CRAN Package Check Results for Package indicspecies

Last updated on 2017-10-16 23:47:30.

Flavor Version Tinstall Tcheck Ttotal Status Flags
r-devel-linux-x86_64-debian-clang 1.7.6 0.87 61.04 61.91 OK
r-devel-linux-x86_64-debian-gcc 1.7.6 0.98 61.00 61.98 OK
r-devel-linux-x86_64-fedora-clang 1.7.6 117.74 OK
r-devel-linux-x86_64-fedora-gcc 1.7.6 118.65 OK
r-devel-windows-ix86+x86_64 1.7.6 3.00 102.00 105.00 OK
r-patched-linux-x86_64 1.7.6 0.84 57.04 57.88 OK
r-patched-solaris-x86 1.7.6 127.00 OK
r-release-linux-x86_64 1.7.6 0.84 58.44 59.27 OK
r-release-windows-ix86+x86_64 1.7.6 2.00 111.00 113.00 OK
r-release-osx-x86_64 1.7.6 ERROR
r-oldrel-windows-ix86+x86_64 1.7.6 5.00 134.00 139.00 OK
r-oldrel-osx-x86_64 1.7.6 OK

Check Details

Version: 1.7.6
Check: package dependencies
Result: NOTE
    Package suggested but not available for checking: ‘rgeos’
Flavor: r-release-osx-x86_64

Version: 1.7.6
Check: examples
Result: ERROR
    Running examples in ‘indicspecies-Ex.R’ failed
    The error most likely occurred in:
    
    > ### Name: nichevar
    > ### Title: Resource niche metrics for a single niche
    > ### Aliases: nichevar nichecentroid nichepref
    >
    > ### ** Examples
    >
    > # Loads example data
    > data(birds)
    >
    > # The niche metrics using distances among resources and assuming equal availability of resources
    > nichepref(birdsbreed, D = resourceD)
     R1 R2 R3 R4 R5
    sp1B 0.50 0.50 0.00 0.0 0.00
    sp2B 0.00 0.25 0.50 0.0 0.25
    sp3B 1.00 0.00 0.00 0.0 0.00
    sp4B 0.65 0.35 0.00 0.0 0.00
    sp5B 0.40 0.20 0.40 0.0 0.00
    sp6B 0.00 0.00 0.35 0.0 0.65
    sp7B 0.50 0.35 0.15 0.0 0.00
    sp8B 0.95 0.00 0.05 0.0 0.00
    sp9B 0.25 0.40 0.35 0.0 0.00
    sp10B 0.00 0.08 0.40 0.2 0.32
    > nichevar(birdsbreed, D = resourceD)
     B
    sp1B 0.13225261
    sp2B 0.12781527
    sp3B 0.00000000
    sp4B 0.12034987
    sp5B 0.18250903
    sp6B 0.08535149
    sp7B 0.16362581
    sp8B 0.03317008
    sp9B 0.16380429
    sp10B 0.20396760
    > nichecentroid(birdsbreed, D = resourceD)
     V1 V2 V3 V4
    sp1B 0.24597349 0.25041608 0.045122608 0.075213112
    sp2B 0.13250560 -0.21553586 0.061091362 -0.058985020
    sp3B 0.22651901 0.48162424 -0.203930962 -0.052807341
    sp4B 0.24013715 0.31977853 -0.029593463 0.036806976
    sp5B 0.19752919 0.09742813 0.025164313 -0.093896341
    sp6B 0.04412588 -0.33760340 -0.146142948 -0.016090090
    sp7B 0.22634779 0.21038621 0.018959229 0.002195533
    sp8B 0.22192256 0.44516013 -0.187746731 -0.064344489
    sp9B 0.20990744 0.04140897 0.108601510 -0.031151012
    sp10B -0.05078743 -0.19448564 -0.005282383 -0.055185385
    >
    > # The niche metrics using distances among resources and computes
    > # 95 percent confidence intervals
    > nichepref(birdsbreed, D = resourceD, mode="multiple",
    + Np = rowSums(birdsbreed), Nq = 100)
    $F
     R1 R2 R3 R4 R5
    sp1B 0.50 0.50 0.00 0.0 0.00
    sp2B 0.00 0.25 0.50 0.0 0.25
    sp3B 1.00 0.00 0.00 0.0 0.00
    sp4B 0.65 0.35 0.00 0.0 0.00
    sp5B 0.40 0.20 0.40 0.0 0.00
    sp6B 0.00 0.00 0.35 0.0 0.65
    sp7B 0.50 0.35 0.15 0.0 0.00
    sp8B 0.95 0.00 0.05 0.0 0.00
    sp9B 0.25 0.40 0.35 0.0 0.00
    sp10B 0.00 0.08 0.40 0.2 0.32
    
