BioC 3.3: CHECK report for cellHTS on morelia

Package: cellHTS

Version: 1.41.3

Command: /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD check --no-vignettes --timings cellHTS_1.41.3.tar.gz

StartedAt: 2016-04-21 00:01:40 -0700 (Thu, 21 Apr 2016)

EndedAt: 2016-04-21 00:03:58 -0700 (Thu, 21 Apr 2016)

EllapsedTime: 138.2 seconds

RetCode: 0

Status:  WARNINGS

CheckDir: cellHTS.Rcheck

Warnings: 1

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### Running command:
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###   /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD check --no-vignettes --timings cellHTS_1.41.3.tar.gz
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* using log directory ‘/Users/biocbuild/bbs-3.3-bioc/meat/cellHTS.Rcheck’
* using R version 3.3.0 beta (2016-04-06 r70435)
* using platform: x86_64-apple-darwin13.4.0 (64-bit)
* using session charset: UTF-8
* using option ‘--no-vignettes’
* checking for file ‘cellHTS/DESCRIPTION’ ... OK
* this is package ‘cellHTS’ version ‘1.41.3’
* package encoding: UTF-8
* checking package namespace information ... OK
* checking package dependencies ... OK
* checking if this is a source package ... OK
* checking if there is a namespace ... OK
* checking for hidden files and directories ... OK
* checking for portable file names ... OK
* checking for sufficient/correct file permissions ... OK
* checking whether package ‘cellHTS’ can be installed ... [12s/12s] WARNING
Found the following significant warnings:
  Warning: Package 'cellHTS' is deprecated and will be removed from Bioconductor
See ‘/Users/biocbuild/bbs-3.3-bioc/meat/cellHTS.Rcheck/00install.out’ for details.
* checking installed package size ... OK
* checking package directory ... OK
* checking ‘build’ directory ... OK
* checking DESCRIPTION meta-information ... OK
* 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 dependencies in R code ... OK
* checking S3 generic/method consistency ... OK
* checking replacement functions ... OK
* checking foreign function calls ... OK
* checking R code for possible problems ... NOTE
Bscore: no visible global function definition for ‘medpolish’
Bscore: no visible global function definition for ‘mad’
QMbyPlate: no visible global function definition for ‘cor’
QMbyPlate : <anonymous>: no visible global function definition for
  ‘par’
QMbyPlate : <anonymous>: no visible global function definition for
  ‘plot’
QMbyPlate : <anonymous>: no visible global function definition for
  ‘abline’
QMbyPlate : <anonymous>: no visible global function definition for
  ‘hist’
QMbyPlate : <anonymous>: no visible global function definition for
  ‘gray’
QMbyPlate : <anonymous>: no visible global function definition for
  ‘rug’
QMbyPlate: no visible global function definition for ‘quantile’
QMexperiment : <anonymous>: no visible global function definition for
  ‘par’
QMexperiment : <anonymous>: no visible global function definition for
  ‘median’
QMexperiment : <anonymous>: no visible global function definition for
  ‘mad’
QMexperiment : <anonymous> : <anonymous>: no visible global function
  definition for ‘mad’
QMexperiment : <anonymous> : <anonymous>: no visible global function
  definition for ‘median’
ROC: no visible global function definition for ‘quantile’
annotate.cellHTS: no visible global function definition for
  ‘read.table’
boxplotwithNA: no visible global function definition for ‘boxplot’
boxplotwithNA: no visible global function definition for ‘IQR’
boxplotwithNA: no visible global function definition for ‘axis’
boxplotwithNA: no visible global function definition for ‘abline’
calcZscores: no visible global function definition for ‘median’
calcZscores: no visible global function definition for ‘mad’
checkDots: no visible global function definition for ‘str’
configure.cellHTS: no visible global function definition for
  ‘read.table’
controlsplot: no visible global function definition for
  ‘colorRampPalette’
controlsplot: no visible global function definition for ‘plot’
controlsplot: no visible global function definition for ‘legend’
controlsplot: no visible global function definition for ‘segments’
controlsplot: no visible global function definition for ‘points’
controlsplot: no visible global function definition for ‘axis’
controlsplot: no visible global function definition for ‘abline’
densityplot: no visible global function definition for
  ‘colorRampPalette’
densityplot: no visible global function definition for ‘density’
densityplot: no visible global function definition for ‘plot’
densityplot: no visible global function definition for ‘lines’
densityplot: no visible global function definition for ‘legend’
envisionPlateReader: no visible global function definition for
  ‘write.table’
imageScreen: no visible global function definition for
  ‘colorRampPalette’
imageScreen: no visible global function definition for ‘par’
imageScreen: no visible global function definition for ‘image’
imageScreen: no visible global function definition for ‘text’
lines.ROC: no visible global function definition for ‘lines’
makePlot: no visible global function definition for ‘pdf’
makePlot: no visible global function definition for ‘dev.off’
makePlot: no visible global function definition for ‘png’
normalizeChannels: no visible global function definition for ‘median’
normalizeChannels: no visible global function definition for ‘mad’
plot.ROC: no visible global function definition for ‘plot’
plot.ROC: no visible global function definition for ‘mtext’
plotPlateLibrary: no visible global function definition for ‘quantile’
readPlateData: no visible global function definition for ‘read.table’
scaleByPlateMedian: no visible global function definition for ‘median’
scaleByPlateNegatives: no visible global function definition for
  ‘median’
sdWithNA: no visible global function definition for ‘sd’
tableOutput: no visible global function definition for ‘read.table’
write.tabdel: no visible global function definition for ‘write.table’
writeReport: no visible binding for global variable ‘median’
writeReport: no visible global function definition for ‘median’
writeReport: no visible global function definition for ‘write.table’
writeTab.cellHTS: no visible global function definition for
  ‘write.table’
Undefined global functions or variables:
  IQR abline axis boxplot colorRampPalette cor density dev.off gray
  hist image legend lines mad median medpolish mtext par pdf plot png
  points quantile read.table rug sd segments str text write.table
Consider adding
  importFrom("grDevices", "colorRampPalette", "dev.off", "gray", "pdf",
             "png")
  importFrom("graphics", "abline", "axis", "boxplot", "hist", "image",
             "legend", "lines", "mtext", "par", "plot", "points", "rug",
             "segments", "text")
  importFrom("stats", "IQR", "cor", "density", "mad", "median",
             "medpolish", "quantile", "sd")
  importFrom("utils", "read.table", "str", "write.table")
to your NAMESPACE file.
* checking Rd files ... OK
* checking Rd metadata ... 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 contents of ‘data’ directory ... OK
* checking data for non-ASCII characters ... OK
* checking data for ASCII and uncompressed saves ... OK
* checking sizes of PDF files under ‘inst/doc’ ... OK
* checking installed files from ‘inst/doc’ ... OK
* checking files in ‘vignettes’ ... OK
* checking examples ... [9s/9s] OK
* checking for unstated dependencies in vignettes ... OK
* checking package vignettes in ‘inst/doc’ ... OK
* checking running R code from vignettes ... SKIPPED
* checking re-building of vignette outputs ... SKIPPED
* checking PDF version of manual ... OK
* DONE

