CRAN Package Check Results for Maintainer Thomas Hoffmann <tjhoffm at gmail.com>

CRAN Package Check Results for Maintainer ‘Thomas Hoffmann <tjhoffm at gmail.com>’

Last updated on 2015-04-24 23:47:13.

Package	NOTE	OK
batch	14
fbati		14
fgui	14
pbatR	14
thgenetics	14

Package batch

Current CRAN status: NOTE: 14

Version: 1.1-4
Check: dependencies in R code
Result: NOTE
    'library' or 'require' call to ‘parallel’ in package code.
     Please use :: or requireNamespace() instead.
     See section 'Suggested packages' in the 'Writing R Extensions' manual.
    ':::' call which should be '::': ‘parallel:::detectCores’
     See the note in ?`:::` about the use of this operator.
Flavors: r-devel-linux-x86_64-debian-gcc, r-devel-windows-ix86+x86_64, r-patched-linux-x86_64, r-release-windows-ix86+x86_64, r-oldrel-windows-ix86+x86_64

Package fbati

Current CRAN status: OK: 14

Package fgui

Current CRAN status: NOTE: 14

Version: 1.0-5
Check: DESCRIPTION meta-information
Result: NOTE
    Package listed in more than one of Depends, Imports, Suggests, Enhances:
     ‘tcltk’
    A package should be listed in only one of these fields.
Flavors: r-devel-linux-x86_64-debian-gcc, r-devel-windows-ix86+x86_64, r-patched-linux-x86_64, r-release-windows-ix86+x86_64, r-oldrel-windows-ix86+x86_64

Version: 1.0-5
Check: dependencies in R code
Result: NOTE
    'library' or 'require' call to ‘tcltk’ in package code.
     Please use :: or requireNamespace() instead.
     See section 'Suggested packages' in the 'Writing R Extensions' manual.
    Package in Depends field not imported from: ‘tools’
     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: ‘tools:::fetchRdDB’
     See the note in ?`:::` about the use of this operator.
Flavors: r-devel-linux-x86_64-debian-gcc, r-devel-windows-ix86+x86_64, r-patched-linux-x86_64, r-release-windows-ix86+x86_64, r-oldrel-windows-ix86+x86_64

Version: 1.0-5
Check: Rd line widths
Result: NOTE
    Rd file 'gui.Rd':
     \examples lines wider than 100 characters:
     gui( summaryStats, helps=list(data="Enter the data as an R vector, e.g. 'c(13,66,44,27)' or enter the text 'rivers' to use a builtin da ... [TRUNCATED]
     ## If you want it modal though, do not do so until the last mgui call, or it will be modal inbetween additions to the menu!
     guiv( lmgui, argFilename=list(csvFilename=NULL), argList=list(response=NULL,explanatory=NULL), callback=lmguiCallback )
     data <- data.frame( mvrnorm( n=100, mu=c(0,0,0), Sigma=matrix(c(1,0.3,0, 0.3,1,0.3, 0,0.3,1),nrow=3) ) )

    These lines will be truncated in the PDF manual.
Flavors: r-devel-linux-x86_64-debian-gcc, r-patched-linux-x86_64

Package pbatR

Current CRAN status: NOTE: 14

Version: 2.2-9
Check: DESCRIPTION meta-information
Result: NOTE
    Package listed in more than one of Depends, Imports, Suggests, Enhances:
     ‘tcltk’
    A package should be listed in only one of these fields.
Flavors: r-devel-linux-x86_64-debian-gcc, r-devel-windows-ix86+x86_64, r-patched-linux-x86_64, r-release-windows-ix86+x86_64, r-oldrel-windows-ix86+x86_64

Version: 2.2-9
Check: dependencies in R code
Result: NOTE
    'library' or 'require' call to ‘rootSolve’ which was already attached by Depends.
     Please remove these calls from your code.
    'library' or 'require' calls in package code:
     ‘kinship2’ ‘tcltk’
     Please use :: or requireNamespace() instead.
     See section 'Suggested packages' in the 'Writing R Extensions' manual.
    Packages in Depends field not imported from:
     ‘rootSolve’ ‘survival’
     These packages need to be imported from (in the NAMESPACE file)
     for when this namespace is loaded but not attached.
Flavors: r-devel-linux-x86_64-debian-gcc, r-devel-windows-ix86+x86_64, r-patched-linux-x86_64, r-release-windows-ix86+x86_64, r-oldrel-windows-ix86+x86_64

