Having trouble running the main function

[Abeltheroy]

when i run the main.py,it shows "Fatal error: unable to initialize theJIT",then it shows
Error in .makeMessage(..., domain = domain) :
3 arguments passed to .Internal(gettext) which requires 2
Error in gettext(fmt, domain = domain, trim = trim) :
3 arguments passed to .Internal(gettext) which requires 2
Error in Ops.numeric_version(R_version_built_under, "4.0.0") :
there is no .Internal function 'compareNumericVersion'

[wdevazelhes]

Hi, thanks a lot for using our repo, could you share the details of your Python environment (such as packages versions etc ?) I believe the error may be due to the dependencies, as the code snippet you provided does not contain any code specific to the current repo

[wdevazelhes]

Also, it seems that maybe the problem is coming from the R package (cf. (R_version_built_under, "4.0.0")) (we use it through rpy2 in python)
Below is a recommended installation script, which should normally install a clean environment, but let us know if it still does not work after using this script:

$ conda create -n ksn -c conda-forge numpy scipy scikit-learn tqdm matplotlib pandas rpy2
$ conda activate ksn
$ pip install libsvmdata benchopt jupyter modopt appdirs

[Abeltheroy]

under the folder prediction,the main.py.Could you please provide the environment requirements? After checking the information, it seems that it is related to the R language environment?

[wdevazelhes]

Yes, indeed you are right, I also believe it is related to R (used with rpy2): the requirements as per the readme are numpy scipy scikit-learn tqdm matplotlib pandas rpy2 libsvmdata benchopt jupyter modopt appdirs, but the recommended installation process is as follows:

With an updated conda:

$ conda create -n ksn -c conda-forge numpy scipy scikit-learn tqdm matplotlib pandas rpy2
$ conda activate ksn
$ pip install libsvmdata benchopt jupyter modopt appdirs

rpy2 seems to have a non-standard install compared to usual Python packages (even on my mac it prompts me something related to the JDK whenever I activate the environment), so I guess it may not work properly if installed differently than in the steps above: let us know if even using the steps above it still does not work 👍🙏

[Abeltheroy]

