• using R version 2.15.1 (2012-06-22)
• using platform: i386-apple-darwin9.8.0 (32-bit)
• using session charset: ASCII
• checking for file 'haplo.stats/DESCRIPTION' ... OK
• this is package 'haplo.stats' version '1.6.3'
• 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 '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
• loading checks for arch 'i386'
  ** 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
• loading checks for arch 'x86_64'
  ** 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 ... OK
• 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 ...
  ** running examples for arch 'i386' ... OK
  ** running examples for arch 'x86_64' ... OK
• checking for unstated dependencies in tests ... OK
• checking tests ...
  ** running tests for arch 'i386' OK
  Running 'test.Ginv.R'
  Comparing 'test.Ginv.Rout' to 'test.Ginv.Rout.save' ... OK
  Running 'test.haplo.em.R'
  Comparing 'test.haplo.em.Rout' to 'test.haplo.em.Rout.save' ...113c113
  < 8 3 f G h2 F g h2 1.00000
  ---
  > 6 3 F g h2 f G h2 1.00000
  115,119c115,119
  < 9 4 f g h1 f G h2 1.00000
  < 6 5 F g h2 F G H 1.00000
  < 8.1 6 f G h2 f G h1 1.00000
  < 8.2 7 f G h2 F g h2 1.00000
  < 1.1 8 F G H F g h1 0.25095
  ---
  > 8 4 f G h2 f g h1 1.00000
  > 1.1 5 F G H F g h2 1.00000
  > 7.1 6 f G h1 f G h2 1.00000
  > 6.1 7 F g h2 f G h2 1.00000
  > 1.2 8 F G H F g h1 0.25095
  121c121
  < 5.1 8 F g h1 F G h1 0.40212
  ---
  > 2.3 8 F G h1 F g h1 0.40212
  123,130c123,130
  < 6.1 8 F g h2 F G h1 0.34694
  < 7.1 9 f G h1 F G h1 0.18357
  < 9.1 9 f g h1 F G h1 0.28450
  < 5.2 9 F g h1 f G h1 0.20861
  < 9.2 9 f g h1 F g h1 0.32331
  < 2.3 10 F G h1 f g h2 0.00000
  < 8.3 10 f G h2 F g h1 0.76212
  < 9.3 10 f g h1 F G h2 0.00000
  ---
  > 2.4 8 F G h1 F g h2 0.34694
  > 2.5 9 F G h1 f G h1 0.18357
  > 2.6 9 F G h1 f g h1 0.28450
  > 5.1 9 F g h1 f G h1 0.20861
  > 5.2 9 F g h1 f g h1 0.32331
  > 2.7 10 F G h1 f g h2 0.00000
  > 5.3 10 F g h1 f G h2 0.76212
  > 3.1 10 F G h2 f g h1 0.00000
  132,144c132,144
  < 8.4 11 f G h2 F G h1 1.00000
  < 3.1 11 F G h2 f G h1 0.00000
  < 1.2 12 F G H F g h1 0.25095
  < 2.4 12 F G h1 F g H 0.00000
  < 5.3 12 F g h1 F G h1 0.40212
  < 5.4 12 F g h1 F G h2 0.00000
  < 6.3 12 F g h2 F G h1 0.34694
  < 7.2 13 f G h1 F G h1 0.18357
  < 9.4 13 f g h1 F G h1 0.28450
  < 5.5 13 F g h1 f G h1 0.20861
  < 5.6 13 F g h1 f g h1 0.32331
  < 7.3 14 f G h1 f g h2 0.00000
  < 9.5 14 f g h1 f G h2 1.00000
  ---
  > 2.8 11 F G h1 f G h2 1.00000
  > 3.2 11 F G h2 f G h1 0.00000
  > 1.3 12 F G H F g h1 0.25095
  > 2.9 12 F G h1 F g H 0.00000
  > 2.10 12 F G h1 F g h1 0.40212
  > 3.3 12 F G h2 F g h1 0.00000
  > 2.11 12 F G h1 F g h2 0.34694
  > 2.12 13 F G h1 f G h1 0.18357
  > 2.13 13 F G h1 f g h1 0.28450
  > 5.4 13 F g h1 f G h1 0.20861
  > 5.5 13 F g h1 f g h1 0.32331
  > 7.2 14 f G h1 f g h2 0.00000
  > 8.1 14 f G h2 f g h1 1.00000
  163c163
  < 5 3 8 6 1.00000
  ---
  > 5 3 6 8 1.00000
  165,168c165,168
  < 7 4 9 8 1.00000
