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CHECK report for Basic4Cseq on merida1

This page was generated on 2020-10-27 12:02:53 -0400 (Tue, 27 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: 2020-10-26 14:42:55 -0400 (Mon, 26 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: /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD check --install=check:Basic4Cseq.install-out.txt --library=/Library/Frameworks/R.framework/Versions/Current/Resources/library --no-vignettes --timings Basic4Cseq_1.25.0.tar.gz
StartedAt: 2020-10-26 23:50:05 -0400 (Mon, 26 Oct 2020)
EndedAt: 2020-10-26 23:54:04 -0400 (Mon, 26 Oct 2020)
EllapsedTime: 239.2 seconds
RetCode: 0
Status:  OK 
CheckDir: Basic4Cseq.Rcheck
Warnings: 0

Command output

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### Running command:
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###   /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD check --install=check:Basic4Cseq.install-out.txt --library=/Library/Frameworks/R.framework/Versions/Current/Resources/library --no-vignettes --timings Basic4Cseq_1.25.0.tar.gz
###
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* using log directory ‘/Users/biocbuild/bbs-3.12-bioc/meat/Basic4Cseq.Rcheck’
* using R version 4.0.3 (2020-10-10)
* using platform: x86_64-apple-darwin17.0 (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 ‘1.25.0’
* 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 ... NOTE
Found the following hidden files and directories:
  .git_fetch_output.txt
  .git_merge_output.txt
These were most likely included in error. See section ‘Package
structure’ in the ‘Writing R Extensions’ manual.
* 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 sizes of PDF files under ‘inst/doc’ ... OK
* checking files in ‘vignettes’ ... OK
* checking examples ... OK
Examples with CPU (user + system) or elapsed time > 5s
                  user system elapsed
readsToFragments 5.107  1.688   6.806
* 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: 1 NOTE
See
  ‘/Users/biocbuild/bbs-3.12-bioc/meat/Basic4Cseq.Rcheck/00check.log’
for details.



Installation output

Basic4Cseq.Rcheck/00install.out

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###
### Running command:
###
###   /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD INSTALL Basic4Cseq
###
##############################################################################
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* installing to library ‘/Library/Frameworks/R.framework/Versions/4.0/Resources/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-class0.0020.0010.010
Data4Cseq0.1340.0050.139
checkRestrictionEnzymeSequence0.0010.0000.001
chooseNearCisFragments0.0190.0050.024
createVirtualFragmentLibrary0.0000.0000.001
drawDigestionFragmentHistogram0.0090.0010.009
drawHeatmap0.0010.0000.001
exportVisualizationFragmentData0.0000.0000.001
getReadDistribution0.2820.0210.304
giveEnzymeSequence0.0020.0010.003
importVisualizationFragmentData0.0160.0140.031
liverData0.0050.0040.009
liverDataRaw0.0030.0030.007
normalizeFragmentData0.0110.0050.016
plotTransInteractions0.0010.0000.001
prepare4CseqData0.0000.0010.001
printBEDFragmentLibrary0.0000.0000.001
printWigFile000
readPointsOfInterestFile0.0040.0010.006
readsToFragments5.1071.6886.806
simulateDigestion0.0030.0000.004
visualizeViewpoint0.0540.0040.060