Multiple platform build/check report for BioC 3.13 - CHECK results for scDblFinder on tokay2

Package: scDblFinder

Version: 1.6.0

Command: C:\Users\biocbuild\bbs-3.13-bioc\R\bin\R.exe CMD check --force-multiarch --install=check:scDblFinder.install-out.txt --library=C:\Users\biocbuild\bbs-3.13-bioc\R\library --no-vignettes --timings scDblFinder_1.6.0.tar.gz

StartedAt: 2021-10-15 05:10:04 -0400 (Fri, 15 Oct 2021)

EndedAt: 2021-10-15 05:16:48 -0400 (Fri, 15 Oct 2021)

EllapsedTime: 403.7 seconds

RetCode: 0

Status: WARNINGS

CheckDir: scDblFinder.Rcheck

Warnings: 3

##############################################################################
##############################################################################
###
### Running command:
###
###   C:\Users\biocbuild\bbs-3.13-bioc\R\bin\R.exe CMD check --force-multiarch --install=check:scDblFinder.install-out.txt --library=C:\Users\biocbuild\bbs-3.13-bioc\R\library --no-vignettes --timings scDblFinder_1.6.0.tar.gz
###
##############################################################################
##############################################################################


* using log directory 'C:/Users/biocbuild/bbs-3.13-bioc/meat/scDblFinder.Rcheck'
* using R version 4.1.1 (2021-08-10)
* 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 '1.6.0'
* 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 ... OK
* checking installed package size ... OK
* checking package directory ... OK
* checking 'build' directory ... OK
* checking DESCRIPTION meta-information ... OK
* 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
* 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
'library' or 'require' call not declared from: 'mbkmeans'
'library' or 'require' call to 'mbkmeans' in package code.
  Please use :: or requireNamespace() instead.
  See section 'Suggested packages' in the 'Writing R Extensions' manual.
':::' call which should be '::': 'mbkmeans:::mbkmeans'
  See the note in ?`:::` about the use of this operator.
* checking S3 generic/method consistency ... OK
* checking replacement functions ... OK
* checking foreign function calls ... OK
* checking R code for possible problems ... NOTE
clusterStickiness: no visible binding for global variable 'sce'
doubletPairwiseEnrichment: no visible binding for global variable 'sce'
plotThresholds: no visible global function definition for 'aes'
plotThresholds: no visible binding for global variable 'threshold'
plotThresholds: no visible binding for global variable 'FNR'
plotThresholds: no visible binding for global variable 'FDR'
plotThresholds: no visible binding for global variable 'dev'
plotThresholds: no visible binding for global variable 'cost'
Undefined global functions or variables:
  FDR FNR aes cost dev sce threshold
* checking Rd files ... WARNING
checkRd: (7) cxds2.Rd:27: Tag \href is invalid in a \code block
* 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 'doubletThresholding':
  'verbose'

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
scDblFinder         8.75   0.31    9.06
doubletThresholding 7.86   0.41    8.27
clusterStickiness   5.77   0.15    5.92
** running examples for arch 'x64' ... OK
Examples with CPU (user + system) or elapsed time > 5s
                    user system elapsed
scDblFinder         7.64   0.29    7.93
doubletThresholding 7.00   0.15    7.15
clusterStickiness   6.09   0.13    6.21
* 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: 3 WARNINGs, 2 NOTEs
See
  'C:/Users/biocbuild/bbs-3.13-bioc/meat/scDblFinder.Rcheck/00check.log'
for details.

##############################################################################
##############################################################################
###
### Running command:
###
###   C:\cygwin\bin\curl.exe -O http://155.52.207.165/BBS/3.13/bioc/src/contrib/scDblFinder_1.6.0.tar.gz && rm -rf scDblFinder.buildbin-libdir && mkdir scDblFinder.buildbin-libdir && C:\Users\biocbuild\bbs-3.13-bioc\R\bin\R.exe CMD INSTALL --merge-multiarch --build --library=scDblFinder.buildbin-libdir scDblFinder_1.6.0.tar.gz && C:\Users\biocbuild\bbs-3.13-bioc\R\bin\R.exe CMD INSTALL scDblFinder_1.6.0.zip && rm scDblFinder_1.6.0.tar.gz scDblFinder_1.6.0.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
  0  820k    0  5189    0     0  63065      0  0:00:13 --:--:--  0:00:13 63280
100  820k  100  820k    0     0  1681k      0 --:--:-- --:--:-- --:--:-- 1681k

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
    TFIDF                                   html  
    addDoublets                             html  
    aggregateFeatures                       html  
    clusterStickiness                       html  
    computeDoubletDensity                   html  
    finding level-2 HTML links ... done

    createDoublets                          html  
    cxds2                                   html  
    data                                    html  
    doubletPairwiseEnrichment               html  
    doubletThresholding                     html  
    fastcluster                             html  
    findDoubletClusters                     html  
    getArtificialDoublets                   html  
    getCellPairs                            html  
    getExpectedDoublets                     html  
    mockDoubletSCE                          html  
    plotDoubletMap                          html  
    plotThresholds                          html  
    propHomotypic                           html  
    recoverDoublets                         html  
    scDblFinder                             html  
    selFeatures                             html  
** 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_1.6.0.zip
* DONE (scDblFinder)
* installing to library 'C:/Users/biocbuild/bbs-3.13-bioc/R/library'
package 'scDblFinder' successfully unpacked and MD5 sums checked


R version 4.1.1 (2021-08-10) -- "Kick Things"
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 
  37.09    1.82   38.92


R version 4.1.1 (2021-08-10) -- "Kick Things"
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 
  40.65    1.25   41.89

name	user	system	elapsed
TFIDF	0.06	0.00	0.06
addDoublets	0.83	0.04	0.86
clusterStickiness	5.77	0.15	5.92
computeDoubletDensity	3.36	0.17	3.54
createDoublets	0.87	0.00	0.87
cxds2	0.86	0.00	0.86
doubletPairwiseEnrichment	4.14	0.11	4.25
doubletThresholding	7.86	0.41	8.27
fastcluster	1.41	0.02	1.43
findDoubletClusters	1.78	0.04	1.85
getArtificialDoublets	0	0	0
getCellPairs	0	0	0
getExpectedDoublets	0.02	0.00	0.02
mockDoubletSCE	0.78	0.00	0.78
propHomotypic	0	0	0
recoverDoublets	0.17	0.00	0.17
scDblFinder	8.75	0.31	9.06
selFeatures	0.86	0.00	0.86

name	user	system	elapsed
TFIDF	0.06	0.00	0.06
addDoublets	0.91	0.03	0.94
clusterStickiness	6.09	0.13	6.21
computeDoubletDensity	3.53	0.14	3.68
createDoublets	0.8	0.0	0.8
cxds2	0.92	0.01	0.94
doubletPairwiseEnrichment	4.76	0.13	4.89
doubletThresholding	7.00	0.15	7.15
fastcluster	1.57	0.00	1.57
findDoubletClusters	1.92	0.02	1.93
getArtificialDoublets	0	0	0
getCellPairs	0.01	0.00	0.02
getExpectedDoublets	0	0	0
mockDoubletSCE	0.75	0.00	0.75
propHomotypic	0	0	0
recoverDoublets	0.14	0.02	0.16
scDblFinder	7.64	0.29	7.93
selFeatures	0.82	0.00	0.82

CHECK results for scDblFinder on tokay2

Summary

Command output

Installation output

Tests output

Example timings