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This page was generated on 2021-10-18 12:03:36 -0400 (Mon, 18 Oct 2021).

CHECK results for Basic4Cseq on nebbiolo2

To the developers/maintainers of the Basic4Cseq package:
- Please allow up to 24 hours (and sometimes 48 hours) for your latest push to git@git.bioconductor.org:packages/Basic4Cseq.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 117/2060HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
Basic4Cseq 1.29.0  (landing page)
Carolin Walter
Snapshot Date: 2021-10-17 14:50:03 -0400 (Sun, 17 Oct 2021)
git_url: https://git.bioconductor.org/packages/Basic4Cseq
git_branch: master
git_last_commit: 12af821
git_last_commit_date: 2021-05-19 12:03:22 -0400 (Wed, 19 May 2021)
nebbiolo2Linux (Ubuntu 20.04.2 LTS) / x86_64  OK    OK    OK  UNNEEDED, same version is already published
riesling1Windows Server 2019 Standard / x64  OK    OK    OK    OK  UNNEEDED, same version is already published
merida1macOS 10.14.6 Mojave / x86_64  OK    OK    OK    OK  UNNEEDED, same version is already published

Summary

Package: Basic4Cseq
Version: 1.29.0
Command: /home/biocbuild/bbs-3.14-bioc/R/bin/R CMD check --install=check:Basic4Cseq.install-out.txt --library=/home/biocbuild/bbs-3.14-bioc/R/library --no-vignettes --timings Basic4Cseq_1.29.0.tar.gz
StartedAt: 2021-10-17 19:08:31 -0400 (Sun, 17 Oct 2021)
EndedAt: 2021-10-17 19:11:39 -0400 (Sun, 17 Oct 2021)
EllapsedTime: 188.0 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-3.14-bioc/R/bin/R CMD check --install=check:Basic4Cseq.install-out.txt --library=/home/biocbuild/bbs-3.14-bioc/R/library --no-vignettes --timings Basic4Cseq_1.29.0.tar.gz
###
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* using log directory ‘/home/biocbuild/bbs-3.14-bioc/meat/Basic4Cseq.Rcheck’
* using R version 4.1.1 (2021-08-10)
* 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 ‘1.29.0’
* 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 (user + system) or elapsed time > 5s
                  user system elapsed
readsToFragments 4.556  1.784   6.341
* 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-3.14-bioc/R/bin/R CMD INSTALL Basic4Cseq
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* installing to library ‘/home/biocbuild/bbs-3.14-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-class0.0010.0000.001
Data4Cseq0.0760.0000.076
checkRestrictionEnzymeSequence0.0000.0000.001
chooseNearCisFragments0.0080.0000.008
createVirtualFragmentLibrary000
drawDigestionFragmentHistogram0.0050.0000.004
drawHeatmap000
exportVisualizationFragmentData000
getReadDistribution0.1470.0200.166
giveEnzymeSequence0.0010.0000.002
importVisualizationFragmentData0.0060.0000.006
liverData0.0010.0030.003
liverDataRaw0.0010.0000.002
normalizeFragmentData0.0040.0000.005
plotTransInteractions000
prepare4CseqData0.0010.0000.000
printBEDFragmentLibrary000
printWigFile000
readPointsOfInterestFile0.0020.0000.002
readsToFragments4.5561.7846.341
simulateDigestion0.0020.0000.002
visualizeViewpoint0.0360.0040.040