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CHECK report for coRdon on malbec1

This page was generated on 2020-04-15 12:14:32 -0400 (Wed, 15 Apr 2020).

Package 363/1823HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
coRdon 1.4.0
Anamaria Elek
Snapshot Date: 2020-04-14 16:46:13 -0400 (Tue, 14 Apr 2020)
URL: https://git.bioconductor.org/packages/coRdon
Branch: RELEASE_3_10
Last Commit: e2fafd9
Last Changed Date: 2019-10-29 13:11:17 -0400 (Tue, 29 Oct 2019)
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 OS X 10.11.6 El Capitan / x86_64  OK  OK  OK  OK UNNEEDED, same version exists in internal repository

Summary

Package: coRdon
Version: 1.4.0
Command: /home/biocbuild/bbs-3.10-bioc/R/bin/R CMD check --install=check:coRdon.install-out.txt --library=/home/biocbuild/bbs-3.10-bioc/R/library --no-vignettes --timings coRdon_1.4.0.tar.gz
StartedAt: 2020-04-15 05:55:38 -0400 (Wed, 15 Apr 2020)
EndedAt: 2020-04-15 05:58:28 -0400 (Wed, 15 Apr 2020)
EllapsedTime: 170.1 seconds
RetCode: 0
Status:  OK 
CheckDir: coRdon.Rcheck
Warnings: 0

Command output

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### Running command:
###
###   /home/biocbuild/bbs-3.10-bioc/R/bin/R CMD check --install=check:coRdon.install-out.txt --library=/home/biocbuild/bbs-3.10-bioc/R/library --no-vignettes --timings coRdon_1.4.0.tar.gz
###
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* using log directory ‘/home/biocbuild/bbs-3.10-bioc/meat/coRdon.Rcheck’
* using R version 3.6.3 (2020-02-29)
* using platform: x86_64-pc-linux-gnu (64-bit)
* using session charset: UTF-8
* using option ‘--no-vignettes’
* checking for file ‘coRdon/DESCRIPTION’ ... OK
* checking extension type ... Package
* this is package ‘coRdon’ version ‘1.4.0’
* 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 ‘coRdon’ 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 contents of ‘data’ directory ... OK
* checking data for non-ASCII characters ... OK
* checking data for ASCII and uncompressed saves ... OK
* checking R/sysdata.rda ... OK
* checking files in ‘vignettes’ ... OK
* checking examples ... OK
Examples with CPU or elapsed time > 5s
                           user system elapsed
reduceCrossTab          192.348  1.104  39.026
codonUsage-expressivity  20.208  0.116   6.450
codonUsage                9.860  0.052   3.472
* checking for unstated dependencies in ‘tests’ ... OK
* checking tests ...
  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

coRdon.Rcheck/00install.out

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###
### Running command:
###
###   /home/biocbuild/bbs-3.10-bioc/R/bin/R CMD INSTALL coRdon
###
##############################################################################
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* installing to library ‘/home/biocbuild/bbs-3.10-bioc/R/library’
* installing *source* package ‘coRdon’ ...
** using staged installation
** R
** data
*** moving datasets to lazyload DB
** inst
** byte-compile and prepare package for lazy loading
** help
*** installing help indices
** 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 (coRdon)

Tests output

coRdon.Rcheck/tests/testthat.Rout


R version 3.6.3 (2020-02-29) -- "Holding the Windsock"
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(coRdon)
> 
> test_check("coRdon")
══ testthat results  ═══════════════════════════════════════════════════════════
[ OK: 26 | SKIPPED: 0 | WARNINGS: 0 | FAILED: 0 ]
> 
> proc.time()
   user  system elapsed 
 22.452   0.288  11.998 

Example timings

coRdon.Rcheck/coRdon-Ex.timings

nameusersystemelapsed
bplot1.8000.0081.029
codonTable-class0.7000.0080.320
codonUsage-expressivity20.208 0.116 6.450
codonUsage9.8600.0523.472
crossTab-class0.0240.0040.028
enrichBarplot1.2920.0000.850
enrichMAplot1.5440.0001.545
enrichMatrix1.9400.0201.035
enrichment1.8080.0081.118
intraBplot2.3400.0241.364
readSet0.1280.0000.130
reduceCrossTab192.348 1.104 39.026
subset0.5600.0080.195