[Bioc-devel] GenVisR vignette build issues

Dan Tenenbaum dtenenba at fredhutch.org
Sat Feb 27 19:39:22 CET 2016

----- 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), (morelia) and (moscato2).

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


> Zach
> --
> Zachary L. Skidmore
> Staff Scientist
> McDonnell Genome Institute
> Washington University in Saint Louis
> ____
> This email message is a private communication. The information transmitted,
> including attachments, is intended only for the person or entity to which it is
> addressed and may contain confidential, privileged, and/or proprietary
> material. Any review, duplication, retransmission, distribution, or other use
> of, or taking of any action in reliance upon, this information by persons or
> entities other than the intended recipient is unauthorized by the sender and is
> prohibited. If you have received this message in error, please contact the
> sender immediately by return email and delete the original message from all
> computer systems. Thank you.
>	[[alternative HTML version deleted]]
> _______________________________________________
> Bioc-devel at r-project.org mailing list
> https://stat.ethz.ch/mailman/listinfo/bioc-devel

More information about the Bioc-devel mailing list