Back to Multiple platform build/check report for BioC 3.8
ABCDEFGHIJKL[M]NOPQRSTUVWXYZ

CHECK report for MPRAnalyze on malbec1

This page was generated on 2019-04-16 11:53:49 -0400 (Tue, 16 Apr 2019).

Package 1002/1649HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
MPRAnalyze 1.0.1
Tal Ashuach
Snapshot Date: 2019-04-15 17:01:12 -0400 (Mon, 15 Apr 2019)
URL: https://git.bioconductor.org/packages/MPRAnalyze
Branch: RELEASE_3_8
Last Commit: ef30857
Last Changed Date: 2019-01-04 13:40:21 -0400 (Fri, 04 Jan 2019)
malbec1 Linux (Ubuntu 16.04.6 LTS) / x86_64  OK  OK [ OK ]UNNEEDED, same version exists in internal repository
merida1 OS X 10.11.6 El Capitan / x86_64  OK  OK  OK  OK UNNEEDED, same version exists in internal repository

Summary

Package: MPRAnalyze
Version: 1.0.1
Command: /home/biocbuild/bbs-3.8-bioc/R/bin/R CMD check --install=check:MPRAnalyze.install-out.txt --library=/home/biocbuild/bbs-3.8-bioc/R/library --no-vignettes --timings MPRAnalyze_1.0.1.tar.gz
StartedAt: 2019-04-16 01:35:00 -0400 (Tue, 16 Apr 2019)
EndedAt: 2019-04-16 01:37:45 -0400 (Tue, 16 Apr 2019)
EllapsedTime: 165.0 seconds
RetCode: 0
Status:  OK 
CheckDir: MPRAnalyze.Rcheck
Warnings: 0

Command output

##############################################################################
##############################################################################
###
### Running command:
###
###   /home/biocbuild/bbs-3.8-bioc/R/bin/R CMD check --install=check:MPRAnalyze.install-out.txt --library=/home/biocbuild/bbs-3.8-bioc/R/library --no-vignettes --timings MPRAnalyze_1.0.1.tar.gz
###
##############################################################################
##############################################################################


* using log directory ‘/home/biocbuild/bbs-3.8-bioc/meat/MPRAnalyze.Rcheck’
* using R version 3.5.3 (2019-03-11)
* 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 ‘1.0.1’
* 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
getAlpha           8.824  0.016   8.845
analyzeComparative 7.920  0.052   7.976
testLrt            5.304  0.024   5.335
* 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

##############################################################################
##############################################################################
###
### Running command:
###
###   /home/biocbuild/bbs-3.8-bioc/R/bin/R CMD INSTALL MPRAnalyze
###
##############################################################################
##############################################################################


* installing to library ‘/home/biocbuild/bbs-3.8-bioc/R/library’
* installing *source* package ‘MPRAnalyze’ ...
** 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
* DONE (MPRAnalyze)

Tests output


Example timings

MPRAnalyze.Rcheck/MPRAnalyze-Ex.timings

nameusersystemelapsed
MpraObject0.0360.0000.036
analyzeComparative7.9200.0527.976
analyzeQuantification3.8800.0843.972
estimateDepthFactors0.0040.0000.007
extractModelParameters1.4040.0081.416
getAlpha8.8240.0168.845
getDistrParam1.8960.0041.901
getFits_DNA2.1440.0002.148
getFits_RNA2.0400.0042.046
setDepthFactors0.0080.0000.008
setModel4.2680.0044.294
simulateMPRA0.1440.0160.159
testCoefficient4.3480.0044.363
testEmpirical3.0480.0043.055
testLrt5.3040.0245.335