Package Version

---

anyio 4.3.0
appdirs 1.4.4
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
Babel 2.14.0
beautifulsoup4 4.12.3
benchopt 1.5.1
bleach 6.1.0
certifi 2024.2.2
cffi 1.16.0
charset-normalizer 3.3.2
click 8.1.7
colorama 0.4.6
comm 0.2.2
contourpy 1.2.0
cryptography 42.0.5
cycler 0.12.1
debugpy 1.8.1
decorator 5.1.1
defusedxml 0.7.1
Deprecated 1.2.14
download 0.3.5
executing 2.0.1
fastjsonschema 2.19.1
fonttools 4.49.0
fqdn 1.5.1
h11 0.14.0
httpcore 1.0.4
httpx 0.27.0
idna 3.6
importlib_metadata 7.0.2
ipykernel 6.29.3
ipython 8.22.2
ipywidgets 8.1.2
isoduration 20.11.0
jedi 0.19.1
Jinja2 3.1.3
joblib 1.3.2
json5 0.9.24
jsonpointer 2.4
jsonschema 4.21.1
jsonschema-specifications 2023.12.1
jupyter 1.0.0
jupyter_client 8.6.1
jupyter-console 6.6.3
jupyter_core 5.7.2
jupyter-events 0.9.1
jupyter-lsp 2.2.4
jupyter_server 2.13.0
jupyter_server_terminals 0.5.3
jupyterlab 4.1.5
jupyterlab_pygments 0.3.0
jupyterlab_server 2.25.4
jupyterlab_widgets 3.0.10
kiwisolver 1.4.5
libsvmdata 0.4.1
line-profiler 4.1.2
Mako 1.3.2
MarkupSafe 2.1.5
matplotlib 3.8.3
matplotlib-inline 0.1.6
mistune 3.0.2
modopt 1.7.1
munkres 1.1.4
nbclient 0.10.0
nbconvert 7.16.2
nbformat 5.10.3
nest-asyncio 1.6.0
notebook 7.1.2
notebook_shim 0.2.4
numpy 1.26.4
overrides 7.7.0
packaging 24.0
pandas 2.2.1
pandocfilters 1.5.1
parso 0.8.3
pillow 10.2.0
pip 24.0
platformdirs 4.2.0
plotly 5.20.0
ply 3.11
prometheus_client 0.20.0
prompt-toolkit 3.0.43
psutil 5.9.8
pure-eval 0.2.2
pyarrow 15.0.1
pycparser 2.21
PyGithub 2.2.0
Pygments 2.17.2
PyJWT 2.8.0
PyNaCl 1.5.0
pyparsing 3.1.2
PyQt5 5.15.9
PyQt5-sip 12.12.2
python-dateutil 2.9.0
python-json-logger 2.0.7
pytz 2024.1
pywin32 306
pywinpty 2.0.13
PyYAML 6.0.1
pyzmq 25.1.2
qtconsole 5.5.1
QtPy 2.4.1
referencing 0.34.0
requests 2.31.0
rfc3339-validator 0.1.4
rfc3986-validator 0.1.1
rpds-py 0.18.0
rpy2 3.5.11
scikit-learn 1.4.1.post1
scipy 1.12.0
Send2Trash 1.8.2
setuptools 69.2.0
simplegeneric 0.8.1
sip 6.7.12
six 1.16.0
sniffio 1.3.1
soupsieve 2.5
stack-data 0.6.3
tenacity 8.2.3
terminado 0.18.1
threadpoolctl 3.3.0
tinycss2 1.2.1
toml 0.10.2
tomli 2.0.1
tornado 6.4
tqdm 4.66.2
traitlets 5.14.2
types-python-dateutil 2.9.0.20240316
typing_extensions 4.10.0
tzdata 2024.1
tzlocal 5.2
uri-template 1.3.0
urllib3 2.2.1
wcwidth 0.2.13
webcolors 1.13
webencodings 0.5.1
websocket-client 1.7.0
wheel 0.42.0
widgetsnbextension 4.0.10
wrapt 1.16.0
zipp 3.18.1
This is the environment. I installed it according to your instructions, but I still got the same error.

[wdevazelhes]

Thanks a lot for the details, looks like you have the same rpy2 version as me (but I didn't check all other packages):
I tried to reproduce the issue by reinstalling the environment from scratch on my machine according to the conda script above, but running main.py works for me then: so here are a few possible reasons which may cause the issue in your case:

• what conda version did you run the script with ? I have 23.7.2 (if you have another version, you may try to relaunch the script above with a new conda 23.7.2 install (with a new env from scratch))
• what python version do you have ? I have 3.12.2 on my environment
• what machine are you running the script on ? I am running on a macbook: if you are running on a different machine (e.g. windows), maybe we can investigate further on why there is a machine specific bug
• Finally, could you maybe print the output of conda list after activating your environment ? This way we can see what channel all packages come from and the corresponding binary reference

Let me know if that helps 👍🙏

[Abeltheroy]

