Re: [R-pkg-devel] Packages required but not available
This advice would apply if the errors were being generated on a computer under the package developer's control... but this looks like it is from a repo submission. That said, if the developer has installed packages not currently in BioC for R4.1.1 they may need to wait for those packages to propagate in the official BioC repo and then to the submission test computers. On September 11, 2021 3:47:32 PM PDT, dbosa...@gmail.com wrote: >Reminder that you have to re-install any packages that your oncoPredict >package depends on for the new R version 4.1.1. Packages are >downloaded/installed to a specific R version. If you switch to another >version, everything needs to be reinstalled. I always get this error after >upgrading or switching R versions. > > � > >If you’ve already reinstalled and are still getting the error, then maybe it >is something with your NAMESPACE or DESCRIPTION file. Like if you are using a >package inside a function, but forget to add it to the DESCRIPTION. Or you >put it in the DESCRIPTION, but forget to add the @import roxygen directive >above your function so that it gets into the NAMESPACE. > > � > >Those are the situations that most commonly generate this error, from what I >have seen. > > � > >From: Danielle Maeser >Sent: Saturday, September 11, 2021 6:28 PM >To: dbosa...@gmail.com; R Package Devel >Subject: Re: [R-pkg-devel] Packages required but not available > > � > >Hi David, > > � > >Yes. I did recently upgrade R. � > > � > >On Sat, Sep 11, 2021 at 4:28 PM <mailto:dbosa...@gmail.com> > wrote: > >Danielle: > >Did you recently upgrade to R 4.1.1? > >David > > >-Original Message- >From: R-package-devel <mailto:r-package-devel-boun...@r-project.org> > On Behalf Of Danielle Maeser >via R-package-devel >Sent: Saturday, September 11, 2021 5:10 PM >To: R Package Devel <mailto:r-package-devel@r-project.org> > >Subject: [R-pkg-devel] Packages required but not available > >Hello, > >I received the following output from my package, oncoPredict. > >However, I don't understand how to correct this error. I've tested the advice >here: >https://stackoverflow.com/questions/14358814/error-in-r-cmd-check-packages-required-but-not-available >without success. > >Any thoughts as to how this error can be fixed? > >Danielle Maeser > > > > > > >*Version: 0.1Check: package dependenciesResult: ERROR � � Packages required >but not available: � � �'org.Hs.eg.db', 'TxDb.Hsapiens.UCSC.hg19.knownGene', >'maftools', � � �'TCGAbiolinks'* > � * � See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’* > >* � � manual.Flavor: r-release-macos-x86_64 ><https://www.r-project.org/nosvn/R.check/r-release-macos-x86_64/oncoPredict-00check.html>* >-- >Ph.D. Student >Bioinformatics and Computational Biology University of Minnesota > > � � � � [[alternative HTML version deleted]] > >__ >R-package-devel@r-project.org <mailto:R-package-devel@r-project.org> mailing >list https://stat.ethz.ch/mailman/listinfo/r-package-devel > > > > > � > -- Sent from my phone. Please excuse my brevity. __ R-package-devel@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/r-package-devel
Re: [R-pkg-devel] Packages required but not available
Reminder that you have to re-install any packages that your oncoPredict package depends on for the new R version 4.1.1. Packages are downloaded/installed to a specific R version. If you switch to another version, everything needs to be reinstalled. I always get this error after upgrading or switching R versions. � If you’ve already reinstalled and are still getting the error, then maybe it is something with your NAMESPACE or DESCRIPTION file. Like if you are using a package inside a function, but forget to add it to the DESCRIPTION. Or you put it in the DESCRIPTION, but forget to add the @import roxygen directive above your function so that it gets into the NAMESPACE. � Those are the situations that most commonly generate this error, from what I have seen. � From: Danielle Maeser Sent: Saturday, September 11, 2021 6:28 PM To: dbosa...@gmail.com; R Package Devel Subject: Re: [R-pkg-devel] Packages required but not available � Hi David, � Yes. I did recently upgrade R. � � On Sat, Sep 11, 2021 at 4:28 PM mailto:dbosa...@gmail.com> > wrote: Danielle: Did you recently upgrade to R 4.1.1? David -Original Message- From: R-package-devel mailto:r-package-devel-boun...@r-project.org> > On Behalf Of Danielle Maeser via R-package-devel Sent: Saturday, September 11, 2021 5:10 PM To: R Package Devel mailto:r-package-devel@r-project.org> > Subject: [R-pkg-devel] Packages required but not available Hello, I received the following output from my package, oncoPredict. However, I don't understand how to correct this error. I've tested the advice here: https://stackoverflow.com/questions/14358814/error-in-r-cmd-check-packages-required-but-not-available without success. Any thoughts as to how this error can be fixed? Danielle Maeser *Version: 0.1Check: package dependenciesResult: ERROR � � Packages required but not available: � � �'org.Hs.eg.db', 'TxDb.Hsapiens.UCSC.hg19.knownGene', 'maftools', � � �'TCGAbiolinks'* � * � See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’* * � � manual.Flavor: r-release-macos-x86_64 <https://www.r-project.org/nosvn/R.check/r-release-macos-x86_64/oncoPredict-00check.html>* -- Ph.D. Student Bioinformatics and Computational Biology University of Minnesota � � � � [[alternative HTML version deleted]] __ R-package-devel@r-project.org <mailto:R-package-devel@r-project.org> mailing list https://stat.ethz.ch/mailman/listinfo/r-package-devel � -- Ph.D. Student Bioinformatics and Computational Biology University of Minnesota � [[alternative HTML version deleted]] __ R-package-devel@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/r-package-devel
Re: [R-pkg-devel] Packages required but not available
Hi David, Yes. I did recently upgrade R. On Sat, Sep 11, 2021 at 4:28 PM wrote: > Danielle: > > Did you recently upgrade to R 4.1.1? > > David > > > -Original Message- > From: R-package-devel On Behalf > Of Danielle Maeser via R-package-devel > Sent: Saturday, September 11, 2021 5:10 PM > To: R Package Devel > Subject: [R-pkg-devel] Packages required but not available > > Hello, > > I received the following output from my package, oncoPredict. > > However, I don't understand how to correct this error. I've tested the > advice here: > > https://stackoverflow.com/questions/14358814/error-in-r-cmd-check-packages-required-but-not-available > without success. > > Any thoughts as to how this error can be fixed? > > Danielle Maeser > > > > > > > *Version: 0.1Check: package dependenciesResult: ERRORPackages required > but not available: 'org.Hs.eg.db', 'TxDb.Hsapiens.UCSC.hg19.knownGene', > 'maftools', 'TCGAbiolinks'* > * See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’* > > *manual.Flavor: r-release-macos-x86_64 > < > https://www.r-project.org/nosvn/R.check/r-release-macos-x86_64/oncoPredict-00check.html > >* > -- > Ph.D. Student > Bioinformatics and Computational Biology University of Minnesota > > [[alternative HTML version deleted]] > > __ > R-package-devel@r-project.org mailing list > https://stat.ethz.ch/mailman/listinfo/r-package-devel > > -- Ph.D. Student Bioinformatics and Computational Biology University of Minnesota [[alternative HTML version deleted]] __ R-package-devel@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/r-package-devel
