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Package 37/462HostnameOS / ArchBUILDCHECKBUILD BIN
aroma.light 1.21.0
Henrik Bengtsson
Snapshot Date: 2011-05-09 07:20:56 -0700 (Mon, 09 May 2011)
URL: https://hedgehog.fhcrc.org/bioconductor/trunk/madman/Rpacks/aroma.light
Last Changed Rev: 54869 / Revision: 55359
Last Changed Date: 2011-04-14 18:05:47 -0700 (Thu, 14 Apr 2011)
wilson2 Linux (openSUSE 11.4) / x86_64  OK  ERROR 
liverpool Windows Server 2003 R2 (32-bit) / x64  OK  ERROR  OK 
gewurz Windows Server 2008 R2 Enterprise (64-bit) / x64  OK [ ERROR ] OK 
pelham Mac OS X Leopard (10.5.8) / i386  OK  ERROR  OK 

Summary

Package: aroma.light
Version: 1.21.0
Command: D:\biocbld\bbs-2.9-bioc\R\bin\R.exe CMD check --no-vignettes --timings aroma.light_1.21.0.tar.gz
StartedAt: 2011-05-09 14:46:04 -0700 (Mon, 09 May 2011)
EndedAt: 2011-05-09 14:47:13 -0700 (Mon, 09 May 2011)
EllapsedTime: 68.9 seconds
RetCode: 1
Status:  ERROR  
CheckDir: aroma.light.Rcheck
Warnings: NA

Command output

* using log directory 'D:/biocbld/bbs-2.9-bioc/meat/aroma.light.Rcheck'
* using R version 2.14.0 Under development (unstable) (2011-04-17 r55484)
* using platform: x86_64-pc-mingw32 (64-bit)
* using session charset: ISO8859-1
* using option '--no-vignettes'
* checking for file 'aroma.light/DESCRIPTION' ... OK
* this is package 'aroma.light' version '1.21.0'
* package encoding: latin1
* checking package name space information ... OK
* checking package dependencies ... OK
* checking if this is a source package ... OK
* checking whether package 'aroma.light' can be installed ... OK
* checking installed package size ... OK
* checking package directory ... OK
* checking for portable file names ... OK
* checking DESCRIPTION meta-information ... OK
* checking top-level files ... OK
* checking index information ... OK
* checking package subdirectories ... OK
* checking R files for non-ASCII characters ... OK
* checking R files for syntax errors ... OK
* checking whether the package can be loaded ... OK
* checking whether the package can be loaded with stated dependencies ... OK
* checking whether the package can be unloaded cleanly ... OK
* checking whether the name space can be loaded with stated dependencies ... OK
* checking whether the name space can be unloaded cleanly ... OK
* checking for unstated dependencies in R code ... OK
* checking S3 generic/method consistency ... OK
* checking replacement functions ... OK
* checking foreign function calls ... OK
* checking R code for possible problems ... OK
* checking Rd files ... OK
* checking Rd metadata ... OK
* checking Rd cross-references ... OK
* checking for missing documentation entries ... OK
* checking for code/documentation mismatches ... OK
* checking Rd \usage sections ... OK
* checking Rd contents ... OK
* checking for unstated dependencies in examples ... NOTE
'library' or 'require' call not declared from: 'R.basic'
* checking examples ... ERROR
Running examples in 'aroma.light-Ex.R' failed
The error most likely occurred in:

