debrowser 1.5.4
Alper Kucukural
| Snapshot Date: 2017-08-15 17:18:21 -0400 (Tue, 15 Aug 2017) | | URL: https://hedgehog.fhcrc.org/bioconductor/trunk/madman/Rpacks/debrowser | | Last Changed Rev: 131941 / Revision: 131943 | | Last Changed Date: 2017-08-15 14:49:45 -0400 (Tue, 15 Aug 2017) |
| malbec1 | Linux (Ubuntu 16.04.1 LTS) / x86_64 | NotNeeded | OK | [ OK ] | |  |
| tokay1 | Windows Server 2012 R2 Standard / x64 | NotNeeded | OK | OK | OK | |
| veracruz1 | OS X 10.11.6 El Capitan / x86_64 | NotNeeded | OK | OK | OK | |
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### Running command:
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### /home/biocbuild/bbs-3.6-bioc/R/bin/R CMD check --no-vignettes --timings debrowser_1.5.4.tar.gz
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* using log directory ‘/home/biocbuild/bbs-3.6-bioc/meat/debrowser.Rcheck’
* using R version 3.4.1 (2017-06-30)
* 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 ‘1.5.4’
* 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 ... 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
* 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 10.816 0.924 27.986
* 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-3.6-bioc/meat/debrowser.Rcheck/00check.log’
for details.
* installing *source* package ‘debrowser’ ...
** R
** inst
** preparing package for lazy loading
No methods found in "IRanges" for requests: ifelse
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 "IRanges" for requests: ifelse
No methods found in "S4Vectors" for requests: rowMeans
No methods found in "S4Vectors" for requests: rowSums
* DONE (debrowser)