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CHECK report for goSTAG on tokay1

This page was generated on 2018-04-12 13:29:16 -0400 (Thu, 12 Apr 2018).

Package 603/1472HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
goSTAG 1.2.0
Brian D. Bennett
Snapshot Date: 2018-04-11 16:45:18 -0400 (Wed, 11 Apr 2018)
URL: https://git.bioconductor.org/packages/goSTAG
Branch: RELEASE_3_6
Last Commit: b517358
Last Changed Date: 2017-10-30 12:41:25 -0400 (Mon, 30 Oct 2017)
malbec1 Linux (Ubuntu 16.04.1 LTS) / x86_64  NotNeeded  OK  OK UNNEEDED, same version exists in internal repository
tokay1 Windows Server 2012 R2 Standard / x64  NotNeeded  OK [ OK ] OK UNNEEDED, same version exists in internal repository
veracruz1 OS X 10.11.6 El Capitan / x86_64  NotNeeded  OK  OK  OK UNNEEDED, same version exists in internal repository

Summary

Package: goSTAG
Version: 1.2.0
Command: rm -rf goSTAG.buildbin-libdir goSTAG.Rcheck && mkdir goSTAG.buildbin-libdir goSTAG.Rcheck && C:\Users\biocbuild\bbs-3.6-bioc\R\bin\R.exe CMD INSTALL --build --merge-multiarch --library=goSTAG.buildbin-libdir goSTAG_1.2.0.tar.gz >goSTAG.Rcheck\00install.out 2>&1 && cp goSTAG.Rcheck\00install.out goSTAG-install.out && C:\Users\biocbuild\bbs-3.6-bioc\R\bin\R.exe CMD check --library=goSTAG.buildbin-libdir --install="check:goSTAG-install.out" --force-multiarch --no-vignettes --timings goSTAG_1.2.0.tar.gz
StartedAt: 2018-04-12 00:29:01 -0400 (Thu, 12 Apr 2018)
EndedAt: 2018-04-12 00:35:58 -0400 (Thu, 12 Apr 2018)
EllapsedTime: 416.7 seconds
RetCode: 0
Status:  OK  
CheckDir: goSTAG.Rcheck
Warnings: 0

Command output

##############################################################################
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###
### Running command:
###
###   rm -rf goSTAG.buildbin-libdir goSTAG.Rcheck && mkdir goSTAG.buildbin-libdir goSTAG.Rcheck && C:\Users\biocbuild\bbs-3.6-bioc\R\bin\R.exe CMD INSTALL --build --merge-multiarch --library=goSTAG.buildbin-libdir goSTAG_1.2.0.tar.gz >goSTAG.Rcheck\00install.out 2>&1 && cp goSTAG.Rcheck\00install.out goSTAG-install.out  &&  C:\Users\biocbuild\bbs-3.6-bioc\R\bin\R.exe CMD check --library=goSTAG.buildbin-libdir --install="check:goSTAG-install.out" --force-multiarch --no-vignettes --timings goSTAG_1.2.0.tar.gz
###
##############################################################################
##############################################################################


* using log directory 'C:/Users/biocbuild/bbs-3.6-bioc/meat/goSTAG.Rcheck'
* using R version 3.4.4 (2018-03-15)
* 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 '1.2.0'
* 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
** checking loading without being on the library search path ... 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 loading without being on the library search path ... 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 installed files from 'inst/doc' ... OK
* checking files in 'vignettes' ... OK
* checking examples ...
** running examples for arch 'i386' ... OK
Examples with CPU or elapsed time > 5s
                               user system elapsed
annotateClusters              28.46   0.16   28.61
groupClusters                 26.22   0.08   26.30
goSTAG-package                25.75   0.01   25.81
plotHeatmap                   22.85   0.03   22.87
performGOEnrichment           21.97   0.05   22.02
performHierarchicalClustering 21.62   0.03   21.66
** running examples for arch 'x64' ... OK
Examples with CPU or elapsed time > 5s
                               user system elapsed
plotHeatmap                   27.83   0.01   27.84
goSTAG-package                21.83   0.03   21.86
annotateClusters              21.43   0.11   21.55
performGOEnrichment           20.06   0.00   20.07
groupClusters                 19.94   0.05   19.99
performHierarchicalClustering 19.83   0.02   19.84
* 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


install for i386

* installing *source* package 'goSTAG' ...
** R
** data
*** moving datasets to lazyload DB
** inst
** preparing 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
In R CMD INSTALL

install for x64

* installing *source* package 'goSTAG' ...
** testing if installed package can be loaded
* MD5 sums
packaged installation of 'goSTAG' as goSTAG_1.2.0.zip
* DONE (goSTAG)
In R CMD INSTALL
In R CMD INSTALL

Tests output

goSTAG.Rcheck/tests_i386/testthat.Rout


R version 3.4.4 (2018-03-15) -- "Someone to Lean On"
Copyright (C) 2018 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")
== testthat results  ===========================================================
OK: 0 SKIPPED: 0 FAILED: 0
> 
> proc.time()
   user  system elapsed 
   3.39    0.20    3.57

goSTAG.Rcheck/tests_x64/testthat.Rout


R version 3.4.4 (2018-03-15) -- "Someone to Lean On"
Copyright (C) 2018 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")
== testthat results  ===========================================================
OK: 0 SKIPPED: 0 FAILED: 0
> 
> proc.time()
   user  system elapsed 
   3.57    0.10    3.70

Example timings

goSTAG.Rcheck/examples_i386/goSTAG-Ex.timings

nameusersystemelapsed
annotateClusters28.46 0.1628.61
goSTAG-package25.75 0.0125.81
goSTAG_example_gene_lists0.000.020.01
goSTAG_go_genes_human0.250.000.25
goSTAG_go_genes_mouse0.250.010.27
goSTAG_go_genes_rat0.060.000.06
groupClusters26.22 0.0826.30
loadGOTerms0.340.020.36
loadGeneLists0.020.000.01
performGOEnrichment21.97 0.0522.02
performHierarchicalClustering21.62 0.0321.66
plotHeatmap22.85 0.0322.87
rat_cancer_therapeutics_gene_lists000

goSTAG.Rcheck/examples_x64/goSTAG-Ex.timings

nameusersystemelapsed
annotateClusters21.43 0.1121.55
goSTAG-package21.83 0.0321.86
goSTAG_example_gene_lists000
goSTAG_go_genes_human0.080.000.08
goSTAG_go_genes_mouse0.250.000.25
goSTAG_go_genes_rat0.050.020.06
groupClusters19.94 0.0519.99
loadGOTerms0.260.010.28
loadGeneLists0.020.000.01
performGOEnrichment20.06 0.0020.07
performHierarchicalClustering19.83 0.0219.84
plotHeatmap27.83 0.0127.84
rat_cancer_therapeutics_gene_lists000