Back to Multiple platform build/check report for BioC 3.14
ABCDEFGHIJKLM[N]OPQRSTUVWXYZ

This page was generated on 2022-01-14 13:05:31 -0500 (Fri, 14 Jan 2022).

HostnameOSArch (*)R versionInstalled pkgs
nebbiolo2Linux (Ubuntu 20.04.4 LTS)x86_644.1.2 (2021-11-01) -- "Bird Hippie" 4327
tokay2Windows Server 2012 R2 Standardx644.1.2 (2021-11-01) -- "Bird Hippie" 4076
machv2macOS 10.14.6 Mojavex86_644.1.2 (2021-11-01) -- "Bird Hippie" 4137
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 nebbiolo2


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? here 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 1299/2083HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
NoRCE 1.6.0  (landing page)
Gulden Olgun
Snapshot Date: 2022-01-13 01:55:04 -0500 (Thu, 13 Jan 2022)
git_url: https://git.bioconductor.org/packages/NoRCE
git_branch: RELEASE_3_14
git_last_commit: 8637123
git_last_commit_date: 2021-11-21 00:38:54 -0500 (Sun, 21 Nov 2021)
nebbiolo2Linux (Ubuntu 20.04.4 LTS) / x86_64  OK    OK    OK  UNNEEDED, same version is already published
tokay2Windows Server 2012 R2 Standard / x64  OK    OK    OK    OK  UNNEEDED, same version is already published
machv2macOS 10.14.6 Mojave / x86_64  OK    OK    OK    OK  UNNEEDED, same version is already published

Summary

Package: NoRCE
Version: 1.6.0
Command: /home/biocbuild/bbs-3.14-bioc/R/bin/R CMD check --install=check:NoRCE.install-out.txt --library=/home/biocbuild/bbs-3.14-bioc/R/library --no-vignettes --timings NoRCE_1.6.0.tar.gz
StartedAt: 2022-01-13 08:45:34 -0500 (Thu, 13 Jan 2022)
EndedAt: 2022-01-13 08:52:24 -0500 (Thu, 13 Jan 2022)
EllapsedTime: 410.4 seconds
RetCode: 0
Status:   OK  
CheckDir: NoRCE.Rcheck
Warnings: 0

Command output

##############################################################################
##############################################################################
###
### Running command:
###
###   /home/biocbuild/bbs-3.14-bioc/R/bin/R CMD check --install=check:NoRCE.install-out.txt --library=/home/biocbuild/bbs-3.14-bioc/R/library --no-vignettes --timings NoRCE_1.6.0.tar.gz
###
##############################################################################
##############################################################################


* using log directory ‘/home/biocbuild/bbs-3.14-bioc/meat/NoRCE.Rcheck’
* using R version 4.1.2 (2021-11-01)
* using platform: x86_64-pc-linux-gnu (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 ‘1.6.0’
* 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      15.330  0.911  57.779
genePathwayEnricher 13.819  0.330  18.451
assembly            12.561  1.465  52.856
reactomeEnrichment   5.637  0.840   6.477
calculateCorr        5.356  0.463   5.819
mirnaGOEnricher      5.435  0.212   5.647
geneGOEnricher       4.779  0.308   5.088
* 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:
###
###   /home/biocbuild/bbs-3.14-bioc/R/bin/R CMD INSTALL NoRCE
###
##############################################################################
##############################################################################


* installing to library ‘/home/biocbuild/bbs-3.14-bioc/R/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 4.1.2 (2021-11-01) -- "Bird Hippie"
Copyright (C) 2021 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(NoRCE)

> 
> test_check("NoRCE")
[ FAIL 0 | WARN 0 | SKIP 0 | PASS 1 ]
> 
> proc.time()
   user  system elapsed 
 10.852   0.901  11.739 

Example timings

NoRCE.Rcheck/NoRCE-Ex.timings

nameusersystemelapsed
KeggEnrichment15.330 0.91157.779
assembly12.561 1.46552.856
brain_disorder_ncRNA0.0030.0000.003
brain_mirna0.0010.0000.001
breastmRNA0.0000.0010.000
calculateCorr5.3560.4635.819
convertGeneID0.5330.0080.542
extractBiotype0.1470.0040.151
filterBiotype0.0630.0000.063
geneGOEnricher4.7790.3085.088
genePathwayEnricher13.819 0.33018.451
geneRegionGOEnricher3.1720.3563.530
geneRegionPathwayEnricher0.9320.1161.423
getGoDag2.7420.2963.414
getKeggDiagram3.1500.2883.814
getNearToExon1.1560.0761.232
getNearToIntron1.2170.1001.317
getReactomeDiagram3.9320.3844.316
getTADOverlap0.0890.0120.101
getUCSC0.1350.0040.139
goEnrichment2.4180.1242.542
listTAD0.0050.0000.005
mirna0.0010.0000.000
mirnaGOEnricher5.4350.2125.647
mirnaPathwayEnricher2.5910.0363.003
mirnaRegionGOEnricher3.7460.3404.086
mirnaRegionPathwayEnricher0.4330.0600.876
mrna0.0010.0000.001
ncRegion000
predictmiTargets1.3500.1492.127
reactomeEnrichment5.6370.8406.477
setParameters000
tad_dmel0.0010.0000.001
tad_hg190.0010.0000.001
tad_hg380.0010.0000.001
tad_mm100.0010.0000.001
writeEnrichment4.5740.2004.775