Open haesleinhuepf opened 1 year ago
kevinyamauchi
commented
1 year ago @haesleinhuepf , I'm a bit confused why it was looking for linux stuff on Windows. Were your collaborators using the WSL? Can you please provide a bit more detail on how their environment was set up?
haesleinhuepf
commented
1 year ago There was no WSL installed. We used mambaforge which was freshly installed. As far as I could see there was nothing special about these computers.
kevinyamauchi
commented
1 year ago Ah, I wonder if we need to do something special for WSL. Were you using WSL on your computer when you tested?
haesleinhuepf
commented
1 year ago No (sorry I edited my post above presumably while you were typing). There is no WSL installed on these machines
jaimergp
commented
1 year ago The __linux package error is an (unfortunate) red herring. It means that it tried to use the Windows variant, but failed and fell back to the Linux one in a last attempt. This can happen when a dependency is not available on Windows. If you enable the verbose solver logs ("set CONDA_VERBOSITY=3" or -vvv), you might be able to pinpoint the solver backtracking. You can also try the new experimental messages in mamba >=1.3 by adding experimental_sat_error_message: true to ~/.condarc. Is CUDA not available on those machines but it is in yours?
haesleinhuepf
commented
1 year ago Is CUDA not available on those machines but it is in yours?
That's a potential difference between the machines. I can check tomorrow.
However, why should this make a difference? None of the devbio-napari dependencies need CUDA...
haesleinhuepf
commented
1 year ago Hi @jaimergp ,
I finally managed to try it on one of the computers. It turns out, devbio-napari 0.8.1 installs fine if it only comes alone. As soon as we install it using this environment.yml file it does not work anymore:
As soon as one changes the line with devbio-napari to devbio-napari=0.6.0 it works. When running
mamba env create -f "environment (1).yml" -vvv > conda_log.txtThe output is here:
Again, any suggestion is very welcome! I'd like to make devbio-napari as compatible with as many packages as possible.
haesleinhuepf
commented
1 year ago As this is tricky to debug, I would undo the changes between devbio napari 0.6.0 and 0.8.1: https://github.com/conda-forge/devbio-napari-feedstock/compare/023fcf3e5742276a2dbdb444429ea647b179db69...ee6da23f02e80bca0c841777e6426360a8f06ea5
We can bring them back later when we better understand how this works. Does anyone object? @kevinyamauchi @jaimergp
kevinyamauchi
commented
1 year ago Works for me! sorry about the installation troubles.
jaimergp
commented
1 year ago I cannot reproduce with micromamba :(
