CRAN Package Check Results for Package dlmap

Last updated on 2020-10-28 18:49:58 CET.

Check Details

Version: 1.13
Check: package dependencies
Result: NOTE
    Package suggested but not available for checking: 'asreml'
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-macos-x86_64, r-release-windows-ix86+x86_64, r-oldrel-macos-x86_64, r-oldrel-windows-ix86+x86_64

Version: 1.13
Check: dependencies in R code
Result: NOTE
    'library' or 'require' calls to packages already attached by Depends:
     'nlme' 'wgaim'
     Please remove these calls from your code.
    'library' or 'require' call to 'asreml' in package code.
     Please use :: or requireNamespace() instead.
     See section 'Suggested packages' in the 'Writing R Extensions' manual.
    Packages in Depends field not imported from:
     'ibdreg' 'mgcv' 'nlme' 'qtl' 'wgaim'
     These packages need to be imported from (in the NAMESPACE file)
     for when this namespace is loaded but not attached.
    Unexported object imported by a ':::' call: 'qtl:::adjust.rf.ri'
     See the note in ?`:::` about the use of this operator.
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-macos-x86_64, r-release-windows-ix86+x86_64, r-oldrel-macos-x86_64, r-oldrel-windows-ix86+x86_64

Version: 1.13
Check: foreign function calls
Result: NOTE
    Foreign function call to a different package:
     .C(cfunc, ..., PACKAGE = "qtl")
    See chapter 'System and foreign language interfaces' 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-windows-ix86+x86_64, r-patched-linux-x86_64, r-patched-solaris-x86, r-release-linux-x86_64, r-release-macos-x86_64, r-release-windows-ix86+x86_64, r-oldrel-macos-x86_64, r-oldrel-windows-ix86+x86_64

Version: 1.13
Check: R code for possible problems
Result: NOTE
    calc.genoprob2: no visible binding for global variable 'mf.k'
    calc.genoprob2: no visible binding for global variable 'mf.cf'
    calc.genoprob2: no visible binding for global variable 'mf.m'
    calc.genoprob2: no visible binding for global variable 'mf.h'
    calc.genoprob2: no visible global function definition for 'nind'
    calc.genoprob2: no visible global function definition for 'nchr'
    calc.genoprob2: no visible global function definition for 'nmar'
    calc.genoprob2: no visible global function definition for
     'getgenonames'
    calcpos: no visible global function definition for 'nchr'
    calcpos: no visible global function definition for 'nind'
    calcpos: no visible global function definition for 'nmar'
    calcpos: no visible global function definition for 'pull.map'
    calcpos: no visible global function definition for 'calc.genoprob'
    cintern : <anonymous>: no visible global function definition for
     'contr.helmert'
    cintern: no visible global function definition for 'pchisq'
    dlcross.cross: no visible global function definition for 'nind'
    dlcross.cross: no visible global function definition for 'fill.geno'
    dlcross.cross: no visible global function definition for 'pull.map'
    dlcross.cross: no visible global function definition for 'est.map'
    dlcross.cross: no visible global function definition for 'replace.map'
    dlcross.dlmap: no visible global function definition for 'read.table'
    dlcross.dlmap: no visible global function definition for 'fill.geno'
    dlcross.dlmap: no visible global function definition for 'est.map'
    dlcross.dlmap: no visible global function definition for 'replace.map'
    dlcross.dlmap: no visible global function definition for 'pull.map'
    dlcross.other: no visible global function definition for 'read.table'
    dlmap: no visible global function definition for 'as.formula'
