- using R version 3.5.3 (2019-03-11)
- using platform: x86_64-w64-mingw32 (64-bit)
- using session charset: ISO8859-1
- checking for file 'vegan/DESCRIPTION' ... OK
- this is package 'vegan' version '2.5-6'
- 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 ... [58s] 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 pragmas in C/C++ headers and code ... 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' ... [43s] OK
- running examples for arch 'x64' ... [44s] OK
- checking for unstated dependencies in 'tests' ... OK
- checking tests ...
- running tests for arch 'i386' ... [11s] OK
Running 'cca-object-tests.R' [4s]
Comparing 'cca-object-tests.Rout' to 'cca-object-tests.Rout.save' ...763c763
< [1] 0.055799
---
> [1] 0.054162
877c877
< Model 4 0.45 1.27 0.18
---
> Model 4 0.45 1.27 0.26
890c890
< Model 4 16.8 1.32 0.08 .
---
> Model 4 16.8 1.32 0.18
892,893d891
< ---
< Signif. codes: 0 '***' 0.001 '**' 0.01 '*' 0.05 '.' 0.1 ' ' 1
905c903
< Model 4 6.14 1.22 0.14
---
> Model 4 6.14 1.22 0.22
918c916
< Model 4 1.07 1.59 0.12
---
> Model 4 1.07 1.59 0.16
931c929
< Model 4 1.03 1.73 0.1
---
> Model 4 1.03 1.73 0.14
944c942
< Model 4 213 1.41 0.1
---
> Model 4 213 1.41 0.14
957c955
< Model 4 203 1.57 0.04 *
---
> Model 4 203 1.57 0.12
959,960d956
< ---
< Signif. codes: 0 '***' 0.001 '**' 0.01 '*' 0.05 '.' 0.1 ' ' 1
979,980c975,976
< Manure 3 86.5 1.03 0.30
< A1 1 89.0 2.00 0.08 .
---
> Manure 3 86.5 1.03 0.46
> A1 1 89.0 2.00 0.04 *
987c983
< Manure 3 87.4 1.30 0.10
---
> Manure 3 87.4 1.30 0.22
993,994c989,990
< Manure 3 68.2 1.12 0.3
< A1 1 69.6 1.48 0.2
---
> Manure 3 68.2 1.12 0.34
> A1 1 69.6 1.48 0.14
999c995
< Manure 3 28.4 1.24 0.20
---
> Manure 3 28.4 1.24 0.26
1005,1006c1001,1002
< Manure 3 26.4 1.32 0.2
< A1 1 28.4 2.46 0.1
---
> Manure 3 26.4 1.32 0.26
> A1 1 28.4 2.46 0.10
1015c1011
< Model 4 0.45 1.27 0.18
---
> Model 4 0.45 1.27 0.26
1024c1020
< Model 4 16.8 1.32 0.08 .
---
> Model 4 16.8 1.32 0.18
1026,1027d1021
< ---
< Signif. codes: 0 '***' 0.001 '**' 0.01 '*' 0.05 '.' 0.1 ' ' 1
1035c1029
< Model 4 6.14 1.22 0.14
---
> Model 4 6.14 1.22 0.22
1044c1038
< Model 4 1.07 1.59 0.12
---
> Model 4 1.07 1.59 0.16
1053c1047
< Model 4 1.03 1.73 0.1
---
> Model 4 1.03 1.73 0.14
1062c1056
< Model 4 213 1.41 0.1
---
> Model 4 213 1.41 0.14
1071c1065
< Model 4 203 1.57 0.04 *
---
> Model 4 203 1.57 0.12
1073,1074d1066
< ---
< Signif. codes: 0 '***' 0.001 '**' 0.01 '*' 0.05 '.' 0.1 ' ' 1
1091,1092c1083,1084
< Manure 3 0.273 1.03 0.34
< A1 1 0.177 2.00 0.08 .
---
> Manure 3 0.273 1.03 0.46
> A1 1 0.177 2.00 0.04 *
1104c1096
< Manure 3 13.3 1.40 0.04 *
---
> Manure 3 13.3 1.40 0.14
1107,1108d1098
< ---
< Signif. codes: 0 '***' 0.001 '**' 0.01 '*' 0.05 '.' 0.1 ' ' 1
1117,1118c1107,1108
< Manure 3 4.28 1.14 0.24
< A1 1 1.86 1.48 0.20
---
> Manure 3 4.28 1.14 0.36
> A1 1 1.86 1.48 0.14
1128c1118
< Manure 3 0.703 1.39 0.14
---
> Manure 3 0.703 1.39 0.22
1139c1129
< Manure 3 0.667 1.49 0.14
---
> Manure 3 0.667 1.49 0.22
1150,1151c1140,1141
< Manure 3 173 1.53 0.04 *
< A1 1 40 1.07 0.40
---
> Manure 3 173 1.53 0.12
> A1 1 40 1.07 0.34
1153,1154d1142
< ---
< Signif. codes: 0 '***' 0.001 '**' 0.01 '*' 0.05 '.' 0.1 ' ' 1
1163,1164c1151,1152
< Manure 3 163 1.68 0.04 *
< A1 1 39 1.22 0.36
---
> Manure 3 163 1.68 0.10
> A1 1 39 1.22 0.28
1166,1167d1153
< ---
< Signif. codes: 0 '***' 0.001 '**' 0.01 '*' 0.05 '.' 0.1 ' ' 1
1177,1178c1163,1164
< Manure 3 0.274 1.03 0.30
< A1 1 0.177 2.00 0.08 .
