Package: PGPC

Version: 1.8.0

Command: /home/biocbuild/bbs-3.7-bioc/R/bin/R CMD check --install=check:PGPC.install-out.txt --library=/home/biocbuild/bbs-3.7-bioc/R/library --no-vignettes --timings PGPC_1.8.0.tar.gz

StartedAt: 2018-07-03 11:13:18 -0400 (Tue, 03 Jul 2018)

EndedAt: 2018-07-03 11:24:09 -0400 (Tue, 03 Jul 2018)

EllapsedTime: 651.1 seconds

RetCode: 0

Status:  OK

CheckDir: PGPC.Rcheck

Warnings: 0

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### Running command:
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###   /home/biocbuild/bbs-3.7-bioc/R/bin/R CMD check --install=check:PGPC.install-out.txt --library=/home/biocbuild/bbs-3.7-bioc/R/library --no-vignettes --timings PGPC_1.8.0.tar.gz
###
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* using log directory ‘/home/biocbuild/bbs-3.7-data-experiment/meat/PGPC.Rcheck’
* using R version 3.5.1 RC (2018-06-24 r74929)
* using platform: x86_64-pc-linux-gnu (64-bit)
* using session charset: UTF-8
* using option ‘--no-vignettes’
* checking for file ‘PGPC/DESCRIPTION’ ... OK
* checking extension type ... Package
* this is package ‘PGPC’ version ‘1.8.0’
* checking package namespace information ... OK
* checking package dependencies ... NOTE
Depends: includes the non-default packages:
  ‘EBImage’ ‘imageHTS’ ‘SearchTrees’ ‘limma’ ‘RColorBrewer’ ‘gplots’
  ‘splots’ ‘ggplot2’ ‘geneplotter’ ‘ChemmineR’ ‘reshape2’ ‘plyr’
Adding so many packages to the search path is excessive and importing
selectively is preferable.
* 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 ‘PGPC’ can be installed ... OK
* checking installed package size ... NOTE
  installed size is 243.9Mb
  sub-directories of 1Mb or more:
    data     172.8Mb
    extdata   70.9Mb
* 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 ... NOTE
Packages in Depends field not imported from:
  ‘ChemmineR’ ‘RColorBrewer’ ‘geneplotter’ ‘ggplot2’ ‘gplots’ ‘plyr’
  ‘reshape2’ ‘splots’
  These packages need to be imported from (in the NAMESPACE file)
  for when this namespace is loaded but not attached.
Unexported object imported by a ':::' call: ‘imageHTS:::writeThumbnail’
  See the note in ?`:::` about the use of this operator.
* checking S3 generic/method consistency ... OK
* checking replacement functions ... OK
* checking foreign function calls ... OK
* checking R code for possible problems ... NOTE
checkConsistency: no visible global function definition for ‘data’
extractFeaturesWithParameter: no visible global function definition for
  ‘write.table’
getCorr: no visible global function definition for ‘cor’
getDist: no visible global function definition for ‘cor’
getFeaturesAllSpots : <anonymous>: no visible global function
  definition for ‘sd’
getInteractions: no visible global function definition for ‘medpolish’
getInteractions : <anonymous>: no visible global function definition
  for ‘mad’
getInteractions: no visible global function definition for ‘p.adjust’
getInteractions: no visible global function definition for ‘cor’
mergeProfiles: no visible global function definition for ‘write.table’
myHeatmap: no visible global function definition for ‘pushViewport’
myHeatmap: no visible global function definition for ‘viewport’
myHeatmap: no visible global function definition for ‘unit’
myHeatmap: no visible global function definition for ‘grid.raster’
myHeatmap: no visible global function definition for ‘grid.text’
myHeatmap: no visible global function definition for ‘gpar’
myHeatmap: no visible global function definition for ‘popViewport’
myHeatmapSingle: no visible global function definition for
  ‘pushViewport’
myHeatmapSingle: no visible global function definition for ‘viewport’
myHeatmapSingle: no visible global function definition for ‘unit’
myHeatmapSingle: no visible global function definition for
  ‘grid.raster’
myHeatmapSingle: no visible global function definition for ‘grid.text’
myHeatmapSingle: no visible global function definition for ‘gpar’
myHeatmapSingle: no visible global function definition for
  ‘popViewport’
orderDim: no visible global function definition for ‘cor’
orderDim: no visible global function definition for ‘hclust’
orderDim: no visible global function definition for ‘as.dist’
plotAll: no visible global function definition for ‘png’
plotAll: no visible global function definition for ‘dev.off’
plotEffects: no visible global function definition for ‘plot’
plotEffects: no visible global function definition for ‘points’
