• using R version 3.0.1 Patched (2013-05-18 r62762)
• using platform: i386-pc-solaris2.10 (32-bit)
• using session charset: UTF-8
• 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 for hidden files and directories ... OK
• checking for portable file names ... OK
• checking for sufficient/correct file permissions ... OK
• checking whether package ‘haplo.stats’ can be installed ... OK
• checking installed package size ... OK
• checking package directory ... 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 ... 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 installed files from ‘inst/doc’ ... OK
• checking examples ... [31s/38s] OK
• checking for unstated dependencies in tests ... OK
• checking tests ... [262s/317s] OK
  Running ‘test.Ginv.R’ [14s/17s]
  Comparing ‘test.Ginv.Rout’ to ‘test.Ginv.Rout.save’ ... OK
  Running ‘test.haplo.em.R’ [65s/78s]
  Comparing ‘test.haplo.em.Rout’ to ‘test.haplo.em.Rout.save’ ...109c109
  < 7 1 f G h1 F g h1 0.42305
  ---
  > 5 1 F g h1 f G h1 0.42305
  113,115c113,115
  < 8 3 f G h2 F g h2 1.00000
  < 10 4 f g h2 f G h1 0.00000
  < 9 4 f g h1 f G h2 1.00000
  ---
  > 6 3 F g h2 f G h2 1.00000
  > 7 4 f G h1 f g h2 0.00000
  > 8 4 f G h2 f g h1 1.00000
  117,126c117,126
  < 8.1 6 f G h2 f G h1 1.00000
  < 8.2 7 f G h2 F g h2 1.00000
  < 5 8 F g h1 F G H 0.25095
  < 4 8 F g H F G h1 0.00000
  < 2.2 8 F G h1 F g h1 0.40212
  < 5.1 8 F g h1 F G h2 0.00000
  < 2.3 8 F G h1 F g h2 0.34694
  < 2.4 9 F G h1 f G h1 0.18357
  < 9.1 9 f g h1 F G h1 0.28450
  < 7.1 9 f G h1 F g h1 0.20861
  ---
  > 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
  > 2.2 8 F G h1 F g H 0.00000
  > 2.3 8 F G h1 F g h1 0.40212
  > 3 8 F G h2 F g h1 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
  128,140c128,140
  < 2.5 10 F G h1 f g h2 0.00000
  < 8.3 10 f G h2 F g h1 0.76212
  < 3 10 F G h2 f g h1 0.00000
  < 6 10 F g h2 f G h1 0.23788
  < 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
  < 4.1 12 F g H F G h1 0.00000
  < 2.6 12 F G h1 F g h1 0.40212
  < 5.3 12 F g h1 F G h2 0.00000
  < 6.1 12 F g h2 F G h1 0.34694
  < 7.2 13 f G h1 F G h1 0.18357
  < 2.7 13 F G h1 f g h1 0.28450
  ---
  > 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
  > 6.2 10 F g h2 f G h1 0.23788
  > 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
  143,144c143,144
  < 10.1 14 f g h2 f G h1 0.00000
  < 9.2 14 f g h1 f G h2 1.00000
  ---
  > 7.2 14 f G h1 f g h2 0.00000
  > 8.1 14 f G h2 f g h1 1.00000
  159c159
  < 1 1 7 5 0.42305
  ---
  > 1 1 5 7 0.42305
  163,165c163,165
  < 5 3 8 6 1.00000
  < 6 4 10 7 0.00000
  < 7 4 9 8 1.00000
  ---
  > 5 3 6 8 1.00000
  > 6 4 7 10 0.00000
  > 7 4 8 9 1.00000
  167,170c167,170
  < 9 6 8 7 1.00000
  < 10 7 8 6 1.00000
  < 11 8 5 1 0.25095
  < 12 8 4 2 0.00000
  ---
  > 9 6 7 8 1.00000
  > 10 7 6 8 1.00000
  > 11 8 1 5 0.25095
  > 12 8 2 4 0.00000
  172c172
  < 14 8 5 3 0.00000
  ---
  > 14 8 3 5 0.00000
  175,176c175,176
  < 17 9 9 2 0.28450
  < 18 9 7 5 0.20861
  ---
  > 17 9 2 9 0.28450
  > 18 9 5 7 0.20861
  179c179
  < 21 10 8 5 0.76212
  ---
  > 21 10 5 8 0.76212
  182c182
  < 24 11 8 2 1.00000
  ---
  > 24 11 2 8 1.00000
  185c185
  < 27 12 4 2 0.00000
  ---
  > 27 12 2 4 0.00000
  187,189c187,189
  < 29 12 5 3 0.00000
  < 30 12 6 2 0.34694
  < 31 13 7 2 0.18357
  ---
  > 29 12 3 5 0.00000
  > 30 12 2 6 0.34694
  > 31 13 2 7 0.18357
  193,194c193,194
  < 35 14 10 7 0.00000
  < 36 14 9 8 1.00000
  ---
  > 35 14 7 10 0.00000
