[Bioc-devel] Nasty function collision

James MacDonald jmacdon at med.umich.edu
Tue Oct 31 17:32:49 CET 2006

I am having a nasty function collision in my affycoretools package that
is causing things to error out. I have tracked the problem down to the
getURL() functions that are defined in RCurl and annaffy. If I load
RCurl first and then annaffy, getURL() is silently masked, probably
because it is an S4 function in annaffy and a regular function in RCurl.

If I do the opposite, R is nice enough to mention that I have just
masked a function from annaffy. 

In the past I got around this problem by importing annaffy rather than
listing it in the Depends line in the DESCRIPTION file, and load()ing it
when needed. This worked out OK because one is likely to be using either
annaffy to create output, or biomaRt, but not usually both, so the
masking problem was a moot point. Having annaffy in Imports ensured that
things like biocLite() would automatically install it as a dependency.

Unfortunately now R CMD check complains about "'library' or 'require'
calls not declared from: annaffy" and points me to Creating R Packages
and the DESCRIPTION file entry, which doesn't really enlighten.

Any suggestions?



James W. MacDonald, M.S.
Affymetrix and cDNA Microarray Core
University of Michigan Cancer Center
1500 E. Medical Center Drive
7410 CCGC
Ann Arbor MI 48109

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