BioC 3.6: CHECK report for Basic4Cseq on tokay1

Package: Basic4Cseq

Version: 1.13.1

Command: rm -rf Basic4Cseq.buildbin-libdir Basic4Cseq.Rcheck && mkdir Basic4Cseq.buildbin-libdir Basic4Cseq.Rcheck && C:\Users\biocbuild\bbs-3.6-bioc\R\bin\R.exe CMD INSTALL --build --merge-multiarch --library=Basic4Cseq.buildbin-libdir Basic4Cseq_1.13.1.tar.gz >Basic4Cseq.Rcheck\00install.out 2>&1 && cp Basic4Cseq.Rcheck\00install.out Basic4Cseq-install.out && C:\Users\biocbuild\bbs-3.6-bioc\R\bin\R.exe CMD check --library=Basic4Cseq.buildbin-libdir --install="check:Basic4Cseq-install.out" --force-multiarch --no-vignettes --timings Basic4Cseq_1.13.1.tar.gz

StartedAt: 2017-08-15 21:51:49 -0400 (Tue, 15 Aug 2017)

EndedAt: 2017-08-15 21:56:33 -0400 (Tue, 15 Aug 2017)

EllapsedTime: 283.7 seconds

RetCode: 0

Status:  OK

CheckDir: Basic4Cseq.Rcheck

Warnings: 0

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### Running command:
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###   rm -rf Basic4Cseq.buildbin-libdir Basic4Cseq.Rcheck && mkdir Basic4Cseq.buildbin-libdir Basic4Cseq.Rcheck && C:\Users\biocbuild\bbs-3.6-bioc\R\bin\R.exe CMD INSTALL --build --merge-multiarch --library=Basic4Cseq.buildbin-libdir Basic4Cseq_1.13.1.tar.gz >Basic4Cseq.Rcheck\00install.out 2>&1 && cp Basic4Cseq.Rcheck\00install.out Basic4Cseq-install.out  &&  C:\Users\biocbuild\bbs-3.6-bioc\R\bin\R.exe CMD check --library=Basic4Cseq.buildbin-libdir --install="check:Basic4Cseq-install.out" --force-multiarch --no-vignettes --timings Basic4Cseq_1.13.1.tar.gz
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* using log directory 'C:/Users/biocbuild/bbs-3.6-bioc/meat/Basic4Cseq.Rcheck'
* using R version 3.4.1 (2017-06-30)
* using platform: x86_64-w64-mingw32 (64-bit)
* using session charset: ISO8859-1
* using option '--no-vignettes'
* checking for file 'Basic4Cseq/DESCRIPTION' ... OK
* checking extension type ... Package
* this is package 'Basic4Cseq' version '1.13.1'
* 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 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
* loading checks for arch 'i386'
** 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 loading without being on the library search path ... OK
* loading checks for arch 'x64'
** 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 loading without being on the library search path ... 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 installed files from 'inst/doc' ... OK
* checking files in 'vignettes' ... OK
* checking examples ...
** running examples for arch 'i386' ... OK
Examples with CPU or elapsed time > 5s
                 user system elapsed
readsToFragments 3.26   2.03     5.3
** running examples for arch 'x64' ... OK
Examples with CPU or elapsed time > 5s
                 user system elapsed
readsToFragments 4.23    2.3    6.53
* 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

install for i386

* installing *source* package 'Basic4Cseq' ...
** R
** data
** inst
** preparing package for lazy loading
** help
*** installing help indices
** building package indices
** installing vignettes
** testing if installed package can be loaded

install for x64

* installing *source* package 'Basic4Cseq' ...
** testing if installed package can be loaded
* MD5 sums
packaged installation of 'Basic4Cseq' as Basic4Cseq_1.13.1.zip
* DONE (Basic4Cseq)

name	user	system	elapsed
Data4Cseq-class	0	0	0
Data4Cseq	0.23	0.02	0.25
checkRestrictionEnzymeSequence	0	0	0
chooseNearCisFragments	0.01	0.00	0.02
createVirtualFragmentLibrary	0	0	0
drawDigestionFragmentHistogram	0	0	0
drawHeatmap	0	0	0
exportVisualizationFragmentData	0	0	0
getReadDistribution	0.08	0.00	0.07
giveEnzymeSequence	0	0	0
importVisualizationFragmentData	0	0	0
liverData	0.01	0.00	0.02
liverDataRaw	0	0	0
normalizeFragmentData	0.00	0.01	0.01
plotTransInteractions	0	0	0
prepare4CseqData	0	0	0
printBEDFragmentLibrary	0.02	0.00	0.02
printWigFile	0	0	0
readPointsOfInterestFile	0	0	0
readsToFragments	3.26	2.03	5.30
simulateDigestion	0	0	0
visualizeViewpoint	0.14	0.00	0.14

name	user	system	elapsed
Data4Cseq-class	0	0	0
Data4Cseq	0.26	0.00	0.26
checkRestrictionEnzymeSequence	0	0	0
chooseNearCisFragments	0.00	0.02	0.02
createVirtualFragmentLibrary	0	0	0
drawDigestionFragmentHistogram	0	0	0
drawHeatmap	0	0	0
exportVisualizationFragmentData	0	0	0
getReadDistribution	0.08	0.00	0.08
giveEnzymeSequence	0.01	0.00	0.02
importVisualizationFragmentData	0	0	0
liverData	0.00	0.01	0.01
liverDataRaw	0	0	0
normalizeFragmentData	0.00	0.02	0.02
plotTransInteractions	0	0	0
prepare4CseqData	0	0	0
printBEDFragmentLibrary	0	0	0
printWigFile	0	0	0
readPointsOfInterestFile	0	0	0
readsToFragments	4.23	2.30	6.53
simulateDigestion	0	0	0
visualizeViewpoint	0.16	0.00	2.24