plotEffects: no visible global function definition for ‘abline’
plotHeatmap: no visible global function definition for ‘heatmap.2’
plotHeatmap: no visible global function definition for
  ‘colorRampPalette’
plotResVsEffect: no visible global function definition for ‘plot’
plotResVsEffect: no visible global function definition for ‘points’
plotResVsValue: no visible global function definition for ‘plot’
plotResiduals: no visible global function definition for ‘plot’
plotResiduals: no visible global function definition for ‘abline’
plotSingleValues: no visible global function definition for ‘ggplot’
plotSingleValues: no visible global function definition for ‘aes’
plotSingleValues: no visible binding for global variable
  ‘concdrug1.micro_M.’
plotSingleValues: no visible binding for global variable ‘value’
plotSingleValues: no visible binding for global variable ‘identifier’
plotSingleValues: no visible binding for global variable ‘variable’
plotSingleValues: no visible global function definition for
  ‘scale_x_log10’
plotSingleValues: no visible global function definition for
  ‘scale_y_continuous’
plotSingleValues: no visible global function definition for ‘theme_bw’
plotSingleValues: no visible global function definition for
  ‘scale_colour_manual’
plotSingleValues: no visible global function definition for ‘labs’
plotSingleValues: no visible binding for global variable ‘experiment’
plotSingleValues: no visible global function definition for
  ‘geom_jitter’
plotSingleValues: no visible global function definition for
  ‘position_jitter’
plotSingleValues: no visible global function definition for
  ‘geom_vline’
plotSummary: no visible binding for global variable
  ‘concdrug1.micro_M.’
plotSummary: no visible global function definition for ‘theme’
plotSummary: no visible global function definition for ‘element_text’
plotSummary: no visible global function definition for ‘ggplot’
plotSummary: no visible global function definition for ‘aes’
plotSummary: no visible binding for global variable ‘sem’
plotSummary: no visible binding for global variable ‘identifier’
plotSummary: no visible global function definition for ‘geom_point’
plotSummary: no visible global function definition for ‘geom_line’
plotSummary: no visible global function definition for ‘scale_x_log10’
plotSummary: no visible global function definition for
  ‘scale_y_continuous’
plotSummary: no visible global function definition for
  ‘scale_colour_manual’
plotSummary: no visible global function definition for ‘geom_errorbar’
plotSummary: no visible global function definition for ‘labs’
plotSummary: no visible binding for global variable ‘experiment’
plotSummary: no visible global function definition for ‘geom_vline’
plotSummaryBarplot: no visible binding for global variable
  ‘concdrug1.micro_M.’
plotSummaryBarplot: no visible global function definition for ‘theme’
plotSummaryBarplot: no visible global function definition for
  ‘element_text’
plotSummaryBarplot: no visible global function definition for ‘ggplot’
plotSummaryBarplot: no visible global function definition for ‘aes’
plotSummaryBarplot: no visible binding for global variable ‘sem’
plotSummaryBarplot: no visible binding for global variable ‘identifier’
plotSummaryBarplot: no visible global function definition for
  ‘position_dodge’
plotSummaryBarplot: no visible global function definition for
  ‘geom_bar’
plotSummaryBarplot: no visible global function definition for
  ‘scale_y_continuous’
plotSummaryBarplot: no visible global function definition for
  ‘scale_fill_manual’
plotSummaryBarplot: no visible global function definition for
  ‘scale_colour_manual’
plotSummaryBarplot: no visible global function definition for
  ‘geom_errorbar’
plotSummaryBarplot: no visible global function definition for ‘labs’
plotSummaryBarplot: no visible binding for global variable ‘experiment’
plotSummaryBarplot: no visible global function definition for ‘xlab’
plotSummaryBarplot: no visible global function definition for
  ‘geom_point’
plotSummaryBarplot: no visible binding for global variable ‘pvalue’
plotSummaryBarplotInhibition: no visible binding for global variable
  ‘concdrug1.micro_M.’
plotSummaryBarplotInhibition: no visible global function definition for
  ‘theme’
plotSummaryBarplotInhibition: no visible global function definition for
  ‘element_text’
plotSummaryBarplotInhibition: no visible global function definition for
  ‘element_blank’
plotSummaryBarplotInhibition: no visible global function definition for
