I want to use the devel container to build R packages... the problem is since the bioconductor/devel containers are based on rocker/rstudio containers, they lack some of the pdf tools in the rocker/r-devel containers... so R CMD check fails as lacking things like qpdf, pdflatex, etc.
So, a suggestion -- should the devel containers be instead based on the rocker/r-devel image?
Or is there a better way to do bioconductor development in a docker container? (so far I've build my own docker images).
This is probably better addressed on the bioc-devel list. That said, your suggestion seems like a good one to me. A devel container should support a full development stack.
I've added the packages needed to build a latex vignette to the devel_base image. pandoc is already present (bundled with RStudio) to support markdown vignettes. The images that are based on devel_base will include these packages next time they build (within 24 hours).
But I'm a bit confused now -- actually, all my vignettes are written in markdown (Rmarkdown to be precise, .Rmd) -- yet when I run R CMD check, it builds PDF versions, requires qpdf/pdflatex etc... But your comment indicates that these are only needed for vignettes written in latex, but this has not been my experience. Did I miss something?
btw, it's in the "checking PDF version of manual" where the errors come in, not vignettes... here's an example from a package with only Rmd vignettes:
* checking running R code from vignettes ...
'choosingUniverse.Rmd' ... OK
'gettingStarted.Rmd' ... OK
'usingLOLACore.Rmd' ... OK
OK
* checking re-building of vignette outputs ... OK
* checking PDF version of manual ... WARNING
LaTeX errors when creating PDF version.
This typically indicates Rd problems.
LaTeX errors found:
! Font T1/cmr/m/n/10=ecrm1000 at 10.0pt not loadable: Metric (TFM) file not fou
nd.
<to be read again>
relax
l.100 \fontencoding\encodingdefault\selectfont
! LaTeX Error: File `inconsolata.sty' not found.
No, I didn't realize you were creating pdf vignettes from markdown. It might be good to share your package with me offline if you want to, and I can make sure that it builds/checks under the docker container.
This is probably better addressed on the bioc-devel list. That said, your suggestion seems like a good one to me. A devel container should support a full development stack.