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CHECK report for BioCor on tokay1

This page was generated on 2020-08-07 12:11:33 -0400 (Fri, 07 Aug 2020).

TO THE DEVELOPERS/MAINTAINERS OF THE BioCor PACKAGE: Please make sure to use the following settings in order to reproduce any error or warning you see on this page.
Package 156/1882HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
BioCor 1.13.0
LluĂ­s Revilla Sancho
Snapshot Date: 2020-08-06 14:50:46 -0400 (Thu, 06 Aug 2020)
URL: https://git.bioconductor.org/packages/BioCor
Branch: master
Last Commit: 992299c
Last Changed Date: 2020-07-09 06:05:18 -0400 (Thu, 09 Jul 2020)
malbec1 Linux (Ubuntu 18.04.4 LTS) / x86_64  OK  OK  OK UNNEEDED, same version exists in internal repository
tokay1 Windows Server 2012 R2 Standard / x64  OK  OK [ OK ] OK UNNEEDED, same version exists in internal repository
merida1 macOS 10.14.6 Mojave / x86_64  OK  OK  OK  OK UNNEEDED, same version exists in internal repository

Summary

Package: BioCor
Version: 1.13.0
Command: C:\Users\biocbuild\bbs-3.12-bioc\R\bin\R.exe CMD check --force-multiarch --install=check:BioCor.install-out.txt --library=C:\Users\biocbuild\bbs-3.12-bioc\R\library --no-vignettes --timings BioCor_1.13.0.tar.gz
StartedAt: 2020-08-07 03:46:17 -0400 (Fri, 07 Aug 2020)
EndedAt: 2020-08-07 03:50:05 -0400 (Fri, 07 Aug 2020)
EllapsedTime: 228.0 seconds
RetCode: 0
Status:  OK  
CheckDir: BioCor.Rcheck
Warnings: 0

Command output

##############################################################################
##############################################################################
###
### Running command:
###
###   C:\Users\biocbuild\bbs-3.12-bioc\R\bin\R.exe CMD check --force-multiarch --install=check:BioCor.install-out.txt --library=C:\Users\biocbuild\bbs-3.12-bioc\R\library --no-vignettes --timings BioCor_1.13.0.tar.gz
###
##############################################################################
##############################################################################


* using log directory 'C:/Users/biocbuild/bbs-3.12-bioc/meat/BioCor.Rcheck'
* using R version 4.0.2 (2020-06-22)
* 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 '1.13.0'
* 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
Examples with CPU (user + system) or elapsed time > 5s
         user system elapsed
mpathSim 5.12   0.05    5.18
** 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


Installation output

BioCor.Rcheck/00install.out

##############################################################################
##############################################################################
###
### Running command:
###
###   C:\cygwin\bin\curl.exe -O https://malbec1.bioconductor.org/BBS/3.12/bioc/src/contrib/BioCor_1.13.0.tar.gz && rm -rf BioCor.buildbin-libdir && mkdir BioCor.buildbin-libdir && C:\Users\biocbuild\bbs-3.12-bioc\R\bin\R.exe CMD INSTALL --merge-multiarch --build --library=BioCor.buildbin-libdir BioCor_1.13.0.tar.gz && C:\Users\biocbuild\bbs-3.12-bioc\R\bin\R.exe CMD INSTALL BioCor_1.13.0.zip && rm BioCor_1.13.0.tar.gz BioCor_1.13.0.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 94065  100 94065    0     0   241k      0 --:--:-- --:--:-- --:--:--  243k

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_1.13.0.zip
* DONE (BioCor)
* installing to library 'C:/Users/biocbuild/bbs-3.12-bioc/R/library'
package 'BioCor' successfully unpacked and MD5 sums checked

Tests output

BioCor.Rcheck/tests_i386/spelling.Rout


R version 4.0.2 (2020-06-22) -- "Taking Off Again"
Copyright (C) 2020 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 
   0.20    0.01    0.20 

BioCor.Rcheck/tests_x64/spelling.Rout


R version 4.0.2 (2020-06-22) -- "Taking Off Again"
Copyright (C) 2020 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 
   0.17    0.01    0.17 

BioCor.Rcheck/tests_i386/testthat.Rout


R version 4.0.2 (2020-06-22) -- "Taking Off Again"
Copyright (C) 2020 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")
== testthat results  ===========================================================
[ OK: 322 | SKIPPED: 0 | WARNINGS: 0 | FAILED: 0 ]
> 
> proc.time()
   user  system elapsed 
  11.12    0.81   11.98 

BioCor.Rcheck/tests_x64/testthat.Rout


R version 4.0.2 (2020-06-22) -- "Taking Off Again"
Copyright (C) 2020 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")
== testthat results  ===========================================================
[ OK: 322 | SKIPPED: 0 | WARNINGS: 0 | FAILED: 0 ]
> 
> proc.time()
   user  system elapsed 
  10.65    0.48   11.12 

Example timings

BioCor.Rcheck/examples_i386/BioCor-Ex.timings

nameusersystemelapsed
AintoB000
addSimilarities000
clusterGeneSim2.030.152.19
clusterSim1.020.101.11
combinadic000
combineScores0.020.000.01
combineSources000
conversions000
diceSim000
duplicateIndices000
geneSim3.200.123.34
mclusterGeneSim1.380.101.47
mclusterSim1.030.031.06
mgeneSim3.940.013.96
mpathSim5.120.055.18
pathSim3.710.003.86
removeDup000
seq2mat0.000.000.03
similarities0.020.000.02
weighted000

BioCor.Rcheck/examples_x64/BioCor-Ex.timings

nameusersystemelapsed
AintoB0.000.010.02
addSimilarities000
clusterGeneSim1.250.031.29
clusterSim0.660.000.66
combinadic000
combineScores0.010.000.01
combineSources000
conversions000
diceSim000
duplicateIndices000
geneSim2.800.052.85
mclusterGeneSim0.830.010.92
mclusterSim0.670.040.70
mgeneSim2.370.012.39
mpathSim2.960.022.97
pathSim2.310.012.32
removeDup0.020.000.02
seq2mat000
similarities000
weighted000