---
> Manure 3 0.274 1.03 0.46
> A1 1 0.177 2.00 0.04 *
1190c1176
< Manure 3 12.4 1.30 0.10
---
> Manure 3 12.4 1.30 0.22
1201,1202c1187,1188
< Manure 3 4.21 1.12 0.3
< A1 1 1.86 1.48 0.2
---
> Manure 3 4.21 1.12 0.34
> A1 1 1.86 1.48 0.14
1212c1198
< Manure 3 0.627 1.24 0.20
---
> Manure 3 0.627 1.24 0.26
1223,1224c1209,1210
< Manure 3 0.594 1.32 0.2
< A1 1 0.367 2.46 0.1
---
> Manure 3 0.594 1.32 0.26
> A1 1 0.367 2.46 0.10
1234,1235c1220,1221
< Manure 3 165 1.46 0.08 .
< A1 1 40 1.07 0.40
---
> Manure 3 165 1.46 0.18
> A1 1 40 1.07 0.34
1237,1238d1222
< ---
< Signif. codes: 0 '***' 0.001 '**' 0.01 '*' 0.05 '.' 0.1 ' ' 1
1247,1248c1231,1232
< Manure 3 155 1.60 0.06 .
< A1 1 39 1.22 0.36
---
> Manure 3 155 1.60 0.18
> A1 1 39 1.22 0.28
1250,1251d1233
< ---
< Signif. codes: 0 '***' 0.001 '**' 0.01 '*' 0.05 '.' 0.1 ' ' 1
1261,1264c1243,1246
< CCA1 1 0.223 2.52 0.14
< CCA2 1 0.123 1.39 0.70
< CCA3 1 0.064 0.72 1.00
< CCA4 1 0.041 0.46 0.90
---
> CCA1 1 0.223 2.52 0.24
> CCA2 1 0.123 1.39 0.58
> CCA3 1 0.064 0.72 0.98
> CCA4 1 0.041 0.46 0.94
1274,1276c1256,1258
< RDA1 1 8.5 2.69 0.08 .
< RDA2 1 4.3 1.36 0.72
< RDA3 1 2.2 0.69 0.96
---
> RDA1 1 8.5 2.69 0.14
> RDA2 1 4.3 1.36 0.60
> RDA3 1 2.2 0.69 0.98
1279,1280d1260
< ---
< Signif. codes: 0 '***' 0.001 '**' 0.01 '*' 0.05 '.' 0.1 ' ' 1
1289,1292c1269,1272
< RDA1 1 2.61 2.08 0.18
< RDA2 1 1.70 1.35 0.76
< RDA3 1 1.10 0.88 0.96
< RDA4 1 0.73 0.58 0.88
---
> RDA1 1 2.61 2.08 0.32
> RDA2 1 1.70 1.35 0.68
> RDA3 1 1.10 0.88 0.92
> RDA4 1 0.73 0.58 0.84
1302,1305c1282,1285
< CAP1 1 0.674 4.00 0.12
< CAP2 1 0.243 1.44 0.78
< CAP3 1 0.105 0.62 0.94
< CAP4 1 0.051 0.30 0.98
---
> CAP1 1 0.674 4.00 0.16
> CAP2 1 0.243 1.44 0.62
> CAP3 1 0.105 0.62 0.96
> CAP4 1 0.051 0.30 0.94
1315,1318c1295,1298
< dbRDA1 1 0.667 4.45 0.10
< dbRDA2 1 0.238 1.59 0.76
< dbRDA3 1 0.091 0.61 0.94
< dbRDA4 1 0.038 0.26 0.96
---
> dbRDA1 1 0.667 4.45 0.16
> dbRDA2 1 0.238 1.59 0.60
> dbRDA3 1 0.091 0.61 0.96
> dbRDA4 1 0.038 0.26 0.94
1328,1330c1308,1310
< CAP1 1 126 3.33 0.14
< CAP2 1 49 1.31 0.80
< CAP3 1 24 0.64 0.98
---
> CAP1 1 126 3.33 0.18
> CAP2 1 49 1.31 0.72
> CAP3 1 24 0.64 1.00
1341,1344c1321,1324
< dbRDA1 1 123 3.81 0.12
< dbRDA2 1 47 1.47 0.74
< dbRDA3 1 22 0.68 0.96
< dbRDA4 1 10 0.31 0.88
---
> dbRDA1 1 123 3.81 0.16
> dbRDA2 1 47 1.47 0.70
> dbRDA3 1 22 0.68 0.98
> dbRDA4 1 10 0.31 0.84
Running 'oecosimu-tests.R' [2s]
Comparing 'oecosimu-tests.Rout' to 'oecosimu-tests.Rout.save' ... OK
Running 'vegan-tests.R' [5s]
Comparing 'vegan-tests.Rout' to 'vegan-tests.Rout.save' ...61c61
< Management 3 0.82392 1.7163 0.03 *
---
> Management 3 0.82392 1.7163 0.02 *
63c63
< spno 1 0.08318 0.5198 0.96
---
> spno 1 0.08318 0.5198 0.95
75,76c75,76
< Management 3 0.55418 1.1544 0.21
< poly(A1, 2) 2 0.32940 1.0292 0.44
---
> Management 3 0.55418 1.1544 0.25
> poly(A1, 2) 2 0.32940 1.0292 0.30
87,92c87,92
< CCA1 1 0.46993 2.9366 0.07 .
< CCA2 1 0.26217 1.6384 0.75
< CCA3 1 0.19308 1.2066 0.97
< CCA4 1 0.18345 1.1464 0.90
< CCA5 1 0.08871 0.5544 0.98
< CCA6 1 0.06104 0.3815 0.93
---
> CCA1 1 0.46993 2.9366 0.09 .
