Multiple platform build/check report for BioC 3.14 - CHECK results for doppelgangR on tokay2

Hostname	OS	Arch (*)	R version	Installed pkgs
nebbiolo2	Linux (Ubuntu 20.04.4 LTS)	x86_64	4.1.3 (2022-03-10) -- "One Push-Up"	4324
tokay2	Windows Server 2012 R2 Standard	x64	4.1.3 (2022-03-10) -- "One Push-Up"	4077
machv2	macOS 10.14.6 Mojave	x86_64	4.1.3 (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*

Package: doppelgangR

Version: 1.22.0

Command: C:\Users\biocbuild\bbs-3.14-bioc\R\bin\R.exe CMD check --force-multiarch --install=check:doppelgangR.install-out.txt --library=C:\Users\biocbuild\bbs-3.14-bioc\R\library --no-vignettes --timings doppelgangR_1.22.0.tar.gz

StartedAt: 2022-04-12 18:49:32 -0400 (Tue, 12 Apr 2022)

EndedAt: 2022-04-12 19:19:38 -0400 (Tue, 12 Apr 2022)

EllapsedTime: 1805.4 seconds

RetCode: 0

Status: OK

CheckDir: doppelgangR.Rcheck

Warnings: 0

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### Running command:
###
###   C:\Users\biocbuild\bbs-3.14-bioc\R\bin\R.exe CMD check --force-multiarch --install=check:doppelgangR.install-out.txt --library=C:\Users\biocbuild\bbs-3.14-bioc\R\library --no-vignettes --timings doppelgangR_1.22.0.tar.gz
###
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* using log directory 'C:/Users/biocbuild/bbs-3.14-bioc/meat/doppelgangR.Rcheck'
* using R version 4.1.3 (2022-03-10)
* using platform: x86_64-w64-mingw32 (64-bit)
* using session charset: ISO8859-1
* using option '--no-vignettes'
* checking for file 'doppelgangR/DESCRIPTION' ... OK
* this is package 'doppelgangR' version '1.22.0'
* 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 'doppelgangR' 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 ... OK
* 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 ... OK
* checking S3 generic/method consistency ... OK
* checking replacement functions ... OK
* checking foreign function calls ... OK
* checking R code for possible problems ... OK
* 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 files in 'vignettes' ... OK
* checking examples ...
** running examples for arch 'i386' ... OK
Examples with CPU (user + system) or elapsed time > 5s
              user system elapsed
plot-methods 15.46   0.99   63.16
corFinder     7.48   0.89   10.14
doppelgangR   4.34   0.31   32.97
** running examples for arch 'x64' ... OK
Examples with CPU (user + system) or elapsed time > 5s
              user system elapsed
plot-methods 10.88   0.88   56.79
corFinder     5.59   0.28    5.87
doppelgangR   3.22   0.33   35.41
* 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: OK

##############################################################################
##############################################################################
###
### Running command:
###
###   C:\cygwin\bin\curl.exe -O http://155.52.207.166/BBS/3.14/bioc/src/contrib/doppelgangR_1.22.0.tar.gz && rm -rf doppelgangR.buildbin-libdir && mkdir doppelgangR.buildbin-libdir && C:\Users\biocbuild\bbs-3.14-bioc\R\bin\R.exe CMD INSTALL --merge-multiarch --build --library=doppelgangR.buildbin-libdir doppelgangR_1.22.0.tar.gz && C:\Users\biocbuild\bbs-3.14-bioc\R\bin\R.exe CMD INSTALL doppelgangR_1.22.0.zip && rm doppelgangR_1.22.0.tar.gz doppelgangR_1.22.0.zip
###
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  % 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 72293  100 72293    0     0   368k      0 --:--:-- --:--:-- --:--:--  369k

install for i386

* installing *source* package 'doppelgangR' ...
** using staged installation
** R
** inst
** byte-compile and prepare package for lazy loading
** help
*** installing help indices
  converting help for package 'doppelgangR'
    finding HTML links ... done
    DoppelGang-class                        html  
    colFinder                               html  
    corFinder                               html  
    doppelgangR-package                     html  
    doppelgangR                             html  
    dst                                     html  
    mst.mle                                 html  
    outlierFinder                           html  
    phenoDist                               html  
    phenoFinder                             html  
    plot-methods                            html  
    smokingGunFinder                        html  
    vectorHammingDist                       html  
    vectorWeightedDist                      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 'doppelgangR' ...
** testing if installed package can be loaded
* MD5 sums
packaged installation of 'doppelgangR' as doppelgangR_1.22.0.zip
* DONE (doppelgangR)
* installing to library 'C:/Users/biocbuild/bbs-3.14-bioc/R/library'
package 'doppelgangR' successfully unpacked and MD5 sums checked


