Re: [Bioc-devel] package build : Warning: 'rgl_init' failed, running with rgl.useNULL = TRUE
- Original Message -
> From: "Diana LOW"
> To: "bioc-devel"
> Sent: Sunday, February 28, 2016 9:25:43 PM
> Subject: [Bioc-devel] package build : Warning: 'rgl_init' failed, running
> with rgl.useNULL = TRUE
> Hi,
>
> I've been getting this error on package build (morelia), and it appears as a
> warning on the zin2 check.
>
> Warning in rgl.init(initValue, onlyNULL) :
>
> RGL: unable to open X11 display
>
> Warning: 'rgl_init' failed, running with rgl.useNULL = TRUE
It's safe to ignore that one.
>
> I am also getting occasional errors like this
> Warning in (if (grepl("\\.[Rr]md$", file)) knit2html else if
> (grepl("\\.[Rr]rst$", :
> It seems you should call rmarkdown::render() instead of knitr::knit2html()
> because confess-vignette.Rmd appears to be an R Markdown v2 document.
> Quitting from lines 2-18 (confess-vignette.Rmd)
> Error: processing vignette 'confess-vignette.Rmd' failed with diagnostics:
Not sure about this one, I can't reproduce it either, will look into it.
> could not find function "doc_date"
You call doc_date in your YAML preamble before you have loaded BiocStyle, so
replac doc_date with BiocStyle::doc_date, likewise with pkg_ver.
>
> http://bioconductor.org/spb_reports/CONFESS_0.99.7_buildreport_20160229000425.html
>
> Any advice on how to deal with this? I cannot replicate the error/warnings
> when
> I build/check/BiocCheck on my system.
>
> Best,
> Diana
>
>
>
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>
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>
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[Bioc-devel] package build : Warning: 'rgl_init' failed, running with rgl.useNULL = TRUE
Hi,
I've been getting this error on package build (morelia), and it appears as a
warning on the zin2 check.
Warning in rgl.init(initValue, onlyNULL) :
RGL: unable to open X11 display
Warning: 'rgl_init' failed, running with rgl.useNULL = TRUE
I am also getting occasional errors like this
Warning in (if (grepl("\\.[Rr]md$", file)) knit2html else if
(grepl("\\.[Rr]rst$", :
It seems you should call rmarkdown::render() instead of knitr::knit2html()
because confess-vignette.Rmd appears to be an R Markdown v2 document.
Quitting from lines 2-18 (confess-vignette.Rmd)
Error: processing vignette 'confess-vignette.Rmd' failed with diagnostics:
could not find function "doc_date"
http://bioconductor.org/spb_reports/CONFESS_0.99.7_buildreport_20160229000425.html
Any advice on how to deal with this? I cannot replicate the error/warnings when
I build/check/BiocCheck on my system.
Best,
Diana
Note: This message may contain confidential information. If this Email/Fax has
been sent to you by mistake, please notify the sender and delete it
immediately. Thank you.
[[alternative HTML version deleted]]
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Re: [Bioc-devel] workflows running Bioc-devel
Hi Dan, Sounds good. In which case, I'll stick to my original plan, i.e., to submit the package for BioC 3.4. We can figure out what to do with the workflow and build system then, if it hasn't already been sorted. Cheers, Aaron Dan Tenenbaum wrote: > Hi, > > This has come up before and probably should be done at some point. > I can be virtually certain that it will not happen before the upcoming (3.3) > release though. > > Thanks. > Dan > > > - Original Message - >> From: "Michael Love" >> To: "Aaron Lun" >> Cc: "bioc-devel" >> Sent: Sunday, February 28, 2016 5:59:41 AM >> Subject: Re: [Bioc-devel] workflows running Bioc-devel >> +1 >> >> I'm also interested in having the option of devel / release workflow >> branches for the reasons Aaron mentions. >> >> I develop software and workflow in tandem but currently there is a >> disconnect in showing publicly how software changes will impact a workflow. >> >> [[alternative HTML version deleted]] >> >> ___ >> Bioc-devel@r-project.org mailing list >> https://stat.ethz.ch/mailman/listinfo/bioc-devel ___ Bioc-devel@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/bioc-devel
Re: [Bioc-devel] workflows running Bioc-devel
Hi, This has come up before and probably should be done at some point. I can be virtually certain that it will not happen before the upcoming (3.3) release though. Thanks. Dan - Original Message - > From: "Michael Love" > To: "Aaron Lun" > Cc: "bioc-devel" > Sent: Sunday, February 28, 2016 5:59:41 AM > Subject: Re: [Bioc-devel] workflows running Bioc-devel > +1 > > I'm also interested in having the option of devel / release workflow > branches for the reasons Aaron mentions. > > I develop software and workflow in tandem but currently there is a > disconnect in showing publicly how software changes will impact a workflow. > > [[alternative HTML version deleted]] > > ___ > Bioc-devel@r-project.org mailing list > https://stat.ethz.ch/mailman/listinfo/bioc-devel ___ Bioc-devel@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/bioc-devel
Re: [Bioc-devel] workflows running Bioc-devel
+1 I'm also interested in having the option of devel / release workflow branches for the reasons Aaron mentions. I develop software and workflow in tandem but currently there is a disconnect in showing publicly how software changes will impact a workflow. [[alternative HTML version deleted]] ___ Bioc-devel@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/bioc-devel
Re: [Bioc-devel] workflows running Bioc-devel
Hi all, Is it possible to get the workflow build system to use an R installation running Bioc-devel for a specific workflow? To give some context, I've been writing a workflow for low-level analysis of single-cell RNA-seq data. Of the many Bioconductor packages it uses, one of them is my own package that isn't quite ready to go into the upcoming 3.3 release. I'd like to have some more time to clean it up (add tests, documentation, etc.) so I was initially aiming to submit the package into BioC 3.4, i.e., the release after the next. However, if the workflow build system only runs on BioC release, I'd have to wait until ~September to submit the workflow (assuming we're still on schedule). This would be slightly annoying, given that the workflow would have been finished for months at that point. The obvious solution would be to allow the building of workflows on Bioc devel, but I don't know how technically possible that would be. Alternatively, I've still got a month before the new package submission deadline, so I can try to clean up the package and get it into 3.3. Any suggestions? Cheers, Aaron ___ Bioc-devel@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/bioc-devel
