[Bioc-devel] autonomics devel : how to reproduce bioc build errors best ?
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 at 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 at r-project.org> on behalf of Aditya Bhagwat via Bioc-devel <bioc-devel at r-project.org> Sent: Wednesday, January 24, 2024 4:03 AM To: bioc-devel at r-project.org <bioc-devel at 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 _______________________________________________ Bioc-devel at r-project.org mailing list https://secure-web.cisco.com/1kGEWsKiRHXb49vrhBt8Gleszb2n4jor7pjkUqB9LOYL8cHoFepm2kp0HGA0Xkb7RxHKPurhd0cB2NUZWLGyVCh6540DyXOIwZJ6fdCaLODRay0wEJomRgHyo_cw3xI6iaEaa3RbjrlouGxOPWGC06hEfe9-grA9THyn66Iao98-QrZx-nxpjGixqwIJ6VACn7Z6N4m3NRbwnxOjiniiuMgbvzGAQwwzkKttEBWGsXdRiLRfBmFElSydwGLqIu6E1dL9wXooFpdkL9b3wcqMBcsrS9XmzghkmFkyCNVgYipgJQEAM1aT7H_yq-Xpa8I_N/https%3A%2F%2Fstat.ethz.ch%2Fmailman%2Flistinfo%2Fbioc-devel This email message may contain legally privileged and/or confidential information. If you are not the intended recipient(s), or the employee or agent responsible for the delivery of this message to the intended recipient(s), you are hereby notified that any disclosure, copying, distribution, or use of this email message is prohibited. If you have received this message in error, please notify the sender immediately by e-mail and delete this email message from your computer. Thank you.
Aditya Bhagwat Translational Proteomics ? Philipps-University Marburg Biological Pharmacological Center ? Room A406 Tel.: +49 6421 28 27403