BioC 3.3: CHECK report for debrowser on oaxaca

Package: debrowser

Version: 1.0.10

Command: /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD check --no-vignettes --timings debrowser_1.0.10.tar.gz

StartedAt: 2016-10-13 00:47:06 -0700 (Thu, 13 Oct 2016)

EndedAt: 2016-10-13 00:52:32 -0700 (Thu, 13 Oct 2016)

EllapsedTime: 325.2 seconds

RetCode: 0

Status:  OK

CheckDir: debrowser.Rcheck

Warnings: 0

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### Running command:
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###   /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD check --no-vignettes --timings debrowser_1.0.10.tar.gz
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* using log directory ‘/Users/biocbuild/bbs-3.3-bioc/meat/debrowser.Rcheck’
* using R version 3.3.1 (2016-06-21)
* using platform: x86_64-apple-darwin13.4.0 (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
* 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
  ‘/Users/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	0.001	0.000	0.001
MAZoom	0.001	0.000	0.001
addID	0.001	0.000	0.001
add_title_pos	0.243	0.003	0.325
all2all	0.167	0.002	0.170
applyFilters	0.001	0.000	0.001
applyFiltersToMergedComparison	0.001	0.001	0.001
cellInfo	0.001	0.000	0.000
clusterData	0.084	0.001	0.086
compareClust	0.001	0.000	0.000
deServer	0.005	0.001	0.006
deUI	0.021	0.003	0.192
getAfterLoadMsg	0.001	0.000	0.001
getColors	0.001	0.000	0.000
getCompSelection	0.005	0.001	0.005
getCondMsg	0.000	0.000	0.001
getConditionSelector	0.001	0.000	0.000
getCutOffSelection	0.003	0.000	0.003
getDataForTables	0	0	0
getDataPrepPanel	0.000	0.000	0.001
getDomains	0.000	0.000	0.001
getDown	0.000	0.000	0.001
getDownloadSection	0.000	0.000	0.001
getEnrichDO	0	0	0
getEnrichGO	0.001	0.000	0.000
getEnrichKEGG	1.170	0.039	1.211
getGOLeftMenu	0.015	0.002	0.016
getGOPlots	0.001	0.000	0.001
getGeneList	0.848	0.023	0.873
getGeneSetData	0	0	0
getGoPanel	0.001	0.000	0.001
getHoverPlots	0.001	0.000	0.001
getInitialMenu	0.001	0.000	0.001
getIntHeatmap	0.001	0.000	0.001
getIntHeatmapVis	0	0	0
getLeftMenu	0.031	0.004	0.034
getLoadingMsg	0.002	0.000	0.002
getLogo	0.001	0.000	0.001
getMainPanel	0.000	0.001	0.001
getMainPanelPlots	0.001	0.000	0.001
getMean	0.001	0.000	0.001
getMergedComparison	0.001	0.000	0.001
getMostVariedList	0.001	0.001	0.001
getNormalizedMatrix	0.011	0.000	0.011
getOrganism	0.001	0.000	0.001
getOrganismBox	0.004	0.001	0.005
getOrganismPathway	0	0	0
getPCAexplained	0.001	0.000	0.001
getPCselection	0.001	0.000	0.001
getProgramTitle	0.001	0.000	0.000
getQCLeftMenu	0.012	0.001	0.014
getQCPanel	0.002	0.001	0.002
getQCPlots	0.001	0.000	0.001
getQCReplot	0.001	0.000	0.001
getSampleNames	0.000	0.000	0.001
getSamples	0.000	0.000	0.001
getSearchData	0.001	0.000	0.001
getSelHeat	0.001	0.000	0.001
getSelectedDatasetInput	0.001	0.000	0.000
getStartPlotsMsg	0.001	0.000	0.001
getStartupMsg	0.001	0.000	0.001
getTableStyle	0.000	0.000	0.001
getToolTipText	0.000	0.000	0.001
getUp	0.000	0.000	0.001
getUpDown	0.001	0.000	0.000
hideObj	0.001	0.000	0.000
installpack	0.001	0.000	0.001
link_brush	0.004	0.000	0.004
load_data	0.000	0.000	0.001
logSliderJScode	0.001	0.000	0.000
mainScatter	0.001	0.000	0.000
panel.cor	0.000	0.000	0.001
panel.hist	0.002	0.000	0.002
plot_pca	1.438	0.044	1.486
prepDESeqOutput	0.001	0.000	0.001
prepDataContainer	0.001	0.000	0.000
prepDataForQC	0.001	0.000	0.001
push	0.001	0.000	0.001
removeCols	0.000	0.000	0.001
round_vals	0.001	0.001	0.000
runDESeq	0.001	0.000	0.000
runHeatmap	0.138	0.006	0.144
run_pca	0.962	0.049	1.014
saveQCPlot	0.001	0.000	0.001
scatterZoom	0.001	0.000	0.000
selectConditions	0	0	0
setFilterParams	0.000	0.000	0.001
showObj	0	0	0
startDEBrowser	0.000	0.000	0.001
textareaInput	0.001	0.000	0.001
togglePanels	0.001	0.000	0.000
volcanoPlot	0.000	0.000	0.001
volcanoZoom	0.001	0.001	0.001