Back to Multiple platform build/check report for BioC 3.12
ABCDEFGHIJKL[M]NOPQRSTUVWXYZ

CHECK report for MPRAnalyze on malbec1

This page was generated on 2021-05-06 12:28:18 -0400 (Thu, 06 May 2021).

To the developers/maintainers of the MPRAnalyze package:
Please make sure to use the following settings in order to reproduce any error or warning you see on this page.
Package 1151/1974HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
MPRAnalyze 1.8.0  (landing page)
Tal Ashuach
Snapshot Date: 2021-05-05 14:51:38 -0400 (Wed, 05 May 2021)
URL: https://git.bioconductor.org/packages/MPRAnalyze
Branch: RELEASE_3_12
Last Commit: 1836ce5
Last Changed Date: 2020-10-27 11:39:16 -0400 (Tue, 27 Oct 2020)
malbec1Linux (Ubuntu 18.04.5 LTS) / x86_64  OK    OK    OK  UNNEEDED, same version exists in internal repository
tokay1Windows Server 2012 R2 Standard / x64  OK    OK    OK    OK  UNNEEDED, same version exists in internal repository
merida1macOS 10.14.6 Mojave / x86_64  OK    OK    OK    OK  UNNEEDED, same version exists in internal repository

Summary

Package: MPRAnalyze
Version: 1.8.0
Command: /home/biocbuild/bbs-3.12-bioc/R/bin/R CMD check --install=check:MPRAnalyze.install-out.txt --library=/home/biocbuild/bbs-3.12-bioc/R/library --no-vignettes --timings MPRAnalyze_1.8.0.tar.gz
StartedAt: 2021-05-06 03:42:54 -0400 (Thu, 06 May 2021)
EndedAt: 2021-05-06 03:46:17 -0400 (Thu, 06 May 2021)
EllapsedTime: 202.3 seconds
RetCode: 0
Status:   OK  
CheckDir: MPRAnalyze.Rcheck
Warnings: 0

Command output

##############################################################################
##############################################################################
###
### Running command:
###
###   /home/biocbuild/bbs-3.12-bioc/R/bin/R CMD check --install=check:MPRAnalyze.install-out.txt --library=/home/biocbuild/bbs-3.12-bioc/R/library --no-vignettes --timings MPRAnalyze_1.8.0.tar.gz
###
##############################################################################
##############################################################################


* using log directory ‘/home/biocbuild/bbs-3.12-bioc/meat/MPRAnalyze.Rcheck’
* using R version 4.0.5 (2021-03-31)
* 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 ‘1.8.0’
* 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 (user + system) or elapsed time > 5s
                     user system elapsed
analyzeComparative 10.760  0.096  10.894
getAlpha            9.348  0.020   9.388
testLrt             5.284  0.016   5.307
* 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-3.12-bioc/R/bin/R CMD INSTALL MPRAnalyze
###
##############################################################################
##############################################################################


* installing to library ‘/home/biocbuild/bbs-3.12-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
MpraObject0.0560.0120.068
analyzeComparative10.760 0.09610.894
analyzeQuantification4.4640.0084.498
estimateDepthFactors0.0080.0000.008
extractModelParameters1.8440.0041.848
getAlpha9.3480.0209.388
getDistrParam2.2160.0082.226
getFits_DNA2.6040.0002.624
getFits_RNA2.4560.0082.465
setDepthFactors0.0040.0000.005
setModel3.9400.0163.963
simulateMPRA0.0760.0000.078
testCoefficient4.5240.0044.533
testEmpirical3.0280.0123.043
testLrt5.2840.0165.307