[Bioc-devel] autonomics devel : how to reproduce bioc build errors best ?

[@dity@@bh@gw@t m@iii@g oii u@i-m@rburg@de]

Thank you Lori and Vince,

Will make it work using your suggestions : )

@Vince : could you send your email once again. I seem to have  
accidentally deleted it and know it was full of helpful information -  
sorry :( !!!

Aditya



> I just tried locally with R-devel and making sure all the package  
> dependencies were updated and can reproduce this.
>
> I suggest making sure you have an updated installation or maybe try  
> using the BIoconductor docker if you don't have access to R-devel.
>
>
> lorikern using jbcj433:~/BioconductorPackages/SoftwarePkg$ R CMD build autonomics
> * checking for file 'autonomics/DESCRIPTION' ... OK
> * preparing 'autonomics':
> * checking DESCRIPTION meta-information ... OK
> * installing the package to build vignettes
> * creating vignettes ... ERROR
> --- re-building ‘autonomics_detailed_manual.Rmd’ using rmarkdown
> Quitting from lines 24-38 [unnamed-chunk-1] (autonomics_detailed_manual.Rmd)
> Error: processing vignette 'autonomics_detailed_manual.Rmd' failed  
> with diagnostics:
> NA/NaN argument
> --- failed re-building ‘autonomics_detailed_manual.Rmd’
>
> --- re-building ‘autonomics_platformaware_analysis.Rmd’ using rmarkdown
>
> Quitting from lines 51-54 [unnamed-chunk-2]  
> (autonomics_platformaware_analysis.Rmd)
> Error: processing vignette 'autonomics_platformaware_analysis.Rmd'  
> failed with diagnostics:
> is_subset : The elements 'pls1', 'pls2' in c("pls1", "pls2") are not  
> in fits(object).
> --- failed re-building ‘autonomics_platformaware_analysis.Rmd’
>
> --- re-building ‘autonomics_unified_modeling.Rmd’ using rmarkdown
>
> Quitting from lines 103-107 [unnamed-chunk-8]  
> (autonomics_unified_modeling.Rmd)
> Error: processing vignette 'autonomics_unified_modeling.Rmd' failed  
> with diagnostics:
> argument "y" is missing, with no default
> --- failed re-building ‘autonomics_unified_modeling.Rmd’
>
> SUMMARY: processing the following files failed:
>   ‘autonomics_detailed_manual.Rmd’
>   ‘autonomics_platformaware_analysis.Rmd’
>   ‘autonomics_unified_modeling.Rmd’
>
> Error: Vignette re-building failed.
> Execution halted
>
>
>
>
> Lori Shepherd - Kern
>
> Bioconductor Core Team
>
> Roswell Park Comprehensive Cancer Center
>
> Department of Biostatistics & Bioinformatics
>
> Elm & Carlton Streets
>
> Buffalo, New York 14263
>
> ________________________________
> From: Bioc-devel <bioc-devel-bounces using r-project.org> on behalf of  
> Aditya Bhagwat via Bioc-devel <bioc-devel using r-project.org>
> Sent: Wednesday, January 24, 2024 4:03 AM
> To: bioc-devel using r-project.org <bioc-devel using r-project.org>
> Subject: [Bioc-devel] autonomics devel : how to reproduce bioc build  
> errors best ?
>
> Dear bioc-devel,
>
> autonomics underwent continued development since its submission two  
> years ago.
> The new functionality was recently pushed to autonomics devel to make
> it accessible to users.
> Not suprisingly, the green traffic lights turned red.
>
> The puzzling thing, though, is that, on my machine, with R env
> variables set as recommended by BioC to mimick the BioC build
> machines, R CMD CHECK runs error-free. On the BioC machines, however,
> it doesnt, and I am having a hard time figuring out why (given that I
> cant reproduce).
>
> Any suggestions to make the puzzle-solving easier ?
>
> Thankyou!
>
> Aditya
>
> --
> Aditya Bhagwat
> Translational Proteomics ∙ Philipps-University Marburg
> Biological Pharmacological Center ∙ Room A406
> Tel.: +49 6421 28 27403
>
>
> --
> Aditya Bhagwat
> Translational Proteomics ∙ Philipps-University Marburg
> Biological Pharmacological Center ∙ Room A406
> Tel.: +49 6421 28 27403
>
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-- 
Aditya Bhagwat
Translational Proteomics ∙ Philipps-University Marburg
Biological Pharmacological Center ∙ Room A406
Tel.: +49 6421 28 27403