[Bioc-devel] Assignments in \usage sections are now causing a WARNING

[Hervé Pagès]

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.

-- 
Hervé Pagès

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