Back to Multiple platform build/check report for BioC 3.15
ABCDEFGHIJKLMNOPQRS[T]UVWXYZ

This page was generated on 2022-03-18 11:08:53 -0400 (Fri, 18 Mar 2022).

HostnameOSArch (*)R versionInstalled pkgs
nebbiolo1Linux (Ubuntu 20.04.4 LTS)x86_64R Under development (unstable) (2022-02-17 r81757) -- "Unsuffered Consequences" 4334
riesling1Windows Server 2019 Standardx64R Under development (unstable) (2021-11-21 r81221) -- "Unsuffered Consequences" 4097
palomino3Windows Server 2022 Datacenterx64R Under development (unstable) (2022-02-17 r81757 ucrt) -- "Unsuffered Consequences" 4083
merida1macOS 10.14.6 Mojavex86_64R Under development (unstable) (2022-03-02 r81842) -- "Unsuffered Consequences" 4134
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 riesling1


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? 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 1990/2090HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
transcriptR 1.23.1  (landing page)
Armen R. Karapetyan
Snapshot Date: 2022-03-17 13:55:23 -0400 (Thu, 17 Mar 2022)
git_url: https://git.bioconductor.org/packages/transcriptR
git_branch: master
git_last_commit: ca08999
git_last_commit_date: 2021-11-20 20:56:28 -0400 (Sat, 20 Nov 2021)
nebbiolo1Linux (Ubuntu 20.04.4 LTS) / x86_64  OK    OK    OK  UNNEEDED, same version is already published
riesling1Windows Server 2019 Standard / x64  OK    OK    OK    OK  
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: transcriptR
Version: 1.23.1
Command: D:\biocbuild\bbs-3.15-bioc\R\bin\R.exe CMD check --no-multiarch --install=check:transcriptR.install-out.txt --library=D:\biocbuild\bbs-3.15-bioc\R\library --no-vignettes --timings transcriptR_1.23.1.tar.gz
StartedAt: 2022-03-17 20:30:51 -0400 (Thu, 17 Mar 2022)
EndedAt: 2022-03-17 20:36:11 -0400 (Thu, 17 Mar 2022)
EllapsedTime: 320.7 seconds
RetCode: 0
Status:   OK  
CheckDir: transcriptR.Rcheck
Warnings: 0

Command output

##############################################################################
##############################################################################
###
### Running command:
###
###   D:\biocbuild\bbs-3.15-bioc\R\bin\R.exe CMD check --no-multiarch --install=check:transcriptR.install-out.txt --library=D:\biocbuild\bbs-3.15-bioc\R\library --no-vignettes --timings transcriptR_1.23.1.tar.gz
###
##############################################################################
##############################################################################


* using log directory 'D:/biocbuild/bbs-3.15-bioc/meat/transcriptR.Rcheck'
* using R Under development (unstable) (2021-11-21 r81221)
* using platform: x86_64-w64-mingw32 (64-bit)
* using session charset: ISO8859-1
* using option '--no-vignettes'
* checking for file 'transcriptR/DESCRIPTION' ... OK
* checking extension type ... Package
* this is package 'transcriptR' version '1.23.1'
* 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 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 5.92   0.43    6.36
* 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

##############################################################################
##############################################################################
###
### Running command:
###
###   D:\biocbuild\bbs-3.15-bioc\R\bin\R.exe CMD INSTALL transcriptR
###
##############################################################################
##############################################################################


* installing to library 'D:/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
  converting help for package 'transcriptR'
    finding HTML links ... done
    ChipDataSet-class                       html  
    TranscriptionDataSet-class              html  
    addFeature-methods                      html  
    annot                                   html  
    finding level-2 HTML links ... done

    annotateTranscripts-methods             html  
    breakTranscriptsByPeaks-methods         html  
    cds                                     html  
    constructCDS                            html  
    constructTDS                            html  
    detectTranscripts-methods               html  
    estimateBackground-methods              html  
    estimateGapDistance-methods             html  
    exportCoverage-methods                  html  
    getConfusionMatrix-methods              html  
    getGenomicAnnot-methods                 html  
    getPeaks-methods                        html  
    getPredictorSignificance-methods        html  
    getProbTreshold-methods                 html  
    getQuadProb-methods                     html  
    getTestedGapDistances-methods           html  
    getTranscripts-methods                  html  
    peaksToBed-methods                      html  
    plotErrorRate-methods                   html  
    plotFeatures-methods                    html  
    plotGenomicAnnot-methods                html  
    plotROC-methods                         html  
    predictStrand-methods                   html  
    predictTssOverlap-methods               html  
    show                                    html  
    tds                                     html  
    transcriptsToBed-methods                html  
** 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)
Making 'packages.html' ...Warning in packageDescription(i, lib.loc = lib, fields = "Title", encoding = "UTF-8") :
  DESCRIPTION file of package 'nullranges' is missing or broken
Warning in packageDescription(i, lib.loc = lib, fields = "Title", encoding = "UTF-8") :
  DESCRIPTION file of package 'PAST' is missing or broken
 done

Tests output

transcriptR.Rcheck/tests/testthat.Rout


R Under development (unstable) (2021-11-21 r81221) -- "Unsuffered Consequences"
Copyright (C) 2021 The R Foundation for Statistical Computing
Platform: x86_64-w64-mingw32/x64 (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 
  44.31    2.32   46.64 

Example timings

transcriptR.Rcheck/transcriptR-Ex.timings

nameusersystemelapsed
addFeature-methods0.080.000.08
annotateTranscripts-methods2.320.162.49
breakTranscriptsByPeaks-methods5.920.436.36
constructCDS000
constructTDS0.120.050.17
detectTranscripts-methods0.910.060.97
estimateBackground-methods0.360.130.48
estimateGapDistance-methods0.750.110.86
exportCoverage-methods0.140.060.21
getConfusionMatrix-methods000
getGenomicAnnot-methods000
getPeaks-methods0.030.000.03
getPredictorSignificance-methods000
getProbTreshold-methods0.000.020.01
getQuadProb-methods0.130.040.17
getTestedGapDistances-methods0.180.000.19
getTranscripts-methods0.180.030.20
peaksToBed-methods3.290.293.58
plotErrorRate-methods0.800.070.88
plotFeatures-methods1.220.001.22
plotGenomicAnnot-methods0.230.000.23
plotROC-methods1.280.021.30
predictStrand-methods3.300.233.53
predictTssOverlap-methods1.170.041.20
show0.170.000.17
transcriptsToBed-methods0.800.100.91