Aha… I think I have taken care of this.
My team just realized that a class level documentation Rd file is required… I
have created this with calls to the methods section, itemized… and we seem to
be good to go.
Thanks!
~luis
On Oct 28, 2013, at 1:54 PM, Luis Rodriguez <luis.f.rodrigu...@gmail.com> wrote:
> Dear Duncan and R-devel,
>
> This advice has cleared my "checking Rd \usage sections" warning—but I am not
> sure I did a good job taking your advice as I cleared this by modifying the
> alias statements, but not invoking \S3method or \S4method.
>
> Thus, I am still a bit stumped on my "checking for missing documentation
> entries … WARNING"
>
> It still reads:
>
> ***
> 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
> ***
>
> My updated \alias and \usage sections are included below.
>
> Based on some archived discussion board material I have read, I am
> considering adding a section that might read something like this for methods
> mod and plot, but my logic seems off as the error does not seem to respond to
> this addition:
>
> \section{Methods}{
> \describe{
> \item{mod}{\code{signature(object = "commcorrelogram")}: Provides a
> shortcut method for \code{mod.commcorrelogram}.}
> }
> }
>
> Does that make sense?
>
> What would you suggest?
>
> I will also work on correcting my approach to invoking \S3 and \S4method.
>
> Thanks!
> ~luis
>
>
> ****comcorrelogram.Rd \alias and \usage sections****
>
> \name{commcorrelogram}
> \docType{class}
> \alias{commcorrelogram}
>
> \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')
> }
>
> ****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',...)
> }
>
> ****mod.comcorrelogram.Rd \alias and \usage sections****
>
>
> On Oct 14, 2013, at 4:21 PM, Duncan Murdoch <murdoch.dun...@gmail.com> wrote:
>
>> 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'
>>>>>
>>>>> ***
>>>>> ______________________________________________
>>>>> R-devel@r-project.org mailing list
>>>>> https://stat.ethz.ch/mailman/listinfo/r-devel
>>>>
>>>
>>
>
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