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CHECK report for MPRAnalyze on malbec2

This page was generated on 2019-10-16 12:16:25 -0400 (Wed, 16 Oct 2019).

Package 1048/1741HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
MPRAnalyze 1.2.0
Tal Ashuach
Snapshot Date: 2019-10-15 17:01:26 -0400 (Tue, 15 Oct 2019)
URL: https://git.bioconductor.org/packages/MPRAnalyze
Branch: RELEASE_3_9
Last Commit: 4f4b51d
Last Changed Date: 2019-05-02 11:54:13 -0400 (Thu, 02 May 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

Summary

Package: MPRAnalyze
Version: 1.2.0
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_1.2.0.tar.gz
StartedAt: 2019-10-16 03:20:59 -0400 (Wed, 16 Oct 2019)
EndedAt: 2019-10-16 03:24:15 -0400 (Wed, 16 Oct 2019)
EllapsedTime: 195.5 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_1.2.0.tar.gz
###
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* using log directory ‘/home/biocbuild/bbs-3.9-bioc/meat/MPRAnalyze.Rcheck’
* using R version 3.6.1 (2019-07-05)
* 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 ‘1.2.0’
* 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
analyzeComparative 10.298  0.096  10.406
getAlpha           10.182  0.040  10.229
testLrt             5.701  0.020   5.725
testCoefficient     5.044  0.018   5.065
* 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
MpraObject0.0330.0040.036
analyzeComparative10.298 0.09610.406
analyzeQuantification4.0070.0234.033
estimateDepthFactors0.0110.0020.014
extractModelParameters1.7940.0001.794
getAlpha10.182 0.04010.229
getDistrParam1.8660.0041.870
getFits_DNA1.4480.0001.448
getFits_RNA2.1500.0082.158
setDepthFactors0.0080.0000.008
setModel3.5570.0043.561
simulateMPRA0.1390.0000.138
testCoefficient5.0440.0185.065
testEmpirical4.1850.0124.197
testLrt5.7010.0205.725