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CHECK report for NoRCE on machv2

This page was generated on 2020-10-17 11:59:05 -0400 (Sat, 17 Oct 2020).

TO THE DEVELOPERS/MAINTAINERS OF THE NoRCE PACKAGE: Please make sure to use the following settings in order to reproduce any error or warning you see on this page.
Package 1199/1905HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
NoRCE 1.0.0
Gulden Olgun
Snapshot Date: 2020-10-16 14:40:19 -0400 (Fri, 16 Oct 2020)
URL: https://git.bioconductor.org/packages/NoRCE
Branch: RELEASE_3_11
Last Commit: bda1f3d
Last Changed Date: 2020-04-27 15:34:50 -0400 (Mon, 27 Apr 2020)
malbec2 Linux (Ubuntu 18.04.4 LTS) / x86_64  OK  OK  OK UNNEEDED, same version exists in internal repository
tokay2 Windows Server 2012 R2 Standard / x64  OK  OK  OK  OK UNNEEDED, same version exists in internal repository
machv2 macOS 10.14.6 Mojave / x86_64  OK  OK [ OK ] OK UNNEEDED, same version exists in internal repository

Summary

Package: NoRCE
Version: 1.0.0
Command: /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD check --install=check:NoRCE.install-out.txt --library=/Library/Frameworks/R.framework/Versions/Current/Resources/library --no-vignettes --timings NoRCE_1.0.0.tar.gz
StartedAt: 2020-10-17 03:31:45 -0400 (Sat, 17 Oct 2020)
EndedAt: 2020-10-17 03:41:24 -0400 (Sat, 17 Oct 2020)
EllapsedTime: 579.5 seconds
RetCode: 0
Status:  OK 
CheckDir: NoRCE.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:NoRCE.install-out.txt --library=/Library/Frameworks/R.framework/Versions/Current/Resources/library --no-vignettes --timings NoRCE_1.0.0.tar.gz
###
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* using log directory ‘/Users/biocbuild/bbs-3.11-bioc/meat/NoRCE.Rcheck’
* using R version 4.0.3 (2020-10-10)
* using platform: x86_64-apple-darwin17.0 (64-bit)
* using session charset: UTF-8
* using option ‘--no-vignettes’
* checking for file ‘NoRCE/DESCRIPTION’ ... OK
* checking extension type ... Package
* this is package ‘NoRCE’ version ‘1.0.0’
* 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 ‘NoRCE’ 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 files in ‘vignettes’ ... OK
* checking examples ... OK
Examples with CPU (user + system) or elapsed time > 5s
                        user system elapsed
genePathwayEnricher   19.384  0.107  21.790
calculateCorr         12.132  0.152  12.303
KeggEnrichment        10.882  0.465  32.376
assembly               8.636  0.413  23.824
writeEnrichment        8.598  0.318   9.065
mirnaGOEnricher        7.411  0.278   7.756
getReactomeDiagram     7.383  0.122   7.527
geneGOEnricher         7.117  0.281   7.505
mirnaRegionGOEnricher  6.850  0.233   7.097
geneRegionGOEnricher   5.687  0.240   6.055
reactomeEnrichment     5.302  0.058   5.370
* 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

NoRCE.Rcheck/00install.out

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### Running command:
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###   /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD INSTALL NoRCE
###
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* installing to library ‘/Library/Frameworks/R.framework/Versions/4.0/Resources/library’
* installing *source* package ‘NoRCE’ ...
** 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 (NoRCE)

Tests output

NoRCE.Rcheck/tests/testthat.Rout


R version 4.0.3 (2020-10-10) -- "Bunny-Wunnies Freak Out"
Copyright (C) 2020 The R Foundation for Statistical Computing
Platform: x86_64-apple-darwin17.0 (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(NoRCE)

> 
> test_check("NoRCE")
══ testthat results  ═══════════════════════════════════════════════════════════
[ OK: 1 | SKIPPED: 0 | WARNINGS: 0 | FAILED: 0 ]
> 
> proc.time()
   user  system elapsed 
 18.333   0.838  22.029 

Example timings

NoRCE.Rcheck/NoRCE-Ex.timings

nameusersystemelapsed
KeggEnrichment10.882 0.46532.376
WikiEnrichment3.5400.1414.865
assembly 8.636 0.41323.824
brain_disorder_ncRNA0.0040.0020.005
brain_mirna0.0010.0010.003
breastmRNA0.0020.0010.003
calculateCorr12.132 0.15212.303
convertGeneID0.5780.0120.594
extractBiotype0.1970.0180.220
filterBiotype0.0350.0020.037
geneGOEnricher7.1170.2817.505
genePathwayEnricher19.384 0.10721.790
geneRegionGOEnricher5.6870.2406.055
geneRegionPathwayEnricher1.7100.0161.922
getGoDag3.0940.0533.352
getKeggDiagram3.5290.0483.781
getNearToExon2.1910.0552.253
getNearToIntron2.0700.0322.104
getReactomeDiagram7.3830.1227.527
getTADOverlap0.1430.0020.144
getUCSC0.2030.0020.206
goEnrichment2.9990.1333.134
listTAD0.0030.0010.004
mirna0.0010.0010.002
mirnaGOEnricher7.4110.2787.756
mirnaPathwayEnricher3.1880.0503.440
mirnaRegionGOEnricher6.8500.2337.097
mirnaRegionPathwayEnricher0.6490.0020.848
mrna0.0010.0020.003
ncRegion0.0020.0020.003
predictmiTargets1.7980.0782.226
reactomeEnrichment5.3020.0585.370
setParameters0.0010.0000.001
tad_dmel0.0010.0010.003
tad_hg190.0010.0020.002
tad_hg380.0010.0010.003
tad_mm100.0020.0010.003
writeEnrichment8.5980.3189.065