CRAN Package Check Results for Package biomod2

Last updated on 2021-10-26 22:57:55 CEST.

Flavor Version Tinstall Tcheck Ttotal Status Flags
r-devel-linux-x86_64-debian-clang 3.5.1 56.61 411.19 467.80 OK
r-devel-linux-x86_64-debian-gcc 3.5.1 51.18 303.08 354.26 OK
r-devel-linux-x86_64-fedora-clang 3.5.1 601.69 NOTE
r-devel-linux-x86_64-fedora-gcc 3.5.1 563.46 NOTE
r-devel-windows-x86_64 3.5.1 95.00 474.00 569.00 OK
r-devel-windows-x86_64-gcc10-UCRT 3.5.1 NOTE
r-patched-linux-x86_64 3.5.1 57.46 394.33 451.79 OK
r-patched-solaris-x86 3.5.1 704.70 NOTE
r-release-linux-x86_64 3.5.1 59.69 390.68 450.37 OK
r-release-macos-arm64 3.5.1 NOTE
r-release-macos-x86_64 3.5.1 NOTE
r-release-windows-ix86+x86_64 3.5.1 96.00 470.00 566.00 OK
r-oldrel-macos-x86_64 3.5.1 NOTE
r-oldrel-windows-ix86+x86_64 3.5.1 133.00 412.00 545.00 ERROR

Check Details

Version: 3.5.1
Check: package dependencies
Result: NOTE
    Imports includes 27 non-default packages.
    Importing from so many packages makes the package vulnerable to any of
    them becoming unavailable. Move as many as possible to Suggests and
    use conditionally.
Flavor: r-devel-linux-x86_64-fedora-clang

Version: 3.5.1
Check: dependencies in R code
Result: NOTE
    Namespace in Imports field not imported from: ‘doParallel’
     All declared Imports should be used.
Flavors: r-devel-linux-x86_64-fedora-clang, r-devel-linux-x86_64-fedora-gcc, r-devel-windows-x86_64-gcc10-UCRT, r-patched-solaris-x86, r-release-macos-arm64, r-release-macos-x86_64, r-oldrel-macos-x86_64

Version: 3.5.1
Check: examples
Result: ERROR
    Running examples in 'biomod2-Ex.R' failed
    The error most likely occurred in:
    
    > ### Name: BIOMOD_FormatingData
    > ### Title: Initialize the datasets for usage in 'biomod2'
    > ### Aliases: BIOMOD_FormatingData
    > ### Keywords: models datasets
    >
    > ### ** Examples
    >
    >
    > # species occurrences
    > DataSpecies <- read.csv(system.file("external/species/mammals_table.csv",
    + package="biomod2"), row.names = 1)
    > head(DataSpecies)
     X_WGS84 Y_WGS84 ConnochaetesGnou GuloGulo PantheraOnca PteropusGiganteus
    1 -94.5 82.00001 0 0 0 0
    2 -91.5 82.00001 0 1 0 0
    3 -88.5 82.00001 0 1 0 0
    4 -85.5 82.00001 0 1 0 0
    5 -82.5 82.00001 0 1 0 0
    6 -79.5 82.00001 0 1 0 0
     TenrecEcaudatus VulpesVulpes
    1 0 0
    2 0 0
    3 0 0
    4 0 0
    5 0 0
    6 0 0
    >
    > # the name of studied species
    > myRespName <- 'GuloGulo'
    >
    > # the presence/absences data for our species
    > myResp <- as.numeric(DataSpecies[,myRespName])
    >
    > # the XY coordinates of species data
    > myRespXY <- DataSpecies[,c("X_WGS84","Y_WGS84")]
    >
    >
    > # Environmental variables extracted from BIOCLIM (bio_3, bio_4, bio_7, bio_11 & bio_12)
    > myExpl = raster::stack( system.file( "external/bioclim/current/bio3.grd",
    + package="biomod2"),
    + system.file( "external/bioclim/current/bio4.grd",
    + package="biomod2"),
    + system.file( "external/bioclim/current/bio7.grd",
    + package="biomod2"),
    + system.file( "external/bioclim/current/bio11.grd",
    + package="biomod2"),
    + system.file( "external/bioclim/current/bio12.grd",
    + package="biomod2"))
    > # 1. Formatting Data
    > myBiomodData <- BIOMOD_FormatingData(resp.var = myResp,
    + expl.var = myExpl,
    + resp.xy = myRespXY,
    + resp.name = myRespName)
    
    -=-=-=-=-=-=-=-=-=-=-=-=-=-= GuloGulo Data Formating -=-=-=-=-=-=-=-=-=-=-=-=-=-=
    
    > No pseudo absences selection !
     ! No data has been set aside for modeling evaluation
    -=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-= Done -=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=
    >
    > myBiomodData
    
    -=-=-=-=-=-=-=-=-=-=-=-=-=-= 'BIOMOD.formated.data' -=-=-=-=-=-=-=-=-=-=-=-=-=-=
    
    sp.name = GuloGulo
    
     661 presences, 1827 true absences and 0 undifined points in dataset
    
    
     5 explanatory variables
    
     bio3 bio4 bio7 bio11
     Min. :10.19 Min. : 72 Min. : 54.5 Min. :-447.75
     1st Qu.:21.22 1st Qu.: 2641 1st Qu.:186.0 1st Qu.:-184.32
     Median :35.00 Median : 6682 Median :306.2 Median : 24.23
     Mean :40.29 Mean : 7358 Mean :310.9 Mean : -2.64
     3rd Qu.:56.35 3rd Qu.:11752 3rd Qu.:424.6 3rd Qu.: 196.30
     Max. :92.00 Max. :22314 Max. :718.0 Max. : 283.00
     bio12
     Min. : 0.028
     1st Qu.: 276.493
     Median : 562.931
     Mean : 853.516
     3rd Qu.:1200.592
     Max. :5431.002
    
    -=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=
    > plot(myBiomodData)
    Error in (function (classes, fdef, mtable) :
     unable to find an inherited method for function 'xmin' for signature '"Extent"'
    Calls: plot ... levelplot -> .local -> .levelplot -> xmin -> <Anonymous>
    Execution halted
Flavor: r-oldrel-windows-ix86+x86_64