  < 8 5 6 1 1.00000
  < 9 6 8 7 1.00000
  < 10 7 8 6 1.00000
  ---
  > 7 4 8 9 1.00000
  > 8 5 1 6 1.00000
  > 9 6 7 8 1.00000
  > 10 7 6 8 1.00000
  171c171
  < 13 8 5 2 0.40212
  ---
  > 13 8 2 5 0.40212
  173,175c173,175
  < 15 8 6 2 0.34694
  < 16 9 7 2 0.18357
  < 17 9 9 2 0.28450
  ---
  > 15 8 2 6 0.34694
  > 16 9 2 7 0.18357
  > 17 9 2 9 0.28450
  177c177
  < 19 9 9 5 0.32331
  ---
  > 19 9 5 9 0.32331
  179,180c179,180
  < 21 10 8 5 0.76212
  < 22 10 9 3 0.00000
  ---
  > 21 10 5 8 0.76212
  > 22 10 3 9 0.00000
  182c182
  < 24 11 8 2 1.00000
  ---
  > 24 11 2 8 1.00000
  186,190c186,190
  < 28 12 5 2 0.40212
  < 29 12 5 3 0.00000
  < 30 12 6 2 0.34694
  < 31 13 7 2 0.18357
  < 32 13 9 2 0.28450
  ---
  > 28 12 2 5 0.40212
  > 29 12 3 5 0.00000
  > 30 12 2 6 0.34694
  > 31 13 2 7 0.18357
  > 32 13 2 9 0.28450
  194c194
  < 36 14 9 8 1.00000
  ---
  > 36 14 8 9 1.00000
  480c480
  < 2 2 12212211 11122122 1.000000e+00 12212211 11122122
  ---
  > 2 2 11122122 12212211 1.000000e+00 12212211 11122122
  484,486c484,486
  < 6 5 12221112 11112211 9.427027e-02 12212211 11121112
  < 7 6 21221112 11121112 1.000000e+00 21221112 11121112
  < 8 7 21221112 12212211 1.000000e+00 12212211 21221112
  ---
  > 6 5 11112211 12221112 9.427027e-02 12212211 11121112
  > 7 6 11121112 21221112 1.000000e+00 21221112 11121112
  > 8 7 12212211 21221112 1.000000e+00 12212211 21221112
  488c488
  < 10 9 11122122 11121112 1.000000e+00 11121112 11122122
  ---
  > 10 9 11121112 11122122 1.000000e+00 11121112 11122122
  490c490
  < 12 11 11122122 11121112 1.000000e+00 11121112 11122122
  ---
  > 12 11 11121112 11122122 1.000000e+00 11121112 11122122
  493c493
  < 15 13 12221112 11112211 9.427027e-02 11121112 12212211
  ---
  > 15 13 11112211 12221112 9.427027e-02 11121112 12212211
  496c496
  < 18 16 21112212 12221112 9.999999e-01 12221112 21112212
  ---
  > 18 16 12221112 21112212 9.999999e-01 12221112 21112212
  498c498
  < 20 17 12212211 11122122 1.000000e+00 12212211 11122122
  ---
  > 20 17 11122122 12212211 1.000000e+00 12212211 11122122
  500c500
  < 22 19 12221112 11121112 1.000000e+00 12221112 11121112
  ---
  > 22 19 11121112 12221112 1.000000e+00 12221112 11121112
  513c513
  < 35 31 11122122 11121112 1.000000e+00 11122122 11121112
  ---
  > 35 31 11121112 11122122 1.000000e+00 11122122 11121112
  515c515
  < 37 33 21221112 11122122 1.000000e+00 11122122 21221112
  ---
  > 37 33 11122122 21221112 1.000000e+00 11122122 21221112
  517c517
  < 39 35 21221112 21112212 1.000000e+00 21221112 21112212
  ---
  > 39 35 21112212 21221112 1.000000e+00 21221112 21112212
  524c524
  < 46 41 12212211 11121112 9.057297e-01 12212211 11121112
  ---
  > 46 41 11121112 12212211 9.057297e-01 12212211 11121112
  527,528c527,528
  < 49 43 11122122 11121112 1.000000e+00 11121112 11122122
  < 50 44 21112212 12212211 1.000000e+00 21112212 12212211
  ---
  > 49 43 11121112 11122122 1.000000e+00 11121112 11122122
  > 50 44 12212211 21112212 1.000000e+00 21112212 12212211
