Last updated on 2020-08-07 01:50:35 CEST.
| Package | NOTE |
|---|---|
| cgh | 12 |
| titan | 12 |
Current CRAN status:
Version: 1.0-7.1
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-windows-ix86+x86_64, r-patched-linux-x86_64, r-patched-solaris-x86, r-release-linux-x86_64, r-release-macos-x86_64, r-release-windows-ix86+x86_64, r-oldrel-macos-x86_64, r-oldrel-windows-ix86+x86_64
Version: 1.0-7.1
Check: R code for possible problems
Result: NOTE
sw.plot : <anonymous>: no visible global function definition for
'median'
sw.plot : <anonymous>: no visible global function definition for 'mad'
sw.plot : my.line: no visible global function definition for 'lines'
sw.plot : island.line: no visible global function definition for
'lines'
sw.plot: no visible global function definition for 'rug'
sw.plot: no visible global function definition for 'axis'
sw.plot: no visible global function definition for 'mtext'
sw.plot: no visible global function definition for 'abline'
sw.plot: no visible global function definition for 'points'
sw.rob : <anonymous>: no visible global function definition for
'median'
sw.rob : <anonymous>: no visible global function definition for 'mad'
sw.threshold : <anonymous>: no visible global function definition for
'median'
sw.threshold : <anonymous>: no visible global function definition for
'mad'
Undefined global functions or variables:
abline axis lines mad median mtext points rug
Consider adding
importFrom("graphics", "abline", "axis", "lines", "mtext", "points",
"rug")
importFrom("stats", "mad", "median")
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-macos-x86_64, r-release-windows-ix86+x86_64
Version: 1.0-7.1
Check: compiled code
Result: NOTE
File ‘cgh/libs/cgh.so’:
Found no call to: ‘R_useDynamicSymbols’
It is good practice to register native routines and to disable symbol
search.
See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual.
Flavors: r-devel-linux-x86_64-fedora-clang, r-devel-linux-x86_64-fedora-gcc
Version: 1.0-7.1
Check: R code for possible problems
Result: NOTE
sw.plot : <anonymous>: no visible global function definition for
‘median’
sw.plot : <anonymous>: no visible global function definition for ‘mad’
sw.plot : my.line: no visible global function definition for ‘lines’
sw.plot : island.line: no visible global function definition for
‘lines’
sw.plot: no visible global function definition for ‘plot’
sw.plot: no visible global function definition for ‘rug’
sw.plot: no visible global function definition for ‘axis’
sw.plot: no visible global function definition for ‘mtext’
sw.plot: no visible global function definition for ‘abline’
sw.plot: no visible global function definition for ‘points’
sw.rob : <anonymous>: no visible global function definition for
‘median’
sw.rob : <anonymous>: no visible global function definition for ‘mad’
sw.threshold : <anonymous>: no visible global function definition for
‘median’
sw.threshold : <anonymous>: no visible global function definition for
‘mad’
Undefined global functions or variables:
abline axis lines mad median mtext plot points rug
Consider adding
importFrom("graphics", "abline", "axis", "lines", "mtext", "plot",
"points", "rug")
importFrom("stats", "mad", "median")
to your NAMESPACE file.
Flavors: r-oldrel-macos-x86_64, r-oldrel-windows-ix86+x86_64
Current CRAN status:
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-macos-x86_64, r-release-windows-ix86+x86_64, r-oldrel-macos-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.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.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.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-macos-x86_64, r-release-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-oldrel-macos-x86_64, r-oldrel-windows-ix86+x86_64