[Bioc-devel] GenVisR vignette build issues

[Dan Tenenbaum]

And already we have a solution, which I can confirm works:

https://github.com/rstudio/rmarkdown/issues/630#issuecomment-189712014

Dan


----- 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 11:31:26 AM
> Subject: Re: [Bioc-devel] GenVisR vignette build issues

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