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faircloth-lab / phyluce

software for UCE (and general) phylogenomics
http://phyluce.readthedocs.org/
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Problem installing phyluce 1.7.1 #235

Closed haxacloruro closed 3 years ago

haxacloruro commented 3 years ago

Hi Brant, previously I had installed phyluce 1.6, and I decided to work with phyluce 1.7.1. I followed the instructions to install Miniconda3 and then phyluce, but I'm having the next issue:

(base) [habromys@mike1 ~]$ conda env create -n phyluce-1.7.1 --file phyluce-1.7.1-py36-Linux-conda.yml Collecting package metadata (repodata.json): done Solving environment: done

==> WARNING: A newer version of conda exists. <== current version: 4.9.2 latest version: 4.10.1

Please update conda by running

$ conda update -n base -c defaults conda

Preparing transaction: done Verifying transaction: failed

CondaVerificationError: The package for mafft located at /work/habromys/test-env/pkgs/mafft-7.475-h516909a_0 appears to be corrupted. The path 'bin/einsi' specified in the package manifest cannot be found.

CondaVerificationError: The package for mafft located at /work/habromys/test-env/pkgs/mafft-7.475-h516909a_0 appears to be corrupted. The path 'bin/fftns' specified in the package manifest cannot be found.

CondaVerificationError: The package for mafft located at /work/habromys/test-env/pkgs/mafft-7.475-h516909a_0 appears to be corrupted. The path 'bin/fftnsi' specified in the package manifest cannot be found.

CondaVerificationError: The package for mafft located at /work/habromys/test-env/pkgs/mafft-7.475-h516909a_0 appears to be corrupted. The path 'bin/ginsi' specified in the package manifest cannot be found.

CondaVerificationError: The package for mafft located at /work/habromys/test-env/pkgs/mafft-7.475-h516909a_0 appears to be corrupted. The path 'bin/linsi' specified in the package manifest cannot be found.

CondaVerificationError: The package for mafft located at /work/habromys/test-env/pkgs/mafft-7.475-h516909a_0 appears to be corrupted. The path 'bin/mafft-distance' specified in the package manifest cannot be found.

CondaVerificationError: The package for mafft located at /work/habromys/test-env/pkgs/mafft-7.475-h516909a_0 appears to be corrupted. The path 'bin/mafft-einsi' specified in the package manifest cannot be found.

CondaVerificationError: The package for mafft located at /work/habromys/test-env/pkgs/mafft-7.475-h516909a_0 appears to be corrupted. The path 'bin/mafft-fftns' specified in the package manifest cannot be found.

CondaVerificationError: The package for mafft located at /work/habromys/test-env/pkgs/mafft-7.475-h516909a_0 appears to be corrupted. The path 'bin/mafft-fftnsi' specified in the package manifest cannot be found.

CondaVerificationError: The package for mafft located at /work/habromys/test-env/pkgs/mafft-7.475-h516909a_0 appears to be corrupted. The path 'bin/mafft-ginsi' specified in the package manifest cannot be found.

CondaVerificationError: The package for mafft located at /work/habromys/test-env/pkgs/mafft-7.475-h516909a_0 appears to be corrupted. The path 'bin/mafft-linsi' specified in the package manifest cannot be found.

CondaVerificationError: The package for mafft located at /work/habromys/test-env/pkgs/mafft-7.475-h516909a_0 appears to be corrupted. The path 'bin/mafft-nwns' specified in the package manifest cannot be found.

CondaVerificationError: The package for mafft located at /work/habromys/test-env/pkgs/mafft-7.475-h516909a_0 appears to be corrupted. The path 'bin/mafft-nwnsi' specified in the package manifest cannot be found.

CondaVerificationError: The package for mafft located at /work/habromys/test-env/pkgs/mafft-7.475-h516909a_0 appears to be corrupted. The path 'bin/mafft-profile' specified in the package manifest cannot be found.

CondaVerificationError: The package for mafft located at /work/habromys/test-env/pkgs/mafft-7.475-h516909a_0 appears to be corrupted. The path 'bin/mafft-qinsi' specified in the package manifest cannot be found.

CondaVerificationError: The package for mafft located at /work/habromys/test-env/pkgs/mafft-7.475-h516909a_0 appears to be corrupted. The path 'bin/mafft-xinsi' specified in the package manifest cannot be found.

CondaVerificationError: The package for mafft located at /work/habromys/test-env/pkgs/mafft-7.475-h516909a_0 appears to be corrupted. The path 'bin/nwns' specified in the package manifest cannot be found.

CondaVerificationError: The package for mafft located at /work/habromys/test-env/pkgs/mafft-7.475-h516909a_0 appears to be corrupted. The path 'bin/nwnsi' specified in the package manifest cannot be found.

CondaVerificationError: The package for trimmomatic located at /work/habromys/test-env/pkgs/trimmomatic-0.39-1 appears to be corrupted. The path 'bin/trimmomatic' specified in the package manifest cannot be found.

It seems that I have a couple of corrupted folders, so I wonder if some files from https://raw.githubusercontent.com/faircloth-lab/phyluce/v1.7.1/distrib/phyluce-1.7.1-py36-Linux-conda.yml are incomplete, or if my problem is something else...

Thank you!

brantfaircloth commented 3 years ago

hmm. the packages should be complete because I test the distributions before making them available. these particular packages are from bioconda, as well, so i’m not sure what happened here. perhaps remove the environment you’ve tried to create, perhaps clean the cache of packages (see conda clean command), and try again.

haxacloruro commented 3 years ago

Thanks for the quick answer! As you said, that was a problem related with the packages from bioconda (...some missing files). We fix them and now Phyluce is working. Best!