CRAN Package Check Results for Package FD

Last updated on 2021-12-03 23:49:57 CET.

Flavor Version Tinstall Tcheck Ttotal Status Flags
r-devel-linux-x86_64-debian-clang 1.0-12 11.73 100.39 112.12 NOTE
r-devel-linux-x86_64-debian-gcc 1.0-12 8.28 60.92 69.20 ERROR
r-devel-linux-x86_64-fedora-clang 1.0-12 151.81 NOTE
r-devel-linux-x86_64-fedora-gcc 1.0-12 129.15 NOTE
r-devel-windows-x86_64-new-UL 1.0-12 22.00 139.00 161.00 NOTE
r-devel-windows-x86_64-new-TK 1.0-12 NOTE
r-devel-windows-x86_64-old 1.0-12 16.00 91.00 107.00 NOTE
r-patched-linux-x86_64 1.0-12 10.97 92.89 103.86 NOTE
r-release-linux-x86_64 1.0-12 11.12 93.26 104.38 NOTE
r-release-macos-arm64 1.0-12 NOTE
r-release-macos-x86_64 1.0-12 NOTE
r-release-windows-ix86+x86_64 1.0-12 26.00 173.00 199.00 NOTE
r-oldrel-macos-x86_64 1.0-12 NOTE
r-oldrel-windows-ix86+x86_64 1.0-12 26.00 176.00 202.00 NOTE

Check Details

Version: 1.0-12
Check: R code for possible problems
Result: NOTE
    dbFD: no visible global function definition for 'dist'
    dbFD: no visible global function definition for 'na.omit'
    dbFD: no visible global function definition for 'hclust'
    dbFD: no visible global function definition for 'cutree'
    dbFD: no visible global function definition for 'aggregate'
    dbFD : divc: no visible global function definition for 'as.dist'
    dbFD: no visible global function definition for 'as.dist'
    fdisp: no visible binding for global variable 'weighted.mean'
    fdisp: no visible global function definition for 'weighted.mean'
    functcomp: no visible global function definition for 'weighted.mean'
    mahaldis: no visible global function definition for 'dist'
    maxent: no visible global function definition for 'coef'
    maxent: no visible global function definition for 'lm'
    maxent.test: no visible global function definition for 'cor'
    maxent.test: no visible global function definition for 'par'
    maxent.test: no visible global function definition for 'abline'
    maxent.test: no visible global function definition for 'text'
    maxent.test: no visible global function definition for 'lines'
    maxent.test: no visible global function definition for 'mtext'
    simul.dbFD : <anonymous>: no visible global function definition for
     'runif'
    simul.dbFD : <anonymous>: no visible global function definition for
     'rnorm'
    simul.dbFD : <anonymous>: no visible global function definition for
     'rlnorm'
    simul.dbFD : fill.abun: no visible global function definition for
     'rlnorm'
    simul.dbFD : fill.abun: no visible global function definition for
     'rnorm'
    simul.dbFD : fill.abun: no visible global function definition for
     'runif'
    simul.dbFD: no visible global function definition for 'cor.test'
    simul.dbFD: no visible global function definition for 'par'
    simul.dbFD: no visible global function definition for 'title'
    simul.dbFD: no visible global function definition for 'mtext'
    simul.dbFD: no visible global function definition for 'boxplot'
    Undefined global functions or variables:
     abline aggregate as.dist boxplot coef cor cor.test cutree dist hclust
     lines lm mtext na.omit par rlnorm rnorm runif text title
     weighted.mean
    Consider adding
     importFrom("graphics", "abline", "boxplot", "lines", "mtext", "par",
     "text", "title")
     importFrom("stats", "aggregate", "as.dist", "coef", "cor", "cor.test",
     "cutree", "dist", "hclust", "lm", "na.omit", "rlnorm",
     "rnorm", "runif", "weighted.mean")
    to your NAMESPACE file.
Flavors: r-devel-linux-x86_64-debian-clang, r-devel-linux-x86_64-debian-gcc, r-devel-linux-x86_64-fedora-clang, r-devel-linux-x86_64-fedora-gcc, r-devel-windows-x86_64-new-UL, r-devel-windows-x86_64-new-TK, r-devel-windows-x86_64-old, r-patched-linux-x86_64, r-release-linux-x86_64, r-release-macos-arm64, r-release-macos-x86_64, r-release-windows-ix86+x86_64, r-oldrel-macos-x86_64, r-oldrel-windows-ix86+x86_64

Version: 1.0-12
Check: for non-standard things in the check directory
Result: NOTE
    Found the following files/directories:
     'vert.txt'
Flavors: r-devel-linux-x86_64-debian-clang, r-devel-linux-x86_64-fedora-clang, r-devel-linux-x86_64-fedora-gcc, r-patched-linux-x86_64, r-release-linux-x86_64

Version: 1.0-12
Check: examples
Result: ERROR
    Running examples in ‘FD-Ex.R’ failed
    The error most likely occurred in:
    
    > base::assign(".ptime", proc.time(), pos = "CheckExEnv")
    > ### Name: FD-package
    > ### Title: Measuring Functional Diversity from Multiple Traits, and Other
    > ### Tools for Functional Ecology
    > ### Aliases: FD-package FD
    > ### Keywords: package
    >
    > ### ** Examples
    >
    > # examples with a dummy dataset
    >
    > ex1 <- gowdis(dummy$trait)
    > ex1
     sp1 sp2 sp3 sp4 sp5 sp6 sp7
    sp2 0.2181884
    sp3 0.5240052 0.6678082
    sp4 0.6737443 0.5610028 0.8225701
    sp5 0.5291113 0.8145699 0.4862253 0.4843264
    sp6 0.6100161 0.5932587 0.2784736 0.7073925 0.6067323
    sp7 0.4484235 0.6863374 0.4848663 0.5575126 0.3023416 0.6187844
    sp8 0.4072834 0.2039443 0.5958904 0.2390962 0.5585525 0.4470207 0.7030186
    >
    > ex2 <- functcomp(dummy$trait, dummy$abun)
    > ex2
     num1 num2 fac1 fac2 ord1 ord2 bin1 bin2
    com1 5.887500 4.037500 C X 2 6 1 1
    com2 4.212500 5.562500 B Z 1 3 0 1
    com3 5.716667 6.166667 A Z 1 3 0 1
    com4 9.000000 2.575000 C Y 5 3 1 1
    com5 4.500000 3.050000 C X 1 6 0 0
    com6 5.095238 5.528571 C Z 2 1 0 1
    com7 7.009091 5.427273 A Z 3 1 0 1
    com8 5.245455 3.572727 C X 2 6 1 0
    com9 6.870000 4.245455 A X 3 2 0 1
    com10 7.427273 3.783333 B X 3 2 1 0
    >
    > ex3 <- dbFD(dummy$trait, dummy$abun)
    Error in dbFD(dummy$trait, dummy$abun) :
     Species labels in 'x' and 'a' need to be identical and ordered alphabetically (or simply in the same order).
    Execution halted
Flavor: r-devel-linux-x86_64-debian-gcc

Version: 1.0-12
Check: compiled code
Result: NOTE
    File ‘FD/libs/FD.so’:
     Found no calls to: ‘R_registerRoutines’, ‘R_useDynamicSymbols’
    
    It is good practice to register native routines and to disable symbol
    search.
    
    See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual.
Flavors: r-devel-linux-x86_64-fedora-clang, r-devel-linux-x86_64-fedora-gcc