CRAN Package Check Results for Package mpMap

Last updated on 2015-07-05 06:46:40.

Flavor Version Tinstall Tcheck Ttotal Status Flags
r-devel-linux-x86_64-debian-clang 1.14 2.98 34.55 37.52 ERROR
r-devel-linux-x86_64-debian-gcc 1.14 3.25 31.89 35.14 ERROR
r-devel-linux-x86_64-fedora-clang 1.14 68.35 ERROR
r-devel-linux-x86_64-fedora-gcc 1.14 62.70 ERROR
r-devel-osx-x86_64-clang 1.14 63.60 ERROR
r-devel-windows-ix86+x86_64 1.14 18.00 118.00 136.00 NOTE
r-patched-linux-x86_64 1.14 3.20 31.84 35.04 ERROR
r-patched-solaris-sparc 1.14 380.00 ERROR
r-patched-solaris-x86 1.14 85.20 ERROR
r-release-linux-x86_64 1.14 3.02 32.97 35.99 ERROR
r-release-osx-x86_64-mavericks 1.14 ERROR
r-release-windows-ix86+x86_64 1.14 23.00 87.00 110.00 NOTE
r-oldrel-windows-ix86+x86_64 1.14 22.00 118.00 140.00 NOTE

Check Details

Version: 1.14
Check: package dependencies
Result: NOTE
    Packages suggested but not available for checking:
     ‘asreml’ ‘happy.hbrem’ ‘VPdtw’
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-patched-linux-x86_64, r-patched-solaris-sparc, r-patched-solaris-x86, r-release-linux-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
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: 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: could not find function "dilation"
    Execution halted
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-patched-linux-x86_64, r-patched-solaris-sparc, r-patched-solaris-x86, 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: package dependencies
Result: NOTE
    Packages suggested but not available for checking: 'asreml' 'happy.hbrem'
Flavors: r-devel-windows-ix86+x86_64, 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’
    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