• using R Under development (unstable) (2012-02-27 r58511)
• using platform: x86_64-pc-mingw32 (64-bit)
• using session charset: ISO8859-1
• 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 whether package 'haplo.stats' can be installed ... OK
• checking installed package size ... OK
• checking package directory ... OK
• checking for portable file names ... 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 'x64'
  ** 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 ... 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 ... NOTE
  File 'd:/Rcompile/CRANpkg/lib/2.15/haplo.stats/libs/i386/haplo.stats.dll':
  Found 'abort', possibly from 'abort' (C)
  File 'd:/Rcompile/CRANpkg/lib/2.15/haplo.stats/libs/x64/haplo.stats.dll':
  Found 'abort', possibly from 'abort' (C)
  
  Compiled code should not call functions which might terminate R nor
  write to stdout/stderr instead of to the console. The detected symbols
  are linked into the code but might come from libraries and not actually
  be called.
  
  See 'Writing portable packages' in the 'Writing R Extensions' manual.
• 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 'x64' ... 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' ...62,66c62,66
  < [1,] 129.301815287 2.020565287 -10.048992 -4.276906e-03 1.4289919
  < [2,] 2.020565287 129.301815287 -10.048992 -4.276902e-03 1.4289919
  < [3,] -10.048991557 -10.048991557 3239.425101 4.098196e+00 -10.6405650
  < [4,] -0.004276905 -0.004276849 4.098196 8.731269e+03 -0.5958503
  < [5,] 1.428991853 1.428991853 -10.640565 -5.958503e-01 255.3999184
  ---
  > [1,] 129.30181529 2.020565287 -10.048992 -4.276933e-03 1.4289919
  > [2,] 2.02056529 129.301815287 -10.048992 -4.276852e-03 1.4289919
  > [3,] -10.04899156 -10.048991553 3239.425101 4.098196e+00 -10.6405650
  > [4,] -0.00427691 -0.004276945 4.098196 8.731269e+03 -0.5958503
  > [5,] 1.42899185 1.428991852 -10.640565 -5.958504e-01 255.3999184
  Running 'test.haplo.em.R'
  Comparing 'test.haplo.em.Rout' to 'test.haplo.em.Rout.save' ...14c14
  < [1] "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"
  16,17c16,17
  < R Under development (unstable) (2012-02-27 r58511)
  < Platform: i386-pc-mingw32/i386 (32-bit)
  ---
  > R version 2.14.0 (2011-10-31)
  > Platform: x86_64-unknown-linux-gnu (64-bit)
  20c20,25
  < [1] C
  ---
  > [1] LC_CTYPE=C LC_NUMERIC=C
  > [3] LC_TIME=C LC_COLLATE=C
  > [5] LC_MONETARY=C LC_MESSAGES=en_US.UTF-8
  > [7] LC_PAPER=C LC_NAME=C
  > [9] LC_ADDRESS=C LC_TELEPHONE=C
  > [11] LC_MEASUREMENT=en_US.UTF-8 LC_IDENTIFICATION=C
  101c106
  < 2 F G h1 0.14328
  ---
  > 2 F G h1 0.14326
  104,106c109,111
  < 5 F g h1 0.16266
  < 6 F g h2 0.14043
  < 7 f G h1 0.08732
  ---
  > 5 F g h1 0.16268
  > 6 F g h2 0.14042
  > 7 f G h1 0.08733
  108c113
  < 9 f g h1 0.13547
  ---
  > 9 f g h1 0.13545
  120,123c125,128
  < 5 1 F g h1 f G h1 0.42280
  < 9 1 f g h1 F G h1 0.57720
  < 4 2 F g H F G h1 0.00000
  < 5.1 2 F g h1 F G H 1.00000
  ---
  > 5 1 F g h1 f G h1 0.42305
  > 2 1 F G h1 f g h1 0.57695
  > 2.1 2 F G h1 F g H 0.00000
  > 1 2 F G H F g h1 1.00000
  125c130
