• using R version 2.14.2 (2012-02-29)
• using platform: i386-pc-mingw32 (32-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 ... OK
• checking sizes of PDF files under '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 version 2.14.2 (2012-02-29)
  < 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 version 2.14.2 (2012-02-29)
  < 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 version 2.14.2 (2012-02-29)
  < 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 version 2.14.2 (2012-02-29)
  < 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 version 2.14.2 (2012-02-29)
  < 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 version 2.14.2 (2012-02-29)
  < 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