Let's keep the discussion on the mailing list. On 12/07/2016 10:58 PM, Stian Lågstad wrote:
I tried doing that now and got another error: "cannot open the connection". I don't know how to investigate that further. Link to new build report: http://bioconductor.org/spb_reports/chimeraviz_buildreport_20161208015500.html
At least the webshot issue is gone. Yes adding it to the Suggests field is of course a dirty hack. The hope being that it would help you quickly work around the build failure on oaxaca.
Do you think the issue could be caused by the warning below? Since I'm only seeing that on oaxaca. "Warning in engine$weave(file, quiet = quiet, encoding = enc) : Pandoc (>= 1.12.3) and/or pandoc-citeproc not available. Falling back to R Markdown v1."
Both pandoc and pandoc-citeproc are on oaxaca: oaxaca:~ biocbuild$ which pandoc /usr/local/bin/pandoc oaxaca:~ biocbuild$ which pandoc-citeproc /usr/local/bin/pandoc-citeproc And pandoc version is >= 1.12.3: oaxaca:~ biocbuild$ pandoc -v | head -n 2 pandoc 1.17.0.2 Compiled with texmath 0.8.5, highlighting-kate 0.6.2. Also we don't see that warning on the daily builds even though many packages use pandoc/pandoc-citeproc for their vignettes. So again, I'm not sure what's going on, sorry. Likely a problem on our side. I suggest you ignore this build error on oaxaca for now. Cheers, H.
Thank you. On Thu, Dec 8, 2016 at 1:07 AM, Hervé Pagès <hpa...@fredhutch.org <mailto: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_20161207152203.html <http://bioconductor.org/spb_reports/chimeraviz_buildreport_20161207152203.html> <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 <hpa...@fredhutch.org <mailto:hpa...@fredhutch.org> <mailto: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/> <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> <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> <mailto: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_20161130173413.html <http://bioconductor.org/spb_reports/chimeraviz_buildreport_20161130173413.html> <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> <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> <tel:%2B47%2041%2080%2080%2025> [[alternative HTML version deleted]] _______________________________________________ Bioc-devel@r-project.org <mailto:Bioc-devel@r-project.org> <mailto: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> <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> <mailto: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> <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> <mailto:hpa...@fredhutch.org <mailto:hpa...@fredhutch.org>> Phone: (206) 667-5791 <tel:%28206%29%20667-5791> <tel:%28206%29%20667-5791> Fax: (206) 667-1319 <tel:%28206%29%20667-1319> <tel:%28206%29%20667-1319> -- Stian Lågstad +47 41 80 80 25 <tel:%2B47%2041%2080%2080%2025> -- 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
