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CHECK report for BioCor on merida1

This page was generated on 2019-04-16 12:00:29 -0400 (Tue, 16 Apr 2019).

Package 141/1649HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
BioCor 1.6.1
Lluís Revilla Sancho
Snapshot Date: 2019-04-15 17:01:12 -0400 (Mon, 15 Apr 2019)
URL: https://git.bioconductor.org/packages/BioCor
Branch: RELEASE_3_8
Last Commit: 421f8ca
Last Changed Date: 2019-02-02 10:35:57 -0400 (Sat, 02 Feb 2019)
malbec1 Linux (Ubuntu 16.04.6 LTS) / x86_64  OK  OK  OK UNNEEDED, same version exists in internal repository
merida1 OS X 10.11.6 El Capitan / x86_64  OK  OK [ OK ] OK UNNEEDED, same version exists in internal repository

Summary

Package: BioCor
Version: 1.6.1
Command: /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD check --install=check:BioCor.install-out.txt --library=/Library/Frameworks/R.framework/Versions/Current/Resources/library --no-vignettes --timings BioCor_1.6.1.tar.gz
StartedAt: 2019-04-15 22:35:55 -0400 (Mon, 15 Apr 2019)
EndedAt: 2019-04-15 22:38:31 -0400 (Mon, 15 Apr 2019)
EllapsedTime: 156.3 seconds
RetCode: 0
Status:  OK 
CheckDir: BioCor.Rcheck
Warnings: 0

Command output

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### Running command:
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###   /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD check --install=check:BioCor.install-out.txt --library=/Library/Frameworks/R.framework/Versions/Current/Resources/library --no-vignettes --timings BioCor_1.6.1.tar.gz
###
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* using log directory ‘/Users/biocbuild/bbs-3.8-bioc/meat/BioCor.Rcheck’
* using R version 3.5.3 (2019-03-11)
* using platform: x86_64-apple-darwin15.6.0 (64-bit)
* using session charset: UTF-8
* using option ‘--no-vignettes’
* checking for file ‘BioCor/DESCRIPTION’ ... OK
* this is package ‘BioCor’ version ‘1.6.1’
* 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:
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###   /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD INSTALL BioCor
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* installing to library ‘/Library/Frameworks/R.framework/Versions/3.5/Resources/library’
* installing *source* package ‘BioCor’ ...
** 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
** building package indices
** installing vignettes
** testing if installed package can be loaded
* DONE (BioCor)

Tests output

BioCor.Rcheck/tests/spelling.Rout


R version 3.5.3 (2019-03-11) -- "Great Truth"
Copyright (C) 2019 The R Foundation for Statistical Computing
Platform: x86_64-apple-darwin15.6.0 (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 
  0.185   0.048   0.207 

BioCor.Rcheck/tests/testthat.Rout


R version 3.5.3 (2019-03-11) -- "Great Truth"
Copyright (C) 2019 The R Foundation for Statistical Computing
Platform: x86_64-apple-darwin15.6.0 (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)
If you use BioCor in published research, please cite:
> 
> test_check("BioCor")
══ testthat results  ═══════════════════════════════════════════════════════════
OK: 322 SKIPPED: 0 FAILED: 0
> 
> proc.time()
   user  system elapsed 
 12.986   0.694  13.854 

Example timings

BioCor.Rcheck/BioCor-Ex.timings

nameusersystemelapsed
AintoB0.0020.0020.004
addSimilarities0.0090.0010.009
clusterGeneSim1.5000.0831.593
clusterSim0.8400.0210.863
combinadic0.0010.0010.001
combineScores0.0110.0010.011
combineSources0.0040.0010.004
conversions0.0000.0000.001
diceSim0.0010.0000.000
duplicateIndices0.0010.0010.001
geneSim3.6670.1423.903
mclusterGeneSim1.0430.0711.124
mclusterSim0.7950.0160.819
mgeneSim3.5360.1203.711
mpathSim3.3230.0703.417
pathSim3.0240.0563.133
removeDup0.0060.0010.006
seq2mat0.0010.0010.002
similarities0.0060.0000.006
weighted0.0020.0000.002