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.ganzfr...@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<lig...@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
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and provide commented, minimal, self-contained, reproducible code.
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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.
