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

[Andrzej Oleś]

Dear Stian,
according to https://github.com/yihui/knitr/releases/tag/v1.14 the
dependency on webshot, which apparently is used to take website
screenshots, is optional and knitr should use fallback mode if webshot is
not available. Webshot has a list of system dependencies, not sure how hard
to fulfill. I wouldn't recommend adding webshot dependency to your packge,
unless you actually intended to use the functionality provided by it.

Cheers,
Andrzej



On Thu, Dec 8, 2016 at 1:07 AM, Hervé Pagès <hpages at fredhutch.org> wrote:

> Not clear to me what's going on, I'm not a knitr/rmarkdown expert.
> What I see is that knitr suggests webshot probably because it needs
> it in some situations. That must be a rare situation though because
> webshot is not installed on our build machines, which means that none
> of the 1298 software packages currently in BioC devel needs it.
>
> So I'm not sure why it would need it for building your vignette, and
> why it would need it only on oaxaca. Anyway maybe it would help to add
> webshot to your Suggests field. That will trigger installation of
> webshot by the SPB before it tries to build/check your package.
> Don't forget to bump again the package version in order to trigger
> a new build by the SPB.
>
> H.
>
> On 12/07/2016 12:31 PM, Stian Lågstad wrote:
>
>> 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
>> <http://bioconductor.org/spb_reports/chimeraviz_buildreport_
>> 20161207152203.html>
>>
>> On Wed, Dec 7, 2016 at 7:42 PM, Hervé Pagès <hpages at fredhutch.org
>> <mailto: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/
>>     <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
>>         <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 <mailto: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
>>             <http://bioconductor.org/spb_reports/chimeraviz_buildreport_
>> 20161130173413.html>
>>             Link to bioconductor submission issue:
>>             https://github.com/Bioconductor/Contributions/issues/206
>>             <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 <tel:%2B47%2041%2080%2080%2025>
>>
>>                     [[alternative HTML version deleted]]
>>
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>>
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>>
>>
>>     --
>>     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 <mailto:hpages at fredhutch.org>
>>     Phone:  (206) 667-5791 <tel:%28206%29%20667-5791>
>>     Fax:    (206) 667-1319 <tel:%28206%29%20667-1319>
>>
>>
>>
>>
>> --
>> Stian Lågstad
>> +47 41 80 80 25
>>
>
> --
> 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
>
> _______________________________________________
> Bioc-devel at r-project.org mailing list
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