> CCA2 1 0.26217 1.6384 0.80
> CCA3 1 0.19308 1.2066 0.89
> CCA4 1 0.18345 1.1464 0.84
> CCA5 1 0.08871 0.5544 0.99
> CCA6 1 0.06104 0.3815 0.90
105c105
< Model 6 59.582 1.6462 0.04 *
---
> Model 6 59.582 1.6462 0.03 *
118,119c118,119
< poly(A1, 2) 2 10.150 0.8413 0.63
< spno 1 3.167 0.5250 0.79
---
> poly(A1, 2) 2 10.150 0.8413 0.69
> spno 1 3.167 0.5250 0.91
131,133c131,133
< Management 3 28.7515 1.5888 0.13
< poly(A1, 2) 2 8.0847 0.6701 0.88
< spno 1 3.1669 0.5250 0.90
---
> Management 3 28.7515 1.5888 0.05 *
> poly(A1, 2) 2 8.0847 0.6701 0.92
> spno 1 3.1669 0.5250 0.93
134a135,136
> ---
> Signif. codes: 0 '***' 0.001 '**' 0.01 '*' 0.05 '.' 0.1 ' ' 1
143,147c145,149
< CAP1 1 25.0252 4.1487 0.03 *
< CAP2 1 15.8759 2.6319 0.39
< CAP3 1 8.0942 1.3419 0.78
< CAP4 1 5.0675 0.8401 0.95
< CAP5 1 3.5671 0.5914 0.96
---
> CAP1 1 25.0252 4.1487 0.02 *
> CAP2 1 15.8759 2.6319 0.45
> CAP3 1 8.0942 1.3419 0.88
> CAP4 1 5.0675 0.8401 0.96
> CAP5 1 3.5671 0.5914 0.95
162c164
< Model 6 1.54840 1.6423 0.14
---
> Model 6 1.54840 1.6423 0.13
172,174c174,176
< Management 3 1.17117 2.4844 0.02 *
< poly(A1, 2) 2 0.30602 0.9737 0.53
< spno 1 0.07121 0.4532 0.84
---
> Management 3 1.17117 2.4844 0.06 .
> poly(A1, 2) 2 0.30602 0.9737 0.54
> spno 1 0.07121 0.4532 0.85
186,188c188,190
< Management 3 0.64888 1.3765 0.22
< poly(A1, 2) 2 0.26160 0.8324 0.69
< spno 1 0.07121 0.4532 0.91
---
> Management 3 0.64888 1.3765 0.25
> poly(A1, 2) 2 0.26160 0.8324 0.66
> spno 1 0.07121 0.4532 0.86
198,201c200,203
< CAP1 1 0.77834 4.9533 0.13
< CAP2 1 0.45691 2.9078 0.48
< CAP3 1 0.14701 0.9355 0.98
< CAP4 1 0.11879 0.7560 0.96
---
> CAP1 1 0.77834 4.9533 0.09 .
> CAP2 1 0.45691 2.9078 0.39
> CAP3 1 0.14701 0.9355 1.00
> CAP4 1 0.11879 0.7560 0.97
204a207,208
> ---
> Signif. codes: 0 '***' 0.001 '**' 0.01 '*' 0.05 '.' 0.1 ' ' 1
215c219
< Model 6 1.25838 1.3106 0.11
---
> Model 6 1.25838 1.3106 0.18
227c231
< Management 3 0.82392 1.7163 0.02 *
---
> Management 3 0.82392 1.7163 0.03 *
229c233
< spno 1 0.08318 0.5198 0.95
---
> spno 1 0.08318 0.5198 0.96
241,243c245,247
< Management 3 0.55418 1.1544 0.33
< poly(A1, 2) 2 0.32940 1.0292 0.44
< spno 1 0.08318 0.5198 0.94
---
> Management 3 0.55418 1.1544 0.28
> poly(A1, 2) 2 0.32940 1.0292 0.46
> spno 1 0.08318 0.5198 0.96
253c257
< CCA1 1 0.46993 2.9366 0.05 *
---
> CCA1 1 0.46993 2.9366 0.10
255,257c259,261
< CCA3 1 0.19308 1.2066 0.93
< CCA4 1 0.18345 1.1464 0.88
< CCA5 1 0.08871 0.5544 0.97
---
> CCA3 1 0.19308 1.2066 0.95
> CCA4 1 0.18345 1.1464 0.85
> CCA5 1 0.08871 0.5544 0.96
260,261d263
< ---
< Signif. codes: 0 '***' 0.001 '**' 0.01 '*' 0.05 '.' 0.1 ' ' 1
404,407c406,409
< CCA1 1 0.27109 2.9561 0.09 .
< CCA2 1 0.14057 1.5329 0.56
< CCA3 1 0.08761 0.9553 0.78
< CCA4 1 0.05624 0.6132 0.76
---
> CCA1 1 0.27109 2.9561 0.07 .
> CCA2 1 0.14057 1.5329 0.48
> CCA3 1 0.08761 0.9553 0.85
> CCA4 1 0.05624 0.6132 0.84
443,445c445,447
< CAP1 1 0.2682 1.3075 0.783
< CAP2 1 0.0685 0.3339 0.998
< CAP3 1 0.0455 0.2217 0.967
---
> CAP1 1 0.2682 1.3075 0.779
> CAP2 1 0.0685 0.3339 0.997
> CAP3 1 0.0455 0.2217 0.964
456,457c458,459
< A 1 0.1316 0.6415 0.680
< B 2 0.2506 0.6108 0.824
---
> A 1 0.1316 0.6415 0.696
> B 2 0.2506 0.6108 0.821
471,473c473,475
< CAP1 1 0.2682 1.3267 0.764
< CAP2 1 0.0685 0.3388 0.993
< CAP3 1 0.0455 0.2249 0.964
---
> CAP1 1 0.2682 1.3267 0.785
> CAP2 1 0.0685 0.3388 0.995
> CAP3 1 0.0455 0.2249 0.961
484,485c486,487
< A 1 0.1316 0.6509 0.693
< B 2 0.2506 0.6198 0.829
---
> A 1 0.1316 0.6509 0.665
> B 2 0.2506 0.6198 0.834
499c501
< RDA1 1 0.2682 1.3075 0.774
---
> RDA1 1 0.2682 1.3075 0.770
501c503
< RDA3 1 0.0455 0.2217 0.964
---
> RDA3 1 0.0455 0.2217 0.962
512,513c514,515
< A 1 0.1316 0.6415 0.669
< B 2 0.2506 0.6108 0.827
---
> A 1 0.1316 0.6415 0.656
> B 2 0.2506 0.6108 0.825
527,529c529,531
< RDA1 1 0.2682 1.3267 0.768
< RDA2 1 0.0685 0.3388 0.995
< RDA3 1 0.0455 0.2249 0.971
---
> RDA1 1 0.2682 1.3267 0.765
> RDA2 1 0.0685 0.3388 0.996
> RDA3 1 0.0455 0.2249 0.969
540,541c542,543
< A 1 0.1316 0.6509 0.695
< B 2 0.2506 0.6198 0.820
---
> A 1 0.1316 0.6509 0.690
> B 2 0.2506 0.6198 0.823
566,570c568,572
< A1 1 0.22476 2.5704 0.010 **
< Moisture 3 0.51898 1.9783 0.009 **
< Management 3 0.39543 1.5074 0.064 .