    $LF
     R1 R2 R3 R4 R5
    sp1B 0.25000000 0.21212121 NA NA NA
    sp2B NA 0.06203474 0.2662860 NA 0.07335907
    sp3B NA NA NA NA NA
    sp4B 0.36538462 0.13200000 NA NA NA
    sp5B 0.17942584 0.04619565 0.1702497 NA NA
    sp6B NA NA 0.1500000 NA 0.37070938
    sp7B 0.26612903 0.12107623 0.0000000 NA NA
    sp8B 0.77981651 NA 0.0000000 NA NA
    sp9B 0.07031828 0.16873890 0.1447182 NA NA
    sp10B NA 0.00000000 0.1925028 0.063384 0.14258132
    
    $UF
     R1 R2 R3 R4 R5
    sp1B 0.7821577 0.7437071 NA NA NA
    sp2B NA 0.4971559 0.7537388 NA 0.4889005
    sp3B NA NA NA NA NA
    sp4B 0.8571429 0.6206897 NA NA NA
    sp5B 0.6443299 0.4582814 0.6725336 NA NA
    sp6B NA NA 0.6216216 NA 0.8333333
    sp7B 0.7881302 0.6150342 0.3631124 NA NA
    sp8B 1.0000000 NA 0.2060440 NA NA
    sp9B 0.4897959 0.6469754 0.6453901 NA NA
    sp10B NA 0.2448522 0.6479847 0.4079914 0.5790549
    
    > nichevar(birdsbreed, D = resourceD, mode="multiple",
    + Np = rowSums(birdsbreed), Nq = 100)
     B LC UC
    sp1B 0.13225261 0.13225261 0.13225261
    sp2B 0.12781527 0.08986727 0.14901541
    sp3B 0.00000000 0.00000000 0.00000000
    sp4B 0.12034987 0.06608697 0.13224710
    sp5B 0.18250903 0.18219550 0.18302165
    sp6B 0.08535149 0.04167193 0.09378101
    sp7B 0.16362581 0.13204100 0.18225082
    sp8B 0.03317008 0.00000000 0.11149844
    sp9B 0.16380429 0.12375650 0.18259092
    sp10B 0.20396760 0.14409736 0.24544019
    > nichecentroid(birdsbreed, D = resourceD, mode="multiple",
    + Np = rowSums(birdsbreed), Nq = 100)
    $C
     V1 V2 V3 V4
    sp1B 0.24597349 0.25041608 0.045122608 0.075213112
    sp2B 0.13250560 -0.21553586 0.061091362 -0.058985020
    sp3B 0.22651901 0.48162424 -0.203930962 -0.052807341
    sp4B 0.24013715 0.31977853 -0.029593463 0.036806976
    sp5B 0.19752919 0.09742813 0.025164313 -0.093896341
    sp6B 0.04412588 -0.33760340 -0.146142948 -0.016090090
    sp7B 0.22634779 0.21038621 0.018959229 0.002195533
    sp8B 0.22192256 0.44516013 -0.187746731 -0.064344489
    sp9B 0.20990744 0.04140897 0.108601510 -0.031151012
    sp10B -0.05078743 -0.19448564 -0.005282383 -0.055185385
    
