CRAN Package Check Results for Package mpMap

Last updated on 2015-08-28 03:48:28.

Flavor Version Tinstall Tcheck Ttotal Status Flags
r-devel-linux-x86_64-debian-clang 1.14 2.87 39.51 42.38 NOTE
r-devel-linux-x86_64-debian-gcc 1.14 3.16 41.02 44.18 NOTE
r-devel-linux-x86_64-fedora-clang 1.14 84.01 NOTE
r-devel-linux-x86_64-fedora-gcc 1.14 80.91 NOTE
r-devel-osx-x86_64-clang 1.14 75.06 NOTE
r-devel-windows-ix86+x86_64 1.14 21.00 137.00 158.00 NOTE
r-patched-linux-x86_64 1.14 3.15 42.80 45.95 NOTE
r-patched-solaris-sparc 1.14 504.80 NOTE
r-patched-solaris-x86 1.14 107.10 NOTE
r-release-linux-x86_64 1.14 3.08 41.64 44.72 NOTE
r-release-osx-x86_64-mavericks 1.14 ERROR
r-release-windows-ix86+x86_64 1.14 24.00 94.00 118.00 NOTE
r-oldrel-windows-ix86+x86_64 1.14 29.00 112.00 141.00 NOTE

Check Details

Version: 1.14
Check: package dependencies
Result: NOTE
    Packages suggested but not available for checking: ‘asreml’ ‘happy.hbrem’
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-windows-ix86+x86_64, r-oldrel-windows-ix86+x86_64

Version: 1.14
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-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: 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.
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: 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.
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: 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.
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: 1.14
Check: Rd line widths
Result: NOTE
    Rd file 'clean.mpcross.Rd':
     \examples lines wider than 100 characters:
     sim.dat <- sim.mpcross(map=map, pedigree=sim.ped, qtl=matrix(data=c(1, 45, .4, 0, 0, 0), nrow=1, ncol=6, byrow=TRUE),seed=1)
    
    Rd file 'findqtl2.Rd':
     \examples lines wider than 100 characters:
     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 ... [TRUNCATED]
    
    Rd file 'fit.Rd':
     \examples lines wider than 100 characters:
     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 ... [TRUNCATED]
    
    Rd file 'mpIM.Rd':
     \examples lines wider than 100 characters:
     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 ... [TRUNCATED]
    
    Rd file 'mpcross.Rd':
     \examples lines wider than 100 characters:
     sim.dat <- sim.mpcross(map=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=TRU ... [TRUNCATED]
    
    Rd file 'mpestrf.Rd':
     \examples lines wider than 100 characters:
     sim.dat <- sim.mpcross(map=map, pedigree=sim.ped, qtl=matrix(data=c(1, 50, .4, 0, 0, 0), nrow=1, ncol=6, byrow=TRUE), seed=1)
    
    Rd file 'mporder.Rd':
     \usage lines wider than 90 characters:
     criterion = c("Path_length", "AR_events", "AR_deviations", "Gradient_raw", "Inertia", "Least_squares", "minXO", "lkhdsum"),
    
    Rd file 'mpprob.Rd':
     \examples lines wider than 100 characters:
     sim.dat <- sim.mpcross(map=sim.map, pedigree=sim.ped, qtl=matrix(data=c(1, 50, .4, 0, 0, 0), nrow=1, ncol=6, byrow=TRUE), seed=1)
    
    Rd file 'plot.mpcross.Rd':
     \examples lines wider than 100 characters:
     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 ... [TRUNCATED]
    
    Rd file 'plot.mpprob.Rd':
     \examples lines wider than 100 characters:
     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 ... [TRUNCATED]
    
    Rd file 'plot.mpqtl.Rd':
     \examples lines wider than 100 characters:
     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 ... [TRUNCATED]
    
    Rd file 'qtlmap.Rd':
     \examples lines wider than 100 characters:
     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 ... [TRUNCATED]
    
