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CHECK report for goSTAG on celaya2

This page was generated on 2019-10-16 12:59:26 -0400 (Wed, 16 Oct 2019).

Package 700/1741HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
goSTAG 1.8.0
Brian D. Bennett
Snapshot Date: 2019-10-15 17:01:26 -0400 (Tue, 15 Oct 2019)
URL: https://git.bioconductor.org/packages/goSTAG
Branch: RELEASE_3_9
Last Commit: 292948c
Last Changed Date: 2019-05-02 11:54:05 -0400 (Thu, 02 May 2019)
malbec2 Linux (Ubuntu 18.04.2 LTS) / x86_64  OK  OK  OK UNNEEDED, same version exists in internal repository
tokay2 Windows Server 2012 R2 Standard / x64  OK  OK  OK  OK UNNEEDED, same version exists in internal repository
celaya2 OS X 10.11.6 El Capitan / x86_64  OK  OK [ OK ] OK UNNEEDED, same version exists in internal repository

Summary

Package: goSTAG
Version: 1.8.0
Command: /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD check --install=check:goSTAG.install-out.txt --library=/Library/Frameworks/R.framework/Versions/Current/Resources/library --no-vignettes --timings goSTAG_1.8.0.tar.gz
StartedAt: 2019-10-16 03:21:44 -0400 (Wed, 16 Oct 2019)
EndedAt: 2019-10-16 03:29:44 -0400 (Wed, 16 Oct 2019)
EllapsedTime: 479.5 seconds
RetCode: 0
Status:  OK 
CheckDir: goSTAG.Rcheck
Warnings: 0

Command output

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### Running command:
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###   /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD check --install=check:goSTAG.install-out.txt --library=/Library/Frameworks/R.framework/Versions/Current/Resources/library --no-vignettes --timings goSTAG_1.8.0.tar.gz
###
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* using log directory ‘/Users/biocbuild/bbs-3.9-bioc/meat/goSTAG.Rcheck’
* using R version 3.6.1 (2019-07-05)
* using platform: x86_64-apple-darwin15.6.0 (64-bit)
* using session charset: UTF-8
* using option ‘--no-vignettes’
* checking for file ‘goSTAG/DESCRIPTION’ ... OK
* checking extension type ... Package
* this is package ‘goSTAG’ version ‘1.8.0’
* 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 ‘goSTAG’ 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 or elapsed time > 5s
                                user system elapsed
annotateClusters              56.853  3.326  62.339
goSTAG-package                55.619  3.003  59.152
plotHeatmap                   51.106  2.888  54.185
groupClusters                 50.638  2.841  53.484
performHierarchicalClustering 49.704  2.835  52.540
performGOEnrichment           49.082  2.784  51.885
* 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

goSTAG.Rcheck/00install.out

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### Running command:
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###   /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD INSTALL goSTAG
###
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* installing to library ‘/Library/Frameworks/R.framework/Versions/3.6/Resources/library’
* installing *source* package ‘goSTAG’ ...
** using staged installation
** R
** data
*** moving datasets to lazyload DB
** 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 (goSTAG)

Tests output

goSTAG.Rcheck/tests/testthat.Rout


R version 3.6.1 (2019-07-05) -- "Action of the Toes"
Copyright (C) 2019 The R Foundation for Statistical Computing
Platform: x86_64-apple-darwin15.6.0 (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(goSTAG)

> 
> test_check("goSTAG")
══ testthat results  ═══════════════════════════════════════════════════════════
[ OK: 0 | SKIPPED: 0 | WARNINGS: 0 | FAILED: 0 ]
> 
> proc.time()
   user  system elapsed 
  5.451   0.599   6.001 

Example timings

goSTAG.Rcheck/goSTAG-Ex.timings

nameusersystemelapsed
annotateClusters56.853 3.32662.339
goSTAG-package55.619 3.00359.152
goSTAG_example_gene_lists0.0040.0020.005
goSTAG_go_genes_human0.0900.0110.101
goSTAG_go_genes_mouse0.1420.0130.155
goSTAG_go_genes_rat0.0850.0030.087
groupClusters50.638 2.84153.484
loadGOTerms0.2810.0270.308
loadGeneLists0.0090.0030.012
performGOEnrichment49.082 2.78451.885
performHierarchicalClustering49.704 2.83552.540
plotHeatmap51.106 2.88854.185
rat_cancer_therapeutics_gene_lists0.0070.0020.008