Package: AUCell

Version: 1.6.1

Command: /home/biocbuild/bbs-3.9-bioc/R/bin/R CMD check --install=check:AUCell.install-out.txt --library=/home/biocbuild/bbs-3.9-bioc/R/library --no-vignettes --timings AUCell_1.6.1.tar.gz

StartedAt: 2019-10-15 23:52:30 -0400 (Tue, 15 Oct 2019)

EndedAt: 2019-10-15 23:58:53 -0400 (Tue, 15 Oct 2019)

EllapsedTime: 382.8 seconds

RetCode: 0

Status:  OK

CheckDir: AUCell.Rcheck

Warnings: 0

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### Running command:
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###   /home/biocbuild/bbs-3.9-bioc/R/bin/R CMD check --install=check:AUCell.install-out.txt --library=/home/biocbuild/bbs-3.9-bioc/R/library --no-vignettes --timings AUCell_1.6.1.tar.gz
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* using log directory ‘/home/biocbuild/bbs-3.9-bioc/meat/AUCell.Rcheck’
* using R version 3.6.1 (2019-07-05)
* using platform: x86_64-pc-linux-gnu (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 ‘1.6.1’
* 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 ‘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 : : no visible global function
  definition for ‘%>%’
AUCell_createViewerApp : : no visible binding for global
  variable ‘tsne1’
AUCell_createViewerApp : : no visible binding for global
  variable ‘tsne2’
AUCell_createViewerApp : : 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_calcAUC           99.594  0.483  17.000
AUCell_buildRankings     97.014  0.407  15.595
AUCell_exploreThresholds 95.709  0.482  18.642
plotTsne_cellProps       90.042  0.426  15.478
AUCell_plotHist          83.377  0.294  12.359
aucellResults-class      83.065  0.289  12.733
AUCell_createViewerApp   79.106  0.251  11.424
AUCell_plotTSNE          47.337  0.137   6.538
* 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: 2 NOTEs
See
  ‘/home/biocbuild/bbs-3.9-bioc/meat/AUCell.Rcheck/00check.log’
for details.

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### Running command:
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###   /home/biocbuild/bbs-3.9-bioc/R/bin/R CMD INSTALL AUCell
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* installing to library ‘/home/biocbuild/bbs-3.9-bioc/R/library’
* installing *source* package ‘AUCell’ ...
** using staged installation
** 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 from temporary location
** testing if installed package can be loaded from final location
** testing if installed package keeps a record of temporary installation path
* DONE (AUCell)

R version 3.6.1 (2019-07-05) -- "Action of the Toes"
Copyright (C) 2019 The R Foundation for Statistical Computing
Platform: x86_64-pc-linux-gnu (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% 
   3    5    6    7   10   16 
 min   1%   5%  10%  50% 100% 
   3    5    6    7   10   16 
══ testthat results  ═══════════════════════════════════════════════════════════
[ OK: 39 | SKIPPED: 0 | WARNINGS: 0 | FAILED: 0 ]
> 
> proc.time()
   user  system elapsed 
611.230   3.230 111.745 

name	user	system	elapsed
AUCell_buildRankings	97.014	0.407	15.595
AUCell_calcAUC	99.594	0.483	17.000
AUCell_createViewerApp	79.106	0.251	11.424
AUCell_exploreThresholds	95.709	0.482	18.642
AUCell_plotHist	83.377	0.294	12.359
AUCell_plotTSNE	47.337	0.137	6.538
GeneSet-methods	0.128	0.004	0.132
aucellResults-class	83.065	0.289	12.733
orderAUC	0	0	0
plotGeneCount	0.003	0.000	0.004
plotTsne_cellProps	90.042	0.426	15.478
updateAucellResults	0.036	0.000	0.036