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CHECK report for scDblFinder on malbec1

This page was generated on 2021-05-06 12:29:01 -0400 (Thu, 06 May 2021).

To the developers/maintainers of the scDblFinder package:
Please make sure to use the following settings in order to reproduce any error or warning you see on this page.
Package 1635/1974HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
scDblFinder 1.4.0  (landing page)
Pierre-Luc Germain
Snapshot Date: 2021-05-05 14:51:38 -0400 (Wed, 05 May 2021)
URL: https://git.bioconductor.org/packages/scDblFinder
Branch: RELEASE_3_12
Last Commit: b3dd92a
Last Changed Date: 2020-10-27 11:51:03 -0400 (Tue, 27 Oct 2020)
malbec1Linux (Ubuntu 18.04.5 LTS) / x86_64  OK    OK    WARNINGS  UNNEEDED, same version exists in internal repository
tokay1Windows Server 2012 R2 Standard / x64  OK    OK    WARNINGS    OK  UNNEEDED, same version exists in internal repository
merida1macOS 10.14.6 Mojave / x86_64  OK    OK    WARNINGS    OK  UNNEEDED, same version exists in internal repository

Summary

Package: scDblFinder
Version: 1.4.0
Command: /home/biocbuild/bbs-3.12-bioc/R/bin/R CMD check --install=check:scDblFinder.install-out.txt --library=/home/biocbuild/bbs-3.12-bioc/R/library --no-vignettes --timings scDblFinder_1.4.0.tar.gz
StartedAt: 2021-05-06 05:42:26 -0400 (Thu, 06 May 2021)
EndedAt: 2021-05-06 05:47:23 -0400 (Thu, 06 May 2021)
EllapsedTime: 296.4 seconds
RetCode: 0
Status:   WARNINGS  
CheckDir: scDblFinder.Rcheck
Warnings: 3

Command output

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###
### Running command:
###
###   /home/biocbuild/bbs-3.12-bioc/R/bin/R CMD check --install=check:scDblFinder.install-out.txt --library=/home/biocbuild/bbs-3.12-bioc/R/library --no-vignettes --timings scDblFinder_1.4.0.tar.gz
###
##############################################################################
##############################################################################


* using log directory ‘/home/biocbuild/bbs-3.12-bioc/meat/scDblFinder.Rcheck’
* using R version 4.0.5 (2021-03-31)
* using platform: x86_64-pc-linux-gnu (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 ‘1.4.0’
* 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:
  ‘bluster’
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 ... WARNING
Subdirectory 'inst/doc' contains invalid file names:
  ‘1_introduction.Rmd’ ‘2_scDblFinder.Rmd’ ‘3_findDoubletClusters.Rmd’
  ‘4_computeDoubletDensity.Rmd’ ‘5_recoverDoublets.Rmd’
  ‘1_introduction.html’ ‘2_scDblFinder.html’
  ‘3_findDoubletClusters.html’ ‘4_computeDoubletDensity.html’
  ‘5_recoverDoublets.html’
Please remove or rename the files.
See section ‘Package subdirectories’ in the ‘Writing R Extensions’
manual.
* 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 ... WARNING
'::' or ':::' imports not declared from:
  ‘ComplexHeatmap’ ‘MASS’ ‘circlize’ ‘dplyr’ ‘viridisLite’
* checking S3 generic/method consistency ... OK
* checking replacement functions ... OK
* checking foreign function calls ... OK
* checking R code for possible problems ... NOTE
.getThresholdStats: no visible binding for global variable ‘w’
Undefined global functions or variables:
  w
* 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 ... WARNING
Documented arguments not in \usage in documentation object 'computeDoubletDensity':
  ‘adjust’

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 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         7.148  0.092   7.250
doubletThresholding 7.016  0.140   7.162
* 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 WARNINGs, 3 NOTEs
See
  ‘/home/biocbuild/bbs-3.12-bioc/meat/scDblFinder.Rcheck/00check.log’
for details.



Installation output

scDblFinder.Rcheck/00install.out

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###
### Running command:
###
###   /home/biocbuild/bbs-3.12-bioc/R/bin/R CMD INSTALL scDblFinder
###
##############################################################################
##############################################################################


* installing to library ‘/home/biocbuild/bbs-3.12-bioc/R/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 4.0.5 (2021-03-31) -- "Shake and Throw"
Copyright (C) 2021 The R Foundation for Statistical Computing
Platform: x86_64-pc-linux-gnu (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 85 ]
> 
> proc.time()
   user  system elapsed 
 43.620   0.556  44.273 

Example timings

scDblFinder.Rcheck/scDblFinder-Ex.timings

nameusersystemelapsed
addDoublets0.5360.0360.569
computeDoubletDensity3.7880.1843.989
createDoublets0.3960.0000.393
cxds20.4480.0000.448
doubletThresholding7.0160.1407.162
fastcluster1.0160.0001.019
findDoubletClusters1.6720.0241.701
getArtificialDoublets0.0080.0000.007
getCellPairs0.0160.0000.016
getExpectedDoublets0.0000.0040.003
mockDoubletSCE0.4640.0000.462
recoverDoublets0.2000.0000.201
scDblFinder7.1480.0927.250
selFeatures0.5360.0000.539