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kmayerb / tcrdist3

flexible CDR based distance metrics
MIT License
53 stars 17 forks source link

Installation error: File name too long #75

Open canuckafar opened 1 year ago

canuckafar commented 1 year ago

Hi there. Having trouble installing tcrdist3 on Linux. Apparently there appears to be a file name that is too long. Any recommendations?

Thank you.

BI

$ pip install git+https://github.com/kmayerb/tcrdist3.git@0.2.2
Defaulting to user installation because normal site-packages is not writeable
Collecting git+https://github.com/kmayerb/tcrdist3.git@0.2.2
  Cloning https://github.com/kmayerb/tcrdist3.git (to revision 0.2.2) to /tmp/pip-req-build-105ty4k_
  Running command git clone --filter=blob:none --quiet https://github.com/kmayerb/tcrdist3.git /tmp/pip-req-build-105ty4k_
  Running command git checkout -q 04b0b8c2573d04a9d2cb77f7a3aeeed3a0eab167
  Resolved https://github.com/kmayerb/tcrdist3.git to commit 04b0b8c2573d04a9d2cb77f7a3aeeed3a0eab167
  Preparing metadata (setup.py) ... done
Requirement already satisfied: dill>=0.3.2 in ./.local/lib/python3.10/site-packages (from tcrdist3==0.2.2) (0.3.5.1)
Requirement already satisfied: fishersapi in ./.local/lib/python3.10/site-packages (from tcrdist3==0.2.2) (0.5)
Requirement already satisfied: hierdiff>=0.4 in ./.local/lib/python3.10/site-packages (from tcrdist3==0.2.2) (0.9)
Requirement already satisfied: numba in ./.local/lib/python3.10/site-packages (from tcrdist3==0.2.2) (0.56.2)
Requirement already satisfied: numpy>=1.16.4 in ./.local/lib/python3.10/site-packages (from tcrdist3==0.2.2) (1.23.3)
Requirement already satisfied: olga>=1.2.1 in ./.local/lib/python3.10/site-packages (from tcrdist3==0.2.2) (1.2.4)
Requirement already satisfied: palmotif>=0.2 in ./.local/lib/python3.10/site-packages (from tcrdist3==0.2.2) (0.4)
Requirement already satisfied: pandas>=0.24.2 in ./.local/lib/python3.10/site-packages (from tcrdist3==0.2.2) (1.5.0)
Requirement already satisfied: parasail>=1.1.17 in ./.local/lib/python3.10/site-packages (from tcrdist3==0.2.2) (1.3.3)
Requirement already satisfied: parmap>=1.5.2 in ./.local/lib/python3.10/site-packages (from tcrdist3==0.2.2) (1.6.0)
Requirement already satisfied: pwseqdist>=0.6 in ./.local/lib/python3.10/site-packages (from tcrdist3==0.2.2) (0.6)
Requirement already satisfied: scipy>=1.4.1 in ./.local/lib/python3.10/site-packages (from tcrdist3==0.2.2) (1.9.1)
Requirement already satisfied: tcrsampler>=0.1.9 in ./.local/lib/python3.10/site-packages (from tcrdist3==0.2.2) (0.1.9)
Requirement already satisfied: zipdist>=0.1.5 in ./.local/lib/python3.10/site-packages (from tcrdist3==0.2.2) (0.1.5)
Requirement already satisfied: jinja2>=2.10.1 in ./.local/lib/python3.10/site-packages (from hierdiff>=0.4->tcrdist3==0.2.2) (3.1.2)
Requirement already satisfied: statsmodels>=0.10 in ./.local/lib/python3.10/site-packages (from hierdiff>=0.4->tcrdist3==0.2.2) (0.13.2)
Requirement already satisfied: joblib>=0.16 in ./.local/lib/python3.10/site-packages (from hierdiff>=0.4->tcrdist3==0.2.2) (1.2.0)
Requirement already satisfied: fisher in ./.local/lib/python3.10/site-packages (from fishersapi->tcrdist3==0.2.2) (0.1.10)
Requirement already satisfied: svgwrite in ./.local/lib/python3.10/site-packages (from palmotif>=0.2->tcrdist3==0.2.2) (1.4.3)
