CRAN Package Check Results for Package geomorph

Last updated on 2021-12-06 05:53:10 CET.

Flavor Version Tinstall Tcheck Ttotal Status Flags
r-devel-linux-x86_64-debian-clang 4.0.1 21.24 326.37 347.61 ERROR
r-devel-linux-x86_64-debian-gcc 4.0.1 18.27 251.10 269.37 ERROR
r-devel-linux-x86_64-fedora-clang 4.0.1 421.80 ERROR
r-devel-linux-x86_64-fedora-gcc 4.0.1 428.52 ERROR
r-devel-windows-x86_64-new-UL 4.0.1 48.00 409.00 457.00 OK
r-devel-windows-x86_64-new-TK 4.0.1 ERROR
r-devel-windows-x86_64-old 4.0.1 35.00 300.00 335.00 OK
r-patched-linux-x86_64 4.0.1 28.46 335.92 364.38 OK
r-release-linux-x86_64 4.0.1 19.73 343.43 363.16 OK
r-release-macos-arm64 4.0.1 OK
r-release-macos-x86_64 4.0.1 OK
r-release-windows-ix86+x86_64 4.0.1 44.00 396.00 440.00 OK
r-oldrel-macos-x86_64 4.0.1 OK
r-oldrel-windows-ix86+x86_64 4.0.1 46.00 393.00 439.00 OK

Check Details

Version: 4.0.1
Check: examples
Result: ERROR
    Running examples in 'geomorph-Ex.R' failed
    The error most likely occurred in:
    
    > base::assign(".ptime", proc.time(), pos = "CheckExEnv")
    > ### Name: morphol.disparity
    > ### Title: Morphological disparity for one or more groups of specimens
    > ### Aliases: morphol.disparity
    > ### Keywords: analysis
    >
    > ### ** Examples
    >
    > data(plethodon)
    > Y.gpa<-gpagen(plethodon$land, print.progress = FALSE) #GPA-alignment
    > gdf <- geomorph.data.frame(Y.gpa, species = plethodon$species,
    + site = plethodon$site)
    >
    > # Morphological disparity for entire data set
    > morphol.disparity(coords ~ 1, groups = NULL, data = gdf,
    + iter = 999, print.progress = FALSE)
    No factor in formula or model terms from which to define groups.
    Procrustes variance:
    0.004923493
    [1] 0.004923493
    >
    > # Morphological disparity for entire data set, accounting for allometry
    > morphol.disparity(coords ~ Csize, groups= NULL, data = gdf,
    + iter = 999, print.progress = FALSE)
    No factor in formula or model terms from which to define groups.
    Procrustes variance:
    0.004663261
    [1] 0.004663261
    >
    > # Morphological disparity without covariates, using overall mean
    > morphol.disparity(coords ~ 1, groups= ~ species*site, data = gdf,
    + iter = 999, print.progress = FALSE)
    
    Call:
    morphol.disparity(f1 = coords ~ 1, groups = ~species * site,
     iter = 999, data = gdf, print.progress = FALSE)
    
    
    
    Randomized Residual Permutation Procedure Used
    1000 Permutations
    
    Procrustes variances for defined groups
     Jord.Allo Jord.Symp Teyah.Allo Teyah.Symp
    0.003825239 0.005937274 0.003355766 0.006575694
    
    
    Pairwise absolute differences between variances
     Jord.Allo Jord.Symp Teyah.Allo Teyah.Symp
    Jord.Allo 0.0000000000 0.002112035 0.0004694738 0.002750455
    Jord.Symp 0.0021120348 0.000000000 0.0025815087 0.000638420
    Teyah.Allo 0.0004694738 0.002581509 0.0000000000 0.003219929
    Teyah.Symp 0.0027504548 0.000638420 0.0032199286 0.000000000
    
    
    P-Values
     Jord.Allo Jord.Symp Teyah.Allo Teyah.Symp
    Jord.Allo 1.000 0.023 0.613 0.002
    Jord.Symp 0.023 1.000 0.008 0.522
    Teyah.Allo 0.613 0.008 1.000 0.001
    Teyah.Symp 0.002 0.522 0.001 1.000
    
    
    >
    > # Morphological partial disparities for overal mean
    > morphol.disparity(coords ~ 1, groups= ~ species*site, partial = TRUE,
    + data = gdf, iter = 999, print.progress = FALSE)
    
    Call:
    morphol.disparity(f1 = coords ~ 1, groups = ~species * site,
     partial = TRUE, iter = 999, data = gdf, print.progress = FALSE)
    
