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sigven / pcgr

Personal Cancer Genome Reporter (PCGR)
https://sigven.github.io/pcgr
MIT License
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post-link script failed for package `bioconda::bioconductor-genomeinfodbdata-1.2.7-r41hdfd78af_1` #195

Closed pdiakumis closed 1 year ago

pdiakumis commented 2 years ago

Reporting this issue we got via email:

Preparing transaction: done
Verifying transaction: done
Executing transaction: done
ERROR conda.core.link:_execute(730): An error occurred while installing package 'bioconda::bioconductor-genomeinfodbdata-1.2.7-r41hdfd78af_1'.
Rolling back transaction: done
class: LinkError
message:
post-link script failed for package bioconda::bioconductor-genomeinfodbdata-1.2.7-r41hdfd78af_1
location of failed script: .../tools/pcgr/PCGR/conda/env/pcgrr/bin/.bioconductor-genomeinfodbdata-post-link.sh
==> script messages <==
<None>
==> script output <==
stdout: .../tools/pcgr/PCGR/conda/env/pcgrr/share/bioconductor-genomeinfodbdata-1.2.7-1/GenomeInfoDbData_1.2.7.tar.gz: FAILED
.../tools/pcgr/PCGR/conda/env/pcgrr/share/bioconductor-genomeinfodbdata-1.2.7-1/GenomeInfoDbData_1.2.7.tar.gz: FAILED
.../tools/pcgr/PCGR/conda/env/pcgrr/share/bioconductor-genomeinfodbdata-1.2.7-1/GenomeInfoDbData_1.2.7.tar.gz: FAILED
ERROR: post-link.sh was unable to download any of the following URLs with the md5sum 74c82f26111062a9ceb3c5331088cd56:
https://bioconductor.org/packages/3.14/data/annotation/src/contrib/GenomeInfoDbData_1.2.7.tar.gz
https://bioarchive.galaxyproject.org/GenomeInfoDbData_1.2.7.tar.gz
https://depot.galaxyproject.org/software/bioconductor-genomeinfodbdata/bioconductor-genomeinfodbdata_1.2.7_src_all.tar.gz

A nice explanation of the issue can be found at https://github.com/bioconda/bioconda-recipes/pull/36797. This has been popping up for me a lot recently, so it's great they got to the bottom of it.

Might need to wait for a bit until some of the relevant conda PRs are merged from their side first.

bujianbusan commented 2 years ago

So，I meet this problem also. Qiime2 2022-8 is not working now.

pdiakumis commented 2 years ago

Hello @bujianbusan Even though this repo is not related to Qiime2, you can try installing the newer version of GenomeInfoDbData from https://anaconda.org/bioconda/bioconductor-genomeinfodbdata/files (note the _2 suffix of that latest version).

pdiakumis commented 1 year ago

This seems to be fixed, since I'm not having any issues with a fresh conda installation. Closing.