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CHECK report for Basic4Cseq on malbec1

This page was generated on 2020-04-15 12:08:26 -0400 (Wed, 15 Apr 2020).

Package 113/1823HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
Basic4Cseq 1.22.0
Carolin Walter
Snapshot Date: 2020-04-14 16:46:13 -0400 (Tue, 14 Apr 2020)
URL: https://git.bioconductor.org/packages/Basic4Cseq
Branch: RELEASE_3_10
Last Commit: 25a3f99
Last Changed Date: 2019-10-29 13:08:53 -0400 (Tue, 29 Oct 2019)
malbec1 Linux (Ubuntu 18.04.4 LTS) / x86_64  OK  OK [ OK ]UNNEEDED, same version exists in internal repository
tokay1 Windows Server 2012 R2 Standard / x64  OK  OK  OK  OK UNNEEDED, same version exists in internal repository
merida1 OS X 10.11.6 El Capitan / x86_64  OK  OK  OK  OK UNNEEDED, same version exists in internal repository

Summary

Package: Basic4Cseq
Version: 1.22.0
Command: /home/biocbuild/bbs-3.10-bioc/R/bin/R CMD check --install=check:Basic4Cseq.install-out.txt --library=/home/biocbuild/bbs-3.10-bioc/R/library --no-vignettes --timings Basic4Cseq_1.22.0.tar.gz
StartedAt: 2020-04-15 02:05:02 -0400 (Wed, 15 Apr 2020)
EndedAt: 2020-04-15 02:08:41 -0400 (Wed, 15 Apr 2020)
EllapsedTime: 219.0 seconds
RetCode: 0
Status:  OK 
CheckDir: Basic4Cseq.Rcheck
Warnings: 0

Command output

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### Running command:
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###   /home/biocbuild/bbs-3.10-bioc/R/bin/R CMD check --install=check:Basic4Cseq.install-out.txt --library=/home/biocbuild/bbs-3.10-bioc/R/library --no-vignettes --timings Basic4Cseq_1.22.0.tar.gz
###
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* using log directory ‘/home/biocbuild/bbs-3.10-bioc/meat/Basic4Cseq.Rcheck’
* using R version 3.6.3 (2020-02-29)
* using platform: x86_64-pc-linux-gnu (64-bit)
* using session charset: UTF-8
* using option ‘--no-vignettes’
* checking for file ‘Basic4Cseq/DESCRIPTION’ ... OK
* checking extension type ... Package
* this is package ‘Basic4Cseq’ 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 for sufficient/correct file permissions ... 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
* 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 or elapsed time > 5s
                  user system elapsed
readsToFragments 4.224  1.452   5.693
* 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:
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###   /home/biocbuild/bbs-3.10-bioc/R/bin/R CMD INSTALL Basic4Cseq
###
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* installing to library ‘/home/biocbuild/bbs-3.10-bioc/R/library’
* installing *source* package ‘Basic4Cseq’ ...
** using staged installation
** R
** data
** inst
** byte-compile and prepare package for lazy loading
** help
*** installing help indices
** 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 (Basic4Cseq)

Tests output


Example timings

Basic4Cseq.Rcheck/Basic4Cseq-Ex.timings

nameusersystemelapsed
Data4Cseq-class0.0000.0000.002
Data4Cseq0.1360.0000.203
checkRestrictionEnzymeSequence0.0000.0000.001
chooseNearCisFragments0.0080.0080.017
createVirtualFragmentLibrary000
drawDigestionFragmentHistogram0.0080.0000.007
drawHeatmap000
exportVisualizationFragmentData0.0000.0000.001
getReadDistribution0.2440.0240.270
giveEnzymeSequence0.0040.0000.012
importVisualizationFragmentData0.0120.0000.013
liverData0.0040.0000.003
liverDataRaw0.0040.0000.002
normalizeFragmentData0.0040.0000.005
plotTransInteractions0.0000.0000.001
prepare4CseqData000
printBEDFragmentLibrary000
printWigFile000
readPointsOfInterestFile0.0040.0000.003
readsToFragments4.2241.4525.693
simulateDigestion0.0040.0000.002
visualizeViewpoint0.0360.0000.038