Back to Multiple platform build/check report for BioC 3.14
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This page was generated on 2022-01-26 13:07:30 -0500 (Wed, 26 Jan 2022).

HostnameOSArch (*)R versionInstalled pkgs
nebbiolo2Linux (Ubuntu 20.04.4 LTS)x86_644.1.2 (2021-11-01) -- "Bird Hippie" 4329
tokay2Windows Server 2012 R2 Standardx644.1.2 (2021-11-01) -- "Bird Hippie" 4080
machv2macOS 10.14.6 Mojavex86_644.1.2 (2021-11-01) -- "Bird Hippie" 4141
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 tokay2


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 1984/2083HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
transcriptR 1.22.0  (landing page)
Armen R. Karapetyan
Snapshot Date: 2022-01-25 01:55:07 -0500 (Tue, 25 Jan 2022)
git_url: https://git.bioconductor.org/packages/transcriptR
git_branch: RELEASE_3_14
git_last_commit: 6605278
git_last_commit_date: 2021-10-26 12:24:18 -0500 (Tue, 26 Oct 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: transcriptR
Version: 1.22.0
Command: C:\Users\biocbuild\bbs-3.14-bioc\R\bin\R.exe CMD check --force-multiarch --install=check:transcriptR.install-out.txt --library=C:\Users\biocbuild\bbs-3.14-bioc\R\library --no-vignettes --timings transcriptR_1.22.0.tar.gz
StartedAt: 2022-01-26 04:10:05 -0500 (Wed, 26 Jan 2022)
EndedAt: 2022-01-26 04:20:22 -0500 (Wed, 26 Jan 2022)
EllapsedTime: 616.9 seconds
RetCode: 0
Status:   OK  
CheckDir: transcriptR.Rcheck
Warnings: 0

Command output

##############################################################################
##############################################################################
###
### Running command:
###
###   C:\Users\biocbuild\bbs-3.14-bioc\R\bin\R.exe CMD check --force-multiarch --install=check:transcriptR.install-out.txt --library=C:\Users\biocbuild\bbs-3.14-bioc\R\library --no-vignettes --timings transcriptR_1.22.0.tar.gz
###
##############################################################################
##############################################################################


* using log directory 'C:/Users/biocbuild/bbs-3.14-bioc/meat/transcriptR.Rcheck'
* using R version 4.1.2 (2021-11-01)
* 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 '1.22.0'
* 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 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
* loading checks for arch 'i386'
** 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
* loading checks for arch 'x64'
** 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 ...
** running examples for arch 'i386' ... OK
Examples with CPU (user + system) or elapsed time > 5s
                                 user system elapsed
breakTranscriptsByPeaks-methods 14.11   0.83   15.56
predictStrand-methods            5.55   0.22    5.77
peaksToBed-methods               5.09   0.11    5.20
** running examples for arch 'x64' ... OK
Examples with CPU (user + system) or elapsed time > 5s
                                 user system elapsed
breakTranscriptsByPeaks-methods 10.29   0.33   10.61
predictStrand-methods            5.21   0.17    5.38
peaksToBed-methods               5.05   0.20    5.25
* checking for unstated dependencies in 'tests' ... OK
* checking tests ...
** running tests for arch 'i386' ...
  Running 'testthat.R'
 OK
** running tests for arch 'x64' ...
  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:
###
###   C:\cygwin\bin\curl.exe -O http://155.52.207.166/BBS/3.14/bioc/src/contrib/transcriptR_1.22.0.tar.gz && rm -rf transcriptR.buildbin-libdir && mkdir transcriptR.buildbin-libdir && C:\Users\biocbuild\bbs-3.14-bioc\R\bin\R.exe CMD INSTALL --merge-multiarch --build --library=transcriptR.buildbin-libdir transcriptR_1.22.0.tar.gz && C:\Users\biocbuild\bbs-3.14-bioc\R\bin\R.exe CMD INSTALL transcriptR_1.22.0.zip && rm transcriptR_1.22.0.tar.gz transcriptR_1.22.0.zip
###
##############################################################################
##############################################################################


