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.o...@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 <hpa...@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 <hpa...@fredhutch.org >>> <mailto:hpa...@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 >>> <stianlags...@gmail.com <mailto:stianlags...@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> >>> >>> [[alternative HTML version deleted]] >>> >>> _______________________________________________ >>> Bioc-devel@r-project.org <mailto:Bioc-devel@r-project.org> >>> mailing list >>> https://stat.ethz.ch/mailman/listinfo/bioc-devel >>> <https://stat.ethz.ch/mailman/listinfo/bioc-devel> >>> >>> >>> _______________________________________________ >>> Bioc-devel@r-project.org <mailto:Bioc-devel@r-project.org> >>> mailing list >>> https://stat.ethz.ch/mailman/listinfo/bioc-devel >>> <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: hpa...@fredhutch.org <mailto:hpa...@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: hpa...@fredhutch.org >> Phone: (206) 667-5791 >> Fax: (206) 667-1319 >> >> _______________________________________________ >> Bioc-devel@r-project.org mailing list >> https://stat.ethz.ch/mailman/listinfo/bioc-devel >> > > -- Stian Lågstad +47 41 80 80 25 [[alternative HTML version deleted]] _______________________________________________ Bioc-devel@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/bioc-devel