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CHECK report for blacksheepr on merida1

This page was generated on 2020-08-11 12:04:34 -0400 (Tue, 11 Aug 2020).

TO THE DEVELOPERS/MAINTAINERS OF THE blacksheepr PACKAGE: Please make sure to use the following settings in order to reproduce any error or warning you see on this page.
Package 185/1885HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
blacksheepr 1.3.0
RugglesLab
Snapshot Date: 2020-08-10 14:50:56 -0400 (Mon, 10 Aug 2020)
URL: https://git.bioconductor.org/packages/blacksheepr
Branch: master
Last Commit: c938295
Last Changed Date: 2020-04-27 15:31:23 -0400 (Mon, 27 Apr 2020)
malbec1 Linux (Ubuntu 18.04.4 LTS) / x86_64  OK  OK  OK UNNEEDED, same version exists in internal repository
nebbiolo1 Linux (Ubuntu 20.04.1 LTS) / x86_64  OK  OK  NA 
tokay1 Windows Server 2012 R2 Standard / x64  OK  OK  OK  OK UNNEEDED, same version exists in internal repository
merida1 macOS 10.14.6 Mojave / x86_64  OK  OK [ OK ] OK UNNEEDED, same version exists in internal repository

Summary

Package: blacksheepr
Version: 1.3.0
Command: /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD check --install=check:blacksheepr.install-out.txt --library=/Library/Frameworks/R.framework/Versions/Current/Resources/library --no-vignettes --timings blacksheepr_1.3.0.tar.gz
StartedAt: 2020-08-11 05:13:17 -0400 (Tue, 11 Aug 2020)
EndedAt: 2020-08-11 05:18:43 -0400 (Tue, 11 Aug 2020)
EllapsedTime: 326.2 seconds
RetCode: 0
Status:  OK 
CheckDir: blacksheepr.Rcheck
Warnings: 0

Command output

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### Running command:
###
###   /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD check --install=check:blacksheepr.install-out.txt --library=/Library/Frameworks/R.framework/Versions/Current/Resources/library --no-vignettes --timings blacksheepr_1.3.0.tar.gz
###
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* using log directory ‘/Users/biocbuild/bbs-3.12-bioc/meat/blacksheepr.Rcheck’
* using R version 4.0.2 (2020-06-22)
* using platform: x86_64-apple-darwin17.0 (64-bit)
* using session charset: UTF-8
* using option ‘--no-vignettes’
* checking for file ‘blacksheepr/DESCRIPTION’ ... OK
* checking extension type ... Package
* this is package ‘blacksheepr’ version ‘1.3.0’
* 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 ‘blacksheepr’ 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
deva               17.203  0.945  18.212
outlier_analysis   11.303  0.039  11.354
deva_results       11.121  0.120  11.254
outlier_heatmap    11.135  0.047  11.196
count_outliers      7.727  0.220   7.962
create_heatmap      6.905  0.275   7.195
make_outlier_table  5.261  0.032   5.307
* 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

blacksheepr.Rcheck/00install.out

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###
### Running command:
###
###   /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD INSTALL blacksheepr
###
##############################################################################
##############################################################################


* installing to library ‘/Library/Frameworks/R.framework/Versions/4.0/Resources/library’
* installing *source* package ‘blacksheepr’ ...
** 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 (blacksheepr)

Tests output

blacksheepr.Rcheck/tests/testthat.Rout


R version 4.0.2 (2020-06-22) -- "Taking Off Again"
Copyright (C) 2020 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(blacksheepr)
> 
> test_check("blacksheepr")
══ testthat results  ═══════════════════════════════════════════════════════════
[ OK: 9 | SKIPPED: 0 | WARNINGS: 0 | FAILED: 0 ]
> 
> proc.time()
   user  system elapsed 
 50.274   0.823  51.152 

Example timings

blacksheepr.Rcheck/blacksheepr-Ex.timings

nameusersystemelapsed
annotationlist_builder0.0190.0030.023
comparison_groupings0.0160.0020.018
count_outliers7.7270.2207.962
create_heatmap6.9050.2757.195
deva17.203 0.94518.212
deva_normalization0.1430.0040.148
deva_results11.121 0.12011.254
make_comparison_columns0.0050.0090.086
make_outlier_table5.2610.0325.307
outlier_analysis11.303 0.03911.354
outlier_heatmap11.135 0.04711.196