R version 4.1.3 (2022-03-10) -- "One Push-Up"
Copyright (C) 2022 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(doppelgangR)
Loading required package: Biobase
Loading required package: BiocGenerics

Attaching package: 'BiocGenerics'

The following objects are masked from 'package:stats':

    IQR, mad, sd, var, xtabs

The following objects are masked from 'package:base':

    Filter, Find, Map, Position, Reduce, anyDuplicated, append,
    as.data.frame, basename, cbind, colnames, dirname, do.call,
    duplicated, eval, evalq, get, grep, grepl, intersect, is.unsorted,
    lapply, mapply, match, mget, order, paste, pmax, pmax.int, pmin,
    pmin.int, rank, rbind, rownames, sapply, setdiff, sort, table,
    tapply, union, unique, unsplit, which.max, which.min

Welcome to Bioconductor

    Vignettes contain introductory material; view with
    'browseVignettes()'. To cite Bioconductor, see
    'citation("Biobase")', and for packages 'citation("pkgname")'.

Loading required package: BiocParallel
> 
> test_check("doppelgangR")
Warning message:
In FUN(...) :
  m and n have different column names in phenoData.  Skipping phenotype checking for this pair.  Set phenoFinger.args=NULL to disable phenotype checking altogether.
[ FAIL 0 | WARN 8 | SKIP 0 | PASS 115 ]

[ FAIL 0 | WARN 8 | SKIP 0 | PASS 115 ]
> 
> proc.time()
   user  system elapsed 
  25.50    1.29  604.71


R version 4.1.3 (2022-03-10) -- "One Push-Up"
Copyright (C) 2022 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(doppelgangR)
Loading required package: Biobase
Loading required package: BiocGenerics

Attaching package: 'BiocGenerics'

The following objects are masked from 'package:stats':

    IQR, mad, sd, var, xtabs

The following objects are masked from 'package:base':

    Filter, Find, Map, Position, Reduce, anyDuplicated, append,
    as.data.frame, basename, cbind, colnames, dirname, do.call,
    duplicated, eval, evalq, get, grep, grepl, intersect, is.unsorted,
    lapply, mapply, match, mget, order, paste, pmax, pmax.int, pmin,
    pmin.int, rank, rbind, rownames, sapply, setdiff, sort, table,
    tapply, union, unique, unsplit, which.max, which.min

Welcome to Bioconductor

    Vignettes contain introductory material; view with
    'browseVignettes()'. To cite Bioconductor, see
    'citation("Biobase")', and for packages 'citation("pkgname")'.

Loading required package: BiocParallel
> 
> test_check("doppelgangR")
Warning message:
In FUN(...) :
  m and n have different column names in phenoData.  Skipping phenotype checking for this pair.  Set phenoFinger.args=NULL to disable phenotype checking altogether.
[ FAIL 0 | WARN 8 | SKIP 0 | PASS 115 ]

[ FAIL 0 | WARN 8 | SKIP 0 | PASS 115 ]
> 
> proc.time()
   user  system elapsed 
  31.76    0.79  735.53

name	user	system	elapsed
corFinder	7.48	0.89	10.14
doppelgangR	4.34	0.31	32.97
dst	0	0	0
mst.mle	0.15	0.00	0.14
outlierFinder	1.96	0.19	2.16
phenoDist	2.80	0.28	3.08
phenoFinder	3.11	0.19	3.29
plot-methods	15.46	0.99	63.16
smokingGunFinder	2.64	0.23	2.87
vectorHammingDist	0	0	0
vectorWeightedDist	0	0	0

name	user	system	elapsed
corFinder	5.59	0.28	5.87
doppelgangR	3.22	0.33	35.41
dst	0	0	0
mst.mle	0.15	0.00	0.14
outlierFinder	1.89	0.16	2.05
phenoDist	2.48	0.23	2.72
phenoFinder	2.89	0.11	3.00
plot-methods	10.88	0.88	56.79
smokingGunFinder	3.36	0.20	3.56
vectorHammingDist	0.02	0.00	0.02
vectorWeightedDist	0	0	0

CHECK results for doppelgangR on tokay2

Summary

Command output

Installation output

Tests output

Example timings