• using R version 2.15.0 Patched (2012-05-26 r59446)
• using platform: i386-pc-solaris2.10 (32-bit)
• using session charset: UTF-8
• checking for file ‘ExomeCNV/DESCRIPTION’ ... OK
• checking extension type ... Package
• this is package ‘ExomeCNV’ version ‘1.2’
• checking package dependencies ... OK
• checking if this is a source package ... OK
• checking if there is a namespace ... NOTE
  As from R 2.14.0 all packages need a namespace.
  One will be generated on installation, but it is better to handcraft a
  NAMESPACE file: R CMD build will produce a suitable starting point.
  CRAN requires a NAMESPACE file for all submissions.
• checking for .dll and .exe files ... OK
• checking whether package ‘ExomeCNV’ 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 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 ... NOTE
  CNV.analyze: warning in png(file, width = 2000, height = 1000, unit =
  "px"): partial argument match of 'unit' to 'units'
  CNV.analyze: warning in png("CNV detection for exons with > " %+%
  coverage.cutoff %+% " coverage.png", width = 2000, height = 1000,
  unit = "px"): partial argument match of 'unit' to 'units'
  CNV.analyze: warning in png("allchr." %+% file, width = 2000, height =
  1000, unit = "px"): partial argument match of 'unit' to 'units'
  CNV.analyze: warning in png("all chromosome CNV detection for exons
  with > " %+% coverage.cutoff %+% " coverage.png", width = 2000,
  height = 1000, unit = "px"): partial argument match of 'unit' to
  'units'
  CNV.analyze: warning in png("CNV detection for exons with > " %+%
  coverage.cutoff %+% " coverage.noDNAcopy.png", width = 2000, height =
  1000, unit = "px"): partial argument match of 'unit' to 'units'
  write.output: warning in png(file = name %+% ".cnv.png", res = 70,
  width = 2000, height = 1200, pointsize = 16): partial argument match
  of 'file' to 'filename'
  do.DNAcopy: no visible binding for global variable ‘chr.hash’
  do.plot.loh: no visible binding for global variable ‘chr.hash’
  get.proper.cnv.positions: no visible binding for global variable
  ‘chr.hash’
  read.all.coverage: no visible binding for global variable
  ‘COVERAGE_HEADER’
  read.eCNV: no visible binding for global variable ‘ecnv’
  strip.chr.name: no visible binding for global variable ‘chr.hash’
• 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 examples ... [19s/113s] OK
• checking PDF version of manual ... OK
  NOTE: There were 2 notes.
  See
  ‘/home/ripley/R/packages/tests32/ExomeCNV.Rcheck/00check.log’
  for details.