sci-mathematics/sage-doc-13 issue
Closed this issue · 13 comments
All other sage related installed fine against dev-lang/python:11.
Forces against dev-lang/python:12
Can you be more precise? Building against py3.12 requires the extra unmasking of gmpy from the sage-on-gentoo overlay.
I've messed up with some unvalidated OP updates. Fixed.
Sorry.
Here's an issue:
sci-mathematics:sage-doc-10.3:20240323-225931.log.gz
- Package: sci-mathematics/sage-doc-10.3:0
- Repository: sage-on-gentoo
- Maintainer: frp.bissey@gmail.com
- USE: abi_x86_64 amd64 elibc_glibc kernel_linux l10n_fr
- FEATURES: network-sandbox preserve-libs sandbox userpriv usersandbox
- Checking whether python3_12 is suitable ...
- dev-lang/python:3.12[readline,sqlite] ...
[ !! ] - Checking whether python3_11 is suitable ...
- dev-lang/python:3.11[readline,sqlite] ...
[ ok ] - python_check_deps ...
-
dev-python/sphinx[python_targets_python3_11(-)] ...
[ ok ]
-
~sci-mathematics/sagemath-standard-10.3[python_targets_python3_11(-),jmol] ...
[ ok ]
-
~sci-mathematics/sage_docbuild-10.3[python_targets_python3_11(-)] ...
[ ok ]
-
dev-python/furo[python_targets_python3_11(-)] ...
[ ok ]
-
dev-python/jupyter-sphinx[python_targets_python3_11(-)] ...
[ ok ]
-
dev-python/sphinx-copybutton[python_targets_python3_11(-)] ...
[ ok ]
-
dev-python/sphinx-inline-tabs[python_targets_python3_11(-)] ...
[ ok ]
[ ok ]
- Using python3.11 to build (via PYTHON_COMPAT iteration)
Unpacking source...
Unpacking sage-doc-10.3.tar.gz to /var/no-tmpfs/portage/sci-mathematics/sage-doc-10.3/work
Source unpacked in /var/no-tmpfs/portage/sci-mathematics/sage-doc-10.3/work
Preparing source in /var/no-tmpfs/portage/sci-mathematics/sage-doc-10.3/work/sage-10.3 ...
- Applying sage-doc-9.5-neutering.patch ...
patching file src/doc/en/reference/misc/index.rst
Hunk #1 succeeded at 212 with fuzz 1 (offset -48 lines).
[ ok ] - Applying sage-doc-10.2-makefile.patch ...
patching file src/doc/Makefile
Hunk #2 succeeded at 40 with fuzz 2.
Hunk #3 succeeded at 63 (offset 3 lines).
[ ok ] - bootstrapping the documentation - be patient
Source prepared.
Configuring source in /var/no-tmpfs/portage/sci-mathematics/sage-doc-10.3/work/sage-10.3 ...
Source configured.
Compiling source in /var/no-tmpfs/portage/sci-mathematics/sage-doc-10.3/work/sage-10.3 ...
make -j1 -l1 doc-html
mkdir -p en/reference/repl
sage -advanced > en/reference/repl/options.txt
make doc-inventory--reference-references
make[1]: Entering directory '/var/no-tmpfs/portage/sci-mathematics/sage-doc-10.3/work/sage-10.3/src/doc'
sage --docbuild --no-pdf-links reference/references inventory
[reference] Matplotlib is building the font cache; this may take a moment.
[reference] building [inventory]: targets for 1 source files that are out of date
[reference] updating environment: [new config] 1 added, 0 changed, 0 removed
[reference] The inventory file is in ../../../build_doc/inventory/en/reference/references.
