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CHECK report for MPRAnalyze on malbec2

This page was generated on 2019-04-09 11:51:58 -0400 (Tue, 09 Apr 2019).

Package 1030/1703HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
MPRAnalyze 1.1.1
Tal Ashuach
Snapshot Date: 2019-04-08 17:01:18 -0400 (Mon, 08 Apr 2019)
URL: https://git.bioconductor.org/packages/MPRAnalyze
Branch: master
Last Commit: 69ed590
Last Changed Date: 2019-01-04 13:40:18 -0400 (Fri, 04 Jan 2019)
malbec2 Linux (Ubuntu 18.04.2 LTS) / x86_64  OK  OK [ OK ]UNNEEDED, same version exists in internal repository
tokay2 Windows Server 2012 R2 Standard / x64  OK  OK  OK  OK UNNEEDED, same version exists in internal repository
celaya2 OS X 10.11.6 El Capitan / x86_64  OK  OK  OK  OK UNNEEDED, same version exists in internal repository
merida2 OS X 10.11.6 El Capitan / x86_64  OK  OK  OK  OK 

Summary

Package: MPRAnalyze
Version: 1.1.1
Command: /home/biocbuild/bbs-3.9-bioc/R/bin/R CMD check --install=check:MPRAnalyze.install-out.txt --library=/home/biocbuild/bbs-3.9-bioc/R/library --no-vignettes --timings MPRAnalyze_1.1.1.tar.gz
StartedAt: 2019-04-09 02:10:42 -0400 (Tue, 09 Apr 2019)
EndedAt: 2019-04-09 02:14:06 -0400 (Tue, 09 Apr 2019)
EllapsedTime: 203.1 seconds
RetCode: 0
Status:  OK 
CheckDir: MPRAnalyze.Rcheck
Warnings: 0

Command output

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### Running command:
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###   /home/biocbuild/bbs-3.9-bioc/R/bin/R CMD check --install=check:MPRAnalyze.install-out.txt --library=/home/biocbuild/bbs-3.9-bioc/R/library --no-vignettes --timings MPRAnalyze_1.1.1.tar.gz
###
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* using log directory ‘/home/biocbuild/bbs-3.9-bioc/meat/MPRAnalyze.Rcheck’
* using R Under development (unstable) (2019-03-18 r76245)
* using platform: x86_64-pc-linux-gnu (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 ‘1.1.1’
* 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
analyzeComparative 11.013  0.095  11.119
getAlpha           10.173  0.056  10.278
* 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


Installation output

MPRAnalyze.Rcheck/00install.out

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### Running command:
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###   /home/biocbuild/bbs-3.9-bioc/R/bin/R CMD INSTALL MPRAnalyze
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* installing to library ‘/home/biocbuild/bbs-3.9-bioc/R/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)

Tests output


Example timings

MPRAnalyze.Rcheck/MPRAnalyze-Ex.timings

nameusersystemelapsed
MpraObject0.0340.0000.034
analyzeComparative11.013 0.09511.119
analyzeQuantification3.5780.0243.611
estimateDepthFactors0.010.000.01
extractModelParameters2.0970.0082.114
getAlpha10.173 0.05610.278
getDistrParam2.4700.0042.475
getFits_DNA2.3880.0042.399
getFits_RNA2.4190.0082.428
setDepthFactors0.0070.0000.007
setModel4.8730.0404.913
simulateMPRA0.1120.0160.128
testCoefficient4.7980.0084.806
testEmpirical4.2990.0084.312
testLrt4.7410.0284.770