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This page was generated on 2021-10-23 14:07:16 -0400 (Sat, 23 Oct 2021).

CHECK results for scDblFinder on merida1

To the developers/maintainers of the scDblFinder package:
- Please allow up to 24 hours (and sometimes 48 hours) for your latest push to git@git.bioconductor.org:packages/scDblFinder.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 1718/2083HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
scDblFinder 1.7.7  (landing page)
Pierre-Luc Germain
Snapshot Date: 2021-10-22 14:50:11 -0400 (Fri, 22 Oct 2021)
git_url: https://git.bioconductor.org/packages/scDblFinder
git_branch: master
git_last_commit: c006f4f
git_last_commit_date: 2021-09-28 09:33:38 -0400 (Tue, 28 Sep 2021)
nebbiolo2Linux (Ubuntu 20.04.2 LTS) / x86_64  OK    OK    OK  UNNEEDED, same version is already published
riesling1Windows Server 2019 Standard / x64  OK    OK    OK    OK  UNNEEDED, same version is already published
merida1macOS 10.14.6 Mojave / x86_64  OK    OK    OK    OK  UNNEEDED, same version is already published

Summary

Package: scDblFinder
Version: 1.7.7
Command: /Library/Frameworks/R.framework/Resources/bin/R CMD check --install=check:scDblFinder.install-out.txt --library=/Library/Frameworks/R.framework/Resources/library --no-vignettes --timings scDblFinder_1.7.7.tar.gz
StartedAt: 2021-10-23 08:50:54 -0400 (Sat, 23 Oct 2021)
EndedAt: 2021-10-23 08:57:58 -0400 (Sat, 23 Oct 2021)
EllapsedTime: 424.0 seconds
RetCode: 0
Status:   OK  
CheckDir: scDblFinder.Rcheck
Warnings: 0

Command output

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### Running command:
###
###   /Library/Frameworks/R.framework/Resources/bin/R CMD check --install=check:scDblFinder.install-out.txt --library=/Library/Frameworks/R.framework/Resources/library --no-vignettes --timings scDblFinder_1.7.7.tar.gz
###
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* using log directory ‘/Users/biocbuild/bbs-3.14-bioc/meat/scDblFinder.Rcheck’
* using R version 4.1.1 Patched (2021-08-22 r80813)
* using platform: x86_64-apple-darwin17.0 (64-bit)
* using session charset: UTF-8
* using option ‘--no-vignettes’
* checking for file ‘scDblFinder/DESCRIPTION’ ... OK
* checking extension type ... Package
* this is package ‘scDblFinder’ version ‘1.7.7’
* package encoding: UTF-8
* 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 ‘scDblFinder’ can be installed ... OK
* checking installed package size ... OK
* checking package directory ... OK
* checking ‘build’ directory ... OK
* checking DESCRIPTION meta-information ... NOTE
Package listed in more than one of Depends, Imports, Suggests, Enhances:
  ‘MASS’
A package should be listed in only one of these fields.
* checking top-level files ... NOTE
File
  LICENSE
is not mentioned in the DESCRIPTION file.
* 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 ‘mbkmeans’ 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
plotThresholds: no visible binding for global variable ‘threshold’
plotThresholds: no visible binding for global variable ‘value’
plotThresholds: no visible binding for global variable ‘variable’
Undefined global functions or variables:
  threshold value variable
* 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 contents of ‘data’ directory ... OK
* checking data for non-ASCII characters ... OK
* checking data for ASCII and uncompressed saves ... OK
* checking files in ‘vignettes’ ... OK
* checking examples ... OK
Examples with CPU (user + system) or elapsed time > 5s
                            user system elapsed
scDblFinder               14.208  0.222  14.473
doubletThresholding       13.871  0.286  14.188
clusterStickiness          8.472  0.199   8.680
doubletPairwiseEnrichment  6.995  0.073   7.079
* 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/scDblFinder.Rcheck/00check.log’
for details.



Installation output

scDblFinder.Rcheck/00install.out

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


* installing to library ‘/Library/Frameworks/R.framework/Versions/4.1/Resources/library’
* installing *source* package ‘scDblFinder’ ...
** using staged installation
** R
** data
** 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 (scDblFinder)

Tests output

scDblFinder.Rcheck/tests/testthat.Rout


R version 4.1.1 Patched (2021-08-22 r80813) -- "Kick Things"
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(scDblFinder)
> test_check("scDblFinder")
[ FAIL 0 | WARN 8 | SKIP 0 | PASS 100 ]
> 
> proc.time()
   user  system elapsed 
 81.046   1.871  83.068 

Example timings

scDblFinder.Rcheck/scDblFinder-Ex.timings

nameusersystemelapsed
TFIDF0.7430.0040.748
addDoublets1.5440.0801.626
clusterStickiness8.4720.1998.680
computeDoubletDensity4.1330.2154.354
createDoublets1.3200.0201.341
cxds21.4520.0291.483
directDblClassification4.6710.0774.757
doubletPairwiseEnrichment6.9950.0737.079
doubletThresholding13.871 0.28614.188
fastcluster2.3710.0222.400
findDoubletClusters2.8330.0242.860
getArtificialDoublets0.0040.0000.005
getCellPairs0.0190.0010.019
getExpectedDoublets0.0040.0000.003
mockDoubletSCE1.2340.0321.271
propHomotypic0.0000.0000.001
recoverDoublets0.1530.0000.154
scDblFinder14.208 0.22214.473
selFeatures1.4220.0201.445