make[1]: Leaving directory '/var/no-tmpfs/portage/sci-mathematics/sage-doc-10.3/work/sage-10.3/src/doc'
make SAGE_DOCBUILD_OPTS=" --no-prune-empty-dirs" doc-inventory--reference-spkg doc-inventory--reference-manifolds doc-inventory--reference-algebras doc-inventory--reference-polynomial_rings doc-inventory--reference-repl doc-inventory--reference-tensor_free_modules doc-inventory--reference-combinat doc-inventory--reference-dynamics doc-inventory--reference-plot3d doc-inventory--reference-arithgroup doc-inventory--reference-graphs doc-inventory--reference-misc doc-inventory--reference-parallel doc-inventory--reference-topology doc-inventory--reference-arithmetic_curves doc-inventory--reference-asymptotic doc-inventory--reference-calculus doc-inventory--reference-categories doc-inventory--reference-coding doc-inventory--reference-coercion doc-inventory--reference-constants doc-inventory--reference-cpython doc-inventory--reference-cryptography doc-inventory--reference-curves doc-inventory--reference-data_structures doc-inventory--reference-databases doc-inventory--reference-diophantine_approximation doc-inventory--reference-discrete_geometry doc-inventory--reference-doctest doc-inventory--reference-documentation doc-inventory--reference-drinfeld_modules doc-inventory--reference-euclidean_spaces doc-inventory--reference-finite_rings doc-inventory--reference-function_fields doc-inventory--reference-functions doc-inventory--reference-game_theory doc-inventory--reference-games doc-inventory--reference-groups doc-inventory--reference-hecke doc-inventory--reference-history_and_license doc-inventory--reference-homology doc-inventory--reference-hyperbolic_geometry doc-inventory--reference-interfaces doc-inventory--reference-knots doc-inventory--reference-lfunctions doc-inventory--reference-libs doc-inventory--reference-logic doc-inventory--reference-matrices doc-inventory--reference-matroids doc-inventory--reference-modabvar doc-inventory--reference-modfrm doc-inventory--reference-modsym doc-inventory--reference-modules doc-inventory--reference-monoids doc-inventory--reference-noncommutative_polynomial_rings doc-inventory--reference-number_fields doc-inventory--reference-numerical doc-inventory--reference-padics doc-inventory--reference-plotting doc-inventory--reference-power_series doc-inventory--reference-probability doc-inventory--reference-quadratic_forms doc-inventory--reference-quat_algebras doc-inventory--reference-quivers doc-inventory--reference-resolutions doc-inventory--reference-riemannian_geometry doc-inventory--reference-rings doc-inventory--reference-rings_numerical doc-inventory--reference-rings_standard doc-inventory--reference-sat doc-inventory--reference-schemes doc-inventory--reference-semirings doc-inventory--reference-sets doc-inventory--reference-stats doc-inventory--reference-structure doc-inventory--reference-valuations
make[1]: Entering directory '/var/no-tmpfs/portage/sci-mathematics/sage-doc-10.3/work/sage-10.3/src/doc'
sage --docbuild --no-pdf-links reference/spkg inventory --no-prune-empty-dirs
[spkg ] building [inventory]: targets for 474 source files that are out of date
