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@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 _______________________________________________ Bioc-devel@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/bioc-devel