< Use 2 0.10910 0.6238 0.922
< Manure 3 0.25490 0.9717 0.519
---
> A1 1 0.22476 2.5704 0.012 *
> Moisture 3 0.51898 1.9783 0.005 **
> Management 3 0.39543 1.5074 0.055 .
> Use 2 0.10910 0.6238 0.927
> Manure 3 0.25490 0.9717 0.518
583,587c585,589
< A1 1 8.1148 2.7156 0.008 **
< Moisture 3 21.6497 2.4150 0.008 **
< Management 3 19.1153 2.1323 0.009 **
< Use 2 4.7007 0.7865 0.730
< Manure 3 9.6257 1.0737 0.377
---
> A1 1 8.1148 2.7156 0.009 **
> Moisture 3 21.6497 2.4150 0.004 **
> Management 3 19.1153 2.1323 0.007 **
> Use 2 4.7007 0.7865 0.724
> Manure 3 9.6257 1.0737 0.360
612c614
< Manure 4 4.7257 5.7006 0.009 **
---
> Manure 4 4.7257 5.7006 0.011 *
673,675c675,677
< Procrustes Sum of Squares (m12 squared): 0.9147
< Correlation in a symmetric Procrustes rotation: 0.292
< Significance: 0.08
---
> Procrustes Sum of Squares (m12 squared): 0.9389
> Correlation in a symmetric Procrustes rotation: 0.2471
> Significance: 0.46
681,695c683,697
< [1] 0.2056649 0.2008622 0.2062525 0.2656158 0.2739148 0.1990895 0.3124461
< [8] 0.2287779 0.2033140 0.2396172 0.1868019 0.2736072 0.1830199 0.2026019
< [15] 0.2402570 0.2286169 0.2791609 0.2214468 0.2356083 0.2188325 0.2097262
< [22] 0.2596154 0.2560289 0.2190367 0.2174689 0.2438396 0.1991101 0.2374612
< [29] 0.2030745 0.2205115 0.2566758 0.1448623 0.2354268 0.2419134 0.3144177
< [36] 0.2368505 0.2442661 0.2272011 0.3184241 0.2200089 0.2598430 0.2301587
< [43] 0.2763337 0.2332606 0.1935269 0.2315727 0.2573623 0.2021127 0.2387335
< [50] 0.2419087 0.2213094 0.2231619 0.2577845 0.2828219 0.2554605 0.2830915
< [57] 0.2342396 0.2137396 0.2151201 0.2432896 0.1956238 0.2055716 0.2329736
< [64] 0.2086125 0.2039124 0.1955711 0.2038045 0.2358886 0.2579199 0.1808128
< [71] 0.2155189 0.2967100 0.2480105 0.2010537 0.2718478 0.2182713 0.2471893
< [78] 0.2310223 0.2007771 0.2902640 0.2392380 0.2551756 0.3476679 0.2632614
< [85] 0.2289929 0.2222382 0.2503562 0.1983700 0.2084773 0.2406556 0.2478302
< [92] 0.2136439 0.3251671 0.2048928 0.3098776 0.2501555 0.2677039 0.2427125
< [99] 0.2693285
---
> [1] 0.2142734 0.2317691 0.2325867 0.2318738 0.2297942 0.2547687 0.2150992
> [8] 0.2856655 0.2323035 0.2430091 0.2607687 0.2653226 0.2127120 0.2482851
> [15] 0.3044707 0.2797892 0.2644764 0.2560291 0.2916665 0.2330199 0.2434141
> [22] 0.2891063 0.2871878 0.2609612 0.2158827 0.2297220 0.2417230 0.2244848
> [29] 0.2177450 0.2528551 0.2616422 0.2584395 0.2412174 0.2244347 0.2264776
> [36] 0.2244727 0.1973865 0.2837535 0.2634514 0.2823068 0.2699507 0.2750179
> [43] 0.2628074 0.2458801 0.2635264 0.2801017 0.2296173 0.1947667 0.2929171
> [50] 0.2422339 0.1831137 0.2688563 0.2555202 0.2043385 0.2287129 0.2366098
> [57] 0.2141830 0.1858646 0.2616734 0.1974915 0.3197986 0.2245312 0.2712518
> [64] 0.2171044 0.2241602 0.2100868 0.2183290 0.2143512 0.2642714 0.2572791
> [71] 0.2806032 0.2401609 0.2063171 0.2016924 0.2684739 0.2484569 0.2200211
> [78] 0.2487178 0.1925942 0.2957915 0.2991842 0.2359773 0.2440686 0.2504427
> [85] 0.2919524 0.2324999 0.2086198 0.2298386 0.2727169 0.3253668 0.2292110
> [92] 0.2193247 0.3517265 0.2777563 0.3713275 0.2330743 0.1986322 0.2027622
> [99] 0.2281227
- running tests for arch 'x64' ... [12s] OK
Running 'cca-object-tests.R' [4s]
Comparing 'cca-object-tests.Rout' to 'cca-object-tests.Rout.save' ...763c763
< [1] 0.055799
---
> [1] 0.054162
877c877
< Model 4 0.45 1.27 0.18
---
> Model 4 0.45 1.27 0.26
890c890
< Model 4 16.8 1.32 0.08 .
