• using R Under development (unstable) (2012-02-09 r58309)
• using platform: x86_64-unknown-linux-gnu (64-bit)
• using session charset: UTF-8
• checking for file ‘pcalg/DESCRIPTION’ ... OK
• this is package ‘pcalg’ version ‘1.1-4’
• checking package namespace information ... OK
• checking package dependencies ... OK
• checking if this is a source package ... OK
• checking if there is a namespace ... OK
• checking for executable files ... OK
• checking whether package ‘pcalg’ can be installed ... [5s/15s] 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
  dsep: warning in wgtMatrix(gS, transp = FALSE): partial argument match
  of 'transp' to 'transpose'
  shd: warning in wgtMatrix(g1, transp = FALSE): partial argument match
  of 'transp' to 'transpose'
  shd: warning in wgtMatrix(g2, transp = FALSE): partial argument match
  of 'transp' to 'transpose'
• 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 sizes of PDF files under ‘inst/doc’ ... OK
• checking installed files from ‘inst/doc’ ... NOTE
  The following files are already in R: ‘jss.bst’, ‘jss.cls’
  Please remove them from your package.
  The following files should probably not be installed:
  ‘Makefile’
  The following directories should probably not be installed:
  ‘auto’, ‘jssStyle’
  
  Consider the use of a .Rinstignore file: see ‘Writing R Extensions’,
  or move the vignette sources from ‘inst/doc’ to ‘vignettes’.
• checking examples ... [42s/126s] OK
• checking for unstated dependencies in tests ... OK
• checking tests ... [126s/380s] OK
  Running ‘test_amat2dag.R’
  Running ‘test_compareGraphs.R’
  Running ‘test_dag2cpdag.R’
  Running ‘test_dsep.R’
  Running ‘test_fci.R’ [22s/66s]
  Running ‘test_gSquareBin.R’
  Running ‘test_gSquareDis.R’
  Running ‘test_getNextSet.R’
  Running ‘test_ida.R’ [8s/23s]
  Running ‘test_idaFast.R’ [7s/20s]
  Running ‘test_pc.R’ [8s/26s]
  Running ‘test_pcAlgo.R’ [6s/18s]
  Running ‘test_pcSelect.R’
  Running ‘test_pcorOrder.R’
  Running ‘test_pdag2dag.R’
  Running ‘test_randomDAG.R’
  Running ‘test_rfci.R’ [37s/111s]
  Running ‘test_rmvDAG.R’
  Running ‘test_shd.R’
  Running ‘test_skeleton.R’ [4s/11s]
  Running ‘test_udag2pag.R’
  Running ‘test_udag2pdag.R’ [12s/35s]
  Running ‘test_wgtMatrix.R’
• checking for unstated dependencies in vignettes ... OK
• checking package vignettes in ‘inst/doc’ ... OK
• checking running R code from vignettes ... [7s/19s] OK
• checking re-building of vignette PDFs ... [10s/35s] OK
• checking PDF version of manual ... OK
  NOTE: There were 2 notes.
  See
  ‘/data/gannet/tmp/ripley/R/packages/tests-devel/pcalg.Rcheck/00check.log’
  for details.