Skip to content
New issue

Have a question about this project? Sign up for a free GitHub account to open an issue and contact its maintainers and the community.

Sign up for GitHub

By clicking “Sign up for GitHub”, you agree to our terms of service and privacy statement. We’ll occasionally send you account related emails.

Already on GitHub? Sign in to your account

Jump to bottom

Installation error: File name too long #75

Open
canuckafar opened this issue Oct 3, 2022 · 3 comments
Open

Installation error: File name too long #75

canuckafar opened this issue Oct 3, 2022 · 3 comments

Comments

@canuckafar
Copy link

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
Copy link
Owner

kmayerb commented Oct 4, 2022 via email

@canuckafar
Copy link
Author

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
Copy link
Owner

kmayerb commented Oct 13, 2022 via email

Sign up for free to join this conversation on GitHub. Already have an account? Sign in to comment
Assignees
No one assigned
Labels
None yet
Projects
None yet
Milestone
No milestone
Development

No branches or pull requests
2 participants
@kmayerb @canuckafar