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This page was generated on 2022-06-27 11:10:11 -0400 (Mon, 27 Jun 2022).

HostnameOSArch (*)R versionInstalled pkgs
nebbiolo1Linux (Ubuntu 20.04.4 LTS)x86_644.2.0 (2022-04-22) -- "Vigorous Calisthenics" 4380
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 transcriptR on nebbiolo1


To the developers/maintainers of the transcriptR package:
- Please allow up to 24 hours (and sometimes 48 hours) for your latest push to git@git.bioconductor.org:packages/transcriptR.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 2037/2140HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
transcriptR 1.24.0  (landing page)
Armen R. Karapetyan
Snapshot Date: 2022-06-26 13:55:11 -0400 (Sun, 26 Jun 2022)
git_url: https://git.bioconductor.org/packages/transcriptR
git_branch: RELEASE_3_15
git_last_commit: d4ab47e
git_last_commit_date: 2022-04-26 11:28:38 -0400 (Tue, 26 Apr 2022)
nebbiolo1Linux (Ubuntu 20.04.4 LTS) / x86_64  OK    OK    OK  UNNEEDED, same version is already published

Summary

Package: transcriptR
Version: 1.24.0
Command: /home/biocbuild/bbs-3.15-bioc/R/bin/R CMD check --install=check:transcriptR.install-out.txt --library=/home/biocbuild/bbs-3.15-bioc/R/library --no-vignettes --timings transcriptR_1.24.0.tar.gz
StartedAt: 2022-06-26 22:18:38 -0400 (Sun, 26 Jun 2022)
EndedAt: 2022-06-26 22:25:28 -0400 (Sun, 26 Jun 2022)
EllapsedTime: 410.3 seconds
RetCode: 0
Status:   OK  
CheckDir: transcriptR.Rcheck
Warnings: 0

Command output

##############################################################################
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### Running command:
###
###   /home/biocbuild/bbs-3.15-bioc/R/bin/R CMD check --install=check:transcriptR.install-out.txt --library=/home/biocbuild/bbs-3.15-bioc/R/library --no-vignettes --timings transcriptR_1.24.0.tar.gz
###
##############################################################################
##############################################################################


* using log directory ‘/home/biocbuild/bbs-3.15-bioc/meat/transcriptR.Rcheck’
* using R version 4.2.0 (2022-04-22)
* using platform: x86_64-pc-linux-gnu (64-bit)
* using session charset: UTF-8
* using option ‘--no-vignettes’
* checking for file ‘transcriptR/DESCRIPTION’ ... OK
* checking extension type ... Package
* this is package ‘transcriptR’ version ‘1.24.0’
* 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 ‘transcriptR’ 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
breakTranscriptsByPeaks-methods 6.421   0.36   6.781
* 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

transcriptR.Rcheck/00install.out

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###
### Running command:
###
###   /home/biocbuild/bbs-3.15-bioc/R/bin/R CMD INSTALL transcriptR
###
##############################################################################
##############################################################################


* installing to library ‘/home/biocbuild/bbs-3.15-bioc/R/library’
* installing *source* package ‘transcriptR’ ...
** using staged installation
** R
** data
** 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 (transcriptR)

Tests output

transcriptR.Rcheck/tests/testthat.Rout


R version 4.2.0 (2022-04-22) -- "Vigorous Calisthenics"
Copyright (C) 2022 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(transcriptR)
> 
> test_check("transcriptR")
[ FAIL 0 | WARN 0 | SKIP 0 | PASS 87 ]
> 
> proc.time()
   user  system elapsed 
 62.850   2.374  65.317 

Example timings

transcriptR.Rcheck/transcriptR-Ex.timings

nameusersystemelapsed
addFeature-methods0.0790.0080.088
annotateTranscripts-methods2.7790.1362.915
breakTranscriptsByPeaks-methods6.4210.3606.781
constructCDS0.0030.0000.003
constructTDS0.2150.0080.224
detectTranscripts-methods1.1290.0441.174
estimateBackground-methods1.2950.0361.331
estimateGapDistance-methods0.8610.0100.871
exportCoverage-methods0.2110.0050.217
getConfusionMatrix-methods0.0030.0000.003
getGenomicAnnot-methods0.0040.0000.003
getPeaks-methods0.0130.0080.021
getPredictorSignificance-methods0.0030.0000.002
getProbTreshold-methods0.0030.0000.002
getQuadProb-methods0.2180.0120.229
getTestedGapDistances-methods0.2180.0120.229
getTranscripts-methods0.2040.0160.219
peaksToBed-methods4.2490.2044.453
plotErrorRate-methods0.8740.0160.890
plotFeatures-methods1.5510.0391.591
plotGenomicAnnot-methods0.3140.0000.314
plotROC-methods1.6860.0761.762
predictStrand-methods4.2690.0804.349
predictTssOverlap-methods1.6400.0881.728
show0.2450.0080.253
transcriptsToBed-methods1.2640.0161.280