BioC 3.4: CHECK report for debrowser on tokay1
This page was generated on 2017-04-15 16:20:53 -0400 (Sat, 15 Apr 2017).
debrowser 1.3.11 Alper Kucukural
Snapshot Date: 2017-04-14 17:17:13 -0400 (Fri, 14 Apr 2017) | URL: https://hedgehog.fhcrc.org/bioconductor/branches/RELEASE_3_4/madman/Rpacks/debrowser | Last Changed Rev: 128388 / Revision: 128728 | Last Changed Date: 2017-04-08 15:06:08 -0400 (Sat, 08 Apr 2017) |
| malbec1 | Linux (Ubuntu 16.04.1 LTS) / x86_64 | NotNeeded | OK | OK | |  |
tokay1 | Windows Server 2012 R2 Standard / x64 | NotNeeded | OK | [ OK ] | OK |  |
morelia | Mac OS X Mavericks (10.9.5) / x86_64 | NotNeeded | OK | OK | OK |  |
Summary
Package: debrowser
|
Version: 1.3.11
|
Command: rm -rf debrowser.buildbin-libdir debrowser.Rcheck && mkdir debrowser.buildbin-libdir debrowser.Rcheck && C:\Users\biocbuild\bbs-3.4-bioc\R\bin\R.exe CMD INSTALL --build --merge-multiarch --library=debrowser.buildbin-libdir debrowser_1.3.11.tar.gz >debrowser.Rcheck\00install.out 2>&1 && cp debrowser.Rcheck\00install.out debrowser-install.out && C:\Users\biocbuild\bbs-3.4-bioc\R\bin\R.exe CMD check --library=debrowser.buildbin-libdir --install="check:debrowser-install.out" --force-multiarch --no-vignettes --timings debrowser_1.3.11.tar.gz
|
StartedAt: 2017-04-14 21:51:55 -0400 (Fri, 14 Apr 2017)
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EndedAt: 2017-04-14 21:59:34 -0400 (Fri, 14 Apr 2017)
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EllapsedTime: 459.4 seconds
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RetCode: 0
|
Status: OK
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CheckDir: debrowser.Rcheck
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Warnings: 0
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Command output
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###
### Running command:
###
### rm -rf debrowser.buildbin-libdir debrowser.Rcheck && mkdir debrowser.buildbin-libdir debrowser.Rcheck && C:\Users\biocbuild\bbs-3.4-bioc\R\bin\R.exe CMD INSTALL --build --merge-multiarch --library=debrowser.buildbin-libdir debrowser_1.3.11.tar.gz >debrowser.Rcheck\00install.out 2>&1 && cp debrowser.Rcheck\00install.out debrowser-install.out && C:\Users\biocbuild\bbs-3.4-bioc\R\bin\R.exe CMD check --library=debrowser.buildbin-libdir --install="check:debrowser-install.out" --force-multiarch --no-vignettes --timings debrowser_1.3.11.tar.gz
###
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* using log directory 'C:/Users/biocbuild/bbs-3.4-bioc/meat/debrowser.Rcheck'
* using R version 3.3.3 (2017-03-06)
* 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 '1.3.11'
* 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 ... 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
* 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 7.06 1.03 18.32
** 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 ... 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: 3 NOTEs
See
'C:/Users/biocbuild/bbs-3.4-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
** help
*** installing help indices
** building package indices
** installing vignettes
** testing if installed package can be loaded
install for x64
* installing *source* package 'debrowser' ...
