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

[Uwe Ligges]

On 08.02.2012 22:10, Martin Morgan wrote:
> 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


Yes, and let me add: you may want to use \dQuote{} and friends rather 
than "real" quotes, use markup for the e-mail address etc.


Uwe Ligges


>>
>> \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]]
>>>>
>>>>
>>>>
>>>>
>>>> ______________________________**________________
>>>> R-help at r-project.org mailing list
>>>> https://stat.ethz.ch/mailman/**listinfo/r-help<https://stat.ethz.ch/mailman/listinfo/r-help>
>>>>
>>>> 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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>> https://stat.ethz.ch/mailman/listinfo/r-help
>> PLEASE do read the posting guide
>> http://www.R-project.org/posting-guide.html
>> and provide commented, minimal, self-contained, reproducible code.
>
>