CRAN Package Check Results for Package titan

Last updated on 2018-10-17 22:52:11 CEST.

Flavor Version Tinstall Tcheck Ttotal Status Flags
r-devel-linux-x86_64-debian-clang 1.0-16 4.11 37.05 41.16 NOTE
r-devel-linux-x86_64-debian-gcc 1.0-16 4.19 29.98 34.17 NOTE
r-devel-linux-x86_64-fedora-clang 1.0-16 50.54 NOTE
r-devel-linux-x86_64-fedora-gcc 1.0-16 48.61 NOTE
r-devel-windows-ix86+x86_64 1.0-16 12.00 52.00 64.00 NOTE
r-patched-linux-x86_64 1.0-16 5.08 35.84 40.92 NOTE
r-patched-solaris-x86 1.0-16 76.40 NOTE
r-release-linux-x86_64 1.0-16 5.17 35.82 40.99 NOTE
r-release-windows-ix86+x86_64 1.0-16 7.00 67.00 74.00 NOTE
r-release-osx-x86_64 1.0-16 NOTE
r-oldrel-windows-ix86+x86_64 1.0-16 9.00 56.00 65.00 NOTE
r-oldrel-osx-x86_64 1.0-16 NOTE

Check Details

Version: 1.0-16
Check: top-level files
Result: NOTE
    Non-standard file/directory found at top level:
     ‘CONTENTS’
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: 1.0-16
Check: dependencies in R code
Result: NOTE
    'library' or 'require' calls to packages already attached by Depends:
     ‘MASS’ ‘boot’ ‘lattice’ ‘splines’ ‘tcltk’
     Please remove these calls from your code.
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-windows-ix86+x86_64, r-release-osx-x86_64, r-oldrel-windows-ix86+x86_64, r-oldrel-osx-x86_64