$ micromamba create -n unused --dry-run --platform=win-64 -f environment.1.yml
__
__ ______ ___ ____ _____ ___ / /_ ____ _
/ / / / __ `__ \/ __ `/ __ `__ \/ __ \/ __ `/
/ /_/ / / / / / / /_/ / / / / / / /_/ / /_/ /
/ .___/_/ /_/ /_/\__,_/_/ /_/ /_/_.___/\__,_/
/_/
conda-forge/win-64 Using cache
conda-forge/noarch Using cache
Transaction
Prefix: /Users/jrodriguez/micromamba/envs/unused
Updating specs:
- aicsimageio=4.9.4
- czifile=2019.7.2
- devbio-napari=0.8.1
- napari=0.4.15
- napari-segment-blobs-and-things-with-membranes=0.3.3
- napari-simpleitk-image-processing=0.4.5
- numpy=1.23.2
- pandas=1.4.3
- pyopencl=2022.1.6
- pyclesperanto-prototype=0.22.0
- python=3.9.12
- scikit-image=0.19.3
- simpleitk=2.1.0
- jupyter=1.0.0
- jupyter_client=7.4.8
- jupyter_console=6.4.4
- jupyter_core=5.1.0
- jupyter_server=1.23.3
- jupyterlab=3.5.1
- jupyterlab_pygments=0.2.2
- jupyterlab_server=2.16.5
- jupytext=1.14.4
- napari-clusters-plotter=0.6.0
- napari-czifile2=0.2.7
- numba=0.56.4
- pip
Package Version Build Channel Size
───────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────
Install:
───────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────
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+ napari-roi 0.1.8 pyhd8ed1ab_0 conda-forge/noarch 18kB
+ napari-segment-blobs-and-things-with-membranes 0.3.3 pyhd8ed1ab_0 conda-forge/noarch 16kB
+ napari-simpleitk-image-processing 0.4.5 pyhd8ed1ab_0 conda-forge/noarch 20kB
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+ openssl 3.1.0 hcfcfb64_0 conda-forge/win-64 7MB
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+ parquet-cpp 1.5.1 2 conda-forge/noarch 3kB
+ parso 0.8.3 pyhd8ed1ab_0 conda-forge/noarch 71kB
+ partd 1.3.0 pyhd8ed1ab_0 conda-forge/noarch 19kB
+ pcre2 10.40 h17e33f8_0 conda-forge/win-64 2MB
+ pickleshare 0.7.5 py_1003 conda-forge/noarch 9kB
+ pillow 9.2.0 py39h595c93f_3 conda-forge/win-64 48MB
+ pint 0.20.1 pyhd8ed1ab_0 conda-forge/noarch 212kB
+ pip 23.0.1 pyhd8ed1ab_0 conda-forge/noarch 1MB
+ pkgutil-resolve-name 1.3.10 pyhd8ed1ab_0 conda-forge/noarch 9kB
+ platformdirs 3.1.1 pyhd8ed1ab_0 conda-forge/noarch 18kB
+ platymatch 0.0.3 pyhd8ed1ab_0 conda-forge/noarch 31kB
+ pluggy 1.0.0 pyhd8ed1ab_5 conda-forge/noarch 16kB
+ ply 3.11 py_1 conda-forge/noarch 45kB
+ pooch 1.7.0 pyha770c72_3 conda-forge/noarch 51kB
+ prometheus_client 0.16.0 pyhd8ed1ab_0 conda-forge/noarch 52kB
+ prompt-toolkit 3.0.38 pyha770c72_0 conda-forge/noarch 269kB
+ prompt_toolkit 3.0.38 hd8ed1ab_0 conda-forge/noarch 6kB
+ psutil 5.9.4 py39ha55989b_0 conda-forge/win-64 379kB
+ psygnal 0.8.1 pyhd8ed1ab_0 conda-forge/noarch 50kB
+ pthread-stubs 0.4 hcd874cb_1001 conda-forge/win-64 6kB
+ pthreads-win32 2.9.1 hfa6e2cd_3 conda-forge/win-64 144kB