Thank you for your answer. I am running on windows and the conda list shows： # Name Version Build Channel
_r-mutex 1.0.1 anacondar_1 conda-forge
anyio 4.3.0 pypi_0 pypi
appdirs 1.4.4 pypi_0 pypi
argon2-cffi 23.1.0 pypi_0 pypi
argon2-cffi-bindings 21.2.0 pypi_0 pypi
arrow 1.3.0 pypi_0 pypi
asttokens 2.4.1 pypi_0 pypi
async-lru 2.0.4 pypi_0 pypi
attrs 23.2.0 pypi_0 pypi
babel 2.14.0 pypi_0 pypi
beautifulsoup4 4.12.3 pypi_0 pypi
benchopt 1.5.1 pypi_0 pypi
bleach 6.1.0 pypi_0 pypi
brotli 1.1.0 hcfcfb64_1 conda-forge
brotli-bin 1.1.0 hcfcfb64_1 conda-forge
bzip2 1.0.8 hcfcfb64_5 conda-forge
ca-certificates 2024.2.2 h56e8100_0 conda-forge
certifi 2024.2.2 pyhd8ed1ab_0 conda-forge
cffi 1.16.0 py312he70551f_0 conda-forge
charset-normalizer 3.3.2 pypi_0 pypi
click 8.1.7 pypi_0 pypi
colorama 0.4.6 pyhd8ed1ab_0 conda-forge
comm 0.2.2 pypi_0 pypi
contourpy 1.2.0 py312h0d7def4_0 conda-forge
cryptography 42.0.5 pypi_0 pypi
cycler 0.12.1 pyhd8ed1ab_0 conda-forge
debugpy 1.8.1 pypi_0 pypi
decorator 5.1.1 pypi_0 pypi
defusedxml 0.7.1 pypi_0 pypi
deprecated 1.2.14 pypi_0 pypi
download 0.3.5 pypi_0 pypi
executing 2.0.1 pypi_0 pypi
fastjsonschema 2.19.1 pypi_0 pypi
fonttools 4.49.0 py312he70551f_0 conda-forge
fqdn 1.5.1 pypi_0 pypi
freetype 2.12.1 hdaf720e_2 conda-forge
gettext 0.21.1 h5728263_0 conda-forge
glib 2.80.0 h39d0aa6_0 conda-forge
glib-tools 2.80.0 h0a98069_0 conda-forge
gst-plugins-base 1.22.9 h001b923_0 conda-forge
gstreamer 1.22.9 hb4038d2_0 conda-forge
h11 0.14.0 pypi_0 pypi
httpcore 1.0.4 pypi_0 pypi
httpx 0.27.0 pypi_0 pypi
icu 73.2 h63175ca_0 conda-forge
idna 3.6 pypi_0 pypi
importlib-metadata 7.0.2 pypi_0 pypi
intel-openmp 2024.0.0 h57928b3_49841 conda-forge
ipykernel 6.29.3 pypi_0 pypi
ipython 8.22.2 pypi_0 pypi
ipywidgets 8.1.2 pypi_0 pypi
isoduration 20.11.0 pypi_0 pypi
jedi 0.19.1 pypi_0 pypi
jinja2 3.1.3 pyhd8ed1ab_0 conda-forge
joblib 1.3.2 pyhd8ed1ab_0 conda-forge
json5 0.9.24 pypi_0 pypi
jsonpointer 2.4 pypi_0 pypi
jsonschema 4.21.1 pypi_0 pypi
jsonschema-specifications 2023.12.1 pypi_0 pypi
jupyter 1.0.0 pypi_0 pypi
jupyter-client 8.6.1 pypi_0 pypi
jupyter-console 6.6.3 pypi_0 pypi
jupyter-core 5.7.2 pypi_0 pypi
jupyter-events 0.9.1 pypi_0 pypi
jupyter-lsp 2.2.4 pypi_0 pypi
jupyter-server 2.13.0 pypi_0 pypi
jupyter-server-terminals 0.5.3 pypi_0 pypi
jupyterlab 4.1.5 pypi_0 pypi
jupyterlab-pygments 0.3.0 pypi_0 pypi
jupyterlab-server 2.25.4 pypi_0 pypi
jupyterlab-widgets 3.0.10 pypi_0 pypi
kiwisolver 1.4.5 py312h0d7def4_1 conda-forge
krb5 1.21.2 heb0366b_0 conda-forge
lcms2 2.16 h67d730c_0 conda-forge
lerc 4.0.0 h63175ca_0 conda-forge
libblas 3.9.0 21_win64_mkl conda-forge
libbrotlicommon 1.1.0 hcfcfb64_1 conda-forge
libbrotlidec 1.1.0 hcfcfb64_1 conda-forge
libbrotlienc 1.1.0 hcfcfb64_1 conda-forge
libcblas 3.9.0 21_win64_mkl conda-forge