[spkg ] updating environment: [new config] 474 added, 0 changed, 0 removed
[spkg ] The inventory file is in ../../../build_doc/inventory/en/reference/spkg.
sage --docbuild --no-pdf-links reference/manifolds inventory --no-prune-empty-dirs
[manifolds] building [inventory]: targets for 88 source files that are out of date
[manifolds] updating environment: [new config] 88 added, 0 changed, 0 removed
/usr/lib/python3.11/site-packages/cysignals/signals.cpython-311-x86_64-linux-gnu.so(+0x8408)[0x7d389e8f0408]
/usr/lib/python3.11/site-packages/cysignals/signals.cpython-311-x86_64-linux-gnu.so(+0x8514)[0x7d389e8f0514]
/usr/lib/python3.11/site-packages/cysignals/signals.cpython-311-x86_64-linux-gnu.so(+0xc3ac)[0x7d389e8f43ac]
/lib64/libc.so.6(+0x39910)[0x7d38a13de910]
/usr/lib64/libecl.so.21.2(si_safe_eval+0x447)[0x7d38445b76a7]
/usr/lib64/libecl.so.21.2(si_string_to_object+0x131)[0x7d3844568821]
/usr/lib/python3.11/site-packages/sage/libs/ecl.cpython-311-x86_64-linux-gnu.so(+0x19ffa)[0x7d38446d9ffa]
/usr/lib/python3.11/site-packages/sage/libs/ecl.cpython-311-x86_64-linux-gnu.so(+0x15304)[0x7d38446d5304]
/usr/lib/python3.11/site-packages/sage/libs/ecl.cpython-311-x86_64-linux-gnu.so(+0xa8a7)[0x7d38446ca8a7]
/usr/lib64/libpython3.11.so.1.0(PyModule_ExecDef+0x70)[0x7d38a1835180]
/usr/lib64/libpython3.11.so.1.0(+0x23a1bd)[0x7d38a183a1bd]
/usr/lib64/libpython3.11.so.1.0(+0x1bb57e)[0x7d38a17bb57e]
/usr/lib64/libpython3.11.so.1.0(_PyEval_EvalFrameDefault+0x4334)[0x7d38a17a9cf4]
/usr/lib64/libpython3.11.so.1.0(+0x1a10ce)[0x7d38a17a10ce]
/usr/lib64/libpython3.11.so.1.0(+0x1bbd75)[0x7d38a17bbd75]
/usr/lib64/libpython3.11.so.1.0(PyObject_CallMethodObjArgs+0x101)[0x7d38a17e3df1]
/usr/lib64/libpython3.11.so.1.0(PyImport_ImportModuleLevelObject+0x33d)[0x7d38a17e317d]
/usr/lib64/libpython3.11.so.1.0(_PyEval_EvalFrameDefault+0x532e)[0x7d38a17aacee]
/usr/lib64/libpython3.11.so.1.0(+0x1a11fc)[0x7d38a17a11fc]
/usr/lib64/libpython3.11.so.1.0(PyEval_EvalCode+0x8e)[0x7d38a1830a5e]
/usr/lib64/libpython3.11.so.1.0(+0x2441e9)[0x7d38a18441e9]
/usr/lib64/libpython3.11.so.1.0(+0x1b3edb)[0x7d38a17b3edb]
/usr/lib64/libpython3.11.so.1.0(_PyEval_EvalFrameDefault+0x4334)[0x7d38a17a9cf4]
/usr/lib64/libpython3.11.so.1.0(+0x1a10ce)[0x7d38a17a10ce]
/usr/lib64/libpython3.11.so.1.0(+0x1bbd75)[0x7d38a17bbd75]
/usr/lib64/libpython3.11.so.1.0(PyObject_CallMethodObjArgs+0x101)[0x7d38a17e3df1]
/usr/lib64/libpython3.11.so.1.0(PyImport_ImportModuleLevelObject+0x33d)[0x7d38a17e317d]
/usr/lib64/libpython3.11.so.1.0(+0x1f3811)[0x7d38a17f3811]
/usr/lib64/libpython3.11.so.1.0(+0x1b3edb)[0x7d38a17b3edb]
/usr/lib/python3.11/site-packages/sage/misc/lazy_import.cpython-311-x86_64-linux-gnu.so(+0x14841)[0x7d389dde5841]
/usr/lib/python3.11/site-packages/sage/misc/lazy_import.cpython-311-x86_64-linux-gnu.so(+0xb3a6)[0x7d389dddc3a6]
/usr/lib/python3.11/site-packages/sage/misc/lazy_import.cpython-311-x86_64-linux-gnu.so(+0xeb92)[0x7d389dddfb92]
/usr/lib64/libpython3.11.so.1.0(_PyObject_MakeTpCall+0x76)[0x7d38a1799bb6]
/usr/lib64/libpython3.11.so.1.0(_PyEval_EvalFrameDefault+0x82f)[0x7d38a17a61ef]
/usr/lib64/libpython3.11.so.1.0(+0x1a10ce)[0x7d38a17a10ce]
