Seth Falcon
2004-Sep-17 21:14 UTC
[R] Help w/ custom pkg: ERROR: installing package indices failed
I'm using R 1.9.1 on Linux and am having trouble installing a package that I've written. Would very much appreciate a hint as to where to look to find my mistake. I can build the package, but when I try to install it, I get an error like: Error in FUN(X[[as.integer(1)]], ...) : subscript out of bounds Execution halted ERROR: installing package indices failed After some trial and error, I find that there is one troublesome Rd file. If I remove it, I can build and install the package. But I can't figure out what's wrong with the Rd file! E.g., in ESS it previews just fine and appears to get built in the transcript below. Below is a transcript of building and installing... Building: $ ls capsim DESCRIPTION R man $ R CMD build capsim * checking for file 'capsim/DESCRIPTION' ... OK * preparing 'capsim': * removing junk files * building 'capsim_1.0.tar.gz' Installing: $ R CMD INSTALL capsim_1.0.tar.gz * Installing *source* package 'capsim' ... ** R ** help >>> Building/Updating help pages for package 'capsim' Formats: text html latex example collect text html latex collectRunData text html latex combineAges text html latex combineAges.single text html latex combineAges3 text html latex combineIncidenceData text html latex combineMortalityData text html latex getAgeAdjustmentCounts text html latex getAllStageIncidence text html latex getMortByStage text html latex getRunResults text html latex getSeerStageInflateMatrix text html latex inflateSeerData text html latex loadIncidenceData text html latex loadMortalityData text html latex loadRRSurvData text html latex loadSeerData text html latex Error in FUN(X[[as.integer(1)]], ...) : subscript out of bounds Execution halted ERROR: installing package indices failed ** Removing '/home/sfalcon/util/lib/R/capsim' Here's the troublesome Rd file: \name{combineAges3} \title{Age adjust data and combine SEER, SEERInflated and model data frames.} \description{ Use \code{getAgeAdjustmentCounts} to get standard population counts and combine age categories using appropriate weights. } \usage{ combineAges3(seer, seerInflated, model, col.names) } \arguments{ \item{seer}{A data frame containing SEER data. Must contain columns ``year'' and ``age''.} \item{seerInflated}{A data frame containing inflated SEER data. Must contain columns ``year'' and ``age''.} \item{model}{A data frame containing model data. Must contain columns ``year'' and ``age''. } \item{col.names}{ Column name of the column in both data frames that should be adjusted. For example, ``incidence'' or ``mortality''. } } \details{ Hmm, not yet. } \value{ A data frame with columns: year, age, and source, \code{col.names}. The source column is a factor with levels ``model'', ``seer'', and ``seerInflated'' indicating the source of the data. } \references{No ref} \author{Seth Falcon} \note{No Notes} \keyword{manip}
Seth Falcon
2004-Sep-17 22:14 UTC
[R] Help w/ custom pkg: ERROR: installing package indices failed
Turns out adding an \alias{} line to the problem Rd file fixed the issue. I'm somewhat surprised that a missing \alias line leads to error in FUN(X[[as.interger(1)]], ...) message. Perhaps there was something else going on (my Rd file is admittedly a bit sloppy)... + seth