  Running 'test.haplo.power.R'
  Comparing 'test.haplo.power.Rout' to 'test.haplo.power.Rout.save' ... OK
  Running 'test.methods.haplo.glm.R'
  Comparing 'test.methods.haplo.glm.Rout' to 'test.methods.haplo.glm.Rout.save' ...181c181
  < hap.77 -4.058363e-08 3.310615e-08 1.093231e-08 -1.238478e-09
  ---
  > hap.77 -4.058363e-08 3.310615e-08 1.093231e-08 -1.238479e-09
  202c202
  < hap.77 -2.569089e-09 8.519476e-10 1.374934e-08 8.440416e-09
  ---
  > hap.77 -2.569089e-09 8.519475e-10 1.374934e-08 8.440416e-09
  206,207d205
  < hap.rare -2.569089e-09 8.519474e-10 1.374934e-08 8.440416e-09
  < hap.rare -2.569089e-09 8.519473e-10 1.374934e-08 8.440416e-09
  209,210c207,210
  < hap.rare -2.569089e-09 8.519477e-10 1.374934e-08 8.440416e-09
  < hap.rare -5.138179e-09 1.703895e-09 2.749868e-08 1.688083e-08
  ---
  > hap.rare -2.569089e-09 8.519473e-10 1.374934e-08 8.440416e-09
  > hap.rare -2.569089e-09 8.519475e-10 1.374934e-08 8.440416e-09
  > hap.rare -2.569089e-09 8.519474e-10 1.374934e-08 8.440416e-09
  > hap.rare -5.138178e-09 1.703895e-09 2.749868e-08 1.688083e-08
  217c217
  < geno.78 8.481883e-02 -3.191332e-06 8.519474e-10 8.519474e-10
  ---
  > geno.78 8.481883e-02 -3.191332e-06 8.519477e-10 8.519475e-10
  237,238c237,238
  < geno.77 3.153900e-07 -4.343015e-06 -1.246208e-05 -2.569089e-09
  < geno.78 2.239790e-07 -2.129393e-06 -8.450638e-06 8.519475e-10
  ---
  > geno.77 3.153900e-07 -4.343015e-06 -1.246208e-05 -2.569090e-09
  > geno.78 2.239790e-07 -2.129393e-06 -8.450638e-06 8.519474e-10
  258,259c258,259
  < geno.77 -2.569089e-09 -2.569089e-09 -2.569089e-09 -5.138178e-09
  < geno.78 8.519476e-10 8.519472e-10 8.519473e-10 1.703895e-09
  ---
  > geno.77 -2.569089e-09 -2.569089e-09 -2.569089e-09 -5.138179e-09
  > geno.78 8.519475e-10 8.519473e-10 8.519475e-10 1.703894e-09
  ** running tests for arch 'x86_64' OK
  Running 'test.Ginv.R'
  Comparing 'test.Ginv.Rout' to 'test.Ginv.Rout.save' ... OK
  Running 'test.haplo.em.R'
  Comparing 'test.haplo.em.Rout' to 'test.haplo.em.Rout.save' ...113c113
  < 8 3 f G h2 F g h2 1.00000
  ---
  > 6 3 F g h2 f G h2 1.00000
  115,119c115,119
  < 9 4 f g h1 f G h2 1.00000
  < 6 5 F g h2 F G H 1.00000
  < 8.1 6 f G h2 f G h1 1.00000
  < 8.2 7 f G h2 F g h2 1.00000
  < 1.1 8 F G H F g h1 0.25095
  ---
  > 8 4 f G h2 f g h1 1.00000
  > 1.1 5 F G H F g h2 1.00000
  > 7.1 6 f G h1 f G h2 1.00000
  > 6.1 7 F g h2 f G h2 1.00000
  > 1.2 8 F G H F g h1 0.25095
  121c121
  < 5.1 8 F g h1 F G h1 0.40212
  ---
  > 2.3 8 F G h1 F g h1 0.40212
  123,130c123,130
  < 6.1 8 F g h2 F G h1 0.34694
  < 7.1 9 f G h1 F G h1 0.18357
  < 9.1 9 f g h1 F G h1 0.28450
  < 5.2 9 F g h1 f G h1 0.20861
  < 9.2 9 f g h1 F g h1 0.32331
  < 2.3 10 F G h1 f g h2 0.00000
  < 8.3 10 f G h2 F g h1 0.76212
  < 9.3 10 f g h1 F G h2 0.00000
  ---
  > 2.4 8 F G h1 F g h2 0.34694
  > 2.5 9 F G h1 f G h1 0.18357
  > 2.6 9 F G h1 f g h1 0.28450
  > 5.1 9 F g h1 f G h1 0.20861
  > 5.2 9 F g h1 f g h1 0.32331
