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 _______________________________________________ Bioc-devel@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. [[alternative HTML version deleted]] _______________________________________________ Bioc-devel@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/bioc-devel