• using R Under development (unstable) (2012-05-22 r59396)
• using platform: x86_64-unknown-linux-gnu (64-bit)
• using session charset: UTF-8
• checking for file ‘PresenceAbsence/DESCRIPTION’ ... OK
• checking extension type ... Package
• this is package ‘PresenceAbsence’ version ‘1.1.5’
• 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 ‘PresenceAbsence’ 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 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 ... OK
• checking Rd files ... NOTE
  prepare_Rd: Kappa.Rd:29-30: Dropping empty section \note
  prepare_Rd: Kappa.Rd:27: Dropping empty section \references
  prepare_Rd: PresenceAbsence.package.Rd:54: Dropping empty section \seealso
  prepare_Rd: auc.Rd:46-47: Dropping empty section \note
  prepare_Rd: auc.roc.plot.Rd:74-75: Dropping empty section \note
  prepare_Rd: auc.roc.plot.Rd:72: Dropping empty section \references
  prepare_Rd: calibration.plot.Rd:56-57: Dropping empty section \note
  prepare_Rd: cmx.Rd:44: Dropping empty section \references
  prepare_Rd: error.threshold.plot.Rd:86-87: Dropping empty section \note
  prepare_Rd: error.threshold.plot.Rd:84: Dropping empty section \references
  prepare_Rd: optimal.thresholds.Rd:102: Dropping empty section \note
  prepare_Rd: pcc.Rd:28-29: Dropping empty section \note
  prepare_Rd: pcc.Rd:26: Dropping empty section \references
  prepare_Rd: predicted.prevalence.Rd:34-35: Dropping empty section \note
  prepare_Rd: predicted.prevalence.Rd:32: Dropping empty section \references
  prepare_Rd: predicted.prevalence.Rd:36: Dropping empty section \seealso
  prepare_Rd: presence.absence.accuracy.Rd:63-64: Dropping empty section \note
  prepare_Rd: presence.absence.accuracy.Rd:61: Dropping empty section \references
  prepare_Rd: presence.absence.hist.Rd:70-71: Dropping empty section \note
  prepare_Rd: presence.absence.hist.Rd:68: Dropping empty section \references
  prepare_Rd: presence.absence.simulation.Rd:40: Dropping empty section \references
  prepare_Rd: presence.absence.simulation.Rd:43: Dropping empty section \seealso
  prepare_Rd: presence.absence.summary.Rd:62-63: Dropping empty section \note
  prepare_Rd: presence.absence.summary.Rd:60: Dropping empty section \references
  prepare_Rd: roc.plot.calculate.Rd:41-42: Dropping empty section \note
  prepare_Rd: roc.plot.calculate.Rd:39: Dropping empty section \references
  prepare_Rd: sensitivity.Rd:27-28: Dropping empty section \note
  prepare_Rd: sensitivity.Rd:25: Dropping empty section \references
  prepare_Rd: specificity.Rd:28-29: Dropping empty section \note
  prepare_Rd: specificity.Rd:26: Dropping empty section \references
• 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 ... [8s/11s] OK
• checking PDF version of manual ... OK
  WARNING: There was 1 warning.
  NOTE: There was 1 note.
  See
  ‘/data/gannet/tmp/ripley/R/packages/tests-devel/PresenceAbsence.Rcheck/00check.log’
  for details.