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lcolladotor / biocthis

Automate package and project setup for Bioconductor packages
https://lcolladotor.github.io/biocthis/
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biocthis::use_bioc_github_action - Error in readRDS(dest) : error reading from connection #20

Closed mdozmorov closed 3 years ago

mdozmorov commented 3 years ago

I'm trying to use the biocthis::use_bioc_github_action() function to set up a BioC-style GitHub Actions workflow for the preciseTAD package. The package builds on ubuntu but fails on macOS and Windows. The error happens at the "Set BiocVersion" stage, "Error in readRDS(dest) : error reading from connection". Example. Any advice? Since this happens on GitHub side, not reporting here, but can move to Bioc support.

mdozmorov commented 3 years ago

Looks like the problem is more global as even the local installation of packages fails with the same error. May it be related to the upcoming R/Bioconductor releases?

mdozmorov commented 3 years ago

The solution, as suggested in https://support.bioconductor.org/p/9136957/, is to adjust BiocManager installation in check-bioc.yml as:

      - name: Install BiocManager
        run: |
          message(paste('****', Sys.time(), 'installing BiocManager ****'))
          # remotes::install_cran("BiocManager")
          remotes::install_github("Bioconductor/BiocManager", ref="ghost-binary-repo")