BioC 3.5: CHECK report for debrowser on oaxaca

Package: debrowser

Version: 1.3.4

Command: /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD check --no-vignettes --timings debrowser_1.3.4.tar.gz

StartedAt: 2017-03-04 01:36:45 -0800 (Sat, 04 Mar 2017)

EndedAt: 2017-03-04 01:42:00 -0800 (Sat, 04 Mar 2017)

EllapsedTime: 314.7 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_1.3.4.tar.gz
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* using log directory ‘/Users/biocbuild/bbs-3.5-bioc/meat/debrowser.Rcheck’
* using R Under development (unstable) (2017-02-15 r72177)
* 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 ‘1.3.4’
* 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 ... NOTE
  installed size is  7.9Mb
  sub-directories of 1Mb or more:
    doc       5.7Mb
    extdata   1.9Mb
* 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 ‘:=’
plot_pca: no visible binding for global variable ‘key’
plot_pca: no visible global function definition for ‘layer_text’
plot_pca: no visible binding for global variable ‘fontSize’
plot_pca: no visible binding for global variable ‘align’
plot_pca: no visible binding for global variable ‘baseline’
plot_pca: no visible binding for global variable ‘stroke’
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:
  := align baseline biocLite conds demodata fill fill.brush fillOpacity
  fillOpacity.hover fit fontSize key layer_text opacity samples
  searched size size.hover stroke
* 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 ... NOTE
'library' or 'require' call not declared from: ‘ReactomePA’
* 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: 4 NOTEs
See
  ‘/Users/biocbuild/bbs-3.5-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	0	0
actionButton	0.085	0.001	0.086
addID	0.001	0.000	0.001
add_title_pos	1.272	0.009	1.329
all2all	0.163	0.021	0.184
applyFilters	0.001	0.000	0.001
applyFiltersToMergedComparison	0.001	0.000	0.001
clusterData	0	0	0
compareClust	0.001	0.000	0.000
correctBatchEffect	0.000	0.000	0.001
deServer	0.010	0.001	0.010
deUI	0.091	0.012	0.172
drawPCAExplained	0.000	0.000	0.001
getAfterLoadMsg	0.001	0.000	0.001
getColorShapeSelection	0.000	0.000	0.001
getColors	0.000	0.000	0.001
getCompSelection	0.019	0.001	0.019
getCondMsg	0.001	0.000	0.000
getConditionSelector	0.001	0.000	0.000
getCutOffSelection	0.093	0.001	0.093
getDataForTables	0.001	0.000	0.000
getDataPrepPanel	0.001	0.000	0.001
getDensityPlot	0.001	0.000	0.001
getDomains	0.001	0.000	0.001
getDown	0.001	0.000	0.001
getDownloadSection	0.001	0.000	0.000
getEnrichDO	0	0	0
getEnrichGO	0.001	0.001	0.001
getEnrichKEGG	0	0	0
getGOLeftMenu	0.077	0.001	0.079
getGOPlots	0.001	0.000	0.001
getGeneList	0.937	0.036	0.974
getGeneSetData	0.000	0.000	0.001
getGoPanel	0.001	0.000	0.000
getHelpButton	0	0	0
getHoverPlots	0.001	0.000	0.001
getIQRPlot	0.000	0.000	0.001
getInitialMenu	0	0	0
getIntHeatmap	0.001	0.000	0.001
getIntHeatmapVis	0.000	0.000	0.001
getLeftMenu	0.001	0.000	0.000
getLegendSelect	0.006	0.001	0.007
getLoadingMsg	0.002	0.000	0.002
getLogo	0.002	0.000	0.002
getMainPanel	0.001	0.000	0.001
getMainPanelPlots	0.001	0.000	0.001
getMean	0.001	0.000	0.001
getMergedComparison	0.001	0.000	0.001
getMethodDetails	0.001	0.000	0.001
getMostVariedList	0.000	0.001	0.001
getNormalizedMatrix	0.081	0.000	0.083
getOrganism	0.000	0.000	0.001
getOrganismBox	0.004	0.000	0.004
getOrganismPathway	0.000	0.000	0.001
getPCAexplained	0.000	0.000	0.001
getPCselection	0.001	0.000	0.001
getProgramTitle	0.001	0.001	0.001
getQCLeftMenu	0.000	0.000	0.001
getQCPanel	0.120	0.003	0.133
getQCPlots	0.001	0.000	0.001
getQCReplot	0.001	0.000	0.001
getSampleNames	0.001	0.001	0.001
getSamples	0.001	0.000	0.001
getSearchData	0.001	0.000	0.000
getSelHeat	0.002	0.000	0.003
getSelectInputBox	0	0	0
getSelectedCols	0.001	0.000	0.001
getSelectedDatasetInput	0.001	0.000	0.001
getShapeColor	0.001	0.001	0.001
getStartPlotsMsg	0.004	0.000	0.004
getStartupMsg	0.004	0.001	0.004
getTableStyle	0.001	0.000	0.000
getTextOnOff	0.004	0.001	0.005
getToolTipPCA	0.000	0.000	0.001
getToolTipText	0.001	0.000	0.001
getUp	0.000	0.000	0.001
getUpDown	0.000	0.000	0.001
hideObj	0	0	0
installpack	0	0	0
link_brush	0.004	0.000	0.005
load_data	0.001	0.000	0.001
logSliderJScode	0	0	0
mainScatter	0	0	0
panel.cor	0.001	0.000	0.001
panel.hist	0.001	0.000	0.001
plot_pca	1.865	0.052	1.919
prepAddQCPlots	0.001	0.000	0.000
prepDEOutput	0.001	0.000	0.001
prepDataContainer	0.000	0.000	0.001
prepDataForQC	0	0	0
push	0.000	0.000	0.001
readMetaData	0.000	0.000	0.001
removeCols	0.001	0.000	0.001
round_vals	0.001	0.000	0.000
runBayseq	0.001	0.001	0.001
runDE	0.000	0.000	0.001
runDESeq	0.001	0.000	0.001
runDESeq2	0.001	0.000	0.000
runEdgeR	0.000	0.001	0.001
runHeatmap	0.397	0.008	0.406
runLimma	0.001	0.000	0.001
run_pca	1.024	0.051	1.076
saveQCPlot	0.001	0.000	0.001
scatterZoom	0.001	0.000	0.001
selectBatchEffect	0.000	0.000	0.001
selectConditions	0	0	0
selectedInput	0.001	0.000	0.000
setFilterParams	0.001	0.000	0.001
showObj	0	0	0
startDEBrowser	0.001	0.000	0.001
textareaInput	0.001	0.000	0.001
togglePanels	0.001	0.000	0.001
volcanoPlot	0.001	0.000	0.001
volcanoZoom	0.001	0.000	0.001