Package: Basic4Cseq

Version: 1.23.0

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_1.23.0.tar.gz

StartedAt: 2020-01-16 01:57:54 -0500 (Thu, 16 Jan 2020)

EndedAt: 2020-01-16 02:04:25 -0500 (Thu, 16 Jan 2020)

EllapsedTime: 390.7 seconds

RetCode: 0

Status:  OK

CheckDir: Basic4Cseq.Rcheck

Warnings: 0

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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_1.23.0.tar.gz
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* using log directory ‘/Users/biocbuild/bbs-3.11-bioc/meat/Basic4Cseq.Rcheck’
* using R Under development (unstable) (2019-12-14 r77572)
* using platform: x86_64-apple-darwin15.6.0 (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 ‘1.23.0’
* 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 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 7.962  5.549  13.521
* 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:
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###   /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)

name	user	system	elapsed
Data4Cseq-class	0.003	0.001	0.004
Data4Cseq	0.166	0.007	0.177
checkRestrictionEnzymeSequence	0.000	0.000	0.001
chooseNearCisFragments	0.021	0.006	0.027
createVirtualFragmentLibrary	0	0	0
drawDigestionFragmentHistogram	0.007	0.001	0.007
drawHeatmap	0.001	0.000	0.001
exportVisualizationFragmentData	0.000	0.001	0.000
getReadDistribution	0.387	0.060	0.448
giveEnzymeSequence	0.004	0.001	0.006
importVisualizationFragmentData	0.022	0.013	0.035
liverData	0.006	0.004	0.011
liverDataRaw	0.006	0.004	0.010
normalizeFragmentData	0.011	0.005	0.016
plotTransInteractions	0.001	0.001	0.001
prepare4CseqData	0.001	0.001	0.001
printBEDFragmentLibrary	0.001	0.000	0.001
printWigFile	0.001	0.000	0.001
readPointsOfInterestFile	0.006	0.002	0.008
readsToFragments	7.962	5.549	13.521
simulateDigestion	0.003	0.001	0.005
visualizeViewpoint	0.068	0.007	0.077