Package: Basic4Cseq

Version: 1.19.1

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_1.19.1.tar.gz

StartedAt: 2019-04-09 00:01:22 -0400 (Tue, 09 Apr 2019)

EndedAt: 2019-04-09 00:06:18 -0400 (Tue, 09 Apr 2019)

EllapsedTime: 295.9 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_1.19.1.tar.gz
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* using log directory ‘/Users/biocbuild/bbs-3.9-bioc/meat/Basic4Cseq.Rcheck’
* using R Under development (unstable) (2019-03-18 r76245)
* 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 ‘1.19.1’
* 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 or elapsed time > 5s
                  user system elapsed
readsToFragments 6.117  4.343  10.461
* 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/3.6/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	0.002	0.000	0.003
Data4Cseq	0.120	0.006	0.130
checkRestrictionEnzymeSequence	0.000	0.001	0.001
chooseNearCisFragments	0.019	0.006	0.024
createVirtualFragmentLibrary	0.001	0.000	0.000
drawDigestionFragmentHistogram	0.008	0.000	0.009
drawHeatmap	0.001	0.000	0.000
exportVisualizationFragmentData	0	0	0
getReadDistribution	0.299	0.011	0.311
giveEnzymeSequence	0.004	0.001	0.007
importVisualizationFragmentData	0.021	0.011	0.033
liverData	0.005	0.005	0.010
liverDataRaw	0.005	0.005	0.011
normalizeFragmentData	0.009	0.005	0.014
plotTransInteractions	0.001	0.000	0.001
prepare4CseqData	0	0	0
printBEDFragmentLibrary	0.000	0.001	0.001
printWigFile	0.001	0.000	0.000
readPointsOfInterestFile	0.005	0.000	0.006
readsToFragments	6.117	4.343	10.461
simulateDigestion	0.002	0.000	0.002
visualizeViewpoint	0.069	0.007	0.078