CRAN Package Check Results for Package QTLRel

Last updated on 2015-07-06 14:48:48.

Flavor Version Tinstall Tcheck Ttotal Status Flags
r-devel-linux-x86_64-debian-clang 0.2-14 2.07 26.07 28.14 NOTE
r-devel-linux-x86_64-debian-gcc 0.2-14 2.49 26.84 29.34 NOTE
r-devel-linux-x86_64-fedora-clang 0.2-14 50.24 NOTE
r-devel-linux-x86_64-fedora-gcc 0.2-14 47.25 NOTE
r-devel-osx-x86_64-clang 0.2-14 46.16 NOTE
r-devel-windows-ix86+x86_64 0.2-14 23.00 48.00 71.00 NOTE
r-patched-linux-x86_64 0.2-14 2.54 26.84 29.38 NOTE
r-patched-solaris-sparc 0.2-14 306.40 NOTE
r-patched-solaris-x86 0.2-14 63.10 NOTE
r-release-linux-x86_64 0.2-14 2.54 26.91 29.45 NOTE
r-release-osx-x86_64-mavericks 0.2-14 NOTE
r-release-windows-ix86+x86_64 0.2-14 17.00 44.00 61.00 NOTE
r-oldrel-windows-ix86+x86_64 0.2-14 20.00 52.00 72.00 NOTE

Check Details

Version: 0.2-14
Check: dependencies in R code
Result: NOTE
    'library' or 'require' call to ‘qtl’ in package code.
     Please use :: or requireNamespace() instead.
     See section 'Suggested 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-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-x86_64, r-release-osx-x86_64-mavericks, r-release-windows-ix86+x86_64, r-oldrel-windows-ix86+x86_64

Version: 0.2-14
Check: foreign function calls
Result: NOTE
    Calls with DUP:
     .C("rgdata2", gdata = as.integer(t(gdat)), nr = as.integer(nr),
     nc = as.integer(nc), ninit = as.integer(ninit), pedigree = as.integer(t(pedd)),
     recomb = as.double(rr), xchr = as.logical(xchr), seed = as.integer(seed),
     DUP = FALSE, PACKAGE = "QTLRel")
     .C("gen_Matrix", x = as.double(t(x)), nr = as.integer(nr), nc = as.integer(nc),
     nn = as.integer(nn), ksp = as.double(t(ksp)), DD = as.double(t(DD)),
     AD = as.double(t(AD)), HH = as.double(t(HH)), MH = as.double(t(MH)),
     DUP = FALSE, PACKAGE = "QTLRel")
     .C("deltaFnc", x = as.integer(t(gdata)), nr = as.integer(nr),
     nc = as.integer(nc), deltac = as.double(t(deltac)), DUP = FALSE,
     PACKAGE = "QTLRel")
     .C("conGenoPrc", mdat = as.integer(mdat[nn, ]), n = as.integer(n),
     dist = as.double(dist), pos = as.double(pos), np = as.integer(np),
     at = as.integer(at), gr = as.integer(gr), method = as.integer(method),
     pdat = as.double(pdat), error = as.logical(err), DUP = FALSE,
     PACKAGE = "QTLRel")
     .C("ibsPrc", prdat = as.double(aperm(prdat, c(3, 2, 1))), nr = as.integer(nr),
     nc = as.integer(nc), ibsc = as.double(t(ibsc)), DUP = FALSE,
     PACKAGE = "QTLRel")
     .C("ibsFnc", gdat = as.integer(t(gdata)), nr = as.integer(nr),
     nc = as.integer(nc), ibsc = as.double(t(ibsc)), DUP = FALSE,
     PACKAGE = "QTLRel")
     .C("kinship", ped = as.integer(t(ped)), nr = as.integer(nrow(ped)),
     nc = as.integer(ncol(ped)), ksp = as.double(ksp), DUP = FALSE,
     PACKAGE = "QTLRel")
    DUP is no longer supported and will be ignored.
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-x86_64, r-release-osx-x86_64-mavericks, r-release-windows-ix86+x86_64

