• using R version 2.8.0 Under development (unstable) (2008-05-12 r45677)
• using session charset: UTF-8
• checking for file 'adegenet/DESCRIPTION' ... OK
• this is package 'adegenet' version '1.1-1'
• checking package dependencies ... OK
• checking if this is a source package ... OK
• checking for executable files ... OK
• checking whether package 'adegenet' can be installed ... OK
• checking package directory ... OK
• checking for portable file names ... OK
• checking for sufficient/correct file permissions ... 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 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 cross-references ... OK
• checking for missing documentation entries ... OK
• checking for code/documentation mismatches ... OK
• checking Rd \usage sections ... OK
• checking data for non-ASCII characters ... OK
• checking line endings in C/C++/Fortran sources/headers ... OK
• checking line endings in Makefiles ... OK
• checking for portable use of $BLAS_LIBS ... OK
• creating adegenet-Ex.R ... OK
• checking examples ... ERROR
  Running examples in 'adegenet-Ex.R' failed.
  The error most likely occurred in:
  
  > ### * spca
  >
  > flush(stderr()); flush(stdout())
  >
  > ### Encoding: UTF-8
  >
  > ### Name: spca
  > ### Title: Spatial principal component analysis
  > ### Aliases: spca print.spca summary.spca plot.spca screeplot.spca
  > ### Keywords: spatial multivariate
  >
  > ### ** Examples
  >
  > ## data(spcaIllus) illustrates the sPCA
  > ## see ?spcaIllus
  > ##
  >
  > example(spcaIllus)
  
  spcIll> if(require(spdep) & require(ade4)){
  spcIll+
  spcIll+ data(spcaIllus)
  spcIll+ attach(spcaIllus)
  spcIll+ ## comparison PCA vs sPCA
  spcIll+
  spcIll+ # PCA
  spcIll+ pca2A <- dudi.pca(dat2A$tab,center=TRUE,scale=FALSE,scannf=FALSE)
  spcIll+ pca2B <- dudi.pca(dat2B$tab,center=TRUE,scale=FALSE,scannf=FALSE)
  spcIll+ pca2C <- dudi.pca(dat2C$tab,center=TRUE,scale=FALSE,scannf=FALSE)
  spcIll+ pca3 <- dudi.pca(dat3$tab,center=TRUE,scale=FALSE,scannf=FALSE,nf=2)
  spcIll+ pca4 <- dudi.pca(dat4$tab,center=TRUE,scale=FALSE,scannf=FALSE,nf=2)
  spcIll+
  spcIll+ # sPCA
  spcIll+ spca2A <- spca(dat2A,xy=dat2A$other$xy,ask=FALSE,type=1,plot=FALSE,scannf=FALSE,nfposi=1,nfnega=0)
  spcIll+
  spcIll+ spca2B <- spca(dat2B,xy=dat2B$other$xy,ask=FALSE,type=1,plot=FALSE,scannf=FALSE,nfposi=1,nfnega=0)
  spcIll+
  spcIll+ spca2C <- spca(dat2C,xy=dat2C$other$xy,ask=FALSE,type=1,plot=FALSE,scannf=FALSE,nfposi=0,nfnega=1)
  spcIll+
  spcIll+ spca3 <- spca(dat3,xy=dat3$other$xy,ask=FALSE,type=1,plot=FALSE,scannf=FALSE,nfposi=1,nfnega=1)
  spcIll+
  spcIll+ spca4 <- spca(dat4,xy=dat4$other$xy,ask=FALSE,type=1,plot=FALSE,scannf=FALSE,nfposi=1,nfnega=1)
  spcIll+
  spcIll+ # an auxiliary function for graphics
  spcIll+ plotaux <- function(x,analysis,axis=1,lab=NULL,...){
  spcIll+ neig <- NULL
  spcIll+ if(inherits(analysis,"spca")) neig <- nb2neig(analysis$lw$neighbours)
  spcIll+ xrange <- range(x$other$xy[,1])
  spcIll+ xlim <- xrange + c(-diff(xrange)*.1 , diff(xrange)*.45)
  spcIll+ yrange <- range(x$other$xy[,2])
  spcIll+ ylim <- yrange + c(-diff(yrange)*.45 , diff(yrange)*.1)
  spcIll+
  spcIll+ s.value(x$other$xy,analysis$li[,axis],include.ori=FALSE,addaxes=FALSE,cgrid=0,grid=FALSE,neig=neig,cleg=0,xlim=xlim,ylim=ylim,
  spcIll+ ...)
  spcIll+
  spcIll+ par(mar=rep(.1,4))
  spcIll+ if(is.null(lab)) lab = gsub("[P]","",x$pop)
  spcIll+ text(x$other$xy, lab=lab, col="blue", cex=1.2, font=2)
  spcIll+ add.scatter({barplot(analysis$eig,col="grey");box();title("Eigenvalues",line=-1)},posi="bottomright",ratio=.3)
  spcIll+ }
  spcIll+
  spcIll+ # plots
  spcIll+ get(getOption("device"))(width=10,height=5)
  spcIll+ par(mfrow=c(1,2))
  spcIll+ plotaux(dat2A,pca2A,sub="dat2A - PCA",pos="bottomleft",csub=2)
  spcIll+ plotaux(dat2A,spca2A,sub="dat2A - sPCA glob1",pos="bottomleft",csub=2)
  spcIll+
  spcIll+ plotaux(dat2B,pca2B,sub="dat2B - PCA",pos="bottomleft",csub=2)
  spcIll+ plotaux(dat2B,spca2B,sub="dat2B - sPCA glob1",pos="bottomleft",csub=2)
  spcIll+
  spcIll+ plotaux(dat2C,pca2C,sub="dat2C - PCA",pos="bottomleft",csub=2)
  spcIll+ plotaux(dat2C,spca2C,sub="dat2C - sPCA loc1",pos="bottomleft",csub=2,axis=2)
  spcIll+
  spcIll+ get(getOption("device"))()
  spcIll+ par(mfrow=c(2,2))
  spcIll+ plotaux(dat3,pca3,sub="dat3 - PCA axis1",pos="bottomleft",csub=2)
  spcIll+ plotaux(dat3,spca3,sub="dat3 - sPCA glob1",pos="bottomleft",csub=2)
  spcIll+ plotaux(dat3,pca3,sub="dat3 - PCA axis2",pos="bottomleft",csub=2,axis=2)
  spcIll+ plotaux(dat3,spca3,sub="dat3 - sPCA loc1",pos="bottomleft",csub=2,axis=2)
  spcIll+
  spcIll+ plotaux(dat4,pca4,lab=dat4$other$sup.pop,sub="dat4 - PCA axis1",pos="bottomleft",csub=2)
  spcIll+ plotaux(dat4,spca4,lab=dat4$other$sup.pop,sub="dat4 - sPCA glob1",pos="bottomleft",csub=2)
  spcIll+ plotaux(dat4,pca4,lab=dat4$other$sup.pop,sub="dat4 - PCA axis2",pos="bottomleft",csub=2,axis=2)
  spcIll+ plotaux(dat4,spca4,lab=dat4$other$sup.pop,sub="dat4 - sPCA loc1",pos="bottomleft",csub=2,axis=2)
  spcIll+
  spcIll+ # detach data
  spcIll+ detach(spcaIllus)
  spcIll+ }
  Loading required package: spdep
  Loading required package: tripack
  Loading required package: sp
  Loading required package: maptools
  Loading required package: foreign
  Loading required package: boot
  Loading required package: spam
  Package 'spam' is loaded. Version0.13-3 (2008-04-21).
  