libclang 15.0.7 default_hde6756a_4 conda-forge
libclang13 15.0.7 default_h85b4d89_4 conda-forge
libdeflate 1.19 hcfcfb64_0 conda-forge
libexpat 2.6.2 h63175ca_0 conda-forge
libffi 3.4.2 h8ffe710_5 conda-forge
libglib 2.80.0 h39d0aa6_0 conda-forge
libhwloc 2.9.3 default_haede6df_1009 conda-forge
libiconv 1.17 hcfcfb64_2 conda-forge
libjpeg-turbo 3.0.0 hcfcfb64_1 conda-forge
liblapack 3.9.0 21_win64_mkl conda-forge
libogg 1.3.4 h8ffe710_1 conda-forge
libpng 1.6.43 h19919ed_0 conda-forge
libsqlite 3.45.2 hcfcfb64_0 conda-forge
libsvmdata 0.4.1 pypi_0 pypi
libtiff 4.6.0 h6e2ebb7_2 conda-forge
libvorbis 1.3.7 h0e60522_0 conda-forge
libwebp-base 1.3.2 hcfcfb64_0 conda-forge
libxcb 1.15 hcd874cb_0 conda-forge
libxml2 2.12.5 hc3477c8_0 conda-forge
libzlib 1.2.13 hcfcfb64_5 conda-forge
line-profiler 4.1.2 pypi_0 pypi
m2w64-bwidget 1.9.10 2 conda-forge
m2w64-bzip2 1.0.6 6 conda-forge
m2w64-expat 2.1.1 2 conda-forge
m2w64-fftw 3.3.4 6 conda-forge
m2w64-flac 1.3.1 3 conda-forge
m2w64-gcc-libgfortran 5.3.0 6 conda-forge
m2w64-gcc-libs 5.3.0 7 conda-forge
m2w64-gcc-libs-core 5.3.0 7 conda-forge
m2w64-gettext 0.19.7 2 conda-forge
m2w64-gmp 6.1.0 2 conda-forge
m2w64-gsl 2.1 2 conda-forge
m2w64-libiconv 1.14 6 conda-forge
m2w64-libjpeg-turbo 1.4.2 3 conda-forge
m2w64-libogg 1.3.2 3 conda-forge
m2w64-libpng 1.6.21 2 conda-forge
m2w64-libsndfile 1.0.26 2 conda-forge
m2w64-libtiff 4.0.6 2 conda-forge
m2w64-libvorbis 1.3.5 2 conda-forge
m2w64-libwinpthread-git 5.0.0.4634.697f757 2 conda-forge
m2w64-libxml2 2.9.3 3 conda-forge
m2w64-mpfr 3.1.4 4 conda-forge
m2w64-pcre2 10.34 0 conda-forge
m2w64-speex 1.2rc2 3 conda-forge
m2w64-speexdsp 1.2rc3 3 conda-forge
m2w64-tcl 8.6.5 3 conda-forge
m2w64-tk 8.6.5 3 conda-forge
m2w64-tktable 2.10 5 conda-forge
m2w64-wineditline 2.101 5 conda-forge
m2w64-xz 5.2.2 2 conda-forge
m2w64-zlib 1.2.8 10 conda-forge
mako 1.3.2 pypi_0 pypi
markupsafe 2.1.5 py312he70551f_0 conda-forge
matplotlib 3.8.3 py312h2e8e312_0 conda-forge
matplotlib-base 3.8.3 py312h26ecaf7_0 conda-forge
matplotlib-inline 0.1.6 pypi_0 pypi
mistune 3.0.2 pypi_0 pypi
mkl 2024.0.0 h66d3029_49657 conda-forge
modopt 1.7.1 pypi_0 pypi
msys2-conda-epoch 20160418 1 conda-forge
munkres 1.1.4 pyh9f0ad1d_0 conda-forge
nbclient 0.10.0 pypi_0 pypi
nbconvert 7.16.2 pypi_0 pypi
nbformat 5.10.3 pypi_0 pypi
nest-asyncio 1.6.0 pypi_0 pypi
notebook 7.1.2 pypi_0 pypi
notebook-shim 0.2.4 pypi_0 pypi
numpy 1.26.4 py312h8753938_0 conda-forge
openjpeg 2.5.2 h3d672ee_0 conda-forge
openssl 3.2.1 hcfcfb64_0 conda-forge
overrides 7.7.0 pypi_0 pypi
packaging 24.0 pyhd8ed1ab_0 conda-forge
pandas 2.2.1 py312h2ab9e98_0 conda-forge
pandocfilters 1.5.1 pypi_0 pypi
parso 0.8.3 pypi_0 pypi
pcre2 10.43 h17e33f8_0 conda-forge
pillow 10.2.0 py312he768995_0 conda-forge
pip 24.0 pyhd8ed1ab_0 conda-forge
