* using log directory ‘/data/gannet/ripley/R/packages/tests-MKL/adaptDA.Rcheck’
* using R Under development (unstable) (2018-01-29 r74182)
* using platform: x86_64-pc-linux-gnu (64-bit)
* using session charset: UTF-8
* using option ‘--no-stop-on-test-error’
* checking for file ‘adaptDA/DESCRIPTION’ ... OK
* checking extension type ... Package
* this is package ‘adaptDA’ version ‘1.0’
* 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 executable files ... OK
* checking for hidden files and directories ... OK
* checking for portable file names ... OK
* checking for sufficient/correct file permissions ... OK
* checking whether package ‘adaptDA’ 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 loading without being on the library search path ... OK
* checking use of S3 registration ... 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 ... NOTE
.amdai.initparam: no visible global function definition for ‘cov’
.amdat.initiparam: no visible global function definition for ‘cov’
amdai: no visible global function definition for ‘cov’
Undefined global functions or variables:
  cov
Consider adding
  importFrom("stats", "cov")
to your NAMESPACE file.
* checking Rd files ... OK
* checking Rd metadata ... OK
* checking Rd line widths ... 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 ‘adaptDA-Ex.R’ failed
The error most likely occurred in:

> ### Name: adaptDA-package
> ### Title: Adaptive Mixture Discriminant Analysis
> ### Aliases: adaptDA-package adaptDA
> ### Keywords: package
> 
> ### ** Examples
> 
> set.seed(12345)
> 
> ## Data simulation
> data(iris)
> Z.data = iris[,-5]
> Z.cls = as.numeric(iris[,5])
> Z.cls[as.numeric(iris[,5]==2)] = 3
> Z.cls[as.numeric(iris[,5]==3)] = 2
> N = 150
> 
> ## Sampling
> ind = sample(1:N,N)
> X.data = Z.data[ind[1:(2*N/3)],]
> X.cls = Z.cls[ind[1:(2*N/3)]]
> X.data = X.data[X.cls!=3,]
> X.cls = X.cls[X.cls!=3]
> Y.data = Z.data[ind[(2*N/3+1):N],]
> Y.cls = Z.cls[ind[(2*N/3+1):N]]
> 
> # Plotting the data
> par(mfrow=c(2,3))#,cex.lab=0.75,cex.axis=0.75,cex.main=0.75,cex.sub=0.75)
> pc = princomp(Z.data)
> x = predict(pc,X.data)
> y = predict(pc,Y.data)
> plot(y,type='n',main='Learning data')
> points(x[,1:2],col=X.cls+1,pch=19,main='Learning data')
> y = predict(pc,Y.data)
> plot(y[,1:2],col=1,pch=19,main='Test data')
> plot(y[,1:2],col=Y.cls+1,pch=19,main='True labels of test data')
> 
> ## Usual classification with QDA
> c1 = qda(X.data,X.cls)
> res1 = predict(c1,Y.data)
> plot(y[,1:2],col=as.numeric(res1$class)+1,pch=19,main='QDA results')
> 
> ## Classification with AMDAi
> c2 = amdai(X.data,X.cls,model='qda')
> B = rep(c(-Inf),5)
> myPRMS <- vector(mode='list', length=7) # vector of lists!
> for (i in 2:5){
+   myPRMS[[i]] = predict(c2,Y.data,K=i)
+   B[i] = myPRMS[[i]]$crit$bic
+ }
Error in solve.default(V[i, , ]) : 
  system is computationally singular: reciprocal condition number = 2.26537e-18
Calls: predict ... .amdai.loglikelihood -> diag -> solve -> solve.default
Execution halted
* checking PDF version of manual ... OK
* DONE

Status: 1 ERROR, 1 NOTE
See
  ‘/data/gannet/ripley/R/packages/tests-MKL/adaptDA.Rcheck/00check.log’
for details.

Time 0:36.36, 21.54 + 3.52