Multiple platform build/check report for BioC 3.14 - CHECK results for transcriptR on tokay2

Hostname	OS	Arch (*)	R version	Installed pkgs
nebbiolo2	Linux (Ubuntu 20.04.4 LTS)	x86_64	4.1.3 (2022-03-10) -- "One Push-Up"	4324
tokay2	Windows Server 2012 R2 Standard	x64	4.1.3 (2022-03-10) -- "One Push-Up"	4077
machv2	macOS 10.14.6 Mojave	x86_64	4.1.3 (2022-03-10) -- "One Push-Up"	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*

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: 2022-04-13 04:16:18 -0400 (Wed, 13 Apr 2022)

EndedAt: 2022-04-13 04:26:36 -0400 (Wed, 13 Apr 2022)

EllapsedTime: 617.5 seconds

RetCode: 0

Status: OK

CheckDir: transcriptR.Rcheck

Warnings: 0

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### 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
###
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* using log directory 'C:/Users/biocbuild/bbs-3.14-bioc/meat/transcriptR.Rcheck'
* using R version 4.1.3 (2022-03-10)
* 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 9.81   0.67   10.49
peaksToBed-methods              5.02   0.14    5.16
** running examples for arch 'x64' ... OK
Examples with CPU (user + system) or elapsed time > 5s
                                user system elapsed
breakTranscriptsByPeaks-methods 8.88   0.24    9.11
* 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

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

  0     0    0     0    0     0      0      0 --:--:-- --:--:-- --:--:--     0
  0 2472k    0  2487    0     0  11935      0  0:03:32 --:--:--  0:03:32 11956
 64 2472k   64 1606k    0     0  1438k      0  0:00:01  0:00:01 --:--:-- 1438k
100 2472k  100 2472k    0     0  1659k      0  0:00:01  0:00:01 --:--:-- 1659k

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


R version 4.1.3 (2022-03-10) -- "One Push-Up"
Copyright (C) 2022 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 
  59.00    2.78   61.84


R version 4.1.3 (2022-03-10) -- "One Push-Up"
Copyright (C) 2022 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 
  59.09    1.79   60.89

name	user	system	elapsed
addFeature-methods	0.23	0.00	0.23
annotateTranscripts-methods	3.3	0.2	3.5
breakTranscriptsByPeaks-methods	9.81	0.67	10.49
constructCDS	0.00	0.02	0.01
constructTDS	0.3	0.0	0.3
detectTranscripts-methods	2.09	0.05	2.14
estimateBackground-methods	0.78	0.03	0.81
estimateGapDistance-methods	1.38	0.06	1.44
exportCoverage-methods	0.31	0.02	0.33
getConfusionMatrix-methods	0	0	0
getGenomicAnnot-methods	0.00	0.01	0.01
getPeaks-methods	0.05	0.02	0.07
getPredictorSignificance-methods	0	0	0
getProbTreshold-methods	0.00	0.01	0.01
getQuadProb-methods	0.29	0.02	0.31
getTestedGapDistances-methods	0.27	0.05	0.32
getTranscripts-methods	0.28	0.03	0.31
peaksToBed-methods	5.02	0.14	5.16
plotErrorRate-methods	1.03	0.03	1.06
plotFeatures-methods	1.53	0.00	1.53
plotGenomicAnnot-methods	0.27	0.01	0.28
plotROC-methods	1.39	0.02	1.41
predictStrand-methods	4.78	0.22	5.00
predictTssOverlap-methods	1.46	0.01	1.47
show	0.26	0.02	0.28
transcriptsToBed-methods	1.30	0.06	1.36

name	user	system	elapsed
addFeature-methods	0.12	0.01	0.14
annotateTranscripts-methods	2.89	0.03	2.93
breakTranscriptsByPeaks-methods	8.88	0.24	9.11
constructCDS	0	0	0
constructTDS	0.20	0.03	0.23
detectTranscripts-methods	1.47	0.06	1.54
estimateBackground-methods	0.42	0.02	0.43
estimateGapDistance-methods	1.00	0.04	1.05
exportCoverage-methods	0.24	0.00	0.23
getConfusionMatrix-methods	0	0	0
getGenomicAnnot-methods	0.01	0.00	0.02
getPeaks-methods	0.05	0.00	0.05
getPredictorSignificance-methods	0	0	0
getProbTreshold-methods	0	0	0
getQuadProb-methods	0.20	0.04	0.24
getTestedGapDistances-methods	0.23	0.00	0.23
getTranscripts-methods	0.24	0.01	0.25
peaksToBed-methods	4.58	0.24	4.81
plotErrorRate-methods	0.93	0.06	1.00
plotFeatures-methods	1.5	0.0	1.5
plotGenomicAnnot-methods	0.28	0.02	0.30
plotROC-methods	1.52	0.02	1.53
predictStrand-methods	4.48	0.16	4.64
predictTssOverlap-methods	1.72	0.00	1.72
show	0.24	0.00	0.24
transcriptsToBed-methods	2.33	0.07	2.40

CHECK results for transcriptR on tokay2

Summary

Command output

Installation output

Tests output

Example timings