• using R version 2.10.0 Patched (2009-11-22 r50534)
  • using session charset: UTF-8
  • checking for file 'asuR/DESCRIPTION' ... OK
  • checking extension type ... Package
  • this is package 'asuR' version '0.08-24'
  • checking package dependencies ... OK
  • checking if this is a source package ... OK
  • checking whether package 'asuR' can be installed ... WARNING
    Found the following significant warnings:
    Warning: ./man/colVars.Rd:28: unexpected '}'
    Warning: ./man/growth.Rd:22: unexpected '}'
    Warning: ./man/inspect.Rd:28: unexpected section header '\description'
    Warning: ./man/inspect.Rd:29: unknown macro '\item'
    Warning: ./man/inspect.Rd:33: unknown macro '\item'
    Warning: ./man/inspect.Rd:37: unknown macro '\item'
    Warning: ./man/mytrees.Rd:18: unexpected '}'
    Warning: ./man/pea.Rd:20: unexpected '}'
    Warning: ./man/wellplate.Rd:34: unexpected '}'
    See http://www.r-project.org/nosvn/R.check/r-patched-linux-x86_64/asuR-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
    dep.glm: no visible binding for global variable ‘my.data’
    lep.glm: no visible binding for global variable ‘response.values’
    lep.glm: no visible binding for global variable ‘my.data’
    nep.lmer: no visible binding for global variable ‘my.data’
    nrp.lmer: no visible binding for global variable ‘fixed.terms.factor’
    nrp.lmer: no visible binding for global variable ‘my.data’
    parseFormula.glm: no visible binding for '<<-' assignment to
    ‘response.var’
    parseFormula.glm: no visible binding for '<<-' assignment to
    ‘response.term’
    parseFormula.glm: no visible binding for '<<-' assignment to
    ‘predict.vars.numeric’
    parseFormula.glm: no visible binding for '<<-' assignment to
    ‘predict.terms.numeric’
    parseFormula.glm: no visible binding for '<<-' assignment to
    ‘index_coef.terms.numeric’
    parseFormula.glm: no visible binding for global variable
    ‘predict.terms.numeric’
    parseFormula.glm: no visible binding for '<<-' assignment to ‘my.data’
    parseFormula.glm: no visible binding for global variable ‘response.var’
    parseFormula.glm: no visible binding for '<<-' assignment to
    ‘intercept.logical’
    parseFormula.lm: no visible binding for '<<-' assignment to
    ‘terms.numeric’
    parseFormula.lm: no visible binding for '<<-' assignment to
    ‘response.var’
    parseFormula.lm: no visible binding for '<<-' assignment to
    ‘response.term’
    parseFormula.lm: no visible binding for '<<-' assignment to
    ‘predict.vars.numeric’
    parseFormula.lm: no visible binding for '<<-' assignment to
    ‘predict.terms.numeric’
    parseFormula.lm: no visible binding for global variable ‘terms.numeric’
    parseFormula.lm: no visible binding for '<<-' assignment to
    ‘my.data.glm’
    parseFormula.lm: no visible binding for global variable ‘response.var’
    parseFormula.lm: no visible binding for '<<-' assignment to
    ‘intercept.logical’
    parseFormula.lmer: no visible binding for '<<-' assignment to
    ‘intercept.logical’
    parseFormula.lmer: no visible binding for '<<-' assignment to
    ‘group.vars’
    parseFormula.lmer: no visible binding for '<<-' assignment to
    ‘effect.vars’
    parseFormula.lmer: no visible binding for '<<-' assignment to
    ‘fixed.terms.numeric’
    parseFormula.lmer: no visible binding for '<<-' assignment to
    ‘fixed.terms.factor’
    rfp.lmer: no visible binding for global variable ‘my.data’
    rfp.lmer: no visible binding for global variable ‘fixed.terms.factor’
    rgp.lmer: no visible binding for global variable ‘my.data’
    rgp.lmer: no visible binding for global variable ‘rand.vars’
    rpp.glm: no visible binding for global variable ‘my.data’
    rpp.glm: no visible binding for global variable ‘predict.terms.numeric’
    rpp.glm: no visible binding for global variable ‘response.values’
    rpp.lm: no visible binding for global variable ‘predict.vars.numeric’
    rpp.lm: no visible binding for global variable ‘response.values.lm’
    dep,glm: no visible binding for global variable ‘my.data’
    lep,glm: no visible binding for global variable ‘response.values’
    lep,glm: no visible binding for global variable ‘my.data’
    nep,lmer: no visible binding for global variable ‘my.data’
    nrp,lmer: no visible binding for global variable ‘fixed.terms.factor’
    nrp,lmer: no visible binding for global variable ‘my.data’
    parseFormula,glm: no visible binding for '<<-' assignment to
