[Bioc-devel] Invalid Parameter - /figure-html

[Obenchain, Valerie]

Hi,

It looks like vignette in TCGAWorkflow hasn't changed except for updating to use BiocManager. This often points to a breaking change in an upstream dependency (244 in your case) or it could be a problem on the builder.

The code chunk causing problems in devel is the call to ELMER::get.TFs().

TF <- get.TFs(data = mae,
              group.col = group.col,
              group1 = group1,
              group2 =  group2,
              mode = "supervised",
              enriched.motif = enriched.motif,
              dir.out = dir.out,
              cores = cores,
              diff.dir = direction,
              label = direction)

On Windows, this either hangs and crashes the R session or produces this error with what looks like a bad file name:

Quitting from lines 2387-2394 (TCGAWorkflow.Rmd)
Error: processing vignette 'TCGAWorkflow.Rmd' failed with diagnostics:
unable to open C:/Users/biocbuild/bbs-3.8-workflows/tmpdir/RtmpuGXyPJ/.heatmap_body_DNA methylation level_1_2348149424d.png

It looks like you were the last one to touch ELMER:

commit fbf589501eb035138d28d69640041547f54c38a4 (HEAD -> master, origin/master, origin/HEAD)
Author: tiagochst <tiagochst using gmail.com><mailto:tiagochst using gmail.com>
Date:   Thu Sep 20 15:39:46 2018 -0300

    fix heatmap plot

R/GetNearbyGenes.R
R/Scatter.plot.R
R/TCGA_pipe.R
R/plots.R

commit 207f80398996bef2a593e67b9e7c12f3ae10a768
Merge: 17b72e7 b8721cb
Author: Tiago Chedraoui Silva <tiagochst using gmail.com><mailto:tiagochst using gmail.com>
Date:   Thu Sep 20 11:34:34 2018 -0700

    Merge branch 'master' of https://github.com/tiagochst/ELMER

commit 17b72e79b42ad19ead302bbab17272575af352e2
Author: Tiago Chedraoui Silva <tiagochst using gmail.com><mailto:tiagochst using gmail.com>
Date:   Thu Sep 20 11:34:26 2018 -0700

    Fixing the cluster within groups for heatmap

R/plots.R
man/heatmapPairs.Rd

Maybe the name of the file in the error message is familiar to you or you could revisit recent changes to ELMER that impacted get.TFs().

Along those lines, how about setting save=FALSE when calling get.TFs()? It takes a significant amount of time to write out all 20+ pdf files and AFAIK only the file with TF ranking is used in plotting. This ranking file could be saved in TCGAWorkflow/data and loaded for plotting. You can point out to the user that save=TRUE is an option they may want but for the purpose of the vignette it doesn't seem necessary.

Thanks.
Valerie


On 9/27/18 7:43 AM, Tiago Chedraoui Silva wrote:

Hello,

The workflow I'm maintaining is giving this message "Invalid Parameter -
/figure-html"  in the devel and release windows environment.

http://bioconductor.org/checkResults/devel/workflows-LATEST/TCGAWorkflow/tokay1-buildsrc.html

It seems other users had the same problem before:
https://stackoverflow.com/questions/48747959/biocstyle-vignettes-invalid-parameter-figure-html?rq=1

Please, someone knows how that could be fixed?

Best regards,
Tiago Chedraoui Silva

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