    dlmap: no visible global function definition for 'asreml.Ainverse'
    dlmap: no visible global function definition for 'Ginv'
    dlmap : <anonymous>: no visible global function definition for 'pnorm'
    dlmap: no visible binding for global variable 'na.omit'
    dlmapdet: no visible global function definition for 'mroot'
    dlmapdet: no visible global function definition for 'C'
    dlmapdet: no visible global function definition for 'as.formula'
    dlmapdet: no visible global function definition for 'groupedData'
    dlmapdet: no visible global function definition for 'lme'
    dlmapdet: no visible global function definition for 'lmeControl'
    dlmapdet: no visible binding for global variable 'na.omit'
    dlmapdet: no visible global function definition for 'anova'
    dlmaploc: no visible global function definition for 'mroot'
    dlmaploc: no visible global function definition for 'as.formula'
    dlmaploc: no visible global function definition for 'groupedData'
    dlmaploc: no visible global function definition for 'lme'
    dlmaploc: no visible global function definition for 'lmeControl'
    dlmaploc: no visible binding for global variable 'na.omit'
    dlmaploc: no visible global function definition for 'anova'
    dltest: no visible global function definition for 'as.formula'
    dltest: no visible global function definition for 'mroot'
    dltest: no visible global function definition for 'asreml'
    dltest: no visible global function definition for 'update'
    dltest: no visible global function definition for 'groupedData'
    dltest: no visible global function definition for 'lme'
    dltest: no visible global function definition for 'lmeControl'
    dltest: no visible binding for global variable 'na.omit'
    nmrk.dlcross: no visible global function definition for 'nmar'
    plot.dlcross: no visible global function definition for 'par'
    plot.dlcross: no visible global function definition for 'hist'
    plot.dlmap: no visible global function definition for 'nchr'
    plot.dlmap: no visible global function definition for 'link.map.cross'
    plot.dlmap: no visible global function definition for 'pull.map'
    plot.dlmap: no visible global function definition for 'find.markerpos'
    plot.dlmap: no visible global function definition for 'polygon'
    plot.dlmap: no visible global function definition for 'segments'
    plot.dlmap: no visible global function definition for 'title'
    profileplot.dlmap: no visible global function definition for 'par'
    profileplot.dlmap: no visible global function definition for 'axis'
    profileplot.dlmap: no visible global function definition for 'abline'
    pvfx: no visible global function definition for 'pchibar'
    qchibar: no visible global function definition for 'qchisq'
    waldtest.asreml: no visible global function definition for 'update'
    Undefined global functions or variables:
     C Ginv abline anova as.formula asreml asreml.Ainverse axis
     calc.genoprob contr.helmert est.map fill.geno find.markerpos
     getgenonames groupedData hist link.map.cross lme lmeControl mf.cf
     mf.h mf.k mf.m mroot na.omit nchr nind nmar par pchibar pchisq pnorm
     polygon pull.map qchisq read.table replace.map segments title update
    Consider adding
     importFrom("graphics", "abline", "axis", "hist", "par", "polygon",
     "segments", "title")
     importFrom("stats", "C", "anova", "as.formula", "contr.helmert",
     "na.omit", "pchisq", "pnorm", "qchisq", "update")
     importFrom("utils", "read.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-macos-x86_64, r-release-windows-ix86+x86_64

