BioC 3.4: CHECK report for debrowser on zin1
This page was generated on 2016-09-21 03:40:40 -0700 (Wed, 21 Sep 2016).
debrowser 1.1.9
Alper Kucukural
| Snapshot Date: 2016-09-19 19:15:14 -0700 (Mon, 19 Sep 2016) | | URL: https://hedgehog.fhcrc.org/bioconductor/trunk/madman/Rpacks/debrowser | | Last Changed Rev: 120388 / Revision: 121152 | | Last Changed Date: 2016-08-24 08:37:27 -0700 (Wed, 24 Aug 2016) |
| zin1 | Linux (Ubuntu 16.04 LTS) / x86_64 | NotNeeded | OK | [ OK ] | |  |
| moscato1 | Windows Server 2008 R2 Standard (64-bit) / x64 | NotNeeded | OK | OK | OK | |
| morelia | Mac OS X Mavericks (10.9.5) / x86_64 | NotNeeded | OK | OK | OK | |
Summary
| 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 |
Command output
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###
### Running command:
###
### /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.
debrowser.Rcheck/00install.out:
* 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)
debrowser.Rcheck/debrowser-Ex.timings:
| 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 |
|