CRAN Package Check Results for Maintainer ‘Karl Broman <broman at wisc.edu>’

Last updated on 2020-12-04 01:51:26 CET.

Package ERROR WARN NOTE OK
aRxiv 12
broman 2 10
lineup 2 10
lineup2 12
mbmixture 12
negenes 12
qtl 5 5 2
qtl2 2 5 5
qtl2convert 12
qtl2fst 12
qtlbook 12
qtlcharts 12
regress 12
simcross 12
xoi 12

Package aRxiv

Current CRAN status: OK: 12

Package broman

Current CRAN status: WARN: 2, OK: 10

Version: 0.71-6
Check: R code for possible problems
Result: NOTE
    excel_fig: no visible global function definition for ‘plot’
    grayplot : hidegrayplot: no visible global function definition for
     ‘plot’
    grayplot_na : hidegrayplot_na: no visible global function definition
     for ‘plot’
    mypairs: no visible global function definition for ‘plot’
    plot_crayons: no visible global function definition for ‘plot’
    triplot: no visible global function definition for ‘plot’
    venn: no visible global function definition for ‘plot’
    Undefined global functions or variables:
     plot
    Consider adding
     importFrom("graphics", "plot")
    to your NAMESPACE file.
Flavors: r-oldrel-macos-x86_64, r-oldrel-windows-ix86+x86_64

Version: 0.71-6
Check: Rd cross-references
Result: WARN
    Missing link or links in documentation object 'grayplot.Rd':
     ‘[base:plot]{base::plot()}’
    
    Missing link or links in documentation object 'grayplot_na.Rd':
     ‘[base:plot]{base::plot()}’
    
    Missing link or links in documentation object 'mypairs.Rd':
     ‘[base:plot]{base::plot()}’
    
    Missing link or links in documentation object 'triplot.Rd':
     ‘[base:plot]{base::plot()}’
    
    See section 'Cross-references' in the 'Writing R Extensions' manual.
Flavors: r-oldrel-macos-x86_64, r-oldrel-windows-ix86+x86_64

Package lineup

Current CRAN status: NOTE: 2, OK: 10

Version: 0.38-3
Check: R code for possible problems
Result: NOTE
    plot2dist: no visible global function definition for ‘plot’
    plotEGclass: no visible global function definition for ‘plot’
    Undefined global functions or variables:
     plot
    Consider adding
     importFrom("graphics", "plot")
    to your NAMESPACE file.
Flavors: r-oldrel-macos-x86_64, r-oldrel-windows-ix86+x86_64

Package lineup2

Current CRAN status: OK: 12

Package mbmixture

Current CRAN status: OK: 12

Package negenes

Current CRAN status: OK: 12

Package qtl

Current CRAN status: ERROR: 5, NOTE: 5, OK: 2

Version: 1.46-2
Check: examples
Result: ERROR
    Running examples in 'qtl-Ex.R' failed
    The error most likely occurred in:
    
    > base::assign(".ptime", proc.time(), pos = "CheckExEnv")
    > ### Name: inferredpartitions
    > ### Title: Identify inferred partitions in mapping QTL to a phylogenetic
    > ### tree
    > ### Aliases: inferredpartitions
    > ### Keywords: print
    >
    > ### ** Examples
    >
    > ## Don't show:
    > set.seed(66787403)
    > ## End(Don't show)
    > # example map; drop X chromosome
    > data(map10)
    > map10 <- map10[1:19]
    > ## Don't show:
    > map10 <- map10[1:4]
    > ## End(Don't show)
    >
    > # simulate data
    > x <- simPhyloQTL(4, partition="AB|CD", crosses=c("AB", "AC", "AD"),
    + map=map10, n.ind=150,
    + model=c(1, 50, 0.5, 0))
    >
    > # run calc.genoprob on each cross
    > ## Not run: x <- lapply(x, calc.genoprob, step=2)
    > ## Don't show:
    > x <- lapply(x, calc.genoprob, step=0)
    > ## End(Don't show)
    >
    > # scan genome, at each position trying all possible partitions
    > out <- scanPhyloQTL(x, method="hk")
    >
    > # inferred partitions
    > inferredpartitions(out, chr=3, lodthreshold=3)
    Warning in min(which(cs >= probthreshold)) :
     no non-missing arguments to min; returning Inf
    Error in 1:wh : result would be too long a vector
    Calls: inferredpartitions
    Execution halted
Flavors: r-devel-linux-x86_64-debian-clang, r-devel-linux-x86_64-debian-gcc

