Multiple platform build/check report for BioC 3.12 - CHECK report for doppelgangR on tokay1

Package: doppelgangR

Version: 1.18.0

Command: C:\Users\biocbuild\bbs-3.12-bioc\R\bin\R.exe CMD check --force-multiarch --install=check:doppelgangR.install-out.txt --library=C:\Users\biocbuild\bbs-3.12-bioc\R\library --no-vignettes --timings doppelgangR_1.18.0.tar.gz

StartedAt: 2021-05-06 02:20:51 -0400 (Thu, 06 May 2021)

EndedAt: 2021-05-06 02:47:28 -0400 (Thu, 06 May 2021)

EllapsedTime: 1596.4 seconds

RetCode: 0

Status: OK

CheckDir: doppelgangR.Rcheck

Warnings: 0

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### Running command:
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###   C:\Users\biocbuild\bbs-3.12-bioc\R\bin\R.exe CMD check --force-multiarch --install=check:doppelgangR.install-out.txt --library=C:\Users\biocbuild\bbs-3.12-bioc\R\library --no-vignettes --timings doppelgangR_1.18.0.tar.gz
###
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* using log directory 'C:/Users/biocbuild/bbs-3.12-bioc/meat/doppelgangR.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 'doppelgangR/DESCRIPTION' ... OK
* this is package 'doppelgangR' version '1.18.0'
* 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 17.23   0.78   61.35
corFinder     7.50   0.85    9.13
doppelgangR   5.11   0.49   33.78
** running examples for arch 'x64' ... OK
Examples with CPU (user + system) or elapsed time > 5s
                  user system elapsed
plot-methods     15.66   0.78   63.72
corFinder         8.47   0.48    9.04
doppelgangR       6.52   0.50   32.18
smokingGunFinder  5.60   0.34    5.95
* 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

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###
### Running command:
###
###   C:\cygwin\bin\curl.exe -O http://172.29.0.3/BBS/3.12/bioc/src/contrib/doppelgangR_1.18.0.tar.gz && rm -rf doppelgangR.buildbin-libdir && mkdir doppelgangR.buildbin-libdir && C:\Users\biocbuild\bbs-3.12-bioc\R\bin\R.exe CMD INSTALL --merge-multiarch --build --library=doppelgangR.buildbin-libdir doppelgangR_1.18.0.tar.gz && C:\Users\biocbuild\bbs-3.12-bioc\R\bin\R.exe CMD INSTALL doppelgangR_1.18.0.zip && rm doppelgangR_1.18.0.tar.gz doppelgangR_1.18.0.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 72764  100 72764    0     0  3820k      0 --:--:-- --:--:-- --:--:-- 4179k

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_1.18.0.zip
* DONE (doppelgangR)
* installing to library 'C:/Users/biocbuild/bbs-3.12-bioc/R/library'
package 'doppelgangR' successfully unpacked and MD5 sums checked


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(doppelgangR)
Loading required package: Biobase
Loading required package: BiocGenerics
Loading required package: parallel

Attaching package: 'BiocGenerics'

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

    clusterApply, clusterApplyLB, clusterCall, clusterEvalQ,
    clusterExport, clusterMap, parApply, parCapply, parLapply,
    parLapplyLB, parRapply, parSapply, parSapplyLB

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 0 | SKIP 0 | PASS 115 ]
> 
> proc.time()
   user  system elapsed 
  21.45    0.90  545.54


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(doppelgangR)
Loading required package: Biobase
Loading required package: BiocGenerics
Loading required package: parallel

Attaching package: 'BiocGenerics'

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

    clusterApply, clusterApplyLB, clusterCall, clusterEvalQ,
    clusterExport, clusterMap, parApply, parCapply, parLapply,
    parLapplyLB, parRapply, parSapply, parSapplyLB

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 0 | SKIP 0 | PASS 115 ]
> 
> proc.time()
   user  system elapsed 
  28.85    0.67  557.46

name	user	system	elapsed
corFinder	7.50	0.85	9.13
doppelgangR	5.11	0.49	33.78
dst	0	0	0
mst.mle	0.11	0.00	0.11
outlierFinder	2.34	0.12	2.47
phenoDist	4.47	0.30	4.76
phenoFinder	4.30	0.37	4.67
plot-methods	17.23	0.78	61.35
smokingGunFinder	4.24	0.28	4.51
vectorHammingDist	0	0	0
vectorWeightedDist	0	0	0

name	user	system	elapsed
corFinder	8.47	0.48	9.04
doppelgangR	6.52	0.50	32.18
dst	0.01	0.00	0.01
mst.mle	0.19	0.00	0.19
outlierFinder	2.52	0.16	2.67
phenoDist	4.33	0.28	4.61
phenoFinder	4.18	0.17	4.36
plot-methods	15.66	0.78	63.72
smokingGunFinder	5.60	0.34	5.95
vectorHammingDist	0	0	0
vectorWeightedDist	0	0	0

CHECK report for doppelgangR on tokay1

Summary

Command output

Installation output

Tests output

Example timings