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

Package: BioCor

Version: 1.16.0

Command: C:\Users\biocbuild\bbs-3.13-bioc\R\bin\R.exe CMD check --force-multiarch --install=check:BioCor.install-out.txt --library=C:\Users\biocbuild\bbs-3.13-bioc\R\library --no-vignettes --timings BioCor_1.16.0.tar.gz

StartedAt: 2021-10-14 20:11:24 -0400 (Thu, 14 Oct 2021)

EndedAt: 2021-10-14 20:15:01 -0400 (Thu, 14 Oct 2021)

EllapsedTime: 216.4 seconds

RetCode: 0

Status: OK

CheckDir: BioCor.Rcheck

Warnings: 0

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###
### Running command:
###
###   C:\Users\biocbuild\bbs-3.13-bioc\R\bin\R.exe CMD check --force-multiarch --install=check:BioCor.install-out.txt --library=C:\Users\biocbuild\bbs-3.13-bioc\R\library --no-vignettes --timings BioCor_1.16.0.tar.gz
###
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* using log directory 'C:/Users/biocbuild/bbs-3.13-bioc/meat/BioCor.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 'BioCor/DESCRIPTION' ... OK
* this is package 'BioCor' version '1.16.0'
* 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 'BioCor' 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 R/sysdata.rda ... OK
* checking files in 'vignettes' ... OK
* checking examples ...
** running examples for arch 'i386' ... OK
** running examples for arch 'x64' ... OK
* checking for unstated dependencies in 'tests' ... OK
* checking tests ...
** running tests for arch 'i386' ...
  Running 'spelling.R'
  Running 'testthat.R'
 OK
** running tests for arch 'x64' ...
  Running 'spelling.R'
  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://155.52.207.165/BBS/3.13/bioc/src/contrib/BioCor_1.16.0.tar.gz && rm -rf BioCor.buildbin-libdir && mkdir BioCor.buildbin-libdir && C:\Users\biocbuild\bbs-3.13-bioc\R\bin\R.exe CMD INSTALL --merge-multiarch --build --library=BioCor.buildbin-libdir BioCor_1.16.0.tar.gz && C:\Users\biocbuild\bbs-3.13-bioc\R\bin\R.exe CMD INSTALL BioCor_1.16.0.zip && rm BioCor_1.16.0.tar.gz BioCor_1.16.0.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  108k  100  108k    0     0   561k      0 --:--:-- --:--:-- --:--:--  562k

install for i386

* installing *source* package 'BioCor' ...
** using staged installation
** R
** byte-compile and prepare package for lazy loading
Creating a generic function from function 'clusterGeneSim' in package 'BioCor'
Creating a generic function from function 'clusterSim' in package 'BioCor'
Creating a generic function from function 'geneSim' in package 'BioCor'
Creating a generic function from function 'mclusterGeneSim' in package 'BioCor'
Creating a generic function from function 'mclusterSim' in package 'BioCor'
Creating a generic function from function 'mgeneSim' in package 'BioCor'
Creating a generic function from function 'mpathSim' in package 'BioCor'
Creating a generic function from function 'pathSim' in package 'BioCor'
** help
*** installing help indices
  converting help for package 'BioCor'
    finding HTML links ... done
    AintoB                                  html  
    BioCor-package                          html  
    addSimilarities                         html  
    clusterGeneSim                          html  
    clusterSim                              html  
    combinadic                              html  
    combineScores                           html  
    combineSources                          html  
    conversions                             html  
    diceSim                                 html  
    duplicateIndices                        html  
    geneSim                                 html  
    incidence-list-method                   html  
    inverseList                             html  
    mclusterGeneSim                         html  
    mclusterSim                             html  
    mgeneSim                                html  
    mpathSim                                html  
    pathSim                                 html  
    removeDup                               html  
    seq2mat                                 html  
    similarities                            html  
    weighted                                html  
*** copying figures
** 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 'BioCor' ...
** testing if installed package can be loaded
* MD5 sums
packaged installation of 'BioCor' as BioCor_1.16.0.zip
* DONE (BioCor)
* installing to library 'C:/Users/biocbuild/bbs-3.13-bioc/R/library'
package 'BioCor' 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.

> if (requireNamespace("spelling", quietly = TRUE)) {
+       spelling::spell_check_test(vignettes = TRUE, error = FALSE, skip_on_cran = TRUE)
+   }
NULL
> 
> proc.time()
   user  system elapsed 
   0.28    0.04    0.37


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.

> if (requireNamespace("spelling", quietly = TRUE)) {
+       spelling::spell_check_test(vignettes = TRUE, error = FALSE, skip_on_cran = TRUE)
+   }
NULL
> 
> proc.time()
   user  system elapsed 
   0.26    0.06    0.31


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(BioCor)
> 
> test_check("BioCor")
[ FAIL 0 | WARN 0 | SKIP 0 | PASS 322 ]
> 
> proc.time()
   user  system elapsed 
  11.01    0.73   11.76


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(BioCor)
> 
> test_check("BioCor")
[ FAIL 0 | WARN 0 | SKIP 0 | PASS 322 ]
> 
> proc.time()
   user  system elapsed 
  11.53    0.48   12.00

name	user	system	elapsed
AintoB	0	0	0
addSimilarities	0.01	0.00	0.02
clusterGeneSim	0.76	0.17	0.94
clusterSim	0.55	0.02	0.56
combinadic	0	0	0
combineScores	0	0	0
combineSources	0.00	0.01	0.02
conversions	0	0	0
diceSim	0	0	0
duplicateIndices	0	0	0
geneSim	2.03	0.10	2.12
mclusterGeneSim	0.67	0.00	0.67
mclusterSim	0.53	0.07	0.61
mgeneSim	1.65	0.04	1.67
mpathSim	3.51	0.04	3.57
pathSim	1.84	0.00	1.85
removeDup	0	0	0
seq2mat	0	0	0
similarities	0	0	0
weighted	0	0	0

name	user	system	elapsed
AintoB	0	0	0
addSimilarities	0	0	0
clusterGeneSim	0.83	0.09	0.92
clusterSim	1.07	0.02	1.09
combinadic	0	0	0
combineScores	0	0	0
combineSources	0	0	0
conversions	0	0	0
diceSim	0	0	0
duplicateIndices	0	0	0
geneSim	2.58	0.09	2.67
mclusterGeneSim	0.73	0.02	0.75
mclusterSim	0.58	0.05	0.63
mgeneSim	1.86	0.06	1.92
mpathSim	3.95	0.05	4.00
pathSim	1.57	0.01	1.58
removeDup	0	0	0
seq2mat	0	0	0
similarities	0	0	0
weighted	0	0	0

CHECK results for BioCor on tokay2

Summary

Command output

Installation output

Tests output

Example timings