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BioC 3.5: CHECK report for debrowser on tokay2

This page was generated on 2017-08-16 13:25:32 -0400 (Wed, 16 Aug 2017).

Package 322/1382HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
debrowser 1.4.5
Alper Kucukural
Snapshot Date: 2017-08-15 17:17:57 -0400 (Tue, 15 Aug 2017)
URL: https://hedgehog.fhcrc.org/bioconductor/branches/RELEASE_3_5/madman/Rpacks/debrowser
Last Changed Rev: 131942 / Revision: 131943
Last Changed Date: 2017-08-15 14:50:57 -0400 (Tue, 15 Aug 2017)
malbec2 Linux (Ubuntu 16.04.1 LTS) / x86_64  NotNeeded  OK  OK YES, new version is higher than in internal repository
tokay2 Windows Server 2012 R2 Standard / x64  NotNeeded  OK [ OK ] OK YES, new version is higher than in internal repository
veracruz2 OS X 10.11.6 El Capitan / x86_64  NotNeeded  OK  OK  OK YES, new version is higher than in internal repository

Summary

Package: debrowser
Version: 1.4.5
Command: rm -rf debrowser.buildbin-libdir debrowser.Rcheck && mkdir debrowser.buildbin-libdir debrowser.Rcheck && C:\Users\biocbuild\bbs-3.5-bioc\R\bin\R.exe CMD INSTALL --build --merge-multiarch --library=debrowser.buildbin-libdir debrowser_1.4.5.tar.gz >debrowser.Rcheck\00install.out 2>&1 && cp debrowser.Rcheck\00install.out debrowser-install.out && C:\Users\biocbuild\bbs-3.5-bioc\R\bin\R.exe CMD check --library=debrowser.buildbin-libdir --install="check:debrowser-install.out" --force-multiarch --no-vignettes --timings debrowser_1.4.5.tar.gz
StartedAt: 2017-08-15 23:08:47 -0400 (Tue, 15 Aug 2017)
EndedAt: 2017-08-15 23:17:51 -0400 (Tue, 15 Aug 2017)
EllapsedTime: 543.6 seconds
RetCode: 0
Status:  OK  
CheckDir: debrowser.Rcheck
Warnings: 0

Command output

##############################################################################
##############################################################################
###
### Running command:
###
###   rm -rf debrowser.buildbin-libdir debrowser.Rcheck && mkdir debrowser.buildbin-libdir debrowser.Rcheck && C:\Users\biocbuild\bbs-3.5-bioc\R\bin\R.exe CMD INSTALL --build --merge-multiarch --library=debrowser.buildbin-libdir debrowser_1.4.5.tar.gz >debrowser.Rcheck\00install.out 2>&1 && cp debrowser.Rcheck\00install.out debrowser-install.out  &&  C:\Users\biocbuild\bbs-3.5-bioc\R\bin\R.exe CMD check --library=debrowser.buildbin-libdir --install="check:debrowser-install.out" --force-multiarch --no-vignettes --timings debrowser_1.4.5.tar.gz
###
##############################################################################
##############################################################################


