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

[Dan Tenenbaum]

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

[Diana LOW (IMCB)]

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 
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immediately. Thank you.

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Re: [Bioc-devel] workflows running Bioc-devel

[Aaron Lun]

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]]
>>
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Re: [Bioc-devel] workflows running Bioc-devel

[Dan Tenenbaum]

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]]
> 
> ___
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Re: [Bioc-devel] workflows running Bioc-devel

[Michael Love]

+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.

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