[Bioc-devel] Question about "Warning: '.local' is deprecated."

Dear all, In one of my packages, flowSpecs, I have over the last weeks gotten this warning message: * checking examples ... WARNING Found the following significant warnings: Warning: '.local' is deprecated. Deprecated functions may be defunct as soon as of the next release of R. See ?Deprecat

Re: [Bioc-devel] GenomicFeatures and/or TxDb.Hsapiens.UCSC.hg19.knownGene issue: missing tibble

EDIT: I found a general solution! (workaround?) I had written a response, but I had an idea, tested it and a few hours later I'm finishing this email. It does work... although not exactly as I intended it to. --- Thanks Martin for looking into this =) I'll respond to your question about makin

Re: [Bioc-devel] Build timeout in windows only

Hi Ruijia, The time for 'R CMD check APAlyzer_1.1.2.tar.gz' on the Linux and Mac builders are 1220.1 sec and 1441.6 sec, respectively. Keep in mind that on Windows it typically takes about twice longer! That's because all examples and unit tests are run for the i386 and x64 archs. So my guess

[Bioc-devel] regutools: request to add more git push access

Hi Nitesh, Could you add me (l.collado-torres) and Alejandro Reyes (what's your svn username Alejandro?) to regutools' list of contributors that have git push access? I think this is what we are supposed to do from re-reading https://github.com/Bioconductor/Contributions/issues/1393#issuecomment-

[Bioc-devel] Build timeout in windows only

Hi BioC-devel, I am the author of the Bioconductor package APAlyzer ( https://bioconductor.org/packages/devel/bioc/html/APAlyzer.html). We are trying to release our updated package (version 1.1.2) to Bioconductor. However, the Build Report ( http://bioconductor.org/checkResults/3.11/bioc-LATEST/AP

Re: [Bioc-devel] GenomicFeatures and/or TxDb.Hsapiens.UCSC.hg19.knownGene issue: missing tibble

I spent a bit of time not understanding why you were being so complicated -- BiocManager::install() finds all CRAN / Bioc dependencies, there's no need to use remotes at all and for debugging purposes it just seemed (still seems?) like you were making trouble for yourself. But eventually... I c

Re: [Bioc-devel] GenomicFeatures and/or TxDb.Hsapiens.UCSC.hg19.knownGene issue: missing tibble

Hi everyone, Charlotte, thank you very much! I didn't know about that issue on `remotes` and the fix attempts. Thank you for the info Martin! However, I have to report that it doesn't seem like switching from remotes::install_deps() to BiocManager::install() fixes the issue. I updated my GitHub A

[Bioc-devel] Final day to submit to devel branch

Tomorrow the devel branch will be frozen and branched to the RELEASE_3_11 branch. Tonight is the last night to commit changes to devel before release 3.11. After tonight any bug fixes will have to be applied to the new release branch as well as devel. Thank you Get Outlook for Android

Re: [Bioc-devel] To Push or Not To Push?

Hi Herve, Thanks for the advice. We have been pretty thorough with our testing, so I think we will do a final check and push today. Best, Chris Get Outlook for Android From: Herv� Pag�s Sent: Saturday, April 25, 2020 11:25:25 PM To: Chri

Re: [Bioc-devel] GenomicFeatures and/or TxDb.Hsapiens.UCSC.hg19.knownGene issue: missing tibble

Thanks Charlotte for the detective work. Annotation packages (TxDb, org, BSgenome, and GenomeInfoDbData, for instance) are distributed only as source – this was a decision made quite a while (years) ago, to save disk space (some of these packages are large, and hosting macOS and Windows binarie

Re: [Bioc-devel] GenomicFeatures and/or TxDb.Hsapiens.UCSC.hg19.knownGene issue: missing tibble

Hi Leo, Martin, it looks like this is related to an issue with the remotes package: https://github.com/r-lib/remotes/issues/296 . It gets the installation order wrong, and tries to install source packages before binaries. This can be a problem with