/usr/lib/python3.11/site-packages/sage/symbolic/expression.cpython-311-x86_64-linux-gnu.so(+0x16dabd)[0x7d3852b6dabd]
/usr/lib/python3.11/site-packages/sage/symbolic/expression.cpython-311-x86_64-linux-gnu.so(+0x1773bf)[0x7d3852b773bf]
/usr/lib/python3.11/site-packages/sage/symbolic/ring.cpython-311-x86_64-linux-gnu.so(+0xe401)[0x7d3852ee3401]
/usr/lib64/libpython3.11.so.1.0(+0x1b3edb)[0x7d38a17b3edb]
/usr/lib64/libpython3.11.so.1.0(+0x1d2f76)[0x7d38a17d2f76]
/usr/lib/python3.11/site-packages/sage/symbolic/ring.cpython-311-x86_64-linux-gnu.so(+0x1d6e1)[0x7d3852ef26e1]
/usr/lib/python3.11/site-packages/sage/symbolic/ring.cpython-311-x86_64-linux-gnu.so(+0x1b6a8)[0x7d3852ef06a8]
/usr/lib64/libpython3.11.so.1.0(+0x1b3edb)[0x7d38a17b3edb]
/usr/lib64/libpython3.11.so.1.0(PyObject_Vectorcall+0x33)[0x7d38a17b3433]
/usr/lib64/libpython3.11.so.1.0(_PyEval_EvalFrameDefault+0x82f)[0x7d38a17a61ef]
/usr/lib64/libpython3.11.so.1.0(+0x1a10ce)[0x7d38a17a10ce]
/usr/lib64/libpython3.11.so.1.0(+0x1d2f76)[0x7d38a17d2f76]
/usr/lib/python3.11/site-packages/sage/misc/classcall_metaclass.cpython-311-x86_64-linux-gnu.so(+0x9938)[0x7d389dcc4938]
/usr/lib64/libpython3.11.so.1.0(_PyObject_MakeTpCall+0x76)[0x7d38a1799bb6]
/usr/lib64/libpython3.11.so.1.0(_PyEval_EvalFrameDefault+0x82f)[0x7d38a17a61ef]
/usr/lib64/libpython3.11.so.1.0(+0x1a11fc)[0x7d38a17a11fc]
/usr/lib64/libpython3.11.so.1.0(PyEval_EvalCode+0x8e)[0x7d38a1830a5e]
/usr/lib64/libpython3.11.so.1.0(+0x24a657)[0x7d38a184a657]
/usr/lib64/libpython3.11.so.1.0(+0x247440)[0x7d38a1847440]
/usr/lib64/libpython3.11.so.1.0(PyRun_StringFlags+0x6c)[0x7d38a183d45c]
/usr/lib64/libpython3.11.so.1.0(+0x24427e)[0x7d38a184427e]
/usr/lib64/libpython3.11.so.1.0(+0x1b3edb)[0x7d38a17b3edb]
/usr/lib64/libpython3.11.so.1.0(PyObject_Vectorcall+0x33)[0x7d38a17b3433]
/usr/lib64/libpython3.11.so.1.0(_PyEval_EvalFrameDefault+0x82f)[0x7d38a17a61ef]
/usr/lib64/libpython3.11.so.1.0(+0x1a10ce)[0x7d38a17a10ce]
/usr/lib64/libpython3.11.so.1.0(_PyEval_EvalFrameDefault+0x4334)[0x7d38a17a9cf4]
/usr/lib64/libpython3.11.so.1.0(+0x1a10ce)[0x7d38a17a10ce]
/usr/lib64/libpython3.11.so.1.0(+0x1e4405)[0x7d38a17e4405]
/usr/lib64/libpython3.11.so.1.0(+0x25a692)[0x7d38a185a692]
/usr/lib64/libpython3.11.so.1.0(PyObject_Vectorcall+0x33)[0x7d38a17b3433]
/usr/lib64/libpython3.11.so.1.0(_PyEval_EvalFrameDefault+0x82f)[0x7d38a17a61ef]
/usr/lib64/libpython3.11.so.1.0(+0x1a11fc)[0x7d38a17a11fc]
/usr/lib64/libpython3.11.so.1.0(PyEval_EvalCode+0x8e)[0x7d38a1830a5e]
/usr/lib64/libpython3.11.so.1.0(+0x2441e9)[0x7d38a18441e9]
/usr/lib64/libpython3.11.so.1.0(+0x1b3edb)[0x7d38a17b3edb]
/usr/lib64/libpython3.11.so.1.0(PyObject_Vectorcall+0x33)[0x7d38a17b3433]
/usr/lib64/libpython3.11.so.1.0(_PyEval_EvalFrameDefault+0x82f)[0x7d38a17a61ef]
/usr/lib64/libpython3.11.so.1.0(+0x1a10ce)[0x7d38a17a10ce]
/usr/lib64/libpython3.11.so.1.0(+0x2584ad)[0x7d38a18584ad]
/usr/lib64/libpython3.11.so.1.0(Py_RunMain+0x113)[0x7d38a1857d33]
/usr/lib64/libpython3.11.so.1.0(Py_BytesMain+0x27)[0x7d38a1824ac7]
/lib64/libc.so.6(+0x23b48)[0x7d38a13c8b48]
/lib64/libc.so.6(__libc_start_main+0x8f)[0x7d38a13c8c0f]
/usr/bin/python3.11(_start+0x21)[0x579452510081]
Attaching gdb to process id 115.
