Hi All,
I am facing a strange problem. I am making a R Package that internally run
various packages and summarizes the results from them.
I am getting this error from the piece of code written below. The text in
red color is throwing
Error in `[.matrix.coo`(x, rw, cl) : Subscripts out of bound
Value of m is 99
This code works fine when I tested it. But money I make library it gives me
error.
I have attached the file names messages.txt which contains the
warnings/messages generated while making R package.
I am out of ideas
Kindly suggest something
regards
vidhu
############################################################################
`sm.quantreg` <-
function(y, lambda = 1.0, tau = 0.5, interpolate = FALSE) {
nona <- !is.na(y)
## Sparse matrices: E, D, and B
if(!interpolate) {
y.nona <- y[nona]
m <- length(y.nona) *1.0
E <- as.matrix.csr(0,m,m)
diag(E) <- 1
* D <- diff(E)*
B <- rbind(E, lambda * D)
ystar <- c(y.nona, rep(0,m-1))
}else {
## interpolate missing values via weighting
y[!nona] <- 0
m <- length(y) *1.0
E <- as.matrix.csr(0,m,m)
diag(E) <- 1
D <- diff(E)
tmp <- as.matrix.csr(0,m,m)
diag(tmp) <- as.numeric(nona)
B <- rbind(tmp, lambda * D)
ystar <- c(y, rep(0,m-1))
}
## use sparse matrices and accompanying mathematical operations
cat ("before try\n")
try(myrq <- rq.fit.sfn(as.matrix.csr(B), ystar, tau))
cat ("after try\n")
if(exists("myrq")) {
if(!interpolate) {
ys <- rep(NA, length(y))
ys[nona] <- myrq$coef
}else {
ys <- myrq$coef
}
}else {
cat("Error triggered within Quantreg algorithm!\n")
ys <- NULL
}
return(ys)
}
##########################
C:\Documents and Settings\Administrator\My Documents>R CMD INSTALL t1
installing to 'c:/R/R-2.6.2/library'
---------- Making package t1 ------------
adding build stamp to DESCRIPTION
installing NAMESPACE file and metadata
making DLL ...
gcc-sjlj -std=gnu99 -IC:/R/R-2.6.2/include -O3 -Wall -c CGHseg_rewrite.c
-o CGHseg_rewrite.o
gcc-sjlj -std=gnu99 -IC:/R/R-2.6.2/include -O3 -Wall -c rowMedians.c -o r
owMedians.o
gcc-sjlj -std=gnu99 -IC:/R/R-2.6.2/include -O3 -Wall -c runavg.c -o runav
g.o
windres --preprocessor="gcc-sjlj -E -xc -DRC_INVOKED" -I C:/R/R-2.6.2/include -
i t1_res.rc -o t1_res.o
gcc-sjlj -std=gnu99 -shared -s -o t1.dll t1.def CGHseg_rewrite.o rowMedians.o
runavg.o t1_res.o -LC:/R/R-2.6.2/bin -lR
... DLL made
installing DLL
installing R files
installing data files
installing man source files
installing indices
not zipping data
installing help
>>> Building/Updating help pages for package 't1'
Formats: text html latex example chm
checkUploadFileFormat text html latex example
runAnalysis text html latex example
runCGHAnalysis text html latex example
preparing package t1 for lazy loading
Loading required package: waveslim
Loading required package: quantreg
Loading required package: SparseM
Loading required package: snapCGH
Loading required package: limma
Loading required package: tilingArray
Loading required package: Biobase
Loading required package: tools
Welcome to Bioconductor
Vignettes contain introductory material. To view, type
'openVignette()'. To cite Bioconductor, see
'citation("Biobase")' and for packages 'citation(pkgname)'.
Loading required package: affy
Loading required package: affyio
Loading required package: preprocessCore
Attaching package: 'affy'
The following object(s) are masked from package:waveslim :
pm
Loading required package: RColorBrewer
Loading required package: grid
Loading required package: strucchange
Loading required package: zoo
Loading required package: sandwich
Loading required package: vsn
Loading required package: genefilter
Loading required package: survival
Loading required package: splines
Attaching package: 'survival'
The following object(s) are masked from package:quantreg :
untangle.specials
Loading required package: geneplotter
Loading required package: annotate
Loading required package: AnnotationDbi
Loading required package: DBI
Loading required package: RSQLite
Loading required package: xtable
Loading required package: lattice
KernSmooth 2.22 installed
Copyright M. P. Wand 1997
Loading required package: pixmap
Loading required package: DNAcopy
Attaching package: 'DNAcopy'
The following object(s) are masked from package:tilingArray :
segment
Loading required package: GLAD
Loading required package: aws
Loading required package: tcltk
Loading Tcl/Tk interface ... done
Loading required package: cluster
Loading required package: aCGH
Loading required package: multtest
Loading required package: sma
Attaching package: 'aCGH'
The following object(s) are masked from package:stats :
heatmap
Attaching package: 'snapCGH'
The following object(s) are masked from package:aCGH :
prop.na
Loading required package: cghFLasso
Loading required package: FASeg
Loading required package: GDD
Warning: 'Sys.putenv' is deprecated.
Use 'Sys.setenv' instead.
See help("Deprecated")
Loading required package: gplots
Loading required package: gtools
Loading required package: gdata
Attaching package: 'gdata'
The following object(s) are masked from package:Biobase :
combine
Attaching package: 'gplots'
The following object(s) are masked from package:multtest :
wapply
The following object(s) are masked from package:stats :
lowess
adding MD5 sums
* DONE (t1)
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