* using log directory 'd:/Rcompile/CRANpkg/local/2.15/haplo.stats.Rcheck' * using R version 2.15.0 (2012-03-30) * 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 ... 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 '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 2.15.0 (2012-03-30) < 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 2.15.0 (2012-03-30) < 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 2.15.0 (2012-03-30) < 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 2.15.0 (2012-03-30) < 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 2.15.0 (2012-03-30) < 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 2.15.0 (2012-03-30) < 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 was 1 note. See 'd:/Rcompile/CRANpkg/local/2.15/haplo.stats.Rcheck/00check.log' for details.