[R-pkg-devel] Packages required but not available

[Jeff Newmiller]

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, dbosak01 using 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.
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>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.  
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>Those are the situations that most commonly generate this error, from what I have seen.  
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>From: Danielle Maeser <maese005 using umn.edu> 
>Sent: Saturday, September 11, 2021 6:28 PM
>To: dbosak01 using gmail.com; R Package Devel <r-package-devel using r-project.org>
>Subject: Re: [R-pkg-devel] Packages required but not available
>
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>Hi David,
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>Yes. I did recently upgrade R. �
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>On Sat, Sep 11, 2021 at 4:28 PM <dbosak01 using gmail.com <mailto:dbosak01 using gmail.com> > wrote:
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>Danielle:
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>Did you recently upgrade to R 4.1.1?
>
>David
>
>
>-----Original Message-----
>From: R-package-devel <r-package-devel-bounces using r-project.org <mailto:r-package-devel-bounces using r-project.org> > On Behalf Of Danielle Maeser via R-package-devel
>Sent: Saturday, September 11, 2021 5:10 PM
>To: R Package Devel <r-package-devel using r-project.org <mailto:r-package-devel using 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
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>*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
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> �  �  �  � [[alternative HTML version deleted]]
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>______________________________________________
>R-package-devel using r-project.org <mailto:R-package-devel using r-project.org>  mailing list https://stat.ethz.ch/mailman/listinfo/r-package-devel
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-- 
Sent from my phone. Please excuse my brevity.