+ pure_eval 0.2.2 pyhd8ed1ab_0 conda-forge/noarch 15kB
+ pyarrow 11.0.0 py39hdb2b141_13_cpu conda-forge/win-64 3MB
+ pyclesperanto-prototype 0.22.0 pyhd8ed1ab_0 conda-forge/noarch 213kB
+ pycodestyle 2.10.0 pyhd8ed1ab_0 conda-forge/noarch 43kB
+ pycparser 2.21 pyhd8ed1ab_0 conda-forge/noarch Cached
+ pydantic 1.10.7 py39ha55989b_0 conda-forge/win-64 2MB
+ pygments 2.14.0 pyhd8ed1ab_0 conda-forge/noarch 824kB
+ pynndescent 0.5.8 pyh1a96a4e_0 conda-forge/noarch 48kB
+ pyopencl 2022.1.6 py39h66837cb_0 conda-forge/win-64 656kB
+ pyopengl 3.1.6 pyhd8ed1ab_1 conda-forge/noarch 888kB
+ pyopenssl 23.1.0 pyhd8ed1ab_0 conda-forge/noarch 128kB
+ pyparsing 3.0.9 pyhd8ed1ab_0 conda-forge/noarch 81kB
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+ pyproject_hooks 1.0.0 pyhd8ed1ab_0 conda-forge/noarch 14kB
+ pyqt 5.15.7 py39hb77abff_3 conda-forge/win-64 4MB
+ pyqt5-sip 12.11.0 py39h99910a6_3 conda-forge/win-64 79kB
+ pyqtgraph 0.13.2 pyhd8ed1ab_0 conda-forge/noarch 680kB
+ pyrsistent 0.19.3 py39ha55989b_0 conda-forge/win-64 91kB
+ pysocks 1.7.1 pyh0701188_6 conda-forge/noarch 19kB
+ pyspellchecker 0.7.0 pyhd8ed1ab_0 conda-forge/noarch 2MB
+ pystackreg 0.2.7 py39h2ba5b7c_1 conda-forge/win-64 73kB
+ pytest 7.2.2 pyhd8ed1ab_0 conda-forge/noarch 237kB
+ python 3.9.12 hcf16a7b_1_cpython conda-forge/win-64 19MB
+ python-build 0.10.0 pyhd8ed1ab_0 conda-forge/noarch 21kB
+ python-dateutil 2.8.2 pyhd8ed1ab_0 conda-forge/noarch 246kB
+ python-fastjsonschema 2.16.3 pyhd8ed1ab_0 conda-forge/noarch 225kB
+ python_abi 3.9 3_cp39 conda-forge/win-64 6kB
+ pytomlpp 1.0.13 py39h1f6ef14_0 conda-forge/win-64 183kB
+ pytools 2022.1.14 pyhd8ed1ab_0 conda-forge/noarch 69kB
+ pytz 2022.7.1 pyhd8ed1ab_0 conda-forge/noarch 186kB
+ pywavelets 1.4.1 py39hc266a54_0 conda-forge/win-64 4MB
+ pywin32 304 py39h99910a6_2 conda-forge/win-64 10MB
+ pywinpty 2.0.10 py39h99910a6_0 conda-forge/win-64 211kB
+ pyyaml 6.0 py39ha55989b_5 conda-forge/win-64 157kB
+ pyzmq 25.0.2 py39hea35a22_0 conda-forge/win-64 401kB
+ qt-main 5.15.8 h720456b_6 conda-forge/win-64 60MB
+ qtconsole 5.4.1 pyhd8ed1ab_0 conda-forge/noarch 7kB
+ qtconsole-base 5.4.1 pyha770c72_0 conda-forge/noarch 98kB
+ qtpy 2.3.0 pyhd8ed1ab_0 conda-forge/noarch 51kB
+ re2 2023.02.02 h63175ca_0 conda-forge/win-64 379kB
+ redlionfish 0.9 py39hcbf5309_2 conda-forge/win-64 34kB
+ reikna 0.8.0 pyhd8ed1ab_0 conda-forge/noarch 97kB
+ requests 2.28.2 pyhd8ed1ab_0 conda-forge/noarch 57kB
+ resource_backed_dask_array 0.1.0 pyhd8ed1ab_1 conda-forge/noarch 11kB
+ rich 13.3.2 pyhd8ed1ab_0 conda-forge/noarch 182kB
+ scikit-image 0.19.3 py39h2ba5b7c_2 conda-forge/win-64 11MB
+ scikit-learn 1.2.2 py39h6fe01c0_0 conda-forge/win-64 7MB
+ scipy 1.10.1 py39hfbf2dce_0 conda-forge/win-64 24MB
