[Bioc-devel] Advice on build error related to webshot, and possibly related to rmarkdown?
Stian Lågstad
stianlagstad at gmail.com
Thu Dec 8 13:21:11 CET 2016
That's my thinking as well: That I should not need webshot. But I gave it a
*shot* anyway :) I'm thinking and hoping that there's an issue with
rmarkdown on oaxaca that can be solved.
On Thu, Dec 8, 2016 at 10:33 AM, Andrzej Oleś <andrzej.oles at gmail.com>
wrote:
> 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_2
>>> 0161207152203.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_2
>>> 0161130173413.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>
>>>
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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
>> https://stat.ethz.ch/mailman/listinfo/bioc-devel
>>
>
>
--
Stian Lågstad
+47 41 80 80 25
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