  < 10 4 f g h2 f G h1 0.00000
  ---
  > 7 4 f G h1 f g h2 0.00000
  127,132c132,137
  < 6.1 5 F g h2 F G H 1.00000
  < 7 6 f G h1 f G h2 1.00000
  < 8.1 7 f G h2 F g h2 1.00000
  < 5.2 8 F g h1 F G H 0.25084
  < 4.1 8 F g H F G h1 0.00000
  < 5.3 8 F g h1 F G h1 0.40211
  ---
  > 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
  > 2.2 8 F G h1 F g H 0.00000
  > 2.3 8 F G h1 F g h1 0.40212
  134,140c139,145
  < 6.2 8 F g h2 F G h1 0.34704
  < 2 9 F G h1 f G h1 0.18357
  < 7.1 9 f G h1 F g h1 0.20850
  < 2.1 9 F G h1 f g h1 0.28464
  < 9.1 9 f g h1 F g h1 0.32330
  < 2.2 10 F G h1 f g h2 0.00000
  < 5.4 10 F g h1 f G h2 0.76211
  ---
  > 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
  142,155c147,160
  < 7.2 10 f G h1 F g h2 0.23789
  < 2.3 11 F G h1 f G h2 1.00000
  < 7.3 11 f G h1 F G h2 0.00000
  < 1 12 F G H F g h1 0.25084
  < 2.4 12 F G h1 F g H 0.00000
  < 2.5 12 F G h1 F g h1 0.40211
  < 3.2 12 F G h2 F g h1 0.00000
  < 2.6 12 F G h1 F g h2 0.34704
  < 7.4 13 f G h1 F G h1 0.18357
  < 7.5 13 f G h1 F g h1 0.20850
  < 9.2 13 f g h1 F G h1 0.28464
  < 5.5 13 F g h1 f g h1 0.32330
  < 7.6 14 f G h1 f g h2 0.00000
  < 8.2 14 f G h2 f g h1 1.00000
  ---
  > 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
  > 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
  170,173c175,178
  < 1 1 5 7 0.42280
  < 2 1 9 2 0.57720
  < 3 2 4 2 0.00000
  < 4 2 5 1 1.00000
  ---
  > 1 1 5 7 0.42305
  > 2 1 2 9 0.57695
  > 3 2 2 4 0.00000
  > 4 2 1 5 1.00000
  175c180
  < 6 4 10 7 0.00000
  ---
  > 6 4 7 10 0.00000
  177c182
  < 8 5 6 1 1.00000
  ---
  > 8 5 1 6 1.00000
  179,182c184,187
  < 10 7 8 6 1.00000
  < 11 8 5 1 0.25084
  < 12 8 4 2 0.00000
  < 13 8 5 2 0.40211
  ---
  > 10 7 6 8 1.00000
  > 11 8 1 5 0.25095
  > 12 8 2 4 0.00000
  > 13 8 2 5 0.40212
  184c189
  < 15 8 6 2 0.34704
  ---
  > 15 8 2 6 0.34694
  186,188c191,193
  < 17 9 7 5 0.20850
  < 18 9 2 9 0.28464
  < 19 9 9 5 0.32330
  ---
  > 17 9 2 9 0.28450
  > 18 9 5 7 0.20861
  > 19 9 5 9 0.32331
  190c195
  < 21 10 5 8 0.76211
  ---
  > 21 10 5 8 0.76212
  192c197
  < 23 10 7 6 0.23789
  ---
  > 23 10 6 7 0.23788
  194,195c199,200
  < 25 11 7 3 0.00000
  < 26 12 1 5 0.25084
  ---
  > 25 11 3 7 0.00000
  > 26 12 1 5 0.25095
  197c202
  < 28 12 2 5 0.40211
  ---
  > 28 12 2 5 0.40212
  199,203c204,208
  < 30 12 2 6 0.34704
  < 31 13 7 2 0.18357
  < 32 13 7 5 0.20850
  < 33 13 9 2 0.28464
  < 34 13 5 9 0.32330
  ---
  > 30 12 2 6 0.34694
  > 31 13 2 7 0.18357
  > 32 13 2 9 0.28450
  > 33 13 5 7 0.20861
  > 34 13 5 9 0.32331
  490c495
  < 1 1 21221112 11121112 1.000000e+00 21221112 11121112
  ---
  > 1 1 11121112 21221112 1.000000e+00 21221112 11121112
  494c499
  < 5 5 12212211 11121112 9.057297e-01 12212211 11121112
  ---
  > 5 5 11121112 12212211 9.057297e-01 12212211 11121112
  500c505
  < 11 10 12221112 12212211 1.000000e+00 12212211 12221112
  ---
  > 11 10 12212211 12221112 1.000000e+00 12212211 12221112
  505c510
  < 16 14 11121112 11112211 1.000000e+00 11121112 11112211
  ---
  > 16 14 11112211 11121112 1.000000e+00 11121112 11112211
  509c514
  < 20 17 12212211 11122122 1.000000e+00 12212211 11122122
