CRAN Package Check Results for Package qtlhot

Last updated on 2017-12-20 00:47:09 CET.

Check Details

Version: 0.9.0
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-windows-ix86+x86_64, r-patched-linux-x86_64, r-patched-solaris-x86, r-release-linux-x86_64, r-release-windows-ix86+x86_64, r-release-osx-x86_64, r-oldrel-windows-ix86+x86_64, r-oldrel-osx-x86_64

Version: 0.9.0
Check: S3 generic/method consistency
Result: NOTE
    Found the following apparent S3 methods exported but not registered:
     parallel.qtlhot
    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-patched-linux-x86_64, r-patched-solaris-x86, r-release-linux-x86_64

Version: 0.9.0
Check: R code for possible problems
Result: NOTE
    CMSTtests : CreateDesignMatrix: no visible global function definition
     for ‘model.matrix’
    CMSTtests : CreateDesignMatrix: no visible global function definition
     for ‘as.formula’
    CMSTtests : ParametricIUCMST: no visible global function definition for
     ‘pnorm’
    CMSTtests : NonparametricIUCMST: no visible global function definition
     for ‘pbinom’
    CMSTtests : GetLogLik: no visible global function definition for
     ‘dnorm’
    CMSTtests: no visible global function definition for ‘cov’
    CMSTtests: no visible global function definition for ‘cov2cor’
    CitTests: no visible global function definition for ‘lm’
    CitTests: no visible global function definition for ‘anova’
    CitTests: no visible global function definition for ‘resid’
    CitTests: no visible global function definition for ‘runif’
    CitTests: no visible global function definition for ‘pf’
    CitTests: no visible global function definition for ‘qnorm’
    CitTests: no visible global function definition for ‘pnorm’
    CitTests: no visible global function definition for ‘sd’
    DropMissing: no visible global function definition for ‘na.omit’
    FDRplot: no visible global function definition for ‘par’
    FDRplot: no visible global function definition for ‘plot’
    FDRplot: no visible global function definition for ‘abline’
    FDRplot: no visible global function definition for ‘points’
    GetCommonQtls : CreateCovMatrix: no visible global function definition
     for ‘formula’
    GetCommonQtls : CreateCovMatrix: no visible global function definition
     for ‘model.matrix’
    MyMultipleTestingSim: no visible global function definition for ‘runif’
    MyMultipleTestingSim2: no visible global function definition for
     ‘runif’
    SimCross1: no visible global function definition for ‘rnorm’
    SimCross2: no visible global function definition for ‘rnorm’
    SimCross3: no visible global function definition for ‘rnorm’
    SimCross4: no visible global function definition for ‘rnorm’
    SimCross5: no visible global function definition for ‘rnorm’
    SimCross6: no visible global function definition for ‘rnorm’
    SimCrossCausal: no visible global function definition for ‘rnorm’
    SimCrossIndep: no visible global function definition for ‘rnorm’
    add.rug: no visible global function definition for ‘par’
    add.rug: no visible global function definition for ‘rug’
    add.rug: no visible global function definition for ‘abline’
    add.rug: no visible global function definition for ‘axis’
    add.rug: no visible global function definition for ‘mtext’
    add.rug: no visible global function definition for ‘title’
    big.phase2: no visible binding for global variable ‘window’
    get.chr.pos: no visible global function definition for ‘rnorm’
    include.hotspots : update.pheno: no visible global function definition
     for ‘rnorm’
    include.hotspots : update.pheno: no visible global function definition
     for ‘runif’
    make.maxlod : tmpfn2: no visible global function definition for
     ‘median’
    myapprox: no visible global function definition for ‘approx’
    normal.trans: no visible global function definition for ‘qnorm’
    p.adjust.np: no visible global function definition for ‘p.adjust’
    parallel.error: no visible global function definition for ‘write.table’
    parallel.message: no visible global function definition for
     ‘write.table’
    plot.bic.aic: no visible global function definition for ‘par’
    plot.bic.aic: no visible global function definition for ‘plot’
    plot.bic.aic: no visible global function definition for ‘abline’
    plot.bic.aic: no visible global function definition for ‘points’
    plot.cit: no visible global function definition for ‘par’
    plot.cit: no visible global function definition for ‘plot’
    plot.cit: no visible global function definition for ‘abline’
    plot.cit: no visible global function definition for ‘points’
    plot.highlod: no visible global function definition for ‘plot’
    plot.hotperm : tmp.plot: no visible global function definition for
     ‘plot’
    plot.hotperm : tmp.plot: no visible global function definition for
     ‘mtext’
    plot.hotperm : tmp.plot: no visible global function definition for
     ‘abline’
    plot.hotperm : tmp.plot: no visible global function definition for
     ‘lines’
