* using log directory 'd:/Rcompile/CRANpkg/local/2.8/SharedHT2.Rcheck' * using R version 2.8.1 beta (2008-12-12 r47183) * using session charset: ISO8859-1 * checking for file 'SharedHT2/DESCRIPTION' ... OK * this is package 'SharedHT2' version '2.0' * checking package name space information ... OK * 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 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 name space can be loaded with stated dependencies ... 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 cross-references ... OK * checking for missing documentation entries ... OK * checking for code/documentation mismatches ... OK * checking Rd \usage sections ... OK * checking data for non-ASCII characters ... OK * checking line endings in C/C++/Fortran sources/headers ... OK * checking line endings in Makefiles ... 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) > > ## Not run: > ##D # If the two bioconductor packages, "affy" and "hgu95av2" are > ##D # installed, replace the above line with > ##D > ##D data(SimAffyDat.ann) > ##D SimAffyDat <- SimAffyDat.ann > ##D > ##D # In general if you have a replicated microarray experiment in > ##D # "MyMicroArrayData" and the corresponding bioconductor annotation > ##D # package is "hguFOOBAR" then, after making sure that packages > ##D # "affy" and "hguFOOBAR" are installed, the enhanced functionality > ##D # is turned on by adding an attribute to your dataframe as follows: > ##D > ##D attr(MyMicroArrayData, "annotation") <- "hguFOOBAR" > ##D > ## End(Not run) > > # 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 = -56430.787031 Scaled convergence tolerance is 0.000840884 Stepsize computed as 0.100000 BUILD 5 -54381.760400 -58352.190382 EXTENSION 7 -54392.623924 -60448.366557 EXTENSION 9 -56430.787031 -65108.692608 LO-REDUCTION 11 -56742.326431 -65108.692608 EXTENSION 13 -58352.190382 -71345.801671 EXTENSION 15 -60448.366557 -77946.883302 EXTENSION 17 -63989.237648 -85835.722727 LO-REDUCTION 19 -65108.692608 -85835.722727 REFLECTION 21 -71345.801671 -88738.117379 LO-REDUCTION 23 -77946.883302 -89352.964565 REFLECTION 25 -85187.997022 -89851.225920 LO-REDUCTION 27 -85835.722727 -90196.133460 HI-REDUCTION 29 -88738.117379 -90196.133460 LO-REDUCTION 31 -89211.111399 -90196.133460 HI-REDUCTION 33 -89352.964565 -90237.454395 HI-REDUCTION 35 -89851.225920 -90237.454395 HI-REDUCTION 37 -90131.136119 -90456.901183 LO-REDUCTION 39 -90170.344060 -90456.901183 REFLECTION 41 -90196.133460 -90617.475080 REFLECTION 43 -90237.454395 -90753.785824 HI-REDUCTION 45 -90392.054678 -90753.785824 REFLECTION 47 -90456.901183 -90766.161611 LO-REDUCTION 49 -90553.692737 -90766.161611 REFLECTION 51 -90617.475080 -90860.344431 LO-REDUCTION 53 -90753.785824 -90862.952191 LO-REDUCTION 55 -90757.550116 -90862.952191 HI-REDUCTION 57 -90766.161611 -90862.952191 REFLECTION 59 -90844.005175 -90921.265532 LO-REDUCTION 61 -90849.038712 -90921.265532 EXTENSION 63 -90860.344431 -90973.642215 HI-REDUCTION 65 -90862.952191 -90973.642215 LO-REDUCTION 67 -90900.260447 -90973.642215 LO-REDUCTION 69 -90921.265532 -90973.642215 LO-REDUCTION 71 -90922.940211 -90973.642215 LO-REDUCTION 73 -90955.705087 -90973.648574 LO-REDUCTION 75 -90958.339693 -90973.648574 LO-REDUCTION 77 -90963.229288 -90973.648574 REFLECTION 79 -90972.604172 -90975.987791 HI-REDUCTION 81 -90972.637793 -90975.987791 