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###
### Running command:
###
###   /home/biocbuild/bbs-3.18-bioc/R/bin/R CMD check --install=check:RcisTarget.install-out.txt --library=/home/biocbuild/bbs-3.18-bioc/R/site-library --timings RcisTarget_1.22.0.tar.gz
###
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* using log directory ‘/home/biocbuild/bbs-3.18-bioc/meat/RcisTarget.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 ‘RcisTarget/DESCRIPTION’ ... OK
* checking extension type ... Package
* this is package ‘RcisTarget’ version ‘1.22.0’
* 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 ‘RcisTarget’ can be installed ... OK
* checking installed package size ... NOTE
  installed size is 12.0Mb
  sub-directories of 1Mb or more:
    data  11.4Mb
* 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 files in ‘vignettes’ ... OK
* checking examples ... ERROR
Running examples in ‘RcisTarget-Ex.R’ failed
The error most likely occurred in:

> base::assign(".ptime", proc.time(), pos = "CheckExEnv")
> ### Name: addSignificantGenes
> ### Title: Add significant genes
> ### Aliases: addSignificantGenes addSignificantGenes,list-method
> ###   addSignificantGenes,character-method
> ###   addSignificantGenes,GeneSet-method
> ###   addSignificantGenes,GeneSetCollection-method getSignificantGenes
> ###   getSignificantGenes,list-method getSignificantGenes,character-method
> ###   getSignificantGenes,factor-method getSignificantGenes,GeneSet-method
> ###   getSignificantGenes,GeneSetCollection-method
> 
> ### ** Examples
> 
> 
> ##################################################
> # Setup & previous steps in the workflow:
> 
> #### Gene sets
> # As example, the package includes an Hypoxia gene set:
> txtFile <- paste(file.path(system.file('examples', package='RcisTarget')),
+                  "hypoxiaGeneSet.txt", sep="/")
> geneLists <- list(hypoxia=read.table(txtFile, stringsAsFactors=FALSE)[,1])
> 
> #### Databases
> ## Motif rankings: Select according to organism and distance around TSS
> ## (See the vignette for URLs to download)
> # motifRankings <- importRankings("hg19-500bp-upstream-7species.mc9nr.feather")
> 
> ## For this example we will use a SUBSET of the ranking/motif databases:
> library(RcisTarget.hg19.motifDBs.cisbpOnly.500bp)
> data(hg19_500bpUpstream_motifRanking_cispbOnly)
> motifRankings <- hg19_500bpUpstream_motifRanking_cispbOnly
> 
> ## Motif - TF annotation:
> data(motifAnnotations_hgnc_v9) # human TFs (for motif collection 9)
> motifAnnotation <- motifAnnotations_hgnc_v9
> 
> ### Run RcisTarget
> # Step 1. Calculate AUC
> motifs_AUC <- calcAUC(geneLists, motifRankings)
> # Step 2. Select significant motifs, add TF annotation & format as table
> motifEnrichmentTable <- addMotifAnnotation(motifs_AUC,
+            motifAnnot=motifAnnotation)
> 
> ##################################################
> 
> ##################################################
> # (This step: Step 3)
> # Identify the genes that have the motif significantly enriched
> # (i.e. genes from the gene set in the top of the ranking)
> par(mfrow=c(1,2))
> motifEnrichmentTable_wGenes <- addSignificantGenes(motifEnrichmentTable,
+                                        genesFormat="geneList",
+                                        plotCurve=TRUE,
+                                        geneSets=geneLists,
+                                        rankings=motifRankings,
+                                        method="aprox")
Error in .getSignificantGenes(geneSet = geneSet, rankings = rankings,  : 
  Package 'zoo' is required to calculate the aproximate RCC distributions.To install it, run:	 install.packages('zoo')
Calls: addSignificantGenes ... .addSignificantGenes -> lapply -> FUN -> .getSignificantGenes
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:
      genesFormat = genesFormat, nCores = nCores, digits = 3, nMean = nMean)`: Package 'zoo' is required to calculate the aproximate RCC distributions.To install it, run:	 install.packages('zoo')
  Backtrace:
      ▆
   1. └─RcisTarget (local) test_Workflow()
   2.   └─RcisTarget (local) .check_addSignificantGenes(...) at test_RcisTarget.R:258:3
   3.     ├─RcisTarget::addSignificantGenes(...) at test_RcisTarget.R:57:3
   4.     └─RcisTarget::addSignificantGenes(...)
   5.       └─RcisTarget:::.addSignificantGenes(...)
   6.         └─base::lapply(...)
   7.           └─RcisTarget (local) FUN(X[[i]], ...)
   8.             └─RcisTarget:::.getSignificantGenes(...)
  
