R Development Page

qfa log file (check_x86_64_linux)

Fri Feb 21 19:51:06 2020: Checking package qfa (SVN revision 701) ...
* using log directory ‘/srv/rf/building/build_2020-02-21-19-46/RF_PKG_CHECK/PKGS/qfa.Rcheck’
* using R version 3.6.3 beta (2020-02-20 r77838)
* using platform: x86_64-pc-linux-gnu (64-bit)
* using session charset: UTF-8
* using option ‘--as-cran’
* checking for file ‘qfa/DESCRIPTION’ ... OK
* this is package ‘qfa’ version ‘0.0-45’
* checking CRAN incoming feasibility ... NOTE
Maintainer: ‘Conor Lawless ’

New submission

Package was archived on CRAN

CRAN repository db overrides:
  X-CRAN-Comment: Archived on 2014-09-19 as vignette locations were
    never updated for R 3.1.0.

The Description field contains
  image analysis software (http://research.ncl.ac.uk/colonyzer) which
Please enclose URLs in angle brackets (<...>).

The Date field is over a month old.

Size of tarball: 5158623 bytes
* checking package namespace information ... OK
* checking package dependencies ... NOTE
Package which this enhances but not available for checking: ‘data.table’
* checking if this is a source package ... OK
* checking if there is a namespace ... OK
* checking for executable files ... OK
* checking for hidden files and directories ... OK
* checking for portable file names ... OK
* checking for sufficient/correct file permissions ... OK
* checking serialization versions ... OK
* checking whether package ‘qfa’ can be installed ... [10s/10s] OK
* checking installed package size ... NOTE
  installed size is 16.4Mb
  sub-directories of 1Mb or more:
    extdata  15.4Mb
* checking package directory ... OK
* checking for future file timestamps ... OK
* checking ‘build’ directory ... OK
* checking DESCRIPTION meta-information ... NOTE
BugReports field is not a suitable URL but appears to contain an email address
  not specified by mailto: nor contained in < >
   use the Contact field instead
* checking top-level files ... OK
* checking for left-over files ... OK
* checking index information ... OK
* checking package subdirectories ... OK
* checking R files for non-ASCII characters ... OK
* checking R files for syntax errors ... OK
* checking whether the package can be loaded ... OK
* checking whether the package can be loaded with stated dependencies ... OK
* checking whether the package can be unloaded cleanly ... OK
* checking whether the namespace can be loaded with stated dependencies ... OK
* checking whether the namespace can be unloaded cleanly ... OK
* checking loading without being on the library search path ... OK
* checking use of S3 registration ... OK
* checking dependencies in R code ... NOTE
'library' or 'require' call to ‘data.table’ in package code.
  Please use :: or requireNamespace() instead.
  See section 'Suggested packages' in the 'Writing R Extensions' manual.
* checking S3 generic/method consistency ... OK
* checking replacement functions ... OK
* checking foreign function calls ... OK
* checking R code for possible problems ... [17s/17s] NOTE
Found an obsolete/platform-specific call in the following function:
  ‘makeVisTool’
Found the platform-specific device:
  ‘x11’
dev.new() is the preferred way to open a new device, in the unlikely
event one is needed.
bctimes: no visible global function definition for ‘read.delim’
buildComplexes: no visible global function definition for ‘read.delim’
buildGO: no visible global function definition for ‘read.delim’
buildPombeGO: no visible global function definition for ‘read.delim’
colonyzer.read: no visible global function definition for ‘read.delim’
colonyzer.read: no visible global function definition for
  ‘installed.packages’
colonyzer.read: no visible binding for global variable ‘read.delim’
complexesFromSource: no visible global function definition for
  ‘read.delim’
correlationReport: no visible global function definition for ‘pdf’
correlationReport: no visible global function definition for ‘par’
correlationReport: no visible global function definition for ‘combn’
correlationReport: no visible global function definition for ‘rainbow’
correlationReport: no visible global function definition for ‘cor’
correlationReport: no visible global function definition for ‘points’
correlationReport: no visible global function definition for ‘hist’
correlationReport: no visible global function definition for ‘dev.off’
data.fit: no visible global function definition for ‘optim’
de.fit: no visible global function definition for ‘runif’
drawSel: no visible global function definition for ‘points’
fastPwMahal: no visible global function definition for ‘dist’
fitnessReport: no visible binding for global variable ‘median’
fitnessReport: no visible binding for global variable ‘var’
fitnessReport: no visible binding for global variable ‘sd’
fitnessReport: no visible global function definition for ‘sessionInfo’
fitnessReport: no visible global function definition for ‘write.table’
getDeadLocations: no visible global function definition for
  ‘read.delim’
getMissingSGA : findFirst: no visible global function definition for
  ‘read.delim’
getMissingSGA : findFirst: no visible global function definition for
  ‘median’
getNeighbours: no visible global function definition for ‘head’
getResults: no visible global function definition for ‘read.delim’
growthcurve: no visible global function definition for ‘tail’
guess: no visible global function definition for ‘smooth.spline’
