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Question: Bioconductor Docker Development container
1
gravatar for Nathan Sheffield
2.2 years ago by
University of Virginia
Nathan Sheffield10 wrote:

Hi, I'm trying to use the bioconductor containers listed here: http://www.bioconductor.org/help/docker/ and announced by @Dan Tenenbaum here: Announcing Docker containers for Bioconductor

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).

ADD COMMENTlink modified 2.2 years ago by Dan Tenenbaum ♦♦ 8.1k • written 2.2 years ago by Nathan Sheffield10

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.

ADD REPLYlink written 2.2 years ago by Sean Davis20k
1
gravatar for Dan Tenenbaum
2.2 years ago by
Dan Tenenbaum ♦♦ 8.1k
United States
Dan Tenenbaum ♦♦ 8.1k wrote:

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).

ADD COMMENTlink modified 2.2 years ago • written 2.2 years ago by Dan Tenenbaum ♦♦ 8.1k

Thanks -- I'll give it a try.

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?

 

ADD REPLYlink written 2.2 years ago by Nathan Sheffield10

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.

 

 

ADD REPLYlink written 2.2 years ago by Nathan Sheffield10

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.

ADD REPLYlink written 2.2 years ago by Dan Tenenbaum ♦♦ 8.1k
1
gravatar for Dan Tenenbaum
2.2 years ago by
Dan Tenenbaum ♦♦ 8.1k
United States
Dan Tenenbaum ♦♦ 8.1k wrote:

I've added texlive-fonts-extra which contains the inconsolata font and fixes this. Currently rebuilding devel_base.

ADD COMMENTlink written 2.2 years ago by Dan Tenenbaum ♦♦ 8.1k
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