Question

Bioconductor Docker Development container

1

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Nathan Sheffield ▴ 10

@nathan-sheffield-7613

Last seen 7 months ago

University of Virginia

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).

docker bioc-devel • 2.1k views

ADD COMMENT • link updated 8.9 years ago by Dan Tenenbaum ★ 8.2k • written 8.9 years ago by Nathan Sheffield ▴ 10

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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 REPLY • link 8.9 years ago Sean Davis 21k

score 1 · Answer 1 · 2015-06-02

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Dan Tenenbaum ★ 8.2k

@dan-tenenbaum-4256

Last seen 3.2 years ago

United States

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 COMMENT • link 8.9 years ago Dan Tenenbaum ★ 8.2k

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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 REPLY • link 8.9 years ago Nathan Sheffield ▴ 10

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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 REPLY • link 8.9 years ago Nathan Sheffield ▴ 10

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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 REPLY • link 8.9 years ago Dan Tenenbaum ★ 8.2k

score 1 · Answer 2 · 2015-06-03

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Dan Tenenbaum ★ 8.2k

@dan-tenenbaum-4256

Last seen 3.2 years ago

United States

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

ADD COMMENT • link 8.9 years ago Dan Tenenbaum ★ 8.2k