Package: AUCell

Version: 1.9.0

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_1.9.0.tar.gz

StartedAt: 2020-01-16 01:52:40 -0500 (Thu, 16 Jan 2020)

EndedAt: 2020-01-16 01:58:15 -0500 (Thu, 16 Jan 2020)

EllapsedTime: 334.5 seconds

RetCode: 0

Status:  WARNINGS

CheckDir: AUCell.Rcheck

Warnings: 2

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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_1.9.0.tar.gz
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* using log directory ‘/Users/biocbuild/bbs-3.11-bioc/meat/AUCell.Rcheck’
* using R Under development (unstable) (2019-12-14 r77572)
* 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 ‘1.9.0’
* 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.
Namespace in Imports field not imported from: ‘BiocGenerics’
  All declared Imports should be used.
Unexported object imported by a ':::' call: ‘S4Vectors:::disableValidity’
  See the note in ?`:::` about the use of this operator.
* 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’
Undefined global functions or variables:
  %>% cell tsne1 tsne2
* checking Rd files ... OK
* checking Rd metadata ... OK
* checking Rd cross-references ... OK
* checking for missing documentation entries ... WARNING
Undocumented S4 methods:
  generic 'cbind' and siglist 'aucellResults'
All user-level objects in a package (including S4 classes and methods)
should have documentation entries.
See chapter ‘Writing R documentation files’ in the ‘Writing R
Extensions’ manual.
* checking for code/documentation mismatches ... OK
* checking Rd \usage sections ... WARNING
Objects in \usage without \alias in documentation object 'aucellResults-class':
  ‘\S4method{cbind}{aucellResults}’

Functions with \usage entries need to have the appropriate \alias
entries, and all their arguments documented.
The \usage entries must correspond to syntactically valid R code.
See chapter ‘Writing R documentation files’ in the ‘Writing R
Extensions’ manual.
* 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 (user + system) or elapsed time > 5s
                           user system elapsed
AUCell_exploreThresholds 10.910  3.631   7.318
AUCell_calcAUC            7.482  4.226   3.758
AUCell_buildRankings      7.293  3.484   2.109
AUCell_plotTSNE           7.022  3.468   2.218
AUCell_createViewerApp    6.285  3.523   3.000
plotTsne_cellProps        5.701  3.664   2.237
AUCell_plotHist           6.485  2.843   1.762
aucellResults-class       5.154  3.222   1.968
* checking for unstated dependencies in ‘tests’ ... OK
* checking tests ...
  Running ‘testthat.R’
 OK
* checking for unstated dependencies in vignettes ... NOTE
'::' or ':::' import not declared from: ‘reshape2’
* 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 WARNINGs, 4 NOTEs
See
  ‘/Users/biocbuild/bbs-3.11-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/4.0/Resources/library’
* installing *source* package ‘AUCell’ ...
** using staged installation
** R
** inst
** byte-compile and prepare package for lazy loading
Creating a new generic function for ‘cbind’ in package ‘AUCell’
** help
*** installing help indices
** building package indices
** installing vignettes
   ‘AUCell.Rmd’ using ‘UTF-8’ 
** 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 Under development (unstable) (2019-12-14 r77572) -- "Unsuffered Consequences"
Copyright (C) 2019 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)

Attaching package: 'AUCell'

The following object is masked from 'package:base':

    cbind

> 
> 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: 41 | SKIPPED: 0 | WARNINGS: 0 | FAILED: 0 ]
> 
> proc.time()
   user  system elapsed 
 70.190  27.763  36.579 

name	user	system	elapsed
AUCell_buildRankings	7.293	3.484	2.109
AUCell_calcAUC	7.482	4.226	3.758
AUCell_createViewerApp	6.285	3.523	3.000
AUCell_exploreThresholds	10.910	3.631	7.318
AUCell_plotHist	6.485	2.843	1.762
AUCell_plotTSNE	7.022	3.468	2.218
GeneSet-methods	1.192	0.015	1.207
aucellResults-class	5.154	3.222	1.968
orderAUC	0.000	0.001	0.000
plotGeneCount	0.008	0.003	0.011
plotTsne_cellProps	5.701	3.664	2.237
updateAucellResults	0.050	0.000	0.051