Version: 2.2-9
Check: foreign function calls
Result: NOTE
    Call with DUP:
     .C("powerR", as.integer(numOffspring), as.integer(numParents),
     as.integer(numFamilies), as.integer(additionalOffspringPhenos),
     as.integer(ascertainment), as.integer(modelGen), as.integer(modelTest),
     as.double(afreqMarker), as.double(penAA), as.double(penAB),
     as.double(penBB), as.double(heritability), as.double(contsAscertainmentLower),
     as.double(contsAscertainmentUpper), as.double(pDiseaseAlleleGivenMarkerAllele),
     as.double(afreqDSL), as.double(qnorm(1 - alpha/2)), as.double(offset),
     as.integer(numSim), as.integer(ITERATION_KILLER), result,
     DUP = FALSE)
    DUP is no longer supported and will be ignored.
Flavors: r-devel-linux-x86_64-debian-gcc, r-devel-windows-ix86+x86_64, r-patched-linux-x86_64, r-release-windows-ix86+x86_64

Version: 2.2-9
Check: R code for possible problems
Result: NOTE
    pen_or1: no visible global function definition for ‘multiroot’
    plot.pedigree: no visible global function definition for
     ‘align.pedigree’
    plotPed: no visible global function definition for ‘pedigree’
Flavors: r-devel-linux-x86_64-debian-gcc, r-devel-windows-ix86+x86_64, r-patched-linux-x86_64, r-release-windows-ix86+x86_64, r-oldrel-windows-ix86+x86_64

Version: 2.2-9
Check: foreign function calls
Result: NOTE
    Call with DUP != TRUE:
     .C("powerR", as.integer(numOffspring), as.integer(numParents),
     as.integer(numFamilies), as.integer(additionalOffspringPhenos),
     as.integer(ascertainment), as.integer(modelGen), as.integer(modelTest),
     as.double(afreqMarker), as.double(penAA), as.double(penAB),
     as.double(penBB), as.double(heritability), as.double(contsAscertainmentLower),
     as.double(contsAscertainmentUpper), as.double(pDiseaseAlleleGivenMarkerAllele),
     as.double(afreqDSL), as.double(qnorm(1 - alpha/2)), as.double(offset),
     as.integer(numSim), as.integer(ITERATION_KILLER), result,
     DUP = FALSE)
    DUP = FALSE is deprecated and will be disabled in future versions of R.
Flavor: r-oldrel-windows-ix86+x86_64

Package thgenetics

Current CRAN status: NOTE: 14

Memtest notes: UBSAN

Version: 0.3-4
Check: foreign function calls
Result: NOTE
    Calls with DUP:
     .C("zstat_pathway_perm", as.double(g), as.integer(m), as.integer(length(m)),
     as.double(aff), as.integer(length(aff)), as.double(thresh),
     as.integer(gsubsetmatrix), as.integer(nrow(gsubsetmatrix)),
     as.integer(use_sign), as.integer(use_weight), as.integer(strategy),
     as.integer(nperm), ret_pvalue, DUP = FALSE)
     .C("zstat_perm", as.double(g), as.integer(m), as.integer(length(m)),
     as.double(aff), as.integer(length(aff)), as.double(thresh),
     as.integer(gsubsetmatrix), as.integer(nrow(gsubsetmatrix)),
     as.integer(use_sign), as.integer(use_weight), as.integer(strategy),
     as.integer(nperm), ret_pvalue, DUP = FALSE)
    DUP is no longer supported and will be ignored.
Flavors: r-devel-linux-x86_64-debian-gcc, r-devel-windows-ix86+x86_64, r-patched-linux-x86_64, r-release-windows-ix86+x86_64

Version: 0.3-4
Check: foreign function calls
Result: NOTE
    Calls with DUP != TRUE:
     .C("zstat_pathway_perm", as.double(g), as.integer(m), as.integer(length(m)),
     as.double(aff), as.integer(length(aff)), as.double(thresh),
     as.integer(gsubsetmatrix), as.integer(nrow(gsubsetmatrix)),
     as.integer(use_sign), as.integer(use_weight), as.integer(strategy),
     as.integer(nperm), ret_pvalue, DUP = FALSE)
     .C("zstat_perm", as.double(g), as.integer(m), as.integer(length(m)),
     as.double(aff), as.integer(length(aff)), as.double(thresh),
     as.integer(gsubsetmatrix), as.integer(nrow(gsubsetmatrix)),
     as.integer(use_sign), as.integer(use_weight), as.integer(strategy),
     as.integer(nperm), ret_pvalue, DUP = FALSE)
    DUP = FALSE is deprecated and will be disabled in future versions of R.
Flavor: r-oldrel-windows-ix86+x86_64