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CHECK report for blacksheepr on malbec1

This page was generated on 2020-08-06 11:46:32 -0400 (Thu, 06 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 185/1882HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
blacksheepr 1.3.0
RugglesLab
Snapshot Date: 2020-08-05 14:50:59 -0400 (Wed, 05 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
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: /home/biocbuild/bbs-3.12-bioc/R/bin/R CMD check --install=check:blacksheepr.install-out.txt --library=/home/biocbuild/bbs-3.12-bioc/R/library --no-vignettes --timings blacksheepr_1.3.0.tar.gz
StartedAt: 2020-08-06 05:01:48 -0400 (Thu, 06 Aug 2020)
EndedAt: 2020-08-06 05:06:13 -0400 (Thu, 06 Aug 2020)
EllapsedTime: 265.1 seconds
RetCode: 0
Status:  OK 
CheckDir: blacksheepr.Rcheck
Warnings: 0

Command output

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### Running command:
###
###   /home/biocbuild/bbs-3.12-bioc/R/bin/R CMD check --install=check:blacksheepr.install-out.txt --library=/home/biocbuild/bbs-3.12-bioc/R/library --no-vignettes --timings blacksheepr_1.3.0.tar.gz
###
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* using log directory ‘/home/biocbuild/bbs-3.12-bioc/meat/blacksheepr.Rcheck’
* using R version 4.0.2 (2020-06-22)
* using platform: x86_64-pc-linux-gnu (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               14.952  0.160  15.276
outlier_analysis    9.348  0.008   9.402
deva_results        9.212  0.036   9.264
create_heatmap      8.392  0.152   8.848
count_outliers      7.412  0.132   7.555
outlier_heatmap     7.516  0.012   7.552
make_outlier_table  5.428  0.028   5.460
* 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:
###
###   /home/biocbuild/bbs-3.12-bioc/R/bin/R CMD INSTALL blacksheepr
###
##############################################################################
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* installing to library ‘/home/biocbuild/bbs-3.12-bioc/R/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-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(blacksheepr)
> 
> test_check("blacksheepr")
══ testthat results  ═══════════════════════════════════════════════════════════
[ OK: 9 | SKIPPED: 0 | WARNINGS: 0 | FAILED: 0 ]
> 
> proc.time()
   user  system elapsed 
 39.712   0.444  41.059 

Example timings

blacksheepr.Rcheck/blacksheepr-Ex.timings

nameusersystemelapsed
annotationlist_builder0.0160.0000.017
comparison_groupings0.0080.0080.018
count_outliers7.4120.1327.555
create_heatmap8.3920.1528.848
deva14.952 0.16015.276
deva_normalization0.0960.0000.113
deva_results9.2120.0369.264
make_comparison_columns0.0040.0000.005
make_outlier_table5.4280.0285.460
outlier_analysis9.3480.0089.402
outlier_heatmap7.5160.0127.552