Installation issue on Arch Linux and Manjaro Linux (code is not running)

[borgch]

Hi!

I installed packages gap, gap-packages and jupyter-notebook from system repository and run

$ sudo install -Dm644 /usr/lib/gap/pkg/jupyterkernel/etc/gap-mode/* -t "/usr/share/jupyter/nbextensions/gap-mode"
$ sudo install -Dm644 /usr/lib/gap/pkg/jupyterkernel/etc/gap-mode.json -t "/usr/share/jupyter/nbconfig/notebook.d"
$ sudo install -Dm644 /usr/lib/gap/pkg/jupyterkernel/etc/jupyter/* -t "/usr/share/jupyter/kernels/gap-4"
$ sudo install -Dm755 /usr/lib/gap/pkg/jupyterkernel/bin/jupyter-kernel-gap -t "/usr/bin"

The issue is that GAP cells are not running. In logs there are errors like

W 2025-08-24 06:54:54.214 ServerApp] Nudge: attempt 10 on kernel 3b2154fe-027e-4df5-9385-74fc55e4f8ab
[W 2025-08-24 06:54:54.215 ServerApp] Nudge: attempt 10 on kernel 3b2154fe-027e-4df5-9385-74fc55e4f8ab
[W 2025-08-24 06:54:54.220 ServerApp] Nudge: attempt 10 on kernel 3b2154fe-027e-4df5-9385-74fc55e4f8ab
[W 2025-08-24 06:54:54.226 ServerApp] Nudge: attempt 10 on kernel 3b2154fe-027e-4df5-9385-74fc55e4f8ab
[W 2025-08-24 06:54:54.231 ServerApp] Nudge: attempt 10 on kernel 3b2154fe-027e-4df5-9385-74fc55e4f8ab

jupyter kernelspec list
Available kernels:
gap-4 /usr/share/jupyter/kernels/gap-4
python3 /usr/share/jupyter/kernels/python3

The python3 kernel is working well, but gap-4 not. The result of jupyter notebook --debug is in the attached file
jupyter-debug.log.

gap

 ┌───────┐   GAP 4.14.0 of 2024-12-05
 │  GAP  │   https://www.gap-system.org
 └───────┘   Architecture: x86_64-pc-linux-gnu-default64-kv9
 Configuration:  gmp 6.3.0, GASMAN, readline
 Loading the library and packages ...
 Packages:   AClib 1.3.2, Alnuth 3.2.1, AtlasRep 2.1.9, AutPGrp 1.11, Browse 1.8.21, CRISP 1.4.6, Cryst 4.1.27, CrystCat 1.1.10, CTblLib 1.3.9, curlInterface 2.4.0, FactInt 1.6.3, 
             FGA 1.5.0, Forms 1.2.12, GAPDoc 1.6.7, genss 1.6.9, IO 4.9.1, IRREDSOL 1.4.4, LAGUNA 3.9.7, orb 4.9.1, Polenta 1.3.10, Polycyclic 2.16, PrimGrp 3.4.4, RadiRoot 2.9, 
             recog 1.4.3, ResClasses 4.7.3, SmallGrp 1.5.4, Sophus 1.27, SpinSym 1.5.2, StandardFF 1.0, TomLib 1.2.11, TransGrp 3.6.5, utils 0.85
 Try '??help' for help. See also '?copyright', '?cite' and '?authors'
gap> LoadPackage("JupyterKernel");
─────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────
