Fix bioc_mentorship_docs

bschilder commented 10 months ago

The main bioc_mentorship_docs page hasn't launched my previous PR with the rworkflows docs to the GH Pages site yet bc the deploy pages GHA has been failing for a long time. https://github.com/Bioconductor/bioc_mentorship_docs/pull/23

I'll make a PR to fix the GHA so that we can use the proper URL in the manuscript (instead of the URL for our forked repo):

https://neurogenomics.github.io/bioc_mentorship_docs/bioc-package.html

to -->

https://bioconductor.github.io/bioc_mentorship_docs/bioc-package.html

bschilder commented 10 months ago

1. Fix permissions

Needed to add a permissions fix to a known issue: https://github.com/neurogenomics/bioc_mentorship_docs/blob/94effe03a8eb6a5964fb96e73400a8984109ac2a/.github/workflows/build_deploy.yaml#L8

2. Fix tinytex

Now tinytex lib installation steps are failing, which is always fun. https://github.com/neurogenomics/bioc_mentorship_docs/actions/runs/6631736756/job/18015889497#step:4:17

Run r-lib/actions/setup-pandoc@v2
/usr/bin/docker exec  4d[8](https://github.com/neurogenomics/bioc_mentorship_docs/actions/runs/6631736756/job/18015889497#step:4:9)6b05676b3bade7d03af1232eb58f0780[9](https://github.com/neurogenomics/bioc_mentorship_docs/actions/runs/6631736756/job/18015889497#step:4:10)7351e5622862cb21f2c9d46d5ca1 sh -c "cat /etc/*release | grep ^ID"
Download pandoc
Install gdebi-core
  sudo apt-get install -y gdebi-core
  Reading package lists...
  Building dependency tree...
  Reading state information...
  E: Unable to locate package gdebi-core
  Error: Failed to install pandoc: The process 'sudo' failed with exit code [10](https://github.com/neurogenomics/bioc_mentorship_docs/actions/runs/6631736756/job/18015889497#step:4:11)0

Should be able to look to how I've resolved this within rworkflows in the past for an answer.

It seems this was due to the introduction of the pandoc installation step:

 - name: Set up pandoc
        uses: r-lib/actions/setup-pandoc@v2

This is an issue bc pandoc is already preinstalled on the Bioc docker container and trying to reinstall is yourself causes problems.

Not sure what the original goal was with installing pandoc manually, but I've:

removed the pandoc installation step
added a system dependencies installation prestep (necessary for installing tinytex)
added a latex installation step
just in case you need it @kevinrue

 - name: 🛠 Install Linux system dependencies  
        run: |
          sysreqs=$(Rscript -e 'cat("apt-get update -y && apt-get install -y", paste(gsub("apt-get install -y ", "", remotes::system_requirements("ubuntu", "20.04")), collapse = " "))')
          echo $sysreqs
          sudo -s eval "$sysreqs"
          sudo apt-get install -y qpdf rsync
        shell: bash {0}

 - name: 🛠 Install latex
        uses: r-lib/actions/setup-tinytex@v2

bschilder commented 10 months ago

PR here: https://github.com/Bioconductor/bioc_mentorship_docs/pull/25

neurogenomics / rworkflows

Fix bioc_mentorship_docs #91

1. Fix permissions

2. Fix tinytex