pdflatex is not available

[bschilder]

Occurs when testing rworkflows with GenomicRanges:
https://github.com/neurogenomics/GenomicRanges/actions/runs/3716368491/jobs/6302613350

Related issues:
https://superuser.com/questions/1038612/where-do-i-get-the-pdflatex-program-for-mac
https://tex.stackexchange.com/questions/429757/pdflatex-problem-with-rstudio
https://stackoverflow.com/questions/29177775/r-cmd-check-not-locating-texi2pdf-on-mac-after-r-3-1-3-upgrade
STAT545-UBC/Discussion#240
https://support.bioconductor.org/p/38232/
r-lib/actions#138

Seems somewhat related to my gist about rendering manual PDFs too:
https://gist.github.com/bschilder/af3960b7d7b911274198e3febae535a9

[bschilder]

Potential solutions

Linux

https://gist.github.com/rain1024/98dd5e2c6c8c28f9ea9d

sudo apt-get install texlive-latex-base texlive-fonts-recommended texlive-fonts-extra texlive-latex-extra

Mac

https://superuser.com/a/1416736
https://gist.github.com/bschilder/af3960b7d7b911274198e3febae535a9

brew install basictex texlive 

Also condensed brew install calls into just two calls, to reduce overhead.

Windows

https://github.com/r-lib/actions/tree/v2/setup-tinytex

      - uses: r-lib/actions/setup-tinytex@v2
 

[NathanSkene]

Added benefit of running it on other packages is finding bugs I guess!

…

________________________________ From: Brian M. Schilder ***@***.***> Sent: 17 December 2022 02:22 To: neurogenomics/rworkflows ***@***.***> Cc: Subscribed ***@***.***> Subject: Re: [neurogenomics/rworkflows] pdflatex is not available (Issue #32) This email from ***@***.*** originates from outside Imperial. Do not click on links and attachments unless you recognise the sender. If you trust the sender, add them to your safe senders list<https://spam.ic.ac.uk/SpamConsole/Senders.aspx> to disable email stamping for this address. Solutions Linux https://gist.github.com/rain1024/98dd5e2c6c8c28f9ea9d sudo apt-get install texlive-latex-base texlive-fonts-recommended texlive-fonts-extra texlive-latex-extra Mac brew install basictex Windows npm install pdflatex — Reply to this email directly, view it on GitHub<#32 (comment)>, or unsubscribe<https://github.com/notifications/unsubscribe-auth/AH5ZPEZQRQSRZCURVRB7OPDWNUPVXANCNFSM6AAAAAATBQA2N4>. You are receiving this because you are subscribed to this thread.Message ID: ***@***.***>

[bschilder]

Finally got this working by adding some new steps to rworkflows action:

rworkflows/action.yml

Line 183 in 7beb0c6

- name: Install latex

Took some troubleshooting with the authors of r-lib/setup-tinytex:
r-lib/actions#670
r-lib/actions#671

The culprit was ultimately BiocStyle::latex, which requires certain latex libraries but doesn't seem to install them or check that they exist first. I've fixed this semi-manually, but really this should probably be handled by BiocStyle so users don't run into issues with dependencies that are unknown to the user until they start digging deep into the documentation and researching latex.

Had a convo with the BiocStyle group to see if there's a way it can install the necessary latex libs, or at least have a function that gives users to list of all latex dependencies:
Bioconductor/BiocStyle#69
Bioconductor/BiocStyle#15