Back to Multiple platform build/check report for BioC 3.15
ABCDEFGHIJKLM[N]OPQRSTUVWXYZ

This page was generated on 2022-08-15 13:23:17 -0400 (Mon, 15 Aug 2022).

HostnameOSArch (*)R versionInstalled pkgs
nebbiolo1Linux (Ubuntu 20.04.4 LTS)x86_644.2.1 (2022-06-23) -- "Funny-Looking Kid" 4365
palomino3Windows Server 2022 Datacenterx644.2.1 (2022-06-23 ucrt) -- "Funny-Looking Kid" 4118
merida1macOS 10.14.6 Mojavex86_644.2.1 (2022-06-23) -- "Funny-Looking Kid" 4183
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 merida1


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 1333/2140HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
NoRCE 1.8.0  (landing page)
Gulden Olgun
Snapshot Date: 2022-08-14 13:55:13 -0400 (Sun, 14 Aug 2022)
git_url: https://git.bioconductor.org/packages/NoRCE
git_branch: RELEASE_3_15
git_last_commit: ffeef02
git_last_commit_date: 2022-04-26 12:03:27 -0400 (Tue, 26 Apr 2022)
nebbiolo1Linux (Ubuntu 20.04.4 LTS) / x86_64  OK    OK    OK  UNNEEDED, same version is already published
palomino3Windows Server 2022 Datacenter / x64  OK    OK    OK    OK  UNNEEDED, same version is already published
merida1macOS 10.14.6 Mojave / x86_64  OK    OK    OK    OK  UNNEEDED, same version is already published

Summary

Package: NoRCE
Version: 1.8.0
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_1.8.0.tar.gz
StartedAt: 2022-08-15 05:24:21 -0400 (Mon, 15 Aug 2022)
EndedAt: 2022-08-15 05:35:19 -0400 (Mon, 15 Aug 2022)
EllapsedTime: 658.3 seconds
RetCode: 0
Status:   OK  
CheckDir: NoRCE.Rcheck
Warnings: 0

Command output

##############################################################################
##############################################################################
###
### 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_1.8.0.tar.gz
###
##############################################################################
##############################################################################


* using log directory ‘/Users/biocbuild/bbs-3.15-bioc/meat/NoRCE.Rcheck’
* using R version 4.2.1 (2022-06-23)
* 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 ‘1.8.0’
* 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
genePathwayEnricher   38.591  0.153  41.632
KeggEnrichment        30.583  0.960  51.637
assembly              25.749  0.616  36.762
calculateCorr         13.894  0.130  14.059
mirnaGOEnricher        9.147  0.370   9.546
geneGOEnricher         8.038  0.277   8.353
writeEnrichment        7.629  0.241   7.895
getReactomeDiagram     6.499  0.111   6.625
mirnaRegionGOEnricher  6.119  0.192   6.331
geneRegionGOEnricher   5.986  0.203   6.206
reactomeEnrichment     5.886  0.051   5.948
* 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 (2022-06-23) -- "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 
 21.499   0.831  22.377 

Example timings

NoRCE.Rcheck/NoRCE-Ex.timings

nameusersystemelapsed
KeggEnrichment30.583 0.96051.637
assembly25.749 0.61636.762
brain_disorder_ncRNA0.0040.0020.005
brain_mirna0.0010.0010.002
breastmRNA0.0010.0010.003
calculateCorr13.894 0.13014.059
convertGeneID0.5550.0230.580
extractBiotype0.2710.0080.282
filterBiotype0.1730.0050.178
geneGOEnricher8.0380.2778.353
genePathwayEnricher38.591 0.15341.632
geneRegionGOEnricher5.9860.2036.206
geneRegionPathwayEnricher1.1190.0061.321
getGoDag3.0700.0933.362
getKeggDiagram3.4270.1033.727
getNearToExon3.0310.0633.101
getNearToIntron2.6540.0392.698
getReactomeDiagram6.4990.1116.625
getTADOverlap0.1790.0010.180
getUCSC0.2490.0010.251
goEnrichment3.8000.1263.946
listTAD0.0060.0000.006
mirna0.0010.0010.002
mirnaGOEnricher9.1470.3709.546
mirnaPathwayEnricher3.0520.1323.376
mirnaRegionGOEnricher6.1190.1926.331
mirnaRegionPathwayEnricher0.8530.0031.048
mrna0.0010.0010.003
ncRegion0.0020.0010.003
predictmiTargets1.9880.0432.462
reactomeEnrichment5.8860.0515.948
setParameters000
tad_dmel0.0010.0020.002
tad_hg190.0020.0020.002
tad_hg380.0010.0010.003
tad_mm100.0010.0010.003
writeEnrichment7.6290.2417.895