* using log directory 'd:/Rcompile/CRANpkg/local/2.4/SharedHT2.Rcheck' * using R version 2.4.1 beta (2006-12-07 r40137) * checking for file 'SharedHT2/DESCRIPTION' ... OK * this is package 'SharedHT2' version '1.425' * checking package dependencies ... OK * checking if this is a source package ... OK * checking whether package 'SharedHT2' can be installed ... 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 syntax errors ... OK * checking R files for non-ASCII characters ... OK * checking whether the package can be loaded ... OK * checking whether the package can be loaded with stated dependencies ... OK * checking whether the name space can be loaded with stated dependencies ... 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 cross-references ... OK * checking for missing documentation entries ... OK * checking for code/documentation mismatches ... OK * checking Rd \usage sections ... OK * checking for CRLF line endings in C/C++/Fortran sources/headers ... OK * checking for portable use of $BLAS_LIBS ... OK * creating SharedHT2-Ex.R ... OK * checking examples ... ERROR Running examples in 'SharedHT2-Ex.R' failed. The error most likely occurred in: > ### * EB.Anova > > flush(stderr()); flush(stdout()) > > ### Name: EB.Anova > ### Title: Per Gene Group Comparison with Empirical Bayes Anova Tests > ### Aliases: EB.Anova > ### Keywords: models multivariate univar robust htest > > ### ** Examples > > > # The included example dataset is a simulated Affymetrix oligonucleotide > # array experiment. Type ?SimAffyDat for details. > > data(SimAffyDat) > > # Fit the Wishart/Inverse Wishart empirical Bayes model and derive per gene > # Shared Variance Hotelling T-Squared (ShHT2) statistics. > > fit.SimAffyDat <- EB.Anova(data=SimAffyDat, labels=c("log2.grp" %,% (1:2)), + H0="zero.means", Var.Struct = "general") Var.Struct = general You have chosen H0: zero.means N = 12625 d = 2 Nelder-Mead direct search function minimizer function value for initial parameters = -69170.115810 Scaled convergence tolerance is 0.000691701 Stepsize computed as 0.100000 BUILD 5 -67393.073961 -70442.670570 EXTENSION 7 -67410.145212 -72369.454663 EXTENSION 9 -69170.115810 -76287.028591 LO-REDUCTION 11 -69659.677724 -76287.028591 EXTENSION 13 -70442.670570 -79934.377010 EXTENSION 15 -72369.454663 -85512.892701 EXTENSION 17 -75365.131595 -90094.128686 LO-REDUCTION 19 -76287.028591 -90094.128686 LO-REDUCTION 21 -79934.377010 -90094.128686 LO-REDUCTION 23 -85512.892701 -90343.673141 LO-REDUCTION 25 -88875.405918 -90343.673141 REFLECTION 27 -89142.417787 -90412.155107 HI-REDUCTION 29 -90094.128686 -90412.155107 HI-REDUCTION 31 -90137.770682 -90541.150851 LO-REDUCTION 33 -90232.620907 -90621.265832 LO-REDUCTION 35 -90343.673141 -90631.424610 HI-REDUCTION 37 -90412.155107 -90676.500677 HI-REDUCTION 39 -90541.150851 -90676.500677 HI-REDUCTION 41 -90621.265832 -90676.500677 HI-REDUCTION 43 -90631.424610 -90701.237261 HI-REDUCTION 45 -90640.153171 -90701.237261 LO-REDUCTION 47 -90669.160014 -90703.432784 HI-REDUCTION 49 -90676.500677 -90705.572180 HI-REDUCTION 51 -90695.186955 -90711.783284 HI-REDUCTION 53 -90701.237261 -90715.458848 HI-REDUCTION 55 -90703.432784 -90715.458848 LO-REDUCTION 57 -90705.572180 -90715.458848 REFLECTION 59 -90711.783284 -90716.718625 HI-REDUCTION 61 -90713.603916 -90718.037991 HI-REDUCTION 63 -90714.146499 -90718.501332 LO-REDUCTION 65 -90715.458848 -90718.646871 REFLECTION 67 -90716.718625 -90718.906452 HI-REDUCTION 69 -90718.037991 -90719.190352 