[Bioc-devel] Help with R CMD check NOTEs

Pariksheet Nanda pariksheet.nanda at uconn.edu
Wed Oct 18 23:02:46 CEST 2017

Hi Anusha,

On Wed, Oct 18, 2017 at 2:30 PM, Anusha Nagari <
Anusha.Nagari at utsouthwestern.edu> wrote:
> Can you please let me know how to go about the following NOTE. Or if this
is something that should be really taken care of for a successful package
build and install:
> * 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
> @Pariksheet: I am working on the groHMM package.

My best guess is you might want to revise your figure label names without
the number.  LaTeX commands like macro names consider numbers to be an
invalid character class.  So you could try replacing instances of fig2 and
fig3 in the vignette with something like figTwo and figThree.

I couldn't reproduce the build NOTE to confirm the fault / fix.  The
bioconductor.org 1.10.0 tarball doesn't see to produce the error, BiocCheck
fails, and I had trouble building the vignette from the GitHub master

Hope that helps.

> Anusha


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