Re: [Bioc-devel] How to change the name of R package that is already published on Bioconductor?

Hi Juanpeng, I notice that the new miRspongeR package also displays the package startup message explaining the name change from miRsponge to miRspongeR.. Note that you only need to have this message in the old miRsponge package (which is now officially deprecated in BioC 3.9). Having the

[Bioc-devel] Community generated annotation deadline is April 24th

Hello Bioconductor Community, Just a reminder that the community generated annotation package deadline is April 24th. Please submit these packages to me by then. Thank you! This email message may contain legally privileged and/or confidential information. If you are not the intended

[Bioc-devel] Bioconductor 3.9 Orgdbs and TxDbs available

Hello Bioconductor Community! The new OrgDb and TxDbs for the Bioconductor 3.9 release are now available. The new Orgdbs are: GO.db_3.8.0.tar.gz org.Ag.eg.db_3.8.0.tar.gz org.At.tair.db_3.8.0.tar.gz org.Bt.eg.db_3.8.0.tar.gz org.Ce.eg.db_3.8.0.tar.gz org.Cf.eg.db_3.8.0.tar.gz

Re: [Bioc-devel] Help needed: Rdisop on Windows "File format not recognized"

Hi, thanks everyone for the input, I now have a few more leads to follow. It would be great to have a general single package builder even for existing packages to check if one has no direct access to the failing architecture. https://win-builder.r-project.org/ is discouraging BioC package

Re: [Bioc-devel] R CMD check testthat failure in tokay2 (devel branch)

Hi Benjamin, Sorry for the late answer. Looks like things have changed a little bit on the report since your original post. What I see on today's report is a test failure on Windows for the i386 arch only:

Re: [Bioc-devel] Dashes in GFF attributes

Hi Valentino, You will have to provide more details concerning the issue. It may be as simple as removing the dashes with `gsub` before using `featureCount`. Please review the posting guidelines for a better idea on how to get help: https://bioconductor.org/help/support/posting-guide/ And

[Bioc-devel] Dashes in GFF attributes

Hi, I hope this is the right place to write. The featureCount function of Rsubread doesn't work if the GFF file contains dashes in the 9th column. https://github.com/Bioconductor/BiocManager/issues/45 I was told to write in bioc-devel. [[alternative HTML version deleted]]

Re: [Bioc-devel] Help needed: Rdisop on Windows "File format not recognized"

I second the idea of reproducing with the Windows build commands, which have to do more than 'just' build for a particular architecture. One might test the hypothesis that it is staged install that is causing the problem with StagedInstalll: no in the DESCRIPTION file. Makevars is

Re: [Bioc-devel] Help needed: Rdisop on Windows "File format not recognized"

I can reproduce the error using R-3.6.0beta and running the following two steps to replicate the Bioc builder commands: R CMD build --keep-empty-dirs --no-resave-data Rdisop rm -rf Rdisop.buildbin-libdir && mkdir Rdisop.buildbin-libdir && C:\Users\biocbuild\bbs-3.9-bioc\R\bin\R.exe CMD INSTALL

[Bioc-devel] Help needed: Rdisop on Windows "File format not recognized"

Hi, with the next release coming up, I am out of wits regarding the failure at http://bioconductor.org/checkResults/devel/bioc-LATEST/Rdisop/tokay2-buildbin.html which exists since before April this year, when we committed some changes to get rid of the RcppClassic dependency. Max Helf