PGPC 1.5.0
Felix Klein
| Snapshot Date: 2017-08-15 09:00:08 -0400 (Tue, 15 Aug 2017) | | URL: https://hedgehog.fhcrc.org/bioc-data/trunk/experiment/pkgs/PGPC | | Last Changed Rev: 4157 / Revision: 4227 | | Last Changed Date: 2017-04-24 16:19:55 -0400 (Mon, 24 Apr 2017) |
| malbec1 | Linux (Ubuntu 16.04.1 LTS) / x86_64 | NotNeeded | OK | [ OK ] | |  |
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### Running command:
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### /home/biocbuild/bbs-3.6-bioc/R/bin/R CMD check --no-vignettes --timings PGPC_1.5.0.tar.gz
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* using log directory ‘/home/biocbuild/bbs-3.6-data-experiment/meat/PGPC.Rcheck’
* using R version 3.4.1 (2017-06-30)
* 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 ‘1.5.0’
* 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 251.8Mb
sub-directories of 1Mb or more:
data 172.8Mb
doc 7.9Mb
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 loading without being on the library search path ... 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 installed files from ‘inst/doc’ ... OK
* checking files in ‘vignettes’ ... OK
* checking examples ... OK
Examples with CPU or elapsed time > 5s
user system elapsed
summarizeWellsExtended 224.912 47.820 273.005
getFeaturesAllSpots 141.156 43.684 185.395
segmentAllSpots 60.540 13.228 73.827
segmentXman 14.224 1.480 15.712
getInteractions 10.336 0.028 10.371
ftrs 8.792 0.064 8.860
datamatrixTransformed 7.736 0.040 7.783
* checking for unstated dependencies in vignettes ... NOTE
'::' or ':::' import not declared from: ‘cellHTS2’
* 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: 6 NOTEs
See
‘/home/biocbuild/bbs-3.6-data-experiment/meat/PGPC.Rcheck/00check.log’
for details.