Loading crypting 0.10.5 (Hashes and Crypto in GAP)
by Markus Pfeiffer (http://www.morphism.de/~markusp/).
maintained by:
   Markus Pfeiffer (http://www.morphism.de/~markusp/) and
   The GAP Team (support@gap-system.org).
Homepage: https://gap-packages.github.io/crypting/
Report issues at https://github.com/gap-packages/crypting/issues
─────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────
─────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────
Loading json 2.2.2 (Reading and Writing JSON)
by Christopher Jefferson (https://heather.cafe/).
Homepage: https://gap-packages.github.io/json/
Report issues at https://github.com/gap-packages/json/issues
─────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────
─────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────
Loading uuid 0.7 (RFC 4122 UUIDs)
by Markus Pfeiffer (http://www.morphism.de/~markusp/).
maintained by:
   The GAP Team (support@gap-system.org).
Homepage: https://gap-packages.github.io/uuid/
Report issues at https://github.com/gap-packages/uuid/issues
─────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────
─────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────
Loading ZeroMQInterface 0.16 (ZeroMQ bindings for GAP)
by Markus Pfeiffer (http://www.morphism.de/~markusp/) and
   Reimer Behrends (http://www.mathematik.uni-kl.de/agag/mitglieder/wissenschaftliche-mitarbeiter/dr-reimer-behrends/).
maintained by:
   The GAP Team (support@gap-system.org).
Homepage: https://gap-packages.github.io/ZeroMQInterface/
Report issues at https://github.com/gap-packages/ZeroMQInterface/issues
─────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────
─────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────
Loading JupyterKernel 1.5.1 (Jupyter kernel written in GAP)
by Markus Pfeiffer (https://markusp.morphism.de/) and
   Manuel Martins (https://github.com/mcmartins).
with contributions by:
   Thomas Breuer,
   Pedro García-Sánchez,
   Sebastian Gutsche,
   Max Horn,
   Fernando Isuru,
   Zachariah Newbery, and
   Sergio Siccha.
maintained by:
   Olexandr Konovalov (https://olexandr-konovalov.github.io/) and
   The GAP Team (support@gap-system.org).
Homepage: https://gap-packages.github.io/JupyterKernel/
Report issues at https://github.com/gap-packages/JupyterKernel/issues
─────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────
true

