- using R version 2.14.0 RC (2011-10-24 r57417)
- using platform: i386-apple-darwin9.8.0 (32-bit)
- using session charset: ASCII
- checking for file 'prabclus/DESCRIPTION' ... OK
- this is package 'prabclus' version '2.2-2'
- checking package dependencies ... NOTE
Package suggested but not available for checking: 'spdep'
- checking if this is a source package ... OK
- checking if there is a namespace ... NOTE
As from R 2.14.0 all packages need a namespace.
One will be generated on installation, but it is better to handcraft a
NAMESPACE file: R CMD build will produce a suitable starting point.
- checking for executable files ... OK
- checking whether package 'prabclus' can be installed ... OK
- checking installed package size ... OK
- checking package directory ... OK
- checking for portable file names ... OK
- checking for sufficient/correct file permissions ... 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 package can be unloaded cleanly ... 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 ... NOTE
build.nblist: no visible global function definition for 'nb2listw'
prab.sarestimate: no visible global function definition for
'errorsarlm'
- checking Rd files ... OK
- checking Rd metadata ... OK
- checking Rd cross-references ... NOTE
Package(s) unavailable to check Rd xrefs: 'spdep'
- 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 examples ... OK
- checking differences from 'prabclus-Ex.Rout' to 'prabclus-Ex.Rout.save' ...
2,6d1
<
< by using mclust, invoked on its own or through another package,
< you accept the license agreement in the mclust LICENSE file
< and at http://www.stat.washington.edu/mclust/license.txt
<
22a18,22
>
> by using mclust, invoked on its own or through another package,
> you accept the license agreement in the mclust LICENSE file
> and at http://www.stat.washington.edu/mclust/license.txt
>
29a30,32
>
> detaching 'package:mclust'
>
279d281
< > # This uses example data file Heterotrigona_indoFO.dat
5170a5173,5177
>
> by using mclust, invoked on its own or through another package,
> you accept the license agreement in the mclust LICENSE file
> and at http://www.stat.washington.edu/mclust/license.txt
>
5176,5183c5183,5191
< [1] 0.4736842 0.3684211 0.4736842 0.5263158 0.3684211 0.4210526 0.3684211
< [8] 0.5263158 0.5263158 0.5263158 0.6842105 0.4210526 0.4210526 0.5263158
< [15] 0.4210526 0.2631579 0.4210526 0.4736842 0.5263158 0.4210526 0.4736842
< [22] 0.4210526 0.5263158 0.4210526 0.6315789 0.5263158 0.4210526 0.4736842
< [29] 0.4210526 0.3684211 0.5263158 0.4736842 0.4736842 0.4210526 0.4736842
< [36] 0.5789474 0.5263158 0.5263158 0.4210526 0.3684211 0.2631579 0.4210526
< [43] 0.3684211 0.4736842 0.5263158 0.4210526 0.4210526 0.2631579 0.5263158
< [50] 0.5263158
---
> [1] 0.38461538 0.15384615 0.38461538 0.53846154 0.69230769 0.07692308
> [7] 0.15384615 0.07692308 0.00000000 0.07692308 0.07692308 0.38461538
> [13] 0.84615385 0.23076923 0.38461538 0.53846154 0.07692308 0.23076923
> [19] 0.15384615 0.15384615 0.00000000 0.23076923 0.15384615 0.76923077
> [25] 0.00000000 0.23076923 0.00000000 0.15384615 0.07692308 0.15384615
> [31] 0.38461538 0.00000000 0.07692308 0.15384615 0.07692308 0.23076923
> [37] 0.07692308 0.53846154 0.38461538 0.38461538 0.38461538 0.00000000
> [43] 0.07692308 0.00000000 0.15384615 0.07692308 0.07692308 0.00000000