Version: 1.46-2
Check: installed package size
Result: NOTE
     installed size is 11.6Mb
     sub-directories of 1Mb or more:
     R 1.7Mb
     contrib 3.8Mb
     doc 3.0Mb
     libs 1.6Mb
Flavors: r-devel-linux-x86_64-fedora-clang, r-devel-windows-ix86+x86_64, r-patched-solaris-x86, r-release-macos-x86_64, r-release-windows-ix86+x86_64, r-oldrel-macos-x86_64, r-oldrel-windows-ix86+x86_64

Version: 1.46-2
Check: examples
Result: ERROR
    Running examples in ‘qtl-Ex.R’ failed
    The error most likely occurred in:
    
    > ### Name: inferredpartitions
    > ### Title: Identify inferred partitions in mapping QTL to a phylogenetic
    > ### tree
    > ### Aliases: inferredpartitions
    > ### Keywords: print
    >
    > ### ** Examples
    >
    > ## Don't show:
    > set.seed(66787403)
    > ## End(Don't show)
    > # example map; drop X chromosome
    > data(map10)
    > map10 <- map10[1:19]
    > ## Don't show:
    > map10 <- map10[1:4]
    > ## End(Don't show)
    >
    > # simulate data
    > x <- simPhyloQTL(4, partition="AB|CD", crosses=c("AB", "AC", "AD"),
    + map=map10, n.ind=150,
    + model=c(1, 50, 0.5, 0))
    >
    > # run calc.genoprob on each cross
    > ## Not run: x <- lapply(x, calc.genoprob, step=2)
    > ## Don't show:
    > x <- lapply(x, calc.genoprob, step=0)
    > ## End(Don't show)
    >
    > # scan genome, at each position trying all possible partitions
    > out <- scanPhyloQTL(x, method="hk")
    >
    > # inferred partitions
    > inferredpartitions(out, chr=3, lodthreshold=3)
    Warning in min(which(cs >= probthreshold)) :
     no non-missing arguments to min; returning Inf
    Error in 1:wh : result would be too long a vector
    Calls: inferredpartitions
    Execution halted
Flavors: r-devel-linux-x86_64-fedora-clang, r-devel-linux-x86_64-fedora-gcc

Version: 1.46-2
Check: running examples for arch ‘i386’
Result: ERROR
    Running examples in 'qtl-Ex.R' failed
    The error most likely occurred in:
    
    > ### Name: inferredpartitions
    > ### Title: Identify inferred partitions in mapping QTL to a phylogenetic
    > ### tree
    > ### Aliases: inferredpartitions
    > ### Keywords: print
    >
    > ### ** Examples
    >
    > ## Don't show:
    > set.seed(66787403)
    > ## End(Don't show)
    > # example map; drop X chromosome
    > data(map10)
    > map10 <- map10[1:19]
    > ## Don't show:
    > map10 <- map10[1:4]
    > ## End(Don't show)
    >
    > # simulate data
    > x <- simPhyloQTL(4, partition="AB|CD", crosses=c("AB", "AC", "AD"),
    + map=map10, n.ind=150,
    + model=c(1, 50, 0.5, 0))
    >
    > # run calc.genoprob on each cross
    > ## Not run: x <- lapply(x, calc.genoprob, step=2)
    > ## Don't show:
    > x <- lapply(x, calc.genoprob, step=0)
    > ## End(Don't show)
    >
    > # scan genome, at each position trying all possible partitions
    > out <- scanPhyloQTL(x, method="hk")
    >
    > # inferred partitions
    > inferredpartitions(out, chr=3, lodthreshold=3)
    Warning in min(which(cs >= probthreshold)) :
     no non-missing arguments to min; returning Inf
    Error in 1:wh : result would be too long a vector
    Calls: inferredpartitions
    Execution halted
Flavor: r-devel-windows-ix86+x86_64

