Hi again,
With the latest R 2.13, there is this new 'R CMD check' warning that is
very easy to fix and affects a few BioC packages:
* checking Rd \usage sections ... WARNING
Assignments in \usage in documentation object 'ilm':
result <- ilm(celfiles, threshold = 350, satLim = 10000)
Functions with \usage entries need to have the appropriate \alias
entries, and all their arguments documented.
The \usage entries must correspond to syntactically valid R code.
See the chapter 'Writing R documentation files' in manual 'Writing R
Extensions'.
All you need to do to get rid of this warning is to *not* use
assignments in the \usage sections of your man pages. For example, the
warning above will go away by just putting
ilm(celfiles, threshold = 350, satLim = 10000)
in the \usage section.
The packages affected by this warning are:
affyILM
CGEN
flowCore
gaggle
GeneSpring
GeneTraffic
PGSEA
PICS
rGADEM
rMAT
SAGx
tigre
tkWidgets
Please let us know if you have any question, thanks!
H.
Herv? Pag?s Program in Computational Biology Division of Public Health Sciences Fred Hutchinson Cancer Research Center 1100 Fairview Ave. N, M2-B876 P.O. Box 19024 Seattle, WA 98109-1024 E-mail: hpages at fhcrc.org Phone: (206) 667-5791 Fax: (206) 667-1319