    
    
    Randomized Residual Permutation Procedure Used
    1000 Permutations
    
    Procrustes variances for defined groups; partial variances (disparities) were calculated.
     Jord.Allo Jord.Symp Teyah.Allo Teyah.Symp
    0.0009808306 0.0015223780 0.0008604527 0.0016860754
    
    Proportion of total disparity for each group:
     Jord.Allo Jord.Symp Teyah.Allo Teyah.Symp
     0.1942340 0.3014767 0.1703956 0.3338937
    
    
    Pairwise absolute differences between variances
     Jord.Allo Jord.Symp Teyah.Allo Teyah.Symp
    Jord.Allo 0.0000000000 0.0005415474 0.0001203779 0.0007052448
    Jord.Symp 0.0005415474 0.0000000000 0.0006619253 0.0001636974
    Teyah.Allo 0.0001203779 0.0006619253 0.0000000000 0.0008256227
    Teyah.Symp 0.0007052448 0.0001636974 0.0008256227 0.0000000000
    
    
    P-Values
     Jord.Allo Jord.Symp Teyah.Allo Teyah.Symp
    Jord.Allo 1.000 0.023 0.613 0.002
    Jord.Symp 0.023 1.000 0.008 0.522
    Teyah.Allo 0.613 0.008 1.000 0.001
    Teyah.Symp 0.002 0.522 0.001 1.000
    
    
    >
    > # Morphological disparity without covariates, using group means
    > morphol.disparity(coords ~ species*site, groups= ~species*site,
    + data = gdf, iter = 999, print.progress = FALSE)
    
    Call:
    morphol.disparity(f1 = coords ~ species * site, groups = ~species *
     site, iter = 999, data = gdf, print.progress = FALSE)
    
    
    
    Randomized Residual Permutation Procedure Used
    1000 Permutations
    
    Procrustes variances for defined groups
     Jord.Allo Jord.Symp Teyah.Allo Teyah.Symp
    0.001933408 0.001790153 0.001732998 0.001785645
    
    
    Pairwise absolute differences between variances
     Jord.Allo Jord.Symp Teyah.Allo Teyah.Symp
    Jord.Allo 0.0000000000 1.432543e-04 2.004103e-04 1.477632e-04
    Jord.Symp 0.0001432543 0.000000e+00 5.715598e-05 4.508825e-06
    Teyah.Allo 0.0002004103 5.715598e-05 0.000000e+00 5.264716e-05
    Teyah.Symp 0.0001477632 4.508825e-06 5.264716e-05 0.000000e+00
    
    
    P-Values
     Jord.Allo Jord.Symp Teyah.Allo Teyah.Symp
    Jord.Allo 1.000 0.684 0.538 0.676
    Jord.Symp 0.684 1.000 0.872 0.989
    Teyah.Allo 0.538 0.872 1.000 0.868
    Teyah.Symp 0.676 0.989 0.868 1.000
    
    
    >
    > # Morphological disparity of different groups than those
    > # described by the linear model
    > morphol.disparity(coords ~ Csize + species*site, groups= ~ species,
    + data = gdf, iter = 999, print.progress = FALSE)
    
    Call:
    morphol.disparity(f1 = coords ~ Csize + species * site, groups = ~species,
     iter = 999, data = gdf, print.progress = FALSE)
    
    
    
    Randomized Residual Permutation Procedure Used
    1000 Permutations
    
    Procrustes variances for defined groups
     Jord Teyah
    0.001847505 0.001590402
    
    
    Pairwise absolute differences between variances
     Jord Teyah
    Jord 0.0000000000 0.0002571036
    Teyah 0.0002571036 0.0000000000
    
    
    P-Values
     Jord Teyah
    Jord 1.000 0.251
    Teyah 0.251 1.000
    
    
    >
    > # Extracting components
    > MD <- morphol.disparity(coords ~ Csize + species*site, groups= ~ species,
    + data = gdf, iter = 999, print.progress = FALSE)
    > MD$Procrustes.var # just the Procrustes variances
     Jord Teyah
    0.001847505 0.001590402
    >
    >
    > ### Morphol.disparity can be used with previously-defined
    > ### procD.lm or lm.rrpp class objects
    >
    > data(plethspecies)
    > Y.gpa<-gpagen(plethspecies$land) #GPA-alignment
    