Version: 1.13
Check: Rd line widths
Result: NOTE
    Rd file 'dlcross.Rd':
     \usage lines wider than 90 characters:
     dlcross(format = c("rqtl", "dlmap", "other"), genobj, pheobj, mapobj, idname="ID", genfile, phefile, mapfile, type, step=0, fixpos=0, e ... [TRUNCATED]
    
    Rd file 'dlmap-internal.Rd':
     \usage lines wider than 90 characters:
     dlcross.dlmap(genobj, pheobj, mapobj, idname, genfile, mapfile, phefile, type, step, fixpos, estmap, ...)
     calc.genoprob2(cross, pos, error.prob=1e-04, map.function=c("haldane", "kosambi", "c-f", "morgan"))
    
    Rd file 'dlmap.Rd':
     \usage lines wider than 90 characters:
     plot(x, chr, max.dist, qcol="light blue", mcol="red", pcol="purple", marker.names=FALSE, ...)
    
    These lines will be truncated in the PDF 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: 1.13
Check: R code for possible problems
Result: NOTE
    calc.genoprob2: no visible binding for global variable ‘mf.k’
    calc.genoprob2: no visible binding for global variable ‘mf.cf’
    calc.genoprob2: no visible binding for global variable ‘mf.m’
    calc.genoprob2: no visible binding for global variable ‘mf.h’
    calc.genoprob2: no visible global function definition for ‘nind’
    calc.genoprob2: no visible global function definition for ‘nchr’
    calc.genoprob2: no visible global function definition for ‘nmar’
    calc.genoprob2: no visible global function definition for
     ‘getgenonames’
    calcpos: no visible global function definition for ‘nchr’
    calcpos: no visible global function definition for ‘nind’
    calcpos: no visible global function definition for ‘nmar’
    calcpos: no visible global function definition for ‘pull.map’
    calcpos: no visible global function definition for ‘calc.genoprob’
    cintern : <anonymous>: no visible global function definition for
     ‘contr.helmert’
    cintern: no visible global function definition for ‘pchisq’
    dlcross.cross: no visible global function definition for ‘nind’
    dlcross.cross: no visible global function definition for ‘fill.geno’
    dlcross.cross: no visible global function definition for ‘pull.map’
    dlcross.cross: no visible global function definition for ‘est.map’
    dlcross.cross: no visible global function definition for ‘replace.map’
    dlcross.dlmap: no visible global function definition for ‘read.table’
    dlcross.dlmap: no visible global function definition for ‘fill.geno’
    dlcross.dlmap: no visible global function definition for ‘est.map’
    dlcross.dlmap: no visible global function definition for ‘replace.map’
    dlcross.dlmap: no visible global function definition for ‘pull.map’
    dlcross.other: no visible global function definition for ‘read.table’
    dlmap: no visible global function definition for ‘as.formula’
    dlmap: no visible global function definition for ‘asreml.Ainverse’
    dlmap: no visible global function definition for ‘Ginv’
    dlmap : <anonymous>: no visible global function definition for ‘pnorm’
    dlmap: no visible binding for global variable ‘na.omit’
    dlmapdet: no visible global function definition for ‘mroot’
    dlmapdet: no visible global function definition for ‘C’
    dlmapdet: no visible global function definition for ‘as.formula’
    dlmapdet: no visible global function definition for ‘groupedData’
    dlmapdet: no visible global function definition for ‘lme’
    dlmapdet: no visible global function definition for ‘lmeControl’
    dlmapdet: no visible binding for global variable ‘na.omit’
    dlmapdet: no visible global function definition for ‘anova’
    dlmaploc: no visible global function definition for ‘mroot’
    dlmaploc: no visible global function definition for ‘as.formula’
    dlmaploc: no visible global function definition for ‘groupedData’
    dlmaploc: no visible global function definition for ‘lme’
    dlmaploc: no visible global function definition for ‘lmeControl’
    dlmaploc: no visible binding for global variable ‘na.omit’
    dlmaploc: no visible global function definition for ‘anova’
    dltest: no visible global function definition for ‘as.formula’
    dltest: no visible global function definition for ‘mroot’
    dltest: no visible global function definition for ‘asreml’
    dltest: no visible global function definition for ‘update’
    dltest: no visible global function definition for ‘groupedData’
    dltest: no visible global function definition for ‘lme’
    dltest: no visible global function definition for ‘lmeControl’
    dltest: no visible binding for global variable ‘na.omit’
    nmrk.dlcross: no visible global function definition for ‘nmar’
    plot.dlcross: no visible global function definition for ‘par’
    plot.dlcross: no visible global function definition for ‘plot’
    plot.dlcross: no visible global function definition for ‘hist’
    plot.dlmap: no visible global function definition for ‘nchr’
    plot.dlmap: no visible global function definition for ‘link.map.cross’
    plot.dlmap: no visible global function definition for ‘pull.map’
    plot.dlmap: no visible global function definition for ‘find.markerpos’
    plot.dlmap: no visible global function definition for ‘polygon’
    plot.dlmap: no visible global function definition for ‘segments’
    plot.dlmap: no visible global function definition for ‘title’
    profileplot.dlmap: no visible global function definition for ‘par’
    profileplot.dlmap: no visible global function definition for ‘plot’
    profileplot.dlmap: no visible global function definition for ‘axis’
    profileplot.dlmap: no visible global function definition for ‘abline’
    pvfx: no visible global function definition for ‘pchibar’
    qchibar: no visible global function definition for ‘qchisq’
    waldtest.asreml: no visible global function definition for ‘update’
    Undefined global functions or variables:
     C Ginv abline anova as.formula asreml asreml.Ainverse axis
     calc.genoprob contr.helmert est.map fill.geno find.markerpos
     getgenonames groupedData hist link.map.cross lme lmeControl mf.cf
     mf.h mf.k mf.m mroot na.omit nchr nind nmar par pchibar pchisq plot
     pnorm polygon pull.map qchisq read.table replace.map segments title
     update
    Consider adding
     importFrom("graphics", "abline", "axis", "hist", "par", "plot",
     "polygon", "segments", "title")
     importFrom("stats", "C", "anova", "as.formula", "contr.helmert",
     "na.omit", "pchisq", "pnorm", "qchisq", "update")
     importFrom("utils", "read.table")
    to your NAMESPACE file.
Flavors: r-oldrel-macos-x86_64, r-oldrel-windows-ix86+x86_64