  > 2.7 10 F G h1 f g h2 0.00000
  > 5.3 10 F g h1 f G h2 0.76212
  > 3.1 10 F G h2 f g h1 0.00000
  132,144c132,144
  < 8.4 11 f G h2 F G h1 1.00000
  < 3.1 11 F G h2 f G h1 0.00000
  < 1.2 12 F G H F g h1 0.25095
  < 2.4 12 F G h1 F g H 0.00000
  < 5.3 12 F g h1 F G h1 0.40212
  < 5.4 12 F g h1 F G h2 0.00000
  < 6.3 12 F g h2 F G h1 0.34694
  < 7.2 13 f G h1 F G h1 0.18357
  < 9.4 13 f g h1 F G h1 0.28450
  < 5.5 13 F g h1 f G h1 0.20861
  < 5.6 13 F g h1 f g h1 0.32331
  < 7.3 14 f G h1 f g h2 0.00000
  < 9.5 14 f g h1 f G h2 1.00000
  ---
  > 2.8 11 F G h1 f G h2 1.00000
  > 3.2 11 F G h2 f G h1 0.00000
  > 1.3 12 F G H F g h1 0.25095
  > 2.9 12 F G h1 F g H 0.00000
  > 2.10 12 F G h1 F g h1 0.40212
  > 3.3 12 F G h2 F g h1 0.00000
  > 2.11 12 F G h1 F g h2 0.34694
  > 2.12 13 F G h1 f G h1 0.18357
  > 2.13 13 F G h1 f g h1 0.28450
  > 5.4 13 F g h1 f G h1 0.20861
  > 5.5 13 F g h1 f g h1 0.32331
  > 7.2 14 f G h1 f g h2 0.00000
  > 8.1 14 f G h2 f g h1 1.00000
  163c163
  < 5 3 8 6 1.00000
  ---
  > 5 3 6 8 1.00000
  165,168c165,168
  < 7 4 9 8 1.00000
  < 8 5 6 1 1.00000
  < 9 6 8 7 1.00000
  < 10 7 8 6 1.00000
  ---
  > 7 4 8 9 1.00000
  > 8 5 1 6 1.00000
  > 9 6 7 8 1.00000
  > 10 7 6 8 1.00000
  171c171
  < 13 8 5 2 0.40212
  ---
  > 13 8 2 5 0.40212
  173,175c173,175
  < 15 8 6 2 0.34694
  < 16 9 7 2 0.18357
  < 17 9 9 2 0.28450
  ---
  > 15 8 2 6 0.34694
  > 16 9 2 7 0.18357
  > 17 9 2 9 0.28450
  177c177
  < 19 9 9 5 0.32331
  ---
  > 19 9 5 9 0.32331
  179,180c179,180
  < 21 10 8 5 0.76212
  < 22 10 9 3 0.00000
  ---
  > 21 10 5 8 0.76212
  > 22 10 3 9 0.00000
  182c182
  < 24 11 8 2 1.00000
  ---
  > 24 11 2 8 1.00000
  186,190c186,190
  < 28 12 5 2 0.40212
  < 29 12 5 3 0.00000
  < 30 12 6 2 0.34694
  < 31 13 7 2 0.18357
  < 32 13 9 2 0.28450
  ---
  > 28 12 2 5 0.40212
  > 29 12 3 5 0.00000
  > 30 12 2 6 0.34694
  > 31 13 2 7 0.18357
  > 32 13 2 9 0.28450
  194c194
  < 36 14 9 8 1.00000
  ---
  > 36 14 8 9 1.00000
  480c480
  < 2 2 12212211 11122122 1.000000e+00 12212211 11122122
  ---
  > 2 2 11122122 12212211 1.000000e+00 12212211 11122122
  484,486c484,486
  < 6 5 12221112 11112211 9.427027e-02 12212211 11121112
  < 7 6 21221112 11121112 1.000000e+00 21221112 11121112
  < 8 7 21221112 12212211 1.000000e+00 12212211 21221112
  ---
  > 6 5 11112211 12221112 9.427027e-02 12212211 11121112
  > 7 6 11121112 21221112 1.000000e+00 21221112 11121112
  > 8 7 12212211 21221112 1.000000e+00 12212211 21221112
  488c488
  < 10 9 11122122 11121112 1.000000e+00 11121112 11122122
  ---
  > 10 9 11121112 11122122 1.000000e+00 11121112 11122122
  490c490
  < 12 11 11122122 11121112 1.000000e+00 11121112 11122122
  ---
  > 12 11 11121112 11122122 1.000000e+00 11121112 11122122
  493c493
  < 15 13 12221112 11112211 9.427027e-02 11121112 12212211
  ---
  > 15 13 11112211 12221112 9.427027e-02 11121112 12212211
  496c496
  < 18 16 21112212 12221112 9.999999e-01 12221112 21112212
  ---
  > 18 16 12221112 21112212 9.999999e-01 12221112 21112212
