Package: AUCell

Version: 1.5.5

Command: /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD check --install=check:AUCell.install-out.txt --library=/Library/Frameworks/R.framework/Versions/Current/Resources/library --no-vignettes --timings AUCell_1.5.5.tar.gz

StartedAt: 2019-04-08 23:19:30 -0400 (Mon, 08 Apr 2019)

EndedAt: 2019-04-08 23:22:59 -0400 (Mon, 08 Apr 2019)

EllapsedTime: 209.9 seconds

RetCode: 0

Status:  OK

CheckDir: AUCell.Rcheck

Warnings: 0

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### Running command:
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###   /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD check --install=check:AUCell.install-out.txt --library=/Library/Frameworks/R.framework/Versions/Current/Resources/library --no-vignettes --timings AUCell_1.5.5.tar.gz
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* using log directory ‘/Users/biocbuild/bbs-3.9-bioc/meat/AUCell.Rcheck’
* using R Under development (unstable) (2018-11-27 r75683)
* using platform: x86_64-apple-darwin15.6.0 (64-bit)
* using session charset: UTF-8
* using option ‘--no-vignettes’
* checking for file ‘AUCell/DESCRIPTION’ ... OK
* checking extension type ... Package
* this is package ‘AUCell’ version ‘1.5.5’
* checking package namespace information ... OK
* checking package dependencies ... NOTE
Package which this enhances but not available for checking: ‘doMC’
* 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 ‘AUCell’ 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 ... 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 dependencies in R code ... NOTE
'library' or 'require' call to ‘rbokeh’ in package code.
  Please use :: or requireNamespace() instead.
  See section 'Suggested packages' in the 'Writing R Extensions' manual.
* checking S3 generic/method consistency ... OK
* checking replacement functions ... OK
* checking foreign function calls ... OK
* checking R code for possible problems ... NOTE
AUCell_createViewerApp : <anonymous>: no visible global function
  definition for ‘%>%’
AUCell_createViewerApp : <anonymous>: no visible binding for global
  variable ‘tsne1’
AUCell_createViewerApp : <anonymous>: no visible binding for global
  variable ‘tsne2’
AUCell_createViewerApp : <anonymous>: no visible binding for global
  variable ‘cell’
orderAUC: no visible global function definition for ‘as.dist’
orderAUC: no visible global function definition for ‘cor’
orderAUC: no visible global function definition for ‘hclust’
Undefined global functions or variables:
  %>% as.dist cell cor hclust tsne1 tsne2
Consider adding
  importFrom("stats", "as.dist", "cor", "hclust")
to your NAMESPACE file.
* 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 files in ‘vignettes’ ... OK
* checking examples ... OK
Examples with CPU or elapsed time > 5s
                          user system elapsed
AUCell_exploreThresholds 8.600  4.606   4.453
AUCell_calcAUC           7.573  4.228   2.585
AUCell_createViewerApp   6.749  4.556   2.138
AUCell_buildRankings     5.935  4.563   1.356
aucellResults-class      5.916  4.442   1.375
plotTsne_cellProps       6.023  4.163   1.508
AUCell_plotHist          5.606  4.216   1.265
AUCell_plotTSNE          6.140  3.646   1.497
* checking for unstated dependencies in ‘tests’ ... OK
* checking tests ...
  Running ‘testthat.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: 3 NOTEs
See
  ‘/Users/biocbuild/bbs-3.9-bioc/meat/AUCell.Rcheck/00check.log’
for details.

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### Running command:
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###   /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD INSTALL AUCell
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* installing to library ‘/Library/Frameworks/R.framework/Versions/3.6/Resources/library’
* installing *source* package ‘AUCell’ ...
** R
** inst
** byte-compile and prepare package for lazy loading
** help
*** installing help indices
** building package indices
** installing vignettes
** testing if installed package can be loaded
* DONE (AUCell)

R Under development (unstable) (2018-11-27 r75683) -- "Unsuffered Consequences"
Copyright (C) 2018 The R Foundation for Statistical Computing
Platform: x86_64-apple-darwin15.6.0 (64-bit)

R is free software and comes with ABSOLUTELY NO WARRANTY.
You are welcome to redistribute it under certain conditions.
Type 'license()' or 'licence()' for distribution details.

R is a collaborative project with many contributors.
Type 'contributors()' for more information and
'citation()' on how to cite R or R packages in publications.

Type 'demo()' for some demos, 'help()' for on-line help, or
'help.start()' for an HTML browser interface to help.
Type 'q()' to quit R.

> library(testthat)
> library(AUCell)
> 
> test_check("AUCell")
 min   1%   5%  10%  50% 100% 
   4    5    6    7   10   15 
 min   1%   5%  10%  50% 100% 
   4    5    6    7   10   15 
══ testthat results  ═══════════════════════════════════════════════════════════
OK: 39 SKIPPED: 0 FAILED: 0
> 
> proc.time()
   user  system elapsed 
 54.674  32.173  22.097 

name	user	system	elapsed
AUCell_buildRankings	5.935	4.563	1.356
AUCell_calcAUC	7.573	4.228	2.585
AUCell_createViewerApp	6.749	4.556	2.138
AUCell_exploreThresholds	8.600	4.606	4.453
AUCell_plotHist	5.606	4.216	1.265
AUCell_plotTSNE	6.140	3.646	1.497
GeneSet-methods	0.193	0.007	0.200
aucellResults-class	5.916	4.442	1.375
orderAUC	0.000	0.000	0.001
plotGeneCount	0.004	0.000	0.004
plotTsne_cellProps	6.023	4.163	1.508
updateAucellResults	0.029	0.000	0.030