html-none] See http://trac.sagemath.org/24531 for details.
[sagemath_doc_html-none] __import__(module_name)
[sagemath_doc_html-none] [libs ] building [inventory]: targets for 39 source files that are out of date
[sagemath_doc_html-none] [libs ] updating environment: [new config] 39 added, 0 changed, 0 removed
[sagemath_doc_html-none] [libs ] WARNING: autodoc: failed to import module 'giac' from module 'sage.libs'; the following exception was raised:
[sagemath_doc_html-none] [libs ] libgsl.so.25: cannot open shared object file: No such file or directory
[sagemath_doc_html-none] [libs ] The inventory files are in local/share/doc/sage/inventory/en/reference/libs.
[sagemath_doc_html-none] Error building the documentation.
[sagemath_doc_html-none] Traceback (most recent call last):
[sagemath_doc_html-none] File "/usr/lib/python3.9/runpy.py", line 197, in _run_module_as_main
[sagemath_doc_html-none] return _run_code(code, main_globals, None,
[sagemath_doc_html-none] File "/usr/lib/python3.9/runpy.py", line 87, in _run_code
[sagemath_doc_html-none] exec(code, run_globals)
[sagemath_doc_html-none] File "/usr/local/sage-9/local/var/lib/sage/venv-python3.9/lib/python3.9/site-packages/sage_docbuild/__main__.py", line 2, in <module>
[sagemath_doc_html-none] main()
[sagemath_doc_html-none] File "/usr/local/sage-9/local/var/lib/sage/venv-python3.9/lib/python3.9/site-packages/sage_docbuild/__init__.py", line 1815, in main
[sagemath_doc_html-none] builder()
[sagemath_doc_html-none] File "/usr/local/sage-9/local/var/lib/sage/venv-python3.9/lib/python3.9/site-packages/sage_docbuild/__init__.py", line 822, in _wrapper
[sagemath_doc_html-none] getattr(DocBuilder, build_type)(self, *args, **kwds)
[sagemath_doc_html-none] File "/usr/local/sage-9/local/var/lib/sage/venv-python3.9/lib/python3.9/site-packages/sage_docbuild/__init__.py", line 133, in f
[sagemath_doc_html-none] runsphinx()
[sagemath_doc_html-none] File "/usr/local/sage-9/local/var/lib/sage/venv-python3.9/lib/python3.9/site-packages/sage_docbuild/sphinxbuild.py", line 323, in runsphinx
[sagemath_doc_html-none] sys.stderr.raise_errors()
[sagemath_doc_html-none] File "/usr/local/sage-9/local/var/lib/sage/venv-python3.9/lib/python3.9/site-packages/sage_docbuild/sphinxbuild.py", line 258, in raise_errors
[sagemath_doc_html-none] raise OSError(self._error)
[sagemath_doc_html-none] OSError: WARNING: autodoc: failed to import module 'giac' from module 'sage.libs'; the following exception was raised:
[sagemath_doc_html-none]
[sagemath_doc_html-none] Note: incremental documentation builds sometimes cause spurious
[sagemath_doc_html-none] error messages. To be certain that these are real errors, run
[sagemath_doc_html-none] "make doc-clean" first and try again.
[sagemath_doc_html-none] make[6]: *** [Makefile:20 : doc-inventory--reference-libs] Erreur 1
[sagemath_doc_html-none] make[5]: *** [Makefile:37 : doc-inventory-reference] Erreur 2
make[4]: *** [Makefile:2789 : sagemath_doc_html-SAGE_DOCS-no-deps] Erreur 2
make[3]: *** [Makefile:2789 : /usr/local/sage-9/local/var/lib/sage/installed/sagemath_doc_html-none] Erreur 2
make[2]: *** [Makefile:2332 : all-start] Erreur 2
make[2] : on quitte le répertoire « /usr/local/sage-9/build/make »
real 18m33,136s
user 29m24,260s
sys 1m6,712s
***************************************************************
Error building Sage.
The following package(s) may have failed to build (not necessarily
during this run of 'make all-start'):
It is safe to delete any log files and build directories, but they
contain information that is helpful for debugging build problems.
