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

[Stian Lågstad]

Thank you both. Could you also advice me on the error I'm receiving
on oaxaca? "there is no package called 'webshot'"
New build report: http://bioconductor.org/spb_reports/chimeraviz_
buildreport_20161207152203.html

On Wed, Dec 7, 2016 at 7:42 PM, Hervé Pagès <hpages at fredhutch.org> wrote:

> 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
>>>
>>
>> _______________________________________________
>> Bioc-devel at r-project.org mailing list
>> https://stat.ethz.ch/mailman/listinfo/bioc-devel
>>
>>
> --
> Hervé Pagès
>
> Program in Computational Biology
> Division of Public Health Sciences
> Fred Hutchinson Cancer Research Center
> 1100 Fairview Ave. N, M1-B514
> P.O. Box 19024
> Seattle, WA 98109-1024
>
> E-mail: hpages at fredhutch.org
> Phone:  (206) 667-5791
> Fax:    (206) 667-1319
>



-- 
Stian Lågstad
+47 41 80 80 25

	[[alternative HTML version deleted]]