[Bioc-devel] package build : Warning: 'rgl_init' failed, running with rgl.useNULL = TRUE

Dan Tenenbaum dtenenba at fredhutch.org
Mon Feb 29 07:19:20 CET 2016

----- Original Message -----
> From: "Diana LOW" <dlow at imcb.a-star.edu.sg>
> To: "bioc-devel" <bioc-devel at r-project.org>
> 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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