BioC 3.5: CHECK report for aroma.light on oaxaca

Package: aroma.light

Version: 3.5.0

Command: /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD check --no-vignettes --timings aroma.light_3.5.0.tar.gz

StartedAt: 2017-03-03 23:08:47 -0800 (Fri, 03 Mar 2017)

EndedAt: 2017-03-03 23:10:25 -0800 (Fri, 03 Mar 2017)

EllapsedTime: 98.0 seconds

RetCode: 1

Status:  ERROR

CheckDir: aroma.light.Rcheck

Warnings: NA

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### Running command:
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###   /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD check --no-vignettes --timings aroma.light_3.5.0.tar.gz
###
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* using log directory ‘/Users/biocbuild/bbs-3.5-bioc/meat/aroma.light.Rcheck’
* using R Under development (unstable) (2017-02-15 r72177)
* using platform: x86_64-apple-darwin13.4.0 (64-bit)
* using session charset: UTF-8
* using option ‘--no-vignettes’
* checking for file ‘aroma.light/DESCRIPTION’ ... OK
* this is package ‘aroma.light’ version ‘3.5.0’
* package encoding: latin1
* checking package namespace information ... OK
* checking package dependencies ... OK
* checking if this is a source package ... OK
* checking if there is a namespace ... OK
* checking for hidden files and directories ... NOTE
Found the following hidden files and directories:
  inst/rsp/.rspPlugins
These were most likely included in error. See section ‘Package
structure’ in the ‘Writing R Extensions’ manual.
* checking for portable file names ... OK
* checking for sufficient/correct file permissions ... OK
* checking whether package ‘aroma.light’ can be installed ... OK
* checking installed package size ... OK
* checking package directory ... OK
* checking DESCRIPTION meta-information ... OK
* checking top-level files ... OK
* checking for left-over 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 namespace can be loaded with stated dependencies ... OK
* checking whether the namespace can be unloaded cleanly ... OK
* checking 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 ... OK
* checking examples ... ERROR
Running examples in ‘aroma.light-Ex.R’ failed
The error most likely occurred in:

> base::assign(".ptime", proc.time(), pos = "CheckExEnv")
> ### Name: robustSmoothSpline
> ### Title: Robust fit of a Smoothing Spline
> ### Aliases: robustSmoothSpline.default robustSmoothSpline
> ### Keywords: smooth robust
> 
> ### ** Examples
> 
> data(cars)
> attach(cars)
> plot(speed, dist, main = "data(cars)  &  robust smoothing splines")
> 
> # Fit a smoothing spline using L_2 norm
> cars.spl <- smooth.spline(speed, dist)
> lines(cars.spl, col = "blue")
> 
> # Fit a smoothing spline using L_1 norm
> cars.rspl <- robustSmoothSpline(speed, dist)
Error in unname(fit$parms["low"]) : 
  invalid type/length (environment/1) in vector allocation
Calls: robustSmoothSpline ... robustSmoothSpline.default -> smooth.spline0 -> unname
Execution halted
* checking for unstated dependencies in ‘tests’ ... OK
* checking tests ...
  Running ‘backtransformAffine.matrix.R’
  Running ‘backtransformPrincipalCurve.matrix.R’
  Running ‘callNaiveGenotypes.R’
  Running ‘distanceBetweenLines.R’
  Running ‘findPeaksAndValleys.R’
  Running ‘fitPrincipalCurve.matrix.R’
  Running ‘fitXYCurve.matrix.R’
  Running ‘iwpca.matrix.R’
  Running ‘likelihood.smooth.spline.R’
  Running ‘medianPolish.matrix.R’
  Running ‘normalizeAffine.matrix.R’
  Running ‘normalizeAverage.list.R’
  Running ‘normalizeAverage.matrix.R’
  Running ‘normalizeCurveFit.matrix.R’
  Running ‘normalizeDifferencesToAverage.R’
  Running ‘normalizeFragmentLength-ex1.R’
  Running ‘normalizeFragmentLength-ex2.R’
  Running ‘normalizeQuantileRank.list.R’
  Running ‘normalizeQuantileRank.matrix.R’
  Running ‘normalizeQuantileSpline.matrix.R’
 ERROR
Running the tests in ‘tests/normalizeQuantileSpline.matrix.R’ failed.
Last 13 lines of output:
  > layout(matrix(c(1,0,2:5), ncol=2, byrow=TRUE))
  > xlim <- range(X, na.rm=TRUE);
  > plotDensity(X, lwd=2, xlim=xlim, main="The three original distributions")
  > 
  > Xn <- normalizeQuantile(X)
  > plotDensity(Xn, lwd=2, xlim=xlim, main="The three normalized distributions")
  > plotXYCurve(X, Xn, xlim=xlim, main="The three normalized distributions")
  > 
  > Xn2 <- normalizeQuantileSpline(X, xTarget=Xn[,1], spar=0.99)
  Error in unname(fit$parms["low"]) : 
    invalid type/length (unknown type #31/1) in vector allocation
  Calls: normalizeQuantileSpline ... robustSmoothSpline.default -> smooth.spline0 -> unname
  In addition: Warning message:
  In unname(fit$parms["low"]) : type 31 is unimplemented in 'type2char'
  Execution halted
* checking PDF version of manual ... OK
* DONE

