• using R Under development (unstable) (2012-02-23 r58468)
• using platform: i686-pc-linux-gnu (32-bit)
• using session charset: UTF-8
• checking for file ‘SNPRelate/DESCRIPTION’ ... OK
• checking extension type ... Package
• this is package ‘SNPRelate’ version ‘0.9.2’
• 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 whether package ‘SNPRelate’ can be installed ... OK
• checking installed package size ... 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 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 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 ... OK
• checking contents of ‘data’ directory ... OK
• checking data for non-ASCII characters ... OK
• checking data for ASCII and uncompressed saves ... OK
• checking line endings in C/C++/Fortran sources/headers ... OK
• checking line endings in Makefiles ... OK
• checking for portable compilation flags in Makevars ... OK
• checking for portable use of $(BLAS_LIBS) and $(LAPACK_LIBS) ... OK
• checking compiled code ... OK
• checking examples ... ERROR
  Running examples in ‘SNPRelate-Ex.R’ failed
  The error most likely occurred in:
  
  > ### Name: SNPRelate-package
  > ### Title: Parallel Computing Toolset for genome-wide association studies
  > ### Aliases: SNPRelate-package SNPRelate
  > ### Keywords: multicore gds GWAS genetics
  >
  > ### ** Examples
  >
  > ####################################################################
  > # Convert the PLINK BED file to the GDS file
  > #
  >
  > # PLINK BED files
  > path <- paste(.path.package("SNPRelate"), "/extdata", sep="")
  > bed.fn <- paste(path, "/plinkhapmap.bed", sep="")
  > bim.fn <- paste(path, "/plinkhapmap.bim", sep="")
  > fam.fn <- paste(path, "/plinkhapmap.fam", sep="")
  > # convert
  > snpgdsBED2GDS(bed.fn, fam.fn, bim.fn, "HapMap.gds")
  Start snpgdsBED2GDS ...
  open /home/hornik/tmp/R.check/r-devel/Work/build/Packages/SNPRelate/extdata/plinkhapmap.bed in the individual-major mode
  open /home/hornik/tmp/R.check/r-devel/Work/build/Packages/SNPRelate/extdata/plinkhapmap.fam DONE.
  open /home/hornik/tmp/R.check/r-devel/Work/build/Packages/SNPRelate/extdata/plinkhapmap.bim DONE.
  Fri Feb 24 23:30:37 2012 store sample id, snp id, position, and chromosome.
  start writing ...
  Fri Feb 24 23:30:37 2012 0%
  Fri Feb 24 23:30:37 2012 100%
  Fri Feb 24 23:30:37 2012 Done.
  >
  >
  > ####################################################################
  > # Principal Component Analysis
  > #
  >
  > # open
  > genofile <- openfn.gds("HapMap.gds")
  >
  > RV <- snpgdsPCA(genofile, num.thread=2)
  Principal Component Analysis (PCA) on SNP genotypes:
  Removing 203 non-autosomal SNPs
  Removing 2 SNPs (monomorphic, < MAF, or > missing rate)
  Working space: 279 samples, 4795 SNPs
  Use 2 CPU cores.
  PCA: the sum of all working genotypes = 1346365
  PCA: Fri Feb 24 23:30:37 2012 0%
  Killed