[Bioc-devel] "there is no package called 'BSgenome.Athaliana.TAIR.TAIR9'"

Martin Morgan mtmorg@n@b|oc @end|ng |rom gm@||@com
Tue Oct 13 00:20:00 CEST 2020

This warning

* checking dependencies in R code ... WARNING
'::' or ':::' import not declared from: ‘BSgenome.Athaliana.TAIR.TAIR9’

means that you have used BSgenome.Athaliana.TAIR.TAIR9 in your code, but you have not declared it in your DESCRIPTION file, either as Imports: or Suggests:. Since it isn't in your DESCRIPTION file, the build system does not know that it should be installed for checking your package.

~/b/git/trena master$ grep Athal DESCRIPTION
~/b/git/trena master$

This is a little surprising, implying that no other package in the build system has this package in the DESCRIPTION file, but...

It looks like this needs to be added to the Imports: field, or perhaps Suggests:


On 10/12/20, 12:36 PM, "Bioc-devel on behalf of Paul Shannon" <bioc-devel-bounces using r-project.org on behalf of paul.thurmond.shannon using gmail.com> wrote:

    My package trena fails on all platforms with this error:

       there is no package called ‘BSgenome.Athaliana.TAIR.TAIR9’

    Is Arabidopsis no longer supported by bioc?  I remember some discussion related to this over the summer.

     - Paul
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