> [49] 0.00000000 0.07692308
5186c5194
< [1] 0.2631579 0.3684211 0.2631579 0.4210526
---
> [1] 0.0000000 0.0000000 0.2307692 0.0000000
5189c5197
< [1] 0.5263158 0.5263158 0.5789474 0.6842105
---
> [1] 0.3846154 0.3846154 0.8461538 0.2307692
5192c5200
< [1] 0.3947368 0.4520124 0.4574899 0.5043860
---
> [1] 0.13461538 0.09502262 0.48520710 0.12820513
5197a5206,5208
>
> detaching 'package:mclust'
>
5497c5508
< Simulation run 3 statistics value= 0.332721
---
> Simulation run 3 statistics value= 0.3327210
5686a5698,5702
>
> by using mclust, invoked on its own or through another package,
> you accept the license agreement in the mclust LICENSE file
> and at http://www.stat.washington.edu/mclust/license.txt
>
5696,5698c5712,5714
< [1] 0 1 0 3 3 7 6 0 8 0 3 0 0 4 1 6 6 7 0 0 0 7 4 1 4 0 6 5 2 1 2 5 0 6 1 0 0 1
< [39] 0 7 1 3 2 2 5 0 1 2 3 1 8 0 0 4 5 2 8 4 0 0 4 1 5 8 0 2 3 0 0 2 0 1 8 4 0 7
< [77] 3 5 0 6
---
> [1] 0 1 0 4 4 7 6 0 8 0 4 0 0 5 1 6 6 7 0 0 0 7 5 1 5 3 6 3 2 1 2 3 0 6 1 0 0 1
> [39] 0 7 1 4 2 2 3 0 1 2 4 1 8 0 0 5 3 2 8 5 0 0 5 1 3 8 0 2 4 0 0 2 0 1 8 5 0 7
> [77] 4 3 0 6
5701,5705c5717,5721
< [1] "N" "1" "N" "3" "3" "7" "6" "N" "8" "N" "3" "N" "N" "4" "1" "6" "6" "7" "N"
< [20] "N" "N" "7" "4" "1" "4" "N" "6" "5" "2" "1" "2" "5" "N" "6" "1" "N" "N" "1"
< [39] "N" "7" "1" "3" "2" "2" "5" "N" "1" "2" "3" "1" "8" "N" "N" "4" "5" "2" "8"
< [58] "4" "N" "N" "4" "1" "5" "8" "N" "2" "3" "N" "N" "2" "N" "1" "8" "4" "N" "7"
< [77] "3" "5" "N" "6"
---
> [1] "N" "1" "N" "4" "4" "7" "6" "N" "8" "N" "4" "N" "N" "5" "1" "6" "6" "7" "N"
> [20] "N" "N" "7" "5" "1" "5" "3" "6" "3" "2" "1" "2" "3" "N" "6" "1" "N" "N" "1"
> [39] "N" "7" "1" "4" "2" "2" "3" "N" "1" "2" "4" "1" "8" "N" "N" "5" "3" "2" "8"
> [58] "5" "N" "N" "5" "1" "3" "8" "N" "2" "4" "N" "N" "2" "N" "1" "8" "5" "N" "7"
> [77] "4" "3" "N" "6"
5763a5780,5782
>
> detaching 'package:mclust'
>
6910,6915c6929,6934
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< [6,] 0.000000 0.00000 0.00000 0.00000 0.000000 0.0000000 0.0000000
---
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> [6,] 0.000000 0.00000 0.00000 0.000000 0.000000 0.0000000 0.0000000
6952,6957c6971,6976
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< [4,] 72.365691 14.82499277 114.493929 20.40709 0.000000 0.0000000 0.0000000
< [5,] 24.676810 21.91348340 69.902641 96.19975 3.581301 0.0000000 0.0000000
< [6,] 100.327519 19.85900594 93.736155 44.97300 0.000000 0.0000000 0.0000000
---
> [1,] 0.00000 0.09669243 8.171236 37.41091 0.000000 0.7199853 0.0000000
> [2,] 5.44301 1.18816242 79.494097 23.09044 0.000000 0.0000000 0.0000000
> [3,] 84.26024 26.49854856 68.599066 38.35432 0.000000 0.0000000 0.7297678
> [4,] 72.36569 14.82499277 114.493929 20.40709 0.000000 0.0000000 0.0000000
> [5,] 24.67681 21.91348340 69.902641 96.19975 3.581301 0.0000000 0.0000000
> [6,] 100.32752 19.85900594 93.736155 44.97300 0.000000 0.0000000 0.0000000
6979,7041c6998,7067
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< [3,] 0.00000 2.206035 0.000000 1.7816330 0.7675381 0.994798 0.000000 0.0000000
< [4,] 0.00000 0.958365 0.000000 0.5883424 0.0000000 64.694774 0.000000 0.7237579
< [5,] 0.00000 0.000000 4.073145 0.0000000 0.0000000 0.000000 5.592687 0.2872582
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< [3,] 62.177392 144.153967 764.64149 16.274348 0.00000 1.0832240 1.128364
