CRAN Package Check Results for Package betaper

Last updated on 2015-07-29 17:47:51.

Flavor Version Tinstall Tcheck Ttotal Status Flags
r-devel-linux-x86_64-debian-clang 1.1-0 2.92 34.71 37.63 NOTE
r-devel-linux-x86_64-debian-gcc 1.1-0 2.75 33.64 36.40 NOTE
r-devel-linux-x86_64-fedora-clang 1.1-0 75.16 NOTE
r-devel-linux-x86_64-fedora-gcc 1.1-0 71.88 NOTE
r-devel-osx-x86_64-clang 1.1-0 63.22 NOTE
r-devel-windows-ix86+x86_64 1.1-0 9.00 59.00 68.00 NOTE
r-patched-linux-x86_64 1.1-0 2.77 33.68 36.45 NOTE
r-patched-solaris-sparc 1.1-0 462.20 NOTE
r-patched-solaris-x86 1.1-0 104.00 NOTE
r-release-linux-x86_64 1.1-0 2.80 33.58 36.38 NOTE
r-release-osx-x86_64-mavericks 1.1-0 NOTE
r-release-windows-ix86+x86_64 1.1-0 10.00 82.00 92.00 NOTE
r-oldrel-windows-ix86+x86_64 1.1-0 11.00 103.00 114.00 NOTE

Check Details

Version: 1.1-0
Check: DESCRIPTION meta-information
Result: NOTE
    Malformed Description field: should contain one or more complete sentences.
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-osx-x86_64-clang, r-devel-windows-ix86+x86_64, r-patched-linux-x86_64, r-patched-solaris-sparc, r-patched-solaris-x86, r-release-linux-x86_64, r-release-osx-x86_64-mavericks, r-release-windows-ix86+x86_64

Version: 1.1-0
Check: dependencies in R code
Result: NOTE
    'library' or 'require' call to ‘vegan’ which was already attached by Depends.
     Please remove these calls from your code.
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-osx-x86_64-clang, r-devel-windows-ix86+x86_64, r-patched-linux-x86_64, r-patched-solaris-sparc, r-patched-solaris-x86, r-release-linux-x86_64, r-release-osx-x86_64-mavericks, r-release-windows-ix86+x86_64, r-oldrel-windows-ix86+x86_64

Version: 1.1-0
Check: S3 generic/method consistency
Result: NOTE
    Found the following apparent S3 methods exported but not registered:
     cca.pertables plot.adonis.pertables plot.cca.pertables
     plot.mantel.pertables plot.rda.pertables print.adonis.pertables
     print.cca.pertables print.mantel.pertables print.pertables
     print.rda.pertables rda.pertables
    See section ‘Registering S3 methods’ in the ‘Writing R Extensions’
    manual.
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-osx-x86_64-clang, r-patched-linux-x86_64, r-patched-solaris-sparc, r-patched-solaris-x86, r-release-linux-x86_64

Version: 1.1-0
Check: R code for possible problems
Result: NOTE
    adonis.pertables: no visible binding for global variable ‘quantile’
    cca.pertables : cca.var: no visible binding for global variable
     ‘cca.formula’
    cca.pertables : cca.var: no visible global function definition for
     ‘anova’
    cca.pertables: no visible binding for global variable ‘quantile’
    cca.pertables: no visible binding for global variable ‘cca.formula’
    cca.pertables: no visible global function definition for ‘anova’
    mantel.pertables : mantel.test: no visible global function definition
     for ‘dist’
    mantel.pertables: no visible binding for global variable ‘quantile’
    mantel.pertables: no visible global function definition for ‘dist’
    plot.adonis.pertables: no visible global function definition for
     ‘layout’
    plot.adonis.pertables: no visible global function definition for ‘par’
    plot.adonis.pertables: no visible global function definition for ‘hist’
    plot.adonis.pertables: no visible global function definition for
     ‘mtext’
    plot.adonis.pertables: no visible global function definition for ‘plot’
    plot.adonis.pertables: no visible global function definition for
     ‘density’
    plot.adonis.pertables: no visible global function definition for
     ‘abline’
    plot.adonis.pertables: no visible global function definition for
     ‘median’
    plot.cca.pertables: no visible global function definition for ‘plot’
    plot.cca.pertables : <anonymous> : <anonymous>: no visible global
     function definition for ‘arrows’
    plot.cca.pertables : <anonymous>: no visible global function definition
     for ‘points’
    plot.cca.pertables: no visible global function definition for ‘points’
    plot.cca.pertables: no visible global function definition for ‘text’
    plot.mantel.pertables: no visible global function definition for
     ‘layout’
    plot.mantel.pertables: no visible global function definition for ‘par’
    plot.mantel.pertables: no visible global function definition for ‘hist’
    plot.mantel.pertables: no visible global function definition for ‘plot’
    plot.mantel.pertables: no visible global function definition for
     ‘density’
    plot.mantel.pertables: no visible global function definition for
     ‘abline’
    plot.mantel.pertables: no visible global function definition for
     ‘median’
    plot.mantel.pertables : <anonymous>: no visible global function
     definition for ‘lines’
    plot.mantel.pertables : <anonymous>: no visible global function
     definition for ‘lowess’
    plot.mantel.pertables: no visible global function definition for
     ‘lines’
    plot.mantel.pertables: no visible global function definition for
     ‘lowess’
    plot.rda.pertables: no visible global function definition for ‘plot’
    plot.rda.pertables : <anonymous> : <anonymous>: no visible global
     function definition for ‘arrows’
    plot.rda.pertables : <anonymous>: no visible global function definition
     for ‘points’
    plot.rda.pertables: no visible global function definition for ‘points’
    plot.rda.pertables: no visible global function definition for ‘text’
    rda.pertables : rda.var: no visible binding for global variable
     ‘rda.formula’
    rda.pertables : rda.var: no visible global function definition for
     ‘anova’
    rda.pertables: no visible binding for global variable ‘quantile’
    rda.pertables: no visible binding for global variable ‘rda.formula’
    rda.pertables: no visible global function definition for ‘anova’
    Undefined global functions or variables:
     abline anova arrows cca.formula density dist hist layout lines lowess
     median mtext par plot points quantile rda.formula text
    Consider adding
     importFrom("graphics", "abline", "arrows", "hist", "layout", "lines",
     "mtext", "par", "plot", "points", "text")
     importFrom("stats", "anova", "density", "dist", "lowess", "median",
     "quantile")
    to your NAMESPACE.
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-ix86+x86_64

