[Bioc-devel] Advice on build error related to webshot, and possibly related to rmarkdown?
Hervé Pagès
hpages at fredhutch.org
Thu Dec 8 18:38:04 CET 2016
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 <hpages at fredhutch.org
> <mailto: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>
> <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>
> <mailto: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/>
> <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
> <stianlagstad at gmail.com <mailto:stianlagstad at gmail.com>
> <mailto: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>
>
> <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]]
>
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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>
> <mailto:hpages at fredhutch.org <mailto:hpages at 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>
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>
>
>
>
> --
> 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: 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
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