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🍊 :bar_chart: :bulb: Orange: Interactive data analysis
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Installing add-ons on Windows updates numpy (and makes Orange useless) #5765

Closed echavezangel closed 2 years ago

echavezangel commented 2 years ago

I am getting a the following problem with data set files ("tab" files) after installing some adds Read error: '''Cannot parse dataset C:/Program Files/Orange/Lib/site-packages/Orange/datasets/housing.tab: Cannot cast ufunc 'contains (vectorized)' output from dtype('O') to dtype('bool') with casting rule 'same_kind' '''

I don't know exactly which is the add causing this problem. This appears after the installation of some adds (network, time series or any except spectroscopy). I updated the orange version 3.30.2 -> 3.31.0 but the problem didn't disappear. The only way to read again "tab" files is uninstalling orange and installing again.

markotoplak commented 2 years ago

On Dec 31 a new version of numpy was released which seemed to get updated during your add-on installation process. The new version of numpy introduced some changes which are incompatible with the current Orange code. We plan to update Orange to support newer numpy versions shortly (the fix was already committed, see #5760).

To confirm that this is the problem could you please open the Orange command prompt and paste the outputs of conda list and conda --version here?

You can solve your problem by installing the previous numpy version manually. Open the Orange command prompt and run conda install numpy=1.21. Please report if that solved your problem. Do not forget to run Orange command prompt as admin.

Does anyone have any idea why would numpy get upgraded when installing add-ons? All but spectroscopy are installed with conda, so It is likely something conda install related. If numpy gets upgraded for at every add-on install (I suspect none has 1.22 as an explicit dependency) we have a problem...

echavezangel commented 2 years ago

Thank you for the answer the installation of previous numpy worked well.

here the full Conda list:

