BioC 3.4: CHECK report for debrowser on zin1

Package: debrowser

Version: 1.1.9

Command: /home/biocbuild/bbs-3.4-bioc/R/bin/R CMD check --no-vignettes --timings debrowser_1.1.9.tar.gz

StartedAt: 2016-09-20 05:22:23 -0700 (Tue, 20 Sep 2016)

EndedAt: 2016-09-20 05:26:06 -0700 (Tue, 20 Sep 2016)

EllapsedTime: 222.8 seconds

RetCode: 0

Status:  OK

CheckDir: debrowser.Rcheck

Warnings: 0

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### Running command:
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###   /home/biocbuild/bbs-3.4-bioc/R/bin/R CMD check --no-vignettes --timings debrowser_1.1.9.tar.gz
###
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* using log directory ‘/home/biocbuild/bbs-3.4-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 ‘1.1.9’
* 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 ... NOTE
The following files look like leftovers:
  ‘debrowser/svn-commit.tmp’
Please remove them from your package.
* 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’
getDensityPlot: no visible binding for global variable ‘samples’
getHoverPlots: no visible binding for global variable ‘conds’
getIQRPlot: no visible global function definition for ‘:=’
getIQRPlot: no visible binding for global variable ‘fill’
getSelectedDatasetInput: no visible binding for global variable
  ‘searched’
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’
plot_pca: no visible global function definition for ‘:=’
runBayseq: no visible binding for global variable ‘fit’
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:
  := biocLite conds demodata fill fill.brush fillOpacity
  fillOpacity.hover fit key opacity samples searched size size.hover
* 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: 2 NOTEs
See
  ‘/home/biocbuild/bbs-3.4-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	0.000	0.001
MAZoom	0.000	0.000	0.001
actionButton	0.004	0.000	0.004
addID	0	0	0
add_title_pos	0.180	0.000	0.184
all2all	0.124	0.000	0.124
applyFilters	0.004	0.000	0.001
applyFiltersToMergedComparison	0	0	0
clusterData	0	0	0
compareClust	0.004	0.000	0.001
deServer	0.004	0.000	0.004
deUI	0.036	0.000	0.138
getAfterLoadMsg	0.000	0.000	0.001
getColors	0	0	0
getCompSelection	0.004	0.000	0.004
getCondMsg	0.004	0.000	0.000
getConditionSelector	0	0	0
getCutOffSelection	0.004	0.000	0.003
getDataForTables	0	0	0
getDataPrepPanel	0.000	0.000	0.001
getDensityPlot	0.000	0.000	0.001
getDomains	0	0	0
getDown	0	0	0
getDownloadSection	0.000	0.000	0.001
getEnrichDO	0.000	0.000	0.001
getEnrichGO	0	0	0
getEnrichKEGG	0.004	0.000	0.000
getGOLeftMenu	0.012	0.000	0.013
getGOPlots	0	0	0
getGeneList	0.628	0.012	0.645
getGeneSetData	0.000	0.000	0.001
getGoPanel	0.000	0.000	0.001
getHelpButton	0	0	0
getHoverPlots	0.000	0.000	0.001
getIQRPlot	0	0	0
getInitialMenu	0.000	0.000	0.001
getIntHeatmap	0.004	0.000	0.000
getIntHeatmapVis	0.000	0.000	0.001
getLeftMenu	0.028	0.004	0.031
getLoadingMsg	0.000	0.000	0.002
getLogo	0.000	0.000	0.001
getMainPanel	0.000	0.000	0.001
getMainPanelPlots	0.004	0.000	0.000
getMean	0.000	0.000	0.001
getMergedComparison	0.000	0.000	0.001
getMethodDetails	0.004	0.000	0.000
getMostVariedList	0	0	0
getNormalizedMatrix	0.016	0.000	0.014
getOrganism	0.000	0.000	0.001
getOrganismBox	0.004	0.000	0.003
getOrganismPathway	0	0	0
getPCAexplained	0.000	0.000	0.001
getPCselection	0	0	0
getProgramTitle	0	0	0
getQCLeftMenu	0.012	0.000	0.012
getQCPanel	0.020	0.000	0.028
getQCPlots	0.000	0.000	0.001
getQCReplot	0	0	0
getSampleNames	0	0	0
getSamples	0.000	0.000	0.001
getSearchData	0.000	0.000	0.001
getSelHeat	0.004	0.000	0.002
getSelectInputBox	0	0	0
getSelectedCols	0	0	0
getSelectedDatasetInput	0.000	0.000	0.001
getStartPlotsMsg	0.004	0.000	0.003
getStartupMsg	0.004	0.000	0.003
getTableStyle	0	0	0
getToolTipPCA	0	0	0
getToolTipText	0.004	0.000	0.001
getUp	0.000	0.000	0.001
getUpDown	0	0	0
hideObj	0	0	0
installpack	0	0	0
link_brush	0.004	0.000	0.004
load_data	0	0	0
logSliderJScode	0	0	0
mainScatter	0.000	0.000	0.001
panel.cor	0.000	0.000	0.001
panel.hist	0.004	0.000	0.001
plot_pca	1.844	0.008	1.853
prepAddQCPlots	0	0	0
prepDEOutput	0	0	0
prepDataContainer	0.000	0.000	0.001
prepDataForQC	0	0	0
push	0	0	0
removeCols	0	0	0
round_vals	0.000	0.000	0.001
runBayseq	0.004	0.000	0.001
runDE	0	0	0
runDESeq	0.000	0.000	0.001
runDESeq2	0.004	0.000	0.001
runEdgeR	0	0	0
runHeatmap	0.116	0.000	0.115
runLimma	0	0	0
run_pca	1.104	0.004	1.105
saveQCPlot	0.000	0.000	0.001
scatterZoom	0.000	0.000	0.001
selectConditions	0	0	0
selectedInput	0	0	0
setFilterParams	0.000	0.000	0.001
showObj	0.000	0.004	0.001
startDEBrowser	0	0	0
textareaInput	0	0	0
togglePanels	0.004	0.000	0.001
volcanoPlot	0.000	0.000	0.001
volcanoZoom	0	0	0