##############################################################################
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###
### Running command:
###
###   /home/biocbuild/bbs-3.17-bioc/R/bin/R CMD check --install=check:enrichTF.install-out.txt --library=/home/biocbuild/bbs-3.17-bioc/R/library --timings enrichTF_1.15.0.tar.gz
###
##############################################################################
##############################################################################


* using log directory ‘/home/biocbuild/bbs-3.17-bioc/meat/enrichTF.Rcheck’
* using R Under development (unstable) (2023-01-14 r83615)
* using platform: aarch64-unknown-linux-gnu (64-bit)
* R was compiled by
    gcc (Ubuntu 11.3.0-1ubuntu1~22.04) 11.3.0
    GNU Fortran (Ubuntu 11.3.0-1ubuntu1~22.04) 11.3.0
* running under: Ubuntu 22.04.1 LTS
* using session charset: UTF-8
* checking for file ‘enrichTF/DESCRIPTION’ ... OK
* checking extension type ... Package
* this is package ‘enrichTF’ version ‘1.15.0’
* 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 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: Pipelines
> ### Title: ready-to-use pipelines
> ### Aliases: Pipelines PECA_TF_enrich GeneReguPipe
> 
> ### ** Examples
> 
> 
> foregroundBedPath <- system.file(package = "enrichTF", "extdata","testregion.bed")
> # This is the whole pipeline example.
> PECA_TF_enrich(inputForegroundBed = foregroundBedPath, genome = "testgenome")
Configure bsgenome ...
Configure bsgenome finished
Configure motifpwm ...
Configure motifpwm finished
Configure motifPWMOBJ ...
Configure motifPWMOBJ finished
Configure RE_gene_corr ...
Configure RE_gene_corr finished
Configure Enhancer_RE_gene_corr ...
Configure Enhancer_RE_gene_corr finished
Configure MotifTFTable ...
Configure MotifTFTable finished
Configure MotifWeights ...
Configure MotifWeights finished
Configure TFgeneRelMtx ...
Configure TFgeneRelMtx finished
Configure SampleName ...
Configure SampleName finished
Configure OpenRegion ...
Configure OpenRegion finished
Configure ConserveRegion ...
Configure ConserveRegion finished
Configure HOMER ...
Configure HOMER finished
Configure OrgDb ...
Configure OrgDb finished
>>>>>>==========================================================
Step Name:pipe_UnzipAndMergeBed
All Parameters for This Step:
|Input:
|    bedInput:
|        "/home/biocbuild/bbs-3.17-bioc/R/library/enrichTF/extdata/testregion.bed"
|Output:
|    bedOutput:
|        "/home/biocbuild/bbs-3.17-bioc/meat/enrichTF.Rcheck/enrichTF-pipeline/Step_03_pipe_UnzipAndMergeBed/testregion.bed"
|Other Parameters:
__________________________________________
Begin to check if it is finished...
2023-02-07 01:00:25.026306
New step. Start processing data: 
processing file:
source:/home/biocbuild/bbs-3.17-bioc/R/library/enrichTF/extdata/testregion.bed
destination:/home/biocbuild/bbs-3.17-bioc/meat/enrichTF.Rcheck/enrichTF-pipeline/Step_03_pipe_UnzipAndMergeBed/testregion.bed
2023-02-07 01:00:25.049267
processing finished
[1] "2023-02-07 01:00:25 UTC"
[1] "2023-02-07 01:00:25 UTC"
[1] "2023-02-07 01:00:25 UTC"
[1] "2023-02-07 01:00:25 UTC"
[1] "2023-02-07 01:00:25 UTC"
[1] "2023-02-07 01:00:25 UTC"
All results have been saved.
==========================================================<<<<<<
 
>>>>>>==========================================================
Step Name:pipe_GenBackground

Attaching package: ‘BiocGenerics’

The following objects are masked from ‘package:stats’:

    IQR, mad, sd, var, xtabs

The following objects are masked from ‘package:base’:

    Filter, Find, Map, Position, Reduce, anyDuplicated, aperm, append,
    as.data.frame, basename, cbind, colnames, dirname, do.call,
    duplicated, eval, evalq, get, grep, grepl, intersect, is.unsorted,
    lapply, mapply, match, mget, order, paste, pmax, pmax.int, pmin,
    pmin.int, rank, rbind, rownames, sapply, setdiff, sort, table,
    tapply, union, unique, unsplit, which.max, which.min


Attaching package: ‘S4Vectors’

The following objects are masked from ‘package:base’:

    I, expand.grid, unname


Attaching package: ‘Biostrings’

