[Bioc-devel] Odd behavior by R CMD check

[Hartley, Stephen (NIH/NHGRI) [F]]

I'm seeing some odd behavior by the R CMD check command for my package, JunctionSeq.

http://bioconductor.org/checkResults/3.3/bioc-LATEST/JunctionSeq/zin2-checksrc.html

It's not technically throwing warnings (just a "NOTE"), but it is claiming that there's no global definition for functions belonging to the default R packages (grDevices, utils, stats, and graphics).

So I get lines like this:
drawGene: no visible global function definition for 'plot.new'

drawGene: no visible global function definition for 'plot.window'

drawGene: no visible global function definition for 'par'

drawGene: no visible global function definition for 'strwidth'

drawGene: no visible global function definition for 'lines'

drawGene: no visible global function definition for 'rect'

drawGene: no visible global function definition for 'segments'

drawGene: no visible global function definition for 'strheight'

Since it's still able to compile the vignette and everything it's clearly not actually having a problem finding these functions at runtime, but I can't figure out what would cause it to throw these notes. I don't get these notes when I run R CMD check locally on any of my test machines (windows, CentOS5 linux and scientific linux 6). And I've had it build with no issues before. I can't see how my recent changes could possibly have caused this ...

Has anyone ever seen this before?

Regards,
Steve Hartley

	[[alternative HTML version deleted]]