Package: enrichTF

Version: 1.3.5

Command: /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD check --install=check:enrichTF.install-out.txt --library=/Library/Frameworks/R.framework/Versions/Current/Resources/library --no-vignettes --timings enrichTF_1.3.5.tar.gz

StartedAt: 2020-01-16 04:08:21 -0500 (Thu, 16 Jan 2020)

EndedAt: 2020-01-16 04:20:40 -0500 (Thu, 16 Jan 2020)

EllapsedTime: 738.5 seconds

RetCode: 0

Status:  OK

CheckDir: enrichTF.Rcheck

Warnings: 0

##############################################################################
##############################################################################
###
### Running command:
###
###   /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD check --install=check:enrichTF.install-out.txt --library=/Library/Frameworks/R.framework/Versions/Current/Resources/library --no-vignettes --timings enrichTF_1.3.5.tar.gz
###
##############################################################################
##############################################################################


* using log directory ‘/Users/biocbuild/bbs-3.11-bioc/meat/enrichTF.Rcheck’
* using R Under development (unstable) (2019-12-14 r77572)
* using platform: x86_64-apple-darwin15.6.0 (64-bit)
* using session charset: UTF-8
* using option ‘--no-vignettes’
* checking for file ‘enrichTF/DESCRIPTION’ ... OK
* checking extension type ... Package
* this is package ‘enrichTF’ version ‘1.3.5’
* 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 ‘enrichTF’ 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
processing,TissueOpennessConserve: no visible binding for global
  variable ‘X2’
Undefined global functions or variables:
  X2
* 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 (user + system) or elapsed time > 5s
                            user system elapsed
GeneOntology              96.794 15.290 112.786
TissueOpennessSpecificity 47.997  2.188  50.239
GenBackground              6.918  0.789   8.623
MotifsInRegions            4.361  1.886   4.744
Pipelines                  3.428  0.561  31.394
* 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-3.11-bioc/meat/enrichTF.Rcheck/00check.log’
for details.

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


* installing to library ‘/Library/Frameworks/R.framework/Versions/4.0/Resources/library’
* installing *source* package ‘enrichTF’ ...
** 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 (enrichTF)

R Under development (unstable) (2019-12-14 r77572) -- "Unsuffered Consequences"
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(enrichTF)
Loading required package: pipeFrame

> 
> test_check("enrichTF")
[1] "2020-01-16 04:20:25 EST"
[1] "2020-01-16 04:20:25 EST"
[1] "2020-01-16 04:20:25 EST"
[1] "2020-01-16 04:20:25 EST"
[1] "2020-01-16 04:20:25 EST"
[1] "2020-01-16 04:20:25 EST"
[1] "2020-01-16 04:20:28 EST"
[1] "2020-01-16 04:20:28 EST"
[1] "2020-01-16 04:20:28 EST"
[1] "2020-01-16 04:20:28 EST"
[1] "2020-01-16 04:20:28 EST"
[1] "2020-01-16 04:20:28 EST"
[1] "2020-01-16 04:20:31 EST"
[1] "2020-01-16 04:20:31 EST"
[1] "2020-01-16 04:20:31 EST"
[1] "2020-01-16 04:20:31 EST"
[1] "2020-01-16 04:20:31 EST"
[1] "2020-01-16 04:20:31 EST"
══ testthat results  ═══════════════════════════════════════════════════════════
[ OK: 9 | SKIPPED: 0 | WARNINGS: 0 | FAILED: 0 ]
> 
> proc.time()
   user  system elapsed 
 36.844   4.433  40.383 

name	user	system	elapsed
GenBackground	6.918	0.789	8.623
GeneOntology	96.794	15.290	112.786
MotifsInRegions	4.361	1.886	4.744
Pipelines	3.428	0.561	31.394
RegionConnectTargetGene	1.225	0.231	1.643
TFsEnrichInRegions	1.353	0.330	1.819
TissueOpennessConserve	0.343	0.062	0.406
TissueOpennessSpecificity	47.997	2.188	50.239
UnzipAndMergeBed	0.197	0.018	0.215