---
> Model 4 16.8 1.32 0.18
892,893d891
< ---
< Signif. codes: 0 '***' 0.001 '**' 0.01 '*' 0.05 '.' 0.1 ' ' 1
905c903
< Model 4 6.14 1.22 0.14
---
> Model 4 6.14 1.22 0.22
918c916
< Model 4 1.07 1.59 0.12
---
> Model 4 1.07 1.59 0.16
931c929
< Model 4 1.03 1.73 0.1
---
> Model 4 1.03 1.73 0.14
944c942
< Model 4 213 1.41 0.1
---
> Model 4 213 1.41 0.14
957c955
< Model 4 203 1.57 0.04 *
---
> Model 4 203 1.57 0.12
959,960d956
< ---
< Signif. codes: 0 '***' 0.001 '**' 0.01 '*' 0.05 '.' 0.1 ' ' 1
979,980c975,976
< Manure 3 86.5 1.03 0.30
< A1 1 89.0 2.00 0.08 .
---
> Manure 3 86.5 1.03 0.46
> A1 1 89.0 2.00 0.04 *
987c983
< Manure 3 87.4 1.30 0.10
---
> Manure 3 87.4 1.30 0.22
993,994c989,990
< Manure 3 68.2 1.12 0.3
< A1 1 69.6 1.48 0.2
---
> Manure 3 68.2 1.12 0.34
> A1 1 69.6 1.48 0.14
999c995
< Manure 3 28.4 1.24 0.20
---
> Manure 3 28.4 1.24 0.26
1005,1006c1001,1002
< Manure 3 26.4 1.32 0.2
< A1 1 28.4 2.46 0.1
---
> Manure 3 26.4 1.32 0.26
> A1 1 28.4 2.46 0.10
1015c1011
< Model 4 0.45 1.27 0.18
---
> Model 4 0.45 1.27 0.26
1024c1020
< Model 4 16.8 1.32 0.08 .
---
> Model 4 16.8 1.32 0.18
1026,1027d1021
< ---
< Signif. codes: 0 '***' 0.001 '**' 0.01 '*' 0.05 '.' 0.1 ' ' 1
1035c1029
< Model 4 6.14 1.22 0.14
---
> Model 4 6.14 1.22 0.22
1044c1038
< Model 4 1.07 1.59 0.12
---
> Model 4 1.07 1.59 0.16
1053c1047
< Model 4 1.03 1.73 0.1
---
> Model 4 1.03 1.73 0.14
1062c1056
< Model 4 213 1.41 0.1
---
> Model 4 213 1.41 0.14
1071c1065
< Model 4 203 1.57 0.04 *
---
> Model 4 203 1.57 0.12
1073,1074d1066
< ---
< Signif. codes: 0 '***' 0.001 '**' 0.01 '*' 0.05 '.' 0.1 ' ' 1
1091,1092c1083,1084
< Manure 3 0.273 1.03 0.34
< A1 1 0.177 2.00 0.08 .
---
> Manure 3 0.273 1.03 0.46
> A1 1 0.177 2.00 0.04 *
1104c1096
< Manure 3 13.3 1.40 0.04 *
---
> Manure 3 13.3 1.40 0.14
1107,1108d1098
< ---
< Signif. codes: 0 '***' 0.001 '**' 0.01 '*' 0.05 '.' 0.1 ' ' 1
1117,1118c1107,1108
< Manure 3 4.28 1.14 0.24
< A1 1 1.86 1.48 0.20
---
> Manure 3 4.28 1.14 0.36
> A1 1 1.86 1.48 0.14
1128c1118
< Manure 3 0.703 1.39 0.14
---
> Manure 3 0.703 1.39 0.22
1139c1129
< Manure 3 0.667 1.49 0.14
---
> Manure 3 0.667 1.49 0.22
1150,1151c1140,1141
< Manure 3 173 1.53 0.04 *
< A1 1 40 1.07 0.40
---
> Manure 3 173 1.53 0.12
> A1 1 40 1.07 0.34
1153,1154d1142
< ---
< Signif. codes: 0 '***' 0.001 '**' 0.01 '*' 0.05 '.' 0.1 ' ' 1
1163,1164c1151,1152
< Manure 3 163 1.68 0.04 *
< A1 1 39 1.22 0.36
---
> Manure 3 163 1.68 0.10
> A1 1 39 1.22 0.28
1166,1167d1153
< ---
< Signif. codes: 0 '***' 0.001 '**' 0.01 '*' 0.05 '.' 0.1 ' ' 1
1177,1178c1163,1164
< Manure 3 0.274 1.03 0.30
< A1 1 0.177 2.00 0.08 .
---
> Manure 3 0.274 1.03 0.46
> A1 1 0.177 2.00 0.04 *
1190c1176
< Manure 3 12.4 1.30 0.10
---
> Manure 3 12.4 1.30 0.22
1201,1202c1187,1188
< Manure 3 4.21 1.12 0.3
< A1 1 1.86 1.48 0.2
---
> Manure 3 4.21 1.12 0.34
> A1 1 1.86 1.48 0.14
1212c1198
< Manure 3 0.627 1.24 0.20
---
> Manure 3 0.627 1.24 0.26
1223,1224c1209,1210
< Manure 3 0.594 1.32 0.2
< A1 1 0.367 2.46 0.1
---
> Manure 3 0.594 1.32 0.26
> A1 1 0.367 2.46 0.10
1234,1235c1220,1221
< Manure 3 165 1.46 0.08 .