  ---
  > 20 17 11122122 12212211 1.000000e+00 12212211 11122122
  514,515c519,520
  < 25 22 11122122 11121112 1.000000e+00 11121112 11122122
  < 26 23 12212211 11121112 9.057297e-01 11121112 12212211
  ---
  > 25 22 11121112 11122122 1.000000e+00 11121112 11122122
  > 26 23 11121112 12212211 9.057297e-01 11121112 12212211
  518c523
  < 29 25 21112212 11122122 1.000000e+00 11122122 21112212
  ---
  > 29 25 11122122 21112212 1.000000e+00 11122122 21112212
  524,525c529,530
  < 35 31 11122122 11121112 1.000000e+00 11122122 11121112
  < 36 32 21112212 11122122 1.000000e+00 11122122 21112212
  ---
  > 35 31 11121112 11122122 1.000000e+00 11122122 11121112
  > 36 32 11122122 21112212 1.000000e+00 11122122 21112212
  527,529c532,534
  < 38 34 11122122 11121112 1.000000e+00 11122122 11121112
  < 39 35 21221112 21112212 1.000000e+00 21221112 21112212
  < 40 36 12221112 11121112 1.000000e+00 11121112 12221112
  ---
  > 38 34 11121112 11122122 1.000000e+00 11122122 11121112
  > 39 35 21112212 21221112 1.000000e+00 21221112 21112212
  > 40 36 11121112 12221112 1.000000e+00 11121112 12221112
  533,535c538,540
  < 44 40 21112212 12212211 1.000000e+00 21112212 12212211
  < 45 40 22212212 11112211 1.142559e-08 21112212 12212211
  < 46 41 12212211 11121112 9.057297e-01 12212211 11121112
  ---
  > 44 40 12212211 21112212 1.000000e+00 21112212 12212211
  > 45 40 11112211 22212212 1.142559e-08 21112212 12212211
  > 46 41 11121112 12212211 9.057297e-01 12212211 11121112
  539c544
  < 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' ...21c21
  < [1] "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"
  23,24c23,24
  < R Under development (unstable) (2012-02-27 r58511)
  < Platform: i386-pc-mingw32/i386 (32-bit)
  ---
  > R version 2.14.0 (2011-10-31)
  > Platform: x86_64-unknown-linux-gnu (64-bit)
  27c27,32
  < [1] C
  ---
  > [1] LC_CTYPE=C LC_NUMERIC=C
  > [3] LC_TIME=C LC_COLLATE=C
  > [5] LC_MONETARY=C LC_MESSAGES=en_US.UTF-8
  > [7] LC_PAPER=C LC_NAME=C
  > [9] LC_ADDRESS=C LC_TELEPHONE=C
  > [11] LC_MEASUREMENT=en_US.UTF-8 LC_IDENTIFICATION=C
  Running 'test.methods.haplo.glm.R'
  Comparing 'test.methods.haplo.glm.Rout' to 'test.methods.haplo.glm.Rout.save' ...12c12
  < [1] "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"
  14,15c14,15
  < R Under development (unstable) (2012-02-27 r58511)
  < Platform: i386-pc-mingw32/i386 (32-bit)
  ---
  > R version 2.14.0 (2011-10-31)
  > Platform: x86_64-unknown-linux-gnu (64-bit)
  18c18,23
  < [1] C
  ---
  > [1] LC_CTYPE=C LC_NUMERIC=C
  > [3] LC_TIME=C LC_COLLATE=C
  > [5] LC_MONETARY=C LC_MESSAGES=en_US.UTF-8
  > [7] LC_PAPER=C LC_NAME=C
  > [9] LC_ADDRESS=C LC_TELEPHONE=C
  > [11] LC_MEASUREMENT=en_US.UTF-8 LC_IDENTIFICATION=C
  187c192
  < geno.138 -2.351610e-01 3.135953e-02 1.061650e-01 6.035697e-02
  ---
  > geno.138 -2.351610e-01 3.135952e-02 1.061650e-01 6.035697e-02
  196c201
  < hap.rare -4.058363e-08 3.310615e-08 1.093231e-08 -1.238478e-09
  ---
  > hap.rare -4.058363e-08 3.310615e-08 1.093231e-08 -1.238479e-09
  211c216
  < hap.34 -2.569089e-09 8.519472e-10 1.374934e-08 8.440416e-09
