Back to Multiple platform build/check report for BioC 3.14
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This page was generated on 2022-04-13 12:08:44 -0400 (Wed, 13 Apr 2022).

HostnameOSArch (*)R versionInstalled pkgs
nebbiolo2Linux (Ubuntu 20.04.4 LTS)x86_644.1.3 (2022-03-10) -- "One Push-Up" 4324
tokay2Windows Server 2012 R2 Standardx644.1.3 (2022-03-10) -- "One Push-Up" 4077
machv2macOS 10.14.6 Mojavex86_644.1.3 (2022-03-10) -- "One Push-Up" 4137
Click on any hostname to see more info about the system (e.g. compilers)      (*) as reported by 'uname -p', except on Windows and Mac OS X

CHECK results for scDblFinder on machv2


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? 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 1.8.0  (landing page)
Pierre-Luc Germain
Snapshot Date: 2022-04-12 01:55:07 -0400 (Tue, 12 Apr 2022)
git_url: https://git.bioconductor.org/packages/scDblFinder
git_branch: RELEASE_3_14
git_last_commit: bd1331d
git_last_commit_date: 2021-10-26 12:55:40 -0400 (Tue, 26 Oct 2021)
nebbiolo2Linux (Ubuntu 20.04.4 LTS) / x86_64  OK    OK    OK  UNNEEDED, same version is already published
tokay2Windows Server 2012 R2 Standard / x64  OK    OK    OK    OK  UNNEEDED, same version is already published
machv2macOS 10.14.6 Mojave / x86_64  OK    OK    OK    OK  UNNEEDED, same version is already published

Summary

Package: scDblFinder
Version: 1.8.0
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_1.8.0.tar.gz
StartedAt: 2022-04-12 18:08:36 -0400 (Tue, 12 Apr 2022)
EndedAt: 2022-04-12 18:16:13 -0400 (Tue, 12 Apr 2022)
EllapsedTime: 457.3 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_1.8.0.tar.gz
###
##############################################################################
##############################################################################


* using log directory ‘/Users/biocbuild/bbs-3.14-bioc/meat/scDblFinder.Rcheck’
* using R version 4.1.3 (2022-03-10)
* 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 ‘1.8.0’
* 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               15.542  0.286  15.909
doubletThresholding       14.968  0.322  15.322
clusterStickiness          8.806  0.176   8.986
doubletPairwiseEnrichment  7.352  0.078   7.442
directDblClassification    4.927  0.076   5.007
* 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

##############################################################################
##############################################################################
###
### 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 4.1.3 (2022-03-10) -- "One Push-Up"
Copyright (C) 2022 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 ]

[ FAIL 0 | WARN 8 | SKIP 0 | PASS 100 ]
> 
> proc.time()
   user  system elapsed 
 85.079   1.918  88.067 

Example timings

scDblFinder.Rcheck/scDblFinder-Ex.timings

nameusersystemelapsed
TFIDF0.0930.0030.096
addDoublets1.5170.1221.641
clusterStickiness8.8060.1768.986
computeDoubletDensity4.0740.2174.294
createDoublets1.3960.0181.416
cxds21.6510.0321.684
directDblClassification4.9270.0765.007
doubletPairwiseEnrichment7.3520.0787.442
doubletThresholding14.968 0.32215.322
fastcluster2.6210.0382.662
findDoubletClusters3.4660.0303.500
getArtificialDoublets0.0070.0000.006
getCellPairs0.0200.0010.020
getExpectedDoublets0.0030.0010.004
mockDoubletSCE1.4720.0141.486
propHomotypic0.0000.0010.001
recoverDoublets0.2000.0020.202
scDblFinder15.542 0.28615.909
selFeatures1.6180.0511.668