BioC 3.5: CHECK report for goSTAG on malbec2

Package: goSTAG

Version: 1.0.1

Command: /home/biocbuild/bbs-3.5-bioc/R/bin/R CMD check --no-vignettes --timings goSTAG_1.0.1.tar.gz

StartedAt: 2017-10-17 23:44:15 -0400 (Tue, 17 Oct 2017)

EndedAt: 2017-10-17 23:49:35 -0400 (Tue, 17 Oct 2017)

EllapsedTime: 320.6 seconds

RetCode: 0

Status:  OK

CheckDir: goSTAG.Rcheck

Warnings: 0

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### Running command:
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###   /home/biocbuild/bbs-3.5-bioc/R/bin/R CMD check --no-vignettes --timings goSTAG_1.0.1.tar.gz
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* using log directory ‘/home/biocbuild/bbs-3.5-bioc/meat/goSTAG.Rcheck’
* using R version 3.4.2 (2017-09-28)
* using platform: x86_64-pc-linux-gnu (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
annotateClusters              41.124  0.060  41.280
groupClusters                 40.748  0.068  40.845
performGOEnrichment           40.460  0.052  40.543
performHierarchicalClustering 39.148  0.052  39.231
plotHeatmap                   38.220  0.044  38.297
goSTAG-package                36.884  0.012  36.924
* 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	41.124	0.060	41.280
goSTAG-package	36.884	0.012	36.924
goSTAG_example_gene_lists	0.000	0.004	0.002
goSTAG_go_genes_human	0.06	0.00	0.06
goSTAG_go_genes_mouse	0.068	0.004	0.072
goSTAG_go_genes_rat	0.064	0.000	0.066
groupClusters	40.748	0.068	40.845
loadGOTerms	0.356	0.000	0.354
loadGeneLists	0.004	0.000	0.005
performGOEnrichment	40.460	0.052	40.543
performHierarchicalClustering	39.148	0.052	39.231
plotHeatmap	38.220	0.044	38.297
rat_cancer_therapeutics_gene_lists	0.004	0.000	0.005