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

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

problem found in ?curatedData-package.Rd?

Thanks in advance!

Ben

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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):

\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]]

	[[alternative HTML version deleted]]

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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