  ---
  > hap.34 -2.569089e-09 8.519476e-10 1.374934e-08 8.440416e-09
  216c221,222
  < hap.rare -2.569089e-09 8.519475e-10 1.374934e-08 8.440416e-09
  ---
  > 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
  219,220c225
  < hap.rare -2.569089e-09 8.519475e-10 1.374934e-08 8.440416e-09
  < hap.rare -5.138179e-09 1.703895e-09 2.749868e-08 1.688083e-08
  ---
  > hap.rare -5.138178e-09 1.703895e-09 2.749868e-08 1.688083e-08
  227c232
  < geno.78 8.481883e-02 -3.191332e-06 8.519474e-10 8.519471e-10
  ---
  > geno.78 8.481883e-02 -3.191332e-06 8.519477e-10 8.519475e-10
  247,248c252,253
  < 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
  269c274
  < geno.78 8.519476e-10 8.519474e-10 8.519475e-10 1.703895e-09
  ---
  > geno.78 8.519475e-10 8.519473e-10 8.519475e-10 1.703894e-09
  ** running tests for arch 'x64' 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' ...14c14
  < [1] "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"
  16,17c16,17
  < R Under development (unstable) (2012-02-27 r58511)
  < Platform: x86_64-pc-mingw32/x64 (64-bit)
  ---
  > R version 2.14.0 (2011-10-31)
  > Platform: x86_64-unknown-linux-gnu (64-bit)
  20c20,25
  < [1] C
  ---
  > [1] LC_CTYPE=C LC_NUMERIC=C
  > [3] LC_TIME=C LC_COLLATE=C
  > [5] LC_MONETARY=C LC_MESSAGES=en_US.UTF-8
  > [7] LC_PAPER=C LC_NAME=C
  > [9] LC_ADDRESS=C LC_TELEPHONE=C
  > [11] LC_MEASUREMENT=en_US.UTF-8 LC_IDENTIFICATION=C
  101c106
  < 2 F G h1 0.14328
  ---
  > 2 F G h1 0.14326
  104,106c109,111
  < 5 F g h1 0.16266
  < 6 F g h2 0.14043
  < 7 f G h1 0.08732
  ---
  > 5 F g h1 0.16268
  > 6 F g h2 0.14042
  > 7 f G h1 0.08733
  108c113
  < 9 f g h1 0.13547
  ---
  > 9 f g h1 0.13545
  120,123c125,128
  < 5 1 F g h1 f G h1 0.42280
  < 9 1 f g h1 F G h1 0.57720
  < 4 2 F g H F G h1 0.00000
  < 5.1 2 F g h1 F G H 1.00000
  ---
  > 5 1 F g h1 f G h1 0.42305
  > 2 1 F G h1 f g h1 0.57695
  > 2.1 2 F G h1 F g H 0.00000
  > 1 2 F G H F g h1 1.00000
  125c130
  < 10 4 f g h2 f G h1 0.00000
  ---
  > 7 4 f G h1 f g h2 0.00000
  127,132c132,137
  < 6.1 5 F g h2 F G H 1.00000
  < 7 6 f G h1 f G h2 1.00000
  < 8.1 7 f G h2 F g h2 1.00000
  < 5.2 8 F g h1 F G H 0.25084
  < 4.1 8 F g H F G h1 0.00000
  < 5.3 8 F g h1 F G h1 0.40211
  ---
  > 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
  > 2.2 8 F G h1 F g H 0.00000
  > 2.3 8 F G h1 F g h1 0.40212
  134,140c139,145
  < 6.2 8 F g h2 F G h1 0.34704
  < 2 9 F G h1 f G h1 0.18357
  < 7.1 9 f G h1 F g h1 0.20850
  < 2.1 9 F G h1 f g h1 0.28464
  < 9.1 9 f g h1 F g h1 0.32330
  < 2.2 10 F G h1 f g h2 0.00000
  < 5.4 10 F g h1 f G h2 0.76211
  ---
  > 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
  142,155c147,160
  < 7.2 10 f G h1 F g h2 0.23789
  < 2.3 11 F G h1 f G h2 1.00000
  < 7.3 11 f G h1 F G h2 0.00000
  < 1 12 F G H F g h1 0.25084
  < 2.4 12 F G h1 F g H 0.00000
  < 2.5 12 F G h1 F g h1 0.40211
  < 3.2 12 F G h2 F g h1 0.00000
  < 2.6 12 F G h1 F g h2 0.34704
  < 7.4 13 f G h1 F G h1 0.18357
  < 7.5 13 f G h1 F g h1 0.20850
  < 9.2 13 f g h1 F G h1 0.28464
  < 5.5 13 F g h1 f g h1 0.32330
  < 7.6 14 f G h1 f g h2 0.00000