The following object is masked from ‘package:base’:

    strsplit

All Parameters for This Step:
|Input:
|    inputForegroundBed:
|        "/home/biocbuild/bbs-3.17-bioc/meat/enrichTF.Rcheck/enrichTF-pipeline/Step_03_pipe_UnzipAndMergeBed/testregion.bed"
|Output:
|    outputForegroundBed:
|        "/home/biocbuild/bbs-3.17-bioc/meat/enrichTF.Rcheck/enrichTF-pipeline/Step_00_pipe_GenBackground/testregion.foreground.bed"
|    outputBackgroundBed:
|        "/home/biocbuild/bbs-3.17-bioc/meat/enrichTF.Rcheck/enrichTF-pipeline/Step_00_pipe_GenBackground/testregion.background.bed"
|    outputRegionBed:
|        "/home/biocbuild/bbs-3.17-bioc/meat/enrichTF.Rcheck/enrichTF-pipeline/Step_00_pipe_GenBackground/testregion.allregion.bed"
|Other Parameters:
|    bsgenome:
|        An object of BSgenome
|    regionLen:
|        1000
|    sampleNumb:
|        0
__________________________________________
Begin to check if it is finished...
[1] "2023-02-07 01:00:25 UTC"
[1] "2023-02-07 01:00:25 UTC"
[1] "2023-02-07 01:00:25 UTC"
[1] "2023-02-07 01:00:25 UTC"
[1] "2023-02-07 01:00:25 UTC"
[1] "2023-02-07 01:00:25 UTC"
2023-02-07 01:00:25.398235
New step. Start processing data: 
2023-02-07 01:00:25.660314
processing finished
[1] "2023-02-07 01:00:25 UTC"
[1] "2023-02-07 01:00:25 UTC"
[1] "2023-02-07 01:00:25 UTC"
[1] "2023-02-07 01:00:25 UTC"
[1] "2023-02-07 01:00:25 UTC"
[1] "2023-02-07 01:00:25 UTC"
All results have been saved.
==========================================================<<<<<<
 
>>>>>>==========================================================
Step Name:pipe_RegionConnectTargetGene
All Parameters for This Step:
|Input:
|    inputForegroundBed:
|        "/home/biocbuild/bbs-3.17-bioc/meat/enrichTF.Rcheck/enrichTF-pipeline/Step_00_pipe_GenBackground/testregion.foreground.bed"
|    inputBackgroundBed:
|        "/home/biocbuild/bbs-3.17-bioc/meat/enrichTF.Rcheck/enrichTF-pipeline/Step_00_pipe_GenBackground/testregion.background.bed"
|Output:
|    outputForegroundBed:
|        "/home/biocbuild/bbs-3.17-bioc/meat/enrichTF.Rcheck/enrichTF-pipeline/Step_04_pipe_RegionConnectTargetGene/testregion.gene.foreground.bed"
|    ouputForgroundGeneTxt:
|        "/home/biocbuild/bbs-3.17-bioc/meat/enrichTF.Rcheck/enrichTF-pipeline/Step_04_pipe_RegionConnectTargetGene/testregion.gene.foreground.txt"
|    outputBackgroundBed:
|        "/home/biocbuild/bbs-3.17-bioc/meat/enrichTF.Rcheck/enrichTF-pipeline/Step_04_pipe_RegionConnectTargetGene/testregion.gene.background.bed"
|    regularGeneCorrBed:
|        "/home/biocbuild/bbs-3.17-bioc/meat/enrichTF.Rcheck/refdir/testgenome/RE_gene_corr.bed"
|    enhancerRegularGeneCorrBed:
|        "/home/biocbuild/bbs-3.17-bioc/meat/enrichTF.Rcheck/refdir/testgenome/Enhancer_RE_gene_corr.bed"
|Other Parameters:
__________________________________________
Begin to check if it is finished...
2023-02-07 01:00:25.706367
New step. Start processing data: 
2023-02-07 01:00:26.774771
processing finished
[1] "2023-02-07 01:00:26 UTC"
[1] "2023-02-07 01:00:26 UTC"
[1] "2023-02-07 01:00:26 UTC"
[1] "2023-02-07 01:00:26 UTC"
[1] "2023-02-07 01:00:26 UTC"
[1] "2023-02-07 01:00:26 UTC"
All results have been saved.
==========================================================<<<<<<
 
>>>>>>==========================================================
Step Name:pipe_FindMotifsInRegions
All Parameters for This Step:
|Input:
|    inputRegionBed:
|        "/home/biocbuild/bbs-3.17-bioc/meat/enrichTF.Rcheck/enrichTF-pipeline/Step_00_pipe_GenBackground/testregion.allregion.bed"
|Output:
|    outputRegionMotifBed:
|        "/home/biocbuild/bbs-3.17-bioc/meat/enrichTF.Rcheck/enrichTF-pipeline/Step_02_pipe_FindMotifsInRegions/testregion.region.motif.bed"
|    outputMotifBed:
|        "/home/biocbuild/bbs-3.17-bioc/meat/enrichTF.Rcheck/enrichTF-pipeline/Step_02_pipe_FindMotifsInRegions/testregion.motif.bed"
|Other Parameters:
|    motifRc:
|        "integrate"
|    pwmObj:
|        An object of PWMatrixList
|    genome:
|        "hg19"
|    threads:
|        2
__________________________________________
Begin to check if it is finished...
[1] "2023-02-07 01:00:26 UTC"
[1] "2023-02-07 01:00:26 UTC"
[1] "2023-02-07 01:00:26 UTC"
[1] "2023-02-07 01:00:26 UTC"
[1] "2023-02-07 01:00:26 UTC"
[1] "2023-02-07 01:00:26 UTC"
The step:`pipe_FindMotifsInRegions` was finished. Nothing to do.
If you need to redo or rerun this step,please call 'clearStepCache(YourStepObject)'or remove file: /home/biocbuild/bbs-3.17-bioc/meat/enrichTF.Rcheck/enrichTF-pipeline/Step_02_pipe_FindMotifsInRegions/pipeFrame.obj.936228c8.rds
==========================================================<<<<<<
 