Requirement already satisfied: matplotlib in ./.local/lib/python3.10/site-packages (from palmotif>=0.2->tcrdist3==0.2.2) (3.6.0)
Requirement already satisfied: pytz>=2020.1 in /usr/lib/python3/dist-packages (from pandas>=0.24.2->tcrdist3==0.2.2) (2022.1)
Requirement already satisfied: python-dateutil>=2.8.1 in ./.local/lib/python3.10/site-packages (from pandas>=0.24.2->tcrdist3==0.2.2) (2.8.2)
Requirement already satisfied: progress>=1.5 in ./.local/lib/python3.10/site-packages (from tcrsampler>=0.1.9->tcrdist3==0.2.2) (1.6)
Requirement already satisfied: feather-format>=0.4.1 in ./.local/lib/python3.10/site-packages (from zipdist>=0.1.5->tcrdist3==0.2.2) (0.4.1)
Requirement already satisfied: llvmlite<0.40,>=0.39.0dev0 in ./.local/lib/python3.10/site-packages (from numba->tcrdist3==0.2.2) (0.39.1)
Requirement already satisfied: setuptools<60 in /usr/lib/python3/dist-packages (from numba->tcrdist3==0.2.2) (59.6.0)
Requirement already satisfied: pyarrow>=0.4.0 in ./.local/lib/python3.10/site-packages (from feather-format>=0.4.1->zipdist>=0.1.5->tcrdist3==0.2.2) (9.0.0)
Requirement already satisfied: MarkupSafe>=2.0 in /usr/lib/python3/dist-packages (from jinja2>=2.10.1->hierdiff>=0.4->tcrdist3==0.2.2) (2.0.1)
Requirement already satisfied: six>=1.5 in /usr/lib/python3/dist-packages (from python-dateutil>=2.8.1->pandas>=0.24.2->tcrdist3==0.2.2) (1.16.0)
Requirement already satisfied: packaging>=21.3 in /usr/lib/python3/dist-packages (from statsmodels>=0.10->hierdiff>=0.4->tcrdist3==0.2.2) (21.3)
Requirement already satisfied: patsy>=0.5.2 in ./.local/lib/python3.10/site-packages (from statsmodels>=0.10->hierdiff>=0.4->tcrdist3==0.2.2) (0.5.2)
Requirement already satisfied: pyparsing>=2.2.1 in /usr/lib/python3/dist-packages (from matplotlib->palmotif>=0.2->tcrdist3==0.2.2) (2.4.7)
Requirement already satisfied: contourpy>=1.0.1 in ./.local/lib/python3.10/site-packages (from matplotlib->palmotif>=0.2->tcrdist3==0.2.2) (1.0.5)
Requirement already satisfied: kiwisolver>=1.0.1 in ./.local/lib/python3.10/site-packages (from matplotlib->palmotif>=0.2->tcrdist3==0.2.2) (1.4.4)
Requirement already satisfied: fonttools>=4.22.0 in ./.local/lib/python3.10/site-packages (from matplotlib->palmotif>=0.2->tcrdist3==0.2.2) (4.37.4)
Requirement already satisfied: pillow>=6.2.0 in /usr/lib/python3/dist-packages (from matplotlib->palmotif>=0.2->tcrdist3==0.2.2) (9.0.1)
Requirement already satisfied: cycler>=0.10 in ./.local/lib/python3.10/site-packages (from matplotlib->palmotif>=0.2->tcrdist3==0.2.2) (0.11.0)
Building wheels for collected packages: tcrdist3
  Building wheel for tcrdist3 (setup.py) ... done
  Created wheel for tcrdist3: filename=tcrdist3-0.2.2-py3-none-any.whl size=2101178 sha256=baca584c02b1f10a5a88c289fbee37c4ecbd4c8e5d946dbd7f209039a1ec5b8c
  Stored in directory: /tmp/pip-ephem-wheel-cache-swopxv8q/wheels/5b/87/da/8bc84e79a0dd1fbdcf9e083340a45dcab784ebdba4cffa91ab
Successfully built tcrdist3
Installing collected packages: tcrdist3
ERROR: Could not install packages due to an OSError: [Errno 36] File name too long: '/home/brant/.local/lib/python3.10/site-packages/tcrdist/data/covid19/mira_epitope_9_2477_FLQSINFVR_FLQSINFVRI_FLYLYALVYF_GLEAPFLYLY_INFVRIIMR_LQSINFVRI_LQSINFVRII_QSINFVRII_SINFVRIIMR_VYFLQSINF_VYFLQSINFV_YFLQSINFVR_YLYALVYFL.tcrdist3.csv'
kmayerb commented 1 year ago

Never seen this problem before. I wonder what version of python you are using in the environment where you are installing tcrdist3?