guess: no visible global function definition for ‘approxfun’
guess: no visible global function definition for ‘uniroot’
guess: no visible global function definition for ‘cor’
iRVisDemo: no visible global function definition for ‘read.delim’
lin.fit: no visible global function definition for ‘lm’
lin.fit: no visible global function definition for ‘par’
lin.fit: no visible global function definition for ‘points’
lin.fit: no visible global function definition for ‘abline’
lin.fit: no visible global function definition for ‘fitted’
lm.epi: no visible global function definition for ‘lm’
lm.epi: no visible global function definition for ‘pdf’
lm.epi: no visible global function definition for ‘hist’
lm.epi: no visible global function definition for ‘qqnorm’
lm.epi: no visible global function definition for ‘sd’
lm.epi: no visible global function definition for ‘abline’
lm.epi: no visible global function definition for ‘dev.off’
loapproxfun: no visible global function definition for ‘loess’
loapproxfun: no visible global function definition for ‘approxfun’
loapproxfun : loex: no visible global function definition for ‘predict’
logdraw: no visible global function definition for ‘points’
logdraw: no visible global function definition for ‘abline’
logdraw: no visible global function definition for ‘curve’
logdraw: no visible global function definition for ‘legend’
makeFitness : AUC: no visible global function definition for
  ‘integrate’
makePDF: no visible global function definition for ‘pdf’
makePDF: no visible global function definition for ‘dev.off’
makeProfiles: no visible global function definition for ‘read.delim’
makeProfiles: no visible binding for global variable ‘sd’
makeVisTool : epiplot: no visible global function definition for
  ‘abline’
makeVisTool : epiplot: no visible global function definition for
  ‘points’
makeVisTool : makePlot: no visible global function definition for
  ‘points’
makeVisTool : makePlot: no visible global function definition for
  ‘text’
makeVisTool : rnkPlot: no visible global function definition for
  ‘points’
makeVisTool : rnkPlot: no visible global function definition for ‘text’
makeVisTool : mouse: no visible global function definition for
  ‘grconvertX’
makeVisTool : mouse: no visible global function definition for
  ‘grconvertY’
makeVisTool : mouse: no visible global function definition for
  ‘browseURL’
makeVisTool : keybd: no visible global function definition for ‘tail’
makeVisTool : keybd: no visible global function definition for ‘pdf’
makeVisTool : keybd: no visible global function definition for
  ‘dev.off’
makeVisTool : keybd: no visible global function definition for ‘png’
makeVisTool : keybd: no visible global function definition for
  ‘cairo_ps’
makeVisTool : keybd: no visible global function definition for ‘rgb’
makeVisTool : keybd: no visible global function definition for
  ‘browseURL’
makeVisTool : visTool: no visible global function definition for ‘rgb’
makeVisTool : visTool: no visible global function definition for ‘x11’
makeVisTool : visTool: no visible global function definition for
  ‘getGraphicsEvent’
makeVisTool : visTool: no visible global function definition for
  ‘dev.off’
normalisePlates: no visible global function definition for ‘median’
numerical_r: no visible global function definition for ‘par’
numerical_r: no visible global function definition for ‘abline’
numerical_r: no visible global function definition for ‘points’
numerical_r: no visible global function definition for ‘mtext’
numerical_r: no visible global function definition for ‘curve’
numerical_r: no visible global function definition for ‘axis’
numericalfitness : nAUCfn: no visible global function definition for
  ‘integrate’
orf2gdict: no visible global function definition for ‘read.delim’
perpRegression: no visible global function definition for ‘optim’
pgis: no visible global function definition for ‘median’
pgis: no visible global function definition for ‘wilcox.test’
pgis : : no visible global function definition for ‘t.test’
pgis: no visible global function definition for ‘t.test’
pgis_bootstrap: no visible global function definition for ‘median’
plateBoxplots: no visible global function definition for ‘pdf’
plateBoxplots: no visible global function definition for ‘boxplot’
plateBoxplots: no visible global function definition for ‘rainbow’
plateBoxplots: no visible global function definition for ‘dev.off’
plotFitsPoints: no visible global function definition for ‘quantile’
plotFitsPoints: no visible binding for global variable ‘col2rgb’
plotFitsPoints: no visible global function definition for ‘rgb’
plotFitsPoints: no visible global function definition for ‘boxplot’
plotFitsPoints: no visible global function definition for ‘points’
plotFitsPoints: no visible global function definition for ‘text’
plotFitsPoints: no visible global function definition for ‘legend’
plotGroupFits: no visible global function definition for ‘quantile’
plotGroupFits: no visible global function definition for ‘rainbow’
plotGroupFits: no visible global function definition for ‘par’
plotGroupFits: no visible global function definition for ‘boxplot’
plotGroupFits: no visible global function definition for ‘points’
plotGroupFits: no visible global function definition for ‘text’
plotGroupFits: no visible global function definition for ‘legend’
plotRepsDF: no visible global function definition for ‘rainbow’
