* using log directory 'd:/Rcompile/CRANpkg/local/3.4/supclust.Rcheck' * using R version 3.4.4 (2018-03-15) * using platform: x86_64-w64-mingw32 (64-bit) * using session charset: ISO8859-1 * checking for file 'supclust/DESCRIPTION' ... OK * this is package 'supclust' version '1.0-7' * package encoding: UTF-8 * 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 for hidden files and directories ... OK * checking for portable file names ... OK * checking whether package 'supclust' can be installed ... OK * checking installed package size ... OK * checking package directory ... OK * checking DESCRIPTION meta-information ... OK * checking top-level files ... OK * checking for left-over 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 ** checking loading without being on the library search path ... OK ** checking use of S3 registration ... 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 loading without being on the library search path ... OK ** checking use of S3 registration ... OK * checking dependencies in R code ... OK * checking S3 generic/method consistency ... OK * checking replacement functions ... OK * checking foreign function calls ... NOTE Call with DUP: .C(R_clusterer, E = as.double(E), X = as.double(X), W = as.double(W), P = as.double(P), y = as.double(y), prob = as.double(prob), theta = as.double(theta), lambda = as.double(lambda * n), n = as.integer(n), g = as.integer(g), m = as.integer(m), p = as.integer(p), critflag = as.integer(critflag), penflag = as.integer(penflag), blockflag = as.integer(blockflag), valiflag = as.integer(valiflag), traceflag = as.integer(trace), genliste = integer(lSize), kriterium = double(lSize), DUP = FALSE) DUP is no longer supported and will be ignored. * checking R code for possible problems ... [6s] NOTE .p.1gen: warning in formatC(id, wid = 6): partial argument match of 'wid' to 'width' .p.1gen: warning in formatC(s, wid = 4): partial argument match of 'wid' to 'width' .p.1gen: warning in formatC(format(c(round(m, digits = digits), 0.735))[1], wid = 7, dig = 3): partial argument match of 'dig' to 'digits' .p.1gen: warning in formatC(format(c(round(m, digits = digits), 0.735))[1], wid = 7, dig = 3): partial argument match of 'wid' to 'width' predict.pelora: warning in matrix(c((1/(1 + exp(-(X[, 1:(noc[i] + 1)] %*% koeff))))), nc = 1): partial argument match of 'nc' to 'ncol' ridge.coef: warning in diag(apply(X, 2, var) * lambda * nrow(X), nr = ncol(X)): partial argument match of 'nr' to 'nrow' aggtrees: no visible global function definition for 'predict' coef.pelora: no visible global function definition for 'fitted' dlda: no visible binding for global variable 'var' logreg: no visible global function definition for 'glm' logreg: no visible binding for global variable 'binomial' logreg: no visible global function definition for 'predict' plot.pelora: no visible global function definition for 'plot' plot.pelora: no visible global function definition for 'text' plot.wilma: no visible global function definition for 'fitted' plot.wilma: no visible global function definition for 'plot' plot.wilma: no visible global function definition for 'text' predict.pelora: no visible global function definition for 'fitted' predict.pelora: no visible global function definition for 'coef' predict.wilma: no visible global function definition for 