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This page was generated on 2021-12-01 17:17:30 -0500 (Wed, 01 Dec 2021).

CHECK results for MPRAnalyze on nebbiolo2

To the developers/maintainers of the MPRAnalyze package:
- Please allow up to 24 hours (and sometimes 48 hours) for your latest push to git@git.bioconductor.org:packages/MPRAnalyze.git to
reflect on this report. See How and When does the builder pull? When will my changes propagate? here for more information.
- Make sure to use the following settings in order to reproduce any error or warning you see on this page.

raw results

Package 1208/2083HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
MPRAnalyze 1.12.0  (landing page)
Tal Ashuach
Snapshot Date: 2021-11-30 04:15:05 -0500 (Tue, 30 Nov 2021)
git_url: https://git.bioconductor.org/packages/MPRAnalyze
git_branch: RELEASE_3_14
git_last_commit: 490525a
git_last_commit_date: 2021-10-26 12:47:13 -0500 (Tue, 26 Oct 2021)
nebbiolo2Linux (Ubuntu 20.04.3 LTS) / x86_64  OK    OK    OK  UNNEEDED, same version is already published
tokay2Windows Server 2012 R2 Standard / x64  OK    OK    OK    OK  UNNEEDED, same version is already published
machv2macOS 10.14.6 Mojave / x86_64  OK    OK    OK    OK  UNNEEDED, same version is already published

Summary

Package: MPRAnalyze
Version: 1.12.0
Command: /home/biocbuild/bbs-3.14-bioc/R/bin/R CMD check --install=check:MPRAnalyze.install-out.txt --library=/home/biocbuild/bbs-3.14-bioc/R/library --no-vignettes --timings MPRAnalyze_1.12.0.tar.gz
StartedAt: 2021-11-30 10:02:14 -0500 (Tue, 30 Nov 2021)
EndedAt: 2021-11-30 10:04:27 -0500 (Tue, 30 Nov 2021)
EllapsedTime: 133.0 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-3.14-bioc/R/bin/R CMD check --install=check:MPRAnalyze.install-out.txt --library=/home/biocbuild/bbs-3.14-bioc/R/library --no-vignettes --timings MPRAnalyze_1.12.0.tar.gz
###
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* using log directory ‘/home/biocbuild/bbs-3.14-bioc/meat/MPRAnalyze.Rcheck’
* using R version 4.1.2 (2021-11-01)
* 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 ‘1.12.0’
* 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
getAlpha           5.628  0.080   5.709
analyzeComparative 5.466  0.096   5.562
* 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-3.14-bioc/R/bin/R CMD INSTALL MPRAnalyze
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* installing to library ‘/home/biocbuild/bbs-3.14-bioc/R/library’
* installing *source* package ‘MPRAnalyze’ ...
** using staged installation
** R
** data
** inst
** 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
MpraObject0.0280.0000.027
analyzeComparative5.4660.0965.562
analyzeQuantification1.8540.0521.906
estimateDepthFactors0.010.000.01
extractModelParameters0.8600.0040.864
getAlpha5.6280.0805.709
getDistrParam0.9030.0400.943
getFits_DNA0.8580.0080.866
getFits_RNA0.8660.0080.874
setDepthFactors0.0050.0000.005
setModel1.6150.0161.630
simulateMPRA0.0460.0190.067
testCoefficient2.4270.0162.443
testEmpirical1.8430.0201.863
testLrt2.3500.0162.365