platformdirs 4.2.0 pypi_0 pypi
plotly 5.20.0 pypi_0 pypi
ply 3.11 py_1 conda-forge
prometheus-client 0.20.0 pypi_0 pypi
prompt-toolkit 3.0.43 pypi_0 pypi
psutil 5.9.8 pypi_0 pypi
pthread-stubs 0.4 hcd874cb_1001 conda-forge
pthreads-win32 2.9.1 hfa6e2cd_3 conda-forge
pure-eval 0.2.2 pypi_0 pypi
pyarrow 15.0.1 pypi_0 pypi
pycparser 2.21 pyhd8ed1ab_0 conda-forge
pygithub 2.2.0 pypi_0 pypi
pygments 2.17.2 pypi_0 pypi
pyjwt 2.8.0 pypi_0 pypi
pynacl 1.5.0 pypi_0 pypi
pyparsing 3.1.2 pyhd8ed1ab_0 conda-forge
pyqt 5.15.9 py312he09f080_5 conda-forge
pyqt5-sip 12.12.2 py312h53d5487_5 conda-forge
python 3.12.2 h2628c8c_0_cpython conda-forge
python-dateutil 2.9.0 pyhd8ed1ab_0 conda-forge
python-json-logger 2.0.7 pypi_0 pypi
python-tzdata 2024.1 pyhd8ed1ab_0 conda-forge
python_abi 3.12 4_cp312 conda-forge
pytz 2024.1 pyhd8ed1ab_0 conda-forge
pywin32 306 pypi_0 pypi
pywinpty 2.0.13 pypi_0 pypi
pyyaml 6.0.1 pypi_0 pypi
pyzmq 25.1.2 pypi_0 pypi
qt-main 5.15.8 h9e85ed6_19 conda-forge
qtconsole 5.5.1 pypi_0 pypi
qtpy 2.4.1 pypi_0 pypi
r-base 4.1.3 hdca333a_12 conda-forge
referencing 0.34.0 pypi_0 pypi
requests 2.31.0 pypi_0 pypi
rfc3339-validator 0.1.4 pypi_0 pypi
rfc3986-validator 0.1.1 pypi_0 pypi
rpds-py 0.18.0 pypi_0 pypi
rpy2 3.5.11 py312r41hd0f9d78_3 conda-forge
scikit-learn 1.4.1.post1 py312hcacafb1_0 conda-forge
scipy 1.12.0 py312h8753938_2 conda-forge
send2trash 1.8.2 pypi_0 pypi
setuptools 69.2.0 pyhd8ed1ab_0 conda-forge
simplegeneric 0.8.1 py_1 conda-forge
sip 6.7.12 py312h53d5487_0 conda-forge
six 1.16.0 pyh6c4a22f_0 conda-forge
sniffio 1.3.1 pypi_0 pypi
soupsieve 2.5 pypi_0 pypi
stack-data 0.6.3 pypi_0 pypi
tbb 2021.11.0 h91493d7_1 conda-forge
tenacity 8.2.3 pypi_0 pypi
terminado 0.18.1 pypi_0 pypi
threadpoolctl 3.3.0 pyhc1e730c_0 conda-forge
tinycss2 1.2.1 pypi_0 pypi
tk 8.6.13 h5226925_1 conda-forge
toml 0.10.2 pyhd8ed1ab_0 conda-forge
tomli 2.0.1 pyhd8ed1ab_0 conda-forge
tornado 6.4 py312he70551f_0 conda-forge
tqdm 4.66.2 pyhd8ed1ab_0 conda-forge
traitlets 5.14.2 pypi_0 pypi
types-python-dateutil 2.9.0.20240316 pypi_0 pypi
typing-extensions 4.10.0 pypi_0 pypi
tzdata 2024a h0c530f3_0 conda-forge
tzlocal 5.2 py312h2e8e312_0 conda-forge
ucrt 10.0.22621.0 h57928b3_0 conda-forge
uri-template 1.3.0 pypi_0 pypi
urllib3 2.2.1 pypi_0 pypi
vc 14.3 hcf57466_18 conda-forge
vc14_runtime 14.38.33130 h82b7239_18 conda-forge
vs2015_runtime 14.38.33130 hcb4865c_18 conda-forge
wcwidth 0.2.13 pypi_0 pypi
webcolors 1.13 pypi_0 pypi
webencodings 0.5.1 pypi_0 pypi
websocket-client 1.7.0 pypi_0 pypi
wheel 0.42.0 pyhd8ed1ab_0 conda-forge
widgetsnbextension 4.0.10 pypi_0 pypi
wrapt 1.16.0 pypi_0 pypi
xorg-libxau 1.0.11 hcd874cb_0 conda-forge
xorg-libxdmcp 1.1.3 hcd874cb_0 conda-forge
xz 5.2.6 h8d14728_0 conda-forge
zipp 3.18.1 pypi_0 pypi
zstd 1.5.5 h12be248_0 conda-forge