< A1 1 40 1.07 0.40
---
> Manure 3 165 1.46 0.18
> A1 1 40 1.07 0.34
1237,1238d1222
< ---
< Signif. codes: 0 '***' 0.001 '**' 0.01 '*' 0.05 '.' 0.1 ' ' 1
1247,1248c1231,1232
< Manure 3 155 1.60 0.06 .
< A1 1 39 1.22 0.36
---
> Manure 3 155 1.60 0.18
> A1 1 39 1.22 0.28
1250,1251d1233
< ---
< Signif. codes: 0 '***' 0.001 '**' 0.01 '*' 0.05 '.' 0.1 ' ' 1
1261,1264c1243,1246
< CCA1 1 0.223 2.52 0.14
< CCA2 1 0.123 1.39 0.70
< CCA3 1 0.064 0.72 1.00
< CCA4 1 0.041 0.46 0.90
---
> CCA1 1 0.223 2.52 0.24
> CCA2 1 0.123 1.39 0.58
> CCA3 1 0.064 0.72 0.98
> CCA4 1 0.041 0.46 0.94
1274,1276c1256,1258
< RDA1 1 8.5 2.69 0.08 .
< RDA2 1 4.3 1.36 0.72
< RDA3 1 2.2 0.69 0.96
---
> RDA1 1 8.5 2.69 0.14
> RDA2 1 4.3 1.36 0.60
> RDA3 1 2.2 0.69 0.98
1279,1280d1260
< ---
< Signif. codes: 0 '***' 0.001 '**' 0.01 '*' 0.05 '.' 0.1 ' ' 1
1289,1292c1269,1272
< RDA1 1 2.61 2.08 0.18
< RDA2 1 1.70 1.35 0.76
< RDA3 1 1.10 0.88 0.96
< RDA4 1 0.73 0.58 0.88
---
> RDA1 1 2.61 2.08 0.32
> RDA2 1 1.70 1.35 0.68
> RDA3 1 1.10 0.88 0.92
> RDA4 1 0.73 0.58 0.84
1302,1305c1282,1285
< CAP1 1 0.674 4.00 0.12
< CAP2 1 0.243 1.44 0.78
< CAP3 1 0.105 0.62 0.94
< CAP4 1 0.051 0.30 0.98
---
> CAP1 1 0.674 4.00 0.16
> CAP2 1 0.243 1.44 0.62
> CAP3 1 0.105 0.62 0.96
> CAP4 1 0.051 0.30 0.94
1315,1318c1295,1298
< dbRDA1 1 0.667 4.45 0.10
< dbRDA2 1 0.238 1.59 0.76
< dbRDA3 1 0.091 0.61 0.94
< dbRDA4 1 0.038 0.26 0.96
---
> dbRDA1 1 0.667 4.45 0.16
> dbRDA2 1 0.238 1.59 0.60
> dbRDA3 1 0.091 0.61 0.96
> dbRDA4 1 0.038 0.26 0.94
1328,1330c1308,1310
< CAP1 1 126 3.33 0.14
< CAP2 1 49 1.31 0.80
< CAP3 1 24 0.64 0.98
---
> CAP1 1 126 3.33 0.18
> CAP2 1 49 1.31 0.72
> CAP3 1 24 0.64 1.00
1341,1344c1321,1324
< dbRDA1 1 123 3.81 0.12
< dbRDA2 1 47 1.47 0.74
< dbRDA3 1 22 0.68 0.96
< dbRDA4 1 10 0.31 0.88
---
> dbRDA1 1 123 3.81 0.16
> dbRDA2 1 47 1.47 0.70
> dbRDA3 1 22 0.68 0.98
> dbRDA4 1 10 0.31 0.84
Running 'oecosimu-tests.R' [2s]
Comparing 'oecosimu-tests.Rout' to 'oecosimu-tests.Rout.save' ... OK
Running 'vegan-tests.R' [6s]
Comparing 'vegan-tests.Rout' to 'vegan-tests.Rout.save' ...61c61
< Management 3 0.82392 1.7163 0.03 *
---
> Management 3 0.82392 1.7163 0.02 *
63c63
< spno 1 0.08318 0.5198 0.96
---
> spno 1 0.08318 0.5198 0.95
75,76c75,76
< Management 3 0.55418 1.1544 0.21
< poly(A1, 2) 2 0.32940 1.0292 0.44
---
> Management 3 0.55418 1.1544 0.25
> poly(A1, 2) 2 0.32940 1.0292 0.30
87,92c87,92
< CCA1 1 0.46993 2.9366 0.07 .
< CCA2 1 0.26217 1.6384 0.75
< CCA3 1 0.19308 1.2066 0.97
< CCA4 1 0.18345 1.1464 0.90
< CCA5 1 0.08871 0.5544 0.98
< CCA6 1 0.06104 0.3815 0.93
---
> CCA1 1 0.46993 2.9366 0.09 .
