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nhoffman / dada2-nf

A Nextflow pipeline for processing 16S rRNA sequences using dada2
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Docker image build no longer successfully installing dada2 #56

Closed dhoogest closed 1 year ago

dhoogest commented 1 year ago

Appears to be an issue with package management? Following is reproduced both in local docker build and via github CI:

* building ‘dada2_1.20.0.tar.gz’

Installing package into ‘/usr/local/lib/R/site-library’
(as ‘lib’ is unspecified)
ERROR: dependency ‘ShortRead’ is not available for package ‘dada2’
* removing ‘/usr/local/lib/R/site-library/dada2’
Warning message:
In i.p(...) :
  installation of package ‘/tmp/Rtmp0zeBsK/file755d947ad/dada2_1.20.0.tar.gz’ had non-zero exit status
'getOption("repos")' replaces Bioconductor standard repositories, see
'?repositories' for details

replacement repositories:
    CRAN: https://cloud.r-project.org/

Bioconductor version 3.16 (BiocManager 1.30.19), R 4.2.2 Patched (2022-11-10)
dhoogest commented 1 year ago

This is corrected with https://github.com/nhoffman/dada2-nf/pull/57