EXTENSION 83 -90973.642215 -90979.377988 LO-REDUCTION 85 -90973.648574 -90979.377988 LO-REDUCTION 87 -90975.272143 -90979.377988 LO-REDUCTION 89 -90975.987791 -90979.377988 LO-REDUCTION 91 -90977.812929 -90979.377988 REFLECTION 93 -90978.408148 -90979.416970 REFLECTION 95 -90978.794826 -90980.180615 HI-REDUCTION 97 -90978.890037 -90980.180615 EXTENSION 99 -90979.377988 -90980.895092 LO-REDUCTION 101 -90979.416970 -90980.895092 REFLECTION 103 -90979.620798 -90980.999814 EXTENSION 105 -90980.180615 -90982.985980 LO-REDUCTION 107 -90980.278315 -90982.985980 EXTENSION 109 -90980.895092 -90984.876804 LO-REDUCTION 111 -90980.999814 -90984.876804 EXTENSION 113 -90981.511753 -90986.052725 EXTENSION 115 -90982.985980 -90991.172399 EXTENSION 117 -90984.271537 -90995.360177 LO-REDUCTION 119 -90984.876804 -90995.360177 EXTENSION 121 -90986.052725 -90999.840239 EXTENSION 123 -90991.172399 -91014.662771 LO-REDUCTION 125 -90994.114778 -91014.662771 EXTENSION 127 -90995.360177 -91026.377051 LO-REDUCTION 129 -90999.840239 -91026.377051 EXTENSION 131 -91011.250169 -91055.351595 LO-REDUCTION 133 -91014.662771 -91055.351595 LO-REDUCTION 135 -91023.892262 -91055.351595 EXTENSION 137 -91026.377051 -91064.599245 REFLECTION 139 -91044.219822 -91074.215541 EXTENSION 141 -91052.194176 -91091.401112 LO-REDUCTION 143 -91055.351595 -91091.401112 LO-REDUCTION 145 -91064.599245 -91091.401112 EXTENSION 147 -91074.215541 -91094.103455 LO-REDUCTION 149 -91075.218280 -91094.103455 EXTENSION 151 -91078.647015 -91121.418198 LO-REDUCTION 153 -91090.204635 -91121.418198 LO-REDUCTION 155 -91091.401112 -91121.418198 LO-REDUCTION 157 -91094.103455 -91121.418198 EXTENSION 159 -91102.643601 -91135.810656 EXTENSION 161 -91113.114114 -91143.394242 LO-REDUCTION 163 -91113.723591 -91143.394242 REFLECTION 165 -91121.418198 -91144.153138 LO-REDUCTION 167 -91134.385412 -91144.153138 EXTENSION 169 -91135.810656 -91146.982668 LO-REDUCTION 171 -91139.788722 -91146.982668 EXTENSION 173 -91143.394242 -91160.360651 LO-REDUCTION 175 -91144.065089 -91160.360651 LO-REDUCTION 177 -91144.153138 -91160.360651 LO-REDUCTION 179 -91146.982668 -91160.360651 EXTENSION 181 -91149.392987 -91171.792906 EXTENSION 183 -91157.189088 -91187.228904 LO-REDUCTION 185 -91157.343979 -91187.228904 LO-REDUCTION 187 -91160.360651 -91187.228904 EXTENSION 189 -91171.792906 -91213.106975 EXTENSION 191 -91182.350206 -91229.203197 LO-REDUCTION 193 -91184.865189 -91229.203197 REFLECTION 195 -91187.228904 -91230.460886 REFLECTION 197 -91213.106975 -91247.370109 REFLECTION 199 -91225.875340 -91249.144958 LO-REDUCTION 201 -91229.203197 -91249.144958 LO-REDUCTION 203 -91230.460886 -91249.144958 EXTENSION 205 -91238.834998 -91264.046331 EXTENSION 207 -91245.756950 -91271.286755 EXTENSION 209 -91247.370109 -91284.711204 LO-REDUCTION 211 -91249.144958 -91284.711204 LO-REDUCTION 213 -91264.046331 -91284.711204 LO-REDUCTION 215 -91271.286755 -91284.711204 LO-REDUCTION 217 -91273.537360 -91284.711204 REFLECTION 219 -91277.862709 -91287.303658 LO-REDUCTION 221 -91278.980994 -91287.303658 REFLECTION 223 -91282.773106 -91290.675668 REFLECTION 225 -91284.711204 -91291.771827 LO-REDUCTION 227 -91287.065375 -91291.771827 LO-REDUCTION 229 -91287.303658 -91291.771827 REFLECTION 231 -91290.675668 -91294.482194 LO-REDUCTION 233 -91291.383704 -91294.482194 LO-REDUCTION 235 -91291.537589 -91294.482194 LO-REDUCTION 