+ send2trash 1.8.0 pyhd8ed1ab_0 conda-forge/noarch 18kB
+ setuptools 67.6.0 pyhd8ed1ab_0 conda-forge/noarch 579kB
+ shellingham 1.5.1 pyhd8ed1ab_0 conda-forge/noarch 14kB
+ simpleitk 2.1.0 py39hc8d2e25_1 conda-forge/win-64 16MB
+ sip 6.7.7 py39h99910a6_0 conda-forge/win-64 498kB
+ six 1.16.0 pyh6c4a22f_0 conda-forge/noarch 14kB
+ sly 0.4 pyhd8ed1ab_0 conda-forge/noarch 27kB
+ slycot 0.5.0.0 py39h3ce7397_1 conda-forge/win-64 2MB
+ snappy 1.1.10 hfb803bf_0 conda-forge/win-64 57kB
+ sniffio 1.3.0 pyhd8ed1ab_0 conda-forge/noarch 14kB
+ snowballstemmer 2.2.0 pyhd8ed1ab_0 conda-forge/noarch 59kB
+ sortedcontainers 2.4.0 pyhd8ed1ab_0 conda-forge/noarch 26kB
+ soupsieve 2.3.2.post1 pyhd8ed1ab_0 conda-forge/noarch 35kB
+ sphinx 6.1.3 pyhd8ed1ab_0 conda-forge/noarch 1MB
+ sphinxcontrib-applehelp 1.0.4 pyhd8ed1ab_0 conda-forge/noarch 29kB
+ sphinxcontrib-devhelp 1.0.2 py_0 conda-forge/noarch 23kB
+ sphinxcontrib-htmlhelp 2.0.1 pyhd8ed1ab_0 conda-forge/noarch 33kB
+ sphinxcontrib-jsmath 1.0.1 py_0 conda-forge/noarch 7kB
+ sphinxcontrib-qthelp 1.0.3 py_0 conda-forge/noarch 26kB
+ sphinxcontrib-serializinghtml 1.1.5 pyhd8ed1ab_2 conda-forge/noarch 28kB
+ sqlite 3.40.0 hcfcfb64_0 conda-forge/win-64 674kB
+ stack_data 0.6.2 pyhd8ed1ab_0 conda-forge/noarch 26kB
+ stackview 0.5.2 pyhd8ed1ab_0 conda-forge/noarch 25kB
+ suitesparse 5.4.0 h5d0cbe0_1 conda-forge/win-64 1MB
+ superqt 0.4.1 pyhd8ed1ab_0 conda-forge/noarch 55kB
+ svt-av1 1.4.1 h63175ca_0 conda-forge/win-64 2MB
+ sympy 1.11.1 pyh04b8f61_3 conda-forge/noarch 5MB
+ tabulate 0.9.0 pyhd8ed1ab_1 conda-forge/noarch 36kB
+ tbb 2021.8.0 h91493d7_0 conda-forge/win-64 154kB
+ tbb-devel 2021.8.0 h91493d7_0 conda-forge/win-64 1MB
+ tblib 1.7.0 pyhd8ed1ab_0 conda-forge/noarch 15kB
+ terminado 0.17.0 pyh08f2357_0 conda-forge/noarch 20kB
+ the-segmentation-game 0.2.0 pyhd8ed1ab_0 conda-forge/noarch 16kB
+ threadpoolctl 3.1.0 pyh8a188c0_0 conda-forge/noarch 18kB
+ tifffile 2022.10.10 pyhd8ed1ab_0 conda-forge/noarch 163kB
+ tinycss2 1.2.1 pyhd8ed1ab_0 conda-forge/noarch 23kB
+ tk 8.6.12 h8ffe710_0 conda-forge/win-64 4MB
+ toml 0.10.2 pyhd8ed1ab_0 conda-forge/noarch 18kB
+ tomli 2.0.1 pyhd8ed1ab_0 conda-forge/noarch 16kB
+ toolz 0.12.0 pyhd8ed1ab_0 conda-forge/noarch 49kB
+ tornado 6.2 py39ha55989b_1 conda-forge/win-64 673kB
+ tqdm 4.65.0 pyhd8ed1ab_1 conda-forge/noarch 88kB
+ traitlets 5.9.0 pyhd8ed1ab_0 conda-forge/noarch 98kB
+ transforms3d 0.4.1 pyhd8ed1ab_0 conda-forge/noarch 3MB
+ typer 0.4.2 pyhd8ed1ab_0 conda-forge/noarch 46kB
+ typing-extensions 4.5.0 hd8ed1ab_0 conda-forge/noarch 10kB
+ typing_extensions 4.5.0 pyha770c72_0 conda-forge/noarch 31kB
+ tzdata 2022g h191b570_0 conda-forge/noarch Cached
+ ucrt 10.0.22621.0 h57928b3_0 conda-forge/win-64 1MB
