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

[Kern, Lori]

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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