[Bioc-devel] Advice on build error related to webshot, and possibly related to rmarkdown?

[Hervé Pagès]

Hi Stian,

The build machines used by the SPB are the same as the machines used
for the daily builds and they already have the latest BiocStyle
installed (BiocStyle 2.3.23). You can see this by going on the daily
build report for devel and clicking on any of the link in the
"Installed pkgs" column in the top table:

   https://bioconductor.org/checkResults/3.5/bioc-LATEST/

However, the SPB report for your package is from Nov 30 so it could
be that it predates the fix in BiocStyle. You can trigger a new build
of your package by just bumping its version on github.

Hope this helps,
H.

On 12/07/2016 07:17 AM, Leonardo Collado Torres wrote:
> Hi Stian,
>
> Install BiocStyle 2.3.20 or newer and that error will go away. See
> https://github.com/Bioconductor/BiocStyle/issues/20 for details.
>
> Best,
> Leo
>
> On Wed, Dec 7, 2016 at 7:44 AM, Stian Lågstad <stianlagstad at gmail.com> wrote:
>> Hi,
>>
>> Could someone please advice me on the errors I'm getting building my
>> package? I'm unable to reproduce them locally.
>>
>> Link to build report:
>> http://bioconductor.org/spb_reports/chimeraviz_buildreport_20161130173413.html
>> Link to bioconductor submission issue:
>> https://github.com/Bioconductor/Contributions/issues/206
>>
>> I'm getting an error on creating my vignette: `argumemt is not a character
>> vector`
>> I also get this: `there is no package called 'webshot'`
>>
>> I believe these could be related to this warning: `Warning in
>> engine$weave(file, quiet = quiet, encoding = enc) : Pandoc (>= 1.12.3)
>> and/or pandoc-citeproc not available. Falling back to R Markdown v1.`
>>
>> I use rmarkdown_1.2 locally without problems. Can someone here assist me?
>>
>> Thank you.
>>
>> --
>> Stian Lågstad
>> +47 41 80 80 25
>>
>>         [[alternative HTML version deleted]]
>>
>> _______________________________________________
>> Bioc-devel at r-project.org mailing list
>> https://stat.ethz.ch/mailman/listinfo/bioc-devel
>
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>

-- 
Hervé Pagès

Program in Computational Biology
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