    $LC
     V1 V2 V3 V4
    sp1B 0.23620302 0.13481200 -0.0799576296 0.01091840
    sp2B 0.08517357 -0.27980623 -0.0615298811 -0.18205766
    sp3B NA NA NA NA
    sp4B 0.23118809 0.18693575 -0.1428423507 -0.02208243
    sp5B 0.17121097 -0.05611120 -0.0778619278 -0.17778121
    sp6B 0.01543970 -0.36612514 -0.2304588056 -0.13560342
    sp7B 0.20129126 0.06048690 -0.0894542433 -0.08037917
    sp8B 0.20585744 0.31771393 -0.2039309622 -0.10267974
    sp9B 0.17925178 -0.08395548 -0.0006147116 -0.13201043
    sp10B -0.21497612 -0.26877955 -0.1064858523 -0.14803559
    
    $UC
     V1 V2 V3 V4
    sp1B 0.25512854 0.35687163 0.16232429 0.135458031
    sp2B 0.17894184 -0.13519328 0.14832524 0.041386005
    sp3B NA NA NA NA
    sp4B 0.25066940 0.42208566 0.10523899 0.106114601
    sp5B 0.22311288 0.25889025 0.11818405 -0.003920792
    sp6B 0.08230087 -0.29964724 -0.03393712 0.065581907
    sp7B 0.24375879 0.34546324 0.14628012 0.086232564
    sp8B 0.22651901 0.48162424 -0.13397031 -0.052807341
    sp9B 0.23557659 0.19140989 0.18980212 0.072928498
    sp10B 0.05998642 -0.09570854 0.07296549 0.025361160
    
    >
    > # Same computations with different resource availability
    > nichepref(birdsbreed, D = resourceD,
    + q = c(0.18, 0.24, 0.22, 0.21, 0.15), mode="multiple")
     R1 R2 R3 R4 R5
    sp1B 0.5714286 0.42857143 0.0000000 0.0000000 0.0000000
    sp2B 0.0000000 0.20912548 0.4562738 0.0000000 0.3346008
    sp3B 1.0000000 0.00000000 0.0000000 0.0000000 0.0000000
    sp4B 0.7123288 0.28767123 0.0000000 0.0000000 0.0000000
    sp5B 0.4559585 0.17098446 0.3730570 0.0000000 0.0000000
    sp6B 0.0000000 0.00000000 0.2685422 0.0000000 0.7314578
    sp7B 0.5648267 0.29653402 0.1386393 0.0000000 0.0000000
    sp8B 0.9587156 0.00000000 0.0412844 0.0000000 0.0000000
    sp9B 0.2989130 0.35869565 0.3423913 0.0000000 0.0000000
    sp10B 0.0000000 0.06364688 0.3471648 0.1818482 0.4073401
    > nichevar(birdsbreed, D = resourceD,
    + q = c(0.18, 0.24, 0.22, 0.21, 0.15), mode="multiple")
     B
    sp1B 0.1295536
    sp2B 0.1320325
    sp3B 0.0000000
    sp4B 0.1084030
    sp5B 0.1827155
    sp6B 0.0736939
    sp7B 0.1579114
    sp8B 0.0276394
    sp9B 0.1718765
    sp10B 0.1962885
    > nichecentroid(birdsbreed, D = resourceD,
    + q = c(0.18, 0.24, 0.22, 0.21, 0.15), mode="multiple")
     V1 V2 V3 V4
    sp1B 0.24319428 0.28344582 0.009543526 0.056924476
    sp2B 0.11538330 -0.23815073 0.019354147 -0.044070792
    sp3B 0.22651901 0.48162424 -0.203930962 -0.052807341
    sp4B 0.23771200 0.34860037 -0.060639867 0.020848262
    sp5B 0.19887707 0.13049445 0.001990427 -0.095108599
    sp6B 0.03278895 -0.34887535 -0.179465029 0.017427941
    sp7B 0.22531187 0.24339492 -0.011349848 -0.008872539
    sp8B 0.22272378 0.45151626 -0.190567836 -0.062333426
    sp9B 0.20899979 0.06605766 0.085564702 -0.039970962
    sp10B -0.05135008 -0.21784274 -0.043129123 -0.032448647
    >
    > # The niche metrics using distances among resources and
    > # computes 95 percent confidence intervals
    > nichepref(birdsbreed, D = resourceD,
    + q = c(0.18, 0.24, 0.22, 0.21, 0.15), mode="multiple", Np = rowSums(birdsbreed), Nq = 100)
    $F
     R1 R2 R3 R4 R5
    sp1B 0.5714286 0.42857143 0.0000000 0.0000000 0.0000000
    sp2B 0.0000000 0.20912548 0.4562738 0.0000000 0.3346008
    sp3B 1.0000000 0.00000000 0.0000000 0.0000000 0.0000000
    sp4B 0.7123288 0.28767123 0.0000000 0.0000000 0.0000000
    sp5B 0.4559585 0.17098446 0.3730570 0.0000000 0.0000000
    sp6B 0.0000000 0.00000000 0.2685422 0.0000000 0.7314578
    sp7B 0.5648267 0.29653402 0.1386393 0.0000000 0.0000000
    sp8B 0.9587156 0.00000000 0.0412844 0.0000000 0.0000000
    sp9B 0.2989130 0.35869565 0.3423913 0.0000000 0.0000000
    sp10B 0.0000000 0.06364688 0.3471648 0.1818482 0.4073401
    