< [4,] 0.000000 39.056608 22.09675 0.000000 47.00413 3.4273383 2.121247
< [5,] 0.000000 4.721707 19.18309 1.444741 0.00000 0.0000000 20.916254
< [6,] 0.000000 0.000000 0.00000 0.000000 0.00000 6.3784003 6.226726
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< [3,] 1.225024 2.627345 0.00000 0.00000 4.057996 8.075579 0.3911095
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< [5,] 0.000000 0.000000 19.39938 28.51305 0.000000 0.000000 0.0000000
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< [6,] 5.020272 274.2270 38.39652 0.000000 0.0000 0.000000 0.00000 0.000000
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---
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> [6,] 1.388640 0.000000 2.232838 0.0000000 0.0000000 0.000000 5.749486
> [,85] [,86] [,87] [,88] [,89] [,90] [,91]
> [1,] 0.0000000 4.114957 0.000000 0.00000 5.709805 42.39022 0.0000000
> [2,] 0.0000000 119.898059 0.000000 12.88441 8.800875 31.64993 0.9771071
> [3,] 0.0000000 62.177392 144.153967 764.64149 16.274348 0.00000 1.0832240
> [4,] 0.7237579 0.000000 39.056608 22.09675 0.000000 47.00413 3.4273383
> [5,] 0.2872582 0.000000 4.721707 19.18309 1.444741 0.00000 0.0000000
> [6,] 0.0000000 0.000000 0.000000 0.00000 0.000000 0.00000 6.3784003
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> [4,] 2.121247 12.0661980 0.00000000 0.00000 0.000000 0.000000 0.00000
> [5,] 20.916254 0.4321756 0.00000000 0.00000 0.000000 0.000000 10.57284
> [6,] 6.226726 4.5634477 0.07314588 0.00000 0.000000 0.000000 0.00000
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> [3,] 0.3911095 0.000000 0.0000 0.00000 0.000000 199.3773 10.125075
> [4,] 1.9842398 4.952285 179.5948 22.80712 0.000000 482.6783 0.000000
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> [6,] 0.0000000 5.020272 274.2270 38.39652 0.000000 0.0000 0.000000
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> [4,] 89.43248 0.000000 7.147122 11.642397 0.000000 4.930563 12.11852
> [5,] 75.67227 1.501258 5.822955 0.000000 0.000000 68.353075 0.00000
> [6,] 0.00000 0.000000 10.483027 0.000000 0.000000 17.950195 0.00000
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> [6,] 14.78211 4.114816 0.000000 0.8339799 0.000000 5.015895 0.000000 0.000000
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> [5,] 2.862917 0.000000 0.2387701 2.056186 0.9576457 0.000000 0.000000 36.26947
> [6,] 1.827326 0.000000 1.5242211 1.874754 1.7932307 0.000000 0.000000 32.01422
> [,136] [,137] [,138] [,139] [,140] [,141] [,142] [,143]
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> [,144]
> [1,] 0.0000000
> [2,] 0.0000000
> [3,] 0.0000000
> [4,] 0.4583918
> [5,] 0.0000000
> [6,] 0.0000000
OK
- checking for unstated dependencies in tests ... OK
- checking tests ... ERROR
Running the tests in 'tests/prabclustests.R' failed.
Last 13 lines of output:
+ file.format="decimal2",neighbors=TRUE)
> vei <- prabinit(prabmatrix=veronica[1:50,],
+ neighborhood=vnb$nblist,nbbetweenregions=FALSE,
+ distance="jaccard")
> print(vei)
Presence-absence matrix object with
50 species and 583 regions,
including species/individuals neighborhoods and
between-species distance matrix of type jaccard .
>
> library(spdep)
Error in library(spdep) : there is no package called 'spdep'
Execution halted
- elapsed time (check, wall clock): 0:44