WARNING: If you now run 'make' again, the build directory of the
same version of the package will, by default, be deleted. Set the
environment variable SAGE_KEEP_BUILT_SPKGS=yes to prevent this.
make[1]: *** [Makefile:39 : all-start] Erreur 1
make[1] : on quitte le répertoire « /usr/local/sage-9 »
make: *** [Makefile:13 : all] Erreur 2
[sagemath_doc_html-none] Warning: Could not import sage.libs.giac libgsl.so.25: cannot open shared object file: No such file or directory
[sagemath_doc_html-none] /usr/local/sage-9/local/var/lib/sage/venv-python3.9/lib/python3.9/site-packages/sage_docbuild/__init__.py:1066: DeprecationWarning: the module sage.libs.ratpoints is deprecated; use pari.ellratpoints or pari.hyperellratpoints instead
[sagemath_doc_html-none] See http://trac.sagemath.org/24531 for details.
[sagemath_doc_html-none] __import__(module_name)
[sagemath_doc_html-none] [libs ] building [inventory]: targets for 39 source files that are out of date
[sagemath_doc_html-none] [libs ] updating environment: [new config] 39 added, 0 changed, 0 removed
[sagemath_doc_html-none] [libs ] WARNING: autodoc: failed to import module 'giac' from module 'sage.libs'; the following exception was raised:
[sagemath_doc_html-none] [libs ] libgsl.so.25: cannot open shared object file: No such file or directory
[sagemath_doc_html-none] [libs ] The inventory files are in local/share/doc/sage/inventory/en/reference/libs.
[sagemath_doc_html-none] Error building the documentation.
[sagemath_doc_html-none] Traceback (most recent call last):
[sagemath_doc_html-none] File "/usr/lib/python3.9/runpy.py", line 197, in _run_module_as_main
[sagemath_doc_html-none] return _run_code(code, main_globals, None,
[sagemath_doc_html-none] File "/usr/lib/python3.9/runpy.py", line 87, in _run_code
[sagemath_doc_html-none] exec(code, run_globals)
[sagemath_doc_html-none] File "/usr/local/sage-9/local/var/lib/sage/venv-python3.9/lib/python3.9/site-packages/sage_docbuild/__main__.py", line 2, in <module>
[sagemath_doc_html-none] main()
[sagemath_doc_html-none] File "/usr/local/sage-9/local/var/lib/sage/venv-python3.9/lib/python3.9/site-packages/sage_docbuild/__init__.py", line 1815, in main
[sagemath_doc_html-none] builder()
[sagemath_doc_html-none] File "/usr/local/sage-9/local/var/lib/sage/venv-python3.9/lib/python3.9/site-packages/sage_docbuild/__init__.py", line 822, in _wrapper
[sagemath_doc_html-none] getattr(DocBuilder, build_type)(self, *args, **kwds)
[sagemath_doc_html-none] File "/usr/local/sage-9/local/var/lib/sage/venv-python3.9/lib/python3.9/site-packages/sage_docbuild/__init__.py", line 133, in f
[sagemath_doc_html-none] runsphinx()
[sagemath_doc_html-none] File "/usr/local/sage-9/local/var/lib/sage/venv-python3.9/lib/python3.9/site-packages/sage_docbuild/sphinxbuild.py", line 323, in runsphinx
[sagemath_doc_html-none] sys.stderr.raise_errors()
[sagemath_doc_html-none] File "/usr/local/sage-9/local/var/lib/sage/venv-python3.9/lib/python3.9/site-packages/sage_docbuild/sphinxbuild.py", line 258, in raise_errors
[sagemath_doc_html-none] raise OSError(self._error)
[sagemath_doc_html-none] OSError: WARNING: autodoc: failed to import module 'giac' from module 'sage.libs'; the following exception was raised:
[sagemath_doc_html-none]
[sagemath_doc_html-none] Note: incremental documentation builds sometimes cause spurious
[sagemath_doc_html-none] error messages. To be certain that these are real errors, run
[sagemath_doc_html-none] "make doc-clean" first and try again.
[sagemath_doc_html-none] make[6]: *** [Makefile:20 : doc-inventory--reference-libs] Erreur 1
[sagemath_doc_html-none] make[5]: *** [Makefile:37 : doc-inventory-reference] Erreur 2
make[4]: *** [Makefile:2789 : sagemath_doc_html-SAGE_DOCS-no-deps] Erreur 2
make[3]: *** [Makefile:2789 : /usr/local/sage-9/local/var/lib/sage/installed/sagemath_doc_html-none] Erreur 2
make[2]: *** [Makefile:2332 : all-start] Erreur 2
make[2] : on quitte le répertoire « /usr/local/sage-9/build/make »
real 18m33,136s
user 29m24,260s
sys 1m6,712s
***************************************************************
Error building Sage.
The following package(s) may have failed to build (not necessarily
during this run of 'make all-start'):
It is safe to delete any log files and build directories, but they
contain information that is helpful for debugging build problems.
