BioC 3.5: CHECK report for goSTAG on veracruz2

Package: goSTAG

Version: 1.0.1

Command: /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD check --no-vignettes --timings goSTAG_1.0.1.tar.gz

StartedAt: 2017-10-18 04:27:21 -0400 (Wed, 18 Oct 2017)

EndedAt: 2017-10-18 04:32:33 -0400 (Wed, 18 Oct 2017)

EllapsedTime: 312.1 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_1.0.1.tar.gz
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* using log directory ‘/Users/biocbuild/bbs-3.5-bioc/meat/goSTAG.Rcheck’
* using R version 3.4.2 (2017-09-28)
* 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 ‘1.0.1’
* 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
plotHeatmap                   38.069  1.018  40.220
annotateClusters              36.665  1.098  38.716
goSTAG-package                36.294  0.987  38.209
performGOEnrichment           35.192  0.985  37.044
performHierarchicalClustering 32.786  0.927  34.568
groupClusters                 32.658  0.929  34.215
* 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	36.665	1.098	38.716
goSTAG-package	36.294	0.987	38.209
goSTAG_example_gene_lists	0.002	0.000	0.003
goSTAG_go_genes_human	0.062	0.004	0.067
goSTAG_go_genes_mouse	0.078	0.001	0.079
goSTAG_go_genes_rat	0.047	0.001	0.048
groupClusters	32.658	0.929	34.215
loadGOTerms	0.360	0.013	0.383
loadGeneLists	0.004	0.001	0.006
performGOEnrichment	35.192	0.985	37.044
performHierarchicalClustering	32.786	0.927	34.568
plotHeatmap	38.069	1.018	40.220
rat_cancer_therapeutics_gene_lists	0.006	0.000	0.006