[Bioc-devel] Help with R CMD check NOTEs

Pariksheet Nanda pariksheet.nanda at uconn.edu
Wed Oct 18 18:19:48 CEST 2017

Hi Anusha

On Wed, Oct 18, 2017 at 12:04 PM, Anusha Nagari
<Anusha.Nagari at utsouthwestern.edu> wrote:
> Depends: includes the non-default packages:
>   ‘MASS’ ‘parallel’ ‘S4Vectors’ ‘IRanges’ ‘GenomeInfoDb’
>   ‘GenomicRanges’ ‘GenomicAlignments’ ‘rtracklayer’
> Adding so many packages to the search path is excessive and importing
> selectively is preferable.

Move those to the "Imports" section in your package DESCRIPTION file.

> * checking re-building of vignette outputs ... NOTE
> Warnings in re-building vignettes:
>   Warning: file stem ‘/fig2’ is not portable
>   Warning: file stem ‘/fig3’ is not portable

Hmm... I think we'll have to look at the exact vignette to see what's
going on.  Presumably that's a LaTeX vignette.  Can you advise the
package name you are working on and/or link to the the source code?

> Anusha


Pariksheet Nanda
PhD Candidate in Genetics and Genomics
System Administrator, Storrs HPC Cluster
University of Connecticut

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