• using R version 2.9.1 Patched (2009-07-02 r48890)
  • using session charset: UTF-8
  • checking for file 'bim/DESCRIPTION' ... OK
  • this is package 'bim' version '1.01-5'
  • checking package dependencies ... OK
  • checking if this is a source package ... OK
  • checking whether package 'bim' can be installed ... WARNING
    Found the following significant warnings:
    Warning: invalid whitespace before brace in file 'bim.qtl.Rd' at ' \item{hpd} {density critical values for high probability density (HPD) region}'
    Warning: unmatched right brace in file 'read.bim.Rd' on line 41
    See http://www.r-project.org/nosvn/R.check/r-patched-linux-x86_64/bim-00install.html for details.
  • checking package directory ... OK
  • checking for portable file names ... OK
  • checking for sufficient/correct file permissions ... OK
  • checking DESCRIPTION meta-information ... NOTE
    Non-standard license specification:
    GPL version 2 or newer
    Standardizable: TRUE
    Standardized license specification:
    GPL (>= 2)
  • checking top-level files ... OK
  • checking index information ... OK
  • checking package subdirectories ... OK
  • checking R files for non-ASCII characters ... OK
  • checking R files for syntax errors ... OK
  • checking whether the package can be loaded ... OK
  • checking whether the package can be loaded with stated dependencies ... OK
  • checking for unstated dependencies in R code ... OK
  • checking S3 generic/method consistency ... OK
  • checking replacement functions ... OK
  • checking foreign function calls ... OK
  • checking R code for possible problems ... NOTE
    bmapqtl.options: no visible binding for global variable
    ‘.bmapqtl.options’
    bmapqtl.options: no visible binding for '<<-' assignment to
    ‘.bmapqtl.options’
    bmapqtl.options.init: no visible binding for '<<-' assignment to
    ‘.bmapqtl.options’
    bmapqtl.options.init: no visible binding for global variable
    ‘.bmapqtl.options’
    read.bim: ... may be used in an incorrect context: read.table(bimfile,
    header = TRUE, na.strings = na.strings, skip = skip, fill = TRUE,
    nrows = nrows, ...)
    read.bmapqtl: no visible binding for '<<-' assignment to
    ‘.bmapqtl.options’
    read.bmapqtl: no visible binding for global variable ‘.bmapqtl.options’
    run.bmapqtl: no visible binding for global variable ‘.bmapqtl.options’
    write.bmapqtl: no visible binding for global variable
    ‘.bmapqtl.options’
    Warning: <anonymous>: ... may be used in an incorrect context:
    read.table(bimfile, header = TRUE, na.strings = na.strings, skip = skip,
    fill = TRUE, nrows = nrows, ...)

    Found possibly global 'T' or 'F' in the following function:
    run.bmapqtl
  • checking Rd files ... OK
  • checking Rd files against version 2 parser ... WARNING
    *** error on file ./man/Bnapus.Rd
    Error : ./man/Bnapus.Rd:35: Unrecognized macro \item

    Warning in parse_Rd("./man/bim.qtl.Rd", encoding = "unknown") :
    bad markup (extra space?) at bim.qtl.Rd:38:13
    Warning: ./man/bim.qtl.Rd:38: Unnecessary braces at ‘{density critical values for high probability density (HPD) region}’
    *** error on file ./man/read.bim.Rd
    Error in parse_Rd("./man/read.bim.Rd", encoding = "unknown") :
    ./man/read.bim.Rd:41:1: unexpected '}'
    40: }
    41: }
    ^

    *** error on file ./man/run.bmapqtl.Rd
    Error : ./man/run.bmapqtl.Rd:52: Unrecognized macro \item

    *** error on file ./man/vern.Rd
    Error : ./man/vern.Rd:28: Unrecognized macro \item

    problems found in ‘Bnapus.Rd’, ‘read.bim.Rd’, ‘run.bmapqtl.Rd’, ‘vern.Rd’
  • checking Rd cross-references ... OK
  • checking for missing documentation entries ... OK
  • checking for code/documentation mismatches ... OK
  • checking Rd \usage sections ... NOTE
    S3 methods shown with full name in documentation object 'bim-internal':
    plot.bim.pattern

    S3 methods shown with full name in documentation object 'bim.effects':
    plot.bim.effects

    S3 methods shown with full name in documentation object 'bim.fdr':
    plot.bim.fdr

    S3 methods shown with full name in documentation object 'bim.':
    plot.bim.qtl

    S3 methods shown with full name in documentation object 'plot.bim':
    plot.bim

    S3 methods shown with full name in documentation object 'plot.bim.diag':
    plot.bim.diag

    S3 methods shown with full name in documentation object 'plot.bim.loci':
    plot.bim.loci

    S3 methods shown with full name in documentation object 'plot.bim.mcmc':
    plot.bim.mcmc

    S3 methods shown with full name in documentation object 'plot.bim.model':
    plot.bim.model

    The \usage entries for S3 methods should use the \method markup and not
    their full name.
    See the chapter 'Writing R documentation files' in manual 'Writing R
    Extensions'.
  • checking data for non-ASCII characters ... OK
  • checking line endings in C/C++/Fortran sources/headers ... OK
  • checking line endings in Makefiles ... OK
  • checking for portable use of $BLAS_LIBS ... OK
  • checking examples ... OK
  • checking package vignettes in 'inst/doc' ... OK
  • checking PDF version of manual ... OK