237 -91291.771827 -91294.482194 REFLECTION 239 -91293.190201 -91295.131418 LO-REDUCTION 241 -91293.270234 -91295.131418 LO-REDUCTION 243 -91293.766033 -91295.131418 HI-REDUCTION 245 -91294.426840 -91295.131418 LO-REDUCTION 247 -91294.482194 -91295.131418 REFLECTION 249 -91294.550360 -91295.187632 REFLECTION 251 -91294.860399 -91295.225508 REFLECTION 253 -91294.943920 -91295.364640 EXTENSION 255 -91295.131418 -91295.516744 REFLECTION 257 -91295.187632 -91295.599899 LO-REDUCTION 259 -91295.225508 -91295.599899 LO-REDUCTION 261 -91295.364640 -91295.599899 LO-REDUCTION 263 -91295.493514 -91295.599899 LO-REDUCTION 265 -91295.516744 -91295.599899 LO-REDUCTION 267 -91295.551135 -91295.612523 HI-REDUCTION 269 -91295.562265 -91295.612523 LO-REDUCTION 271 -91295.573300 -91295.612523 LO-REDUCTION 273 -91295.596293 -91295.612523 HI-REDUCTION 275 -91295.599899 -91295.613738 HI-REDUCTION 277 -91295.605880 -91295.613738 REFLECTION 279 -91295.610680 -91295.615364 HI-REDUCTION 281 -91295.612523 -91295.616045 HI-REDUCTION 283 -91295.612635 -91295.616764 HI-REDUCTION 285 -91295.613738 -91295.616764 HI-REDUCTION 287 -91295.615364 -91295.617106 HI-REDUCTION 289 -91295.616045 -91295.617479 LO-REDUCTION 291 -91295.616509 -91295.617489 Exiting from Nelder Mead minimizer 293 function evaluations used > > # Top 20 genes (sorted by decreasing ShHT2 statistic) and model summary > > fit.SimAffyDat Top 20 Genes: $table Rank RowNum GeneId log2.grp1 log2.grp2 ShHT2.stat ShHT2.p-val 1 1 34 1030_s_at 1.92 2.22 111.0 3.891e-06 2 2 61 1055_g_at 1.90 1.98 90.5 7.918e-06 3 3 5 1004_at 1.90 2.07 88.9 8.435e-06 4 4 21 1019_g_at 1.89 1.90 84.5 1.006e-05 5 5 56 1050_at 2.03 2.03 83.9 1.029e-05 6 6 92 1083_s_at 1.96 1.82 81.6 1.132e-05 7 7 72 1065_at 1.97 1.77 81.6 1.133e-05 8 8 99 108_g_at 1.91 1.87 81.4 1.142e-05 9 9 25 1022_f_at 1.96 1.90 81.3 1.146e-05 10 10 27 1024_at 1.93 1.91 80.9 1.169e-05 11 11 1 1000_at 1.91 2.14 80.7 1.179e-05 12 12 95 1086_at 1.90 1.99 80.4 1.193e-05 13 13 8 1007_s_at 2.08 1.94 80.2 1.202e-05 14 14 59 1053_at 1.98 1.86 79.0 1.265e-05 15 15 37 1033_g_at 1.95 1.81 77.2 1.369e-05 16 16 38 1034_at 2.00 1.88 77.2 1.371e-05 17 17 60 1054_at 1.99 2.02 77.0 1.382e-05 18 18 74 1067_at 1.98 1.99 77.0 1.385e-05 19 19 73 1066_at 2.15 2.31 75.8 1.459e-05 20 20 33 102_at 1.95 1.83 75.8 1.463e-05 FDR.stepdown=0.05 1 3.960e-06 2 7.921e-06 3 1.188e-05 4 1.584e-05 5 1.980e-05 6 2.376e-05 7 2.772e-05 8 3.168e-05 9 3.564e-05 10 3.960e-05 11 4.356e-05 12 4.752e-05 13 5.149e-05 14 5.545e-05 15 5.941e-05 16 6.337e-05 17 6.733e-05 18 7.129e-05 19 7.525e-05 20 7.921e-05 $call TopGenes(obj = x) $msg [1] "Top 20 Genes: \n" 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 9.19774423 0.113020314 0 rate11 0.13110407 0.005202196 0 rate12 0.08792183 0.003770973 0 rate22 0.12770890 0.004018018 0 > > # Same screen output & opens html browser with genelist linked to GeneCards database. > # Type ?TopGenes for help > > # Note: part of the 'enhanced functionality' is floating gene names > # over the links to the gene identifiers but there is more .... > # see the help under TopGenes (well ... more on that later...) > > print(fit.SimAffyDat, browse = TRUE) Error in shell.exec("file://" %,% file) : file association for 'f' not available or invalid Calls: print ... print.fit.n.data -> TopGenes -> eval -> eval -> htmtbl -> shell.exec Execution halted