'fitted' print.wilma: no visible global function definition for 'fitted' ridge.coef: no visible binding for global variable 'var' sign.change: no visible binding for global variable 'cov' standardize.genes: no visible binding for global variable 'sd' Undefined global functions or variables: binomial coef cov fitted glm plot predict sd text var Consider adding importFrom("graphics", "plot", "text") importFrom("stats", "binomial", "coef", "cov", "fitted", "glm", "predict", "sd", "var") to your NAMESPACE file. * 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 compilation flags in Makevars ... OK * checking for GNU extensions in Makefiles ... OK * checking for portable use of $(BLAS_LIBS) and $(LAPACK_LIBS) ... OK * checking compiled code ... OK * checking examples ... ** running examples for arch 'i386' ... [26s] OK ** running examples for arch 'x64' ... [23s] OK * checking for unstated dependencies in 'tests' ... OK * checking tests ... ** running tests for arch 'i386' ... [7s] OK Running 'pelora-ex.R' [6s] Comparing 'pelora-ex.Rout' to 'pelora-ex.Rout.save' ...100,114c100,114 < Entry 1 : Gene 69 (flipped) < Entry 2 : Gene 225 (flipped) < Entry 3 : Gene 126 < Entry 4 : Gene 100 (flipped) < Entry 5 : Gene 204 (flipped) < Entry 6 : Gene 20 (flipped) < Entry 7 : Gene 215 (flipped) < Entry 8 : Gene 228 (flipped) < Entry 9 : Gene 105 (flipped) < Entry 10 : Gene 186 < Entry 11 : Gene 173 (flipped) < Entry 12 : Gene 218 (flipped) < Entry 13 : Gene 222 < Entry 14 : Gene 123 (flipped) < Entry 15 : Gene 58 (flipped) --- > Entry 1 : Gene 69 > Entry 2 : Gene 225 > Entry 3 : Gene 126 (flipped) > Entry 4 : Gene 100 > Entry 5 : Gene 204 > Entry 6 : Gene 20 > Entry 7 : Gene 215 > Entry 8 : Gene 228 > Entry 9 : Gene 105 > Entry 10 : Gene 186 (flipped) > Entry 11 : Gene 173 > Entry 12 : Gene 218 > Entry 13 : Gene 222 (flipped) > Entry 14 : Gene 123 > Entry 15 : Gene 58 135c135 < -0.04619694 4.04250968 -4.92367256 4.75737556 --- > -0.04619694 4.04250968 4.92367256 4.75737556 139,176c139,176 < 1 -0.2285066 0.12432003 -0.33983410 < 2 -0.2017373 0.04138686 -0.38015308 < 3 -0.2615608 0.04055937 -0.39419765 < 4 -0.2780412 0.09475581 -0.34197622 < 5 -0.2723402 0.09896039 -0.36545322 < 6 -0.2570126 0.10788684 -0.30544423 < 7 -0.2582871 0.06090086 -0.29378052 < 8 -0.2432369 0.01509041 -0.38560155 < 9 -0.2800386 0.05157562 -0.34834236 < 10 -0.2349189 0.05628643 -0.30459387 < 11 -0.3159678 0.10866037 -0.33425831 < 12 -0.3399309 0.01791853 -0.39402569 < 13 -0.3098570 0.06796453 -0.35068307 < 14 -0.2911981 -0.01395371 -0.36716178 < 15 -0.2804411 0.11240865 -0.35376125 < 16 -0.2989401 0.04680822 -0.34514395 < 17 -0.3064803 0.03457211 -0.29166647 < 18 -0.3009477 0.04104916 -0.36065756 < 19 -0.2803658 0.01647425 -0.34734494 < 20 -0.3619075 0.02772715 -0.36860677 < 21 -0.2534279 0.06582762 -0.32617354 < 22 -0.2767475 0.05673009 -0.33408313 < 23 -0.2594244 0.06804213 -0.33286369 < 24 -0.2686963 0.05743951 -0.37159634 < 25 -0.2493578 0.07558631 -0.33871439 < 26 -0.3445316 0.05378141 -0.37364051 < 27 -0.2656955 0.09953485 -0.35245539 < 28 0.1830933 -0.33047470 0.02750604 < 29 0.2351452 -0.33496886 0.08166425 < 30 0.1945311 -0.39994464 0.07867998 < 31 0.2281800 -0.35522562 0.04344020 < 32 0.2371330 -0.36371202 0.10003395 < 33 0.2427357 -0.31841017 0.07078407 < 34 0.2418461 -0.35177789 0.05783627 < 35 0.1971921 -0.33679719 0.04908993 < 36 0.2026620 -0.34749665 0.08493945 < 37 0.2051926 -0.31614019 0.12107278 < 38 0.2108391 -0.32627858 0.07758265 --- > 1 -0.2285066 -0.12432003 -0.33983410 > 2 -0.2017373 -0.04138686 -0.38015308 > 3 -0.2615608 -0.04055937 -0.39419765 > 4 -0.2780412 -0.09475581 -0.34197622 > 5 -0.2723402 -0.09896039 -0.36545322 > 6 -0.2570126 -0.10788684 -0.30544423 > 7 -0.2582871 -0.06090086 -0.29378052 > 8 -0.2432369 -0.01509041 -0.38560155 > 9 -0.2800386 -0.05157562 -0.34834236 > 10 -0.2349189 -0.05628643 -0.30459387 > 11 -0.3159678 -0.10866037 -0.33425831 > 12 -0.3399309 -0.01791853 -0.39402569 > 13 -0.3098570 -0.06796453 -0.35068307 > 14 -0.2911981 0.01395371 -0.36716178 > 15 -0.2804411 -0.11240865 -0.35376125 > 16 -0.2989401 -0.04680822 -0.34514395 > 17 -0.3064803 -0.03457211 -0.29166647 > 18 -0.3009477 -0.04104916 -0.36065756 > 19 -0.2803658 -0.01647425 -0.34734494 > 20 -0.3619075 -0.02772715 -0.36860677 > 21 -0.2534279 -0.06582762 -0.32617354 > 22 -0.2767475 -0.05673009 -0.33408313 > 23 -0.2594244 -0.06804213 -0.33286369 > 24 -0.2686963 -0.05743951 -0.37159634 > 25 -0.2493578 -0.07558631 -0.33871439 > 26 -0.3445316 -0.05378141 -0.37364051 > 27 -0.2656955 -0.09953485 -0.35245539 > 28 0.1830933 0.33047470 0.02750604 > 29 0.2351452 0.33496886 0.08166425 > 30 0.1945311 0.39994464 0.07867998 > 31 0.2281800 0.35522562 0.04344020 > 32 0.2371330 0.36371202 0.10003395 > 33 0.2427357 0.31841017 0.07078407 > 34 0.2418461 0.35177789 0.05783627 > 35 0.1971921 0.33679719 0.04908993 > 36 0.2026620 0.34749665 0.08493945 > 37 0.2051926 0.31614019 0.12107278 > 38 0.2108391 0.32627858 0.07758265 263,265c263,265 < 1 0.1799321 0.19641747 0.4566692 < 2 0.3055774 0.04751572 -0.0557937 < 3 -0.1820159 0.25441379 -0.0938568 --- > 1 0.1799321 -0.19641747 0.4566692 > 2 0.3055774 -0.04751572 -0.0557937 > 3 -0.1820159 -0.25441379 -0.0938568 507,521c507,521 < Entry 1 : Gene 69 (flipped) : Name V69 < Entry 2 : Gene 225 (flipped) : Name V225 < Entry 3 : Gene 126 : Name V126 < Entry 4 : Gene 100 (flipped) : Name V100 < Entry 5 : Gene 204 (flipped) : Name V204 < Entry 6 : Gene 20 (flipped) : Name V20 < Entry 7 : Gene 215 (flipped) : Name V215 < Entry 8 : Gene 228 (flipped) : Name V228 < Entry 9 : Gene 105 (flipped) : Name V105 < Entry 10 : Gene 186 : Name V186 < Entry 11 : Gene 173 (flipped) : Name V173 < Entry 12 : Gene 218 (flipped) : Name V218 < Entry 13 : Gene 222 : Name V222 < Entry 14 : Gene 123 (flipped) : Name V123 < Entry 15 : Gene 58 (flipped) : Name V58 --- > Entry 1 : Gene 69 : Name V69 > Entry 2 : Gene 225 : Name V225 > Entry 3 : Gene 126 (flipped) : Name V126 > Entry 4 : Gene 100 : Name V100 > Entry 5 : Gene 204 : Name V204 > Entry 6 : Gene 20 : Name V20 > Entry 7 : Gene 215 : Name V215 > Entry 8 : Gene 228 : Name V228 > Entry 9 : Gene 105 : Name V105 > Entry 10 : Gene 186 (flipped) : Name V186 > Entry 11 : Gene 173 : Name V173 > Entry 12 : Gene 218 : Name V218 > Entry 13 : Gene 222 (flipped) : Name V222 > Entry 14 : Gene 123 : Name V123 > Entry 15 : Gene 58 : Name V58 542c542 < -0.04619694 4.04250968 -4.92367256 4.75737556 --- > -0.04619694 4.04250968 4.92367256 4.75737556 546,583c546,583 < 1 -0.2285066 0.12432003 -0.33983410 < 2 -0.2017373 0.04138686 -0.38015308 < 3 -0.2615608 0.04055937 -0.39419765 < 4 -0.2780412 0.09475581 -0.34197622 < 5 -0.2723402 0.09896039 -0.36545322 < 6 -0.2570126 