> CCA2 1 0.26217 1.6384 0.80
> CCA3 1 0.19308 1.2066 0.89
> CCA4 1 0.18345 1.1464 0.84
> CCA5 1 0.08871 0.5544 0.99
> CCA6 1 0.06104 0.3815 0.90
105c105
< Model 6 59.582 1.6462 0.04 *
---
> Model 6 59.582 1.6462 0.03 *
118,119c118,119
< poly(A1, 2) 2 10.150 0.8413 0.63
< spno 1 3.167 0.5250 0.79
---
> poly(A1, 2) 2 10.150 0.8413 0.69
> spno 1 3.167 0.5250 0.91
131,133c131,133
< Management 3 28.7515 1.5888 0.13
< poly(A1, 2) 2 8.0847 0.6701 0.88
< spno 1 3.1669 0.5250 0.90
---
> Management 3 28.7515 1.5888 0.05 *
> poly(A1, 2) 2 8.0847 0.6701 0.92
> spno 1 3.1669 0.5250 0.93
134a135,136
> ---
> Signif. codes: 0 '***' 0.001 '**' 0.01 '*' 0.05 '.' 0.1 ' ' 1
143,147c145,149
< CAP1 1 25.0252 4.1487 0.03 *
< CAP2 1 15.8759 2.6319 0.39
< CAP3 1 8.0942 1.3419 0.78
< CAP4 1 5.0675 0.8401 0.95
< CAP5 1 3.5671 0.5914 0.96
---
> CAP1 1 25.0252 4.1487 0.02 *
> CAP2 1 15.8759 2.6319 0.45
> CAP3 1 8.0942 1.3419 0.88
> CAP4 1 5.0675 0.8401 0.96
> CAP5 1 3.5671 0.5914 0.95
162c164
< Model 6 1.54840 1.6423 0.14
---
> Model 6 1.54840 1.6423 0.13
172,174c174,176
< Management 3 1.17117 2.4844 0.02 *
< poly(A1, 2) 2 0.30602 0.9737 0.53
< spno 1 0.07121 0.4532 0.84
---
> Management 3 1.17117 2.4844 0.06 .
> poly(A1, 2) 2 0.30602 0.9737 0.54
> spno 1 0.07121 0.4532 0.85
186,188c188,190
< Management 3 0.64888 1.3765 0.22
< poly(A1, 2) 2 0.26160 0.8324 0.69
< spno 1 0.07121 0.4532 0.91
---
> Management 3 0.64888 1.3765 0.25
> poly(A1, 2) 2 0.26160 0.8324 0.66
> spno 1 0.07121 0.4532 0.86
198,201c200,203
< CAP1 1 0.77834 4.9533 0.13
< CAP2 1 0.45691 2.9078 0.48
< CAP3 1 0.14701 0.9355 0.98
< CAP4 1 0.11879 0.7560 0.96
---
> CAP1 1 0.77834 4.9533 0.09 .
> CAP2 1 0.45691 2.9078 0.39
> CAP3 1 0.14701 0.9355 1.00
> CAP4 1 0.11879 0.7560 0.97
204a207,208
> ---
> Signif. codes: 0 '***' 0.001 '**' 0.01 '*' 0.05 '.' 0.1 ' ' 1
215c219
< Model 6 1.25838 1.3106 0.11
---
> Model 6 1.25838 1.3106 0.18
227c231
< Management 3 0.82392 1.7163 0.02 *
---
> Management 3 0.82392 1.7163 0.03 *
229c233
< spno 1 0.08318 0.5198 0.95
---
> spno 1 0.08318 0.5198 0.96
241,243c245,247
< Management 3 0.55418 1.1544 0.33
< poly(A1, 2) 2 0.32940 1.0292 0.44
< spno 1 0.08318 0.5198 0.94
---
> Management 3 0.55418 1.1544 0.28
> poly(A1, 2) 2 0.32940 1.0292 0.46
> spno 1 0.08318 0.5198 0.96
253c257
< CCA1 1 0.46993 2.9366 0.05 *
---
> CCA1 1 0.46993 2.9366 0.10
255,257c259,261
< CCA3 1 0.19308 1.2066 0.93
< CCA4 1 0.18345 1.1464 0.88
< CCA5 1 0.08871 0.5544 0.97
---
> CCA3 1 0.19308 1.2066 0.95
> CCA4 1 0.18345 1.1464 0.85
> CCA5 1 0.08871 0.5544 0.96
260,261d263
< ---
< Signif. codes: 0 '***' 0.001 '**' 0.01 '*' 0.05 '.' 0.1 ' ' 1
404,407c406,409
< CCA1 1 0.27109 2.9561 0.09 .
< CCA2 1 0.14057 1.5329 0.56
< CCA3 1 0.08761 0.9553 0.78
< CCA4 1 0.05624 0.6132 0.76
---
> CCA1 1 0.27109 2.9561 0.07 .
> CCA2 1 0.14057 1.5329 0.48
> CCA3 1 0.08761 0.9553 0.85
> CCA4 1 0.05624 0.6132 0.84
443,445c445,447
< CAP1 1 0.2682 1.3075 0.783
< CAP2 1 0.0685 0.3339 0.998
< CAP3 1 0.0455 0.2217 0.967
---
> CAP1 1 0.2682 1.3075 0.779
> CAP2 1 0.0685 0.3339 0.997
> CAP3 1 0.0455 0.2217 0.964
456,457c458,459
< A 1 0.1316 0.6415 0.680
< B 2 0.2506 0.6108 0.824
---
> A 1 0.1316 0.6415 0.696
> B 2 0.2506 0.6108 0.821
471,473c473,475
< CAP1 1 0.2682 1.3267 0.764
< CAP2 1 0.0685 0.3388 0.993
< CAP3 1 0.0455 0.2249 0.964
---
> CAP1 1 0.2682 1.3267 0.785
> CAP2 1 0.0685 0.3388 0.995
> CAP3 1 0.0455 0.2249 0.961
484,485c486,487
< A 1 0.1316 0.6509 0.693
< B 2 0.2506 0.6198 0.829
---
> A 1 0.1316 0.6509 0.665
> B 2 0.2506 0.6198 0.834
499c501
< RDA1 1 0.2682 1.3075 0.774
---
> RDA1 1 0.2682 1.3075 0.770
501c503
< RDA3 1 0.0455 0.2217 0.964
---
> RDA3 1 0.0455 0.2217 0.962
512,513c514,515
< A 1 0.1316 0.6415 0.669
< B 2 0.2506 0.6108 0.827
---
> A 1 0.1316 0.6415 0.656
> B 2 0.2506 0.6108 0.825
527,529c529,531
< RDA1 1 0.2682 1.3267 0.768
< RDA2 1 0.0685 0.3388 0.995
< RDA3 1 0.0455 0.2249 0.971
---
> RDA1 1 0.2682 1.3267 0.765
> RDA2 1 0.0685 0.3388 0.996
> RDA3 1 0.0455 0.2249 0.969
540,541c542,543
< A 1 0.1316 0.6509 0.695
< B 2 0.2506 0.6198 0.820
---
> A 1 0.1316 0.6509 0.690
> B 2 0.2506 0.6198 0.823
566,570c568,572
< A1 1 0.22476 2.5704 0.010 **
< Moisture 3 0.51898 1.9783 0.009 **
< Management 3 0.39543 1.5074 0.064 .
