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This page was generated on 2021-09-25 12:06:13 -0400 (Sat, 25 Sep 2021).

CHECK results for proActiv on merida1

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: /Library/Frameworks/R.framework/Resources/bin/R CMD check --install=check:proActiv.install-out.txt --library=/Library/Frameworks/R.framework/Resources/library --no-vignettes --timings proActiv_1.3.4.tar.gz
StartedAt: 2021-09-25 06:31:10 -0400 (Sat, 25 Sep 2021)
EndedAt: 2021-09-25 06:42:24 -0400 (Sat, 25 Sep 2021)
EllapsedTime: 674.6 seconds
RetCode: 0
Status:   OK  
CheckDir: proActiv.Rcheck
Warnings: 0

Command output

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### Running command:
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###   /Library/Frameworks/R.framework/Resources/bin/R CMD check --install=check:proActiv.install-out.txt --library=/Library/Frameworks/R.framework/Resources/library --no-vignettes --timings proActiv_1.3.4.tar.gz
###
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* using log directory ‘/Users/biocbuild/bbs-3.14-bioc/meat/proActiv.Rcheck’
* using R version 4.1.1 Patched (2021-08-22 r80813)
* using platform: x86_64-apple-darwin17.0 (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 37.980  0.130  38.177
integrateProactiv         14.338  0.100  14.459
getAlternativePromoters    9.670  0.137   9.820
boxplotPromoters           6.512  0.081   6.603
plotHeatmap                6.444  0.029   6.482
plotPCA                    5.961  0.024   5.996
proActiv                   5.849  0.061   5.917
* 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:
###
###   /Library/Frameworks/R.framework/Resources/bin/R CMD INSTALL proActiv
###
##############################################################################
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* installing to library ‘/Library/Frameworks/R.framework/Versions/4.1/Resources/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 Patched (2021-08-22 r80813) -- "Kick Things"
Copyright (C) 2021 The R Foundation for Statistical Computing
Platform: x86_64-apple-darwin17.0 (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 
268.588   4.089 266.306 

Example timings

proActiv.Rcheck/proActiv-Ex.timings

nameusersystemelapsed
PromoterAnnotation-class0.1370.0120.150
boxplotPromoters6.5120.0816.603
getAlternativePromoters9.6700.1379.820
integrateProactiv14.338 0.10014.459
plotHeatmap6.4440.0296.482
plotPCA5.9610.0245.996
preparePromoterAnnotation37.980 0.13038.177
proActiv5.8490.0615.917