CRAN Package Check Results for Package mpMap

Last updated on 2017-11-20 23:49:47 CET.

Flavor Version Tinstall Tcheck Ttotal Status Flags
r-release-osx-x86_64 1.14 ERROR

Check Details

Version: 1.14
Check: package dependencies
Result: NOTE
    Packages suggested but not available for checking:
     ‘asreml’ ‘happy.hbrem’ ‘Heatplus’ ‘VPdtw’
Flavor: r-release-osx-x86_64

Version: 1.14
Check: DESCRIPTION meta-information
Result: NOTE
    Malformed Description field: should contain one or more complete sentences.
Flavor: r-release-osx-x86_64

Version: 1.14
Check: dependencies in R code
Result: NOTE
    'library' or 'require' calls to packages already attached by Depends:
     ‘gdata’ ‘seriation’
     Please remove these calls from your code.
    'library' or 'require' calls in package code:
     ‘Heatplus’ ‘VPdtw’ ‘aod’ ‘asreml’ ‘happy.hbrem’ ‘lattice’
     Please use :: or requireNamespace() instead.
     See section 'Suggested packages' in the 'Writing R Extensions' manual.
    Packages in Depends field not imported from:
     ‘gdata’ ‘seriation’ ‘wgaim’
     These packages need to be imported from (in the NAMESPACE file)
     for when this namespace is loaded but not attached.
    ':::' call which should be '::': ‘qtl:::readMWril’
     See the note in ?`:::` about the use of this operator.
    Unexported objects imported by ':::' calls:
     ‘qtl:::adjust.rf.ri’ ‘qtl:::plot.scanone’ ‘qtl:::ripple.perm1’
     ‘qtl:::ripple.perm2’ ‘qtl:::testchr’
     See the note in ?`:::` about the use of this operator.
Flavor: r-release-osx-x86_64

Version: 1.14
Check: foreign function calls
Result: NOTE
    Foreign function calls to a different package:
     .C("R_reorgRIgenoprob", ..., PACKAGE = "qtl")
     .C(cfunc, ..., PACKAGE = "qtl")
     .C(func, ..., PACKAGE = "qtl")
    See chapter ‘System and foreign language interfaces’ in the ‘Writing R
    Extensions’ manual.
Flavor: r-release-osx-x86_64