  < 8.2 14 f G h2 f g h1 1.00000
  ---
  > 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
  > 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
  170,173c175,178
  < 1 1 5 7 0.42280
  < 2 1 9 2 0.57720
  < 3 2 4 2 0.00000
  < 4 2 5 1 1.00000
  ---
  > 1 1 5 7 0.42305
  > 2 1 2 9 0.57695
  > 3 2 2 4 0.00000
  > 4 2 1 5 1.00000
  175c180
  < 6 4 10 7 0.00000
  ---
  > 6 4 7 10 0.00000
  177c182
  < 8 5 6 1 1.00000
  ---
  > 8 5 1 6 1.00000
  179,182c184,187
  < 10 7 8 6 1.00000
  < 11 8 5 1 0.25084
  < 12 8 4 2 0.00000
  < 13 8 5 2 0.40211
  ---
  > 10 7 6 8 1.00000
  > 11 8 1 5 0.25095
  > 12 8 2 4 0.00000
  > 13 8 2 5 0.40212
  184c189
  < 15 8 6 2 0.34704
  ---
  > 15 8 2 6 0.34694
  186,188c191,193
  < 17 9 7 5 0.20850
  < 18 9 2 9 0.28464
  < 19 9 9 5 0.32330
  ---
  > 17 9 2 9 0.28450
  > 18 9 5 7 0.20861
  > 19 9 5 9 0.32331
  190c195
  < 21 10 5 8 0.76211
  ---
  > 21 10 5 8 0.76212
  192c197
  < 23 10 7 6 0.23789
  ---
  > 23 10 6 7 0.23788
  194,195c199,200
  < 25 11 7 3 0.00000
  < 26 12 1 5 0.25084
  ---
  > 25 11 3 7 0.00000
  > 26 12 1 5 0.25095
  197c202
  < 28 12 2 5 0.40211
  ---
  > 28 12 2 5 0.40212
  199,203c204,208
  < 30 12 2 6 0.34704
  < 31 13 7 2 0.18357
  < 32 13 7 5 0.20850
  < 33 13 9 2 0.28464
  < 34 13 5 9 0.32330
  ---
  > 30 12 2 6 0.34694
  > 31 13 2 7 0.18357
  > 32 13 2 9 0.28450
  > 33 13 5 7 0.20861
  > 34 13 5 9 0.32331
  490c495
  < 1 1 21221112 11121112 1.000000e+00 21221112 11121112
  ---
  > 1 1 11121112 21221112 1.000000e+00 21221112 11121112
  494c499
  < 5 5 12212211 11121112 9.057297e-01 12212211 11121112
  ---
  > 5 5 11121112 12212211 9.057297e-01 12212211 11121112
  500c505
  < 11 10 12221112 12212211 1.000000e+00 12212211 12221112
  ---
  > 11 10 12212211 12221112 1.000000e+00 12212211 12221112
  505c510
  < 16 14 11121112 11112211 1.000000e+00 11121112 11112211
  ---
  > 16 14 11112211 11121112 1.000000e+00 11121112 11112211
  509c514
  < 20 17 12212211 11122122 1.000000e+00 12212211 11122122
  ---
  > 20 17 11122122 12212211 1.000000e+00 12212211 11122122
  514,515c519,520
  < 25 22 11122122 11121112 1.000000e+00 11121112 11122122
  < 26 23 12212211 11121112 9.057297e-01 11121112 12212211
  ---
  > 25 22 11121112 11122122 1.000000e+00 11121112 11122122
  > 26 23 11121112 12212211 9.057297e-01 11121112 12212211
  518c523
  < 29 25 21112212 11122122 1.000000e+00 11122122 21112212
  ---
  > 29 25 11122122 21112212 1.000000e+00 11122122 21112212
  524,525c529,530
  < 35 31 11122122 11121112 1.000000e+00 11122122 11121112
  < 36 32 21112212 11122122 1.000000e+00 11122122 21112212
  ---
  > 35 31 11121112 11122122 1.000000e+00 11122122 11121112
  > 36 32 11122122 21112212 1.000000e+00 11122122 21112212
  527,529c532,534
  < 38 34 11122122 11121112 1.000000e+00 11122122 11121112
  < 39 35 21221112 21112212 1.000000e+00 21221112 21112212
  < 40 36 12221112 11121112 1.000000e+00 11121112 12221112
  ---
  > 38 34 11121112 11122122 1.000000e+00 11122122 11121112
  > 39 35 21112212 21221112 1.000000e+00 21221112 21112212
  > 40 36 11121112 12221112 1.000000e+00 11121112 12221112
  533,535c538,540
