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CHECK report for goSTAG on malbec1

This page was generated on 2019-04-16 11:52:33 -0400 (Tue, 16 Apr 2019).

Package 668/1649HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
goSTAG 1.6.1
Brian D. Bennett
Snapshot Date: 2019-04-15 17:01:12 -0400 (Mon, 15 Apr 2019)
URL: https://git.bioconductor.org/packages/goSTAG
Branch: RELEASE_3_8
Last Commit: b36ec25
Last Changed Date: 2018-11-29 17:00:58 -0400 (Thu, 29 Nov 2018)
malbec1 Linux (Ubuntu 16.04.6 LTS) / x86_64  OK  OK [ OK ]UNNEEDED, same version exists in internal repository
merida1 OS X 10.11.6 El Capitan / x86_64  OK  OK  OK  OK UNNEEDED, same version exists in internal repository

Summary

Package: goSTAG
Version: 1.6.1
Command: /home/biocbuild/bbs-3.8-bioc/R/bin/R CMD check --install=check:goSTAG.install-out.txt --library=/home/biocbuild/bbs-3.8-bioc/R/library --no-vignettes --timings goSTAG_1.6.1.tar.gz
StartedAt: 2019-04-16 00:22:35 -0400 (Tue, 16 Apr 2019)
EndedAt: 2019-04-16 00:30:27 -0400 (Tue, 16 Apr 2019)
EllapsedTime: 472.3 seconds
RetCode: 0
Status:  OK 
CheckDir: goSTAG.Rcheck
Warnings: 0

Command output

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### Running command:
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###   /home/biocbuild/bbs-3.8-bioc/R/bin/R CMD check --install=check:goSTAG.install-out.txt --library=/home/biocbuild/bbs-3.8-bioc/R/library --no-vignettes --timings goSTAG_1.6.1.tar.gz
###
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* using log directory ‘/home/biocbuild/bbs-3.8-bioc/meat/goSTAG.Rcheck’
* using R version 3.5.3 (2019-03-11)
* using platform: x86_64-pc-linux-gnu (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 ‘1.6.1’
* 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
groupClusters                 64.744  0.012  65.029
performGOEnrichment           63.968  0.004  64.290
performHierarchicalClustering 63.456  0.008  63.859
goSTAG-package                62.752  0.028  63.053
annotateClusters              62.652  0.108  63.071
plotHeatmap                   58.248  0.012  58.473
* 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:
###
###   /home/biocbuild/bbs-3.8-bioc/R/bin/R CMD INSTALL goSTAG
###
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* installing to library ‘/home/biocbuild/bbs-3.8-bioc/R/library’
* installing *source* package ‘goSTAG’ ...
** 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
* DONE (goSTAG)

Tests output

goSTAG.Rcheck/tests/testthat.Rout


R version 3.5.3 (2019-03-11) -- "Great Truth"
Copyright (C) 2019 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(goSTAG)

> 
> test_check("goSTAG")
══ testthat results  ═══════════════════════════════════════════════════════════
OK: 0 SKIPPED: 0 FAILED: 0
> 
> proc.time()
   user  system elapsed 
  3.920   0.108   4.041 

Example timings

goSTAG.Rcheck/goSTAG-Ex.timings

nameusersystemelapsed
annotateClusters62.652 0.10863.071
goSTAG-package62.752 0.02863.053
goSTAG_example_gene_lists0.0040.0000.002
goSTAG_go_genes_human0.0720.0000.074
goSTAG_go_genes_mouse0.1040.0000.104
goSTAG_go_genes_rat0.0960.0000.095
groupClusters64.744 0.01265.029
loadGOTerms0.2760.0000.279
loadGeneLists0.0080.0000.006
performGOEnrichment63.968 0.00464.290
performHierarchicalClustering63.456 0.00863.859
plotHeatmap58.248 0.01258.473
rat_cancer_therapeutics_gene_lists0.0040.0000.007