EXTENSION 71 -90718.501332 -90721.875013 HI-REDUCTION 73 -90718.646871 -90721.875013 EXTENSION 75 -90718.906452 -90724.799305 LO-REDUCTION 77 -90719.190352 -90724.799305 LO-REDUCTION 79 -90720.772859 -90724.799305 LO-REDUCTION 81 -90721.875013 -90724.799305 EXTENSION 83 -90722.303842 -90726.491019 LO-REDUCTION 85 -90723.502721 -90726.491019 EXTENSION 87 -90724.201491 -90729.465379 LO-REDUCTION 89 -90724.799305 -90729.465379 LO-REDUCTION 91 -90726.370583 -90729.465379 EXTENSION 93 -90726.491019 -90732.219522 LO-REDUCTION 95 -90727.631630 -90732.219522 EXTENSION 97 -90728.646936 -90732.960917 EXTENSION 99 -90729.465379 -90737.853296 LO-REDUCTION 101 -90730.701715 -90737.853296 EXTENSION 103 -90732.219522 -90745.752014 LO-REDUCTION 105 -90732.960917 -90745.752014 EXTENSION 107 -90736.185189 -90751.823785 EXTENSION 109 -90737.853296 -90759.797280 EXTENSION 111 -90739.212566 -90767.227723 EXTENSION 113 -90745.752014 -90789.709837 LO-REDUCTION 115 -90751.823785 -90789.709837 EXTENSION 117 -90759.797280 -90829.610253 LO-REDUCTION 119 -90767.227723 -90829.610253 EXTENSION 121 -90786.834881 -90855.729379 EXTENSION 123 -90789.709837 -90883.734256 EXTENSION 125 -90812.497954 -90896.970370 EXTENSION 127 -90829.610253 -90957.618772 HI-REDUCTION 129 -90855.729379 -90957.618772 LO-REDUCTION 131 -90883.734256 -90957.618772 LO-REDUCTION 133 -90888.202865 -90957.618772 HI-REDUCTION 135 -90896.970370 -90957.618772 EXTENSION 137 -90931.096507 -91038.135148 LO-REDUCTION 139 -90946.201985 -91038.135148 LO-REDUCTION 141 -90950.662116 -91038.135148 LO-REDUCTION 143 -90957.618772 -91038.135148 EXTENSION 145 -90989.303044 -91105.181174 LO-REDUCTION 147 -90997.113503 -91105.181174 LO-REDUCTION 149 -91023.874013 -91105.181174 EXTENSION 151 -91038.135148 -91144.089482 LO-REDUCTION 153 -91062.293660 -91144.089482 EXTENSION 155 -91099.886173 -91198.158899 LO-REDUCTION 157 -91105.181174 -91198.158899 LO-REDUCTION 159 -91122.109602 -91198.158899 EXTENSION 161 -91144.089482 -91210.942686 REFLECTION 163 -91169.045987 -91219.448066 REFLECTION 165 -91196.602745 -91244.232203 LO-REDUCTION 167 -91198.158899 -91244.232203 HI-REDUCTION 169 -91210.942686 -91244.232203 LO-REDUCTION 171 -91219.448066 -91244.232203 LO-REDUCTION 173 -91220.855913 -91244.232203 LO-REDUCTION 175 -91222.199941 -91244.232203 LO-REDUCTION 177 -91227.690471 -91244.232203 REFLECTION 179 -91235.598636 -91248.461207 LO-REDUCTION 181 -91237.594067 -91248.461207 EXTENSION 183 -91241.507624 -91256.265825 LO-REDUCTION 185 -91244.232203 -91256.265825 LO-REDUCTION 187 -91246.224581 -91256.265825 EXTENSION 189 -91248.461207 -91267.455321 LO-REDUCTION 191 -91255.083238 -91267.455321 EXTENSION 193 -91255.255250 -91277.551656 LO-REDUCTION 195 -91256.265825 -91277.551656 REFLECTION 197 -91266.818920 -91278.147162 EXTENSION 199 -91267.455321 -91282.544194 REFLECTION 201 -91271.103942 -91286.274496 LO-REDUCTION 203 -91277.551656 -91286.274496 LO-REDUCTION 205 -91278.147162 -91286.274496 EXTENSION 207 -91282.544194 -91291.446527 LO-REDUCTION 209 -91283.409564 -91291.446527 REFLECTION 211 -91284.778821 -91292.273637 REFLECTION 213 -91286.274496 -91292.786780 LO-REDUCTION 215 -91289.353226 -91292.875025 REFLECTION 217 -91291.446527 -91293.895129 HI-REDUCTION 219 -91292.273637 -91293.895129 HI-REDUCTION 221 -91292.786780 -91293.895129 HI-REDUCTION 223 -91292.875025 -91293.895129 REFLECTION 225 -91293.367426 -91294.656728 LO-REDUCTION 227 -91293.652270 -91294.656728 HI-REDUCTION 229 -91293.669065 -91294.656728 REFLECTION 231 -91293.895129 -91294.779971 HI-REDUCTION 233 -91294.151363 -91294.779971 REFLECTION 235 -91294.170080 -91294.892570 LO-REDUCTION 237 -91294.420573 -91294.892570 EXTENSION 239 -91294.656728 -91295.373978 LO-REDUCTION 241 -91294.779971 -91295.373978 LO-REDUCTION 243 -91294.874230 -91295.373978 LO-REDUCTION 245 -91294.892570 -91295.373978 REFLECTION 247 -91295.138835 -91295.546682 LO-REDUCTION 249 -91295.344783 -91295.546682 LO-REDUCTION 251 -91295.360440 -91295.546682 HI-REDUCTION 253 -91295.373978 -91295.546682 LO-REDUCTION 255 -91295.408928 -91295.546682 LO-REDUCTION 257 -91295.436978 -91295.546682 REFLECTION 259 -91295.442404 -91295.581566 LO-REDUCTION 261 -91295.531358 -91295.581566 HI-REDUCTION 263 -91295.532352 -91295.581566 REFLECTION 265 -91295.546682 -91295.591827 LO-REDUCTION 267 -91295.563307 -91295.594070 REFLECTION 269 -91295.580769 -91295.607813 HI-REDUCTION 271 -91295.581566 -91295.607813 LO-REDUCTION 273 -91295.591827 -91295.607813 LO-REDUCTION 275 -91295.594070 -91295.607813 LO-REDUCTION 277 -91295.595352 -91295.607813 REFLECTION 279 -91295.601349 -91295.610220 HI-REDUCTION 281 -91295.602472 -91295.610220 EXTENSION 283 -91295.606551 -91295.615343 LO-REDUCTION 285 -91295.606967 -91295.615343 LO-REDUCTION 287 -91295.607813 -91295.615343 LO-REDUCTION 289 -91295.610220 -91295.615343 LO-REDUCTION 291 -91295.611686 -91295.615343 LO-REDUCTION 293 -91295.612319 -91295.615343 LO-REDUCTION 295 -91295.612614 -91295.615343 REFLECTION 297 -91295.613933 -91295.615910 EXTENSION 299 -91295.614319 -91295.616706 EXTENSION 301 -91295.614871 -91295.617491 LO-REDUCTION 303 -91295.615343 -91295.617491 LO-REDUCTION 305 -91295.615910 -91295.617552 LO-REDUCTION 307 -91295.616706 -91295.617552 Exiting from Nelder Mead minimizer 309 function evaluations used > > # Top 20 genes (sorted by decreasing ShHT2 statistic) and model summary > > fit.SimAffyDat Top 20 Genes: RowNum GeneId .grp1 .grp2 ShHT2.stat ShHT2.p-val FDR.stepdown=0.05 1 34 1030_s_at 1.92 2.22 111.0 3.899e-06 3.960e-06 2 61 1055_g_at 1.90 1.98 90.5 7.937e-06 7.921e-06 3 5 1004_at 1.90 2.07 88.9 8.455e-06 1.188e-05 4 21 1019_g_at 1.89 1.90 84.5 1.008e-05 1.584e-05 5 56 1050_at 2.03 2.03 83.9 1.032e-05 1.980e-05 6 92 1083_s_at 1.96 1.82 81.6 1.135e-05 2.376e-05 7 72 1065_at 1.97 1.77 81.6 1.136e-05 2.772e-05 8 99 108_g_at 1.91 1.87 81.4 1.145e-05 3.168e-05 9 25 1022_f_at 1.96 1.90 81.3 1.149e-05 3.564e-05 10 27 1024_at 1.93 1.91 80.9 1.171e-05 3.960e-05 11 1 1000_at 1.91 2.14 80.6 1.182e-05 4.356e-05 12 95 1086_at 1.90 1.99 80.4 1.196e-05 4.752e-05 13 8 1007_s_at 2.08 1.94 80.2 1.205e-05 5.149e-05 14 59 1053_at 1.98 1.86 79.0 1.268e-05 5.545e-05 15 37 1033_g_at 1.95 1.81 77.2 1.373e-05 5.941e-05 16 38 1034_at 2.00 1.88 77.2 1.374e-05 6.337e-05 17 60 1054_at 1.99 2.02 77.0 1.386e-05 6.733e-05 18 74 1067_at 1.98 1.99 77.0 1.388e-05 7.129e-05 19 73 1066_at 2.15 2.31 75.8 1.463e-05 7.525e-05 20 33 102_at 1.95 1.83 75.7 1.467e-05 7.921e-05 Multivariate Normal/Inverse Wishart model fit: EB.Anova(data = SimAffyDat, labels = c("log2.grp" %,% (1:2)), H0 = "zero.means", Var.Struct = "general") est. std.err p-val shape 9.19585258 0.094149937 0 rate11 0.13108054 0.005201749 0 rate12 0.08791208 0.003769974 0 rate22 0.12766667 0.004017959 0 > > # Same screen output & opens html browser with genelist linked to GeneCards database. > # Type ?TopGenes for help > > print(fit.SimAffyDat, browse = TRUE) Error in shell.exec("file://" %,% file) : access to 'file://d:\temp\Rtmp3875qb\temp678418be' denied Execution halted