On 13-10-14 1:54 PM, Luis Rodríguez wrote:
Thanks Duncan (and othersin R-devel).
I clearly got away from this project, but I am still quite interested in
resolving this issue and getting these codes into the CRAN.
Some attempts to repair the documentation have occurred in the intervening
time, so I am including slightly updated error messages and the relevant tops
of the Rd files, as requested by Duncan. See below.
Thanks again!
~luis
<<<<my "missing documentation entries">>>>
* checking for missing documentation entries ... WARNING
Undocumented S4 classes:
‘commcorrelogram’
Undocumented S4 methods:
generic 'mod' and siglist 'commcorrelogram'
generic 'plot' and siglist 'commcorrelogram,missing'
All user-level objects in a package (including S4 classes and methods)
should have documentation entries.
See the chapter ‘Writing R documentation files’ in the ‘Writing R
Extensions’ manual.
<<<<my "missing documentation entries">>>>
I am also getting a * checking Rd \usage sections … WARNING, but your message
makes me think this is related to the above. JIC, here is that error message:
<<<<my "\usage section" Warning>>>>
* checking Rd \usage sections ... WARNING
Objects in \usage without \alias in documentation object 'commcorrelogram':
‘plot.commcorrelogram’
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 the ‘Writing R
<<<<my "\usage section" Warning>>>>
****comcorrelogram.Rd \alias and \usage sections****
\name{commcorrelogram}
\docType{class}
\alias{commcorrelogram}
\alias{mod,commcorrelogram}
\alias{plot,commcorrelogram,missing}
Those aliases look like S4 documentation, not S3 as the comment states.
\title{
Community Correlogram
}
\description{
Function \code{commcorrelogram} computes community correlograms using either
the multivariate Mantel statistic (Mantel, 1957) or the ANOSIM R metric
(Clarke, 1993), and includes functionality for both directional analyses and
combinations of temporal and spatial analyses. Mantel correlogram proposed by
Sokal (1986) and Oden and Sokal (1986). ANOSIM correlogram suggested here.
}
\usage{
commcorrelogram(sampleData, sampleTime = NULL, sampleLocation = NULL,
LocationNames = NULL, option = 1, metric = "anosim", lagNumber, lagSize,
lagTol, numTests = 999, anisotropic = FALSE, azimuth, azimuthTol,
bandwidth, dipAngle, dipTol, dipBandwidth, distmeth = "bray",
mantmeth = "spearman", adj = "holm", prog = TRUE, alternative =
"one.sided")
# S3 method for class 'community.correlogram'
plot.commcorrelogram(x, y, alpha=0.05, …)
}
You should use \S3method{plot}{commcorrelogram}(x, y, alpha = 0.05, ...)
(or maybe \S4method ...).
****comcorrelogram.Rd \alias and \usage sections****
****mod.comcorrelogram.Rd \alias and \usage sections****
\name{mod.commcorrelogram}
\alias{mod.commcorrelogram}
\alias{mod}
\title{
Community Correlogram Model
}
\description{
Function mod.commcorrelogram automatically fits a Gaussian curve to the
significance plot of a commcorrelogram object and calculates the correlation
range of the data.
}
\usage{
mod.commcorrelogram(object,Ch=1,Cc=5,Cw=0.01,plot=T,alpha=0.05
,alternative='one.tailed',pw=5,lgpos='topleft',...)
}
Again, use \S3method.
****mod.comcorrelogram.Rd \alias and \usage sections****
On Sep 9, 2013, at 2:49 PM, Duncan Murdoch <murdoch.dun...@gmail.com> wrote:
On 09/09/2013 3:23 PM, Luis Rodríguez wrote:
Dear R-devel,
I am a relative novice in R, but I am eager to post a new package my group
developed in CRAN, but I am stumped by a set of documentation related warnings
created by R CMD check.
So, my current plan is to recreate the documentation by religiously applying
and modifying the skeleton codes that can be generated by R. In the meantime, I
thought I'd post to the discussion group to see if maybe someone with more
experience had some useful advice. Below you'll see a snippet of the key
documentation warnings that we are stumped on.
lagSelect and mod are functions created by my group, as is commcorrelogram. My
belief is that they are clearly documented, but I suspect that our novice
source code and documentation is not quite hitting what R CMD check is looking
for.
This message usually indicates that you don't have the relevant \alias{}
defined correctly. If you do, please post the top of one or two of the Rd
files, and we can tell you what's missing. (I'd like to see at least the
\alias{} and \usage{} sections.)
Duncan Murdoch
If anyone has advice on how to pass R CMD check, it would be greatly
appreciated.
~luis
***
* checking for missing documentation entries ... WARNING
Undocumented code objects:
‘lagSelect’ ‘mod’
Undocumented S4 classes:
‘commcorrelogram’
Undocumented S4 methods:
generic 'mod' and siglist 'commcorrelogram'
generic 'plot' and siglist 'commcorrelogram,missing'
***
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