[borgch]

On a laptop with older version of python everything works. I figured out to install these versions of python and python packages to venv, and this approach works:

(venv) $ python --version
Python 3.12.7
(venv) $ =uv pip freeze
anyio==4.6.2.post1
argcomplete==3.4.0
argon2-cffi==23.1.0
argon2-cffi-bindings==21.2.0
arrow==1.3.0
asttokens==2.4.1
async-lru==2.0.4
attrs==23.2.0
autocommand==2.2.2
babel==2.15.0
beautifulsoup4==4.12.3
bleach==6.1.0
certifi==2024.8.30
cffi==1.17.1
chardet==5.2.0
charset-normalizer==3.4.0
click==8.1.7
colorama==0.4.6
comm==0.2.2
cryptography==43.0.3
dbus-python==1.3.2
debugpy==1.8.16
decorator==5.1.1
defusedxml==0.7.1
docopt==0.6.2
executing==2.1.0
fastjsonschema==2.20.0
filelock==3.16.1
fqdn==1.5.1
h11==0.14.0
httpcore==1.0.5
httpx==0.27.2
idna==3.10
importlib-metadata==7.2.1
ipykernel==6.29.5
ipython==8.29.0
isoduration==20.11.0
jaraco-collections==5.0.1
jaraco-context==5.3.0
jaraco-functools==4.0.2
jaraco-text==4.0.0
jedi==0.19.1
jinja2==3.1.4
json5==0.10.0
jsonpointer==3.0.0
jsonschema==4.23.0
jsonschema-specifications==2023.12.1
jupyter-client==8.6.3
jupyter-collaboration-ui==1.1.0
jupyter-core==5.7.2
jupyter-docprovider==1.1.0
jupyter-events==0.10.0
jupyter-lsp==2.2.6
jupyter-server==2.14.2
jupyter-server-fileid==0.9.3
jupyter-server-terminals==0.5.3
jupyter-server-ydoc==1.1.0
jupyter-ydoc==3.0.2
jupyterlab==4.3.3
jupyterlab-pygments==0.3.0
jupyterlab-server==2.27.3
markdown-it-py==3.0.0
markupsafe==2.1.5
matplotlib-inline==0.1.7
mdurl==0.1.2
meson==1.6.0
mistune==3.0.2
more-itertools==10.3.0
nbclient==0.10.1
nbconvert==7.16.4
nbformat==5.10.4
nest-asyncio==1.6.0
notebook==7.3.1
notebook-shim==0.2.4
npyscreen==4.10.5
opentimelineio==0.17.0
ordered-set==4.1.0
overrides==7.7.0
packaging==24.2
pandocfilters==1.5.1
parso==0.8.4
pexpect==4.9.0
pillow==11.0.0
platformdirs==4.3.6
prometheus-client==0.21.0
prompt-toolkit==3.0.48
psutil==6.1.0
ptyprocess==0.7.0
pure-eval==0.2.3
pyaaf2==1.7.1
pycairo==1.27.0
pycparser==2.22
pycrdt==0.10.8
pycrdt-websocket==0.15.3
pycups==2.0.4
pygments==2.18.0
pygobject==3.50.0
pymupdf==1.25.0
pypdf==5.1.0
pyqt5==5.15.11
pyqt5-qt5==5.15.17
pyqt5-sip==12.16.1
pysmbc==1.0.25.1
python-dateutil==2.9.0
python-json-logger==2.0.7
pytz==2024.2
pyyaml==6.0.2
pyzmq==25.1.2
referencing==0.35.1
reportlab==4.2.2
requests==2.32.3
rfc3339-validator==0.1.4
rfc3986-validator==0.1.1
rich==13.9.4
rpds-py==0.19.0
ruamel-yaml==0.18.6
ruamel-yaml-clib==0.2.12
send2trash==1.8.3
setuptools==75.2.0
six==1.16.0
sniffio==1.3.1
soupsieve==2.6
sqlite-anyio==0.2.3
stack-data==0.6.3
terminado==0.18.1
tinycss2==1.4.0
tomli==2.0.1
tornado==6.4.1
tqdm==4.67.1
traitlets==5.14.3
trove-classifiers==2024.10.21.16
types-python-dateutil==2.9.0.20250822
typing-extensions==4.12.2
uc-micro-py==1.0.3
udiskie==2.5.3
uri-template==1.3.0
urllib3==1.26.20
validate-pyproject==0.22
wcwidth==0.2.13
webcolors==24.11.1
webencodings==0.5.1
websocket-client==1.8.0
wheel==0.45.0
zipp==3.21.0

System versions (not working configurations):

