Package: goSTAG

Version: 1.4.0

Command: C:\Users\biocbuild\bbs-3.7-bioc\R\bin\R.exe CMD check --force-multiarch --install=check:goSTAG.install-out.txt --library=C:\Users\biocbuild\bbs-3.7-bioc\R\library --no-vignettes --timings goSTAG_1.4.0.tar.gz

StartedAt: 2018-10-17 02:29:50 -0400 (Wed, 17 Oct 2018)

EndedAt: 2018-10-17 02:38:18 -0400 (Wed, 17 Oct 2018)

EllapsedTime: 507.7 seconds

RetCode: 0

Status:  OK

CheckDir: goSTAG.Rcheck

Warnings: 0

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### Running command:
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###   C:\Users\biocbuild\bbs-3.7-bioc\R\bin\R.exe CMD check --force-multiarch --install=check:goSTAG.install-out.txt --library=C:\Users\biocbuild\bbs-3.7-bioc\R\library --no-vignettes --timings goSTAG_1.4.0.tar.gz
###
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* using log directory 'C:/Users/biocbuild/bbs-3.7-bioc/meat/goSTAG.Rcheck'
* using R version 3.5.1 Patched (2018-07-24 r75005)
* 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 '1.4.0'
* 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 data for ASCII and uncompressed saves ... OK
* checking files in 'vignettes' ... OK
* checking examples ...
** running examples for arch 'i386' ... OK
Examples with CPU or elapsed time > 5s
                               user system elapsed
performGOEnrichment           41.25   0.02   41.27
plotHeatmap                   37.35   0.03   37.38
performHierarchicalClustering 32.56   0.02   32.59
goSTAG-package                32.11   0.08   32.19
annotateClusters              31.69   0.28   31.96
groupClusters                 31.84   0.04   31.90
** running examples for arch 'x64' ... OK
Examples with CPU or elapsed time > 5s
                               user system elapsed
goSTAG-package                37.34   0.03   37.37
annotateClusters              31.38   0.11   31.49
plotHeatmap                   30.24   0.02   30.25
groupClusters                 27.72   0.03   27.75
performGOEnrichment           26.00   0.03   26.05
performHierarchicalClustering 23.09   0.00   23.09
* 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

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###
### Running command:
###
###   C:\cygwin\bin\curl.exe -O https://malbec2.bioconductor.org/BBS/3.7/bioc/src/contrib/goSTAG_1.4.0.tar.gz && rm -rf goSTAG.buildbin-libdir && mkdir goSTAG.buildbin-libdir && C:\Users\biocbuild\bbs-3.7-bioc\R\bin\R.exe CMD INSTALL --merge-multiarch --build --library=goSTAG.buildbin-libdir goSTAG_1.4.0.tar.gz && C:\Users\biocbuild\bbs-3.7-bioc\R\bin\R.exe CMD INSTALL goSTAG_1.4.0.zip && rm goSTAG_1.4.0.tar.gz goSTAG_1.4.0.zip
###
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  % Total    % Received % Xferd  Average Speed   Time    Time     Time  Current
                                 Dload  Upload   Total   Spent    Left  Speed

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100 1574k  100 1574k    0     0  17.6M      0 --:--:-- --:--:-- --:--:-- 18.9M

install for i386

* installing *source* package 'goSTAG' ...
** 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
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_1.4.0.zip
* DONE (goSTAG)
In R CMD INSTALL
In R CMD INSTALL
* installing to library 'C:/Users/biocbuild/bbs-3.7-bioc/R/library'
package 'goSTAG' successfully unpacked and MD5 sums checked
In R CMD INSTALL

R version 3.5.1 Patched (2018-07-24 r75005) -- "Feather Spray"
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 
   4.03    0.10    4.12 

R version 3.5.1 Patched (2018-07-24 r75005) -- "Feather Spray"
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 
   3.20    0.07    3.26