Full_Name: Laurent
Version: R-2.0.0-beta-from-a-week-ago
OS: linux
Submission from: (NULL) (202.156.6.77)
When running 'R CMD check' for a package that contains the symbol '%'
in the signature of a function (say the default parameter for a string
argument is like "10% - 20%"), the 'codoc' part of the check throws a
warning about mismatching doc and codoc.
While the '%' has apparently to be escaped in the .Rnw (otherwise
latex soon figures out that what is after on the same line is a
comment), the warning remains whether or not '%' is escaped in the
code.
The package 'splicegear' in Bioconductor (in the section "devel") is
what brought me to submit a bug report.
If we run your splicegear from BioC devel (1.1.0) through R CMD check
from a current version of R (as you are actually supposed to when filing
a bug report), we get
* checking Rd \usage sections ... WARNING
Bad \usage lines found in documentation object 'buildSpliceSites':
queryPALSdb(query, disp = c("data", "browser"),
field = c("keyword", "ug_id", "gb_id", "cluster_count"),
species = c("human", "mouse"),
e.value = "1e-1",
ident.threshold = c("90
verbose = FALSE)
getPALSdbURL(query, disp = c("data", "browser"),
field = c("keyword", "ug_id", "gb_id", "cluster_count"),
species = c("human", "mouse"),
e.value = "1e-1",
ident.threshold = c("90
verbose = FALSE)
Bad \usage lines found in documentation object 'grid.expand.gp':
grid.numeric2npc(x, xlim=NULL, lower.blank=0, upper.blank=0
Bad \usage lines found in documentation object 'grid.plot.Probes':
grid.plot.SpliceExprSet(function (x, probes.opt = list(), expr.opt = list(col = NA, lty = 1:6),
fig.xratio = c(2, 1), fig.yratio = c(2, 1), probepos.yscale = NULL,
ylim = NULL, ...)
as the usage entries are syntactically invalid.
This is because (see R-exts) % in Rd files *ALWAYS* indicates an Rd
comment:
The "comment" character `%' and unpaired braces(1) _always_ need
to be escaped by `\' ...
in your case, your
splicegear/man/buildSpliceSites.Rd: ident.threshold = c("90% 50b", "95% 50b", "90% 45b"),
splicegear/man/buildSpliceSites.Rd: ident.threshold = c("90% 50b", "95% 50b", "90% 45b"),
should use
ident.threshold = c("90\% 50b", "95\% 50b", "90\% 45b"),
Hth
-k