[Bioc-devel] function name clash between TFBSTools and graphics

Martin Morgan mtmorgan at fredhutch.org
Wed Feb 11 16:47:20 CET 2015

On 02/11/2015 05:52 AM, Elena Grassi wrote:
> Hello,
> I've just submitted a package and I'm trying to address the last
> issues thanks to the automated building system (if it's inappropriate
> to ask here before hearing from the reviewer please ignore this mail
> and excuse me!).
> I am still getting BUILD BIN warnings:
> http://bioconductor.org/spb_reports/MatrixRider_0.99.2_buildreport_20150211025737.html
>>From what I can see the problem is:
> "
> Warning: replacing previous import by 'graphics::plot' when loading 'seqLogo'

this is actually generated by the seqLogo package (it had imports(stats4); 
importFrom(graphics, "plot") in the NAMESPACE file, but stats4 has exported and 
hence seqLogo was importing an (S4) plot generic already). I have updated 
seqLogo to address this and other minor changes; I guess this will be reflected 
in a subsequent build of your package (but maybe not until the seqLogo changes 
propagate some time tomorrow; I'm not 100% sure of how the single package 
builder satisfies its dependencies.) Whatever the case, this was 'not your problem'.

Thanks for being a conscientious developer!


> "
> I'm doing:
> importFrom(TFBSTools, PFMatrix, PFMatrixList)
> in my NAMESPACE.
> I've also tried with importClassesFrom(TFBSTools, PFMatrix, PFMatrixList) with
> the same results (at least on my BUILD bin, I'm sorry to have
> submitted the package before solving this issue but I did not know
> that it would have issued a build WARNING).
> As long as seqLogo is a method available for PFMatrix I don't know how
> to solve the issue.
> graphics is brought in by...? I think that the original seqLogo method
> by the seqLogo package
> is imported by TFBSTools itself.
> (I'm also wondering why in the daily build system for TFBSTools the
> warning appears but it is
> not listed as WARNINGS: is it a difference in the reporting system or
> I am completely off the scent of the real issue here? :) )
> Thank you very much,
> E.

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