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CHECK report for BioCor on malbec1

This page was generated on 2020-08-12 11:20:32 -0400 (Wed, 12 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 156/1885HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
BioCor 1.13.0
Lluís Revilla Sancho
Snapshot Date: 2020-08-11 14:50:16 -0400 (Tue, 11 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
nebbiolo1 Linux (Ubuntu 20.04.1 LTS) / x86_64  OK  OK  OK 
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: /home/biocbuild/bbs-3.12-bioc/R/bin/R CMD check --install=check:BioCor.install-out.txt --library=/home/biocbuild/bbs-3.12-bioc/R/library --no-vignettes --timings BioCor_1.13.0.tar.gz
StartedAt: 2020-08-12 04:11:04 -0400 (Wed, 12 Aug 2020)
EndedAt: 2020-08-12 04:13:43 -0400 (Wed, 12 Aug 2020)
EllapsedTime: 159.1 seconds
RetCode: 0
Status:  OK 
CheckDir: BioCor.Rcheck
Warnings: 0

Command output

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###
### Running command:
###
###   /home/biocbuild/bbs-3.12-bioc/R/bin/R CMD check --install=check:BioCor.install-out.txt --library=/home/biocbuild/bbs-3.12-bioc/R/library --no-vignettes --timings BioCor_1.13.0.tar.gz
###
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* using log directory ‘/home/biocbuild/bbs-3.12-bioc/meat/BioCor.Rcheck’
* using R version 4.0.2 (2020-06-22)
* using platform: x86_64-pc-linux-gnu (64-bit)
* using session charset: UTF-8
* 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 for sufficient/correct file permissions ... 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
* 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 ... OK
* checking for unstated dependencies in ‘tests’ ... OK
* checking tests ...
  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

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### Running command:
###
###   /home/biocbuild/bbs-3.12-bioc/R/bin/R CMD INSTALL BioCor
###
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* installing to library ‘/home/biocbuild/bbs-3.12-bioc/R/library’
* 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
*** 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
* DONE (BioCor)

Tests output

BioCor.Rcheck/tests/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-pc-linux-gnu (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 
  0.228   0.028   0.253 

BioCor.Rcheck/tests/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-pc-linux-gnu (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 
 13.416   0.272  13.747 

Example timings

BioCor.Rcheck/BioCor-Ex.timings

nameusersystemelapsed
AintoB0.0040.0000.001
addSimilarities0.0000.0040.006
clusterGeneSim1.7600.0121.775
clusterSim0.9720.0120.997
combinadic000
combineScores0.0080.0000.006
combineSources0.0000.0000.002
conversions0.0040.0000.000
diceSim0.0000.0000.001
duplicateIndices000
geneSim3.7760.0563.936
mclusterGeneSim1.1640.0201.187
mclusterSim0.6520.0120.664
mgeneSim2.0120.0082.025
mpathSim4.5000.0124.543
pathSim3.0280.0043.033
removeDup0.0000.0040.005
seq2mat0.0040.0000.001
similarities0.0040.0000.006
weighted0.0000.0000.001