Status: 1 WARNING, 1 NOTE
See
  ‘/Users/biocbuild/bbs-3.3-bioc/meat/cellHTS.Rcheck/00check.log’
for details.

* installing *source* package ‘cellHTS’ ...
** R
** data
** inst
** preparing package for lazy loading
** help
*** installing help indices
** building package indices
** installing vignettes
** testing if installed package can be loaded
Warning: Package 'cellHTS' is deprecated and will be removed from Bioconductor
  version 3.4. Please consider using 'cellHTS2' which offers better
  functionality for working with multiple screens and with
  multi-channel screens.
* DONE (cellHTS)

name	user	system	elapsed
Bscore	0.544	0.030	0.578
ROC	0.013	0.003	0.016
annotate	0.000	0.001	0.001
bdgpbiomart	0.248	0.011	0.262
configure	0.000	0.000	0.001
data-KcViab	0.175	0.007	0.182
data-KcViabSmall	0.013	0.004	0.016
getEnVisionRawData	0.105	0.003	0.111
getLibraryPlate	0.015	0.003	0.019
getMatrix	0.013	0.003	0.016
imageScreen	0.047	0.004	0.051
normalizeChannels	0.001	0.000	0.002
normalizePlates	0.013	0.003	0.017
oneRowPerId	0.005	0.000	0.004
plotPlateLibrary	0.923	0.029	1.004
plotSpatialEffects	0.298	0.008	0.305
print.cellHTS	0.013	0.002	0.015
readPlateData	0.281	0.007	0.304
screenMatch	0.191	0.011	0.202
summarizeChannels	0.001	0.001	0.002
summarizeReplicates	0.026	0.003	0.029
write.tabdel	0.028	0.005	0.032
writeReport	0.014	0.003	0.018
writeTab	0.018	0.004	0.021