* using log directory 'C:/Users/biocbuild/bbs-3.5-bioc/meat/debrowser.Rcheck'
* using R version 3.4.1 (2017-06-30)
* using platform: x86_64-w64-mingw32 (64-bit)
* using session charset: ISO8859-1
* using option '--no-vignettes'
* checking for file 'debrowser/DESCRIPTION' ... OK
* checking extension type ... Package
* this is package 'debrowser' version '1.4.5'
* 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 whether package 'debrowser' can be installed ... OK
* checking installed package size ... NOTE
  installed size is  8.8Mb
  sub-directories of 1Mb or more:
    doc       6.3Mb
    extdata   2.1Mb
* 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
* loading checks for arch 'i386'
** 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
* loading checks for arch 'x64'
** 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'
bookmarkServer: no visible binding for global variable 'NUL'
bookmarkServer : <anonymous>: no visible global function definition for
  'updateStore'
deServer: no visible binding for global variable 'debrowser'
deServer: no visible binding for global variable 'googleAuth'
deUI: no visible global function definition for 'initStore'
deUI: no visible global function definition for 'googleAuthUI'
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'
getJsonObj: no visible global function definition for 'with_shiny'
getJsonObj: no visible binding for global variable 'get_user_info'
getJsonObj: no visible global function definition for 'updateStore'
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 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'
startDEBrowser: no visible binding for global variable
  '.startdebrowser.called'
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:
  .startdebrowser.called := NUL align baseline biocLite conds debrowser
  demodata fill fill.brush fillOpacity fillOpacity.hover fit fontSize
  get_user_info googleAuth googleAuthUI initStore key opacity samples
  searched size size.hover stroke updateStore with_shiny
* 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 ...
** running examples for arch 'i386' ... OK
Examples with CPU or elapsed time > 5s
     user system elapsed
deUI 9.15   1.41    35.3
** running examples for arch 'x64' ... OK
* checking for unstated dependencies in 'tests' ... OK
* checking tests ...
** running tests for arch 'i386' ...
  Running 'test-demo.R'
  Running 'test-deseq.R'
  Running 'test-null.R'
  Running 'test-ui.R'
 OK
** running tests for arch 'x64' ...
  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
  'C:/Users/biocbuild/bbs-3.5-bioc/meat/debrowser.Rcheck/00check.log'
for details.


debrowser.Rcheck/00install.out:


install for i386

* installing *source* package 'debrowser' ...
** R
** inst
** preparing package for lazy loading
No methods found in "S4Vectors" for requests: rowMeans
No methods found in "S4Vectors" for requests: rowSums
** help
*** installing help indices
** building package indices
** installing vignettes
** testing if installed package can be loaded
No methods found in "S4Vectors" for requests: rowMeans
No methods found in "S4Vectors" for requests: rowSums

install for x64

* installing *source* package 'debrowser' ...
** testing if installed package can be loaded
No methods found in "S4Vectors" for requests: rowMeans
No methods found in "S4Vectors" for requests: rowSums
* MD5 sums
packaged installation of 'debrowser' as debrowser_1.4.5.zip
* DONE (debrowser)

debrowser.Rcheck/examples_i386/debrowser-Ex.timings:

nameusersystemelapsed
MAPlot000
MAZoom0.020.000.01
actionButton0.050.000.05
addDataCols000
addID000
add_title_pos0.810.020.84
all2all0.140.000.14
applyFilters000
applyFiltersToMergedComparison000
bookmarkServer000
bookmarkUI000
clusterData000
compareClust000
copy2newDirectory000
correctBatchEffect000
deServer0.010.000.02
deUI 9.15 1.4135.30
drawPCAExplained000
getAfterLoadMsg000
getColorShapeSelection000
getColors000
getCompSelection0.030.000.03
getCondMsg000
getConditionSelector000
getConditionSelectorFromMeta000
getCutOffSelection0.090.000.09
getDataForTables000
getDataPrepPanel000
getDensityPlot000
getDomains000
getDown000
getDownloadSection000
getEnrichDO000
getEnrichGO000
getEnrichKEGG000
getGOLeftMenu0.120.000.12
getGOPlots000
getGeneList0.830.150.98
getGeneSetData000
getGoPanel0.010.000.02
getHelpButton000
getHoverPlots000
getIQRPlot000
getInitialMenu000
getIntHeatmap000
getIntHeatmapVis000
getJsonObj000
getLeftMenu000
getLegendSelect0.020.000.01
getLoadingMsg000
getLogo000
getMainPanel000
getMainPanelPlots0.010.000.02
getMainPlotsLeftMenu000
getMean000
getMergedComparison000
getMethodDetails000
getMostVariedList000
getNormalizedMatrix0.070.020.08
getOrganism000
getOrganismBox000
getOrganismPathway000
getPCAexplained1.570.031.61
getPCselection000
getProgramTitle000
getQCLeftMenu000
getQCPanel0.050.000.08
getQCPlots000
getQCReplot000
getSampleNames000
getSamples000
getSearchData000
getSelHeat000
getSelectInputBox000
getSelectedCols000
getSelectedDatasetInput000
getShapeColor000
getStartPlotsMsg000
getStartupMsg0.010.000.01
getTableStyle000
getTextOnOff000
getToolTipPCA000
getToolTipText000
getUp000
getUpDown000
get_state_id000
hideObj000
installpack000
link_brush0.020.000.02
load_data000
loadpack0.030.040.06
loadpacks0.230.360.59
logSliderJScode000
mainScatter000
panel.cor000
panel.hist0.020.000.02
plot_pca1.150.011.17
prepAddQCPlots000
prepDEOutput000
prepDataContainer000
prepDataForQC0.020.000.02
push000
readMetaData000
removeBookmark000
removeCols000
round_vals000
runBayseq000
runDE000
runDESeq000
runDESeq2000
runEdgeR000
runHeatmap0.340.000.34
runLimma000
run_pca1.050.001.05
saveQCPlot000
scatterZoom000
selectBatchEffect000
selectConditions000
selectedInput000
setFilterParams000
showObj000
startDEBrowser000
textareaInput000
togglePanels000
volcanoPlot000
volcanoZoom000