WARNING: If you now run 'make' again, the build directory of the
same version of the package will, by default, be deleted. Set the
environment variable SAGE_KEEP_BUILT_SPKGS=yes to prevent this.
make[1]: *** [Makefile:39 : all-start] Erreur 1
make[1] : on quitte le répertoire « /usr/local/sage-9 »
make: *** [Makefile:13 : all] Erreur 2
```
Suggestions ?
Dima Pasechnik
Dec 10, 2021, 5:56:00 AM12/10/21
to sage-support
Everything that depends on updated Debian libs has to be rebuilt - looks like
make giac-clean
is needed too, for sure.
> --
> You received this message because you are subscribed to the Google Groups "sage-support" group.
> To unsubscribe from this group and stop receiving emails from it, send an email to sage-support...@googlegroups.com.
> To view this discussion on the web visit https://groups.google.com/d/msgid/sage-support/f93cf900-d04f-4a70-9222-ccd0712c4bfan%40googlegroups.com.
make giac-clean
is needed too, for sure.
> You received this message because you are subscribed to the Google Groups "sage-support" group.
> To unsubscribe from this group and stop receiving emails from it, send an email to sage-support...@googlegroups.com.
> To view this discussion on the web visit https://groups.google.com/d/msgid/sage-support/f93cf900-d04f-4a70-9222-ccd0712c4bfan%40googlegroups.com.
Emmanuel Charpentier
Dec 10, 2021, 10:39:53 AM12/10/21
to sage-support
make giac-clean && make did it !
(Alla cinese) 10^4 thanks !
Emmanuel Charpentier
Dec 10, 2021, 12:13:42 PM12/10/21
to sage-support
Now, at the end of a Sage session, I get :
sage: quit
Exiting Sage (CPU time 0m5.63s, Wall time 97m53.10s).
------------------------------------------------------------------------
/usr/local/sage-9/local/var/lib/sage/venv-python3.9/lib/python3.9/site-packages/cysignals/signals.cpython-39-x86_64-linux-gnu.so(+0x7e1b)[0x7fe106cabe1b]
/usr/local/sage-9/local/var/lib/sage/venv-python3.9/lib/python3.9/site-packages/cysignals/signals.cpython-39-x86_64-linux-gnu.so(+0x7ec9)[0x7fe106cabec9]
/usr/local/sage-9/local/var/lib/sage/venv-python3.9/lib/python3.9/site-packages/cysignals/signals.cpython-39-x86_64-linux-gnu.so(+0xafa3)[0x7fe106caefa3]
/lib/x86_64-linux-gnu/libpthread.so.0(+0x138e0)[0x7fe1099888e0]
/usr/lib/x86_64-linux-gnu/libflint-2.8.2.so(_fmpz_cleanup_mpz_content+0x6a)[0x7fe0b651279a]
/usr/local/sage-9/local/var/lib/sage/venv-python3.9/lib/python3.9/site-packages/sage/libs/flint/flint.cpython-39-x86_64-linux-gnu.so(+0x2e29)[0x7fe0a2a71e29]
python3[0x52326b]
python3(_PyEval_EvalFrameDefault+0x53d1)[0x5149c1]
python3[0x50e2d1]
python3(_PyFunction_Vectorcall+0x3db)[0x525f3b]
python3(_PyEval_EvalFrameDefault+0x53d1)[0x5149c1]
python3[0x50e2d1]
python3(_PyFunction_Vectorcall+0x3db)[0x525f3b]
python3[0x63a580]
python3[0x6287ad]
python3(Py_FinalizeEx+0x4d)[0x62841d]
python3(Py_RunMain+0x170)[0x61eff0]
python3(Py_BytesMain+0x29)[0x606df9]
/lib/x86_64-linux-gnu/libc.so.6(__libc_start_main+0xea)[0x7fe1097d5e4a]
python3(_start+0x2a)[0x606cfa]
------------------------------------------------------------------------
Attaching gdb to process id 174166.
Cannot find gdb installed
GDB is not installed.
Install gdb for enhanced tracebacks.
------------------------------------------------------------------------
Unhandled SIGSEGV: A segmentation fault occurred.
This probably occurred because a *compiled* module has a bug
in it and is not properly wrapped with sig_on(), sig_off().
Python will now terminate.
------------------------------------------------------------------------
Segmentation fault
Both from a terminal session and from emacs‘s sage_shell_mode. I don’t see anything when I stop-and-close a Jupyter notebook.
Thoughts ?
Reply all
Reply to author
Forward
0 new messages