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This page was generated on 2022-08-06 11:07:58 -0400 (Sat, 06 Aug 2022).

HostnameOSArch (*)R versionInstalled pkgs
nebbiolo2Linux (Ubuntu 20.04.4 LTS)x86_644.2.1 (2022-06-23) -- "Funny-Looking Kid" 4371
palomino4Windows Server 2022 Datacenterx644.2.1 (2022-06-23 ucrt) -- "Funny-Looking Kid" 4155
lconwaymacOS 12.2.1 Montereyx86_644.2.1 Patched (2022-07-09 r82577) -- "Funny-Looking Kid" 4155
Click on any hostname to see more info about the system (e.g. compilers)      (*) as reported by 'uname -p', except on Windows and Mac OS X

CHECK results for NoRCE on lconway


To the developers/maintainers of the NoRCE package:
- Please allow up to 24 hours (and sometimes 48 hours) for your latest push to git@git.bioconductor.org:packages/NoRCE.git to
reflect on this report. See How and When does the builder pull? When will my changes propagate? for more information.
- Make sure to use the following settings in order to reproduce any error or warning you see on this page.

raw results

Package 1332/2137HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
NoRCE 1.9.0  (landing page)
Gulden Olgun
Snapshot Date: 2022-08-05 14:00:05 -0400 (Fri, 05 Aug 2022)
git_url: https://git.bioconductor.org/packages/NoRCE
git_branch: master
git_last_commit: 982c70b
git_last_commit_date: 2022-04-26 12:03:27 -0400 (Tue, 26 Apr 2022)
nebbiolo2Linux (Ubuntu 20.04.4 LTS) / x86_64  OK    OK    OK  UNNEEDED, same version is already published
palomino4Windows Server 2022 Datacenter / x64  OK    OK    OK    NA  
lconwaymacOS 12.2.1 Monterey / x86_64  OK    OK    OK    OK  UNNEEDED, same version is already published

Summary

Package: NoRCE
Version: 1.9.0
Command: /Library/Frameworks/R.framework/Resources/bin/R CMD check --install=check:NoRCE.install-out.txt --library=/Library/Frameworks/R.framework/Resources/library --no-vignettes --timings NoRCE_1.9.0.tar.gz
StartedAt: 2022-08-05 21:39:46 -0400 (Fri, 05 Aug 2022)
EndedAt: 2022-08-05 21:46:50 -0400 (Fri, 05 Aug 2022)
EllapsedTime: 424.0 seconds
RetCode: 0
Status:   OK  
CheckDir: NoRCE.Rcheck
Warnings: 0

Command output

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###
### Running command:
###
###   /Library/Frameworks/R.framework/Resources/bin/R CMD check --install=check:NoRCE.install-out.txt --library=/Library/Frameworks/R.framework/Resources/library --no-vignettes --timings NoRCE_1.9.0.tar.gz
###
##############################################################################
##############################################################################


* using log directory ‘/Users/biocbuild/bbs-3.16-bioc/meat/NoRCE.Rcheck’
* using R version 4.2.1 Patched (2022-07-09 r82577)
* 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 ‘1.9.0’
* 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 LazyData ... 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
KeggEnrichment      15.026  0.675  61.038
genePathwayEnricher 13.977  0.116  17.909
assembly            10.297  0.333  46.435
geneGOEnricher       5.850  0.315   6.188
calculateCorr        5.886  0.269   6.171
* 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

##############################################################################
##############################################################################
###
### Running command:
###
###   /Library/Frameworks/R.framework/Resources/bin/R CMD INSTALL NoRCE
###
##############################################################################
##############################################################################


* installing to library ‘/Library/Frameworks/R.framework/Versions/4.2/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 4.2.1 Patched (2022-07-09 r82577) -- "Funny-Looking Kid"
Copyright (C) 2022 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")
[ FAIL 0 | WARN 0 | SKIP 0 | PASS 1 ]
> 
> proc.time()
   user  system elapsed 
 11.689   0.576  12.262 

Example timings

NoRCE.Rcheck/NoRCE-Ex.timings

nameusersystemelapsed
KeggEnrichment15.026 0.67561.038
assembly10.297 0.33346.435
brain_disorder_ncRNA0.0020.0010.003
brain_mirna0.0010.0010.003
breastmRNA0.0010.0010.002
calculateCorr5.8860.2696.171
convertGeneID0.3290.0250.358
extractBiotype0.1690.0070.176
filterBiotype0.1090.0040.113
geneGOEnricher5.8500.3156.188
genePathwayEnricher13.977 0.11617.909
geneRegionGOEnricher3.0320.1293.185
geneRegionPathwayEnricher0.6100.0410.875
getGoDag1.7610.0892.792
getKeggDiagram2.3300.1102.836
getNearToExon1.3640.0401.409
getNearToIntron1.4060.0561.468
getReactomeDiagram4.4890.0964.609
getTADOverlap0.1150.0010.116
getUCSC0.1690.0020.171
goEnrichment2.5200.2242.804
listTAD0.0050.0010.005
mirna0.0010.0010.002
mirnaGOEnricher4.4570.3414.873
mirnaPathwayEnricher1.7740.0752.238
mirnaRegionGOEnricher3.7010.1473.858
mirnaRegionPathwayEnricher0.5200.0030.730
mrna0.0010.0010.002
ncRegion0.0000.0010.002
predictmiTargets1.3230.0521.575
reactomeEnrichment3.7370.0413.785
setParameters0.0000.0010.001
tad_dmel0.0010.0010.002
tad_hg190.0000.0010.001
tad_hg380.0010.0010.001
tad_mm100.0010.0010.002
writeEnrichment4.6170.2464.893