  % Total    % Received % Xferd  Average Speed   Time    Time     Time  Current
                                 Dload  Upload   Total   Spent    Left  Speed

  0     0    0     0    0     0      0      0 --:--:-- --:--:-- --:--:--     0
 69 2472k   69 1728k    0     0  2050k      0  0:00:01 --:--:--  0:00:01 2050k
100 2472k  100 2472k    0     0  2219k      0  0:00:01  0:00:01 --:--:-- 2221k

install for i386

* 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

install for x64

* installing *source* package 'transcriptR' ...
** testing if installed package can be loaded
* MD5 sums
packaged installation of 'transcriptR' as transcriptR_1.22.0.zip
* DONE (transcriptR)
* installing to library 'C:/Users/biocbuild/bbs-3.14-bioc/R/library'
package 'transcriptR' successfully unpacked and MD5 sums checked

Tests output

transcriptR.Rcheck/tests_i386/testthat.Rout


R version 4.1.2 (2021-11-01) -- "Bird Hippie"
Copyright (C) 2021 The R Foundation for Statistical Computing
Platform: i386-w64-mingw32/i386 (32-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 
  59.09    3.00   62.06 

transcriptR.Rcheck/tests_x64/testthat.Rout


R version 4.1.2 (2021-11-01) -- "Bird Hippie"
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 
  62.98    1.81   64.79 

Example timings

transcriptR.Rcheck/examples_i386/transcriptR-Ex.timings

nameusersystemelapsed
addFeature-methods0.160.000.16
annotateTranscripts-methods3.120.173.29
breakTranscriptsByPeaks-methods14.11 0.8315.56
constructCDS000
constructTDS0.440.040.50
detectTranscripts-methods2.630.333.65
estimateBackground-methods0.540.000.55
estimateGapDistance-methods1.060.051.11
exportCoverage-methods0.290.030.31
getConfusionMatrix-methods000
getGenomicAnnot-methods0.010.000.01
getPeaks-methods0.080.000.08
getPredictorSignificance-methods0.000.010.02
getProbTreshold-methods0.000.020.01
getQuadProb-methods0.390.030.42
getTestedGapDistances-methods0.450.010.47
getTranscripts-methods0.520.050.57
peaksToBed-methods5.090.115.20
plotErrorRate-methods1.080.021.10
plotFeatures-methods1.500.031.53
plotGenomicAnnot-methods0.290.000.30
plotROC-methods1.550.001.54
predictStrand-methods5.550.225.77
predictTssOverlap-methods1.510.001.51
show0.400.000.41
transcriptsToBed-methods1.500.071.57

transcriptR.Rcheck/examples_x64/transcriptR-Ex.timings

nameusersystemelapsed
addFeature-methods0.220.000.22
annotateTranscripts-methods3.250.043.30
breakTranscriptsByPeaks-methods10.29 0.3310.61
constructCDS000
constructTDS0.200.030.23
detectTranscripts-methods1.470.061.53
estimateBackground-methods0.430.050.49
estimateGapDistance-methods1.080.031.10
exportCoverage-methods0.350.020.36
getConfusionMatrix-methods000
getGenomicAnnot-methods0.000.010.02
getPeaks-methods0.070.000.08
getPredictorSignificance-methods0.020.000.01
getProbTreshold-methods000
getQuadProb-methods0.330.030.36
getTestedGapDistances-methods0.330.040.36
getTranscripts-methods0.260.010.28
peaksToBed-methods5.050.205.25
plotErrorRate-methods1.030.021.05
plotFeatures-methods1.640.021.66
plotGenomicAnnot-methods0.340.000.34
plotROC-methods1.580.011.59
predictStrand-methods5.210.175.38
predictTssOverlap-methods1.640.051.69
show0.250.020.26
transcriptsToBed-methods2.790.032.83