    $LF
     R1 R2 R3 R4 R5
    sp1B 0.2941176 0.20000000 NA NA NA
    sp2B NA 0.06639004 0.21641118 NA 0.1087695
    sp3B NA NA NA NA NA
    sp4B 0.4375000 0.09090909 NA NA NA
    sp5B 0.1916674 0.03279299 0.17177914 NA NA
    sp6B NA NA 0.08872458 NA 0.4761905
    sp7B 0.2760000 0.11049532 0.03310105 NA NA
    sp8B 0.8252427 NA 0.00000000 NA NA
    sp9B 0.1123110 0.15625000 0.13973129 NA NA
    sp10B NA 0.00000000 0.15718563 0.043379 0.1985628
    
    $UF
     R1 R2 R3 R4 R5
    sp1B 0.7941176 0.7012987 NA NA NA
    sp2B NA 0.4645119 0.7017376 NA 0.6222222
    sp3B NA NA NA NA NA
    sp4B 0.9067164 0.5526316 NA NA NA
    sp5B 0.7115261 0.3936731 0.6511054 NA NA
    sp6B NA NA 0.5200000 NA 0.9090909
    sp7B 0.7954630 0.5567010 0.3636364 NA NA
    sp8B 1.0000000 NA 0.1707317 NA NA
    sp9B 0.5865103 0.6206897 0.6041369 NA NA
    sp10B NA 0.1836597 0.5648665 0.363789 0.6655290
    
    > nichevar(birdsbreed, D = resourceD,
    + q = c(0.18, 0.24, 0.22, 0.21, 0.15), mode="multiple", Np = rowSums(birdsbreed), Nq = 100)
     B LC UC
    sp1B 0.1295536 0.10567628 0.13225261
    sp2B 0.1320325 0.10463708 0.15156412
    sp3B 0.0000000 0.00000000 0.00000000
    sp4B 0.1084030 0.05328359 0.13221525
    sp5B 0.1827155 0.18261967 0.18300311
    sp6B 0.0736939 0.02940119 0.09358017
    sp7B 0.1579114 0.11799408 0.18203040
    sp8B 0.0276394 0.00000000 0.10470398
    sp9B 0.1718765 0.14179136 0.18297491
    sp10B 0.1962885 0.13702023 0.24270306
    > nichecentroid(birdsbreed, D = resourceD,
    + q = c(0.18, 0.24, 0.22, 0.21, 0.15), mode="multiple", Np = rowSums(birdsbreed), Nq = 100)
    $C
     V1 V2 V3 V4
    sp1B 0.24319428 0.28344582 0.009543526 0.056924476
    sp2B 0.11538330 -0.23815073 0.019354147 -0.044070792
    sp3B 0.22651901 0.48162424 -0.203930962 -0.052807341
    sp4B 0.23771200 0.34860037 -0.060639867 0.020848262
    sp5B 0.19887707 0.13049445 0.001990427 -0.095108599
    sp6B 0.03278895 -0.34887535 -0.179465029 0.017427941
    sp7B 0.22531187 0.24339492 -0.011349848 -0.008872539
    sp8B 0.22272378 0.45151626 -0.190567836 -0.062333426
    sp9B 0.20899979 0.06605766 0.085564702 -0.039970962
    sp10B -0.05135008 -0.21784274 -0.043129123 -0.032448647
    