** testing if installed package can be loaded
* MD5 sums
packaged installation of 'debrowser' as debrowser_1.3.11.zip
* DONE (debrowser)
debrowser.Rcheck/examples_i386/debrowser-Ex.timings:
name | user | system | elapsed
|
MAPlot | 0 | 0 | 0 |
|
MAZoom | 0 | 0 | 0 |
|
actionButton | 0 | 0 | 0 |
|
addDataCols | 0.02 | 0.00 | 0.02 |
|
addID | 0 | 0 | 0 |
|
add_title_pos | 0.23 | 0.02 | 0.25 |
|
all2all | 0.17 | 0.01 | 0.19 |
|
applyFilters | 0.02 | 0.00 | 0.01 |
|
applyFiltersToMergedComparison | 0 | 0 | 0 |
|
bookmarkServer | 0 | 0 | 0 |
|
bookmarkUI | 0 | 0 | 0 |
|
clusterData | 0 | 0 | 0 |
|
compareClust | 0 | 0 | 0 |
|
copy2newDirectory | 0.02 | 0.00 | 0.02 |
|
correctBatchEffect | 0 | 0 | 0 |
|
deServer | 0 | 0 | 0 |
|
deUI | 7.06 | 1.03 | 18.32 |
|
drawPCAExplained | 0 | 0 | 0 |
|
getAfterLoadMsg | 0 | 0 | 0 |
|
getColorShapeSelection | 0 | 0 | 0 |
|
getColors | 0 | 0 | 0 |
|
getCompSelection | 0 | 0 | 0 |
|
getCondMsg | 0 | 0 | 0 |
|
getConditionSelector | 0 | 0 | 0 |
|
getConditionSelectorFromMeta | 0 | 0 | 0 |
|
getCutOffSelection | 0 | 0 | 0 |
|
getDataForTables | 0 | 0 | 0 |
|
getDataPrepPanel | 0 | 0 | 0 |
|
getDensityPlot | 0 | 0 | 0 |
|
getDomains | 0 | 0 | 0 |
|
getDown | 0 | 0 | 0 |
|
getDownloadSection | 0 | 0 | 0 |
|
getEnrichDO | 0 | 0 | 0 |
|
getEnrichGO | 0 | 0 | 0 |
|
getEnrichKEGG | 0 | 0 | 0 |
|
getGOLeftMenu | 0.02 | 0.00 | 0.01 |
|
getGOPlots | 0 | 0 | 0 |
|
getGeneList | 0.80 | 0.13 | 0.92 |
|
getGeneSetData | 0 | 0 | 0 |
|
getGoPanel | 0 | 0 | 0 |
|
getHelpButton | 0 | 0 | 0 |
|
getHoverPlots | 0 | 0 | 0 |
|
getIQRPlot | 0 | 0 | 0 |
|
getInitialMenu | 0 | 0 | 0 |
|
getIntHeatmap | 0 | 0 | 0 |
|
getIntHeatmapVis | 0 | 0 | 0 |
|
getJsonObj | 0 | 0 | 0 |
|
getLeftMenu | 0 | 0 | 0 |
|
getLegendSelect | 0.02 | 0.00 | 0.02 |
|
getLoadingMsg | 0 | 0 | 0 |
|
getLogo | 0 | 0 | 0 |
|
getMainPanel | 0 | 0 | 0 |
|
getMainPanelPlots | 0 | 0 | 0 |
|
getMainPlotsLeftMenu | 0 | 0 | 0 |
|
getMean | 0 | 0 | 0 |
|
getMergedComparison | 0 | 0 | 0 |
|
getMethodDetails | 0 | 0 | 0 |
|
getMostVariedList | 0 | 0 | 0 |
|
getNormalizedMatrix | 0.02 | 0.00 | 0.02 |
|
getOrganism | 0 | 0 | 0 |
|
getOrganismBox | 0 | 0 | 0 |
|
getOrganismPathway | 0 | 0 | 0 |
|
getPCAexplained | 2.06 | 0.01 | 2.07 |
|
getPCselection | 0 | 0 | 0 |
|
getProgramTitle | 0 | 0 | 0 |
|
getQCLeftMenu | 0 | 0 | 0 |
|
getQCPanel | 0.03 | 0.00 | 0.05 |
|
getQCPlots | 0 | 0 | 0 |
|
getQCReplot | 0 | 0 | 0 |
|
getSampleNames | 0 | 0 | 0 |
|
getSamples | 0 | 0 | 0 |
|
getSearchData | 0 | 0 | 0 |
|
getSelHeat | 0 | 0 | 0 |
|
getSelectInputBox | 0 | 0 | 0 |
|
getSelectedCols | 0 | 0 | 0 |
|
getSelectedDatasetInput | 0 | 0 | 0 |
|
getShapeColor | 0 | 0 | 0 |
|
getStartPlotsMsg | 0 | 0 | 0 |
