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This page was generated on 2021-09-25 12:05:12 -0400 (Sat, 25 Sep 2021).

CHECK results for proActiv on nebbiolo2

To the developers/maintainers of the proActiv package:
- Please allow up to 24 hours (and sometimes 48 hours) for your latest push to git@git.bioconductor.org:packages/proActiv.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 1421/2034HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
proActiv 1.3.4  (landing page)
Joseph Lee
Snapshot Date: 2021-09-24 14:50:08 -0400 (Fri, 24 Sep 2021)
git_url: https://git.bioconductor.org/packages/proActiv
git_branch: master
git_last_commit: a0df319
git_last_commit_date: 2021-06-23 06:28:09 -0400 (Wed, 23 Jun 2021)
nebbiolo2Linux (Ubuntu 20.04.2 LTS) / x86_64  OK    OK    OK  UNNEEDED, same version is already published
riesling1Windows Server 2019 Standard / x64  OK    OK    OK    OK  UNNEEDED, same version is already published
merida1macOS 10.14.6 Mojave / x86_64  OK    OK    OK    OK  UNNEEDED, same version is already published

Summary

Package: proActiv
Version: 1.3.4
Command: /home/biocbuild/bbs-3.14-bioc/R/bin/R CMD check --install=check:proActiv.install-out.txt --library=/home/biocbuild/bbs-3.14-bioc/R/library --no-vignettes --timings proActiv_1.3.4.tar.gz
StartedAt: 2021-09-24 21:08:25 -0400 (Fri, 24 Sep 2021)
EndedAt: 2021-09-24 21:16:01 -0400 (Fri, 24 Sep 2021)
EllapsedTime: 456.4 seconds
RetCode: 0
Status:   OK  
CheckDir: proActiv.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:proActiv.install-out.txt --library=/home/biocbuild/bbs-3.14-bioc/R/library --no-vignettes --timings proActiv_1.3.4.tar.gz
###
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* using log directory ‘/home/biocbuild/bbs-3.14-bioc/meat/proActiv.Rcheck’
* using R version 4.1.1 (2021-08-10)
* using platform: x86_64-pc-linux-gnu (64-bit)
* using session charset: UTF-8
* using option ‘--no-vignettes’
* checking for file ‘proActiv/DESCRIPTION’ ... OK
* this is package ‘proActiv’ version ‘1.3.4’
* 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 ‘proActiv’ 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 LazyData ... 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
preparePromoterAnnotation 20.864  0.340  21.208
integrateProactiv          9.050  0.164   9.196
getAlternativePromoters    4.969  0.148   5.104
* checking for unstated dependencies in ‘tests’ ... OK
* checking tests ...
  Running ‘testthat.R’
 OK
* 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

proActiv.Rcheck/00install.out

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### Running command:
###
###   /home/biocbuild/bbs-3.14-bioc/R/bin/R CMD INSTALL proActiv
###
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* installing to library ‘/home/biocbuild/bbs-3.14-bioc/R/library’
* installing *source* package ‘proActiv’ ...
** using staged installation
** R
** data
*** moving datasets to lazyload DB
** inst
** byte-compile and prepare package for lazy loading
** help
*** installing help indices
*** copying figures
** 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 (proActiv)

Tests output

proActiv.Rcheck/tests/testthat.Rout


R version 4.1.1 (2021-08-10) -- "Kick Things"
Copyright (C) 2021 The R Foundation for Statistical Computing
Platform: x86_64-pc-linux-gnu (64-bit)

R is free software and comes with ABSOLUTELY NO WARRANTY.
You are welcome to redistribute it under certain conditions.
Type 'license()' or 'licence()' for distribution details.

R is a collaborative project with many contributors.
Type 'contributors()' for more information and
'citation()' on how to cite R or R packages in publications.

Type 'demo()' for some demos, 'help()' for on-line help, or
'help.start()' for an HTML browser interface to help.
Type 'q()' to quit R.

> library(testthat)
> library(proActiv)

Attaching package: 'proActiv'

The following object is masked from 'package:stats':

    filter

> 
> test_check("proActiv")
[ FAIL 0 | WARN 0 | SKIP 0 | PASS 22 ]
> 
> proc.time()
   user  system elapsed 
167.651   5.172 168.443 

Example timings

proActiv.Rcheck/proActiv-Ex.timings

nameusersystemelapsed
PromoterAnnotation-class0.0570.0000.057
boxplotPromoters4.5910.1404.722
getAlternativePromoters4.9690.1485.104
integrateProactiv9.0500.1649.196
plotHeatmap3.5900.0763.652
plotPCA3.3230.0563.374
preparePromoterAnnotation20.864 0.34021.208
proActiv3.2650.0323.292