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This page was generated on 2022-10-19 13:23:23 -0400 (Wed, 19 Oct 2022).

HostnameOSArch (*)R versionInstalled pkgs
nebbiolo1Linux (Ubuntu 20.04.5 LTS)x86_644.2.1 (2022-06-23) -- "Funny-Looking Kid" 4386
palomino3Windows Server 2022 Datacenterx644.2.1 (2022-06-23 ucrt) -- "Funny-Looking Kid" 4138
merida1macOS 10.14.6 Mojavex86_644.2.1 (2022-06-23) -- "Funny-Looking Kid" 4205
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: 2022-10-18 13:55:19 -0400 (Tue, 18 Oct 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 20.04.5 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: 2022-10-19 05:32:16 -0400 (Wed, 19 Oct 2022)
EndedAt: 2022-10-19 05:42:59 -0400 (Wed, 19 Oct 2022)
EllapsedTime: 642.5 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_1.8.0.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   38.862  0.151  41.612
KeggEnrichment        29.907  0.876  49.850
assembly              24.846  0.428  35.003
calculateCorr         13.257  0.166  13.440
mirnaGOEnricher       10.231  0.310  10.572
geneGOEnricher         7.798  0.301   8.120
writeEnrichment        7.165  0.234   7.417
getReactomeDiagram     6.395  0.116   6.524
mirnaRegionGOEnricher  5.808  0.195   6.022
geneRegionGOEnricher   5.680  0.206   5.904
reactomeEnrichment     5.728  0.079   5.816
* 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 
 20.622   0.825  21.448 

Example timings

NoRCE.Rcheck/NoRCE-Ex.timings

nameusersystemelapsed
KeggEnrichment29.907 0.87649.850
assembly24.846 0.42835.003
brain_disorder_ncRNA0.0030.0010.005
brain_mirna0.0010.0010.002
breastmRNA0.0010.0010.003
calculateCorr13.257 0.16613.440
convertGeneID0.5530.0280.584
extractBiotype0.2770.0100.288
filterBiotype0.1700.0050.175
geneGOEnricher7.7980.3018.120
genePathwayEnricher38.862 0.15141.612
geneRegionGOEnricher5.6800.2065.904
geneRegionPathwayEnricher1.0740.0041.276
getGoDag2.9280.0883.214
getKeggDiagram3.6740.1374.011
getNearToExon2.6390.0422.683
getNearToIntron2.4520.0452.501
getReactomeDiagram6.3950.1166.524
getTADOverlap0.1520.0010.154
getUCSC0.2170.0010.218
goEnrichment3.3910.1463.554
listTAD0.0070.0000.007
mirna0.0020.0010.003
mirnaGOEnricher10.231 0.31010.572
mirnaPathwayEnricher2.7030.0782.983
mirnaRegionGOEnricher5.8080.1956.022
mirnaRegionPathwayEnricher0.7780.0060.973
mrna0.0010.0010.001
ncRegion0.0010.0010.002
predictmiTargets1.8600.0502.549
reactomeEnrichment5.7280.0795.816
setParameters0.0000.0010.001
tad_dmel0.0010.0010.003
tad_hg190.0020.0010.003
tad_hg380.0010.0010.003
tad_mm100.0020.0020.003
writeEnrichment7.1650.2347.417