[wdevazelhes]

Thanks a lot, the environment looks similar to mine (there are a few differences though, such as m2w64 which is installed, we may look into that later), but I guess the environment may be OK, but looking online, I found someone saying that if you have already a pre-existing installation of R, this may cause errors: is this the case ? (i.e. do you have a pre-existing installation of R on your machine ?)

If so, you may be able to specify not to use it, by adding the snippet from that answer, e.g. at the beginning of main.py: https://stackoverflow.com/a/71050531/5635843

Let me know if this helps 👍

[Abeltheroy]

I also found this article before. I had installed the R environment and set up ‘import os’ according to the article.
os.environ['R_HOME'] = '/Users//anaconda3/envs//lib/R'', but the JIT error still pops up. I just uninstalled R and it shows up again. 'R_HOME must be set in the environment or Registry'

[wdevazelhes]

For the path of R, did you put the one you wrote above (i.e. '/Users//anaconda3/envs//lib/R') ?
If so, I think this would not be the right one, given that you use Windows (which has a backslash not slash), that your username is Abeltheroy (replace if applicable), and the name of the conda environment is ksn (replace Anaconda3 by Miniconda3 if applicable), it should most likely look like something like this (can you confirm that this "R" file is indeed present on your machine at the written location below ?):

import os
os.environ['R_HOME'] =  'C:\Users\Abeltheroy\Anaconda3\envs\ksn\lib\R'

Otherwise, when saying "uninstalled R", do you mean you uninstalled the machine-wise R, or the R from the environment ? (it should be the machine-wise R, not the one from the environment, i.e. you shouldn't run any conda uninstall command, or delete any file from the conda env)

Let me know if this helps ?

[wdevazelhes]

Sorry if this does not help, it is hard for me to debug it because I don't have a windows machine.. Also, this seems related to a problem installing/executing rpy2, but not to a problem about the repo itself..
Let me know if the above works, if not, I may look into it a bit, but I won't be able to do much..