Thanks so much for your explanation! I will probably wait for the newer version of Rsubreads to fix it.
On Mon, Aug 16, 2021 at 9:16 PM Hervé Pagès <hpages.on.git...@gmail.com> wrote: > Hi Ruijia, > > I think this is due to recent changes to Rsubread. You can actually see > the same error here for Rsubread: > > > > http://bioconductor.org/checkResults/devel/bioc-LATEST/Rsubread/nebbiolo2-buildsrc.html > > These recent changes to Rsubread did not propagate yet which makes > things a little hard to reproduce i.e. you can't just use > BiocManager::install() to get the latest Rsubread. Instead you need to > install it directly from git.bioconductor.org > (https://git.bioconductor.org/packages/Rsubread). This is what the build > system does. > > FWIW the reasons the latest changes to Rsubread didn't propagate yet is > because the package fails to pass 'R CMD build' and also because the > changes have not been followed by a version bump. Last version bump was > on July 6 from 2.7.2 to 2.7.3. > > Cheers, > H. > > > On 15/08/2021 17:24, Ruijia Wang wrote: > > Hi BioC-devel, > > > > I am the author of the Bioconductor package APAlyzer ( > > https://bioconductor.org/packages/release/bioc/html/APAlyzer.html). I > > current noticed there is an ERROR in the building report of our latest > dev > > version (1.7.3) on the page of Bioconductor ( > > > http://bioconductor.org/checkResults/devel/bioc-LATEST/APAlyzer/nebbiolo2-checksrc.html > > ). > > > >> > >> * Error: object 'fout_annot' not found** Backtrace:* > >> > >> * 1. └─APAlyzer::PASEXP_IPA(...) test_IPA_analysis.R:10:8* > >> * 2. └─Rsubread::featureCounts(...)** 3. > └─base::file.remove(fout_annot)* > > > > > > However, I can not repeat this error using R 4.1 and Bioconductor 3.14 on > > my end with either *R CMD check* or > *BiocCheck("APAlyzer_1.7.3.tar.gz").* And > > I don't recall any of the code updating would trigger the error of > > *base::file.remove()*. Could you help me to figure out how to fix/bypass > > this issue in the building report of Bioconductor? Thanks in advance! > > > > Best, > > Ruijia > > > > [[alternative HTML version deleted]] > > > > _______________________________________________ > > Bioc-devel@r-project.org mailing list > > https://stat.ethz.ch/mailman/listinfo/bioc-devel > > > > -- > Hervé Pagès > > Bioconductor Core Team > hpages.on.git...@gmail.com > [[alternative HTML version deleted]] _______________________________________________ Bioc-devel@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/bioc-devel