debrowser.Rcheck/examples_x64/debrowser-Ex.timings:

nameusersystemelapsed
MAPlot000
MAZoom000
actionButton0.060.000.06
addDataCols000
addID000
add_title_pos1.130.001.16
all2all0.170.000.17
applyFilters000
applyFiltersToMergedComparison000
bookmarkServer000
bookmarkUI000
clusterData000
compareClust000
copy2newDirectory0.010.000.01
correctBatchEffect000
deServer000
deUI0.710.322.08
drawPCAExplained000
getAfterLoadMsg000
getColorShapeSelection000
getColors000
getCompSelection0.050.000.04
getCondMsg000
getConditionSelector000
getConditionSelectorFromMeta000
getCutOffSelection0.220.000.22
getDataForTables000
getDataPrepPanel000
getDensityPlot000
getDomains000
getDown000
getDownloadSection000
getEnrichDO000
getEnrichGO000
getEnrichKEGG000
getGOLeftMenu0.130.000.12
getGOPlots000
getGeneList1.030.111.14
getGeneSetData0.010.000.02
getGoPanel000
getHelpButton000
getHoverPlots000
getIQRPlot000
getInitialMenu000
getIntHeatmap000
getIntHeatmapVis000
getJsonObj000
getLeftMenu000
getLegendSelect0.020.000.02
getLoadingMsg000
getLogo000
getMainPanel000
getMainPanelPlots000
getMainPlotsLeftMenu000
getMean000
getMergedComparison000
getMethodDetails000
getMostVariedList000
getNormalizedMatrix0.060.000.06
getOrganism000
getOrganismBox000
getOrganismPathway000
getPCAexplained2.510.032.55
getPCselection000
getProgramTitle000
getQCLeftMenu000
getQCPanel0.080.020.10
getQCPlots000
getQCReplot000
getSampleNames000
getSamples000
getSearchData000
getSelHeat000
getSelectInputBox000
getSelectedCols000
getSelectedDatasetInput000
getShapeColor000
getStartPlotsMsg000
getStartupMsg0.020.000.02
getTableStyle000
getTextOnOff000
getToolTipPCA0.010.000.01
getToolTipText000
getUp000
getUpDown000
get_state_id000
hideObj000
installpack000
link_brush000
load_data000
loadpack0.030.050.08
loadpacks0.240.310.54
logSliderJScode000
mainScatter000
panel.cor000
panel.hist000
plot_pca1.430.011.46
prepAddQCPlots000
prepDEOutput000
prepDataContainer000
prepDataForQC000
push000
readMetaData000
removeBookmark000
removeCols000
round_vals000
runBayseq000
runDE000
runDESeq000
runDESeq2000
runEdgeR000
runHeatmap0.340.020.36
runLimma000
run_pca1.210.001.20
saveQCPlot000
scatterZoom000
selectBatchEffect000
selectConditions000
selectedInput000
setFilterParams000
showObj000
startDEBrowser000
textareaInput000
togglePanels000
volcanoPlot000
volcanoZoom000