Version: 1.0-16
Check: R code for possible problems
Result: NOTE
    titan : titan.widget : widget2: warning in matrix(FALSE, nr = ngene, nc
     = 2): partial argument match of ‘nr’ to ‘nrow’
    titan : titan.widget : widget2: warning in matrix(FALSE, nr = ngene, nc
     = 2): partial argument match of ‘nc’ to ‘ncol’
    titan : titan.widget : widget2: warning in matrix(FALSE, nr = ngene, nc
     = 1): partial argument match of ‘nr’ to ‘nrow’
    titan : titan.widget : widget2: warning in matrix(FALSE, nr = ngene, nc
     = 1): partial argument match of ‘nc’ to ‘ncol’
    titan : titan.input : data.levels : dummy: warning in matrix(nr = len,
     nc = nlevels): partial argument match of ‘nr’ to ‘nrow’
    titan : titan.input : data.levels : dummy: warning in matrix(nr = len,
     nc = nlevels): partial argument match of ‘nc’ to ‘ncol’
    titan : titan.input : data.levels: warning in matrix(nr =
     length(dat$x), nc = ncontr.rx): partial argument match of ‘nr’ to
     ‘nrow’
    titan : titan.input : data.levels: warning in matrix(nr =
     length(dat$x), nc = ncontr.rx): partial argument match of ‘nc’ to
     ‘ncol’
    titan : titan.create.formulae: warning in matrix(NA, nr =
     input$data$levels$ngene, nc = input$data$levels$ncontr.rx + 1):
     partial argument match of ‘nr’ to ‘nrow’
    titan : titan.create.formulae: warning in matrix(NA, nr =
     input$data$levels$ngene, nc = input$data$levels$ncontr.rx + 1):
     partial argument match of ‘nc’ to ‘ncol’
    titan : titan.interpolate: warning in matrix(NA, nr =
     length(gene.valid), nc = 1 + nrx1): partial argument match of ‘nr’ to
     ‘nrow’
    titan : titan.interpolate: warning in matrix(NA, nr =
     length(gene.valid), nc = 1 + nrx1): partial argument match of ‘nc’ to
     ‘ncol’
    titan : titan.interpolate: warning in matrix(NA, nr = ngene1, nc =
     nrx1): partial argument match of ‘nr’ to ‘nrow’
    titan : titan.interpolate: warning in matrix(NA, nr = ngene1, nc =
     nrx1): partial argument match of ‘nc’ to ‘ncol’
    titan : titan.interpolate: warning in matrix(NA, nr = ngene0, nc =
     nrx1): partial argument match of ‘nr’ to ‘nrow’
    titan : titan.interpolate: warning in matrix(NA, nr = ngene0, nc =
     nrx1): partial argument match of ‘nc’ to ‘ncol’
    titan : titan.interpolate: warning in matrix(colMeans(log10fold.g0), nr
     = ngene1, nc = nrx1, byrow = TRUE): partial argument match of ‘nr’ to
     ‘nrow’
    titan : titan.interpolate: warning in matrix(colMeans(log10fold.g0), nr
     = ngene1, nc = nrx1, byrow = TRUE): partial argument match of ‘nc’ to
     ‘ncol’
    titan : titan.bootstrap : boot.fun: warning in matrix(NA, nr = ngene0,
     nc = nrx1): partial argument match of ‘nr’ to ‘nrow’
    titan : titan.bootstrap : boot.fun: warning in matrix(NA, nr = ngene0,
     nc = nrx1): partial argument match of ‘nc’ to ‘ncol’
    titan : titan.bootstrap : boot.fun: warning in matrix(NA, nr = ngene1,
     nc = nrx1): partial argument match of ‘nr’ to ‘nrow’
    titan : titan.bootstrap : boot.fun: warning in matrix(NA, nr = ngene1,
     nc = nrx1): partial argument match of ‘nc’ to ‘ncol’
    titan : titan.bootstrap : boot.fun: warning in
     matrix(colMeans(theta.star.g0), nc = nrx1, nr = ngene1, byrow =
     TRUE): partial argument match of ‘nr’ to ‘nrow’
    titan : titan.bootstrap : boot.fun: warning in
     matrix(colMeans(theta.star.g0), nc = nrx1, nr = ngene1, byrow =
     TRUE): partial argument match of ‘nc’ to ‘ncol’
    titan : titan.bootstrap.baselineonly : boot.fun: warning in matrix(NA,
     nr = (ngene1 - 1) * ngene1/2, nc = 1): partial argument match of ‘nr’
     to ‘nrow’
    titan : titan.bootstrap.baselineonly : boot.fun: warning in matrix(NA,
     nr = (ngene1 - 1) * ngene1/2, nc = 1): partial argument match of ‘nc’
     to ‘ncol’
    titan : print.titanboot: warning in matrix(NA, nr = len, nc = 7):
     partial argument match of ‘nr’ to ‘nrow’
    titan : print.titanboot: warning in matrix(NA, nr = len, nc = 7):
     partial argument match of ‘nc’ to ‘ncol’
    titan : titan.widget : widget2: no visible global function definition
     for ‘runif’
    titan : titan.input : data.levels: no visible global function
     definition for ‘contr.treatment’
    titan : titan.input: no visible global function definition for
     ‘relevel’
    titan : titan.load.file: no visible global function definition for
     ‘read.table’
    titan : titan.create.formulae: no visible global function definition
     for ‘as.formula’
    titan : titan.regression : dropWald: no visible global function
     definition for ‘drop.scope’
    titan : titan.regression : dropWald: no visible global function
     definition for ‘pt’
    titan : titan.regression : dropWald: no visible global function
     definition for ‘update.formula’
    titan : titan.regression : dropWald: no visible global function
     definition for ‘formula’
    titan : titan.regression : dropWald: no visible global function
     definition for ‘as.formula’
    titan : titan.regression : dropWald: no visible global function
     definition for ‘update’
    titan : titan.regression: no visible global function definition for
     ‘coef’
    titan : titan.find.coefs: no visible global function definition for
     ‘coef’
    titan : titan.interpolate.line : pred.y: no visible global function
     definition for ‘predict’
    titan : titan.plot: no visible global function definition for ‘pdf’
    titan : titan.plot: no visible global function definition for ‘dev.off’
    titan : titan.plot: no visible global function definition for ‘par’
    titan : titan.plot.gene : titan.plot.generx: no visible global function
     definition for ‘predict’
    titan : titan.plot.gene : titan.plot.generx: no visible global function
     definition for ‘qt’
    titan : titan.plot.gene: no visible global function definition for
     ‘par’
    titan : titan.plot.gene: no visible global function definition for
     ‘plot.new’
    titan : titan.plot.gene: no visible global function definition for
     ‘plot’
    titan : titan.manualFlag: no visible global function definition for
     ‘par’
    titan : titan.manualFlag: no visible global function definition for
     ‘write.table’
    titan : titan.bootstrap : boot.fun: no visible global function
     definition for ‘update’
    titan : titan.bootstrap.baselineonly : boot.fun: no visible global
     function definition for ‘update’
    titan : titan.printreg: no visible global function definition for
     ‘coef’
    titan : print.titanboot: no visible global function definition for
     ‘na.omit’
    titan : print.titanboot: no visible global function definition for ‘sd’
    Undefined global functions or variables:
     as.formula coef contr.treatment dev.off drop.scope formula na.omit
     par pdf plot plot.new predict pt qt read.table relevel runif sd
     update update.formula write.table
    Consider adding
     importFrom("grDevices", "dev.off", "pdf")
     importFrom("graphics", "par", "plot", "plot.new")
     importFrom("stats", "as.formula", "coef", "contr.treatment",
     "drop.scope", "formula", "na.omit", "predict", "pt", "qt",
     "relevel", "runif", "sd", "update", "update.formula")
     importFrom("utils", "read.table", "write.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-windows-ix86+x86_64, r-release-osx-x86_64, r-oldrel-windows-ix86+x86_64, r-oldrel-osx-x86_64