    $LC
     V1 V2 V3 V4
    sp1B 0.233814444 0.15793281 -0.11053587 -0.004799671
    sp2B 0.055433283 -0.31301753 -0.12777820 -0.171624084
    sp3B NA NA NA NA
    sp4B 0.230699316 0.22431193 -0.15041532 -0.025298814
    sp5B 0.171257865 -0.03870453 -0.10129505 -0.172570058
    sp6B 0.007622826 -0.37389721 -0.25343456 -0.092194618
    sp7B 0.204301925 0.08056110 -0.11912116 -0.070073327
    sp8B 0.208840355 0.34137768 -0.20393096 -0.097180986
    sp9B 0.182179240 -0.07771384 -0.02783273 -0.130026890
    sp10B -0.195257099 -0.29917996 -0.15411088 -0.130402534
    
    $UC
     V1 V2 V3 V4
    sp1B 0.25363738 0.3921243 0.14323462 0.125645412
    sp2B 0.16577312 -0.1573519 0.13109452 0.058759489
    sp3B NA NA NA NA
    sp4B 0.24805115 0.4302446 0.07172056 0.088885199
    sp5B 0.22235254 0.3072538 0.10749251 -0.008473783
    sp6B 0.06909561 -0.3127768 -0.07275067 0.091260655
    sp7B 0.24199932 0.3726107 0.10723906 0.071857585
    sp8B 0.22651901 0.4816242 -0.14493022 -0.052807341
    sp9B 0.23455998 0.2317047 0.18163924 0.063077949
    sp10B 0.04497187 -0.1229974 0.05066744 0.046520106
    
    >
    > # The following example defines a function to calculate the area of the niche
    > # It requires package 'rgeos'
    > library(rgeos)
    Error in library(rgeos) : there is no package called ‘rgeos’
    Execution halted
Flavor: r-release-osx-x86_64

Version: 1.7.6
Check: re-building of vignette outputs
Result: NOTE
    Error in re-building vignettes:
     ...
    Loading required package: permute
    Warning in wilcox.test.default(indvar.barcelona$B, indvar.moia$B) :
     cannot compute exact p-value with ties
    Warning in wilcox.test.default(Spec.ind.barcelona, Spec.ind.moia) :
     cannot compute exact p-value with ties
    Warning in wilcox.test.default(O.barcelona.ind, O.moia.ind) :
     cannot compute exact p-value with ties
    Error in texi2dvi(file = file, pdf = TRUE, clean = clean, quiet = quiet, :
     Running 'texi2dvi' on 'PigeonExample.tex' failed.
    LaTeX errors:
    ! LaTeX Error: File `authblk.sty' not found.
    
    Type X to quit or <RETURN> to proceed,
    or enter new name. (Default extension: sty)
    
    ! Emergency stop.
    <read *>
    
    l.5 ^^M
    
    ! ==> Fatal error occurred, no output PDF file produced!
    Calls: buildVignettes -> texi2pdf -> texi2dvi
    Execution halted
Flavor: r-release-osx-x86_64