  > 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
  483c483
  < 5 5 12212211 11121112 9.057297e-01 12212211 11121112
  ---
  > 5 5 11121112 12212211 9.057297e-01 12212211 11121112
  485,486c485,486
  < 7 6 21221112 11121112 1.000000e+00 21221112 11121112
  < 8 7 21221112 12212211 1.000000e+00 12212211 21221112
  ---
  > 7 6 11121112 21221112 1.000000e+00 21221112 11121112
  > 8 7 12212211 21221112 1.000000e+00 12212211 21221112
  490c490
  < 12 11 11122122 11121112 1.000000e+00 11121112 11122122
  ---
  > 12 11 11121112 11122122 1.000000e+00 11121112 11122122
  492c492
  < 14 13 12212211 11121112 9.057297e-01 11121112 12212211
  ---
  > 14 13 11121112 12212211 9.057297e-01 11121112 12212211
  494c494
  < 16 14 11121112 11112211 1.000000e+00 11121112 11112211
  ---
  > 16 14 11112211 11121112 1.000000e+00 11121112 11112211
  497c497
  < 19 16 22212212 11121112 1.097747e-07 12221112 21112212
  ---
  > 19 16 11121112 22212212 1.097747e-07 12221112 21112212
  502c502
  < 24 21 21221112 21112212 1.000000e+00 21221112 21112212
  ---
  > 24 21 21112212 21221112 1.000000e+00 21221112 21112212
  504c504
  < 26 23 12212211 11121112 9.057297e-01 11121112 12212211
  ---
  > 26 23 11121112 12212211 9.057297e-01 11121112 12212211
  510c510
  < 32 28 21221112 12212211 1.000000e+00 12212211 21221112
  ---
  > 32 28 12212211 21221112 1.000000e+00 12212211 21221112
  518c518
  < 40 36 12221112 11121112 1.000000e+00 11121112 12221112
  ---
  > 40 36 11121112 12221112 1.000000e+00 11121112 12221112
  522,523c522,523
  < 44 40 21112212 12212211 1.000000e+00 21112212 12212211
  < 45 40 22212212 11112211 1.142559e-08 21112212 12212211
  ---
  > 44 40 12212211 21112212 1.000000e+00 21112212 12212211
  > 45 40 11112211 22212212 1.142559e-08 21112212 12212211
  528c528
  < 50 44 21112212 12212211 1.000000e+00 21112212 12212211
  ---
  > 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’ [180s/219s]
  Comparing ‘test.methods.haplo.glm.Rout’ to ‘test.methods.haplo.glm.Rout.save’ ...180,181c180,181
  < hap.34 -4.058363e-08 3.310615e-08 1.093231e-08 -1.238479e-09
  < hap.77 -4.058363e-08 3.310615e-08 1.093231e-08 -1.238478e-09
  ---
  > hap.34 -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
  184a185
  > hap.rare -4.058363e-08 3.310615e-08 1.093231e-08 -1.238478e-09
  188d188
  < hap.rare -4.058363e-08 3.310615e-08 1.093231e-08 -1.238478e-09
  201,202c201,202
  < hap.34 -2.569090e-09 8.519475e-10 1.374934e-08 8.440416e-09
  < hap.77 -2.569089e-09 8.519477e-10 1.374934e-08 8.440416e-09
  ---
  > hap.34 -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 8.519475e-10 1.374934e-08 8.440416e-09
  < hap.rare -2.569089e-09 8.519475e-10 1.374934e-08 8.440416e-09
  209c207,209
  < hap.rare -2.569089e-09 8.519476e-10 1.374934e-08 8.440416e-09
  ---
  > 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
  215c215
  < geno.34 9.399166e-02 -3.651328e-06 -1.238478e-09 -1.238479e-09
  ---
  > geno.34 9.399166e-02 -3.651328e-06 -1.238478e-09 -1.238478e-09
  217c217
  < geno.78 8.481883e-02 -3.191332e-06 8.519475e-10 8.519476e-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
  257,259c257,259
  < geno.34 -1.238478e-09 -1.238479e-09 -1.238479e-09 -2.476957e-09
  < geno.77 -2.569089e-09 -2.569089e-09 -2.569089e-09 -5.138178e-09
  < geno.78 8.519475e-10 8.519473e-10 8.519475e-10 1.703895e-09
  ---
  > geno.34 -1.238478e-09 -1.238478e-09 -1.238478e-09 -2.476957e-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