BioC 3.3: CHECK report for debrowser on zin2

Package: debrowser

Version: 1.0.10

Command: /home/biocbuild/bbs-3.3-bioc/R/bin/R CMD check --no-vignettes --timings debrowser_1.0.10.tar.gz

StartedAt: 2016-10-13 01:09:16 -0700 (Thu, 13 Oct 2016)

EndedAt: 2016-10-13 01:13:45 -0700 (Thu, 13 Oct 2016)

EllapsedTime: 268.7 seconds

RetCode: 0

Status:  OK

CheckDir: debrowser.Rcheck

Warnings: 0

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### Running command:
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###   /home/biocbuild/bbs-3.3-bioc/R/bin/R CMD check --no-vignettes --timings debrowser_1.0.10.tar.gz
###
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* using log directory ‘/home/biocbuild/bbs-3.3-bioc/meat/debrowser.Rcheck’
* using R version 3.3.1 (2016-06-21)
* using platform: x86_64-pc-linux-gnu (64-bit)
* using session charset: UTF-8
* using option ‘--no-vignettes’
* checking for file ‘debrowser/DESCRIPTION’ ... OK
* checking extension type ... Package
* this is package ‘debrowser’ version ‘1.0.10’
* 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 ‘debrowser’ can be installed ... OK
* 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 loading without being on the library search path ... 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
MAPlot: no visible global function definition for ‘:=’
MAPlot: no visible binding for global variable ‘size’
MAPlot: no visible binding for global variable ‘size.hover’
MAPlot: no visible binding for global variable ‘fillOpacity’
MAPlot: no visible binding for global variable ‘fillOpacity.hover’
MAPlot: no visible binding for global variable ‘fill.brush’
MAPlot: no visible binding for global variable ‘opacity’
MAPlot: no visible binding for global variable ‘key’
MAZoom: no visible global function definition for ‘:=’
MAZoom: no visible binding for global variable ‘size’
MAZoom: no visible binding for global variable ‘size.hover’
MAZoom: no visible binding for global variable ‘key’
getHoverPlots: no visible binding for global variable ‘conds’
getIntHeatmap: no visible global function definition for ‘:=’
getIntHeatmap: no visible binding for global variable ‘size’
getIntHeatmap: no visible binding for global variable ‘size.hover’
getIntHeatmap: no visible binding for global variable ‘fillOpacity’
getIntHeatmap: no visible binding for global variable
  ‘fillOpacity.hover’
getIntHeatmap: no visible binding for global variable ‘fill.brush’
getIntHeatmap: no visible binding for global variable ‘opacity’
getIntHeatmap: no visible binding for global variable ‘key’
getIntHeatmap: no visible binding for global variable ‘strokeWidth’
getPCAexplained: no visible binding for global variable ‘PCs’
getPCAexplained: no visible binding for global variable ‘explained’
installpack: no visible global function definition for ‘biocLite’
load_data: no visible binding for global variable ‘demodata’
mainScatter: no visible global function definition for ‘:=’
mainScatter: no visible binding for global variable ‘size’
mainScatter: no visible binding for global variable ‘size.hover’
mainScatter: no visible binding for global variable ‘fillOpacity’
mainScatter: no visible binding for global variable ‘fillOpacity.hover’
mainScatter: no visible binding for global variable ‘fill.brush’
mainScatter: no visible binding for global variable ‘opacity’
mainScatter: no visible binding for global variable ‘key’
scatterZoom: no visible global function definition for ‘:=’
scatterZoom: no visible binding for global variable ‘size’
scatterZoom: no visible binding for global variable ‘size.hover’
scatterZoom: no visible binding for global variable ‘key’
volcanoPlot: no visible global function definition for ‘:=’
volcanoPlot: no visible binding for global variable ‘size’
volcanoPlot: no visible binding for global variable ‘size.hover’
volcanoPlot: no visible binding for global variable ‘fillOpacity’
volcanoPlot: no visible binding for global variable ‘fillOpacity.hover’
volcanoPlot: no visible binding for global variable ‘fill.brush’
volcanoPlot: no visible binding for global variable ‘opacity’
volcanoPlot: no visible binding for global variable ‘key’
volcanoZoom: no visible global function definition for ‘:=’
volcanoZoom: no visible binding for global variable ‘size’
volcanoZoom: no visible binding for global variable ‘size.hover’
volcanoZoom: no visible binding for global variable ‘key’
Undefined global functions or variables:
  := PCs biocLite conds demodata explained fill.brush fillOpacity
  fillOpacity.hover key opacity size size.hover strokeWidth
* 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 installed files from ‘inst/doc’ ... OK
* checking files in ‘vignettes’ ... OK
* checking examples ... OK
Examples with CPU or elapsed time > 5s
               user system elapsed
getEnrichKEGG 1.048  0.052   5.497
* checking for unstated dependencies in ‘tests’ ... OK
* checking tests ...
  Running ‘test-demo.R’
  Running ‘test-deseq.R’
  Running ‘test-null.R’
  Running ‘test-ui.R’
 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 NOTE
See
  ‘/home/biocbuild/bbs-3.3-bioc/meat/debrowser.Rcheck/00check.log’
for details.

