[Bioc-devel] workflow building issues on mac and windows

[Leonardo Collado Torres]

Hi,

I recently got a workflow accepted and I've been trying to get the
workflow builder to successfully complete on Mac and Windows which is
based on bioc-release. Note that the workflow did build properly on
those operating systems using the SPB (bioc-devel).


## Linux: working

After looking at
https://hedgehog.fhcrc.org/bioconductor/trunk/madman/workflows/cytofWorkflow
and https://hedgehog.fhcrc.org/bioconductor/trunk/madman/workflows/rnaseqGene
I was able to:

(1) get the figure references and captions working using captioner
(2) actually get the figures to show
(3) use the new layout (thanks to vignettes/.html_output)

Since the build completes on Linux,
http://bioconductor.org/help/workflows/recountWorkflow/ is now live.
Only the links to the Mac and Windows binaries fail.


## Mac: could be a permissions issue

The issue with Mac is (details at
http://docbuilder.bioconductor.org:8080/job/recountWorkflow/label=vagrantmac/9/console)
is that I eventually run into this error:

Quitting from lines 735-747 (recount-workflow.Rmd)
Error: processing vignette 'recount-workflow.Rmd' failed with diagnostics:
UCSC library operation failed
Execution halted


The referenced lines break because of:

regions <- expressed_regions("SRP045638", "chr21", cutoff = 5L,
    maxClusterGap = 3000L)

This code uses rtracklayer::import.bw() with a URL that gets
forwarded. I made sure that I am requiring the latest bioc-release
rtracklayer in the description file, so this leads me to think that
this issue is a repeat of
https://stat.ethz.ch/pipermail/bioc-devel/2016-August/009599.html
where the solution involved changing some permissions. Dan stated in
that thread (3rd email): "Actually it looks like it was a permissions
issue with the directory /tmp/udcCache. I removed this directory (as
superuser) and that error no longer happens."

Does this sound like something that could be happening in the Mac builder?



## Windows: figure and pandoc-citeproc issues


In Windows, I see warnings like this:

Invalid Parameter - -trim
Warning: running command 'C:\Windows\system32\cmd.exe /c convert
"exondeanalysis1-1.png" -trim "exondeanalysis1-1.png"' had status 4
Warning in shell(paste(c(cmd, args), collapse = " ")) :
  'convert "exondeanalysis1-1.png" -trim "exondeanalysis1-1.png"'
execution failed with error code 4

Details at http://docbuilder.bioconductor.org:8080/job/recountWorkflow/label=winbuilder1/9/console.
I originally thought that it was related to the figure paths, which is
why I added this knitr code:

knitr::opts_chunk$set(fig.path = "")

But that didn't resolve the issue. I get these warnings only with
BiocStyle::html_document2 and not with BiocStyle::html_document
(http://docbuilder.bioconductor.org:8080/job/recountWorkflow/label=winbuilder1/7/console
using v0.99.28).

Ultimately, the warnings might not matter. Though I don't see them on
the build reports for other workflows (cytofWorkflow, rnaseqGene).

The Windows builds fail (with BiocStyle::html_document2 or
BiocStyle::html_document) with error messages like this:

pandoc.exe: Error running filter pandoc-citeproc Filter returned error
status 1073807366 Warning: running command
'"C:/Progra~2/Pandoc/pandoc" +RTS -K512m -RTS recount-workflow.utf8.md
--to html --from
markdown+autolink_bare_uris+ascii_identifiers+tex_math_single_backslash
--output recount-workflow.html --smart --email-obfuscation none
--self-contained --standalone --section-divs --table-of-contents
--toc-depth 3 --template
"C:\Windows\TEMP\RtmpchKz3E/BiocStyle/template.html" --no-highlight
--variable highlightjs=1 --number-sections --css
"C:\PROGRA~1\R\R-34~1.0\library\BIOCST~1\RESOUR~1\html\BIOCON~2.CSS"
--variable "theme:bootstrap" --include-in-header
"C:\Windows\TEMP\RtmpchKz3E\rmarkdown-str3ec7c88cea.html" --mathjax
--variable "mathjax-url:https://mathjax.rstudio.com/latest/MathJax.js?config=TeX-AMS-MML_HTMLorMML"
--bibliography recount-workflow.bib --filter pandoc-citeproc' had
status 83 Error: processing vignette 'recount-workflow.Rmd' failed
with diagnostics: pandoc document conversion failed with error 83
Execution halted

(from http://docbuilder.bioconductor.org:8080/job/recountWorkflow/label=winbuilder1/9/console)


Googling the error pointed me towards having weird symbols on the .bib
file. So I removed some accents and the like, but I still get this
error. I am using a csl file for the bibliography and like I said,
this works with the SPB whose last build report was
http://bioconductor.org/spb_reports/recountWorkflow_buildreport_20170807114418.html
(v0.99.18). There's not much different between that version and
0.99.30 as you can see at
https://github.com/LieberInstitute/recountWorkflow/commits/master **.

The Linux machine has pandoc 1.19.2.1 installed
(http://bioconductor.org/help/workflows/recountWorkflow/#session-information)
and I guess that the Windows one has the same version. But maybe that
could be the issue. BiocStyle 2.5.15 is installed in the Linux machine
too (Bioconductor/BiocStyle at 2a1ba75) which is newer than the latest
bioc-release (2.4.1), but again, I assume that the Windows machine has
the same version.



Anyhow, I haven't been able to fix these issues and was wondering if
anyone else had ideas that could resolve them. Regardless, I'm happy
that I got http://bioconductor.org/help/workflows/recountWorkflow/ up
and looking good ^^. It's just the links to the Mac/Windows
binaries...


Thank you,
Leo



** I've been pushing changes via svn, I know that workflows are not
part of the git transition. I just keep everything in sync manually
with the GitHub repo.


Leonardo Collado Torres, Ph. D., Data Scientist
Lieber Institute for Brain Development
855 N Wolfe St, Suite 300
Baltimore, MD 21205
Website: http://lcolladotor.github.io