>>>>>>==========================================================
Step Name:pipe_TFsEnrichInRegions
All Parameters for This Step:
|Input:
|    inputRegionBed:
|        "/home/biocbuild/bbs-3.17-bioc/meat/enrichTF.Rcheck/enrichTF-pipeline/Step_00_pipe_GenBackground/testregion.allregion.bed"
|    inputRegionMotifBed:
|        "/home/biocbuild/bbs-3.17-bioc/meat/enrichTF.Rcheck/enrichTF-pipeline/Step_02_pipe_FindMotifsInRegions/testregion.region.motif.bed"
|    inputForegroundGeneBed:
|        "/home/biocbuild/bbs-3.17-bioc/meat/enrichTF.Rcheck/enrichTF-pipeline/Step_04_pipe_RegionConnectTargetGene/testregion.gene.foreground.bed"
|    inputBackgroundGeneBed:
|        "/home/biocbuild/bbs-3.17-bioc/meat/enrichTF.Rcheck/enrichTF-pipeline/Step_04_pipe_RegionConnectTargetGene/testregion.gene.background.bed"
|    inputMotifWeights:
|        "/home/biocbuild/bbs-3.17-bioc/meat/enrichTF.Rcheck/refdir/testgenome/MotifWeights.RData"
|    inputTFgeneRelMtx:
|        "/home/biocbuild/bbs-3.17-bioc/meat/enrichTF.Rcheck/refdir/testgenome/TFgeneRelMtx.RData"
|    inputMotifTFTable:
|        "/home/biocbuild/bbs-3.17-bioc/meat/enrichTF.Rcheck/refdir/testgenome/MotifTFTable.RData"
|Output:
|    outputTFsEnrichTxt:
|        "/home/biocbuild/bbs-3.17-bioc/meat/enrichTF.Rcheck/enrichTF-pipeline/Step_05_pipe_TFsEnrichInRegions/testregion.PECA_TF_enrich.txt"
|Other Parameters:
__________________________________________
Begin to check if it is finished...
2023-02-07 01:00:26.872046
New step. Start processing data: 
Killed
* 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 ...
  ‘enrichTF.Rmd’ using ‘UTF-8’... OK
 NONE
* checking re-building of vignette outputs ... ERROR
Error(s) in re-building vignettes:
  ...
--- re-building ‘enrichTF.Rmd’ using rmarkdown
Killed

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

Status: 2 ERRORs, 1 NOTE
See
  ‘/home/biocbuild/bbs-3.17-bioc/meat/enrichTF.Rcheck/00check.log’
for details.

##############################################################################
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###
### Running command:
###
###   /home/biocbuild/bbs-3.17-bioc/R/bin/R CMD INSTALL enrichTF
###
##############################################################################
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* installing to library ‘/home/biocbuild/bbs-3.17-bioc/R/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) (2023-01-14 r83615) -- "Unsuffered Consequences"
Copyright (C) 2023 The R Foundation for Statistical Computing
Platform: aarch64-unknown-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")
[1] "2023-02-07 01:01:06 UTC"
[1] "2023-02-07 01:01:06 UTC"
[1] "2023-02-07 01:01:06 UTC"
[1] "2023-02-07 01:01:06 UTC"
[1] "2023-02-07 01:01:06 UTC"
[1] "2023-02-07 01:01:06 UTC"
[1] "2023-02-07 01:01:08 UTC"
[1] "2023-02-07 01:01:08 UTC"
[1] "2023-02-07 01:01:08 UTC"
[1] "2023-02-07 01:01:08 UTC"
[1] "2023-02-07 01:01:08 UTC"
[1] "2023-02-07 01:01:08 UTC"
[1] "2023-02-07 01:01:09 UTC"
[1] "2023-02-07 01:01:09 UTC"
[1] "2023-02-07 01:01:09 UTC"
[1] "2023-02-07 01:01:09 UTC"
[1] "2023-02-07 01:01:09 UTC"
[1] "2023-02-07 01:01:09 UTC"
[ FAIL 0 | WARN 0 | SKIP 0 | PASS 9 ]
> 
> proc.time()
   user  system elapsed 
 26.014   2.402  34.740