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CHECK report for AUCell on celaya2

This page was generated on 2019-10-16 13:00:55 -0400 (Wed, 16 Oct 2019).

Package 94/1741HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
AUCell 1.6.1
Sara Aibar
Snapshot Date: 2019-10-15 17:01:26 -0400 (Tue, 15 Oct 2019)
URL: https://git.bioconductor.org/packages/AUCell
Branch: RELEASE_3_9
Last Commit: 2668bb4
Last Changed Date: 2019-06-05 05:50:10 -0400 (Wed, 05 Jun 2019)
malbec2 Linux (Ubuntu 18.04.2 LTS) / x86_64  OK  OK  OK UNNEEDED, same version exists in internal repository
tokay2 Windows Server 2012 R2 Standard / x64  OK  OK  OK  OK UNNEEDED, same version exists in internal repository
celaya2 OS X 10.11.6 El Capitan / x86_64  OK  OK [ OK ] OK UNNEEDED, same version exists in internal repository

Summary

Package: AUCell
Version: 1.6.1
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_1.6.1.tar.gz
StartedAt: 2019-10-16 00:40:44 -0400 (Wed, 16 Oct 2019)
EndedAt: 2019-10-16 00:45:28 -0400 (Wed, 16 Oct 2019)
EllapsedTime: 284.1 seconds
RetCode: 0
Status:  OK 
CheckDir: AUCell.Rcheck
Warnings: 0

Command output

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### Running 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_1.6.1.tar.gz
###
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* using log directory ‘/Users/biocbuild/bbs-3.9-bioc/meat/AUCell.Rcheck’
* using R version 3.6.1 (2019-07-05)
* 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 ‘1.6.1’
* 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 : : 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_exploreThresholds 9.753  5.209   5.878
AUCell_calcAUC           9.113  4.549   3.382
aucellResults-class      8.132  4.261   2.230
AUCell_plotTSNE          7.187  3.921   1.781
plotTsne_cellProps       7.213  3.842   1.660
AUCell_buildRankings     6.585  4.324   1.578
AUCell_createViewerApp   6.153  4.373   2.183
AUCell_plotHist          5.319  4.296   1.483
* 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.



Installation output

AUCell.Rcheck/00install.out

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###
### Running command:
###
###   /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’ ...
** 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)

Tests output

AUCell.Rcheck/tests/testthat.Rout


R version 3.6.1 (2019-07-05) -- "Action of the Toes"
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)
> 
> 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 
 60.007  31.652  29.855 

Example timings

AUCell.Rcheck/AUCell-Ex.timings

nameusersystemelapsed
AUCell_buildRankings6.5854.3241.578
AUCell_calcAUC9.1134.5493.382
AUCell_createViewerApp6.1534.3732.183
AUCell_exploreThresholds9.7535.2095.878
AUCell_plotHist5.3194.2961.483
AUCell_plotTSNE7.1873.9211.781
GeneSet-methods0.3270.0120.339
aucellResults-class8.1324.2612.230
orderAUC000
plotGeneCount0.0060.0010.008
plotTsne_cellProps7.2133.8421.660
updateAucellResults0.0350.0010.035