Version: 1.1-0
Check: Rd line widths
Result: NOTE
    Rd file 'adonis.pertables.Rd':
     \examples lines wider than 100 characters:
     # Define a new index that includes the terms used in the \code{Amazonia} dataset to define undetermined taxa at different taxonomic lev ... [TRUNCATED]
     #Generate a pertables object (i.e. a list of biological data tables simulated from taxonomic uncertainty)
     # Assess the effects of taxonomic uncertainty on a Mantel test of biological dissimilarity correlated to soil dissimilarity among site ... [TRUNCATED]
    
    Rd file 'cca.pertables.Rd':
     \examples lines wider than 100 characters:
     # Define a new index that includes the terms used in the \code{Amazonia} dataset to define undetermined
     #Generate a pertables object (i.e. a list of biological data tables simulated from taxonomic uncertainty)
     # Assess the effects of taxonomic uncertainty on a CCA analysis of biological data explained by all the
    
    Rd file 'mantel.pertables.Rd':
     \usage lines wider than 90 characters:
     mantel.pertables(pertab, env, dist.method = "bray", binary = FALSE, cor.method = "pearson", permutations = 100)
     plot(x, xlab = "Environmental distance", ylab = "Sorensen's similarity index", pch = 19, ...)
     \examples lines wider than 100 characters:
     # Define a new index that includes the terms used in the \code{Amazonia} dataset to define undetermined taxa at different taxonomic lev ... [TRUNCATED]
     #Generate a pertables object (i.e. a list of biological data tables simulated from taxonomic uncertainty)
     # Assess the effects of taxonomic uncertainty on a Mantel test of biological dissimilarity correlated to soil dissimilarity among site ... [TRUNCATED]
    
    Rd file 'pertables.Rd':
     \examples lines wider than 100 characters:
     # Define a new index that includes the terms used in the \code{Amazonia} dataset to define undetermined taxa at different taxonomic lev ... [TRUNCATED]
     #Generate a pertables object (i.e. a list of biological data tables simulated from taxonomic uncertainty)
    
    Rd file 'rda.pertables.Rd':
     \examples lines wider than 100 characters:
     # Define a new index that includes the terms used in the \code{Amazonia} dataset to define undetermined taxa at different taxonomic lev ... [TRUNCATED]
     #Generate a pertables object (i.e. a list of biological data tables simulated from taxonomic uncertainty)
     # Assess the effects of taxonomic uncertainty on a RDA analysis of biological data explained by all the environmental variables of the ... [TRUNCATED]
    
    These lines will be truncated in the PDF manual.
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-patched-linux-x86_64, r-release-linux-x86_64

Version: 1.1-0
Check: Rd \usage sections
Result: NOTE
    S3 methods shown with full name in documentation object 'cca.pertables':
     ‘cca.pertables’
    
    S3 methods shown with full name in documentation object 'rda.pertables':
     ‘rda.pertables’
    
    The \usage entries for S3 methods should use the \method markup and not
    their full name.
    See chapter ‘Writing R documentation files’ in the ‘Writing R
    Extensions’ manual.
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-osx-x86_64-clang, r-devel-windows-ix86+x86_64, r-patched-linux-x86_64, r-patched-solaris-sparc, r-patched-solaris-x86, r-release-linux-x86_64, r-release-osx-x86_64-mavericks, r-release-windows-ix86+x86_64, r-oldrel-windows-ix86+x86_64

Version: 1.1-0
Check: R code for possible problems
Result: NOTE
    cca.pertables : cca.var: no visible binding for global variable
     ‘cca.formula’
    cca.pertables: no visible binding for global variable ‘cca.formula’
    rda.pertables : rda.var: no visible binding for global variable
     ‘rda.formula’
    rda.pertables: no visible binding for global variable ‘rda.formula’
    Undefined global functions or variables:
     cca.formula rda.formula
Flavor: r-devel-osx-x86_64-clang

Version: 1.1-0
Check: R code for possible problems
Result: NOTE
    cca.pertables : cca.var: no visible binding for global variable
     ‘cca.formula’
    cca.pertables: no visible binding for global variable ‘cca.formula’
    rda.pertables : rda.var: no visible binding for global variable
     ‘rda.formula’
    rda.pertables: no visible binding for global variable ‘rda.formula’
Flavors: r-patched-linux-x86_64, r-patched-solaris-sparc, r-patched-solaris-x86, r-release-linux-x86_64, r-release-osx-x86_64-mavericks, r-release-windows-ix86+x86_64, r-oldrel-windows-ix86+x86_64