[Bioc-devel] Incorrect Rd files

Herve Pages hpages at fhcrc.org
Mon Feb 6 20:08:37 CET 2006

Hi all,

Due to a recent change in R-devel, "R CMD check" now validates
the Rd files. The consequence is that some Bioconductor packages that
used to pass the "R CMD check" test with no problems now get some
warnings because some Rd files with unknown sections are detected.

Packages affected by the "Rd files with unknown sections" warning
are the following:
  - aCGH
  - affxparser
  - affy
  - affypdnn
  - bim
  - bioDist
  - biomaRt
  - DynDoc
  - genArise
  - GraphAT
  - hopach
  - ideogram
  - impute
  - limma
  - makecdfenv
  - MantelCorr
  - MergeMaid
  - Mfuzz
  - multtest
  - OLIN
  - pairseqsim
  - RankProd
  - simpleaffy
  - simulatorAPMS
  - snapCGH
  - stam

All the above packages contain one or more incorrect sections in their
Rd files resulting in incorrect ouput (or at least, not the intended 
The most frequent errors are:
  a) An empty \alias section.
  b) \notes instead of \note.
  c) The markup command \code being used as a section command.
  d) A \warnings (or \warning, or \Warning) section. There is no such 
     command. Use \section(Warning}{...}
  e) \detail (or \Details) instead of \details.
  f) \ref (or \reference) instead of |\references.|
|  g) \doctype (or ||\docTye) ||instead of ||\docType.|
|  h) \syntax (or \syntaxis) instead of \usage.|
|  i) The markup command \email being used as a section command.|
|  j) \example instead of ||\examples.|
|  k) The use of \creatingobjects, \slots, \methods or \nodes as section
     commands.|| There is no such section commands.|||
|  l) The markup command \url being used as a section command.|

Please, see "Writing R documentation files" (section 2 of the "Writing R 
manual) for more information.



Hervé Pagès
E-mail: hpages at fhcrc.org
Phone: (206) 667-5791
Fax: (206) 667-1319

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