[Bioc-devel] Error: DLL 'rgl' not found: maybe not installed for this architecture?

Pages, Herve hp@ge@ @end|ng |rom |redhutch@org
Thu Aug 29 17:48:02 CEST 2019


Hi,

On 8/23/19 14:38, Venu Thatikonda wrote:
> Hi,
> 
> During one of my R packages bioc review, I see the following 2 errors,
> 
> one:
> 
> Error in library.dynam(dynlib, pkg, lib) :
>    DLL 'rgl' not found: maybe not installed for this architecture?
> Error: .onLoad failed in loadNamespace() for 'rgl', details:
>    call: NULL
>    error: 	Loading rgl's DLL failed.
> Execution halted
> ERROR: lazy loading failed for package 'ALPS'
> * removing 'C:/Users/pkgbuild/packagebuilder/workers/jobs/1215/2a61338/ALPS.buildbin-libdir/ALPS'
> 

For some reasons we had a broken installation of rgl on the Windows 
builders. This should be fixed now. Sorry for that.

> I'm not using any functions from 'rgl', not sure why it is a required
> dependency. Or is there any key detail am I missing? R CMD build, check
> BiocCheck are very clean on my system.

You're not using any function from rgl but I suspect you depend on some 
package that depends on rgl. So your package depends **indirectly** on 
rgl. This means that when you load your package, rgl gets loaded too 
(see sessionInfo() after loading your package).

> 
> Two:
> 
>      * ERROR: System Files found that should not be git tracked:
>          ALPS.Rproj
> 
> 
> Based on this discussion (
> https://urldefense.proofpoint.com/v2/url?u=https-3A__community.rstudio.com_t_should-2Drproj-2Dfiles-2Dbe-2Dadded-2Dto-2Dgitignore_1269&d=DwICAg&c=eRAMFD45gAfqt84VtBcfhQ&r=BK7q3XeAvimeWdGbWY_wJYbW0WYiZvSXAJJKaaPhzWA&m=8Zrvz7lJB0ilLGOQT4Xj-V07HpjBtgN2hCX9TAtwztk&s=bNlefMI8tSDVTK1Yk3jOBMNAiNMaE5A2NXTJo-iSNg0&e= ),
> it is in fact a bit useful not adding PACKAGE.Rproj to .gitignore.

That check seems unjustified to me. Also it seems that adding ALPS.Rproj 
to your .gitignore won't make this error go away. I would suggest that 
you open an issue for it at:

   https://github.com/Bioconductor/BiocCheck/issues

In the meantime hopefully you can convince the reviewer of your package 
to ignore this error.

> Do all bioc packages require adding *Rproj to gitignore?

FWIW I see more than 200 BioC software packages with a PACKAGE.Rproj 
file in their git repo. AFAIK this file has never caused any problem. 
It's automatically ignored by 'R CMD build' and 'R CMD INSTALL' so 
everything is fine.

Best,
H.

> 
> Here is the report, if it's helpful.
> 
> https://urldefense.proofpoint.com/v2/url?u=http-3A__bioconductor.org_spb-5Freports_ALPS-5Fbuildreport-5F20190823145032.html&d=DwICAg&c=eRAMFD45gAfqt84VtBcfhQ&r=BK7q3XeAvimeWdGbWY_wJYbW0WYiZvSXAJJKaaPhzWA&m=8Zrvz7lJB0ilLGOQT4Xj-V07HpjBtgN2hCX9TAtwztk&s=KMJ8PJKE39eKYpi42dIbQlGrfQdm1CDHvdrFq-M-rww&e=
> 
> Thank you & have a ncie day!
> 

-- 
Hervé Pagès

Program in Computational Biology
Division of Public Health Sciences
Fred Hutchinson Cancer Research Center
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P.O. Box 19024
Seattle, WA 98109-1024

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