Package: hypeR

Version: 1.0.0

Command: /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD check --install=check:hypeR.install-out.txt --library=/Library/Frameworks/R.framework/Versions/Current/Resources/library --no-vignettes --timings hypeR_1.0.0.tar.gz

StartedAt: 2019-10-16 03:43:43 -0400 (Wed, 16 Oct 2019)

EndedAt: 2019-10-16 03:45:52 -0400 (Wed, 16 Oct 2019)

EllapsedTime: 128.4 seconds

RetCode: 0

Status:  OK

CheckDir: hypeR.Rcheck

Warnings: 0

##############################################################################
##############################################################################
###
### Running command:
###
###   /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD check --install=check:hypeR.install-out.txt --library=/Library/Frameworks/R.framework/Versions/Current/Resources/library --no-vignettes --timings hypeR_1.0.0.tar.gz
###
##############################################################################
##############################################################################


* using log directory ‘/Users/biocbuild/bbs-3.9-bioc/meat/hypeR.Rcheck’
* using R version 3.6.1 (2019-07-05)
* using platform: x86_64-apple-darwin15.6.0 (64-bit)
* using session charset: UTF-8
* using option ‘--no-vignettes’
* checking for file ‘hypeR/DESCRIPTION’ ... OK
* this is package ‘hypeR’ version ‘1.0.0’
* package encoding: UTF-8
* 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 ‘hypeR’ 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 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 ... NOTE
.hyper_enrichment: no visible global function definition for ‘is’
.hyper_enrichment: no visible global function definition for ‘p.adjust’
.hyper_enrichment: no visible global function definition for ‘rjust’
.hyper_enrichment: no visible global function definition for ‘quantile’
.hyper_enrichment: no visible global function definition for ‘phyper’
download_gsets: no visible binding for global variable ‘gs_name’
download_gsets: no visible binding for global variable ‘gene_symbol’
download_gsets: no visible binding for global variable ‘.’
download_msigdb: no visible binding for global variable ‘gs_cat’
download_msigdb: no visible binding for global variable ‘gs_subcat’
download_msigdb: no visible global function definition for
  ‘packageVersion’
hyp_plot: no visible global function definition for ‘head’
hyp_show : : no visible binding for global variable
  ‘symbols’
hyp_to_table: no visible global function definition for ‘write.table’
hypeR: no visible global function definition for ‘is’
hypeR: no visible global function definition for ‘complete.cases’
Undefined global functions or variables:
  . complete.cases gene_symbol gs_cat gs_name gs_subcat head is
  p.adjust packageVersion phyper quantile rjust symbols write.table
Consider adding
  importFrom("graphics", "symbols")
  importFrom("methods", "is")
  importFrom("stats", "complete.cases", "p.adjust", "phyper", "quantile")
  importFrom("utils", "head", "packageVersion", "write.table")
to your NAMESPACE file (and ensure that your DESCRIPTION Imports field
contains 'methods').
* 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 files in ‘vignettes’ ... OK
* checking examples ... OK
Examples with CPU or elapsed time > 5s
                  user system elapsed
db_get          27.656  5.238  32.898
download_msigdb 22.808  5.069  27.878
* 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: 1 NOTE
See
  ‘/Users/biocbuild/bbs-3.9-bioc/meat/hypeR.Rcheck/00check.log’
for details.

##############################################################################
##############################################################################
###
### Running command:
###
###   /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD INSTALL hypeR
###
##############################################################################
##############################################################################


* installing to library ‘/Library/Frameworks/R.framework/Versions/3.6/Resources/library’
* installing *source* package ‘hypeR’ ...
** using staged installation
** R
** inst
** byte-compile and prepare package for lazy loading
** help
*** installing help indices
** building package indices
** installing vignettes
** testing if installed package can be loaded from temporary location
** testing if installed package can be loaded from final location
** testing if installed package keeps a record of temporary installation path
* DONE (hypeR)

R version 3.6.1 (2019-07-05) -- "Action of the Toes"
Copyright (C) 2019 The R Foundation for Statistical Computing
Platform: x86_64-apple-darwin15.6.0 (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(hypeR)
> 
> test_check("hypeR")
Number of genes =  24 
Number of gene sets =  674 
Background population size =  2520 
P-Value cutoff =  1 
FDR cutoff =  0.05 
══ testthat results  ═══════════════════════════════════════════════════════════
[ OK: 11 | SKIPPED: 0 | WARNINGS: 0 | FAILED: 0 ]
> 
> proc.time()
   user  system elapsed 
  2.470   0.361   2.774 

name	user	system	elapsed
db_get	27.656	5.238	32.898
db_info	0.001	0.000	0.001
download_gsets	0.083	0.024	0.107
download_msigdb	22.808	5.069	27.878
ex_get	0.032	0.002	0.035
hyp_plot	0.482	0.082	0.570
hyp_show	0.191	0.036	0.231
hyp_to_excel	0.234	0.025	0.260
hyp_to_table	0.139	0.009	0.148
hypeR	0.143	0.010	0.152