Version: 0.2-14
Check: R code for possible problems
Result: NOTE
    .hapSim: no visible global function definition for ‘reorder’
    .hapSim: no visible global function definition for ‘runif’
    AICb: no visible global function definition for ‘model.frame’
    AICb: no visible global function definition for ‘model.matrix’
    AICf: no visible global function definition for ‘model.frame’
    AICf: no visible global function definition for ‘model.matrix’
    AICmove: no visible global function definition for ‘model.frame’
    AICmove: no visible global function definition for ‘model.matrix’
    estRR: no visible global function definition for ‘lm’
    estRR: no visible global function definition for ‘logLik’
    estVC.1: no visible global function definition for ‘var’
    estVC.1: no visible global function definition for ‘optim’
    estVC.2: no visible global function definition for ‘var’
    estVC.2 : optfct.b: no visible global function definition for ‘lm.wfit’
    estVC.2: no visible global function definition for ‘optimize’
    estVC.2: no visible global function definition for ‘optim’
    estVC.3: no visible global function definition for ‘var’
    estVC.3 : optfct.b: no visible binding for global variable ‘par’
    estVC.3 : optfct.b: no visible global function definition for ‘lm.wfit’
    estVC.3: no visible global function definition for ‘nlm’
    estVC.3: no visible global function definition for ‘optim’
    estVC.4: no visible global function definition for ‘var’
    estVC.4 : optfct.b: no visible binding for global variable ‘par’
    estVC.4 : optfct.b: no visible global function definition for ‘lm.wfit’
    estVC.4: no visible global function definition for ‘nlminb’
    estVC.4: no visible global function definition for ‘optim’
    estVC.default: no visible global function definition for ‘model.frame’
    estVC.default: no visible global function definition for
     ‘model.response’
    estVC.default: no visible global function definition for ‘model.matrix’
    fns4.2: no visible global function definition for ‘uniroot’
    fs2n: no visible global function definition for ‘uniroot’
    genoImpute.Pr: no visible global function definition for ‘rmultinom’
    genoImpute.default: no visible global function definition for
     ‘rmultinom’
    genoPos: no visible global function definition for ‘reorder’
    genoProb.default: no visible global function definition for ‘reorder’
    gls: no visible global function definition for ‘model.matrix’
    gls: no visible global function definition for ‘model.response’
    gls: no visible global function definition for ‘model.frame’
    gls: no visible global function definition for ‘lm’
    lmGls: no visible global function definition for ‘model.response’
    lmGls: no visible global function definition for ‘model.matrix’
    lmGls: no visible binding for global variable ‘contrasts’
    lmGls: no visible global function definition for ‘lm’
    mAIC.HK: no visible global function definition for ‘model.frame’
    mAIC.HK: no visible global function definition for ‘model.response’
    mAIC.HK: no visible global function definition for ‘model.matrix’
    mAIC.default: no visible global function definition for ‘model.frame’
    mAIC.default: no visible global function definition for
     ‘model.response’
    mAIC.default: no visible global function definition for ‘model.matrix’
    ped.opt: no visible global function definition for ‘reorder’
    pedRecode: no visible global function definition for ‘reorder’
    pedRecode.0: no visible global function definition for ‘reorder’
    plot.lrt: no visible global function definition for ‘reorder’
    plot.lrt: no visible global function definition for ‘plot’
    plot.lrt: no visible global function definition for ‘lines’
    plot.lrt: no visible global function definition for ‘abline’
    plot.lrt: no visible global function definition for ‘axis’
    plot.scanTwo: no visible global function definition for ‘image’
    plot.scanTwo: no visible global function definition for
     ‘terrain.colors’
    plot.scanTwo: no visible global function definition for ‘axis’
    plot.scanTwo: no visible global function definition for ‘mtext’
    plot.scanTwo: no visible global function definition for ‘lines’
    plotit: no visible global function definition for ‘xyplot’
    plotit : <anonymous>: no visible global function definition for
     ‘panel.xyplot’
    plotit : <anonymous>: no visible global function definition for
     ‘panel.abline’
    plotit : <anonymous>: no visible global function definition for
     ‘panel.superpose’
    plotit: no visible global function definition for ‘reorder’
    plotit: no visible global function definition for ‘plot’
    plotit: no visible global function definition for ‘lines’
    plotit: no visible global function definition for ‘abline’
    plotit: no visible global function definition for ‘axis’
    qk: no visible global function definition for ‘uniroot’
    qkolm: no visible global function definition for ‘uniroot’
    qqPlot.default: no visible global function definition for ‘ppoints’
    qqPlot.default: no visible global function definition for ‘approx’
    qqPlot.default: no visible global function definition for ‘quantile’
    qqPlot.default: no visible global function definition for ‘plot’
    qqPlot.default: no visible global function definition for ‘points’
    qqPlot.default: no visible global function definition for ‘abline’
    qqPlot.default: no visible global function definition for ‘lines’
    qtlVar: no visible global function definition for ‘var’
    qtlVar: no visible global function definition for ‘runif’
    rem: no visible global function definition for ‘terms’
    scanOne.0: no visible global function definition for ‘lm’
    scanOne.0: no visible global function definition for ‘logLik’
    scanOne.0: no visible global function definition for ‘anova’
    scanOne.0: no visible global function definition for ‘formula’
    scanOne.1: no visible global function definition for ‘lm’
    scanOne.1: no visible global function definition for ‘logLik’
    scanOne.1: no visible global function definition for ‘anova’
    scanOne.1: no visible global function definition for ‘formula’
    scanOne.2: no visible global function definition for ‘lm’
    scanOne.2: no visible global function definition for ‘logLik’
    scanOne.2: no visible global function definition for ‘anova’
    scanOne.2: no visible global function definition for ‘formula’
    scanTwo.1: no visible global function definition for ‘lm’
    scanTwo.1: no visible global function definition for ‘logLik’
    scanTwo.2: no visible global function definition for ‘lm’
    scanTwo.2: no visible global function definition for ‘logLik’
    Undefined global functions or variables:
     abline anova approx axis contrasts formula image lines lm lm.wfit
     logLik model.frame model.matrix model.response mtext nlm nlminb optim
     optimize panel.abline panel.superpose panel.xyplot par plot points
     ppoints quantile reorder rmultinom runif terms terrain.colors uniroot
     var xyplot
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

