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

[Hervé Pagès]

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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>     --
>     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