• using R Under development (unstable) (2012-05-22 r59405)
• using platform: x86_64-unknown-linux-gnu (64-bit)
• using session charset: UTF-8
• checking for file ‘kinship2/DESCRIPTION’ ... OK
• this is package ‘kinship2’ version ‘1.3.3’
• 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 ‘kinship2’ can be installed ... [9s/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 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
  besthint: warning in align.pedigree(ped, packed = TRUE, align = TRUE,
  width = 8, hint = newhint): partial argument match of 'hint' to
  'hints'
• 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’ ... OK
• checking examples ... OK
• checking for unstated dependencies in tests ... OK
• checking tests ... [40s/58s] OK
  Running ‘failure.R’
  Comparing ‘failure.Rout’ to ‘failure.Rout.save’ ...4a5,11
  >
  > Attaching package: 'Matrix'
  >
  > The following object(s) are masked from 'package:base':
  >
  > det
  >
  Running ‘kin1.R’
  Comparing ‘kin1.Rout’ to ‘kin1.Rout.save’ ...6a7,13
  >
  > Attaching package: 'Matrix'
  >
  > The following object(s) are masked from 'package:base':
  >
  > det
  >
  Running ‘makefam.R’
  Comparing ‘makefam.Rout’ to ‘makefam.Rout.save’ ...3a4,10
  >
  > Attaching package: 'Matrix'
  >
  > The following object(s) are masked from 'package:base':
  >
  > det
  >
  Running ‘subscript.R’
  Comparing ‘subscript.Rout’ to ‘subscript.Rout.save’ ...6a7,13
  >
  > Attaching package: 'Matrix'
  >
  > The following object(s) are masked from 'package:base':
  >
  > det
  >
  Running ‘test.pedigree.legend.R’
  Comparing ‘test.pedigree.legend.Rout’ to ‘test.pedigree.legend.Rout.save’ ...6a7,13
  >
  > Attaching package: 'Matrix'
  >
  > The following object(s) are masked from 'package:base':
  >
  > det
  >
  Running ‘test.pedigree.shrink.R’
  Comparing ‘test.pedigree.shrink.Rout’ to ‘test.pedigree.shrink.Rout.save’ ...10a11,17
  >
  > Attaching package: 'Matrix'
  >
  > The following object(s) are masked from 'package:base':
  >
  > det
  >
  Running ‘test.pedigree.trim.R’
  Comparing ‘test.pedigree.trim.Rout’ to ‘test.pedigree.trim.Rout.save’ ...3a4,10
  >
  > Attaching package: 'Matrix'
  >
  > The following object(s) are masked from 'package:base':
  >
  > det
  >
  Running ‘test.pedigree.unrelated.R’
  Comparing ‘test.pedigree.unrelated.Rout’ to ‘test.pedigree.unrelated.Rout.save’ ...14a15,21
  >
  > Attaching package: 'Matrix'
  >
  > The following object(s) are masked from 'package:base':
  >
  > det
  >
  Running ‘twin.R’
  Comparing ‘twin.Rout’ to ‘twin.Rout.save’ ...3a4,10
  >
  > Attaching package: 'Matrix'
  >
  > The following object(s) are masked from 'package:base':
  >
  > det
  >
• checking for unstated dependencies in vignettes ... OK
• checking package vignettes in ‘inst/doc’ ... OK
• checking running R code from vignettes ... OK
• checking re-building of vignette PDFs ... [6s/12s] OK
• checking PDF version of manual ... OK
  NOTE: There was 1 note.
  See
  ‘/data/gannet/tmp/ripley/R/packages/tests-devel/kinship2.Rcheck/00check.log’
  for details.