• using R Under development (unstable) (2012-05-22 r59405)
• using platform: x86_64-unknown-linux-gnu (64-bit)
• using session charset: UTF-8
• checking for file ‘msProcess/DESCRIPTION’ ... OK
• checking extension type ... Package
• this is package ‘msProcess’ version ‘1.0.6’
• checking package dependencies ... OK
• checking if this is a source package ... OK
• checking if there is a namespace ... WARNING
  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 executable files ... OK
• checking whether package ‘msProcess’ can be installed ... [11s/17s] OK
• checking installed package size ... NOTE
  installed size is 5.9Mb
  sub-directories of 1Mb or more:
  data1 1.2Mb
  data2 1.2Mb
• 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 loading without being on the library search path ... 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
  msAlignMRD: warning in wavMODWT(peak.hist.smoothed, wavelet = "haar",
  n.level = level - 2): partial argument match of 'n.level' to
  'n.levels'
  msPeakMRD: warning in wavMODWT(y, wavelet = "haar", n.level = n.level):
  partial argument match of 'n.level' to 'n.levels'
  msPeakMRD: warning in wavMODWT(y, wavelet = "d4", n.level = n.level):
  partial argument match of 'n.level' to 'n.levels'
  plot.msSet: warning in msPlot(matlines = z$matlines, matpoints =
  z$matpoints, abline = z$abline, text = z$text, main = main, xlab =
  xlab, ylab = "intensity", offset = offset, ...): partial argument
  match of 'matlines' to 'matlines.'
  plot.msSet: warning in msPlot(matlines = z$matlines, matpoints =
  z$matpoints, abline = z$abline, text = z$text, main = main, xlab =
  xlab, ylab = "intensity", offset = offset, ...): partial argument
  match of 'matpoints' to 'matpoints.'
  plot.msSet: warning in msPlot(matlines = z$matlines, matpoints =
  z$matpoints, abline = z$abline, text = z$text, main = main, xlab =
  xlab, ylab = "intensity", offset = offset, ...): partial argument
  match of 'abline' to 'abline.'
  plot.msSet: warning in msPlot(matlines = z$matlines, matpoints =
  z$matpoints, abline = z$abline, text = z$text, main = main, xlab =
  xlab, ylab = "intensity", offset = offset, ...): partial argument
  match of 'text' to 'text.'
  writeBinBlocks: warning in dir(path, pattern = paste("^", pattern,
  "\\.[0-9]+$", sep = ""), full = TRUE): partial argument match of
  'full' to 'full.names'
  assignEvent: no visible binding for global variable ‘newhist’
  binblocks2SQLite: no visible global function definition for ‘dbDriver’
  binblocks2SQLite: no visible global function definition for ‘dbConnect’
  binblocks2SQLite: no visible global function definition for
  ‘dbExistsTable’
  binblocks2SQLite: no visible global function definition for
  ‘dbRemoveTable’
  binblocks2SQLite : <anonymous>: no visible global function definition
  for ‘dbWriteTable’
  binblocks2SQLite: no visible global function definition for
  ‘dbDisconnect’
  cypherGenXML2Bin: no visible global function definition for
  ‘parseXMLPathFile’
  cypherGenXMList2BinBlocks : <anonymous>: no visible global function
  definition for ‘parseXMLPathFile’
  cypherGenXMList2BinBlocks: no visible global function definition for
  ‘parseXMLPathFile’
  importBin2Sqlite: no visible global function definition for ‘dbDriver’
  importBin2Sqlite: no visible global function definition for ‘dbConnect’
  importBin2Sqlite: no visible global function definition for
  ‘make.db.names.default’
  importBin2Sqlite: no visible global function definition for
  ‘dbWriteTable’
  importBin2Sqlite: no visible global function definition for
  ‘dbGetQuery’
  importBin2Sqlite: no visible global function definition for
  ‘dbRemoveTable’
  importBin2Sqlite: no visible global function definition for
  ‘dbDisconnect’
  importXMLDir: no visible binding for global variable ‘ErrorClass’
  msAlignCluster: possible error in dist(logmz[peak.unique], metric =
  "euclidean"): unused argument(s) (metric = "euclidean")
  msAssign: possible error in assign(x, value, frame = envir): unused
  argument(s) (frame = envir)
  msCalibrate: no visible global function definition for ‘l1fit’
  msCalibrate: no visible global function definition for ‘rreg’
  msGet: possible error in get(x, frame = envir): unused argument(s)
  (frame = envir)
  msHelp: no visible global function definition for ‘platform’
  msHelp: no visible global function definition for ‘attached.where’
  msHelp: no visible global function definition for ‘quoteSyntax’
  msHelp: no visible global function definition for ‘searchPaths’
  msHelp: no visible global function definition for ‘callBrowse’
  msImport: no visible global function definition for ‘base.path.name’
  msImport: no visible global function definition for ‘importData’
  msImportCiphergenXML: no visible global function definition for
  ‘parseXMLPathFile’
  msLaunchExample: no visible global function definition for ‘guiOpen’
  msObjects: possible error in objects(classes = "msSet"): unused
  argument(s) (classes = "msSet")
  msPlot: no visible global function definition for ‘regMatch’
  msQualify: no visible global function definition for ‘princompRob’
  predict.msQualify: no visible global function definition for
  ‘predict.princomp’
  throwEvent: no visible binding for global variable ‘msProcessEnv’
• 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 ... WARNING
  ‘::’ or ‘:::’ import not declared from: ‘splus2R’
• checking contents of ‘data’ directory ... OK
• checking data for non-ASCII characters ... OK
• checking data for ASCII and uncompressed saves ... OK
• checking sizes of PDF files under ‘inst/doc’ ... OK
• checking installed files from ‘inst/doc’ ... OK
• checking examples ... [52s/75s] OK
• checking PDF version of manual ... OK
  WARNING: There were 2 warnings.
  NOTE: There were 2 notes.
  See
  ‘/data/gannet/tmp/ripley/R/packages/tests-devel/msProcess.Rcheck/00check.log’
  for details.