$ python --version
Python 3.13.7
$ pip freeze
alabaster==1.0.0
anyio==4.10.0
apparmor==4.1.1
argcomplete==3.6.2
argon2-cffi==25.1.0
argon2-cffi-bindings==25.1.0
asciidoc==10.2.1
asttokens==3.0.0
async-lru==2.0.5
attrs==25.3.0
autocommand==2.2.2
babel==2.17.0
beautifulsoup4==4.13.4
bleach==6.2.0
certifi==2025.8.3
cffi==1.17.1
chardet==5.2.0
charset-normalizer==3.4.3
click==8.2.1
colorama==0.4.6
comm==0.2.3
contourpy==1.3.3
conway-polynomials==0.10
cryptography==45.0.6
cvxopt==1.3.2
cycler==0.12.1
cypari2==2.2.2
cysignals==1.12.4
decorator==5.2.1
defusedxml==0.7.1
docutils==0.21.2
executing==2.2.0
fastjsonschema==2.21.2
filelock==3.19.1
fonttools==4.59.1
fpylll==0.6.4
gi-docgen==2025.4
gmpy2==2.2.1
h11==0.16.0
httpcore==1.0.9
httpx==0.28.1
idna==3.10
imagesize==1.4.1
importlib_metadata==8.7.0
ipykernel==6.30.1
ipython==9.4.0
ipython_pygments_lexers==1.1.1
ipywidgets==8.1.7
jaraco.collections==5.1.0
jaraco.context==6.0.1
jaraco.functools==4.1.0
jaraco.text==4.0.0
jedi==0.19.2
Jinja2==3.1.6
json5==0.12.1
jsonschema==4.25.1
jsonschema-specifications==2025.4.1
jupyter-events==0.12.0
jupyter_client==8.6.3
jupyter_core==5.8.1
jupyter_server==2.17.0
jupyterlab==4.4.6
jupyterlab_pygments==0.3.0
jupyterlab_server==2.27.3
kiwisolver==1.4.7
legacy-cgi==2.6.3
LibAppArmor==4.1.1
lrcalc==2.0.0
lxml==6.0.1
Mako==1.3.10.dev0
Markdown==3.8.2
markdown-it-py==4.0.0
MarkupSafe==3.0.2
matplotlib==3.10.5
matplotlib-inline==0.1.7
mdurl==0.1.2
memory_allocator==0.1.4
mercurial==7.1
meson==1.8.4
mistune==3.1.3
more-itertools==10.7.0
mpmath==1.3.0
nbclient==0.10.2
nbconvert==7.16.6
nbformat==5.10.4
nest_asyncio==1.6.0
networkx==3.5
notebook==7.4.5
notebook_shim==0.2.4
numpy==2.3.2
OpenTimelineIO==0.17.0
overrides==7.7.0
packaging==25.0
pandas==2.3.1
pandocfilters==1.5.1
parso==0.8.4
pdfCropMargins @ file:///home/boris/.cache/yay/pdfcropmargins/src/pdfCropMargins-2.2.0-py3-none-any.whl#sha256=7d0d3b9c0bfc46d75b640513279a226e0f95c52b172faaac15181015132ed946
pexpect==4.9.0
pillow==11.3.0
platformdirs==4.3.8
pooch==1.8.2
pplpy==0.8.10
primecountpy==0.1.1
prometheus_client==0.22.1
prompt_toolkit==3.0.51
psutil==7.0.0
ptyprocess==0.7.0
pure_eval==0.2.3
pyaaf2==1.7.1
pycparser==2.22
pygdbmi==0.11.0.0
Pygments==2.19.2
PyGObject==3.52.3
PyMuPDF==1.26.3
pyparsing==3.2.3
pypdf==6.0.0
python-dateutil==2.9.0
python-json-logger==3.3.0
python-magic==0.4.27
pytz==2025.2
PyYAML==6.0.2
pyzmq==27.0.2
referencing==0.36.2
requests==2.32.5
rich==14.1.0
roman-numerals-py==3.1.0
rpds-py==0.27.1
rpy2==3.6.2
rpy2-rinterface==3.6.2
rpy2-robjects==3.6.1
ruamel.yaml==0.18.10
ruamel.yaml.clib==0.2.12
sagemath==10.7
scipy==1.16.1
Send2Trash==1.8.3
sentry-sdk==2.35.0
setuptools==80.9.0
six==1.17.0
smartypants==2.0.2
smbus==1.1
sniffio==1.3.1
snowballstemmer==2.2.0
soupsieve==2.7
Sphinx==8.2.3
sphinxcontrib-applehelp==2.0.0
sphinxcontrib-devhelp==2.0.0
sphinxcontrib-htmlhelp==2.1.0
sphinxcontrib-jsmath==1.0.1
sphinxcontrib-qthelp==2.0.0
sphinxcontrib-serializinghtml==2.0.0
stack_data==0.6.3
sympy==1.14.0
TBB==0.2
tinycss2==1.4.0
tornado==6.4.2
tqdm==4.67.1
traitlets==5.14.3
typing_extensions==4.14.1
typogrify==2.1.0
tzlocal==5.3.1
urllib3==2.5.0
wcwidth==0.2.13
webencodings==0.5.1
websocket-client==1.8.0
wheel==0.45.1
zipp==3.21.0

More detailed instructions: https://bbs.archlinux.org/viewtopic.php?pid=2258199#p2258199