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

[dbos@k01 m@iii@g oii gm@ii@com]

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:

Danielle:

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






*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>*
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Ph.D. Student
Bioinformatics and Computational Biology University of Minnesota

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-- 

Ph.D. Student

Bioinformatics and  Computational  Biology

University of Minnesota

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