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CHECK report for scDblFinder on tokay1

This page was generated on 2021-05-06 12:33:27 -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: C:\Users\biocbuild\bbs-3.12-bioc\R\bin\R.exe CMD check --force-multiarch --install=check:scDblFinder.install-out.txt --library=C:\Users\biocbuild\bbs-3.12-bioc\R\library --no-vignettes --timings scDblFinder_1.4.0.tar.gz
StartedAt: 2021-05-06 06:38:03 -0400 (Thu, 06 May 2021)
EndedAt: 2021-05-06 06:44:32 -0400 (Thu, 06 May 2021)
EllapsedTime: 389.3 seconds
RetCode: 0
Status:   WARNINGS   
CheckDir: scDblFinder.Rcheck
Warnings: 4

Command output

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###
### Running command:
###
###   C:\Users\biocbuild\bbs-3.12-bioc\R\bin\R.exe CMD check --force-multiarch --install=check:scDblFinder.install-out.txt --library=C:\Users\biocbuild\bbs-3.12-bioc\R\library --no-vignettes --timings scDblFinder_1.4.0.tar.gz
###
##############################################################################
##############################################################################


* using log directory 'C:/Users/biocbuild/bbs-3.12-bioc/meat/scDblFinder.Rcheck'
* using R version 4.0.5 (2021-03-31)
* using platform: x86_64-w64-mingw32 (64-bit)
* using session charset: ISO8859-1
* 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 whether package 'scDblFinder' can be installed ... WARNING
Found the following significant warnings:
  Rd warning: C:/Users/biocbuild/bbs-3.12-bioc/tmpdir/RtmpYbUcrY/R.INSTALLe2864734699/scDblFinder/man/scDblFinder.Rd:37: file link 'SingleCellExperiment-class' in package 'SingleCellExperiment' does not exist and so has been treated as a topic
  Rd warning: C:/Users/biocbuild/bbs-3.12-bioc/tmpdir/RtmpYbUcrY/R.INSTALLe2864734699/scDblFinder/man/selFeatures.Rd:17: file link 'SingleCellExperiment-class' in package 'SingleCellExperiment' does not exist and so has been treated as a topic
See 'C:/Users/biocbuild/bbs-3.12-bioc/meat/scDblFinder.Rcheck/00install.out' for details.
* 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
* loading checks for arch 'i386'
** 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
* loading checks for arch 'x64'
** 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 ...
** running examples for arch 'i386' ... OK
Examples with CPU (user + system) or elapsed time > 5s
                      user system elapsed
doubletThresholding   8.92   0.40    9.39
scDblFinder           6.15   0.25    6.40
computeDoubletDensity 5.33   0.18    5.50
** running examples for arch 'x64' ... OK
Examples with CPU (user + system) or elapsed time > 5s
                    user system elapsed
scDblFinder         8.82   0.29    9.12
doubletThresholding 7.50   0.34    8.03
* checking for unstated dependencies in 'tests' ... OK
* checking tests ...
** running tests for arch 'i386' ...
  Running 'testthat.R'
 OK
** running tests for arch 'x64' ...
  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 WARNINGs, 3 NOTEs
See
  'C:/Users/biocbuild/bbs-3.12-bioc/meat/scDblFinder.Rcheck/00check.log'
for details.



Installation output

scDblFinder.Rcheck/00install.out

##############################################################################
##############################################################################
###
### Running command:
###
###   C:\cygwin\bin\curl.exe -O http://172.29.0.3/BBS/3.12/bioc/src/contrib/scDblFinder_1.4.0.tar.gz && rm -rf scDblFinder.buildbin-libdir && mkdir scDblFinder.buildbin-libdir && C:\Users\biocbuild\bbs-3.12-bioc\R\bin\R.exe CMD INSTALL --merge-multiarch --build --library=scDblFinder.buildbin-libdir scDblFinder_1.4.0.tar.gz && C:\Users\biocbuild\bbs-3.12-bioc\R\bin\R.exe CMD INSTALL scDblFinder_1.4.0.zip && rm scDblFinder_1.4.0.tar.gz scDblFinder_1.4.0.zip
###
##############################################################################
##############################################################################