  [ FAIL 1 | WARN 0 | SKIP 0 | PASS 45 ]
  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 ...
  ‘RcisTarget_MainTutorial.Rmd’... failed
  ‘Tutorial_AnalysisOfGenomicRegions.Rmd’... OK
  ‘Tutorial_AnalysisWithBackground.Rmd’... OK
 ERROR
Errors in running code in vignettes:
when running code in ‘RcisTarget_MainTutorial.Rmd’
  ...
4: EPAS1 (directAnnotation). 
5:                           
6:                           

> motifEnrichmentTable_wGenes <- addSignificantGenes(motifEnrichmentTable, 
+     rankings = motifRankings, geneSets = geneLists)

  When sourcing ‘RcisTarget_MainTutorial.R’:
Error: Package 'zoo' is required to calculate the aproximate RCC distributions.To install it, run:	 install.packages('zoo')
Execution halted

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

Quitting from lines  at lines 339-343 [addSignificantGenes] (RcisTarget_MainTutorial.Rmd)
Error: processing vignette 'RcisTarget_MainTutorial.Rmd' failed with diagnostics:
Package 'zoo' is required to calculate the aproximate RCC distributions.To install it, run:	 install.packages('zoo')
--- failed re-building ‘RcisTarget_MainTutorial.Rmd’

--- re-building ‘Tutorial_AnalysisOfGenomicRegions.Rmd’ using rmarkdown
trying URL 'https://gbiomed.kuleuven.be/apps/lcb/i-cisTarget/examples/input_files/human/peaks/Encode_GATA1_peaks.bed'
Content type 'application/vnd.realvnc.bed' length 23897 bytes (23 KB)
==================================================
downloaded 23 KB

--- finished re-building ‘Tutorial_AnalysisOfGenomicRegions.Rmd’

--- re-building ‘Tutorial_AnalysisWithBackground.Rmd’ using rmarkdown
--- finished re-building ‘Tutorial_AnalysisWithBackground.Rmd’

SUMMARY: processing the following file failed:
  ‘RcisTarget_MainTutorial.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/RcisTarget.Rcheck/00check.log’
for details.

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###
### Running command:
###
###   /home/biocbuild/bbs-3.18-bioc/R/bin/R CMD INSTALL RcisTarget
###
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* installing to library ‘/home/biocbuild/bbs-3.18-bioc/R/site-library’
* installing *source* package ‘RcisTarget’ ...
** using staged installation
** R
** data
** 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 (RcisTarget)

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(RcisTarget)
> 
> test_check("RcisTarget")
[ FAIL 1 | WARN 0 | SKIP 0 | PASS 45 ]

══ Failed tests ════════════════════════════════════════════════════════════════
── Error ('test_RcisTarget.R:283:1'): RcisTarget workflow tests ────────────────
Error in `.getSignificantGenes(geneSet = geneSet, rankings = rankings, 
    signifRankingNames = unname(unlist(subset(enrRnkT_ByGs, select = rnkType))), 
    method = method, maxRank = maxRank, plotCurve = plotCurve, 
    genesFormat = genesFormat, nCores = nCores, digits = 3, nMean = nMean)`: Package 'zoo' is required to calculate the aproximate RCC distributions.To install it, run:	 install.packages('zoo')
Backtrace:
    ▆
 1. └─RcisTarget (local) test_Workflow()
 2.   └─RcisTarget (local) .check_addSignificantGenes(...) at test_RcisTarget.R:258:3
 3.     ├─RcisTarget::addSignificantGenes(...) at test_RcisTarget.R:57:3
 4.     └─RcisTarget::addSignificantGenes(...)
 5.       └─RcisTarget:::.addSignificantGenes(...)
 6.         └─base::lapply(...)
 7.           └─RcisTarget (local) FUN(X[[i]], ...)
 8.             └─RcisTarget:::.getSignificantGenes(...)

[ FAIL 1 | WARN 0 | SKIP 0 | PASS 45 ]
Error: Test failures
Execution halted