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 | |
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### Running command:
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### /home/biocbuild/bbs-3.4-bioc/R/bin/R CMD check --no-vignettes --timings debrowser_1.3.11.tar.gz
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* using log directory ‘/home/biocbuild/bbs-3.4-bioc/meat/debrowser.Rcheck’
* using R version 3.3.3 (2017-03-06)
* 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 ‘1.3.11’
* 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 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’
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 ... OK
Examples with CPU or elapsed time > 5s
user system elapsed
deUI 9.704 0.592 12.96
* 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: 3 NOTEs
See
‘/home/biocbuild/bbs-3.4-bioc/meat/debrowser.Rcheck/00check.log’
for details.