The filename in question is not essential. You could fork the repo, delete that file and install using

pip install git+https://github.com/*YOURUSERNAME*/tcrdist3.git@ @.**>LATEST_TAG*

If that isn't something you are familiar with I can delete file in question and create a new version for you to install. Let me know.

best, K

On Mon, Oct 3, 2022 at 2:58 PM canuckafar @.***> wrote:

Hi there. Having trouble installing tcrdist3 on Linux. Apparently there appears to be a file name that is too long. Any recommendations?

Thank you.

BI

$ pip install @. Defaulting to user installation because normal site-packages is not writeable Collecting @. Cloning https://github.com/kmayerb/tcrdist3.git (to revision 0.2.2) to /tmp/pip-req-build-105ty4k Running command git clone --filter=blob:none --quiet https://github.com/kmayerb/tcrdist3.git /tmp/pip-req-build-105ty4k Running command git checkout -q 04b0b8c2573d04a9d2cb77f7a3aeeed3a0eab167 Resolved https://github.com/kmayerb/tcrdist3.git to commit 04b0b8c2573d04a9d2cb77f7a3aeeed3a0eab167 Preparing metadata (setup.py) ... done Requirement already satisfied: dill>=0.3.2 in ./.local/lib/python3.10/site-packages (from tcrdist3==0.2.2) (0.3.5.1) Requirement already satisfied: fishersapi in ./.local/lib/python3.10/site-packages (from tcrdist3==0.2.2) (0.5) Requirement already satisfied: hierdiff>=0.4 in ./.local/lib/python3.10/site-packages (from tcrdist3==0.2.2) (0.9) Requirement already satisfied: numba in ./.local/lib/python3.10/site-packages (from tcrdist3==0.2.2) (0.56.2) Requirement already satisfied: numpy>=1.16.4 in ./.local/lib/python3.10/site-packages (from tcrdist3==0.2.2) (1.23.3) Requirement already satisfied: olga>=1.2.1 in ./.local/lib/python3.10/site-packages (from tcrdist3==0.2.2) (1.2.4) Requirement already satisfied: palmotif>=0.2 in ./.local/lib/python3.10/site-packages (from tcrdist3==0.2.2) (0.4) Requirement already satisfied: pandas>=0.24.2 in ./.local/lib/python3.10/site-packages (from tcrdist3==0.2.2) (1.5.0) Requirement already satisfied: parasail>=1.1.17 in ./.local/lib/python3.10/site-packages (from tcrdist3==0.2.2) (1.3.3) Requirement already satisfied: parmap>=1.5.2 in ./.local/lib/python3.10/site-packages (from tcrdist3==0.2.2) (1.6.0) Requirement already satisfied: pwseqdist>=0.6 in ./.local/lib/python3.10/site-packages (from tcrdist3==0.2.2) (0.6) Requirement already satisfied: scipy>=1.4.1 in ./.local/lib/python3.10/site-packages (from tcrdist3==0.2.2) (1.9.1) Requirement already satisfied: tcrsampler>=0.1.9 in ./.local/lib/python3.10/site-packages (from tcrdist3==0.2.2) (0.1.9) Requirement already satisfied: zipdist>=0.1.5 in ./.local/lib/python3.10/site-packages (from tcrdist3==0.2.2) (0.1.5) Requirement already satisfied: jinja2>=2.10.1 in ./.local/lib/python3.10/site-packages (from hierdiff>=0.4->tcrdist3==0.2.2) (3.1.2) Requirement already satisfied: statsmodels>=0.10 in ./.local/lib/python3.10/site-packages (from hierdiff>=0.4->tcrdist3==0.2.2) (0.13.2) Requirement already satisfied: joblib>=0.16 in ./.local/lib/python3.10/site-packages (from hierdiff>=0.4->tcrdist3==0.2.2) (1.2.0) Requirement already satisfied: fisher in ./.local/lib/python3.10/site-packages (from fishersapi->tcrdist3==0.2.2) (0.1.10) Requirement already satisfied: svgwrite in ./.local/lib/python3.10/site-packages (from palmotif>=0.2->tcrdist3==0.2.2) (1.4.3) Requirement already satisfied: matplotlib in ./.local/lib/python3.10/site-packages (from palmotif>=0.2->tcrdist3==0.2.2) (3.6.0) Requirement already satisfied: pytz>=2020.1 in /usr/lib/python3/dist-packages (from pandas>=0.24.2->tcrdist3==0.2.2) (2022.1) Requirement