BioC 3.5: CHECK report for goSTAG on toluca2

Package: goSTAG

Version: 0.99.5

Command: /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD check --no-vignettes --timings goSTAG_0.99.5.tar.gz

StartedAt: 2017-04-23 04:51:13 -0400 (Sun, 23 Apr 2017)

EndedAt: 2017-04-23 04:53:23 -0400 (Sun, 23 Apr 2017)

EllapsedTime: 129.9 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_0.99.5.tar.gz
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* using log directory ‘/Users/biocbuild/bbs-3.5-bioc/meat/goSTAG.Rcheck’
* using R Under development (unstable) (2017-02-15 r72187)
* using platform: x86_64-apple-darwin13.4.0 (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 ‘0.99.5’
* 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      5.367  0.045   5.432
annotateClusters 5.218  0.126   5.350
goSTAG-package   5.278  0.048   5.335
* 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	5.218	0.126	5.350
goSTAG-package	5.278	0.048	5.335
goSTAG_example_gene_lists	0.003	0.001	0.003
goSTAG_go_genes_human	0.082	0.004	0.086
goSTAG_go_genes_mouse	0.223	0.001	0.224
goSTAG_go_genes_rat	0.053	0.003	0.056
groupClusters	3.698	0.035	3.737
loadGOTerms	0.482	0.011	0.493
loadGeneLists	0.007	0.001	0.008
performGOEnrichment	3.873	0.041	3.934
performHierarchicalClustering	4.210	0.030	4.271
plotHeatmap	5.367	0.045	5.432
rat_cancer_therapeutics_gene_lists	0.004	0.001	0.005