Version: 1.14
Check: R code for possible problems
Result: NOTE
    CR_calcLD: no visible global function definition for ‘lowerTriangle’
    calc.genoprob2: no visible binding for global variable ‘step’
    cintern : <anonymous>: no visible global function definition for
     ‘contr.helmert’
    cintern: no visible global function definition for ‘pchisq’
    fill: no visible global function definition for ‘upperTriangle<-’
    fill: no visible global function definition for ‘lowerTriangle<-’
    fill: no visible global function definition for ‘lowerTriangle’
    fill: no visible global function definition for ‘upperTriangle’
    findqtl2: no visible global function definition for ‘dilation’
    fit.mpqtl: no visible global function definition for ‘update’
    fit.mpqtl: no visible global function definition for ‘as.formula’
    fit.mpqtl: no visible global function definition for ‘coef’
    fit.mpqtl: no visible global function definition for ‘wald.test’
    fit.mpqtl: no visible global function definition for ‘vcov’
    gen8ped: no visible global function definition for ‘combn’
    generate_obs: no visible global function definition for ‘runif’
    generate_pheno: no visible global function definition for ‘rnorm’
    getpval: no visible global function definition for ‘pf’
    mapcomp: no visible global function definition for ‘cor’
    mpIM: no visible global function definition for ‘update’
    mpIM: no visible global function definition for ‘na.omit’
    mpIM: no visible global function definition for ‘as.formula’
    mpIM: no visible global function definition for ‘lm’
    mpIM: no visible global function definition for ‘stepAIC’
    mpIM: no visible global function definition for ‘coef’
    mpIM: no visible global function definition for ‘wald.test’
    mpIM: no visible global function definition for ‘vcov’
    mpcalcld: no visible global function definition for ‘combn’
    mpcalcld: no visible global function definition for ‘lowerTriangle<-’
    mpcalcld: no visible global function definition for ‘upperTriangle<-’
    mpcalcld: no visible global function definition for ‘upperTriangle’
    mpestrf: no visible global function definition for ‘combn’
    mpestrf: no visible global function definition for ‘lowerTriangle<-’
    mpestrf: no visible global function definition for ‘upperTriangle<-’
    mpestrf: no visible global function definition for ‘upperTriangle’
    mporder: no visible global function definition for ‘as.dist’
    mporder : <anonymous>: no visible global function definition for
     ‘seriate’
    mporder: no visible binding for global variable ‘get_order’
    mpprob: no visible global function definition for ‘happy’
    mpprob: no visible global function definition for ‘hdesign’
    mpsegrat: no visible global function definition for ‘pchisq’
    plot.mapcomp: no visible global function definition for ‘xyplot’
    plot.mpcross: no visible global function definition for ‘par’
    plot.mpcross: no visible global function definition for ‘hist’
    plot.mpcross: no visible global function definition for ‘plot’
    plot.mpcross: no visible global function definition for
     ‘upperTriangle<-’
    plot.mpcross: no visible global function definition for ‘upperTriangle’
    plot.mpcross: no visible global function definition for
     ‘lowerTriangle<-’
    plot.mpcross: no visible global function definition for ‘lowerTriangle’
    plot.mpcross: no visible global function definition for ‘heatmap_2’
    plot.mpprob: no visible global function definition for ‘barplot’
    plot.mpprob: no visible global function definition for ‘par’
    plot.mpprob: no visible global function definition for ‘heatmap’
    plot.mpqtl: no visible global function definition for ‘rect’
    plotlink.map: no visible global function definition for ‘par’
    plotlink.map: no visible global function definition for ‘plot’
    plotlink.map: no visible global function definition for ‘axis’
    plotlink.map: no visible global function definition for ‘text’
    plotlink.map: no visible global function definition for ‘segments’
    plotlink.map: no visible global function definition for ‘lines’
    plotlink.map: no visible global function definition for ‘title’
    read.mpcross: no visible global function definition for ‘read.table’
    sim.sigthr: no visible global function definition for ‘var’
    sim.sigthr: no visible global function definition for ‘rnorm’
    supportinterval: no visible global function definition for ‘qchisq’
    supportinterval: no visible global function definition for ‘pchisq’
    wald.test.asreml: no visible global function definition for ‘update’
    write2cross: no visible global function definition for ‘rnorm’
    write2cross: no visible global function definition for ‘write.csv’
    write2cross: no visible global function definition for ‘write.table’
    write2happy: no visible global function definition for ‘write.table’
    Undefined global functions or variables:
     as.dist as.formula axis barplot coef combn contr.helmert cor dilation
     get_order happy hdesign heatmap heatmap_2 hist lines lm lowerTriangle
     lowerTriangle<- na.omit par pchisq pf plot qchisq read.table rect
     rnorm runif segments seriate step stepAIC text title update
     upperTriangle upperTriangle<- var vcov wald.test write.csv
     write.table xyplot
    Consider adding
     importFrom("graphics", "axis", "barplot", "hist", "lines", "par",
     "plot", "rect", "segments", "text", "title")
     importFrom("stats", "as.dist", "as.formula", "coef", "contr.helmert",
     "cor", "heatmap", "lm", "na.omit", "pchisq", "pf", "qchisq",
     "rnorm", "runif", "step", "update", "var", "vcov")
     importFrom("utils", "combn", "read.table", "write.csv", "write.table")
    to your NAMESPACE file.
Flavor: r-release-osx-x86_64

Version: 1.14
Check: Rd cross-references
Result: NOTE
    Package unavailable to check Rd xrefs: ‘Heatplus’
Flavor: r-release-osx-x86_64

Version: 1.14
Check: examples
Result: ERROR
    Running examples in ‘mpMap-Ex.R’ failed
    The error most likely occurred in:
    
    > ### Name: findqtl2
    > ### Title: Detect a second QTL in a QTL profile from (composite) interval
    > ### mapping
    > ### Aliases: findqtl2
    >
    > ### ** Examples
    >
    > sim.map <- sim.map(len=rep(100, 2), n.mar=11, include.x=FALSE, eq.spacing=TRUE)
    > sim.ped <- sim.mpped(4, 1, 500, 6, 1)
    > sim.dat <- sim.mpcross(map=sim.map, pedigree=sim.ped, qtl=matrix(data=c(1, 10, .4, 0, 0, 0, 1, 70, 0, .35, 0, 0), nrow=2, ncol=6, byrow=TRUE), seed=1)
    > mpp.dat <- mpprob(sim.dat, program="qtl", step=2)
    [1] "No chromosomes specified, will default to all"
     --Read the following data:
     500 individuals
     20 markers
     2 phenotypes
    > mpq.dat <- mpIM(object=mpp.dat, ncov=0, responsename="pheno")
     --Read the following data:
     500 individuals
     20 markers
     2 phenotypes
    Loading required package: aod
    ------Analyzing Chr 1 ----------
    ------Analyzing Chr 2 ----------
    > mpq2 <- findqtl2(mpq.dat, drop=2)
    Loading required package: VPdtw
    Warning in library(package, lib.loc = lib.loc, character.only = TRUE, logical.return = TRUE, :
     there is no package called ‘VPdtw’
    Error in dilation(cpv2, dwindow) : could not find function "dilation"
    Calls: findqtl2
    Execution halted
Flavor: r-release-osx-x86_64