    plot.hotperm : tmp.plot: no visible global function definition for
     ‘text’
    plot.hotperm : tmp.plot: no visible global function definition for
     ‘par’
    plot.hotperm: no visible global function definition for ‘par’
    plot.hotperm: no visible global function definition for ‘plot’
    plot.hotperm: no visible global function definition for ‘abline’
    plot.hotperm: no visible global function definition for ‘mtext’
    plot.hotperm: no visible global function definition for ‘lines’
    plot.hotperm: no visible global function definition for ‘text’
    plot.hotperm: no visible global function definition for ‘title’
    plot.hotsize: no visible global function definition for ‘plot’
    plot.hotsize: no visible global function definition for ‘abline’
    plot.hotsize: no visible global function definition for ‘axis’
    plot.hotsize: no visible global function definition for ‘mtext’
    plot.non.par.cmst: no visible global function definition for ‘par’
    plot.non.par.cmst: no visible global function definition for ‘plot’
    plot.non.par.cmst: no visible global function definition for ‘abline’
    plot.non.par.cmst: no visible global function definition for ‘points’
    plot.par.cmst: no visible global function definition for ‘par’
    plot.par.cmst: no visible global function definition for ‘plot’
    plot.par.cmst: no visible global function definition for ‘abline’
    plot.par.cmst: no visible global function definition for ‘points’
    plot.par.cmst.joint: no visible global function definition for ‘par’
    plot.par.cmst.joint: no visible global function definition for ‘plot’
    plot.par.cmst.joint: no visible global function definition for ‘abline’
    plot.par.cmst.joint: no visible global function definition for ‘points’
    qtlhot.phase1: no visible global function definition for ‘write.table’
    sexbatch.covar: no visible global function definition for ‘formula’
    sexbatch.covar: no visible global function definition for
     ‘model.matrix’
    sim.null.pheno.data: no visible global function definition for ‘rnorm’
    sliding.bar.plot : create.rug: no visible global function definition
     for ‘median’
    sliding.bar.plot: no visible global function definition for ‘par’
    sliding.bar.plot: no visible global function definition for ‘plot’
    sliding.bar.plot: no visible global function definition for ‘rug’
    sliding.bar.plot: no visible global function definition for ‘axis’
    sliding.bar.plot: no visible global function definition for ‘mtext’
    sliding.bar.plot: no visible global function definition for ‘segments’
    slidingbar.plot: no visible global function definition for ‘image’
    slidingbar.plot: no visible global function definition for ‘mtext’
    slidingbar.plot: no visible global function definition for ‘abline’
    slidingbar.plot: no visible global function definition for ‘par’
    slidingbar.plot: no visible global function definition for ‘axis’
    Undefined global functions or variables:
     abline anova approx as.formula axis cov cov2cor dnorm formula image
     lines lm median model.matrix mtext na.omit p.adjust par pbinom pf
     plot pnorm points qnorm resid rnorm rug runif sd segments text title
     window write.table
    Consider adding
     importFrom("graphics", "abline", "axis", "image", "lines", "mtext",
     "par", "plot", "points", "rug", "segments", "text", "title")
     importFrom("stats", "anova", "approx", "as.formula", "cov", "cov2cor",
     "dnorm", "formula", "lm", "median", "model.matrix",
     "na.omit", "p.adjust", "pbinom", "pf", "pnorm", "qnorm",
     "resid", "rnorm", "runif", "sd", "window")
     importFrom("utils", "write.table")
    to your NAMESPACE file.
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-windows-ix86+x86_64, r-patched-linux-x86_64, r-patched-solaris-x86, r-release-linux-x86_64, r-release-windows-ix86+x86_64, r-release-osx-x86_64, r-oldrel-windows-ix86+x86_64, r-oldrel-osx-x86_64

Version: 0.9.0
Check: compiled code
Result: NOTE
    File ‘qtlhot/libs/qtlhot.so’:
     Found no calls to: ‘R_registerRoutines’, ‘R_useDynamicSymbols’
    
    It is good practice to register native routines and to disable symbol
    search.
    
    See ‘Writing portable packages’ 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-patched-linux-x86_64, r-release-linux-x86_64

Version: 0.9.0
Check: re-building of vignette outputs
Result: NOTE
    Error in re-building vignettes:
     ...
    Loading required package: qtl
    Loading required package: lattice
    Loading required package: corpcor
    Loading required package: mnormt
    Error in texi2dvi(file = file, pdf = TRUE, clean = clean, quiet = quiet, :
     Running 'texi2dvi' on 'cmst.tex' failed.
    LaTeX errors:
    ! LaTeX Error: File `epsf.sty' not found.
    
    Type X to quit or <RETURN> to proceed,
    or enter new name. (Default extension: sty)
    
    ! Emergency stop.
    <read *>
    
    l.7 \usepackage
     {epsfig}^^M
    ! ==> Fatal error occurred, no output PDF file produced!
    Calls: buildVignettes -> texi2pdf -> texi2dvi
    Execution halted
Flavor: r-release-osx-x86_64