BioC 3.3: CHECK report for debrowser on morelia

Package: debrowser

Version: 0.99.2

Command: /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD check --no-vignettes --timings debrowser_0.99.2.tar.gz

StartedAt: 2016-04-21 01:23:43 -0700 (Thu, 21 Apr 2016)

EndedAt: 2016-04-21 01:36:00 -0700 (Thu, 21 Apr 2016)

EllapsedTime: 736.7 seconds

RetCode: 0

Status:  OK

CheckDir: debrowser.Rcheck

Warnings: 0

##############################################################################
##############################################################################
###
### Running command:
###
###   /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD check --no-vignettes --timings debrowser_0.99.2.tar.gz
###
##############################################################################
##############################################################################


* using log directory ‘/Users/biocbuild/bbs-3.3-bioc/meat/debrowser.Rcheck’
* using R version 3.3.0 beta (2016-04-06 r70435)
* 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 ‘0.99.2’
* 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 ... [25s/28s] 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’
getPCAexplained: no visible binding for global variable ‘PCs’
getPCAexplained: no visible binding for global variable ‘explained’
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 conds demodata explained fill.brush fillOpacity
  fillOpacity.hover key opacity 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 ... [18s/18s] OK
* checking for unstated dependencies in ‘tests’ ... OK
* checking tests ...
  Running ‘test-demo.R’ [1s/1s]
  Running ‘test-deseq.R’ [412s/421s]
  Running ‘test-null.R’ [13s/13s]
  Running ‘test-ui.R’ [13s/13s]
 [440s/449s] 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	0.001	0.001
addID	0.001	0.000	0.001
add_title_pos	0.291	0.007	0.421
all2all	0.256	0.003	0.279
applyFilters	0.001	0.000	0.001
clusterData	0.057	0.001	0.066
compareClust	0.001	0.000	0.000
deServer	0.011	0.002	0.017
deUI	0.091	0.008	0.177
getAfterLoadMsg	0.001	0.000	0.002
getColors	0.000	0.000	0.001
getCompSelection	0.007	0.000	0.008
getCondMsg	0	0	0
getConditionSelector	0.000	0.000	0.001
getCutOffSelection	0.005	0.000	0.006
getDataPrepPanel	0.000	0.000	0.001
getDomains	0.001	0.000	0.001
getDownloadSection	0.001	0.000	0.001
getEnrichDO	0.000	0.000	0.001
getEnrichGO	0.000	0.001	0.001
getEnrichKEGG	0.804	0.023	0.828
getGOLeftMenu	0.016	0.001	0.017
getGOPlots	0.000	0.000	0.001
getGeneList	0.467	0.002	0.469
getGeneSetData	0.001	0.000	0.001
getGoPanel	0.001	0.000	0.001
getHoverPlots	0.001	0.001	0.001
getInitialMenu	0.001	0.000	0.001
getLeftMenu	0.033	0.003	0.037
getLoadingMsg	0.002	0.000	0.003
getLogo	0.002	0.000	0.002
getMainPanel	0.001	0.000	0.001
getMainPanelPlots	0.000	0.000	0.001
getMean	0.001	0.000	0.000
getMergedComparison	0.001	0.000	0.001
getMostVariedList	0.001	0.000	0.001
getNormalizedMatrix	0.013	0.001	0.012
getPCAexplained	0.001	0.000	0.001
getPCselection	0.001	0.000	0.001
getProgramTitle	0.000	0.000	0.001
getQCLeftMenu	0.013	0.001	0.014
getQCPanel	0.000	0.000	0.001
getQCPlotArea	0.001	0.000	0.000
getQCPlots	0.001	0.000	0.001
getSampleNames	0.001	0.000	0.001
getSamples	0.001	0.000	0.000
getSelectedDatasetInput	0.001	0.000	0.001
getStartPlotsMsg	0.001	0.000	0.001
getStartupMsg	0.001	0.000	0.001
getTableStyle	0.001	0.000	0.001
getToolTipText	0.000	0.000	0.001
hideObj	0	0	0
link_brush	0.005	0.000	0.005
load_data	0.001	0.000	0.001
logSliderJScode	0.001	0.000	0.001
mainScatter	0.001	0.000	0.001
panel.cor	0.001	0.000	0.002
panel.hist	0.001	0.000	0.001
plot_pca	1.980	0.047	2.042
prepDESeqOutput	0.000	0.000	0.001
prepDataContainer	0.001	0.000	0.001
prepDataForQC	0.001	0.000	0.001
push	0.000	0.000	0.001
round_vals	0.001	0.000	0.001
runDESeq	0.001	0.000	0.001
runHeatmap	0.149	0.006	0.157
run_pca	0.778	0.057	0.837
saveQCPlot	0.000	0.000	0.001
scatterZoom	0.001	0.000	0.001
selectConditions	0.001	0.000	0.001
showObj	0.001	0.000	0.001
startDEBrowser	0.001	0.000	0.001
textareaInput	0.002	0.001	0.001
togglePanels	0.001	0.000	0.001
volcanoPlot	0.001	0.000	0.001
volcanoZoom	0.001	0.000	0.001