  < 44 40 21112212 12212211 1.000000e+00 21112212 12212211
  < 45 40 22212212 11112211 1.142559e-08 21112212 12212211
  < 46 41 12212211 11121112 9.057297e-01 12212211 11121112
  ---
  > 44 40 12212211 21112212 1.000000e+00 21112212 12212211
  > 45 40 11112211 22212212 1.142559e-08 21112212 12212211
  > 46 41 11121112 12212211 9.057297e-01 12212211 11121112
  539c544
  < 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' ...21c21
  < [1] "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"
  23,24c23,24
  < R Under development (unstable) (2012-02-27 r58511)
  < Platform: x86_64-pc-mingw32/x64 (64-bit)
  ---
  > R version 2.14.0 (2011-10-31)
  > Platform: x86_64-unknown-linux-gnu (64-bit)
  27c27,32
  < [1] C
  ---
  > [1] LC_CTYPE=C LC_NUMERIC=C
  > [3] LC_TIME=C LC_COLLATE=C
  > [5] LC_MONETARY=C LC_MESSAGES=en_US.UTF-8
  > [7] LC_PAPER=C LC_NAME=C
  > [9] LC_ADDRESS=C LC_TELEPHONE=C
  > [11] LC_MEASUREMENT=en_US.UTF-8 LC_IDENTIFICATION=C
  Running 'test.methods.haplo.glm.R'
  Comparing 'test.methods.haplo.glm.Rout' to 'test.methods.haplo.glm.Rout.save' ...12c12
  < [1] "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"
  14,15c14,15
  < R Under development (unstable) (2012-02-27 r58511)
  < Platform: x86_64-pc-mingw32/x64 (64-bit)
  ---
  > R version 2.14.0 (2011-10-31)
  > Platform: x86_64-unknown-linux-gnu (64-bit)
  18c18,23
  < [1] C
  ---
  > [1] LC_CTYPE=C LC_NUMERIC=C
  > [3] LC_TIME=C LC_COLLATE=C
  > [5] LC_MONETARY=C LC_MESSAGES=en_US.UTF-8
  > [7] LC_PAPER=C LC_NAME=C
  > [9] LC_ADDRESS=C LC_TELEPHONE=C
  > [11] LC_MEASUREMENT=en_US.UTF-8 LC_IDENTIFICATION=C
  187c192
  < geno.138 -2.351610e-01 3.135953e-02 1.061650e-01 6.035697e-02
  ---
  > geno.138 -2.351610e-01 3.135952e-02 1.061650e-01 6.035697e-02
  190,191c195,196
  < 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
  196c201
  < hap.rare -4.058363e-08 3.310615e-08 1.093231e-08 -1.238478e-09
  ---
  > hap.rare -4.058363e-08 3.310615e-08 1.093231e-08 -1.238479e-09
  211,212c216,217
  < hap.34 -2.569089e-09 8.519474e-10 1.374934e-08 8.440416e-09
  < hap.77 -2.569089e-09 8.519473e-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
  216,217d220
  < hap.rare -2.569089e-09 8.519474e-10 1.374934e-08 8.440416e-09
  < hap.rare -2.569089e-09 8.519476e-10 1.374934e-08 8.440416e-09
  218a222
  > hap.rare -2.569089e-09 8.519473e-10 1.374934e-08 8.440416e-09
  219a224
  > hap.rare -2.569089e-09 8.519474e-10 1.374934e-08 8.440416e-09
  227c232
  < geno.78 8.481883e-02 -3.191332e-06 8.519478e-10 8.519473e-10
  ---
  > geno.78 8.481883e-02 -3.191332e-06 8.519477e-10 8.519475e-10
  247,248c252,253
  < 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
  267c272
  < geno.34 -1.238478e-09 -1.238478e-09 -1.238479e-09 -2.476957e-09
  ---
  > geno.34 -1.238478e-09 -1.238478e-09 -1.238478e-09 -2.476957e-09
  269c274
  < geno.78 8.519476e-10 8.519474e-10 8.519475e-10 1.703895e-09
  ---
  > geno.78 8.519475e-10 8.519473e-10 8.519475e-10 1.703894e-09
• checking PDF version of manual ... OK
  NOTE: There were 2 notes.
  See
  'd:/Rcompile/CRANpkg/local/2.15/haplo.stats.Rcheck/00check.log'
  for details.