  ‘ggplot’
plotSummaryBarplotInhibition: no visible global function definition for
  ‘aes’
plotSummaryBarplotInhibition: no visible binding for global variable
  ‘inhibition’
plotSummaryBarplotInhibition: no visible binding for global variable
  ‘sem’
plotSummaryBarplotInhibition: no visible binding for global variable
  ‘identifier’
plotSummaryBarplotInhibition: no visible global function definition for
  ‘position_dodge’
plotSummaryBarplotInhibition: no visible global function definition for
  ‘geom_bar’
plotSummaryBarplotInhibition: no visible global function definition for
  ‘scale_y_continuous’
plotSummaryBarplotInhibition: no visible global function definition for
  ‘scale_fill_manual’
plotSummaryBarplotInhibition: no visible global function definition for
  ‘scale_colour_manual’
plotSummaryBarplotInhibition: no visible global function definition for
  ‘geom_errorbar’
plotSummaryBarplotInhibition: no visible global function definition for
  ‘labs’
plotSummaryBarplotInhibition: no visible binding for global variable
  ‘experiment’
plotSummaryBarplotInhibition: no visible global function definition for
  ‘xlab’
plotSummaryBarplotInhibition: no visible global function definition for
  ‘ylab’
plotSummaryBarplotInhibition: no visible global function definition for
  ‘geom_point’
plotSummaryBarplotInhibition: no visible binding for global variable
  ‘pvalue’
selectByStability: no visible global function definition for ‘lm’
selectByStability : <anonymous>: no visible global function definition
  for ‘cor’
summarizeWellsExtended: no visible binding for global variable ‘sd’
summarizeWellsExtended: no visible binding for global variable
  ‘quantile’
summarizeWellsExtended: no visible global function definition for
  ‘write.table’
Undefined global functions or variables:
  abline aes as.dist colorRampPalette concdrug1.micro_M. cor data
  dev.off element_blank element_text experiment geom_bar geom_errorbar
  geom_jitter geom_line geom_point geom_vline ggplot gpar grid.raster
  grid.text hclust heatmap.2 identifier inhibition labs lm mad
  medpolish p.adjust plot png points popViewport position_dodge
  position_jitter pushViewport pvalue quantile scale_colour_manual
  scale_fill_manual scale_x_log10 scale_y_continuous sd sem theme
  theme_bw unit value variable viewport write.table xlab ylab
Consider adding
  importFrom("grDevices", "colorRampPalette", "dev.off", "png")
  importFrom("graphics", "abline", "plot", "points")
  importFrom("stats", "as.dist", "cor", "hclust", "lm", "mad",
             "medpolish", "p.adjust", "quantile", "sd")
  importFrom("utils", "data", "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 ... NOTE
  Note: found 28 marked Latin-1 strings
* checking data for ASCII and uncompressed saves ... OK
* checking line endings in Makefiles ... OK
* checking for GNU extensions in Makefiles ... OK
* checking include directives in Makefiles ... OK
* checking files in ‘vignettes’ ... OK
* checking examples ... OK
Examples with CPU or elapsed time > 5s
                          user system elapsed
summarizeWellsExtended 217.368 15.384 233.121
getFeaturesAllSpots    140.736 15.980 157.605
segmentAllSpots         62.144  4.112  66.346
segmentXman             13.816  0.616  14.444
getInteractions         10.156  0.008  10.191
ftrs                     9.140  0.140   9.463
datamatrixTransformed    8.308  0.100   8.819
* 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: 5 NOTEs
See
  ‘/home/biocbuild/bbs-3.7-data-experiment/meat/PGPC.Rcheck/00check.log’
for details.

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### Running command:
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###   /home/biocbuild/bbs-3.7-bioc/R/bin/R CMD INSTALL PGPC
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* installing to library ‘/home/biocbuild/bbs-3.7-bioc/R/library’
* installing *source* package ‘PGPC’ ...
** R
** data
** inst
** byte-compile and prepare package for lazy loading
** help
*** installing help indices
** building package indices
** installing vignettes
** testing if installed package can be loaded
* DONE (PGPC)

name	user	system	elapsed
datamatrixTransformed	8.308	0.100	8.819
ftrs	9.140	0.140	9.463
getFeaturesAllSpots	140.736	15.980	157.605
getInteractions	10.156	0.008	10.191
interactions	1.232	0.004	1.233
mergeProfiles	0	0	0
segmentAllSpots	62.144	4.112	66.346
segmentXman	13.816	0.616	14.444
selected	0.132	0.000	0.163
summarizeWellsExtended	217.368	15.384	233.121