  498c498
  < 20 17 12212211 11122122 1.000000e+00 12212211 11122122
  ---
  > 20 17 11122122 12212211 1.000000e+00 12212211 11122122
  500c500
  < 22 19 12221112 11121112 1.000000e+00 12221112 11121112
  ---
  > 22 19 11121112 12221112 1.000000e+00 12221112 11121112
  513c513
  < 35 31 11122122 11121112 1.000000e+00 11122122 11121112
  ---
  > 35 31 11121112 11122122 1.000000e+00 11122122 11121112
  515c515
  < 37 33 21221112 11122122 1.000000e+00 11122122 21221112
  ---
  > 37 33 11122122 21221112 1.000000e+00 11122122 21221112
  517c517
  < 39 35 21221112 21112212 1.000000e+00 21221112 21112212
  ---
  > 39 35 21112212 21221112 1.000000e+00 21221112 21112212
  524c524
  < 46 41 12212211 11121112 9.057297e-01 12212211 11121112
  ---
  > 46 41 11121112 12212211 9.057297e-01 12212211 11121112
  527,528c527,528
  < 49 43 11122122 11121112 1.000000e+00 11121112 11122122
  < 50 44 21112212 12212211 1.000000e+00 21112212 12212211
  ---
  > 49 43 11121112 11122122 1.000000e+00 11121112 11122122
  > 50 44 12212211 21112212 1.000000e+00 21112212 12212211
  Running 'test.haplo.power.R'
  Comparing 'test.haplo.power.Rout' to 'test.haplo.power.Rout.save' ... OK
  Running 'test.methods.haplo.glm.R'
  Comparing 'test.methods.haplo.glm.Rout' to 'test.methods.haplo.glm.Rout.save' ...181c181
  < hap.77 -4.058363e-08 3.310615e-08 1.093231e-08 -1.238478e-09
  ---
  > hap.77 -4.058363e-08 3.310615e-08 1.093231e-08 -1.238479e-09
  202c202
  < hap.77 -2.569089e-09 8.519476e-10 1.374934e-08 8.440416e-09
  ---
  > hap.77 -2.569089e-09 8.519475e-10 1.374934e-08 8.440416e-09
  206,207d205
  < hap.rare -2.569089e-09 8.519474e-10 1.374934e-08 8.440416e-09
  < hap.rare -2.569089e-09 8.519473e-10 1.374934e-08 8.440416e-09
  209,210c207,210
  < hap.rare -2.569089e-09 8.519477e-10 1.374934e-08 8.440416e-09
  < hap.rare -5.138179e-09 1.703895e-09 2.749868e-08 1.688083e-08
  ---
  > hap.rare -2.569089e-09 8.519473e-10 1.374934e-08 8.440416e-09
  > hap.rare -2.569089e-09 8.519475e-10 1.374934e-08 8.440416e-09
  > hap.rare -2.569089e-09 8.519474e-10 1.374934e-08 8.440416e-09
  > hap.rare -5.138178e-09 1.703895e-09 2.749868e-08 1.688083e-08
  217c217
  < geno.78 8.481883e-02 -3.191332e-06 8.519474e-10 8.519474e-10
  ---
  > geno.78 8.481883e-02 -3.191332e-06 8.519477e-10 8.519475e-10
  237,238c237,238
  < geno.77 3.153900e-07 -4.343015e-06 -1.246208e-05 -2.569089e-09
  < geno.78 2.239790e-07 -2.129393e-06 -8.450638e-06 8.519475e-10
  ---
  > geno.77 3.153900e-07 -4.343015e-06 -1.246208e-05 -2.569090e-09
  > geno.78 2.239790e-07 -2.129393e-06 -8.450638e-06 8.519474e-10
  258,259c258,259
  < geno.77 -2.569089e-09 -2.569089e-09 -2.569089e-09 -5.138178e-09
  < geno.78 8.519476e-10 8.519472e-10 8.519473e-10 1.703895e-09
  ---
  > geno.77 -2.569089e-09 -2.569089e-09 -2.569089e-09 -5.138179e-09
  > geno.78 8.519475e-10 8.519473e-10 8.519475e-10 1.703894e-09
• checking PDF version of manual ... OK
• elapsed time (check, wall clock): 5:08