Errors checking a library

"michael watson (IAH-C)" <michael.watson at bbsrc.ac.uk> writes:

I am writing an R library.  

A whole library? Shouldn't you try a package first?

The documentation for one of my functions
includes an example that I *know* works - simply cut and paste into R on
either Windows and Linux and it works perfectly, no errors or warnings,
nothing, nyet.

However, when I run "R CMD check" on the library, I get an error.  I am
running R CMD check on linux, and the offending piece of code appears to
be:

cox[cox$group %in% onc,]

"cox" is a data frame, one of the columns of which is group, which
contains numbers.  "onc" is a vector of numbers.

The output on Linux from R CMD check is this:

# lots of code
# lots of code
cox[cox$group

+
+
+ # the rest of my code
Error: syntax error
Execution halted

As can be seen, my code "cox[cox$group %in% onc,]" seems to have been
executed incorrectly.  Does R CMD check have a problem with the "%in%"
operator?  It would seem that R has somehow got mixed up and has lost
the rest of my command.

Think: What is the comment character in .Rd files?

Checking out src/library/base/man/match.Rd should be enlightening, but
since you might not have R sources installed, here are the relevant
bits:

\name{match}
\alias{match}
\alias{\%in\%}
\title{Value Matching}
\description{
  \code{match} returns a vector of the positions of (first) matches of
  its first argument in its second.

  \code{\%in\%} is a more intuitive interface as a binary operator,
  which returns a logical vector indicating if there is a match or not
  for its left operand.
}
\usage{
match(x, table, nomatch = NA, incomparables = FALSE)

x \%in\% table
}
....
\examples{
## The intersection of two sets :
intersect <- function(x, y) y[match(x, y, nomatch = 0)]
intersect(1:10,7:20)

1:10 \%in\% c(1,3,5,9)
sstr <- c("c","ab","B","bba","c","@","bla","a","Ba","\%")
sstr[sstr \%in\% c(letters,LETTERS)]

"\%w/o\%" <- function(x,y) x[!x \%in\% y] #--  x without y
(1:10) \%w/o\% c(3,7,12)
}
\keyword{manip}

O__  ---- Peter Dalgaard             Blegdamsvej 3  
  c/ /'_ --- Dept. of Biostatistics     2200 Cph. N   
 (*) \(*) -- University of Copenhagen   Denmark      Ph: (+45) 35327918
~~~~~~~~~~ - (p.dalgaard at biostat.ku.dk)             FAX: (+45) 35327907