Hi Hervé, Can share with me the issue page of Rsubread? It seems listed neither on the Bioconductor page nor on Github. Thanks.
On Wed, Aug 18, 2021 at 4:36 AM Hervé Pagès <hpages.on.git...@gmail.com> wrote: > There's been no activity on Rsubread since Aug 8. You might want to open > an issue on GitHub. It might help. > > H. > > On 17/08/2021 16:26, Ruijia Wang wrote: > > 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 > > <mailto: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 > > < > 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 > > <http://git.bioconductor.org> > > (https://git.bioconductor.org/packages/Rsubread > > <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 > > <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 > > < > 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 <mailto:Bioc-devel@r-project.org> > > mailing list > > > https://stat.ethz.ch/mailman/listinfo/bioc-devel > > <https://stat.ethz.ch/mailman/listinfo/bioc-devel> > > > > > > > -- > > Hervé Pagès > > > > Bioconductor Core Team > > hpages.on.git...@gmail.com <mailto:hpages.on.git...@gmail.com> > > > > -- > 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