< Use 2 0.10910 0.6238 0.922
< Manure 3 0.25490 0.9717 0.519
---
> A1 1 0.22476 2.5704 0.012 *
> Moisture 3 0.51898 1.9783 0.005 **
> Management 3 0.39543 1.5074 0.055 .
> Use 2 0.10910 0.6238 0.927
> Manure 3 0.25490 0.9717 0.518
583,587c585,589
< A1 1 8.1148 2.7156 0.008 **
< Moisture 3 21.6497 2.4150 0.008 **
< Management 3 19.1153 2.1323 0.009 **
< Use 2 4.7007 0.7865 0.730
< Manure 3 9.6257 1.0737 0.377
---
> A1 1 8.1148 2.7156 0.009 **
> Moisture 3 21.6497 2.4150 0.004 **
> Management 3 19.1153 2.1323 0.007 **
> Use 2 4.7007 0.7865 0.724
> Manure 3 9.6257 1.0737 0.360
612c614
< Manure 4 4.7257 5.7006 0.009 **
---
> Manure 4 4.7257 5.7006 0.011 *
673,675c675,677
< Procrustes Sum of Squares (m12 squared): 0.9147
< Correlation in a symmetric Procrustes rotation: 0.292
< Significance: 0.08
---
> Procrustes Sum of Squares (m12 squared): 0.9389
> Correlation in a symmetric Procrustes rotation: 0.2471
> Significance: 0.46
681,695c683,697
< [1] 0.2056649 0.2008622 0.2062525 0.2656158 0.2739148 0.1990895 0.3124461
< [8] 0.2287779 0.2033140 0.2396172 0.1868019 0.2736072 0.1830199 0.2026019
< [15] 0.2402570 0.2286169 0.2791609 0.2214468 0.2356083 0.2188325 0.2097262
< [22] 0.2596154 0.2560289 0.2190367 0.2174689 0.2438396 0.1991101 0.2374612
< [29] 0.2030745 0.2205115 0.2566758 0.1448623 0.2354268 0.2419134 0.3144177
< [36] 0.2368505 0.2442661 0.2272011 0.3184241 0.2200089 0.2598430 0.2301587
< [43] 0.2763337 0.2332606 0.1935269 0.2315727 0.2573623 0.2021127 0.2387335
< [50] 0.2419087 0.2213094 0.2231619 0.2577845 0.2828219 0.2554605 0.2830915
< [57] 0.2342396 0.2137396 0.2151201 0.2432896 0.1956238 0.2055716 0.2329736
< [64] 0.2086125 0.2039124 0.1955711 0.2038045 0.2358886 0.2579199 0.1808128
< [71] 0.2155189 0.2967100 0.2480105 0.2010537 0.2718478 0.2182713 0.2471893
< [78] 0.2310223 0.2007771 0.2902640 0.2392380 0.2551756 0.3476679 0.2632614
< [85] 0.2289929 0.2222382 0.2503562 0.1983700 0.2084773 0.2406556 0.2478302
< [92] 0.2136439 0.3251671 0.2048928 0.3098776 0.2501555 0.2677039 0.2427125
< [99] 0.2693285
---
> [1] 0.2142734 0.2317691 0.2325867 0.2318738 0.2297942 0.2547687 0.2150992
> [8] 0.2856655 0.2323035 0.2430091 0.2607687 0.2653226 0.2127120 0.2482851
> [15] 0.3044707 0.2797892 0.2644764 0.2560291 0.2916665 0.2330199 0.2434141
> [22] 0.2891063 0.2871878 0.2609612 0.2158827 0.2297220 0.2417230 0.2244848
> [29] 0.2177450 0.2528551 0.2616422 0.2584395 0.2412174 0.2244347 0.2264776
> [36] 0.2244727 0.1973865 0.2837535 0.2634514 0.2823068 0.2699507 0.2750179
> [43] 0.2628074 0.2458801 0.2635264 0.2801017 0.2296173 0.1947667 0.2929171
> [50] 0.2422339 0.1831137 0.2688563 0.2555202 0.2043385 0.2287129 0.2366098
> [57] 0.2141830 0.1858646 0.2616734 0.1974915 0.3197986 0.2245312 0.2712518
> [64] 0.2171044 0.2241602 0.2100868 0.2183290 0.2143512 0.2642714 0.2572791
> [71] 0.2806032 0.2401609 0.2063171 0.2016924 0.2684739 0.2484569 0.2200211
> [78] 0.2487178 0.1925942 0.2957915 0.2991842 0.2359773 0.2440686 0.2504427
> [85] 0.2919524 0.2324999 0.2086198 0.2298386 0.2727169 0.3253668 0.2292110
> [92] 0.2193247 0.3517265 0.2777563 0.3713275 0.2330743 0.1986322 0.2027622
> [99] 0.2281227
- checking for unstated dependencies in vignettes ... OK
- checking package vignettes in 'inst/doc' ... OK
- checking re-building of vignette outputs ... [47s] OK
- checking PDF version of manual ... OK
- DONE
Status: OK