Version: 0.2-14
Check: compiled code
Result: NOTE
    File ‘QTLRel/libs/QTLRel.so’:
     Found ‘rand’, possibly from ‘rand’ (C)
     Object: ‘rgdat.o’
     Found ‘srand’, possibly from ‘srand’ (C)
     Object: ‘rgdat.o’
    
    Compiled code should not call entry points which might terminate R nor
    write to stdout/stderr instead of to the console, nor the system RNG.
    
    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-patched-solaris-sparc, r-patched-solaris-x86, r-release-linux-x86_64

Version: 0.2-14
Check: R code for possible problems
Result: NOTE
    plotit: no visible global function definition for ‘xyplot’
    plotit : <anonymous>: no visible global function definition for
     ‘panel.xyplot’
    plotit : <anonymous>: no visible global function definition for
     ‘panel.abline’
    plotit : <anonymous>: no visible global function definition for
     ‘panel.superpose’
    Undefined global functions or variables:
     panel.abline panel.superpose panel.xyplot xyplot
Flavor: r-devel-osx-x86_64-clang

Version: 0.2-14
Check: compiled code
Result: NOTE
    File ‘QTLRel/libs/QTLRel.so’:
     Found ‘_rand’, possibly from ‘rand’ (C)
     Object: ‘rgdat.o’
     Found ‘_srand’, possibly from ‘srand’ (C)
     Object: ‘rgdat.o’
    
    Compiled code should not call entry points which might terminate R nor
    write to stdout/stderr instead of to the console, nor the system RNG.
    
