• using R version 2.15.2 (2012-10-26)
• using platform: i386-apple-darwin9.8.0 (32-bit)
• using session charset: ASCII
• checking for file 'trio/DESCRIPTION' ... OK
• checking extension type ... Package
• this is package 'trio' version '2.0.2'
• checking package namespace information ... OK
• checking package dependencies ... NOTE
  Packages suggested but not available for checking:
  'siggenes' 'logicFS'
• checking if this is a source package ... OK
• checking if there is a namespace ... OK
• checking for executable files ... OK
• checking whether package 'trio' 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 for left-over 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 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
  colTDTebam: no visible global function definition for 'ebam'
  colTDTsam: no visible global function definition for 'sam'
  gtdt.null.approx2: no visible global function definition for 'denspr'
  trio.permTest: no visible global function definition for 'triologreg'
  trioBagging: no visible global function definition for 'triologreg'
  trioFS.formula: no visible global function definition for 'getXy'
  trioLR.default: no visible global function definition for 'triologreg'
  trioLR.formula: no visible global function definition for 'getXy'
• checking Rd files ... OK
• checking Rd metadata ... OK
• checking Rd cross-references ... NOTE
  Package(s) unavailable to check Rd xrefs: 'siggenes', 'logicFS'
• 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' ... OK
• checking examples ... OK
• checking for unstated dependencies in vignettes ... OK
• checking package vignettes in 'inst/doc' ... OK
• checking running R code from vignettes ... WARNING
  Errors in running code in vignettes:
  when running code in 'trio.Rnw'
  ...
  > my.control <- lrControl(start = 1, end = -3, iter = 1000,
  + output = -4)
  
  > lr.out <- trioLR(trio.bin, control = my.control, rand = 9876543)
  Warning in library(package, lib.loc = lib.loc, character.only = TRUE, logical.return = TRUE, :
  there is no package called 'logicFS'
  
  When sourcing 'trio.R':
  Error: Package logicFS >= 1.28.1 is required.
  Execution halted
  
• checking re-building of vignette PDFs ... NOTE
  Error in re-building vignettes:
  ...
  Loading required package: survival
  Loading required package: splines
  Loading required package: haplo.stats
  Warning in library(package, lib.loc = lib.loc, character.only = TRUE, logical.return = TRUE, :
  there is no package called 'logicFS'
  
  Error: processing vignette 'trio.Rnw' failed with diagnostics:
  chunk 41
  Error in trioLR.default(x$bin[, -1], x$bin[, 1], ...) :
  Package logicFS >= 1.28.1 is required.
  Execution halted
  
• checking PDF version of manual ... OK
  WARNING: There was 1 warning.
  NOTE: There were 4 notes.
  See
  '/Volumes/XT3/Rdev-web/QA/Simon/packages/leopard-universal/results/2.15/trio.Rcheck/00check.log'
  for details.
• elapsed time (check, wall clock): 2:25