    Performing GPA
    
     |
     | | 0%
     |
     |================== | 25%
     |
     |=================================== | 50%
     |
     |======================================================================| 100%
    
    Making projections... Finished!
    > gp.end<-factor(c(0,0,1,0,0,1,1,0,0)) #endangered species vs. rest
    > names(gp.end)<-plethspecies$phy$tip
    >
    > gdf <- geomorph.data.frame(Y.gpa, phy = plethspecies$phy,
    + gp.end = gp.end)
    Error in geomorph.data.frame(Y.gpa, phy = plethspecies$phy, gp.end = gp.end) :
     Inputs have different numbers of observations
    Execution halted
Flavors: r-devel-linux-x86_64-debian-clang, r-devel-linux-x86_64-debian-gcc

Version: 4.0.1
Check: examples
Result: ERROR
    Running examples in ‘geomorph-Ex.R’ failed
    The error most likely occurred in:
    
    > ### Name: morphol.disparity
    > ### Title: Morphological disparity for one or more groups of specimens
    > ### Aliases: morphol.disparity
    > ### Keywords: analysis
    >
    > ### ** Examples
    >
    > data(plethodon)
    > Y.gpa<-gpagen(plethodon$land, print.progress = FALSE) #GPA-alignment
    > gdf <- geomorph.data.frame(Y.gpa, species = plethodon$species,
    + site = plethodon$site)
    >
    > # Morphological disparity for entire data set
    > morphol.disparity(coords ~ 1, groups = NULL, data = gdf,
    + iter = 999, print.progress = FALSE)
    No factor in formula or model terms from which to define groups.
    Procrustes variance:
    0.004923493
    [1] 0.004923493
    >
    > # Morphological disparity for entire data set, accounting for allometry
    > morphol.disparity(coords ~ Csize, groups= NULL, data = gdf,
    + iter = 999, print.progress = FALSE)
    No factor in formula or model terms from which to define groups.
    Procrustes variance:
    0.004663261
    [1] 0.004663261
    >
    > # Morphological disparity without covariates, using overall mean
    > morphol.disparity(coords ~ 1, groups= ~ species*site, data = gdf,
    + iter = 999, print.progress = FALSE)
    
    Call:
    morphol.disparity(f1 = coords ~ 1, groups = ~species * site,
     iter = 999, data = gdf, print.progress = FALSE)
    
    
    
    Randomized Residual Permutation Procedure Used
    1000 Permutations
    
    Procrustes variances for defined groups
     Jord.Allo Jord.Symp Teyah.Allo Teyah.Symp
    0.003825239 0.005937274 0.003355766 0.006575694
    
    
    Pairwise absolute differences between variances
     Jord.Allo Jord.Symp Teyah.Allo Teyah.Symp
    Jord.Allo 0.0000000000 0.002112035 0.0004694738 0.002750455
    Jord.Symp 0.0021120348 0.000000000 0.0025815087 0.000638420
    Teyah.Allo 0.0004694738 0.002581509 0.0000000000 0.003219929
    Teyah.Symp 0.0027504548 0.000638420 0.0032199286 0.000000000
    
    
    P-Values
     Jord.Allo Jord.Symp Teyah.Allo Teyah.Symp
    Jord.Allo 1.000 0.023 0.613 0.002
    Jord.Symp 0.023 1.000 0.008 0.522
    Teyah.Allo 0.613 0.008 1.000 0.001
    Teyah.Symp 0.002 0.522 0.001 1.000
    
    
    >
    > # Morphological partial disparities for overal mean
    > morphol.disparity(coords ~ 1, groups= ~ species*site, partial = TRUE,
    + data = gdf, iter = 999, print.progress = FALSE)
    
    Call:
    morphol.disparity(f1 = coords ~ 1, groups = ~species * site,
     partial = TRUE, iter = 999, data = gdf, print.progress = FALSE)
    
    
    
    Randomized Residual Permutation Procedure Used
    1000 Permutations
    
    Procrustes variances for defined groups; partial variances (disparities) were calculated.
     Jord.Allo Jord.Symp Teyah.Allo Teyah.Symp
    0.0009808306 0.0015223780 0.0008604527 0.0016860754
    
    Proportion of total disparity for each group:
     Jord.Allo Jord.Symp Teyah.Allo Teyah.Symp
     0.1942340 0.3014767 0.1703956 0.3338937
    