    Rd file 'sim.mpcross.Rd':
     \examples lines wider than 100 characters:
     sim.dat <- sim.mpcross(map=map, pedigree=sim.ped, qtl=matrix(data=c(1, 50, .4, 0, 0, 0), nrow=1, ncol=6, byrow=TRUE), seed=1)
    
    Rd file 'subset.mpcross.Rd':
     \examples lines wider than 100 characters:
     sim.dat <- sim.mpcross(map=map, pedigree=ped, qtl=matrix(data=c(1, 10, .4, 0, 0, 0, 1, 70, 0, .35, 0, 0), nrow=2, ncol=6, byrow=TRUE), ... [TRUNCATED]
    
    Rd file 'summary.mpcross.Rd':
     \examples lines wider than 100 characters:
     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 ... [TRUNCATED]
    
    Rd file 'summary.mpprob.Rd':
     \examples lines wider than 100 characters:
     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 ... [TRUNCATED]
    
    Rd file 'summary.mpqtl.Rd':
     \examples lines wider than 100 characters:
     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 ... [TRUNCATED]
    
    Rd file 'supportinterval.Rd':
     \examples lines wider than 100 characters:
     sim.dat <- sim.mpcross(map=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=TRU ... [TRUNCATED]
    
    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: 1.14
Check: R code for possible problems
Result: NOTE
    CR_calcLD: no visible global function definition for ‘lowerTriangle’
    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 ‘wald.test’
    mpIM: no visible global function definition for ‘stepAIC’
    mpIM: no visible global function definition for ‘wald.test’
    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 ‘lowerTriangle<-’
    mpestrf: no visible global function definition for ‘upperTriangle<-’
    mpestrf: no visible global function definition for ‘upperTriangle’
    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’
    plot.mapcomp: no visible global function definition for ‘xyplot’
    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’
    Undefined global functions or variables:
     dilation get_order happy hdesign heatmap_2 lowerTriangle
     lowerTriangle<- seriate stepAIC upperTriangle upperTriangle<-
     wald.test xyplot
Flavor: r-devel-osx-x86_64-clang

Version: 1.14
Check: R code for possible problems
Result: NOTE
    CR_calcLD: no visible global function definition for ‘lowerTriangle’
    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 ‘wald.test’
    mpIM: no visible global function definition for ‘stepAIC’
    mpIM: no visible global function definition for ‘wald.test’
    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 ‘lowerTriangle<-’
    mpestrf: no visible global function definition for ‘upperTriangle<-’
    mpestrf: no visible global function definition for ‘upperTriangle’
    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’
    plot.mapcomp: no visible global function definition for ‘xyplot’
    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’
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: 1.14
Check: package dependencies
Result: NOTE
    Packages suggested but not available for checking:
     ‘asreml’ ‘happy.hbrem’ ‘Heatplus’
Flavor: r-release-osx-x86_64-mavericks

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

Version: 1.14
Check: examples
Result: ERROR
    Running examples in ‘mpMap-Ex.R’ failed
    The error most likely occurred in:
    
    > ### Name: mpestrf
    > ### Title: Estimate pairwise recombination fractions between markers
    > ### Aliases: mpestrf
    >
    > ### ** Examples
    >
    > map <- sim.map(len=100, n.mar=11, eq.spacing=TRUE, include.x=FALSE)
    > sim.ped <- sim.mpped(4, 1, 500, 6, 1)
    > sim.dat <- sim.mpcross(map=map, pedigree=sim.ped, qtl=matrix(data=c(1, 50, .4, 0, 0, 0), nrow=1, ncol=6, byrow=TRUE), seed=1)
    > dat.rf <- mpestrf(sim.dat)
    > plot(dat.rf)
    Loading required package: Heatplus
    Warning in library(package, lib.loc = lib.loc, character.only = TRUE, logical.return = TRUE, :
     there is no package called ‘Heatplus’
    Error in plot.mpcross(dat.rf) : could not find function "heatmap_2"
    Calls: plot -> plot.mpcross
    Execution halted
Flavor: r-release-osx-x86_64-mavericks