Traceback (most recent call last):
File "/usr/lib/python-exec/python3.11/cysignals-CSI", line 225, in
main(args)
File "/usr/lib/python-exec/python3.11/cysignals-CSI", line 174, in main
trace = run_gdb(args.pid, not args.nocolor)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File "/usr/lib/python-exec/python3.11/cysignals-CSI", line 98, in run_gdb
stdout, stderr = cmd.communicate(gdb_commands(pid, color))
^^^^^^^^^^^^^^^^^^^^^^^^
File "/usr/lib/python-exec/python3.11/cysignals-CSI", line 71, in gdb_commands
with open(script, 'rb') as f:
^^^^^^^^^^^^^^^^^^
FileNotFoundError: [Errno 2] No such file or directory: '/usr/lib/python-exec/python3.11/../share/cysignals/cysignals-CSI-helper.py'
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.
make[1]: *** [Makefile:28: doc-inventory--reference-manifolds] Segmentation fault
make[1]: Leaving directory '/var/no-tmpfs/portage/sci-mathematics/sage-doc-10.3/work/sage-10.3/src/doc'
make: *** [Makefile:41: doc-inventory-reference] Error 2
- ERROR: sci-mathematics/sage-doc-10.3::sage-on-gentoo failed (compile phase):
- emake failed
- If you need support, post the output of
emerge --info '=sci-mathematics/sage-doc-10.3::sage-on-gentoo'
, - the complete build log and the output of
emerge -pqv '=sci-mathematics/sage-doc-10.3::sage-on-gentoo'
. - The complete build log is located at '/var/log/portage/sci-mathematics:sage-doc-10.3:20240323-225931.log.gz'.
- For convenience, a symlink to the build log is located at '/var/no-tmpfs/portage/sci-mathematics/sage-doc-10.3/temp/build.log.gz'.
- The ebuild environment file is located at '/var/no-tmpfs/portage/sci-mathematics/sage-doc-10.3/temp/environment'.
- Working directory: '/var/no-tmpfs/portage/sci-mathematics/sage-doc-10.3/work/sage-10.3/src/doc'
- S: '/var/no-tmpfs/portage/sci-mathematics/sage-doc-10.3/work/sage-10.3'
A file present below seems misadressed:
equery f cysignals
- Searching for cysignals ...
- Contents of dev-python/cysignals-1.11.4:
/usr
/usr/bin
/usr/bin/cysignals-CSI -> ../lib/python-exec/python-exec2
/usr/lib
/usr/lib/python-exec
/usr/lib/python-exec/python3.11
/usr/lib/python-exec/python3.11/cysignals-CSI
/usr/lib/python3.11
/usr/lib/python3.11/site-packages
/usr/lib/python3.11/site-packages/cysignals
/usr/lib/python3.11/site-packages/cysignals-1.11.4.dist-info
/usr/lib/python3.11/site-packages/cysignals-1.11.4.dist-info/METADATA
/usr/lib/python3.11/site-packages/cysignals-1.11.4.dist-info/RECORD
/usr/lib/python3.11/site-packages/cysignals-1.11.4.dist-info/WHEEL
/usr/lib/python3.11/site-packages/cysignals-1.11.4.dist-info/top_level.txt
/usr/lib/python3.11/site-packages/cysignals/init.py
/usr/lib/python3.11/site-packages/cysignals/pycache
/usr/lib/python3.11/site-packages/cysignals/pycache/init.cpython-311.opt-1.pyc
/usr/lib/python3.11/site-packages/cysignals/pycache/init.cpython-311.opt-2.pyc
/usr/lib/python3.11/site-packages/cysignals/pycache/init.cpython-311.pyc
/usr/lib/python3.11/site-packages/cysignals/alarm.cpython-311-x86_64-linux-gnu.so
/usr/lib/python3.11/site-packages/cysignals/cysignals_config.h
/usr/lib/python3.11/site-packages/cysignals/macros.h
/usr/lib/python3.11/site-packages/cysignals/memory.pxd
/usr/lib/python3.11/site-packages/cysignals/pselect.cpython-311-x86_64-linux-gnu.so
