* using log directory 'd:/Rcompile/CRANpkg/local/3.3/vegan.Rcheck' * using R version 3.3.3 (2017-03-06) * using platform: x86_64-w64-mingw32 (64-bit) * using session charset: ISO8859-1 * checking for file 'vegan/DESCRIPTION' ... OK * this is package 'vegan' version '2.5-1' * 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 'vegan' can be installed ... OK * checking installed package size ... OK * checking package directory ... OK * checking 'build' 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 ... OK * checking R code for possible problems ... OK * 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 sizes of PDF files under 'inst/doc' ... OK * checking installed files from 'inst/doc' ... OK * checking files in 'vignettes' ... OK * checking examples ... ** running examples for arch 'i386' ... [52s] OK ** running examples for arch 'x64' ... [60s] OK * checking for unstated dependencies in 'tests' ... OK * checking tests ... ** running tests for arch 'i386' ... [14s] OK Running 'cca-object-tests.R' [3s] Comparing 'cca-object-tests.Rout' to 'cca-object-tests.Rout.save' ...618,623c618,623 < 1 1.78665 -1.5160 -1.5583 -1.09080 -0.25833 0.92271 < 2 0.01705 -0.6581 0.9301 0.28816 0.57516 0.05239 < 3 0.44007 -0.3970 1.1270 0.21113 0.09235 -0.44842 < 4 0.54915 -0.3741 0.4416 0.09204 0.16597 -0.47429 < 5 0.66299 0.3274 1.2512 2.07857 -0.69303 0.11522 < 6 0.34304 0.4884 1.1823 1.87243 -0.05482 0.40479 --- > 1 -1.78665 -1.5160 -1.5583 -1.09080 -0.25833 0.92271 > 2 -0.01705 -0.6581 0.9301 0.28816 0.57516 0.05239 > 3 -0.44007 -0.3970 1.1270 0.21113 0.09235 -0.44842 > 4 -0.54915 -0.3741 0.4416 0.09204 0.16597 -0.47429 > 5 -0.66299 0.3274 1.2512 2.07857 -0.69303 0.11522 > 6 -0.34304 0.4884 1.1823 1.87243 -0.05482 0.40479 630,635c630,635 < 1 1.14324 -0.517750 -0.13719 -0.20653 -0.25833 0.92271 < 2 0.40891 0.006731 0.84283 1.43257 0.57516 0.05239 < 3 0.80504 -0.897322 0.08099 -0.29345 0.09235 -0.44842 < 4 0.82758 -0.872017 0.06645 -0.28765 0.16597 -0.47429 < 5 -0.05034 -0.082513 1.27197 0.07874 -0.69303 0.11522 < 6 0.40060 0.423583 0.98106 0.19462 -0.05482 0.40479 --- > 1 -1.14324 -0.517750 -0.13719 -0.20653 -0.25833 0.92271 > 2 -0.40891 0.006731 0.84283 1.43257 0.57516 0.05239 > 3 -0.80504 -0.897322 0.08099 -0.29345 0.09235 -0.44842 > 4 -0.82758 -0.872017 0.06645 -0.28765 0.16597 -0.47429 > 5 0.05034 -0.082513 1.27197 0.07874 -0.69303 0.11522 > 6 -0.40060 0.423583 0.98106 0.19462 -0.05482 0.40479 642,645c642,645 < Manure.L 0.1792 -0.26684 -0.09723 0.22382 0 0 < Manure.Q 0.3484 -0.37781 -0.18544 -0.17142 0 0 < Manure.C 0.3848 -0.05946 0.21300 -0.70283 0 0 < A1 -0.6766 -0.36898 0.46068 -0.06145 0 0 --- > Manure.L -0.1792 -0.26684 -0.09723 0.22382 0 0 > Manure.Q -0.3484 -0.37781 -0.18544 -0.17142 0 0 > Manure.C -0.3848 -0.05946 0.21300 -0.70283 0 0 > A1 0.6766 -0.36898 0.46068 -0.06145 