already satisfied: python-dateutil>=2.8.1 in ./.local/lib/python3.10/site-packages (from pandas>=0.24.2->tcrdist3==0.2.2) (2.8.2) Requirement already satisfied: progress>=1.5 in ./.local/lib/python3.10/site-packages (from tcrsampler>=0.1.9->tcrdist3==0.2.2) (1.6) Requirement already satisfied: feather-format>=0.4.1 in ./.local/lib/python3.10/site-packages (from zipdist>=0.1.5->tcrdist3==0.2.2) (0.4.1) Requirement already satisfied: llvmlite<0.40,>=0.39.0dev0 in ./.local/lib/python3.10/site-packages (from numba->tcrdist3==0.2.2) (0.39.1) Requirement already satisfied: setuptools<60 in /usr/lib/python3/dist-packages (from numba->tcrdist3==0.2.2) (59.6.0) Requirement already satisfied: pyarrow>=0.4.0 in ./.local/lib/python3.10/site-packages (from feather-format>=0.4.1->zipdist>=0.1.5->tcrdist3==0.2.2) (9.0.0) Requirement already satisfied: MarkupSafe>=2.0 in /usr/lib/python3/dist-packages (from jinja2>=2.10.1->hierdiff>=0.4->tcrdist3==0.2.2) (2.0.1) Requirement already satisfied: six>=1.5 in /usr/lib/python3/dist-packages (from python-dateutil>=2.8.1->pandas>=0.24.2->tcrdist3==0.2.2) (1.16.0) Requirement already satisfied: packaging>=21.3 in /usr/lib/python3/dist-packages (from statsmodels>=0.10->hierdiff>=0.4->tcrdist3==0.2.2) (21.3) Requirement already satisfied: patsy>=0.5.2 in ./.local/lib/python3.10/site-packages (from statsmodels>=0.10->hierdiff>=0.4->tcrdist3==0.2.2) (0.5.2) Requirement already satisfied: pyparsing>=2.2.1 in /usr/lib/python3/dist-packages (from matplotlib->palmotif>=0.2->tcrdist3==0.2.2) (2.4.7) Requirement already satisfied: contourpy>=1.0.1 in ./.local/lib/python3.10/site-packages (from matplotlib->palmotif>=0.2->tcrdist3==0.2.2) (1.0.5) Requirement already satisfied: kiwisolver>=1.0.1 in ./.local/lib/python3.10/site-packages (from matplotlib->palmotif>=0.2->tcrdist3==0.2.2) (1.4.4) Requirement already satisfied: fonttools>=4.22.0 in ./.local/lib/python3.10/site-packages (from matplotlib->palmotif>=0.2->tcrdist3==0.2.2) (4.37.4) Requirement already satisfied: pillow>=6.2.0 in /usr/lib/python3/dist-packages (from matplotlib->palmotif>=0.2->tcrdist3==0.2.2) (9.0.1) Requirement already satisfied: cycler>=0.10 in ./.local/lib/python3.10/site-packages (from matplotlib->palmotif>=0.2->tcrdist3==0.2.2) (0.11.0) Building wheels for collected packages: tcrdist3 Building wheel for tcrdist3 (setup.py) ... done Created wheel for tcrdist3: filename=tcrdist3-0.2.2-py3-none-any.whl size=2101178 sha256=baca584c02b1f10a5a88c289fbee37c4ecbd4c8e5d946dbd7f209039a1ec5b8c Stored in directory: /tmp/pip-ephem-wheel-cache-swopxv8q/wheels/5b/87/da/8bc84e79a0dd1fbdcf9e083340a45dcab784ebdba4cffa91ab Successfully built tcrdist3 Installing collected packages: tcrdist3 ERROR: Could not install packages due to an OSError: [Errno 36] File name too long: '/home/brant/.local/lib/python3.10/site-packages/tcrdist/data/covid19/mira_epitope_9_2477_FLQSINFVR_FLQSINFVRI_FLYLYALVYF_GLEAPFLYLY_INFVRIIMR_LQSINFVRI_LQSINFVRII_QSINFVRII_SINFVRIIMR_VYFLQSINF_VYFLQSINFV_YFLQSINFVR_YLYALVYFL.tcrdist3.csv'

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canuckafar commented 1 year ago

Thanks for the advice. Indeed I was not that familiar with forking on Github, but I read about it and was able to accomplish what you recommended and have also been able to install tcrdist after removing the offending file (what a long name BTW!).

Will try using the software and will see how things worked.

Again, thank you.

kmayerb commented 1 year ago

Thanks for the update.

Also don't forget that using Google Collab easily allows one to pip install tcrdist3==0.2.2 for exploring the package.

Best, K