[Bioc-devel] GenVisR vignette build issues

Dan Tenenbaum dtenenba at fredhutch.org
Sat Feb 27 20:31:26 CET 2016

Seems to be an issue with the theme. I filed https://github.com/rstudio/rmarkdown/issues/630 .

----- Original Message -----
> From: "Dan Tenenbaum" <dtenenba at fredhutch.org>
> To: "Zach Skidmore" <zskidmor at genome.wustl.edu>
> Cc: "bioc-devel" <bioc-devel at r-project.org>
> Sent: Saturday, February 27, 2016 10:39:22 AM
> Subject: Re: [Bioc-devel] GenVisR vignette build issues

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

More information about the Bioc-devel mailing list