Version: 1.46-2
Check: running examples for arch ‘x64’
Result: ERROR
    Running examples in 'qtl-Ex.R' failed
    The error most likely occurred in:
    
    > ### Name: inferredpartitions
    > ### Title: Identify inferred partitions in mapping QTL to a phylogenetic
    > ### tree
    > ### Aliases: inferredpartitions
    > ### Keywords: print
    >
    > ### ** Examples
    >
    > ## Don't show:
    > set.seed(66787403)
    > ## End(Don't show)
    > # example map; drop X chromosome
    > data(map10)
    > map10 <- map10[1:19]
    > ## Don't show:
    > map10 <- map10[1:4]
    > ## End(Don't show)
    >
    > # simulate data
    > x <- simPhyloQTL(4, partition="AB|CD", crosses=c("AB", "AC", "AD"),
    + map=map10, n.ind=150,
    + model=c(1, 50, 0.5, 0))
    >
    > # run calc.genoprob on each cross
    > ## Not run: x <- lapply(x, calc.genoprob, step=2)
    > ## Don't show:
    > x <- lapply(x, calc.genoprob, step=0)
    > ## End(Don't show)
    >
    > # scan genome, at each position trying all possible partitions
    > out <- scanPhyloQTL(x, method="hk")
    >
    > # inferred partitions
    > inferredpartitions(out, chr=3, lodthreshold=3)
    Warning in min(which(cs >= probthreshold)) :
     no non-missing arguments to min; returning Inf
    Error in 1:wh : result would be too long a vector
    Calls: inferredpartitions
    Execution halted
Flavor: r-devel-windows-ix86+x86_64

Package qtl2

Current CRAN status: WARN: 2, NOTE: 5, OK: 5

Additional issues

clang-UBSAN

Version: 0.22-11
Check: installed package size
Result: NOTE
     installed size is 50.4Mb
     sub-directories of 1Mb or more:
     extdata 3.3Mb
     libs 45.8Mb
Flavors: r-devel-linux-x86_64-fedora-clang, r-devel-windows-ix86+x86_64, r-patched-solaris-x86, r-release-macos-x86_64, r-release-windows-ix86+x86_64, r-oldrel-macos-x86_64, r-oldrel-windows-ix86+x86_64

Version: 0.22-11
Check: R code for possible problems
Result: NOTE
    plot_genes : plot_genes_internal: no visible global function definition
     for ‘plot’
    plot_onegeno : plot_onegeno_internal: no visible global function
     definition for ‘plot’
    plot_peaks : plot_peaks_internal: no visible global function definition
     for ‘plot’
    plot_pxg : plot_pxg_internal: no visible global function definition for
     ‘plot’
    plot_scan1 : plot_scan1_internal: no visible global function definition
     for ‘plot’
    Undefined global functions or variables:
     plot
    Consider adding
     importFrom("graphics", "plot")
    to your NAMESPACE file.
Flavors: r-oldrel-macos-x86_64, r-oldrel-windows-ix86+x86_64

Version: 0.22-11
Check: Rd cross-references
Result: WARN
    Missing link or links in documentation object 'plot_genes.Rd':
     ‘[base:plot]{base::plot()}’
    
    Missing link or links in documentation object 'plot_pxg.Rd':
     ‘[base:plot]{base::plot()}’
    
    See section 'Cross-references' in the 'Writing R Extensions' manual.
Flavors: r-oldrel-macos-x86_64, r-oldrel-windows-ix86+x86_64

Package qtl2convert

Current CRAN status: OK: 12

Package qtl2fst

Current CRAN status: OK: 12

Package qtlbook

Current CRAN status: OK: 12

Package qtlcharts

Current CRAN status: OK: 12

Package regress

Current CRAN status: OK: 12

Package simcross

Current CRAN status: OK: 12

Package xoi

Current CRAN status: OK: 12