_py-xgboost-mutex 2.0 cpu_0 anyio 3.4.0 py38haa244fe_0 anyqt 0.0.13 pyh6c4a22f_0 asteval 0.9.25 pypi_0 pypi backcall 0.2.0 pyh9f0ad1d_0 backports 1.0 py_2 backports.functools_lru_cache 1.6.4 pyhd8ed1ab_0 baycomp 1.0.2 py_1 blas 2.112 openblas blas-devel 3.9.0 12_win64_openblas bottleneck 1.3.2 py38h6f4d8f0_5 brotli 1.0.9 h8ffe710_6 brotli-bin 1.0.9 h8ffe710_6 brotlipy 0.7.0 py38h294d835_1003 ca-certificates 2021.10.8 h5b45459_0 cachecontrol 0.12.10 pyhd8ed1ab_0 catboost 1.0.3 py38haa244fe_1 certifi 2021.10.8 py38haa244fe_1 cffi 1.15.0 py38hd8c33c5_0 chardet 4.0.0 py38haa244fe_2 charset-normalizer 2.0.8 pyhd8ed1ab_0 colorama 0.4.4 pyh9f0ad1d_0 colorcet 3.0.0 pypi_0 pypi commonmark 0.9.1 py_0 cryptography 36.0.0 py38hb7941b4_0 cycler 0.11.0 pyhd8ed1ab_0 debugpy 1.5.1 py38h885f38d_0 decorator 5.1.0 pyhd8ed1ab_0 dictdiffer 0.9.0 pyhd8ed1ab_0 docutils 0.18.1 py38haa244fe_0 entrypoints 0.3 pyhd8ed1ab_1003 et_xmlfile 1.0.1 py_1001 extranormal3 0.0.3 pypi_0 pypi fonttools 4.28.2 py38h294d835_0 freetype 2.10.4 h546665d_1 future 0.18.2 py38haa244fe_4 h11 0.12.0 pyhd8ed1ab_0 h2 4.1.0 py38haa244fe_0 h5py 3.6.0 pypi_0 pypi hpack 4.0.0 pyh9f0ad1d_0 httpcore 0.13.7 pyhd8ed1ab_0 httpx 0.19.0 py38haa244fe_0 hyperframe 6.0.1 pyhd8ed1ab_0 icu 68.2 h0e60522_0 idna 3.1 pyhd3deb0d_0 importlib-metadata 4.8.2 py38haa244fe_0 importlib_metadata 4.8.2 hd8ed1ab_0 ipykernel 6.5.1 py38h595d716_0 ipython 7.30.1 py38haa244fe_0 ipython_genutils 0.2.0 py_1 jbig 2.1 h8d14728_2003 jedi 0.18.1 py38haa244fe_0 joblib 1.1.0 pyhd8ed1ab_0 jpeg 9d h8ffe710_0 jupyter_client 7.1.0 pyhd8ed1ab_0 jupyter_core 4.9.1 py38haa244fe_1 keyring 23.4.0 py38haa244fe_0 keyrings.alt 4.0.2 pyhd3deb0d_0 kiwisolver 1.3.2 py38hbd9d945_1 lcms2 2.12 h2a16943_0 lerc 3.0 h0e60522_0 libblas 3.9.0 12_win64_openblas libbrotlicommon 1.0.9 h8ffe710_6 libbrotlidec 1.0.9 h8ffe710_6 libbrotlienc 1.0.9 h8ffe710_6 libcblas 3.9.0 12_win64_openblas libclang 11.1.0 default_h5c34c98_1 libdeflate 1.8 h8ffe710_0 libflang 5.0.0 h6538335_20180525 liblapack 3.9.0 12_win64_openblas liblapacke 3.9.0 12_win64_openblas libopenblas 0.3.18 pthreads_hc469a61_0 libpng 1.6.37 h1d00b33_2 libsodium 1.0.18 h8d14728_1 libtiff 4.3.0 hd413186_2 libxgboost 1.5.0 h0e60522_1 libzlib 1.2.11 h8ffe710_1013 llvm-meta 5.0.0 0 lmfit 1.0.3 pypi_0 pypi lockfile 0.12.2 py_1 lz4-c 1.9.3 h8ffe710_1 m2w64-gcc-libgfortran 5.3.0 6 m2w64-gcc-libs 5.3.0 7 m2w64-gcc-libs-core 5.3.0 7 m2w64-gmp 6.1.0 2 m2w64-libwinpthread-git 5.0.0.4634.697f757 2 matplotlib-base 3.5.0 py38h1f000d6_0 matplotlib-inline 0.1.3 pyhd8ed1ab_0 msgpack-python 1.0.3 py38hbd9d945_0 msys2-conda-epoch 20160418 1 munkres 1.1.4 pyh9f0ad1d_0 nest-asyncio 1.5.4 pyhd8ed1ab_0 networkx 2.6.3 pyhd8ed1ab_1 numpy 1.19.5 py38h09042cb_2 (This version was before the installation of the Add) olefile 0.46 pyh9f0ad1d_1 openblas 0.3.18 pthreads_h543f93c_0 openjpeg 2.4.0 hb211442_1 openmp 5.0.0 vc14_1 [vc14] openpyxl 