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@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-boun...@r-project.org> on behalf of
Aditya Bhagwat via Bioc-devel <bioc-devel@r-project.org>
Sent: Wednesday, January 24, 2024 4:03 AM
To: bioc-devel@r-project.org <bioc-devel@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
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