Hello BioC community, I have been trying unsuccessfully for a week now to update both release and dev branches of the netDx packages but am still getting build errors.
Today I got a build error for the release branch: https://bioconductor.org/checkResults/3.11/bioc-LATEST/netDx/malbec2-buildsrc.html I tried to reproduce the error in the following way: 1. I have a BioC docker that runs R 4.0.0 and Biobase 2.48.0 (from sessionInfo()). 2. I ran a fresh "git clone" to get the latest netDx. "git clone https://git.bioconductor.org/packages/netDx"; , after the URL on the build page above. 3. Switched to release branch "git checkout RELEASE_3_11" 4. Reinstalled netDx "R CMD INSTALL netDx" and confirmed using sessionInfo(); netDx_1.0.1 5. Set up Renvirons as mentioned on the build page and launched R also as suggested there, after declaring the corresponding variable. 6. The offending vignette is "Predict_CaseControl_from_CNV.Rmd". So I first ran "knitr::purl("Predict_CaseControl_from_CNV.Rmd") , and then removed the suppressMessages() around the offending function call, "buildPredictor_sparseGenetic()". 7. Ran "source("Predict_CaseControl_from_CNV.R"). And it ran through successfully. What am I missing? Is it that the snapshot date it from June 10 but the build page is from June 11 so I need to wait for the changes to kick in? I'm also getting errors with the devel branch, so will probably separately write about that (sigh). Thanks,Shraddha -- Shraddha Pai, PhD http://shraddhapai.com ; @spaiglass on Twitter Post-doctoral Fellow, http://baderlab.org The Donnelly Centre for Cellular and Biomolecular Research University of Toronto [[alternative HTML version deleted]] _______________________________________________ Bioc-devel@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/bioc-devel
