Back to Multiple platform build/check report for BioC 3.14
ABCDEF[G]HIJKLMNOPQRSTUVWXYZ

This page was generated on 2022-01-14 13:06:29 -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 tokay2


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: C:\Users\biocbuild\bbs-3.14-bioc\R\bin\R.exe CMD check --force-multiarch --install=check:goSTAG.install-out.txt --library=C:\Users\biocbuild\bbs-3.14-bioc\R\library --no-vignettes --timings goSTAG_1.18.0.tar.gz
StartedAt: 2022-01-13 20:27:12 -0500 (Thu, 13 Jan 2022)
EndedAt: 2022-01-13 20:34:08 -0500 (Thu, 13 Jan 2022)
EllapsedTime: 416.2 seconds
RetCode: 0
Status:   OK  
CheckDir: goSTAG.Rcheck
Warnings: 0

Command output

##############################################################################
##############################################################################
###
### Running command:
###
###   C:\Users\biocbuild\bbs-3.14-bioc\R\bin\R.exe CMD check --force-multiarch --install=check:goSTAG.install-out.txt --library=C:\Users\biocbuild\bbs-3.14-bioc\R\library --no-vignettes --timings goSTAG_1.18.0.tar.gz
###
##############################################################################
##############################################################################


* using log directory 'C:/Users/biocbuild/bbs-3.14-bioc/meat/goSTAG.Rcheck'
* using R version 4.1.2 (2021-11-01)
* using platform: x86_64-w64-mingw32 (64-bit)
* using session charset: ISO8859-1
* 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 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
* loading checks for arch 'i386'
** 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
* loading checks for arch 'x64'
** 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 ...
** running examples for arch 'i386' ... OK
Examples with CPU (user + system) or elapsed time > 5s
                               user system elapsed
groupClusters                 26.09   0.07   26.17
performGOEnrichment           24.87   0.00   24.87
goSTAG-package                22.25   0.04   22.29
performHierarchicalClustering 21.63   0.00   21.64
annotateClusters              20.89   0.28   21.17
plotHeatmap                   20.50   0.00   20.52
** running examples for arch 'x64' ... OK
Examples with CPU (user + system) or elapsed time > 5s
                               user system elapsed
groupClusters                 20.68   0.05   20.73
plotHeatmap                   20.43   0.00   20.44
performGOEnrichment           19.14   0.00   19.14
goSTAG-package                18.96   0.03   19.01
annotateClusters              18.36   0.09   18.45
performHierarchicalClustering 17.86   0.00   17.86
* checking for unstated dependencies in 'tests' ... OK
* checking tests ...
** running tests for arch 'i386' ...
  Running 'testthat.R'
 OK
** running tests for arch 'x64' ...
  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

##############################################################################
##############################################################################
###
### Running command:
###
###   C:\cygwin\bin\curl.exe -O http://155.52.207.166/BBS/3.14/bioc/src/contrib/goSTAG_1.18.0.tar.gz && rm -rf goSTAG.buildbin-libdir && mkdir goSTAG.buildbin-libdir && C:\Users\biocbuild\bbs-3.14-bioc\R\bin\R.exe CMD INSTALL --merge-multiarch --build --library=goSTAG.buildbin-libdir goSTAG_1.18.0.tar.gz && C:\Users\biocbuild\bbs-3.14-bioc\R\bin\R.exe CMD INSTALL goSTAG_1.18.0.zip && rm goSTAG_1.18.0.tar.gz goSTAG_1.18.0.zip
###
##############################################################################
##############################################################################


  % Total    % Received % Xferd  Average Speed   Time    Time     Time  Current
                                 Dload  Upload   Total   Spent    Left  Speed

  0     0    0     0    0     0      0      0 --:--:-- --:--:-- --:--:--     0
 74 1576k   74 1168k    0     0  2397k      0 --:--:-- --:--:-- --:--:-- 2398k
100 1576k  100 1576k    0     0  2659k      0 --:--:-- --:--:-- --:--:-- 2658k

install for i386

* 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
  converting help for package 'goSTAG'
    finding HTML links ... done
    annotateClusters                        html  
    goSTAG-package                          html  
    goSTAG_example_gene_lists               html  
    goSTAG_go_genes_human                   html  
    goSTAG_go_genes_mouse                   html  
    goSTAG_go_genes_rat                     html  
    groupClusters                           html  
    loadGOTerms                             html  
    loadGeneLists                           html  
    performGOEnrichment                     html  
    performHierarchicalClustering           html  
    plotHeatmap                             html  
    rat_cancer_therapeutics_gene_lists      html  
** 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

install for x64

* installing *source* package 'goSTAG' ...
** testing if installed package can be loaded
* MD5 sums
packaged installation of 'goSTAG' as goSTAG_1.18.0.zip
* DONE (goSTAG)
* installing to library 'C:/Users/biocbuild/bbs-3.14-bioc/R/library'
package 'goSTAG' successfully unpacked and MD5 sums checked

Tests output

goSTAG.Rcheck/tests_i386/testthat.Rout


R version 4.1.2 (2021-11-01) -- "Bird Hippie"
Copyright (C) 2021 The R Foundation for Statistical Computing
Platform: i386-w64-mingw32/i386 (32-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 
   4.51    0.28    4.78 

goSTAG.Rcheck/tests_x64/testthat.Rout


R version 4.1.2 (2021-11-01) -- "Bird Hippie"
Copyright (C) 2021 The R Foundation for Statistical Computing
Platform: x86_64-w64-mingw32/x64 (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 
   5.07    0.25    5.32 

Example timings

goSTAG.Rcheck/examples_i386/goSTAG-Ex.timings

nameusersystemelapsed
annotateClusters20.89 0.2821.17
goSTAG-package22.25 0.0422.29
goSTAG_example_gene_lists000
goSTAG_go_genes_human0.060.000.06
goSTAG_go_genes_mouse0.080.000.08
goSTAG_go_genes_rat0.050.000.05
groupClusters26.09 0.0726.17
loadGOTerms0.180.000.17
loadGeneLists0.000.000.02
performGOEnrichment24.87 0.0024.87
performHierarchicalClustering21.63 0.0021.64
plotHeatmap20.50 0.0020.52
rat_cancer_therapeutics_gene_lists000

goSTAG.Rcheck/examples_x64/goSTAG-Ex.timings

nameusersystemelapsed
annotateClusters18.36 0.0918.45
goSTAG-package18.96 0.0319.01
goSTAG_example_gene_lists000
goSTAG_go_genes_human0.100.000.09
goSTAG_go_genes_mouse0.120.000.14
goSTAG_go_genes_rat0.10.00.1
groupClusters20.68 0.0520.73
loadGOTerms0.130.000.13
loadGeneLists000
performGOEnrichment19.14 0.0019.14
performHierarchicalClustering17.86 0.0017.86
plotHeatmap20.43 0.0020.44
rat_cancer_therapeutics_gene_lists000