Back to Multiple platform build/check report for BioC 3.14
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This page was generated on 2022-01-14 13:05:15 -0500 (Fri, 14 Jan 2022).

HostnameOSArch (*)R versionInstalled pkgs
nebbiolo2Linux (Ubuntu 20.04.4 LTS)x86_644.1.2 (2021-11-01) -- "Bird Hippie" 4327
tokay2Windows Server 2012 R2 Standardx644.1.2 (2021-11-01) -- "Bird Hippie" 4076
machv2macOS 10.14.6 Mojavex86_644.1.2 (2021-11-01) -- "Bird Hippie" 4137
Click on any hostname to see more info about the system (e.g. compilers)      (*) as reported by 'uname -p', except on Windows and Mac OS X

CHECK results for goSTAG on nebbiolo2


To the developers/maintainers of the goSTAG package:
- Please allow up to 24 hours (and sometimes 48 hours) for your latest push to git@git.bioconductor.org:packages/goSTAG.git to
reflect on this report. See How and When does the builder pull? When will my changes propagate? here for more information.
- Make sure to use the following settings in order to reproduce any error or warning you see on this page.

raw results

Package 805/2083HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
goSTAG 1.18.0  (landing page)
Brian D. Bennett
Snapshot Date: 2022-01-13 01:55:04 -0500 (Thu, 13 Jan 2022)
git_url: https://git.bioconductor.org/packages/goSTAG
git_branch: RELEASE_3_14
git_last_commit: a62fde0
git_last_commit_date: 2021-10-26 12:32:39 -0500 (Tue, 26 Oct 2021)
nebbiolo2Linux (Ubuntu 20.04.4 LTS) / x86_64  OK    OK    OK  UNNEEDED, same version is already published
tokay2Windows Server 2012 R2 Standard / x64  OK    OK    OK    OK  UNNEEDED, same version is already published
machv2macOS 10.14.6 Mojave / x86_64  OK    OK    OK    OK  UNNEEDED, same version is already published

Summary

Package: goSTAG
Version: 1.18.0
Command: /home/biocbuild/bbs-3.14-bioc/R/bin/R CMD check --install=check:goSTAG.install-out.txt --library=/home/biocbuild/bbs-3.14-bioc/R/library --no-vignettes --timings goSTAG_1.18.0.tar.gz
StartedAt: 2022-01-13 07:51:41 -0500 (Thu, 13 Jan 2022)
EndedAt: 2022-01-13 07:58:50 -0500 (Thu, 13 Jan 2022)
EllapsedTime: 428.8 seconds
RetCode: 0
Status:   OK  
CheckDir: goSTAG.Rcheck
Warnings: 0

Command output

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### Running command:
###
###   /home/biocbuild/bbs-3.14-bioc/R/bin/R CMD check --install=check:goSTAG.install-out.txt --library=/home/biocbuild/bbs-3.14-bioc/R/library --no-vignettes --timings goSTAG_1.18.0.tar.gz
###
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* using log directory ‘/home/biocbuild/bbs-3.14-bioc/meat/goSTAG.Rcheck’
* using R version 4.1.2 (2021-11-01)
* 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 ‘1.18.0’
* 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 LazyData ... 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
performGOEnrichment           57.870  0.072  62.623
plotHeatmap                   56.997  0.100  68.942
groupClusters                 44.836  0.040  44.876
annotateClusters              39.292  0.108  39.401
performHierarchicalClustering 38.386  0.132  38.518
goSTAG-package                34.919  0.036  34.964
* 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-3.14-bioc/R/bin/R CMD INSTALL goSTAG
###
##############################################################################
##############################################################################


* installing to library ‘/home/biocbuild/bbs-3.14-bioc/R/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 4.1.2 (2021-11-01) -- "Bird Hippie"
Copyright (C) 2021 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")
[ FAIL 0 | WARN 0 | SKIP 0 | PASS 0 ]
> 
> proc.time()
   user  system elapsed 
  7.687   0.264   7.964 

Example timings

goSTAG.Rcheck/goSTAG-Ex.timings

nameusersystemelapsed
annotateClusters39.292 0.10839.401
goSTAG-package34.919 0.03634.964
goSTAG_example_gene_lists0.0020.0000.001
goSTAG_go_genes_human0.080.000.08
goSTAG_go_genes_mouse0.0820.0000.081
goSTAG_go_genes_rat0.0570.0040.061
groupClusters44.836 0.04044.876
loadGOTerms0.2640.0040.268
loadGeneLists0.0060.0000.006
performGOEnrichment57.870 0.07262.623
performHierarchicalClustering38.386 0.13238.518
plotHeatmap56.997 0.10068.942
rat_cancer_therapeutics_gene_lists0.0050.0000.005