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###
### Running command:
###
###   /home/biocbuild/bbs-3.18-bioc/R/bin/R CMD check --install=check:enrichTF.install-out.txt --library=/home/biocbuild/bbs-3.18-bioc/R/site-library --timings enrichTF_1.18.0.tar.gz
###
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* using log directory ‘/home/biocbuild/bbs-3.18-bioc/meat/enrichTF.Rcheck’
* using R version 4.3.3 (2024-02-29)
* using platform: x86_64-pc-linux-gnu (64-bit)
* R was compiled by
    gcc (Ubuntu 11.4.0-1ubuntu1~22.04) 11.4.0
    GNU Fortran (Ubuntu 11.4.0-1ubuntu1~22.04) 11.4.0
* running under: Ubuntu 22.04.4 LTS
* using session charset: UTF-8
* checking for file ‘enrichTF/DESCRIPTION’ ... OK
* checking extension type ... Package
* this is package ‘enrichTF’ version ‘1.18.0’
* 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 ‘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 loading without being on the library search path ... OK
* checking startup messages can be suppressed ... 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 global function
  definition for ‘as’
processing,TissueOpennessConserve: no visible binding for global
  variable ‘X2’
processing,TissueOpennessSpecificity: no visible global function
  definition for ‘as’
Undefined global functions or variables:
  X2 as
Consider adding
  importFrom("methods", "as")
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 ... ERROR
Running examples in ‘enrichTF-Ex.R’ failed
The error most likely occurred in:

> base::assign(".ptime", proc.time(), pos = "CheckExEnv")
> ### Name: GenBackground
> ### Title: Generate background regions and reset the size of foreground
> ###   regions
> ### Aliases: GenBackground enrichGenBackground,Step-method
> ###   enrichGenBackground genBackground
> 
> ### ** Examples
> 
> setGenome("testgenome") #Use "hg19","hg38",etc. for your application
Configure bsgenome ...
Error in get_data_annotation_contrib_url(type) : 
  Install 'BiocManager' from CRAN to get 'BioCann' contrib.url
Calls: setGenome ... checkAndInstallBSgenome -> <Anonymous> -> get_data_annotation_contrib_url
Execution halted
* checking for unstated dependencies in ‘tests’ ... OK
* checking tests ...
  Running ‘testthat.R’
 ERROR
Running the tests in ‘tests/testthat.R’ failed.
Last 13 lines of output:
  Backtrace:
      ▆
   1. └─pipeFrame::setGenome("testgenome") at test-pipe.R:8:5
   2.   └─base::lapply(checkAndInstall, function(cai) cai())
   3.     └─pipeFrame (local) FUN(X[[i]], ...)
   4.       └─enrichTF (local) cai()
   5.         └─pipeFrame::runWithFinishCheck(...)
   6.           └─enrichTF (local) func(NULL)
   7.             └─pipeFrame::checkAndInstallBSgenome(refFilePath, genome)
   8.               └─BSgenome::available.genomes()
   9.                 └─BSgenome:::get_data_annotation_contrib_url(type)
  
  [ FAIL 1 | WARN 0 | SKIP 0 | PASS 0 ]
  Error: Test failures
  Execution halted
* checking for unstated dependencies in vignettes ... OK
* checking package vignettes in ‘inst/doc’ ... OK
* checking running R code from vignettes ...
  ‘enrichTF.Rmd’ using ‘UTF-8’... failed
 ERROR
Errors in running code in vignettes:
when running code in ‘enrichTF.Rmd’
  ...
> foregroundBedPath <- system.file(package = "enrichTF", 
+     "extdata", "testregion.bed")

> PECA_TF_enrich(inputForegroundBed = foregroundBedPath, 
+     genome = "testgenome")
Configure bsgenome ...

  When sourcing ‘enrichTF.R’:
Error: Install 'BiocManager' from CRAN to get 'BioCann' contrib.url
Execution halted

* checking re-building of vignette outputs ... NOTE
Error(s) in re-building vignettes:
  ...
--- re-building ‘enrichTF.Rmd’ using rmarkdown

Quitting from lines  at lines 58-62 [unnamed-chunk-1] (enrichTF.Rmd)
Error: processing vignette 'enrichTF.Rmd' failed with diagnostics:
Install 'BiocManager' from CRAN to get 'BioCann' contrib.url
--- failed re-building ‘enrichTF.Rmd’

SUMMARY: processing the following file failed:
  ‘enrichTF.Rmd’

Error: Vignette re-building failed.
Execution halted

* checking PDF version of manual ... OK
* DONE

Status: 3 ERRORs, 2 NOTEs
See
  ‘/home/biocbuild/bbs-3.18-bioc/meat/enrichTF.Rcheck/00check.log’
for details.

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###
### Running command:
###
###   /home/biocbuild/bbs-3.18-bioc/R/bin/R CMD INSTALL enrichTF
###
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* installing to library ‘/home/biocbuild/bbs-3.18-bioc/R/site-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 version 4.3.3 (2024-02-29) -- "Angel Food Cake"
Copyright (C) 2024 The R Foundation for Statistical Computing
Platform: x86_64-pc-linux-gnu (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")
[ FAIL 1 | WARN 0 | SKIP 0 | PASS 0 ]

══ Failed tests ════════════════════════════════════════════════════════════════
── Error ('test-pipe.R:8:5'): test whole pipeline ──────────────────────────────
Error in `get_data_annotation_contrib_url(type)`: Install 'BiocManager' from CRAN to get 'BioCann' contrib.url
Backtrace:
    ▆
 1. └─pipeFrame::setGenome("testgenome") at test-pipe.R:8:5
 2.   └─base::lapply(checkAndInstall, function(cai) cai())
 3.     └─pipeFrame (local) FUN(X[[i]], ...)
 4.       └─enrichTF (local) cai()
 5.         └─pipeFrame::runWithFinishCheck(...)
 6.           └─enrichTF (local) func(NULL)
 7.             └─pipeFrame::checkAndInstallBSgenome(refFilePath, genome)
 8.               └─BSgenome::available.genomes()
 9.                 └─BSgenome:::get_data_annotation_contrib_url(type)

[ FAIL 1 | WARN 0 | SKIP 0 | PASS 0 ]
Error: Test failures
Execution halted