plotRepsDF: no visible global function definition for ‘rect’
plotRepsDF: no visible global function definition for ‘par’
plotRepsDF: no visible global function definition for ‘points’
plotRepsDF: no visible global function definition for ‘legend’
plotRow: no visible global function definition for ‘rasterImage’
plotRow: no visible global function definition for ‘median’
plotSimilarFit: no visible global function definition for ‘quantile’
plotSimilarFit: no visible global function definition for ‘head’
plotSimilarFit: no visible global function definition for ‘par’
plotSimilarFit: no visible global function definition for ‘boxplot’
plotSimilarFit: no visible global function definition for ‘points’
plotSimilarFit: no visible global function definition for ‘text’
prepareTimecourse: no visible global function definition for ‘quantile’
qfa.epi: no visible binding for global variable ‘median’
qfa.epi: no visible global function definition for ‘p.adjust’
qfa.epiplot: no visible global function definition for ‘abline’
qfa.epiplot: no visible global function definition for ‘points’
qfa.epiplot: no visible global function definition for ‘text’
qfa.epiplot: no visible global function definition for ‘cor’
qfa.epiplot: no visible global function definition for ‘legend’
qfa.fit: no visible global function definition for ‘lsf.str’
qfa.plot: no visible global function definition for ‘pdf’
qfa.plot: no visible global function definition for ‘par’
qfa.plot: no visible global function definition for ‘frame’
qfa.plot: no visible global function definition for ‘title’
qfa.plot: no visible global function definition for ‘dev.off’
readMer: no visible global function definition for ‘read.delim’
readSGD: no visible global function definition for ‘read.delim’
report.epi: no visible global function definition for ‘sessionInfo’
report.epi: no visible global function definition for ‘write.table’
reportExpts: no visible global function definition for ‘tail’
reportExpts: no visible global function definition for ‘head’
reportExpts: no visible global function definition for ‘write.table’
rod.read: no visible global function definition for ‘read.delim’
rod.write: no visible global function definition for ‘write.table’
similarities: no visible global function definition for ‘cov’
similarities: no visible global function definition for ‘cor’
similarities: no visible global function definition for ‘dist’
sterr: no visible global function definition for ‘var’
summarise: no visible global function definition for ‘aggregate’
summarise: no visible global function definition for ‘formula’
summarise: no visible global function definition for ‘setNames’
summaryPlots: no visible global function definition for ‘par’
summaryPlots: no visible global function definition for ‘hist’
summaryPlots: no visible global function definition for ‘boxplot’
summaryPlots: no visible global function definition for ‘title’
testSlope: no visible global function definition for ‘lm’
timecourseImages: no visible global function definition for ‘par’
timecourseImages: no visible global function definition for ‘text’
Undefined global functions or variables:
  abline aggregate approxfun axis boxplot browseURL cairo_ps col2rgb
  combn cor cov curve dev.off dist fitted formula frame
  getGraphicsEvent grconvertX grconvertY head hist installed.packages
  integrate legend lm loess lsf.str median mtext optim p.adjust par pdf
  png points predict qqnorm quantile rainbow rasterImage read.delim
  rect rgb runif sd sessionInfo setNames smooth.spline t.test tail text
  title uniroot var wilcox.test write.table x11
Consider adding
  importFrom("grDevices", "cairo_ps", "col2rgb", "dev.off",
             "getGraphicsEvent", "pdf", "png", "rainbow", "rgb", "x11")
  importFrom("graphics", "abline", "axis", "boxplot", "curve", "frame",
             "grconvertX", "grconvertY", "hist", "legend", "mtext",
             "par", "points", "rasterImage", "rect", "text", "title")
  importFrom("stats", "aggregate", "approxfun", "cor", "cov", "dist",
             "fitted", "formula", "integrate", "lm", "loess", "median",
             "optim", "p.adjust", "predict", "qqnorm", "quantile",
             "runif", "sd", "setNames", "smooth.spline", "t.test",
             "uniroot", "var", "wilcox.test")
  importFrom("utils", "browseURL", "combn", "head", "installed.packages",
             "lsf.str", "read.delim", "sessionInfo", "tail",
             "write.table")
to your NAMESPACE file.
* checking Rd files ... OK
* checking Rd metadata ... OK
* checking Rd line widths ... OK
* checking Rd cross-references ... OK
* checking for missing documentation entries ... OK
* checking for code/documentation mismatches ... OK
* checking Rd \usage sections ... OK
* checking Rd contents ... OK
* checking for unstated dependencies in examples ... OK
* checking sizes of PDF files under ‘inst/doc’ ... OK
* checking installed files from ‘inst/doc’ ... OK
* checking files in ‘vignettes’ ... OK
* checking examples ... [3s/3s] OK
* checking for unstated dependencies in vignettes ... OK
* checking package vignettes in ‘inst/doc’ ... OK
* checking re-building of vignette outputs ... [3s/3s] OK
* checking PDF version of manual ... OK
* checking for detritus in the temp directory ... OK
* DONE

Status: 6 NOTEs
See
  ‘/srv/rf/building/build_2020-02-21-19-46/RF_PKG_CHECK/PKGS/qfa.Rcheck/00check.log’
for details.


Run time: 85.09 seconds.