• 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 ‘ppiPre/DESCRIPTION’ ... OK
• checking extension type ... Package
• this is package ‘ppiPre’ 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.
• checking for executable files ... OK
• checking whether package ‘ppiPre’ 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
  CheckAnnotationPackage: no visible global function definition for
  ‘biocLite’
  GetGOMap: no visible binding for global variable ‘ppiPreEnv’
  GetGOParents: no visible binding for global variable ‘ppiPreEnv’
  GetLatestCommonAncestor: no visible binding for global variable
  ‘ppiPreEnv’
  GetOntology: no visible binding for global variable ‘ppiPreEnv’
  IntelliGOGetParents: no visible binding for global variable ‘ppiPreEnv’
  TCSSComputeIC: no visible binding for global variable ‘ppiPreEnv’
  TCSSCompute_ICA: no visible binding for global variable ‘ppiPreEnv’
  TCSSGetAncestors: no visible binding for global variable ‘ppiPreEnv’
  TCSSGetChildren: no visible binding for global variable ‘ppiPreEnv’
  TCSSGetOffsprings: no visible binding for global variable ‘ppiPreEnv’
  WangMethod: no visible binding for global variable ‘ppiPreEnv’
  WangSemVal: no visible binding for global variable ‘ppiPreCache’
• 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 ... WARNING
  
  Note: significantly better compression could be obtained
  by using R CMD build --resave-data
  old_size new_size compress
  Info_Contents_BP_anopheles.rda 61Kb 16Kb xz
  Info_Contents_BP_arabidopsis.rda 61Kb 17Kb xz
  Info_Contents_BP_bovine.rda 64Kb 18Kb xz
  Info_Contents_BP_canine.rda 65Kb 19Kb xz
  Info_Contents_BP_chicken.rda 62Kb 17Kb xz
  Info_Contents_BP_chimp.rda 65Kb 19Kb xz
  Info_Contents_BP_ecolik12.rda 52Kb 10Kb xz
  Info_Contents_BP_ecsakai.rda 49Kb 8Kb xz
  Info_Contents_BP_fly.rda 62Kb 17Kb xz
  Info_Contents_BP_human.rda 68Kb 21Kb xz
  Info_Contents_BP_malaria.rda 54Kb 12Kb xz
  Info_Contents_BP_mouse.rda 66Kb 20Kb xz
  Info_Contents_BP_pig.rda 62Kb 17Kb xz
  Info_Contents_BP_rat.rda 70Kb 23Kb xz
  Info_Contents_BP_rhesus.rda 65Kb 19Kb xz
  Info_Contents_BP_worm.rda 59Kb 15Kb xz
  Info_Contents_BP_xenopus.rda 64Kb 18Kb xz
  Info_Contents_BP_yeast.rda 60Kb 16Kb xz
  Info_Contents_BP_zebrafish.rda 59Kb 15Kb xz
  Info_Contents_CC_anopheles.rda 10Kb 8Kb bzip2
  Info_Contents_CC_arabidopsis.rda 10Kb 9Kb bzip2
  Info_Contents_CC_bovine.rda 10Kb 9Kb bzip2
  Info_Contents_CC_canine.rda 10Kb 9Kb bzip2
  Info_Contents_CC_chicken.rda 10Kb 8Kb bzip2
  Info_Contents_CC_chimp.rda 10Kb 9Kb bzip2
  Info_Contents_CC_fly.rda 10Kb 9Kb bzip2
  Info_Contents_CC_human.rda 11Kb 5Kb xz
  Info_Contents_CC_mouse.rda 11Kb 9Kb bzip2
  Info_Contents_CC_pig.rda 10Kb 8Kb bzip2
  Info_Contents_CC_rat.rda 12Kb 5Kb xz
  Info_Contents_CC_rhesus.rda 10Kb 9Kb bzip2
  Info_Contents_CC_xenopus.rda 10Kb 9Kb bzip2
  Info_Contents_CC_yeast.rda 11Kb 9Kb bzip2
  Info_Contents_MF_anopheles.rda 28Kb 8Kb xz
  Info_Contents_MF_arabidopsis.rda 30Kb 9Kb xz
  Info_Contents_MF_bovine.rda 30Kb 9Kb xz
  Info_Contents_MF_canine.rda 30Kb 9Kb xz
  Info_Contents_MF_chicken.rda 29Kb 9Kb xz
  Info_Contents_MF_chimp.rda 29Kb 9Kb xz
  Info_Contents_MF_ecolik12.rda 24Kb 6Kb xz
  Info_Contents_MF_ecsakai.rda 24Kb 5Kb xz
  Info_Contents_MF_fly.rda 30Kb 9Kb xz
  Info_Contents_MF_human.rda 31Kb 10Kb xz
  Info_Contents_MF_malaria.rda 27Kb 7Kb xz
  Info_Contents_MF_mouse.rda 31Kb 10Kb xz
  Info_Contents_MF_pig.rda 28Kb 8Kb xz
  Info_Contents_MF_rat.rda 32Kb 11Kb xz
  Info_Contents_MF_rhesus.rda 30Kb 9Kb xz
  Info_Contents_MF_worm.rda 28Kb 8Kb xz
  Info_Contents_MF_xenopus.rda 29Kb 9Kb xz
  Info_Contents_MF_yeast.rda 30Kb 9Kb xz
  Info_Contents_MF_zebrafish.rda 29Kb 9Kb xz
• checking examples ... [5s/5s] OK
• checking PDF version of manual ... OK
  WARNING: There was 1 warning.
  NOTE: There were 2 notes.
  See
  ‘/home/hornik/tmp/R.check/r-devel/Work/PKGS/ppiPre.Rcheck/00check.log’
  for details.