• using R version 2.10.0 Patched (2009-11-05 r50317)
  • 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: ./man/Bnapus.Rd:35: unknown macro '\item'
    Warning: ./man/Bnapus.Rd:36: unknown macro '\item'
    Warning: ./man/Bnapus.Rd:37: unknown macro '\item'
    Warning: ./man/Bnapus.Rd:38: unknown macro '\item'
    Warning: ./man/Bnapus.Rd:43: unknown macro '\item'
    Warning: ./man/Bnapus.Rd:47: unknown macro '\item'
    Warning: ./man/Bnapus.Rd:48: unknown macro '\item'
    Warning: ./man/Bnapus.Rd:52: unknown macro '\item'
    Warning: ./man/Bnapus.Rd:58: unknown macro '\item'
    Warning: bad markup (extra space?) at bim.qtl.Rd:38:13
    Warning: ./man/read.bim.Rd:41: unexpected '}'
    Warning: ./man/run.bmapqtl.Rd:52: unknown macro '\item'
    Warning: ./man/run.bmapqtl.Rd:53: unknown macro '\item'
    Warning: ./man/run.bmapqtl.Rd:59: unknown macro '\item'
    Warning: ./man/run.bmapqtl.Rd:68: unknown macro '\item'
    Warning: ./man/vern.Rd:28: unknown macro '\item'
    Warning: ./man/vern.Rd:29: unknown macro '\item'
    Warning: ./man/vern.Rd:33: unknown macro '\item'
    Warning: ./man/vern.Rd:38: unknown macro '\item'
    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 ... WARNING
    prepare_Rd: Bnapus.Rd:35: unknown macro '\item'
    prepare_Rd: Bnapus.Rd:36: unknown macro '\item'
    prepare_Rd: Bnapus.Rd:37: unknown macro '\item'
    prepare_Rd: Bnapus.Rd:38: unknown macro '\item'
    prepare_Rd: Bnapus.Rd:43: unknown macro '\item'
    prepare_Rd: Bnapus.Rd:47: unknown macro '\item'
    prepare_Rd: Bnapus.Rd:48: unknown macro '\item'
    prepare_Rd: Bnapus.Rd:52: unknown macro '\item'
    prepare_Rd: Bnapus.Rd:58: unknown macro '\item'
    prepare_Rd: bad markup (extra space?) at bim.qtl.Rd:38:13
    checkRd: (5) bmapqtl.options.Rd:53: Tag \eqn is invalid in a \code block
    prepare_Rd: read.bim.Rd:41: unexpected '}'
    prepare_Rd: run.bmapqtl.Rd:52: unknown macro '\item'
    prepare_Rd: run.bmapqtl.Rd:53: unknown macro '\item'
    prepare_Rd: run.bmapqtl.Rd:59: unknown macro '\item'
    prepare_Rd: run.bmapqtl.Rd:68: unknown macro '\item'
    prepare_Rd: vern.Rd:28: unknown macro '\item'
    prepare_Rd: vern.Rd:29: unknown macro '\item'
    prepare_Rd: vern.Rd:33: unknown macro '\item'
    prepare_Rd: vern.Rd:38: unknown macro '\item'
  • checking Rd metadata ... OK
  • checking Rd cross-references ... WARNING
    Obsolete package(s) ‘modreg’ in Rd xrefs
    Missing link(s) in documentation object './man/bim.effects.Rd':
    ‘[base]{plot}’

    Missing link(s) in documentation object './man/bim.fdr.Rd':
    ‘[base]{plot}’

    Missing link(s) in documentation object './man/bim.qtl.Rd':
    ‘[base]{plot}’

    Missing link(s) in documentation object './man/plot.bim.Rd':
    ‘[base]{plot}’

    Missing link(s) in documentation object './man/plot.bim.diag.Rd':
    ‘[base]{plot}’ ‘[base]{boxplot}’

    Missing link(s) in documentation object './man/plot.bim.loci.Rd':
    ‘[base]{plot}’

    Missing link(s) in documentation object './man/plot.bim.mcmc.Rd':
    ‘[base]{plot}’

    Missing link(s) in documentation object './man/plot.bim.model.Rd':
    ‘[base]{plot}’

    See the information in section 'Cross-references' of the 'Writing R
    Extensions' manual.
  • 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