[Bioc-devel] GenVisR vignette build issues

[Dan Tenenbaum]

----- Original Message -----
> From: "Zach Skidmore" <zskidmor at genome.wustl.edu>
> To: "bioc-devel" <bioc-devel at r-project.org>
> Sent: Saturday, February 27, 2016 10:04:19 AM
> Subject: [Bioc-devel] GenVisR vignette build issues

> Hi All,
> 
> Recently the vignette in the GenVisR package has been causing Check
> Errors, Specifically the error is:
> 
> pandoc: Could not fetch /tabsets.js
> /tabsets.js: openBinaryFile: does not exist (No such file or directory)
> Error: processing vignette 'GenVisR_intro.Rmd' failed with diagnostics:
> pandoc document conversion failed with error 67
> Execution halted
> 
> I cannot reproduce the error on my local system, some searching suggests
> that the problem might be with rmarkdown however I have the latest
> version installed. Is there anyway to tell what version Bioc is using?
> 

Yes, on the build report page (https://www.bioconductor.org/checkResults/devel/bioc-LATEST/) there is a table listing the build machines and the rightmost column (installed pkgs) is clickable, it tells you what version of each package is installed on each machine. In this case version 0.9.5 of rmarkdown is installed on all 3 machines.

Note that the Bioconductor build system cannot install anything newer than what is on CRAN or Bioconductor (for example, nothing from GitHub). What version of rmarkdown are you using?

Also, what version of pandoc (pandoc --version)? The build system has installed 1.13.2 (on zin2), 1.16.0.1 (morelia) and 1.16.0.2 (moscato2).

And while we're at it, what version of R? Be sure to use a recent R-devel.

Dan

> Zach
> 
> --
> Zachary L. Skidmore
> Staff Scientist
> McDonnell Genome Institute
> Washington University in Saint Louis
> 
> 
> 
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