BioC 3.6: CHECK report for goSTAG on veracruz1

Package: goSTAG

Version: 1.1.3

Command: /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD check --no-vignettes --timings goSTAG_1.1.3.tar.gz

StartedAt: 2017-08-16 03:56:13 -0400 (Wed, 16 Aug 2017)

EndedAt: 2017-08-16 04:02:01 -0400 (Wed, 16 Aug 2017)

EllapsedTime: 347.8 seconds

RetCode: 0

Status:  OK

CheckDir: goSTAG.Rcheck

Warnings: 0

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### Running command:
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###   /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD check --no-vignettes --timings goSTAG_1.1.3.tar.gz
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* using log directory ‘/Users/biocbuild/bbs-3.6-bioc/meat/goSTAG.Rcheck’
* using R version 3.4.1 (2017-06-30)
* using platform: x86_64-apple-darwin15.6.0 (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 ‘1.1.3’
* 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 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 ... OK
Examples with CPU or elapsed time > 5s
                                user system elapsed
goSTAG-package                42.116  0.928  44.337
annotateClusters              41.477  1.000  43.782
groupClusters                 40.361  0.877  42.481
plotHeatmap                   38.781  0.858  40.627
performHierarchicalClustering 38.407  0.840  40.338
performGOEnrichment           38.181  0.852  40.144
* 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

* installing *source* package ‘goSTAG’ ...
** R
** data
*** moving datasets to lazyload DB
** inst
** preparing package for lazy loading
** help
*** installing help indices
** building package indices
** installing vignettes
** testing if installed package can be loaded
* DONE (goSTAG)

name	user	system	elapsed
annotateClusters	41.477	1.000	43.782
goSTAG-package	42.116	0.928	44.337
goSTAG_example_gene_lists	0.003	0.000	0.003
goSTAG_go_genes_human	0.070	0.004	0.077
goSTAG_go_genes_mouse	0.077	0.001	0.083
goSTAG_go_genes_rat	0.064	0.001	0.066
groupClusters	40.361	0.877	42.481
loadGOTerms	0.372	0.012	0.391
loadGeneLists	0.005	0.001	0.007
performGOEnrichment	38.181	0.852	40.144
performHierarchicalClustering	38.407	0.840	40.338
plotHeatmap	38.781	0.858	40.627
rat_cancer_therapeutics_gene_lists	0.006	0.001	0.006