    ‘response.var’
    parseFormula,glm: no visible binding for '<<-' assignment to
    ‘response.term’
    parseFormula,glm: no visible binding for '<<-' assignment to
    ‘predict.vars.numeric’
    parseFormula,glm: no visible binding for '<<-' assignment to
    ‘predict.terms.numeric’
    parseFormula,glm: no visible binding for '<<-' assignment to
    ‘index_coef.terms.numeric’
    parseFormula,glm: no visible binding for global variable
    ‘predict.terms.numeric’
    parseFormula,glm: no visible binding for '<<-' assignment to ‘my.data’
    parseFormula,glm: no visible binding for global variable ‘response.var’
    parseFormula,glm: no visible binding for '<<-' assignment to
    ‘intercept.logical’
    parseFormula,lm: no visible binding for '<<-' assignment to
    ‘terms.numeric’
    parseFormula,lm: no visible binding for '<<-' assignment to
    ‘response.var’
    parseFormula,lm: no visible binding for '<<-' assignment to
    ‘response.term’
    parseFormula,lm: no visible binding for '<<-' assignment to
    ‘predict.vars.numeric’
    parseFormula,lm: no visible binding for '<<-' assignment to
    ‘predict.terms.numeric’
    parseFormula,lm: no visible binding for global variable ‘terms.numeric’
    parseFormula,lm: no visible binding for '<<-' assignment to
    ‘my.data.glm’
    parseFormula,lm: no visible binding for global variable ‘response.var’
    parseFormula,lm: no visible binding for '<<-' assignment to
    ‘intercept.logical’
    parseFormula,lmer: no visible binding for '<<-' assignment to
    ‘intercept.logical’
    parseFormula,lmer: no visible binding for '<<-' assignment to
    ‘group.vars’
    parseFormula,lmer: no visible binding for '<<-' assignment to
    ‘effect.vars’
    parseFormula,lmer: no visible binding for '<<-' assignment to
    ‘fixed.terms.numeric’
    parseFormula,lmer: no visible binding for '<<-' assignment to
    ‘fixed.terms.factor’
    rfp,lmer: no visible binding for global variable ‘my.data’
    rfp,lmer: no visible binding for global variable ‘fixed.terms.factor’
    rgp,lmer: no visible binding for global variable ‘my.data’
    rgp,lmer: no visible binding for global variable ‘rand.vars’
    rpp,glm: no visible binding for global variable ‘my.data’
    rpp,glm: no visible binding for global variable ‘predict.terms.numeric’
    rpp,glm: no visible binding for global variable ‘response.values’
    rpp,lm: no visible binding for global variable ‘predict.vars.numeric’
    rpp,lm: no visible binding for global variable ‘response.values.lm’
  • checking Rd files ... WARNING
    prepare_Rd: colVars.Rd:28: unexpected '}'
    prepare_Rd: growth.Rd:22: unexpected '}'
    prepare_Rd: identifyControl.Rd:16-17: Dropping empty section \details
    prepare_Rd: inspect.Rd:28: unexpected section header '\description'
    prepare_Rd: inspect.Rd:29: unknown macro '\item'
    prepare_Rd: inspect.Rd:33: unknown macro '\item'
    prepare_Rd: inspect.Rd:37: unknown macro '\item'
    prepare_Rd: mytrees.Rd:18: unexpected '}'
    prepare_Rd: parseFormula.glm.Rd:14-15: Dropping empty section \details
    prepare_Rd: parseFormula.glm.Rd:16-18: Dropping empty section \value
    prepare_Rd: parseFormula.lm.Rd:14-15: Dropping empty section \details
    prepare_Rd: parseFormula.lmer.Rd:14-15: Dropping empty section \details
    prepare_Rd: parseFormula.lmer.Rd:16-18: Dropping empty section \value
    prepare_Rd: pea.Rd:20: unexpected '}'
    prepare_Rd: wellplate.Rd:34: unexpected '}'
  • checking Rd metadata ... WARNING
    Rd files with duplicated name 'parseFormula':
    parseFormula.Rd parseFormula.lm.Rd
  • checking Rd cross-references ... OK
  • checking for missing documentation entries ... OK
  • checking for code/documentation mismatches ... OK
  • checking Rd \usage sections ... OK
  • checking data for non-ASCII characters ... OK
  • checking examples ... OK
  • checking package vignettes in 'inst/doc' ... NOTE
    *** PDFLaTeX Errors ***
    File /home/hornik/tmp/R.check/r-patched/Work/PKGS/asuR.Rcheck/inst/doc/coursenotes.Rnw :
    Running 'texi2dvi' on 'coursenotes.tex' failed.
    LaTeX errors:
    ! LaTeX Error: File `mySlides.sty' not found.
    Type X to quit or <RETURN> to proceed,
    or enter new name. (Default extension: sty)
    ! Emergency stop.
    <read *>
    l.12 \usepackage
    {myR}^^M
    ! ==> Fatal error occurred, no output PDF file produced!
  • checking PDF version of manual ... OK