    
    Pairwise absolute differences between variances
     Jord.Allo Jord.Symp Teyah.Allo Teyah.Symp
    Jord.Allo 0.0000000000 0.0005415474 0.0001203779 0.0007052448
    Jord.Symp 0.0005415474 0.0000000000 0.0006619253 0.0001636974
    Teyah.Allo 0.0001203779 0.0006619253 0.0000000000 0.0008256227
    Teyah.Symp 0.0007052448 0.0001636974 0.0008256227 0.0000000000
    
    
    P-Values
     Jord.Allo Jord.Symp Teyah.Allo Teyah.Symp
    Jord.Allo 1.000 0.023 0.613 0.002
    Jord.Symp 0.023 1.000 0.008 0.522
    Teyah.Allo 0.613 0.008 1.000 0.001
    Teyah.Symp 0.002 0.522 0.001 1.000
    
    
    >
    > # Morphological disparity without covariates, using group means
    > morphol.disparity(coords ~ species*site, groups= ~species*site,
    + data = gdf, iter = 999, print.progress = FALSE)
    
    Call:
    morphol.disparity(f1 = coords ~ species * site, groups = ~species *
     site, iter = 999, data = gdf, print.progress = FALSE)
    
    
    
    Randomized Residual Permutation Procedure Used
    1000 Permutations
    
    Procrustes variances for defined groups
     Jord.Allo Jord.Symp Teyah.Allo Teyah.Symp
    0.001933408 0.001790153 0.001732998 0.001785645
    
    
    Pairwise absolute differences between variances
     Jord.Allo Jord.Symp Teyah.Allo Teyah.Symp
    Jord.Allo 0.0000000000 1.432543e-04 2.004103e-04 1.477632e-04
    Jord.Symp 0.0001432543 0.000000e+00 5.715598e-05 4.508825e-06
    Teyah.Allo 0.0002004103 5.715598e-05 0.000000e+00 5.264716e-05
    Teyah.Symp 0.0001477632 4.508825e-06 5.264716e-05 0.000000e+00
    
    
    P-Values
     Jord.Allo Jord.Symp Teyah.Allo Teyah.Symp
    Jord.Allo 1.000 0.684 0.538 0.676
    Jord.Symp 0.684 1.000 0.872 0.989
    Teyah.Allo 0.538 0.872 1.000 0.868
    Teyah.Symp 0.676 0.989 0.868 1.000
    
    
    >
    > # Morphological disparity of different groups than those
    > # described by the linear model
    > morphol.disparity(coords ~ Csize + species*site, groups= ~ species,
    + data = gdf, iter = 999, print.progress = FALSE)
    
    Call:
    morphol.disparity(f1 = coords ~ Csize + species * site, groups = ~species,
     iter = 999, data = gdf, print.progress = FALSE)
    
    
    
    Randomized Residual Permutation Procedure Used
    1000 Permutations
    
    Procrustes variances for defined groups
     Jord Teyah
    0.001847505 0.001590402
    
    
    Pairwise absolute differences between variances
     Jord Teyah
    Jord 0.0000000000 0.0002571036
    Teyah 0.0002571036 0.0000000000
    
    
    P-Values
     Jord Teyah
    Jord 1.000 0.251
    Teyah 0.251 1.000
    
    
    >
    > # Extracting components
    > MD <- morphol.disparity(coords ~ Csize + species*site, groups= ~ species,
    + data = gdf, iter = 999, print.progress = FALSE)
    > MD$Procrustes.var # just the Procrustes variances
     Jord Teyah
    0.001847505 0.001590402
    >
    >
    > ### Morphol.disparity can be used with previously-defined
    > ### procD.lm or lm.rrpp class objects
    >
    > data(plethspecies)
    > Y.gpa<-gpagen(plethspecies$land) #GPA-alignment
    
    Performing GPA
    
     |
     | | 0%
     |
     |================== | 25%
     |
     |=================================== | 50%
     |
     |======================================================================| 100%
    
    Making projections... Finished!
    > gp.end<-factor(c(0,0,1,0,0,1,1,0,0)) #endangered species vs. rest
    > names(gp.end)<-plethspecies$phy$tip
    >
    > gdf <- geomorph.data.frame(Y.gpa, phy = plethspecies$phy,
    + gp.end = gp.end)
    Error in geomorph.data.frame(Y.gpa, phy = plethspecies$phy, gp.end = gp.end) :
     Inputs have different numbers of observations
    Execution halted
Flavors: r-devel-linux-x86_64-fedora-clang, r-devel-linux-x86_64-fedora-gcc, r-devel-windows-x86_64-new-TK