0.10788684 -0.30544423 < 7 -0.2582871 0.06090086 -0.29378052 < 8 -0.2432369 0.01509041 -0.38560155 < 9 -0.2800386 0.05157562 -0.34834236 < 10 -0.2349189 0.05628643 -0.30459387 < 11 -0.3159678 0.10866037 -0.33425831 < 12 -0.3399309 0.01791853 -0.39402569 < 13 -0.3098570 0.06796453 -0.35068307 < 14 -0.2911981 -0.01395371 -0.36716178 < 15 -0.2804411 0.11240865 -0.35376125 < 16 -0.2989401 0.04680822 -0.34514395 < 17 -0.3064803 0.03457211 -0.29166647 < 18 -0.3009477 0.04104916 -0.36065756 < 19 -0.2803658 0.01647425 -0.34734494 < 20 -0.3619075 0.02772715 -0.36860677 < 21 -0.2534279 0.06582762 -0.32617354 < 22 -0.2767475 0.05673009 -0.33408313 < 23 -0.2594244 0.06804213 -0.33286369 < 24 -0.2686963 0.05743951 -0.37159634 < 25 -0.2493578 0.07558631 -0.33871439 < 26 -0.3445316 0.05378141 -0.37364051 < 27 -0.2656955 0.09953485 -0.35245539 < 28 0.1830933 -0.33047470 0.02750604 < 29 0.2351452 -0.33496886 0.08166425 < 30 0.1945311 -0.39994464 0.07867998 < 31 0.2281800 -0.35522562 0.04344020 < 32 0.2371330 -0.36371202 0.10003395 < 33 0.2427357 -0.31841017 0.07078407 < 34 0.2418461 -0.35177789 0.05783627 < 35 0.1971921 -0.33679719 0.04908993 < 36 0.2026620 -0.34749665 0.08493945 < 37 0.2051926 -0.31614019 0.12107278 < 38 0.2108391 -0.32627858 0.07758265 --- > 1 -0.2285066 -0.12432003 -0.33983410 > 2 -0.2017373 -0.04138686 -0.38015308 > 3 -0.2615608 -0.04055937 -0.39419765 > 4 -0.2780412 -0.09475581 -0.34197622 > 5 -0.2723402 -0.09896039 -0.36545322 > 6 -0.2570126 -0.10788684 -0.30544423 > 7 -0.2582871 -0.06090086 -0.29378052 > 8 -0.2432369 -0.01509041 -0.38560155 > 9 -0.2800386 -0.05157562 -0.34834236 > 10 -0.2349189 -0.05628643 -0.30459387 > 11 -0.3159678 -0.10866037 -0.33425831 > 12 -0.3399309 -0.01791853 -0.39402569 > 13 -0.3098570 -0.06796453 -0.35068307 > 14 -0.2911981 0.01395371 -0.36716178 > 15 -0.2804411 -0.11240865 -0.35376125 > 16 -0.2989401 -0.04680822 -0.34514395 > 17 -0.3064803 -0.03457211 -0.29166647 > 18 -0.3009477 -0.04104916 -0.36065756 > 19 -0.2803658 -0.01647425 -0.34734494 > 20 -0.3619075 -0.02772715 -0.36860677 > 21 -0.2534279 -0.06582762 -0.32617354 > 22 -0.2767475 -0.05673009 -0.33408313 > 23 -0.2594244 -0.06804213 -0.33286369 > 24 -0.2686963 -0.05743951 -0.37159634 > 25 -0.2493578 -0.07558631 -0.33871439 > 26 -0.3445316 -0.05378141 -0.37364051 > 27 -0.2656955 -0.09953485 -0.35245539 > 28 0.1830933 0.33047470 0.02750604 > 29 0.2351452 0.33496886 0.08166425 > 30 0.1945311 0.39994464 0.07867998 > 31 0.2281800 0.35522562 0.04344020 > 32 0.2371330 0.36371202 0.10003395 > 33 0.2427357 0.31841017 0.07078407 > 34 0.2418461 0.35177789 0.05783627 > 35 0.1971921 0.33679719 0.04908993 > 36 0.2026620 0.34749665 0.08493945 > 37 0.2051926 0.31614019 0.12107278 > 38 0.2108391 0.32627858 0.07758265 670,672c670,672 < 1 0.1799321 0.19641747 0.4566692 < 2 0.3055774 0.04751572 -0.0557937 < 3 -0.1820159 0.25441379 -0.0938568 --- > 1 0.1799321 -0.19641747 0.4566692 > 2 0.3055774 -0.04751572 -0.0557937 > 3 -0.1820159 -0.25441379 -0.0938568 Running 'wilma-ex.R' [1s] Comparing 'wilma-ex.Rout' to 'wilma-ex.Rout.save' ... OK ** running tests for arch 'x64' ... [8s] OK Running 'pelora-ex.R' [6s] Comparing 'pelora-ex.Rout' to 'pelora-ex.Rout.save' ... OK Running 'wilma-ex.R' [2s] Comparing 'wilma-ex.Rout' to 'wilma-ex.Rout.save' ... OK * checking PDF version of manual ... OK * DONE Status: 2 NOTEs