CRAN Package Check Results for Package betaper

Last updated on 2015-07-02 23:46:59.

Flavor Version Tinstall Tcheck Ttotal Status Flags
r-devel-linux-x86_64-debian-clang 1.1-0 2.80 33.52 36.32 NOTE
r-devel-linux-x86_64-debian-gcc 1.1-0 2.72 32.83 35.55 NOTE
r-devel-linux-x86_64-fedora-clang 1.1-0 74.80 NOTE
r-devel-linux-x86_64-fedora-gcc 1.1-0 68.33 NOTE
r-devel-osx-x86_64-clang 1.1-0 68.15 NOTE
r-devel-windows-ix86+x86_64 1.1-0 8.00 56.00 64.00 NOTE
r-patched-linux-x86_64 1.1-0 2.86 33.74 36.60 NOTE
r-patched-solaris-sparc 1.1-0 460.10 NOTE
r-patched-solaris-x86 1.1-0 105.90 NOTE
r-release-linux-x86_64 1.1-0 2.92 33.56 36.48 NOTE
r-release-osx-x86_64-mavericks 1.1-0 NOTE
r-release-windows-ix86+x86_64 1.1-0 8.00 51.00 59.00 NOTE
r-oldrel-windows-ix86+x86_64 1.1-0 12.00 68.00 80.00 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
Flavors: r-devel-linux-x86_64-debian-clang, 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
    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’
Flavor: r-devel-linux-x86_64-debian-gcc

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-devel-osx-x86_64-clang, 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