CRAN Package Check Results for Package titan

Last updated on 2017-11-17 22:47:39.

Flavor Version Tinstall Tcheck Ttotal Status Flags
r-devel-linux-x86_64-debian-clang 1.0-16 1.12 33.96 35.08 NOTE
r-devel-linux-x86_64-debian-gcc 1.0-16 1.28 32.22 33.50 NOTE
r-devel-linux-x86_64-fedora-clang 1.0-16 46.68 NOTE
r-devel-linux-x86_64-fedora-gcc 1.0-16 46.98 NOTE
r-devel-windows-ix86+x86_64 1.0-16 8.00 76.00 84.00 NOTE
r-patched-linux-x86_64 1.0-16 1.06 34.22 35.28 NOTE
r-patched-solaris-x86 1.0-16 67.30 NOTE
r-release-linux-x86_64 1.0-16 1.12 33.00 34.12 NOTE
r-release-windows-ix86+x86_64 1.0-16 4.00 75.00 79.00 NOTE
r-release-osx-x86_64 1.0-16 NOTE
r-oldrel-windows-ix86+x86_64 1.0-16 4.00 58.00 62.00 NOTE
r-oldrel-osx-x86_64 1.0-16 WARN

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

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

Version: 1.0-16
Check: dependencies in R code
Result: NOTE
    Invalid MIT-MAGIC-COOKIE-1 key'library' or 'require' calls to packages already attached by Depends:
     ‘MASS’ ‘boot’ ‘lattice’ ‘splines’ ‘tcltk’
     Please remove these calls from your code.
Flavor: r-oldrel-osx-x86_64

Version: 1.0-16
Check: S3 generic/method consistency
Result: WARN
    Invalid MIT-MAGIC-COOKIE-1 key
    See section ‘Generic functions and methods’ in the ‘Writing R
    Extensions’ manual.
Flavor: r-oldrel-osx-x86_64

Version: 1.0-16
Check: replacement functions
Result: WARN
    Invalid MIT-MAGIC-COOKIE-1 key
    The argument of a replacement function which corresponds to the right
    hand side must be named ‘value’.
Flavor: r-oldrel-osx-x86_64

Version: 1.0-16
Check: foreign function calls
Result: NOTE
    Invalid MIT-MAGIC-COOKIE-1 key
    See chapter ‘System and foreign language interfaces’ in the ‘Writing R
    Extensions’ manual.
Flavor: r-oldrel-osx-x86_64

Version: 1.0-16
Check: R code for possible problems
Result: NOTE
    Invalid MIT-MAGIC-COOKIE-1 keytitan : 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.
Flavor: r-oldrel-osx-x86_64

Version: 1.0-16
Check: for missing documentation entries
Result: WARN
    Invalid MIT-MAGIC-COOKIE-1 key
    All user-level objects in a package should have documentation entries.
    See chapter ‘Writing R documentation files’ in the ‘Writing R
    Extensions’ manual.
Flavor: r-oldrel-osx-x86_64

Version: 1.0-16
Check: for code/documentation mismatches
Result: WARN
    Invalid MIT-MAGIC-COOKIE-1 key
    Invalid MIT-MAGIC-COOKIE-1 key
    Invalid MIT-MAGIC-COOKIE-1 key
Flavor: r-oldrel-osx-x86_64

Version: 1.0-16
Check: Rd \usage sections
Result: NOTE
    Invalid MIT-MAGIC-COOKIE-1 key
    The \usage entries for S3 methods should use the \method markup and not
    their full name.
    See chapter ‘Writing R documentation files’ in the ‘Writing R
    Extensions’ manual.
Flavor: r-oldrel-osx-x86_64