Status: 2 ERRORs, 1 NOTE
See
  ‘/Users/biocbuild/bbs-3.5-bioc/meat/aroma.light.Rcheck/00check.log’
for details.

R Under development (unstable) (2017-02-15 r72177) -- "Unsuffered Consequences"
Copyright (C) 2017 The R Foundation for Statistical Computing
Platform: x86_64-apple-darwin13.4.0 (64-bit)

R is free software and comes with ABSOLUTELY NO WARRANTY.
You are welcome to redistribute it under certain conditions.
Type 'license()' or 'licence()' for distribution details.

R is a collaborative project with many contributors.
Type 'contributors()' for more information and
'citation()' on how to cite R or R packages in publications.

Type 'demo()' for some demos, 'help()' for on-line help, or
'help.start()' for an HTML browser interface to help.
Type 'q()' to quit R.

> library("aroma.light")
aroma.light v3.5.0 (2016-09-16) successfully loaded. See ?aroma.light for help.
> 
> # Simulate three samples with on average 20% missing values
> N <- 10000
> X <- cbind(rnorm(N, mean=3, sd=1),
+            rnorm(N, mean=4, sd=2),
+            rgamma(N, shape=2, rate=1))
> X[sample(3*N, size=0.20*3*N)] <- NA_real_
> 
> # Plot the data
> layout(matrix(c(1,0,2:5), ncol=2, byrow=TRUE))
> xlim <- range(X, na.rm=TRUE);
> plotDensity(X, lwd=2, xlim=xlim, main="The three original distributions")
> 
> Xn <- normalizeQuantile(X)
> plotDensity(Xn, lwd=2, xlim=xlim, main="The three normalized distributions")
> plotXYCurve(X, Xn, xlim=xlim, main="The three normalized distributions")
> 
> Xn2 <- normalizeQuantileSpline(X, xTarget=Xn[,1], spar=0.99)
Error in unname(fit$parms["low"]) : 
  invalid type/length (unknown type #31/1) in vector allocation
Calls: normalizeQuantileSpline ... robustSmoothSpline.default -> smooth.spline0 -> unname
In addition: Warning message:
In unname(fit$parms["low"]) : type 31 is unimplemented in 'type2char'
Execution halted

* installing *source* package ‘aroma.light’ ...
** R
** inst
** preparing package for lazy loading
** help
*** installing help indices
** building package indices
** testing if installed package can be loaded
* DONE (aroma.light)

name	user	system	elapsed
backtransformAffine	0.044	0.001	0.045
backtransformPrincipalCurve	0.647	0.019	0.732
calibrateMultiscan	0.001	0.000	0.000
callNaiveGenotypes	1.018	0.018	1.036
distanceBetweenLines	0.159	0.002	0.162
findPeaksAndValleys	0.051	0.002	0.053
fitPrincipalCurve	0.930	0.012	0.945
fitXYCurve	0.056	0.003	0.060
iwpca	0.102	0.001	0.103
likelihood.smooth.spline	0.144	0.002	0.148
medianPolish	0.005	0.000	0.020
normalizeAffine	9.470	0.052	9.527
normalizeCurveFit	9.206	0.046	9.260
normalizeDifferencesToAverage	0.193	0.007	0.216
normalizeFragmentLength	0.816	0.019	0.843
normalizeQuantileRank	0.256	0.007	0.272
normalizeQuantileRank.matrix	0.050	0.002	0.051
normalizeQuantileSpline	0.826	0.013	0.840
normalizeTumorBoost	0.420	0.009	0.494