+ umap-learn 0.5.3 py39hcbf5309_0 conda-forge/win-64 135kB
+ unicodedata2 15.0.0 py39ha55989b_0 conda-forge/win-64 507kB
+ urllib3 1.26.15 pyhd8ed1ab_0 conda-forge/noarch 113kB
+ vc 14.3 hb6edc58_10 conda-forge/win-64 16kB
+ vispy 0.9.6 py39h5d4886f_1 conda-forge/win-64 2MB
+ vs2015_runtime 14.34.31931 h4c5c07a_10 conda-forge/win-64 725kB
+ wcwidth 0.2.6 pyhd8ed1ab_0 conda-forge/noarch 29kB
+ webencodings 0.5.1 py_1 conda-forge/noarch 12kB
+ websocket-client 1.5.1 pyhd8ed1ab_0 conda-forge/noarch 44kB
+ wheel 0.40.0 pyhd8ed1ab_0 conda-forge/noarch 56kB
+ widgetsnbextension 4.0.6 pyhd8ed1ab_0 conda-forge/noarch 846kB
+ win32_setctime 1.1.0 pyhd8ed1ab_0 conda-forge/noarch 7kB
+ win_inet_pton 1.1.0 pyhd8ed1ab_6 conda-forge/noarch 8kB
+ winpty 0.4.3 4 conda-forge/win-64 1MB
+ wrapt 1.15.0 py39ha55989b_0 conda-forge/win-64 52kB
+ x264 1!164.3095 h8ffe710_2 conda-forge/win-64 1MB
+ x265 3.5 h2d74725_3 conda-forge/win-64 6MB
+ xarray 2023.3.0 pyhd8ed1ab_0 conda-forge/noarch 670kB
+ xmlschema 1.11.3 pyhd8ed1ab_0 conda-forge/noarch 332kB
+ xorg-libxau 1.0.9 hcd874cb_0 conda-forge/win-64 58kB
+ xorg-libxdmcp 1.1.3 hcd874cb_0 conda-forge/win-64 68kB
+ xz 5.2.6 h8d14728_0 conda-forge/win-64 218kB
+ yaml 0.2.5 h8ffe710_2 conda-forge/win-64 63kB
+ zarr 2.14.2 pyhd8ed1ab_0 conda-forge/noarch 156kB
+ zeromq 4.3.4 h0e60522_1 conda-forge/win-64 9MB
+ zfp 1.0.0 h63175ca_3 conda-forge/win-64 283kB
+ zict 2.2.0 pyhd8ed1ab_0 conda-forge/noarch 20kB
+ zipp 3.15.0 pyhd8ed1ab_0 conda-forge/noarch 17kB
+ zlib 1.2.13 hcfcfb64_4 conda-forge/win-64 116kB
+ zlib-ng 2.0.7 hcfcfb64_0 conda-forge/win-64 91kB
+ zstd 1.5.2 h12be248_6 conda-forge/win-64 288kB
Summary:
Install: 422 packages
Total download: 822MB
Solution to issue cannot be found in the documentation.
Issue
Hi @goanpeca @jaimergp , CC @kevinyamauchi ,
I recently had issues installing devbio-napari using mamba on two Windows (!) computers of collaborators. Installing version 0.8.1 failed with an error containing:
Installing devbio-napari 0.6.0 worked fine. Between these versions, we changed this: https://github.com/conda-forge/devbio-napari-feedstock/compare/023fcf3e5742276a2dbdb444429ea647b179db69...ee6da23f02e80bca0c841777e6426360a8f06ea5
Note: Also on my Windows computer devbio-napari 0.8.1 installs properly. It was not obvious what differentiates their Windows 10 config from mine.
Could you do me a favour and check carefully if these changes were done properly? I'm not so much an expert in these OS-dependent conda-forge-thingies. It meet the collaborators weekly so I could test updates to the conda-forge package on their machines. The issue was reproducible.
Big thanks!
Best, Robert
Installed packages
Environment info