* installing *source* package ‘debrowser’ ...
** R
** inst
** preparing package for lazy loading
** help
*** installing help indices
** building package indices
** installing vignettes
** testing if installed package can be loaded
* DONE (debrowser)

name	user	system	elapsed
MAPlot	0.000	0.004	0.001
MAZoom	0	0	0
addID	0.001	0.000	0.001
add_title_pos	0.222	0.000	0.285
all2all	0.141	0.000	0.154
applyFilters	0.000	0.000	0.001
applyFiltersToMergedComparison	0.001	0.000	0.000
cellInfo	0.000	0.000	0.001
clusterData	0.083	0.000	0.086
compareClust	0.001	0.000	0.000
deServer	0.005	0.000	0.008
deUI	0.023	0.000	0.096
getAfterLoadMsg	0.001	0.000	0.001
getColors	0.000	0.000	0.001
getCompSelection	0.006	0.000	0.005
getCondMsg	0.000	0.000	0.001
getConditionSelector	0.001	0.000	0.000
getCutOffSelection	0.003	0.000	0.004
getDataForTables	0.001	0.000	0.000
getDataPrepPanel	0.000	0.000	0.001
getDomains	0.001	0.000	0.000
getDown	0.000	0.000	0.001
getDownloadSection	0.001	0.000	0.000
getEnrichDO	0.000	0.000	0.001
getEnrichGO	0.001	0.000	0.000
getEnrichKEGG	1.048	0.052	5.497
getGOLeftMenu	0.014	0.000	0.014
getGOPlots	0.001	0.000	0.001
getGeneList	0.649	0.024	0.679
getGeneSetData	0.001	0.000	0.001
getGoPanel	0	0	0
getHoverPlots	0.001	0.000	0.001
getInitialMenu	0	0	0
getIntHeatmap	0	0	0
getIntHeatmapVis	0.000	0.000	0.001
getLeftMenu	0.024	0.000	0.024
getLoadingMsg	0.001	0.000	0.001
getLogo	0.001	0.000	0.001
getMainPanel	0	0	0
getMainPanelPlots	0.001	0.000	0.001
getMean	0	0	0
getMergedComparison	0	0	0
getMostVariedList	0.001	0.000	0.001
getNormalizedMatrix	0.008	0.000	0.008
getOrganism	0.001	0.000	0.001
getOrganismBox	0.001	0.004	0.004
getOrganismPathway	0	0	0
getPCAexplained	0.001	0.000	0.001
getPCselection	0.001	0.000	0.001
getProgramTitle	0	0	0
getQCLeftMenu	0.005	0.004	0.009
getQCPanel	0.001	0.000	0.001
getQCPlots	0.001	0.000	0.001
getQCReplot	0	0	0
getSampleNames	0	0	0
getSamples	0.001	0.000	0.001
getSearchData	0.001	0.000	0.001
getSelHeat	0	0	0
getSelectedDatasetInput	0.001	0.000	0.000
getStartPlotsMsg	0.001	0.000	0.001
getStartupMsg	0.001	0.000	0.001
getTableStyle	0.001	0.000	0.001
getToolTipText	0	0	0
getUp	0	0	0
getUpDown	0.001	0.000	0.001
hideObj	0	0	0
installpack	0	0	0
link_brush	0.003	0.000	0.003
load_data	0.001	0.000	0.001
logSliderJScode	0	0	0
mainScatter	0	0	0
panel.cor	0.000	0.004	0.001
panel.hist	0.000	0.000	0.001
plot_pca	1.495	0.008	1.523
prepDESeqOutput	0.001	0.000	0.001
prepDataContainer	0.001	0.000	0.001
prepDataForQC	0.001	0.000	0.000
push	0.000	0.000	0.001
removeCols	0.001	0.000	0.000
round_vals	0.000	0.000	0.001
runDESeq	0.001	0.000	0.000
runHeatmap	0.146	0.000	0.146
run_pca	1.125	0.000	1.125
saveQCPlot	0.001	0.000	0.001
scatterZoom	0	0	0
selectConditions	0	0	0
setFilterParams	0.001	0.000	0.001
showObj	0	0	0
startDEBrowser	0	0	0
textareaInput	0.001	0.000	0.001
togglePanels	0	0	0
volcanoPlot	0	0	0
volcanoZoom	0.000	0.004	0.001