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

2 messages · Elena Grassi, Martin Morgan

Original
Elena Grassi
# 
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
"
Warning: replacing previous import by 'graphics::plot' when loading 'seqLogo'
"

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.
Martin Morgan
#
On 02/11/2015 05:52 AM, Elena Grassi wrote:
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!

Martin