Multiple platform build/check report for BioC 3.13 - CHECK results for transcriptR on tokay2

Package: transcriptR

Version: 1.20.0

Command: C:\Users\biocbuild\bbs-3.13-bioc\R\bin\R.exe CMD check --force-multiarch --install=check:transcriptR.install-out.txt --library=C:\Users\biocbuild\bbs-3.13-bioc\R\library --no-vignettes --timings transcriptR_1.20.0.tar.gz

StartedAt: 2021-10-15 06:51:28 -0400 (Fri, 15 Oct 2021)

EndedAt: 2021-10-15 07:01:41 -0400 (Fri, 15 Oct 2021)

EllapsedTime: 613.3 seconds

RetCode: 0

Status: OK

CheckDir: transcriptR.Rcheck

Warnings: 0

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### Running command:
###
###   C:\Users\biocbuild\bbs-3.13-bioc\R\bin\R.exe CMD check --force-multiarch --install=check:transcriptR.install-out.txt --library=C:\Users\biocbuild\bbs-3.13-bioc\R\library --no-vignettes --timings transcriptR_1.20.0.tar.gz
###
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* using log directory 'C:/Users/biocbuild/bbs-3.13-bioc/meat/transcriptR.Rcheck'
* using R version 4.1.1 (2021-08-10)
* 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 '1.20.0'
* 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 9.03   0.87    9.91
peaksToBed-methods              8.06   0.20   11.64
predictStrand-methods           6.03   0.20    6.24
** running examples for arch 'x64' ... OK
Examples with CPU (user + system) or elapsed time > 5s
                                user system elapsed
breakTranscriptsByPeaks-methods 9.95   0.40   10.36
peaksToBed-methods              5.01   0.17    5.18
predictStrand-methods           4.97   0.14    5.11
* 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://155.52.207.165/BBS/3.13/bioc/src/contrib/transcriptR_1.20.0.tar.gz && rm -rf transcriptR.buildbin-libdir && mkdir transcriptR.buildbin-libdir && C:\Users\biocbuild\bbs-3.13-bioc\R\bin\R.exe CMD INSTALL --merge-multiarch --build --library=transcriptR.buildbin-libdir transcriptR_1.20.0.tar.gz && C:\Users\biocbuild\bbs-3.13-bioc\R\bin\R.exe CMD INSTALL transcriptR_1.20.0.zip && rm transcriptR_1.20.0.tar.gz transcriptR_1.20.0.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
 53 2473k   53 1332k    0     0  2556k      0 --:--:-- --:--:-- --:--:-- 2557k
100 2473k  100 2473k    0     0  3129k      0 --:--:-- --:--:-- --:--:-- 3127k

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_1.20.0.zip
* DONE (transcriptR)
* installing to library 'C:/Users/biocbuild/bbs-3.13-bioc/R/library'
package 'transcriptR' successfully unpacked and MD5 sums checked


R version 4.1.1 (2021-08-10) -- "Kick Things"
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 
  63.62    2.98   66.61


R version 4.1.1 (2021-08-10) -- "Kick Things"
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 
  57.70    1.34   59.01

name	user	system	elapsed
addFeature-methods	0.15	0.00	0.15
annotateTranscripts-methods	3.32	0.38	3.69
breakTranscriptsByPeaks-methods	9.03	0.87	9.91
constructCDS	0.02	0.00	0.02
constructTDS	0.28	0.04	0.31
detectTranscripts-methods	1.64	0.09	1.73
estimateBackground-methods	0.53	0.03	0.57
estimateGapDistance-methods	1.08	0.03	1.11
exportCoverage-methods	0.37	0.05	0.42
getConfusionMatrix-methods	0.02	0.00	0.01
getGenomicAnnot-methods	0	0	0
getPeaks-methods	0.09	0.01	0.11
getPredictorSignificance-methods	0	0	0
getProbTreshold-methods	0.02	0.00	0.02
getQuadProb-methods	1.66	0.07	1.86
getTestedGapDistances-methods	0.43	0.00	0.83
getTranscripts-methods	0.44	0.03	0.53
peaksToBed-methods	8.06	0.20	11.64
plotErrorRate-methods	2.00	0.11	2.11
plotFeatures-methods	1.69	0.05	1.73
plotGenomicAnnot-methods	0.45	0.01	0.47
plotROC-methods	1.36	0.08	1.44
predictStrand-methods	6.03	0.20	6.24
predictTssOverlap-methods	1.50	0.05	1.54
show	0.29	0.00	0.30
transcriptsToBed-methods	1.75	0.03	1.78

name	user	system	elapsed
addFeature-methods	0.27	0.00	0.27
annotateTranscripts-methods	3.07	0.14	3.22
breakTranscriptsByPeaks-methods	9.95	0.40	10.36
constructCDS	0	0	0
constructTDS	0.19	0.04	0.22
detectTranscripts-methods	1.62	0.10	1.73
estimateBackground-methods	0.47	0.02	0.48
estimateGapDistance-methods	1.08	0.02	1.10
exportCoverage-methods	0.25	0.00	0.25
getConfusionMatrix-methods	0	0	0
getGenomicAnnot-methods	0.00	0.01	0.01
getPeaks-methods	0.08	0.00	0.08
getPredictorSignificance-methods	0	0	0
getProbTreshold-methods	0.00	0.02	0.02
getQuadProb-methods	0.23	0.00	0.23
getTestedGapDistances-methods	0.25	0.00	0.25
getTranscripts-methods	0.22	0.01	0.24
peaksToBed-methods	5.01	0.17	5.18
plotErrorRate-methods	1.02	0.05	1.06
plotFeatures-methods	1.65	0.10	1.75
plotGenomicAnnot-methods	0.36	0.00	0.36
plotROC-methods	1.70	0.03	1.75
predictStrand-methods	4.97	0.14	5.11
predictTssOverlap-methods	1.72	0.00	1.72
show	0.19	0.04	0.23
transcriptsToBed-methods	1.86	0.05	1.91

CHECK results for transcriptR on tokay2

Summary

Command output

Installation output

Tests output

Example timings