  % Total    % Received % Xferd  Average Speed   Time    Time     Time  Current
                                 Dload  Upload   Total   Spent    Left  Speed

  0     0    0     0    0     0      0      0 --:--:-- --:--:-- --:--:--     0
100  517k  100  517k    0     0  12.0M      0 --:--:-- --:--:-- --:--:-- 12.3M

install for i386

* installing *source* package 'scDblFinder' ...
** using staged installation
** R
** data
** inst
** byte-compile and prepare package for lazy loading
** help
*** installing help indices
  converting help for package 'scDblFinder'
    finding HTML links ... done
    addDoublets                             html  
    computeDoubletDensity                   html  
    finding level-2 HTML links ... done

    createDoublets                          html  
    cxds2                                   html  
    data                                    html  
    doubletThresholding                     html  
    fastcluster                             html  
    findDoubletClusters                     html  
    getArtificialDoublets                   html  
    getCellPairs                            html  
    getExpectedDoublets                     html  
    mockDoubletSCE                          html  
    plotDoubletMap                          html  
    recoverDoublets                         html  
    scDblFinder                             html  
Rd warning: C:/Users/biocbuild/bbs-3.12-bioc/tmpdir/RtmpYbUcrY/R.INSTALLe2864734699/scDblFinder/man/scDblFinder.Rd:37: file link 'SingleCellExperiment-class' in package 'SingleCellExperiment' does not exist and so has been treated as a topic
    selFeatures                             html  
Rd warning: C:/Users/biocbuild/bbs-3.12-bioc/tmpdir/RtmpYbUcrY/R.INSTALLe2864734699/scDblFinder/man/selFeatures.Rd:17: file link 'SingleCellExperiment-class' in package 'SingleCellExperiment' does not exist and so has been treated as a topic
** 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

install for x64

* installing *source* package 'scDblFinder' ...
** testing if installed package can be loaded
* MD5 sums
packaged installation of 'scDblFinder' as scDblFinder_1.4.0.zip
* DONE (scDblFinder)
* installing to library 'C:/Users/biocbuild/bbs-3.12-bioc/R/library'
package 'scDblFinder' successfully unpacked and MD5 sums checked

Tests output

scDblFinder.Rcheck/tests_i386/testthat.Rout


R version 4.0.5 (2021-03-31) -- "Shake and Throw"
Copyright (C) 2021 The R Foundation for Statistical Computing
Platform: i386-w64-mingw32/i386 (32-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 
  33.26    1.57   34.84 

scDblFinder.Rcheck/tests_x64/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-w64-mingw32/x64 (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 
  35.21    0.90   36.10 

Example timings

scDblFinder.Rcheck/examples_i386/scDblFinder-Ex.timings

nameusersystemelapsed
addDoublets0.670.020.69
computeDoubletDensity5.330.185.50
createDoublets0.30.00.3
cxds20.330.030.36
doubletThresholding8.920.409.39
fastcluster0.970.041.00
findDoubletClusters1.640.061.70
getArtificialDoublets000
getCellPairs0.010.000.01
getExpectedDoublets000
mockDoubletSCE0.30.00.3
recoverDoublets0.190.010.20
scDblFinder6.150.256.40
selFeatures0.330.030.36

scDblFinder.Rcheck/examples_x64/scDblFinder-Ex.timings

nameusersystemelapsed
addDoublets0.470.020.48
computeDoubletDensity4.260.094.38
createDoublets0.290.000.30
cxds20.470.030.50
doubletThresholding7.500.348.03
fastcluster0.880.020.89
findDoubletClusters1.750.031.78
getArtificialDoublets0.010.000.02
getCellPairs000
getExpectedDoublets000
mockDoubletSCE0.330.020.34
recoverDoublets0.240.000.24
scDblFinder8.820.299.12
selFeatures0.490.020.50