Package: goSTAG

Version: 1.11.0

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_1.11.0.tar.gz

StartedAt: 2020-01-16 05:04:21 -0500 (Thu, 16 Jan 2020)

EndedAt: 2020-01-16 05:13:06 -0500 (Thu, 16 Jan 2020)

EllapsedTime: 524.5 seconds

RetCode: 0

Status:  OK

CheckDir: goSTAG.Rcheck

Warnings: 0

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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_1.11.0.tar.gz
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* using log directory ‘/Users/biocbuild/bbs-3.11-bioc/meat/goSTAG.Rcheck’
* using R Under development (unstable) (2019-12-14 r77572)
* 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 ‘1.11.0’
* 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 (user + system) or elapsed time > 5s
                                user system elapsed
annotateClusters              57.854  3.276  61.451
groupClusters                 57.235  2.843  60.515
goSTAG-package                54.671  3.007  57.764
plotHeatmap                   53.405  2.934  56.344
performHierarchicalClustering 52.918  2.896  55.819
performGOEnrichment           50.293  2.772  53.080
* 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

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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/4.0/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)

R Under development (unstable) (2019-12-14 r77572) -- "Unsuffered Consequences"
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 
  8.419   0.781   9.145 

name	user	system	elapsed
annotateClusters	57.854	3.276	61.451
goSTAG-package	54.671	3.007	57.764
goSTAG_example_gene_lists	0.004	0.002	0.005
goSTAG_go_genes_human	0.098	0.012	0.111
goSTAG_go_genes_mouse	0.089	0.013	0.102
goSTAG_go_genes_rat	0.069	0.008	0.076
groupClusters	57.235	2.843	60.515
loadGOTerms	0.239	0.023	0.272
loadGeneLists	0.008	0.005	0.013
performGOEnrichment	50.293	2.772	53.080
performHierarchicalClustering	52.918	2.896	55.819
plotHeatmap	53.405	2.934	56.344
rat_cancer_therapeutics_gene_lists	0.008	0.003	0.010