  Type demo( spam) for some demos, help( Spam) for an overview of this package.
  
  Loading required package: Matrix
  Loading required package: lattice
  
  Attaching package: 'lattice'
  
  
  The following object(s) are masked from package:boot :
  
  melanoma
  
  
  Attaching package: 'Matrix'
  
  
  The following object(s) are masked from package:spam :
  
  norm
  
  
  The following object(s) are masked from package:stats :
  
  xtabs
  
  Loading required package: ade4
  
  Attaching package: 'ade4'
  
  
  The following object(s) are masked from package:base :
  
  within
  
  Warning in any(col.w) : coercing argument of type 'double' to logical
  Warning in any(row.w) : coercing argument of type 'double' to logical
  Warning in any(col.w) : coercing argument of type 'double' to logical
  Warning in any(row.w) : coercing argument of type 'double' to logical
  Warning in any(col.w) : coercing argument of type 'double' to logical
  Warning in any(row.w) : coercing argument of type 'double' to logical
  Warning in any(col.w) : coercing argument of type 'double' to logical
  Warning in any(row.w) : coercing argument of type 'double' to logical
  Warning in any(col.w) : coercing argument of type 'double' to logical
  Warning in any(row.w) : coercing argument of type 'double' to logical
  Warning in any(col.w) : coercing argument of type 'double' to logical
  Warning in any(row.w) : coercing argument of type 'double' to logical
  Warning in any(col.w) : coercing argument of type 'double' to logical
  Warning in any(row.w) : coercing argument of type 'double' to logical
  Warning in any(col.w) : coercing argument of type 'double' to logical
  Warning in any(row.w) : coercing argument of type 'double' to logical
  Warning in any(col.w) : coercing argument of type 'double' to logical
  Warning in any(row.w) : coercing argument of type 'double' to logical
  Warning in any(col.w) : coercing argument of type 'double' to logical
  Warning in any(row.w) : coercing argument of type 'double' to logical
  Error in get(getOption("device")) : invalid first argument
  Calls: example -> source -> eval.with.vis -> eval.with.vis -> get
  Execution halted