|
getStartupMsg | 0 | 0 | 0 |
|
getTableStyle | 0 | 0 | 0 |
|
getTextOnOff | 0 | 0 | 0 |
|
getToolTipPCA | 0 | 0 | 0 |
|
getToolTipText | 0 | 0 | 0 |
|
getUp | 0 | 0 | 0 |
|
getUpDown | 0 | 0 | 0 |
|
get_state_id | 0 | 0 | 0 |
|
hideObj | 0 | 0 | 0 |
|
installpack | 0 | 0 | 0 |
|
link_brush | 0 | 0 | 0 |
|
load_data | 0 | 0 | 0 |
|
loadpack | 0.02 | 0.05 | 0.07 |
|
loadpacks | 0.13 | 0.27 | 0.39 |
|
logSliderJScode | 0 | 0 | 0 |
|
mainScatter | 0 | 0 | 0 |
|
panel.cor | 0 | 0 | 0 |
|
panel.hist | 0 | 0 | 0 |
|
plot_pca | 0.98 | 0.03 | 1.01 |
|
prepAddQCPlots | 0 | 0 | 0 |
|
prepDEOutput | 0.02 | 0.00 | 0.02 |
|
prepDataContainer | 0 | 0 | 0 |
|
prepDataForQC | 0 | 0 | 0 |
|
push | 0 | 0 | 0 |
|
readMetaData | 0 | 0 | 0 |
|
removeBookmark | 0 | 0 | 0 |
|
removeCols | 0 | 0 | 0 |
|
round_vals | 0 | 0 | 0 |
|
runBayseq | 0 | 0 | 0 |
|
runDE | 0 | 0 | 0 |
|
runDESeq | 0 | 0 | 0 |
|
runDESeq2 | 0 | 0 | 0 |
|
runEdgeR | 0.01 | 0.00 | 0.01 |
|
runHeatmap | 0.13 | 0.00 | 0.13 |
|
runLimma | 0 | 0 | 0 |
|
run_pca | 1.07 | 0.05 | 1.12 |
|
saveQCPlot | 0 | 0 | 0 |
|
scatterZoom | 0 | 0 | 0 |
|
selectBatchEffect | 0 | 0 | 0 |
|
selectConditions | 0 | 0 | 0 |
|
selectedInput | 0 | 0 | 0 |
|
setFilterParams | 0 | 0 | 0 |
|
showObj | 0 | 0 | 0 |
|
startDEBrowser | 0 | 0 | 0 |
|
textareaInput | 0 | 0 | 0 |
|
togglePanels | 0 | 0 | 0 |
|
volcanoPlot | 0 | 0 | 0 |
|
volcanoZoom | 0 | 0 | 0 |
|
debrowser.Rcheck/examples_x64/debrowser-Ex.timings:
name | user | system | elapsed
|
MAPlot | 0 | 0 | 0 |
|
MAZoom | 0 | 0 | 0 |
|
actionButton | 0 | 0 | 0 |
|
addDataCols | 0 | 0 | 0 |
|
addID | 0 | 0 | 0 |
|
add_title_pos | 0.21 | 0.00 | 0.21 |
|
all2all | 0.12 | 0.00 | 0.12 |
|
applyFilters | 0 | 0 | 0 |
|
applyFiltersToMergedComparison | 0 | 0 | 0 |
|
bookmarkServer | 0 | 0 | 0 |
|
bookmarkUI | 0 | 0 | 0 |
|
clusterData | 0 | 0 | 0 |
|
compareClust | 0 | 0 | 0 |
|
copy2newDirectory | 0 | 0 | 0 |
|
correctBatchEffect | 0 | 0 | 0 |
|
deServer | 0.01 | 0.00 | 0.01 |
|
deUI | 0.24 | 0.21 | 1.22 |
|
drawPCAExplained | 0 | 0 | 0 |
|
getAfterLoadMsg | 0 | 0 | 0 |
|
getColorShapeSelection | 0 | 0 | 0 |
|
getColors | 0 | 0 | 0 |
|
getCompSelection | 0.02 | 0.00 | 0.01 |
|
getCondMsg | 0 | 0 | 0 |
|
getConditionSelector | 0 | 0 | 0 |
|
getConditionSelectorFromMeta | 0 | 0 | 0 |
|
getCutOffSelection | 0 | 0 | 0 |
|
getDataForTables | 0 | 0 | 0 |
|
getDataPrepPanel | 0 | 0 | 0 |
|
getDensityPlot | 0 | 0 | 0 |
|
getDomains | 0 | 0 | 0 |
|
getDown | 0 | 0 | 0 |
|
getDownloadSection | 0 | 0 | 0 |
|
getEnrichDO | 0 | 0 | 0 |
|
getEnrichGO | 0 | 0 | 0 |
|
getEnrichKEGG | 0 | 0 | 0 |
|
getGOLeftMenu | 0.01 | 0.02 | 0.03 |
|
getGOPlots | 0 | 0 | 0 |
|
