Package: MPRAnalyze

Version: 1.2.0

Command: /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD check --install=check:MPRAnalyze.install-out.txt --library=/Library/Frameworks/R.framework/Versions/Current/Resources/library --no-vignettes --timings MPRAnalyze_1.2.0.tar.gz

StartedAt: 2019-10-16 04:51:05 -0400 (Wed, 16 Oct 2019)

EndedAt: 2019-10-16 04:55:38 -0400 (Wed, 16 Oct 2019)

EllapsedTime: 273.3 seconds

RetCode: 0

Status:  OK

CheckDir: MPRAnalyze.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:MPRAnalyze.install-out.txt --library=/Library/Frameworks/R.framework/Versions/Current/Resources/library --no-vignettes --timings MPRAnalyze_1.2.0.tar.gz
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* using log directory ‘/Users/biocbuild/bbs-3.9-bioc/meat/MPRAnalyze.Rcheck’
* using R version 3.6.1 (2019-07-05)
* using platform: x86_64-apple-darwin15.6.0 (64-bit)
* using session charset: UTF-8
* using option ‘--no-vignettes’
* checking for file ‘MPRAnalyze/DESCRIPTION’ ... OK
* checking extension type ... Package
* this is package ‘MPRAnalyze’ version ‘1.2.0’
* package encoding: UTF-8
* 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 ‘MPRAnalyze’ 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 or elapsed time > 5s
                        user system elapsed
getAlpha              15.735  0.579  16.317
analyzeComparative    14.505  0.585  15.090
testLrt                7.884  0.208   8.177
testCoefficient        7.044  0.215   7.271
setModel               6.568  0.136   6.716
analyzeQuantification  5.725  0.117   5.843
testEmpirical          5.692  0.110   5.811
* 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 MPRAnalyze
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* installing to library ‘/Library/Frameworks/R.framework/Versions/3.6/Resources/library’
* installing *source* package ‘MPRAnalyze’ ...
** using staged installation
** R
** data
** 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 (MPRAnalyze)

name	user	system	elapsed
MpraObject	0.027	0.001	0.028
analyzeComparative	14.505	0.585	15.090
analyzeQuantification	5.725	0.117	5.843
estimateDepthFactors	0.016	0.001	0.016
extractModelParameters	3.425	0.070	3.494
getAlpha	15.735	0.579	16.317
getDistrParam	3.320	0.079	3.399
getFits_DNA	3.225	0.076	3.301
getFits_RNA	2.606	0.069	2.676
setDepthFactors	0.010	0.000	0.011
setModel	6.568	0.136	6.716
simulateMPRA	0.111	0.039	0.149
testCoefficient	7.044	0.215	7.271
testEmpirical	5.692	0.110	5.811
testLrt	7.884	0.208	8.177