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This page was generated on 2024-12-23 12:04 -0500 (Mon, 23 Dec 2024).

HostnameOSArch (*)R versionInstalled pkgs
nebbiolo2Linux (Ubuntu 24.04.1 LTS)x86_644.4.2 (2024-10-31) -- "Pile of Leaves" 4744
palomino8Windows Server 2022 Datacenterx644.4.2 (2024-10-31 ucrt) -- "Pile of Leaves" 4487
merida1macOS 12.7.5 Montereyx86_644.4.2 (2024-10-31) -- "Pile of Leaves" 4515
kjohnson1macOS 13.6.6 Venturaarm644.4.2 (2024-10-31) -- "Pile of Leaves" 4467
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

Package 2179/2289HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
transcriptR 1.34.0  (landing page)
Armen R. Karapetyan
Snapshot Date: 2024-12-19 13:00 -0500 (Thu, 19 Dec 2024)
git_url: https://git.bioconductor.org/packages/transcriptR
git_branch: RELEASE_3_20
git_last_commit: 9f6196d
git_last_commit_date: 2024-10-29 10:05:55 -0500 (Tue, 29 Oct 2024)
nebbiolo2Linux (Ubuntu 24.04.1 LTS) / x86_64  OK    OK    OK  UNNEEDED, same version is already published
palomino8Windows Server 2022 Datacenter / x64  OK    OK    OK    OK  UNNEEDED, same version is already published
merida1macOS 12.7.5 Monterey / x86_64  OK    OK    OK    OK  UNNEEDED, same version is already published
kjohnson1macOS 13.6.6 Ventura / arm64  OK    OK    OK    OK  UNNEEDED, same version is already published


CHECK results for transcriptR on nebbiolo2

To the developers/maintainers of the transcriptR package:
- 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 Troubleshooting Build Report for more information.
- Use the following Renviron settings to reproduce errors and warnings.
- If 'R CMD check' started to fail recently on the Linux builder(s) over a missing dependency, add the missing dependency to 'Suggests:' in your DESCRIPTION file. See Renviron.bioc for more information.

raw results


Summary

Package: transcriptR
Version: 1.34.0
Command: /home/biocbuild/bbs-3.20-bioc/R/bin/R CMD check --install=check:transcriptR.install-out.txt --library=/home/biocbuild/bbs-3.20-bioc/R/site-library --timings transcriptR_1.34.0.tar.gz
StartedAt: 2024-12-20 06:15:53 -0500 (Fri, 20 Dec 2024)
EndedAt: 2024-12-20 06:23:32 -0500 (Fri, 20 Dec 2024)
EllapsedTime: 459.5 seconds
RetCode: 0
Status:   OK  
CheckDir: transcriptR.Rcheck
Warnings: 0

Command output

##############################################################################
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###
### Running command:
###
###   /home/biocbuild/bbs-3.20-bioc/R/bin/R CMD check --install=check:transcriptR.install-out.txt --library=/home/biocbuild/bbs-3.20-bioc/R/site-library --timings transcriptR_1.34.0.tar.gz
###
##############################################################################
##############################################################################


* using log directory ‘/home/biocbuild/bbs-3.20-bioc/meat/transcriptR.Rcheck’
* using R version 4.4.2 (2024-10-31)
* using platform: x86_64-pc-linux-gnu
* R was compiled by
    gcc (Ubuntu 13.2.0-23ubuntu4) 13.2.0
    GNU Fortran (Ubuntu 13.2.0-23ubuntu4) 13.2.0
* running under: Ubuntu 24.04.1 LTS
* using session charset: UTF-8
* checking for file ‘transcriptR/DESCRIPTION’ ... OK
* checking extension type ... Package
* this is package ‘transcriptR’ version ‘1.34.0’
* 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 code 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 loading without being on the library search path ... 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 7.748  0.338   8.086
* checking for unstated dependencies in ‘tests’ ... OK
* checking tests ...
  Running ‘testthat.R’
 OK
* checking for unstated dependencies in vignettes ... OK
* checking package vignettes ... OK
* checking re-building of vignette outputs ... OK
* checking PDF version of manual ... OK
* DONE

Status: OK


Installation output

transcriptR.Rcheck/00install.out

##############################################################################
##############################################################################
###
### Running command:
###
###   /home/biocbuild/bbs-3.20-bioc/R/bin/R CMD INSTALL transcriptR
###
##############################################################################
##############################################################################


* installing to library ‘/home/biocbuild/bbs-3.20-bioc/R/site-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 4.4.2 (2024-10-31) -- "Pile of Leaves"
Copyright (C) 2024 The R Foundation for Statistical Computing
Platform: x86_64-pc-linux-gnu

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 
 54.835   1.681  56.513 

Example timings

transcriptR.Rcheck/transcriptR-Ex.timings

nameusersystemelapsed
addFeature-methods0.0960.0150.111
annotateTranscripts-methods2.7830.5153.298
breakTranscriptsByPeaks-methods7.7480.3388.086
constructCDS0.0030.0000.003
constructTDS0.2130.0200.233
detectTranscripts-methods1.2050.0711.277
estimateBackground-methods0.3480.0240.371
estimateGapDistance-methods0.8650.0380.902
exportCoverage-methods0.2110.0120.223
getConfusionMatrix-methods0.0020.0000.003
getGenomicAnnot-methods0.0040.0000.004
getPeaks-methods0.0200.0020.022
getPredictorSignificance-methods0.0030.0000.002
getProbTreshold-methods0.0030.0000.002
getQuadProb-methods0.2160.0150.230
getTestedGapDistances-methods0.2300.0280.259
getTranscripts-methods0.2160.0100.226
peaksToBed-methods4.4510.2814.733
plotErrorRate-methods0.9240.0300.954
plotFeatures-methods1.9270.0792.005
plotGenomicAnnot-methods0.4970.0340.530
plotROC-methods0.6110.0310.642
predictStrand-methods3.4040.1213.526
predictTssOverlap-methods0.6240.0050.630
show0.2120.0120.226
transcriptsToBed-methods2.4690.1822.651