0 0 651,654c651,654 < Manure1 -0.16965 0.17776 -0.399584 -1.1193 0 0 < Manure2 0.07803 0.45741 1.074105 0.3951 0 0 < Manure3 -0.64476 -0.01896 -0.776980 0.6413 0 0 < Manure4 0.92529 -0.76236 0.003417 -0.2625 0 0 --- > Manure1 0.16965 0.17776 -0.399584 -1.1193 0 0 > Manure2 -0.07803 0.45741 1.074105 0.3951 0 0 > Manure3 0.64476 -0.01896 -0.776980 0.6413 0 0 > Manure4 -0.92529 -0.76236 0.003417 -0.2625 0 0 1067,1069c1067,1069 < 1 1.851007e+00 3.639809e+00 1.737905e-32 3.9674722 1.259496e-32 0.3922993 < 2 1.732986e-01 1.317109e-32 1.554692e-32 0.4063197 5.089012e-01 1.4998711 < 3 2.379831e-02 3.681363e-01 1.684991e-33 0.7581053 1.570413e-33 1.2938972 --- > 1 1.851007e+00 3.639809e+00 2.179007e-32 3.9674722 5.479544e-32 0.3922993 > 2 1.732986e-01 4.282631e-31 1.871117e-31 0.4063197 5.089012e-01 1.4998711 > 3 2.379831e-02 3.681363e-01 1.435946e-32 0.7581053 5.720843e-35 1.2938972 1071,1072c1071,1072 < 5 1.029318e+03 8.849107e+02 1.628428e-30 1461.1270610 2.665671e+03 5962.9242543 < 6 4.980356e+02 7.907080e+02 3.236982e-31 1305.5834487 3.788022e+02 340.8905896 --- > 5 1.029318e+03 8.849107e+02 5.438392e-30 1461.1270610 2.665671e+03 5962.9242543 > 6 4.980356e+02 7.907080e+02 1.879929e-29 1305.5834487 3.788022e+02 340.8905896 1074,1076c1074,1076 < 1 0.1839542 3.860986e-01 5.662338e-01 2.707376e-34 2.024020e-01 5.6097489 < 2 1.0958050 4.334666e-34 6.626819e-34 3.647552e-33 9.548267e-33 1.3981269 < 3 0.2525391 5.300503e-01 7.773465e-01 6.110718e-33 2.778648e-01 0.4890614 --- > 1 0.1839542 3.860986e-01 5.662338e-01 2.908269e-32 2.024020e-01 5.6097489 > 2 1.0958050 4.624667e-33 4.559223e-32 4.811614e-31 1.600456e-31 1.3981269 > 3 0.2525391 5.300503e-01 7.773465e-01 2.515477e-32 2.778648e-01 0.4890614 1078,1079c1078,1079 < 5 2774.2054183 9.710452e-30 3.656853e-29 6.625018e-34 1.968319e+02 1891.5365604 < 6 1136.6970365 1.330792e-29 3.611963e-29 4.336807e-31 1.758783e+02 1754.8637411 --- > 5 2774.2054183 1.192148e-30 3.496696e-30 4.069428e-29 1.968319e+02 1891.5365604 > 6 1136.6970365 8.588488e-30 2.798993e-30 1.146502e-29 1.758783e+02 1754.8637411 1081,1083c1081,1083 < 1 3.434455e-33 2.084959e-31 6.831603e-02 5.994900e-01 11.2960850 5.848718e-33 < 2 1.066064e-32 2.536554e-01 8.431592e-34 3.838539e-32 0.2701750 1.487614e+00 < 3 5.447475e-33 5.496586e-33 9.378675e-02 8.230018e-01 0.6544776 1.805005e-32 --- > 1 2.994391e-33 3.584712e-32 6.831603e-02 5.994900e-01 11.2960850 6.665583e-31 > 2 3.946001e-32 2.536554e-01 8.405610e-32 1.714565e-32 0.2701750 1.487614e+00 > 3 2.869981e-33 5.444020e-32 9.378675e-02 8.230018e-01 0.6544776 2.693864e-33 1085,1086c1085,1086 < 5 1.745468e-29 4.590436e-31 1.889735e+03 1.713283e+03 1189.9211411 2.825358e+03 < 6 1.764709e-29 3.968264e-30 1.688564e+03 1.530896e+03 458.1039637 1.367050e+03 --- > 5 2.121726e-30 9.674570e-30 1.889735e+03 1.713283e+03 1189.9211411 