CRAN Package Check Results for Package betaper

Last updated on 2014-04-25 05:47:12.

Flavor Version Tinstall Tcheck Ttotal Status Flags
r-devel-linux-x86_64-debian-clang 1.1-0 0.96 14.85 15.81 NOTE
r-devel-linux-x86_64-debian-gcc 1.1-0 1.04 15.60 16.64 NOTE
r-devel-linux-x86_64-fedora-clang 1.1-0 30.63 NOTE
r-devel-linux-x86_64-fedora-gcc 1.1-0 28.37 NOTE
r-devel-osx-x86_64-clang 1.1-0 32.52 NOTE
r-devel-osx-x86_64-gcc 1.1-0 ERROR
r-devel-windows-ix86+x86_64 1.1-0 3.00 24.00 27.00 NOTE
r-patched-linux-x86_64 1.1-0 0.92 15.36 16.29 NOTE
r-patched-solaris-sparc 1.1-0 170.80 NOTE
r-patched-solaris-x86 1.1-0 42.30 NOTE
r-release-linux-ix86 1.1-0 2.00 30.00 32.00 NOTE
r-release-linux-x86_64 1.1-0 0.92 14.55 15.47 NOTE
r-release-osx-x86_64-mavericks 1.1-0 WARN
r-release-osx-x86_64-snowleopard 1.1-0 NOTE
r-release-windows-ix86+x86_64 1.1-0 4.00 24.00 28.00 NOTE
r-oldrel-windows-ix86+x86_64 1.1-0 4.00 27.00 31.00 NOTE

Check Details

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.
    See the information on DESCRIPTION files in the chapter ‘Creating R
    packages’ of 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-ix86, r-release-linux-x86_64, r-release-osx-x86_64-mavericks, r-release-osx-x86_64-snowleopard, 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’
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-ix86, r-release-linux-x86_64, r-release-osx-x86_64-mavericks, r-release-osx-x86_64-snowleopard, r-release-windows-ix86+x86_64, r-oldrel-windows-ix86+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 the 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-ix86, r-release-linux-x86_64, r-release-osx-x86_64-mavericks, r-release-osx-x86_64-snowleopard, r-release-windows-ix86+x86_64, r-oldrel-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-fedora-clang, r-devel-linux-x86_64-fedora-gcc

Version: 1.1-0
Check: package dependencies
Result: ERROR
    Package required but not available: ‘vegan’
    
    See the information on DESCRIPTION files in the chapter ‘Creating R
    packages’ of the ‘Writing R Extensions’ manual.
Flavor: r-devel-osx-x86_64-gcc

Version: 1.1-0
Check: PDF version of manual
Result: WARNING
    LaTeX errors when creating PDF version.
    This typically indicates Rd problems.
    LaTeX errors found:
    ! LaTeX Error: File `upquote.sty' not found.
    
    Type X to quit or <RETURN> to proceed,
    or enter new name. (Default extension: sty)
    
    2c9b771/Rd2.tex:8: ==> Fatal error occurred, no output PDF file produced!
Flavor: r-release-osx-x86_64-mavericks