getGeneList | 0.64 | 0.12 | 0.77 |
|
getGeneSetData | 0 | 0 | 0 |
|
getGoPanel | 0 | 0 | 0 |
|
getHelpButton | 0 | 0 | 0 |
|
getHoverPlots | 0 | 0 | 0 |
|
getIQRPlot | 0 | 0 | 0 |
|
getInitialMenu | 0 | 0 | 0 |
|
getIntHeatmap | 0 | 0 | 0 |
|
getIntHeatmapVis | 0 | 0 | 0 |
|
getJsonObj | 0 | 0 | 0 |
|
getLeftMenu | 0 | 0 | 0 |
|
getLegendSelect | 0 | 0 | 0 |
|
getLoadingMsg | 0 | 0 | 0 |
|
getLogo | 0 | 0 | 0 |
|
getMainPanel | 0 | 0 | 0 |
|
getMainPanelPlots | 0 | 0 | 0 |
|
getMainPlotsLeftMenu | 0 | 0 | 0 |
|
getMean | 0 | 0 | 0 |
|
getMergedComparison | 0 | 0 | 0 |
|
getMethodDetails | 0 | 0 | 0 |
|
getMostVariedList | 0 | 0 | 0 |
|
getNormalizedMatrix | 0.05 | 0.00 | 0.05 |
|
getOrganism | 0 | 0 | 0 |
|
getOrganismBox | 0.01 | 0.00 | 0.02 |
|
getOrganismPathway | 0 | 0 | 0 |
|
getPCAexplained | 1.74 | 0.05 | 1.78 |
|
getPCselection | 0 | 0 | 0 |
|
getProgramTitle | 0 | 0 | 0 |
|
getQCLeftMenu | 0 | 0 | 0 |
|
getQCPanel | 0.03 | 0.00 | 0.03 |
|
getQCPlots | 0 | 0 | 0 |
|
getQCReplot | 0 | 0 | 0 |
|
getSampleNames | 0 | 0 | 0 |
|
getSamples | 0 | 0 | 0 |
|
getSearchData | 0 | 0 | 0 |
|
getSelHeat | 0 | 0 | 0 |
|
getSelectInputBox | 0.01 | 0.00 | 0.01 |
|
getSelectedCols | 0 | 0 | 0 |
|
getSelectedDatasetInput | 0 | 0 | 0 |
|
getShapeColor | 0 | 0 | 0 |
|
getStartPlotsMsg | 0 | 0 | 0 |
|
getStartupMsg | 0 | 0 | 0 |
|
getTableStyle | 0 | 0 | 0 |
|
getTextOnOff | 0.02 | 0.00 | 0.02 |
|
getToolTipPCA | 0 | 0 | 0 |
|
getToolTipText | 0 | 0 | 0 |
|
getUp | 0 | 0 | 0 |
|
getUpDown | 0 | 0 | 0 |
|
get_state_id | 0 | 0 | 0 |
|
hideObj | 0 | 0 | 0 |
|
installpack | 0 | 0 | 0 |
|
link_brush | 0 | 0 | 0 |
|
load_data | 0 | 0 | 0 |
|
loadpack | 0.00 | 0.05 | 0.04 |
|
loadpacks | 0.14 | 0.17 | 0.31 |
|
logSliderJScode | 0 | 0 | 0 |
|
mainScatter | 0 | 0 | 0 |
|
panel.cor | 0.02 | 0.00 | 0.02 |
|
panel.hist | 0 | 0 | 0 |
|
plot_pca | 1.09 | 0.02 | 1.11 |
|
prepAddQCPlots | 0 | 0 | 0 |
|
prepDEOutput | 0 | 0 | 0 |
|
prepDataContainer | 0 | 0 | 0 |
|
prepDataForQC | 0 | 0 | 0 |
|
push | 0 | 0 | 0 |
|
readMetaData | 0 | 0 | 0 |
|
removeBookmark | 0 | 0 | 0 |
|
removeCols | 0 | 0 | 0 |
|
round_vals | 0 | 0 | 0 |
|
runBayseq | 0 | 0 | 0 |
|
runDE | 0 | 0 | 0 |
|
runDESeq | 0 | 0 | 0 |
|
runDESeq2 | 0 | 0 | 0 |
|
runEdgeR | 0 | 0 | 0 |
|
runHeatmap | 0.14 | 0.00 | 0.14 |
|
runLimma | 0 | 0 | 0 |
|
run_pca | 1.17 | 0.00 | 1.17 |
|
saveQCPlot | 0 | 0 | 0 |
|
scatterZoom | 0 | 0 | 0 |
|
selectBatchEffect | 0 | 0 | 0 |
|
selectConditions | 0 | 0 | 0 |
|
selectedInput | 0 | 0 | 0 |
|
setFilterParams | 0 | 0 | 0 |
|
showObj | 0 | 0 | 0 |
|
startDEBrowser | 0 | 0 | 0 |
|
textareaInput | 0 | 0 | 0 |
|
togglePanels | 0 | 0 | 0 |
|
volcanoPlot | 0 | 0 | 0 |
|
volcanoZoom | 0 | 0 | 0 |
|