2.825358e+03 > 6 4.230712e-31 4.106410e-30 1.688564e+03 1.530896e+03 458.1039637 1.367050e+03 1088,1090c1088,1090 < 1 6.895259e+00 0.19124551 2.314134e-01 7.205523e-02 1.2079134 2.766842e-34 < 2 2.988364e-02 2.63662504 1.768460e-32 8.735773e-33 0.2167341 2.961703e-33 < 3 1.134247e+00 0.06239637 3.176928e-01 9.892005e-02 1.6582678 9.905076e-34 --- > 1 6.895259e+00 0.19124551 2.314134e-01 7.205523e-02 1.2079134 0.000000e+00 > 2 2.988364e-02 2.63662504 4.420245e-31 1.078842e-32 0.2167341 7.160739e-31 > 3 1.134247e+00 0.06239637 3.176928e-01 9.892005e-02 1.6582678 2.242288e-33 1092,1093c1092,1093 < 5 1.466608e+03 855.98844449 2.250450e+02 5.386319e+03 621.3141300 6.987294e-30 < 6 3.541864e+02 912.87493994 2.010879e+02 7.068395e+03 555.1724187 4.564657e-30 --- > 5 1.466608e+03 855.98844449 2.250450e+02 5.386319e+03 621.3141300 4.789513e-29 > 6 3.541864e+02 912.87493994 2.010879e+02 7.068395e+03 555.1724187 4.089123e-29 1095,1097c1095,1097 < 1 0.88826070 1.290404e-30 4.640375e-01 2.425893e-30 7.634084e-01 1.025041e-01 < 2 0.06495429 4.128717e-33 2.007862e-04 4.708545e+00 1.035890e+00 2.107223e-33 < 3 0.09221991 2.130891e-32 4.817673e-02 6.535235e-32 2.358079e-02 1.407214e-01 --- > 1 0.88826070 1.954244e-31 4.640375e-01 1.222203e-31 7.634084e-01 1.025041e-01 > 2 0.06495429 3.365544e-34 2.007862e-04 4.708545e+00 1.035890e+00 3.880418e-32 > 3 0.09221991 1.356119e-32 4.817673e-02 1.479680e-32 2.358079e-02 1.407214e-01 1099,1100c1099,1100 < 5 39.97309955 9.407841e+01 4.725006e+02 9.215259e-29 3.454806e+02 2.813065e-29 < 6 22.80149615 1.777212e+04 1.689403e+03 1.102013e-28 2.937072e+03 3.403099e-29 --- > 5 39.97309955 9.407841e+01 4.725006e+02 5.901182e-29 3.454806e+02 3.164998e-30 > 6 22.80149615 1.777212e+04 1.689403e+03 3.078362e-30 2.937072e+03 1.379339e-29 1133c1133,1134 < numeric(0) --- > > [1,] 1193,1198c1194,1199 < Achimill 0.015342931 1.733414e-34 0.03535925 < Agrostol 0.038101789 6.872132e-34 0.04400950 < Airaprae 0.025813313 3.760269e-35 0.07828527 < Alopgeni 0.048789228 3.923213e-34 0.04641737 < Anthodor 0.014146632 6.284224e-35 0.07969556 < Bellpere 0.006973897 4.410958e-35 0.03076871 --- > Achimill 0.015342931 6.319458e-35 0.03535925 > Agrostol 0.038101789 7.854183e-34 0.04400950 > Airaprae 0.025813313 2.193409e-34 0.07828527 > Alopgeni 0.048789228 2.166671e-33 0.04641737 > Anthodor 0.014146632 2.678246e-34 0.07969556 > Bellpere 0.006973897 2.949080e-33 0.03076871 1230,1234c1231,1235 < Manure.L 0.3363608 -0.4690057 -0.1455160 0.1966932 < Manure.Q 0.4608444 -0.4679955 -0.1955898 -0.1061713 < Manure.C 0.3505782 -0.0507461 0.1547750 -0.2998918 < Manure^4 0.2669010 0.1008842 0.5385750 0.0872403 < A1 -0.5693913 -0.2908300 0.3091850 -0.0242160 --- > Manure.L -0.3363608 -0.4690057 -0.1455160 0.1966932 > Manure.Q -0.4608444 -0.4679955 -0.1955898 -0.1061713 > Manure.C -0.3505782 -0.0507461 0.1547750 -0.2998918 > Manure^4 -0.2669010 0.1008842 0.5385750 0.0872403 > A1 0.5693913 -0.2908300 0.3091850 -0.0242160 1446,1451c1447,1452 < ManagementHF 0.05723350 0.2059983 0.007271835 -0.39636572 < ManagementNM 2.14856017 0.7651671 3.369400423 1.57734022 < ManagementSF -0.11222605 0.6842717 0.007712919 -0.47394178 < Manure.L 1.50644728 -0.3419042 2.138959205 1.50184559 < Manure.Q -0.83513374 -0.6857571 -1.906088364 -0.97681891 < Manure.C 0.77167591 0.1002141 1.217675445 0.03048179 --- > ManagementHF -0.05723350 0.2059983 0.007271835 -0.39636572 > ManagementNM -2.14856017 0.7651671 3.369400423 1.57734022 > ManagementSF 0.11222605 0.6842717 0.007712919 -0.47394178 > Manure.L -1.50644728 -0.3419042 2.138959205 1.50184559 > Manure.Q 0.83513374 -0.6857571 -1.906088364 -0.97681891 > Manure.C -0.77167591 0.1002141 1.217675445 0.03048179 1453c1454 < A1 -0.07499906 -0.0841729 0.048383354 -0.01927336 --- > A1 0.07499906 -0.0841729 0.048383354 -0.01927336 Running 'oecosimu-tests.R' [3s] Comparing 'oecosimu-tests.Rout' to 'oecosimu-tests.Rout.save' ...932c932 < row sums: [1] "Mean relative difference: 0.4253934" --- > row sums: [1] "Mean relative difference: 0.4160623" 934,936c934,936 < fill: [1] "Mean relative difference: 0.3552492" < row freqs: [1] "Mean relative difference: 0.3997879" < col freqs: [1] "Mean relative difference: 0.356383" --- > fill: [1] "Mean relative difference: 0.3566138" > row freqs: [1] "Mean relative difference: 0.406423" > col freqs: [1] "Mean relative difference: 0.3577495" Running 'vegan-tests.R' [7s] Comparing 'vegan-tests.Rout' to 'vegan-tests.Rout.save' ...682c682 < ... Procrustes: rmse 2.812037e-05 max resid 9.047785e-05 --- > ... Procrustes: rmse 2.260742e-06 max resid 5.293932e-06 686c686 < ... Procrustes: rmse 2.724763e-05 max resid 8.660655e-05 --- > ... Procrustes: rmse 3.225938e-06 max resid 7.314283e-06 692c692 < ... Procrustes: rmse 2.295609e-05 max resid 6.384851e-05 --- > ... Procrustes: rmse 2.295609e-05 max resid 6.384852e-05 796c796 < Run 18 stress 0.1843198 --- > Run 18 stress 0.1843197 890c890 < [1] -1.332268e-15 2.220446e-15 --- > [1] -1.509903e-14 1.110223e-14 893c893 < [1] -2.886580e-15 5.329071e-15 --- > [1] -1.287859e-14 1.731948e-14 ** running tests for arch 'x64' ... [15s] OK Running 'cca-object-tests.R' [4s] Comparing 'cca-object-tests.Rout' to 'cca-object-tests.Rout.save' ...1133c1133,1134 < numeric(0) --- > > [1,] Running 'oecosimu-tests.R' [3s] Comparing 'oecosimu-tests.Rout' to 'oecosimu-tests.Rout.save' ... OK Running 'vegan-tests.R' [7s] Comparing 'vegan-tests.Rout' to 'vegan-tests.Rout.save' ... OK * checking for unstated dependencies in vignettes ... OK * checking package vignettes in 'inst/doc' ... OK * checking re-building of vignette outputs ... [66s] OK * checking PDF version of manual ... OK * DONE Status: OK