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This page was generated on 2021-11-26 15:05:42 -0500 (Fri, 26 Nov 2021).

CHECK results for AUCell on machv2

To the developers/maintainers of the AUCell package:
- Please allow up to 24 hours (and sometimes 48 hours) for your latest push to git@git.bioconductor.org:packages/AUCell.git to
reflect on this report. See How and When does the builder pull? When will my changes propagate? here for more information.
- Make sure to use the following settings in order to reproduce any error or warning you see on this page.

raw results

Package 98/2083HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
AUCell 1.16.0  (landing page)
Sara Aibar
Snapshot Date: 2021-11-25 04:15:05 -0500 (Thu, 25 Nov 2021)
git_url: https://git.bioconductor.org/packages/AUCell
git_branch: RELEASE_3_14
git_last_commit: dfde2b6
git_last_commit_date: 2021-10-26 12:38:06 -0500 (Tue, 26 Oct 2021)
nebbiolo2Linux (Ubuntu 20.04.3 LTS) / x86_64  OK    OK    OK  UNNEEDED, same version is already published
tokay2Windows Server 2012 R2 Standard / x64  OK    ERROR  skippedskipped
machv2macOS 10.14.6 Mojave / x86_64  OK    OK    OK    OK  UNNEEDED, same version is already published

Summary

Package: AUCell
Version: 1.16.0
Command: /Library/Frameworks/R.framework/Resources/bin/R CMD check --install=check:AUCell.install-out.txt --library=/Library/Frameworks/R.framework/Resources/library --no-vignettes --timings AUCell_1.16.0.tar.gz
StartedAt: 2021-11-25 13:55:46 -0500 (Thu, 25 Nov 2021)
EndedAt: 2021-11-25 14:00:32 -0500 (Thu, 25 Nov 2021)
EllapsedTime: 286.1 seconds
RetCode: 0
Status:   OK  
CheckDir: AUCell.Rcheck
Warnings: 0

Command output

##############################################################################
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###
### Running command:
###
###   /Library/Frameworks/R.framework/Resources/bin/R CMD check --install=check:AUCell.install-out.txt --library=/Library/Frameworks/R.framework/Resources/library --no-vignettes --timings AUCell_1.16.0.tar.gz
###
##############################################################################
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* using log directory ‘/Users/biocbuild/bbs-3.14-bioc/meat/AUCell.Rcheck’
* using R version 4.1.2 (2021-11-01)
* using platform: x86_64-apple-darwin17.0 (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 ‘1.16.0’
* 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 ... NOTE
  installed size is  5.1Mb
  sub-directories of 1Mb or more:
    doc   4.3Mb
* 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
Namespace in Imports field not imported from: ‘S4Vectors’
  All declared Imports should be used.
* 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’
plotEmb_rgb : <anonymous>: no visible global function definition for
  ‘rgb’
Undefined global functions or variables:
  %>% cell rgb tsne1 tsne2
Consider adding
  importFrom("grDevices", "rgb")
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 installed files from ‘inst/doc’ ... OK
* checking files in ‘vignettes’ ... OK
* checking examples ... OK
* 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: 4 NOTEs
See
  ‘/Users/biocbuild/bbs-3.14-bioc/meat/AUCell.Rcheck/00check.log’
for details.



Installation output

AUCell.Rcheck/00install.out

##############################################################################
##############################################################################
###
### Running command:
###
###   /Library/Frameworks/R.framework/Resources/bin/R CMD INSTALL AUCell
###
##############################################################################
##############################################################################


* installing to library ‘/Library/Frameworks/R.framework/Versions/4.1/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
   ‘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)

Tests output

AUCell.Rcheck/tests/testthat.Rout


R version 4.1.2 (2021-11-01) -- "Bird Hippie"
Copyright (C) 2021 The R Foundation for Statistical Computing
Platform: x86_64-apple-darwin17.0 (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 
[ FAIL 0 | WARN 0 | SKIP 0 | PASS 42 ]
> 
> proc.time()
   user  system elapsed 
 26.858   1.495  28.364 

Example timings

AUCell.Rcheck/AUCell-Ex.timings

nameusersystemelapsed
AUCell_buildRankings0.9350.0530.989
AUCell_calcAUC2.5750.0472.625
AUCell_createViewerApp3.7420.5684.315
AUCell_exploreThresholds3.6710.1793.855
AUCell_plotHist1.0610.0111.074
AUCell_plotTSNE1.3230.0131.341
GeneSet-methods0.2530.0120.264
aucellResults-class1.9910.0112.003
orderAUC0.0010.0000.000
plotGeneCount0.0070.0010.008
plotTsne_cellProps1.2810.0571.341
updateAucellResults0.0990.0090.109