[R] Error in Rd[[which]] : subscript out of bounds

[Martin Morgan]

On 02/08/2012 12:13 PM, Ben Ganzfried wrote:
> Hi Uwe,
>
> Thanks for the help.  R version 2.14.0 (2011-10-31).  The file in question
> looks like this (w/ a few minor edits for privacy):

There are two 'description' entries; the second might be combined with 
the existing 'details'. Martin

>
> \name{curatedData-package}
> \alias{curatedData-package}
> \alias{curatedData}
> \docType{package}
> \title{Cancer Gene Expression Analysis}
> \description{The curatedData package provides relevant functions and data
> for gene expression analysis in cancer patients.}
> \details{
> \tabular{ll}{
> Package: \tab curatedData\cr
> Type: \tab Package\cr
> Version: \tab 1.0\cr
> Date: \tab 2012-2-03\cr
> License: \tab Artistic-2.0\cr
> Depends: \tab R (>= 2.10.0), affy\cr
> }
> }
> \author{
> Benjamin F. Ganzfried, et al.
>
> Department of Biostatistics and Computational Biology, Dana-Farber Cancer
> Institute, Harvard School of Public Health
>
> Maintainer: ben.ganzfried at gmail.com
> }
> \description{
> Please refer to the following key.
>
> For "summarygrade": low = 1, 2, LMP.  High= 3,4,23.
>
> For "summarystage": early = 1,2, 12. late=3,4,23,34.
>
> For "T": Stage (1-4).  If multiple stages given (eg 34), use the highest.
>
> For "substage": substage (abcd).  For cases like ab, bc, use highest given.
>
> For "G": Grade (1-4): If multiple given, ie 12, 23, use highest given.
>
> For "N": N (0/1): degree of spread to regional lymph nodes.
>
> For "M": M (0/1): presence of metastasis.
>
> For "pltx": patient treated with platin.
>
> For "tax": patient treated with taxol.
>
> For "neo": patient treated with neoadjuvant treatment.
>
> For "primary_therapy_outcome_success": response to any kind of therapy
> (including radiation only).
>
> For "chemo_response": platinum resistance: refractory=3mo or less,
> resistant=6mo or less, sensitive=12mo or higher.
>
> For "inferred_chemo_response": inferred platinum resistance:
> refractory=death in 6mo or less, sensitive=survival for 12mo or more.
>
> For "debulking": amount of residual disease (optimal =<1mm,
> suboptimal=>1mm).
> }
>
>
>
>
> 2012/2/8 Uwe Ligges<ligges at statistik.tu-dortmund.de>
>
>>
>>
>> On 08.02.2012 18:44, Ben Ganzfried wrote:
>>
>>> Hi--
>>>
>>> I googled the above error and found previous postings about this error on
>>> the list.  I was having a little difficulty implementing the advice
>>> though.
>>>   The suggestions were to use: traceback() and checkRd().  I'm using R in
>>> the directory in which the .Rd file with the problem is located, but I'm
>>> having difficulty figuring out how to proceed.  I've looked through the
>>> help pages for traceback() and checkRd(), and would greatly appreciate any
>>> advice for how to find the errors and fix them.
>>>
>>> The specific error I am getting when trying to check my package is:
>>>
>>> * checking Rd files ... WARNING
>>> Error in Rd[[which]] : subscript out of bounds
>>>
>>
>> Which R version (assuming R-2.14.1 or R-devel)? Can you make the file
>> available?
>>
>> Uwe Ligges
>>
>>
>>
>>> problem found in ‘curatedData-package.Rd’
>>>
>>> Thanks in advance!
>>>
>>> Ben
>>>
>>>         [[alternative HTML version deleted]]
>>>
>>>
>>>
>>>
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>>> PLEASE do read the posting guide http://www.R-project.org/**
>>> posting-guide.html<http://www.R-project.org/posting-guide.html>
>>> and provide commented, minimal, self-contained, reproducible code.
>>>
>>
>
> 	[[alternative HTML version deleted]]
>
>
>
>
> ______________________________________________
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> PLEASE do read the posting guide http://www.R-project.org/posting-guide.html
> and provide commented, minimal, self-contained, reproducible code.


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