• using R version 2.14.2 RC (2012-02-23 r58468)
• using platform: i686-pc-linux-gnu (32-bit)
• using session charset: UTF-8
• checking for file ‘MetaQC/DESCRIPTION’ ... OK
• checking extension type ... Package
• this is package ‘MetaQC’ version ‘0.1.8’
• checking package namespace information ... OK
• checking package dependencies ... NOTE
  Package suggested but not available for checking: ‘doSMP’
• checking if this is a source package ... OK
• checking if there is a namespace ... OK
• checking for executable files ... OK
• checking whether package ‘MetaQC’ 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 ... NOTE
  GMT2List: no visible binding for global variable ‘x’
  MetaQC: no visible global function definition for ‘startWorkers’
  MetaQC: no visible global function definition for ‘registerDoSMP’
  MetaQC : Cleanup: no visible global function definition for
  ‘stopWorkers’
  MetaQC : .ConvertToGeneSetIdx: no visible binding for global variable
  ‘g’
  MetaQC : .ConvertToGeneSetIdx: no visible binding for global variable
  ‘d’
  MetaQC : .CalcPval: no visible binding for global variable ‘i’
  MetaQC : .CalcPval: no visible binding for global variable ‘w’
  MetaQC : .CalcPval: no visible binding for global variable ‘j’
  MetaQC : .CalcPval: no visible binding for global variable ‘b’
  MetaQC : EQC: no visible binding for global variable ‘g’
  MetaQC : EQC: no visible binding for global variable ‘w’
  MetaQC : AQCg: no visible binding for global variable ‘i’
  MetaQC : AQCp: no visible binding for global variable ‘i’
  MetaQC : CQCg: no visible binding for global variable ‘dat’
  MetaQC : CQCg: no visible binding for global variable ‘pv’
  MetaQC : CQCg: no visible binding for global variable ‘i’
  MetaQC : CQCp: no visible binding for global variable ‘dat’
  MetaQC : CQCp: no visible binding for global variable ‘pv’
  MetaQC : CQCp: no visible binding for global variable ‘ii’
  MetaQC : CQCp: no visible binding for global variable ‘jj’
  MetaQC : CQCp: no visible binding for global variable ‘i’
  MetaQC : IQC: no visible binding for global variable ‘i’
  MetaQC : .CalcDistOfStudies: no visible binding for global variable
  ‘ii’
  MetaQC : .CalcDistOfStudies: no visible binding for global variable
  ‘jj’
  MetaQC : .CalcScores: no visible binding for global variable ‘d’
  cleanup: no visible global function definition for ‘stopWorkers’
  requireAll: no visible global function definition for ‘biocLite’
• checking Rd files ... NOTE
  prepare_Rd: MetaQC-package.Rd:30-31: Dropping empty section \seealso
  prepare_Rd: MetaQC.Rd:55-57: Dropping empty section \details
  prepare_Rd: MetaQC.Rd:71-73: Dropping empty section \note
  prepare_Rd: cleanup.Rd:22-24: Dropping empty section \details
  prepare_Rd: cleanup.Rd:34-36: Dropping empty section \note
  prepare_Rd: plot.proto.Rd:25-27: Dropping empty section \details
  prepare_Rd: plot.proto.Rd:37-39: Dropping empty section \note
  prepare_Rd: print.proto.Rd:25-27: Dropping empty section \details
  prepare_Rd: print.proto.Rd:37-39: Dropping empty section \note
  prepare_Rd: requireAll.Rd:19-21: Dropping empty section \details
  prepare_Rd: requireAll.Rd:31-33: Dropping empty section \note
  prepare_Rd: requireAll.Rd:25-27: Dropping empty section \references
  prepare_Rd: requireAll.Rd:37-39: Dropping empty section \seealso
  prepare_Rd: runQC.Rd:38-40: Dropping empty section \details
  prepare_Rd: runQC.Rd:50-52: Dropping empty section \note
• 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 ... NOTE
  S3 methods shown with full name in documentation object 'plot.proto':
  ‘plot.proto’
  
  S3 methods shown with full name in documentation object 'print.proto':
  ‘print.proto’
  
  The \usage entries for S3 methods should use the \method markup and not
  their full name.
  See the chapter ‘Writing R documentation files’ in the ‘Writing R
  Extensions’ manual.
• 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 ... OK
• checking PDF version of manual ... OK