• 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 ‘haplo.stats/DESCRIPTION’ ... OK
• this is package ‘haplo.stats’ version ‘1.5.5’
• 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 ‘haplo.stats’ 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 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
  glm.fit.nowarn: no visible binding for global variable ‘n’
  haplo.glm: no visible binding for global variable ‘eta’
• 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 line endings in C/C++/Fortran sources/headers ... OK
• checking line endings in Makefiles ... OK
• checking for portable use of $(BLAS_LIBS) and $(LAPACK_LIBS) ... OK
• checking compiled code ... OK
• checking sizes of PDF files under ‘inst/doc’ ... OK
• checking installed files from ‘inst/doc’ ... OK
• checking examples ... [31s/40s] OK
• checking for unstated dependencies in tests ... OK
• checking tests ... [268s/361s] OK
  Running ‘test.Ginv.R’ [9s/12s]
  Comparing ‘test.Ginv.Rout’ to ‘test.Ginv.Rout.save’ ... OK
  Running ‘test.haplo.em.R’ [72s/98s]
  Comparing ‘test.haplo.em.Rout’ to ‘test.haplo.em.Rout.save’ ...14c14
  < [1] "LC_CTYPE=C;LC_NUMERIC=C;LC_TIME=C;LC_COLLATE=C;LC_MONETARY=C;LC_MESSAGES=en_GB.utf-8;LC_PAPER=C;LC_NAME=C;LC_ADDRESS=C;LC_TELEPHONE=C;LC_MEASUREMENT=en_GB.utf-8;LC_IDENTIFICATION=C"
  ---
  > [1] "LC_CTYPE=C;LC_NUMERIC=C;LC_TIME=C;LC_COLLATE=C;LC_MONETARY=C;LC_MESSAGES=en_US.UTF-8;LC_PAPER=C;LC_NAME=C;LC_ADDRESS=C;LC_TELEPHONE=C;LC_MEASUREMENT=en_US.UTF-8;LC_IDENTIFICATION=C"
  16c16
  < R Under development (unstable) (2012-05-22 r59405)
  ---
  > R version 2.14.0 (2011-10-31)
  22c22
  < [5] LC_MONETARY=C LC_MESSAGES=en_GB.utf-8
  ---
  > [5] LC_MONETARY=C LC_MESSAGES=en_US.UTF-8
  25c25
  < [11] LC_MEASUREMENT=en_GB.utf-8 LC_IDENTIFICATION=C
  ---
  > [11] LC_MEASUREMENT=en_US.UTF-8 LC_IDENTIFICATION=C
  Running ‘test.haplo.power.R’
  Comparing ‘test.haplo.power.Rout’ to ‘test.haplo.power.Rout.save’ ...21c21
  < [1] "LC_CTYPE=C;LC_NUMERIC=C;LC_TIME=C;LC_COLLATE=C;LC_MONETARY=C;LC_MESSAGES=en_GB.utf-8;LC_PAPER=C;LC_NAME=C;LC_ADDRESS=C;LC_TELEPHONE=C;LC_MEASUREMENT=en_GB.utf-8;LC_IDENTIFICATION=C"
  ---
  > [1] "LC_CTYPE=C;LC_NUMERIC=C;LC_TIME=C;LC_COLLATE=C;LC_MONETARY=C;LC_MESSAGES=en_US.UTF-8;LC_PAPER=C;LC_NAME=C;LC_ADDRESS=C;LC_TELEPHONE=C;LC_MEASUREMENT=en_US.UTF-8;LC_IDENTIFICATION=C"
  23c23
  < R Under development (unstable) (2012-05-22 r59405)
  ---
  > R version 2.14.0 (2011-10-31)
  29c29
  < [5] LC_MONETARY=C LC_MESSAGES=en_GB.utf-8
  ---
  > [5] LC_MONETARY=C LC_MESSAGES=en_US.UTF-8
  32c32
  < [11] LC_MEASUREMENT=en_GB.utf-8 LC_IDENTIFICATION=C
  ---
  > [11] LC_MEASUREMENT=en_US.UTF-8 LC_IDENTIFICATION=C
  Running ‘test.methods.haplo.glm.R’ [186s/248s]
  Comparing ‘test.methods.haplo.glm.Rout’ to ‘test.methods.haplo.glm.Rout.save’ ...12c12
  < [1] "LC_CTYPE=C;LC_NUMERIC=C;LC_TIME=C;LC_COLLATE=C;LC_MONETARY=C;LC_MESSAGES=en_GB.utf-8;LC_PAPER=C;LC_NAME=C;LC_ADDRESS=C;LC_TELEPHONE=C;LC_MEASUREMENT=en_GB.utf-8;LC_IDENTIFICATION=C"
  ---
  > [1] "LC_CTYPE=C;LC_NUMERIC=C;LC_TIME=C;LC_COLLATE=C;LC_MONETARY=C;LC_MESSAGES=en_US.UTF-8;LC_PAPER=C;LC_NAME=C;LC_ADDRESS=C;LC_TELEPHONE=C;LC_MEASUREMENT=en_US.UTF-8;LC_IDENTIFICATION=C"
  14c14
  < R Under development (unstable) (2012-05-22 r59405)
  ---
  > R version 2.14.0 (2011-10-31)
  20c20
  < [5] LC_MONETARY=C LC_MESSAGES=en_GB.utf-8
  ---
  > [5] LC_MONETARY=C LC_MESSAGES=en_US.UTF-8
  23c23
  < [11] LC_MEASUREMENT=en_GB.utf-8 LC_IDENTIFICATION=C
  ---
  > [11] LC_MEASUREMENT=en_US.UTF-8 LC_IDENTIFICATION=C
• checking PDF version of manual ... OK
  NOTE: There was 1 note.
  See
  ‘/data/gannet/tmp/ripley/R/packages/tests-devel/haplo.stats.Rcheck/00check.log’
  for details.