> assign(".ptime", proc.time(), pos = "CheckExEnv")
> ### Name: normalizeAffine.matrix
> ### Title: Weighted affine normalization between channels and arrays
> ### Aliases: normalizeAffine.matrix normalizeAffine.matrix
> ### Keywords: methods
> 
> ### ** Examples
> 
> pathname <- system.file("data-ex", "PMT-RGData.dat", package="aroma.light")
> rg <- read.table(pathname, header=TRUE, sep="\t")
> nbrOfScans <- max(rg$slide)
> 
> rg <- as.list(rg)
> for (field in c("R", "G"))
+   rg[[field]] <- matrix(as.double(rg[[field]]), ncol=nbrOfScans)
> rg$slide <- rg$spot <- NULL
> rg <- as.matrix(as.data.frame(rg))
> colnames(rg) <- rep(c("R", "G"), each=nbrOfScans)
> 
> layout(matrix(c(1,2,0,3,4,0,5,6,7), ncol=3, byrow=TRUE))
> 
> rgC <- rg
> for (channel in c("R", "G")) {
+   sidx <- which(colnames(rg) == channel)
+   channelColor <- switch(channel, R="red", G="green");
+ 
+   # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -
+   # The raw data
+   # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -
+   plotMvsAPairs(rg[,sidx])
+   title(main=paste("Observed", channel))
+   box(col=channelColor)
+  
+   # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -
+   # The calibrated data
+   # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -
+   rgC[,sidx] <- calibrateMultiscan(rg[,sidx], average=NULL)
+ 
+   plotMvsAPairs(rgC[,sidx])
+   title(main=paste("Calibrated", channel))
+   box(col=channelColor)
+ } # for (channel ...)
> 
> 
> # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -
> # The average calibrated data
> #
> # Note how the red signals are weaker than the green. The reason
> # for this can be that the scale factor in the green channel is
> # greater than in the red channel, but it can also be that there
> # is a remaining relative difference in bias between the green
> # and the red channel, a bias that precedes the scanning.
> # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -
> rgCA <- rg
> for (channel in c("R", "G")) {
+   sidx <- which(colnames(rg) == channel)
+   rgCA[,sidx] <- calibrateMultiscan(rg[,sidx])
+ }
> 
> rgCAavg <- matrix(NA, nrow=nrow(rgCA), ncol=2)
> colnames(rgCAavg) <- c("R", "G");
> for (channel in c("R", "G")) {
+   sidx <- which(colnames(rg) == channel)
+   rgCAavg[,channel] <- apply(rgCA[,sidx], MARGIN=1, FUN=median, na.rm=TRUE);
+ }
> 
> # Add some "fake" outliers
> outliers <- 1:600
> rgCAavg[outliers,"G"] <- 50000;
> 
> plotMvsA(rgCAavg)
> title(main="Average calibrated (AC)")
> 
> # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -
> # Normalize data
> # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -
> # Weight-down outliers when normalizing
> weights <- rep(1, nrow(rgCAavg));
> weights[outliers] <- 0.001;
> 
> # Affine normalization of channels
> rgCANa <- normalizeAffine(rgCAavg, weights=weights)
> # It is always ok to rescale the affine normalized data if its
> # done on (R,G); not on (A,M)! However, this is only needed for
> # esthetic purposes.
> rgCANa <- rgCANa *2^1.4
> plotMvsA(rgCANa)
> title(main="Normalized AC")
> 
> # Curve-fit (lowess) normalization
> rgCANlw <- normalizeLowess(rgCAavg, weights=weights)
Warning in normalizeCurveFit.matrix(X, method = "lowess", ...) :
  Weights were rounded to {0,1} since 'lowess' normalization supports only zero-one weights.
> plotMvsA(rgCANlw, col="orange", add=TRUE)
> 
> # Curve-fit (loess) normalization
> rgCANl <- normalizeLoess(rgCAavg, weights=weights)
> plotMvsA(rgCANl, col="red", add=TRUE)
> 
> # Curve-fit (robust spline) normalization
> rgCANrs <- normalizeRobustSpline(rgCAavg, weights=weights)
Error: with(spline.prep, { .... is not TRUE
Execution halted

aroma.light.Rcheck/00install.out:

* installing *source* package 'aroma.light' ...
** R
** inst
** preparing package for lazy loading
R.methodsS3 v1.2.1 (2010-09-18) successfully loaded. See ?R.methodsS3 for help.
** help
*** installing help indices
** building package indices ...
** testing if installed package can be loaded

* DONE (aroma.light)

aroma.light.Rcheck/aroma.light-Ex.timings:

nameusersystemelapsed
backtransformAffine.matrix000
backtransformPrincipalCurve.matrix0.770.001.46
calibrateMultiscan.matrix000
callNaiveGenotypes.numeric0.750.010.88
distanceBetweenLines0.040.000.03
findPeaksAndValleys.density0.060.000.06
fitPrincipalCurve.matrix0.500.000.56
fitXYCurve.matrix0.080.000.08
iwpca.matrix0.030.000.03
likelihood.smooth.spline0.220.000.28
medianPolish.matrix0.020.000.02