/usr/lib/python3.11/site-packages/cysignals/pysignals.cpython-311-x86_64-linux-gnu.so
/usr/lib/python3.11/site-packages/cysignals/pysignals.pxd
/usr/lib/python3.11/site-packages/cysignals/signals.cpython-311-x86_64-linux-gnu.so
/usr/lib/python3.11/site-packages/cysignals/signals.pxd
/usr/lib/python3.11/site-packages/cysignals/struct_signals.h
/usr/lib/python3.11/site-packages/cysignals/tests.cpython-311-x86_64-linux-gnu.so
/usr/share
/usr/share/cysignals
/usr/share/cysignals/cysignals-CSI-helper.py
/usr/share/doc
/usr/share/doc/cysignals-1.11.4
/usr/share/doc/cysignals-1.11.4/README.rst.lzma
OK, that looks like two bugs rolled into one. First, the new in tree cysignals
is not patched properly. Possibly, my patch was obsolete, if it has been imported - just checked, no patch for this behavior in the gentoo main tree. Second, there appear to be an issue with libecl
from dev-lisp/ecl
. I would be tempted to rebuild ecl
to see if it fixes thing.
Also, does sage starts?
user@amd64 ~ $ sage
┌────────────────────────────────────────────────────────────────────┐
│ SageMath version 10.3, Release Date: 2024-03-19 │
│ Using Python 3.11.8. Type "help()" for help. │
└────────────────────────────────────────────────────────────────────┘
[U] dev-lisp/ecl
Available versions: 21.2.1-r5(0/21.2.1)^t 23.9.9-r1(0/23.9.9)^t {X cxx debug emacs gengc precisegc +threads +unicode CPU_FLAGS_X86="sse"}
Installed versions: 21.2.1-r5(0/21.2.1)^t(22:21:40 27/01/2024)(emacs -X -cxx -debug -gengc -precisegc -threads -unicode CPU_FLAGS_X86="sse")
Homepage: https://common-lisp.net/project/ecl/
Description: ECL is an embeddable Common Lisp implementation
OK, so sage starts, it is not that libecl or the binding to it is completely broken. But doing specific with it is.
I also may have incorrectly locked sage to ecl-21, when it should be able to use ecl-23. I'll look into that.
OK, you can upgrade ecl after synchronising the overlay with
emaint sync -r sage-on-gentoo
emerge -uv ecl --nodeps
emerge -1v maxima sagemath-standard
new ecl maxima & sagemath-standard[-doc] went fine.
amd64 ~ # eix sage-doc
[I] sci-mathematics/sage-doc [1]
Available versions: (~)10.3^mt **9999*l^mt {doc-pdf L10N="ca de es fr hu it ja pt ru tr"}
Installed versions: 10.3^mt(21:18:28 24/03/2024)(-doc-pdf L10N="fr -ca -de -es -hu -it -ja -pt -ru -tr")
went fine too.
However
USE=doc-pdf emerge sci-mathematics/sage-doc
fails for some reason, possibly specific on my side:
Would you mind to have a look at:
sci-mathematics:sage-doc-10.3:20240324-182724.log.gz
For doc-pdf, you may have missed the news https://github.com/cschwan/sage-on-gentoo/blob/master/metadata/news/2023-12-27-sage-doc-10.3.beta4-and-after/2023-12-27-sage-doc-10.3.beta4-and-after.en.txt
Some stuff changed since then, and maybe I should post an update. texlive-2023 has entered the main tree but is masked. If you want doc-pdf you need to link tools/package.keywords/texlive-2023
in both /etc/portage/package_acceptkeywords
and /etc/portage/package.unmask
there is also the licenses and .use file.
Clear enough +.
Yes indeed, texlive-2023 version constraint could help others.
The sage-doc ebuild needed to have >=texlive-2023 for the doc-pdf useflag, but for some reasons I forgot to do it. Corrected now, anyone wanting doc-pdf will find they need texlive-2023.