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CHECK report for Basic4Cseq on riesling1

This page was generated on 2020-10-24 11:04:33 -0400 (Sat, 24 Oct 2020).

TO THE DEVELOPERS/MAINTAINERS OF THE Basic4Cseq PACKAGE: Please make sure to use the following settings in order to reproduce any error or warning you see on this page.
Package 118/1974HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
Basic4Cseq 1.25.0
Carolin Walter
Snapshot Date: 2020-10-23 14:40:36 -0400 (Fri, 23 Oct 2020)
URL: https://git.bioconductor.org/packages/Basic4Cseq
Branch: master
Last Commit: e3986b9
Last Changed Date: 2020-04-27 14:38:54 -0400 (Mon, 27 Apr 2020)
malbec1 Linux (Ubuntu 18.04.4 LTS) / x86_64  OK  OK  OK UNNEEDED, same version exists in internal repository
nebbiolo1 Linux (Ubuntu 20.04.1 LTS) / x86_64  OK  OK  OK 
tokay1 Windows Server 2012 R2 Standard / x64  OK  OK  OK  OK UNNEEDED, same version exists in internal repository
riesling1 Windows Server 2019 Standard / x64  OK  OK [ OK ] OK 
merida1 macOS 10.14.6 Mojave / x86_64  OK  OK  OK  OK UNNEEDED, same version exists in internal repository

Summary

Package: Basic4Cseq
Version: 1.25.0
Command: D:\biocbuild\bbs-3.12-bioc\R\bin\R.exe CMD check --force-multiarch --install=check:Basic4Cseq.install-out.txt --library=D:\biocbuild\bbs-3.12-bioc\R\library --no-vignettes --timings Basic4Cseq_1.25.0.tar.gz
StartedAt: 2020-10-24 01:41:03 -0400 (Sat, 24 Oct 2020)
EndedAt: 2020-10-24 01:44:42 -0400 (Sat, 24 Oct 2020)
EllapsedTime: 218.9 seconds
RetCode: 0
Status:  OK  
CheckDir: Basic4Cseq.Rcheck
Warnings: 0

Command output

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### Running command:
###
###   D:\biocbuild\bbs-3.12-bioc\R\bin\R.exe CMD check --force-multiarch --install=check:Basic4Cseq.install-out.txt --library=D:\biocbuild\bbs-3.12-bioc\R\library --no-vignettes --timings Basic4Cseq_1.25.0.tar.gz
###
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* using log directory 'D:/biocbuild/bbs-3.12-bioc/meat/Basic4Cseq.Rcheck'
* using R version 4.0.3 (2020-10-10)
* using platform: x86_64-w64-mingw32 (64-bit)
* using session charset: ISO8859-1
* using option '--no-vignettes'
* checking for file 'Basic4Cseq/DESCRIPTION' ... OK
* checking extension type ... Package
* this is package 'Basic4Cseq' version '1.25.0'
* 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 'Basic4Cseq' 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
** running examples for arch 'x64' ... 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

Basic4Cseq.Rcheck/00install.out

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###
### Running command:
###
###   C:\cygwin\bin\curl.exe -O http://172.29.0.3/BBS/3.12/bioc/src/contrib/Basic4Cseq_1.25.0.tar.gz && rm -rf Basic4Cseq.buildbin-libdir && mkdir Basic4Cseq.buildbin-libdir && D:\biocbuild\bbs-3.12-bioc\R\bin\R.exe CMD INSTALL --merge-multiarch --build --library=Basic4Cseq.buildbin-libdir Basic4Cseq_1.25.0.tar.gz && D:\biocbuild\bbs-3.12-bioc\R\bin\R.exe CMD INSTALL Basic4Cseq_1.25.0.zip && rm Basic4Cseq_1.25.0.tar.gz Basic4Cseq_1.25.0.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
100  218k  100  218k    0     0  4855k      0 --:--:-- --:--:-- --:--:-- 4855k

install for i386

* installing *source* package 'Basic4Cseq' ...
** using staged installation
** R
** data
** inst
** byte-compile and prepare package for lazy loading
** help
*** installing help indices
  converting help for package 'Basic4Cseq'
    finding HTML links ... done
    Data4Cseq-class                         html  
    Data4Cseq                               html  
    checkRestrictionEnzymeSequence          html  
    chooseNearCisFragments                  html  
    createVirtualFragmentLibrary            html  
    drawDigestionFragmentHistogram          html  
    drawHeatmap                             html  
    exportVisualizationFragmentData         html  
    getReadDistribution                     html  
    giveEnzymeSequence                      html  
    importVisualizationFragmentData         html  
    liverData                               html  
    liverDataRaw                            html  
    normalizeFragmentData                   html  
    plotTransInteractions                   html  
    prepare4CseqData                        html  
    printBEDFragmentLibrary                 html  
    printWigFile                            html  
    readPointsOfInterestFile                html  
    readsToFragments                        html  
    simulateDigestion                       html  
    visualizeViewpoint                      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 'Basic4Cseq' ...
** testing if installed package can be loaded
* MD5 sums
packaged installation of 'Basic4Cseq' as Basic4Cseq_1.25.0.zip
* DONE (Basic4Cseq)
* installing to library 'D:/biocbuild/bbs-3.12-bioc/R/library'
package 'Basic4Cseq' successfully unpacked and MD5 sums checked

Tests output


Example timings

Basic4Cseq.Rcheck/examples_i386/Basic4Cseq-Ex.timings

nameusersystemelapsed
Data4Cseq-class000
Data4Cseq0.100.000.09
checkRestrictionEnzymeSequence000
chooseNearCisFragments0.020.000.02
createVirtualFragmentLibrary000
drawDigestionFragmentHistogram000
drawHeatmap000
exportVisualizationFragmentData000
getReadDistribution0.160.000.15
giveEnzymeSequence000
importVisualizationFragmentData0.000.020.01
liverData0.000.010.02
liverDataRaw000
normalizeFragmentData0.000.010.04
plotTransInteractions000
prepare4CseqData000
printBEDFragmentLibrary000
printWigFile000
readPointsOfInterestFile000
readsToFragments3.260.523.78
simulateDigestion000
visualizeViewpoint0.030.000.04

Basic4Cseq.Rcheck/examples_x64/Basic4Cseq-Ex.timings

nameusersystemelapsed
Data4Cseq-class000
Data4Cseq0.070.000.08
checkRestrictionEnzymeSequence000
chooseNearCisFragments0.000.010.02
createVirtualFragmentLibrary000
drawDigestionFragmentHistogram000
drawHeatmap000
exportVisualizationFragmentData000
getReadDistribution0.130.000.12
giveEnzymeSequence0.020.000.02
importVisualizationFragmentData000
liverData000
liverDataRaw000
normalizeFragmentData000
plotTransInteractions000
prepare4CseqData000
printBEDFragmentLibrary000
printWigFile000
readPointsOfInterestFile000
readsToFragments3.460.744.21
simulateDigestion000
visualizeViewpoint0.040.010.06