    See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual.
Flavors: r-devel-osx-x86_64-clang, r-release-osx-x86_64-mavericks

Version: 0.2-14
Check: compiled code
Result: NOTE
    File 'QTLRel/libs/i386/QTLRel.dll':
     Found 'rand', possibly from 'rand' (C)
     Object: 'rgdat.o'
     Found 'srand', possibly from 'srand' (C)
     Object: 'rgdat.o'
    File 'QTLRel/libs/x64/QTLRel.dll':
     Found 'rand', possibly from 'rand' (C)
     Object: 'rgdat.o'
     Found 'srand', possibly from 'srand' (C)
     Object: 'rgdat.o'
    
    Compiled code should not call entry points which might terminate R nor
    write to stdout/stderr instead of to the console, nor the system RNG.
    
    See 'Writing portable packages' in the 'Writing R Extensions' manual.
Flavors: r-devel-windows-ix86+x86_64, r-release-windows-ix86+x86_64, r-oldrel-windows-ix86+x86_64

Version: 0.2-14
Check: R code for possible problems
Result: NOTE
    plotit: no visible global function definition for ‘xyplot’
    plotit : <anonymous>: no visible global function definition for
     ‘panel.xyplot’
    plotit : <anonymous>: no visible global function definition for
     ‘panel.abline’
    plotit : <anonymous>: no visible global function definition for
     ‘panel.superpose’
Flavors: r-patched-linux-x86_64, r-patched-solaris-sparc, r-patched-solaris-x86, r-release-linux-x86_64, r-release-osx-x86_64-mavericks, r-release-windows-ix86+x86_64, r-oldrel-windows-ix86+x86_64

Version: 0.2-14
Check: foreign function calls
Result: NOTE
    Calls with DUP != TRUE:
     .C("rgdata2", gdata = as.integer(t(gdat)), nr = as.integer(nr),
     nc = as.integer(nc), ninit = as.integer(ninit), pedigree = as.integer(t(pedd)),
     recomb = as.double(rr), xchr = as.logical(xchr), seed = as.integer(seed),
     DUP = FALSE, PACKAGE = "QTLRel")
     .C("gen_Matrix", x = as.double(t(x)), nr = as.integer(nr), nc = as.integer(nc),
     nn = as.integer(nn), ksp = as.double(t(ksp)), DD = as.double(t(DD)),
     AD = as.double(t(AD)), HH = as.double(t(HH)), MH = as.double(t(MH)),
     DUP = FALSE, PACKAGE = "QTLRel")
     .C("deltaFnc", x = as.integer(t(gdata)), nr = as.integer(nr),
     nc = as.integer(nc), deltac = as.double(t(deltac)), DUP = FALSE,
     PACKAGE = "QTLRel")
     .C("conGenoPrc", mdat = as.integer(mdat[nn, ]), n = as.integer(n),
     dist = as.double(dist), pos = as.double(pos), np = as.integer(np),
     at = as.integer(at), gr = as.integer(gr), method = as.integer(method),
     pdat = as.double(pdat), error = as.logical(err), DUP = FALSE,
     PACKAGE = "QTLRel")
     .C("ibsPrc", prdat = as.double(aperm(prdat, c(3, 2, 1))), nr = as.integer(nr),
     nc = as.integer(nc), ibsc = as.double(t(ibsc)), DUP = FALSE,
     PACKAGE = "QTLRel")
     .C("ibsFnc", gdat = as.integer(t(gdata)), nr = as.integer(nr),
     nc = as.integer(nc), ibsc = as.double(t(ibsc)), DUP = FALSE,
     PACKAGE = "QTLRel")
     .C("kinship", ped = as.integer(t(ped)), nr = as.integer(nrow(ped)),
     nc = as.integer(ncol(ped)), ksp = as.double(ksp), DUP = FALSE,
     PACKAGE = "QTLRel")
    DUP = FALSE is deprecated and will be disabled in future versions of R.
Flavor: r-oldrel-windows-ix86+x86_64