3.0.9 pyhd8ed1ab_0 openssl 1.1.1l h8ffe710_0 opentsne 0.6.1 py38he5193b3_1 orange-canvas-core 0.1.23 pyhd8ed1ab_0 orange-spectroscopy 0.6.3 pypi_0 pypi orange-widget-base 4.15.1 pyhd8ed1ab_0 orange3 3.30.2 py38h5d928e2_0 packaging 21.3 pyhd8ed1ab_0 pandas 1.3.4 py38h5d928e2_1 param 1.12.0 pypi_0 pypi parso 0.8.3 pyhd8ed1ab_0 pebble 4.6.3 pypi_0 pypi pickleshare 0.7.5 py_1003 pillow 8.4.0 py38h794f750_0 pip 21.3.1 pyhd8ed1ab_0 prompt-toolkit 3.0.22 pyha770c72_0 py-xgboost 1.5.0 py38haa244fe_1 pycparser 2.21 pyhd8ed1ab_0 pyct 0.4.8 pypi_0 pypi pygments 2.10.0 pyhd8ed1ab_0 pyopenssl 21.0.0 pyhd8ed1ab_0 pyparsing 3.0.6 pyhd8ed1ab_0 pyqt 5.12.3 py38haa244fe_8 pyqt-impl 5.12.3 py38h885f38d_8 pyqt5-sip 4.19.18 py38h885f38d_8 pyqtchart 5.12 py38h885f38d_8 pyqtgraph 0.12.2 pyhd8ed1ab_0 pyqtwebengine 5.12.1 py38h885f38d_8 pysocks 1.7.1 py38haa244fe_4 python 3.8.8 h7840368_0_cpython python-dateutil 2.8.2 pyhd8ed1ab_0 python-louvain 0.15 pyhd3deb0d_0 python_abi 3.8 2_cp38 pytz 2021.3 pyhd8ed1ab_0 pywin32 302 py38h294d835_2 pywin32-ctypes 0.2.0 py38haa244fe_1004 pyyaml 6.0 py38h294d835_3 pyzmq 22.3.0 py38h09162b1_1 qasync 0.22.0 pyhd8ed1ab_0 qt 5.12.9 h5909a2a_4 qtconsole 5.2.1 pyhd8ed1ab_0 qtpy 1.11.2 pyhd8ed1ab_0 renishawwire 0.1.15 pypi_0 pypi requests 2.26.0 pyhd8ed1ab_1 rfc3986 1.5.0 pyhd8ed1ab_0 scikit-learn 0.23.2 py38ha09990b_3 scipy 1.5.3 py38h5f893b4_0 serverfiles 0.3.0 py_0 setuptools 59.4.0 py38haa244fe_0 six 1.16.0 pyh6c4a22f_0 sniffio 1.2.0 py38haa244fe_2 spectral 0.22.4 pypi_0 pypi sqlite 3.37.0 h8ffe710_0 threadpoolctl 3.0.0 pyh8a188c0_0 tk 8.6.11 h8ffe710_1 tornado 6.1 py38h294d835_2 traitlets 5.1.1 pyhd8ed1ab_0 typing_extensions 4.0.1 pyha770c72_0 ucrt 10.0.20348.0 h57928b3_0 uncertainties 3.1.6 pypi_0 pypi unicodedata2 13.0.0.post2 py38h294d835_4 urllib3 1.26.7 pyhd8ed1ab_0 vc 14.2 hb210afc_5 vs2015_runtime 14.29.30037 h902a5da_5 wcwidth 0.2.5 pyh9f0ad1d_2 wheel 0.37.0 pyhd8ed1ab_1 win_inet_pton 1.1.0 py38haa244fe_3 xgboost 1.5.0 py38haa244fe_1 xlrd 2.0.1 pyhd8ed1ab_3 xlsxwriter 3.0.2 pyhd8ed1ab_0 xz 5.2.5 h62dcd97_1 yaml 0.2.5 he774522_0 zeromq 4.3.4 h0e60522_1 zipp 3.6.0 pyhd8ed1ab_0 zlib 1.2.11 h8ffe710_1013 zstd 1.5.0 h6255e5f_0

Conda --ver : conda 4.9.2

markotoplak commented 2 years ago

@echavezangel, thanks! Reopening because it needs to be seen why (or if) installing add-ons on Windows upgrades numpy. If it does, we also need new Windows packages.

markotoplak commented 2 years ago

I tried 3 add-ons on a test Windows computer. I confirm, Text really forced the numpy upgrade. Interesting, it seems that one of its dependencies requires numpy newer that 1.19, at least on conda-forge.

To somewhat fix this issue or at least make Orange users suffer from it less often:

PrimozGodec commented 2 years ago

Now the new release of Orange3-text is made. Updating it to the newest version 1.6.2 should also fix Orange since it updates it.