##############################################################################
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###
### Running command:
###
###   /Library/Frameworks/R.framework/Resources/bin/R CMD check --install=check:circRNAprofiler.install-out.txt --library=/Library/Frameworks/R.framework/Resources/library --no-vignettes --timings circRNAprofiler_1.20.0.tar.gz
###
##############################################################################
##############################################################################


* using log directory ‘/Users/biocbuild/bbs-3.20-bioc/meat/circRNAprofiler.Rcheck’
* using R version 4.4.2 (2024-10-31)
* using platform: x86_64-apple-darwin20
* R was compiled by
    Apple clang version 14.0.0 (clang-1400.0.29.202)
    GNU Fortran (GCC) 12.2.0
* running under: macOS Monterey 12.7.6
* using session charset: UTF-8
* using option ‘--no-vignettes’
* checking for file ‘circRNAprofiler/DESCRIPTION’ ... OK
* checking extension type ... Package
* this is package ‘circRNAprofiler’ version ‘1.20.0’
* 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 ‘circRNAprofiler’ 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 code 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
.fixCoordsWithGTF: no visible binding for global variable ‘startUpBSE’
.fixCoordsWithGTF: no visible binding for global variable ‘endDownBSE’
.fixCoordsWithGTF: no visible binding for global variable ‘start’
.fixCoordsWithGTF: no visible binding for global variable ‘end’
.getAllTranscripts: no visible binding for global variable ‘gene_name’
.getAllTranscripts: no visible binding for global variable ‘type’
.getAllTranscripts: no visible binding for global variable
  ‘transcript_id’
.getAllTranscripts: no visible binding for global variable ‘width’
.getAllTranscripts: no visible binding for global variable ‘len’
.getAntisenseCircRNAs: no visible binding for global variable
  ‘gene_name’
.getAntisenseCircRNAs: no visible binding for global variable ‘strand’
.getAntisenseCircRNAs: no visible binding for global variable ‘strand1’
.getAntisenseCircRNAs: no visible binding for global variable
  ‘gene_name1’
.getBSEsFromTranscript: no visible binding for global variable ‘start’
.getBSEsFromTranscript: no visible binding for global variable ‘end’
.getBSEsFromTranscript: no visible binding for global variable
  ‘exon_number’
.getCentralMatches: no visible binding for global variable ‘tm’
.getCentralMatches: no visible binding for global variable ‘cwcm’
.getCompensatoryMatches: no visible binding for global variable ‘tm’
.getCompensatoryMatches: no visible binding for global variable ‘cwcm’
.getComplRepeats: no visible binding for global variable ‘name’
.getComplRepeats: no visible binding for global variable ‘name.1’
.getComplRepeats: no visible binding for global variable ‘gr’
.getComplRepeats: no visible binding for global variable ‘gr.1’
.getComplRepeats: no visible binding for global variable ‘strand’
.getComplRepeats: no visible binding for global variable ‘strand.1’
.getFlankIntronFirst: no visible binding for global variable
  ‘exon_number’
.getFlankIntronLast: no visible binding for global variable
  ‘exon_number’
.getFlankIntrons: no visible binding for global variable ‘exon_number’
.getLengthBSEfi: no visible binding for global variable ‘endUpIntron’
.getLengthBSEfi: no visible binding for global variable ‘startUpIntron’
.getLengthBSEfi: no visible binding for global variable ‘endUpBSE’
.getLengthBSEfi: no visible binding for global variable ‘startUpBSE’
.getLengthBSEfi: no visible binding for global variable ‘endDownBSE’
.getLengthBSEfi: no visible binding for global variable ‘startDownBSE’
.getLengthBSEfi: no visible binding for global variable ‘endDownIntron’
.getLengthBSEfi: no visible binding for global variable
  ‘startDownIntron’
.getLengthBSEfi: no visible binding for global variable ‘lenUpBSE’
.getLengthBSEfi: no visible binding for global variable ‘lenDownBSE’
.getLengthBSEfi: no visible binding for global variable ‘lenUpIntron’
.getLengthBSEfi: no visible binding for global variable ‘lenDownIntron’
.getLengthBSEfi: no visible binding for global variable
  ‘meanLengthBSEs’
.getLengthBSEfi: no visible binding for global variable
  ‘meanLengthIntrons’
.getLengthCirc: no visible binding for global variable ‘exon_number’
.getLengthCirc: no visible binding for global variable ‘width’
.getRBPmotifsAttract: no visible binding for global variable ‘Organism’
.getRBPmotifsAttract: no visible binding for global variable
  ‘Gene_name’
.getRBPmotifsAttract: no visible binding for global variable ‘Motif’
.getRBPmotifsMEME: no visible binding for global variable ‘path’
.getSeedMatches: no visible binding for global variable ‘ncm’
.getSeedMatches: no visible binding for global variable ‘tm’
.getSeedMatches: no visible binding for global variable ‘cwcm’
.getTranscriptToAnalyze: no visible binding for global variable
  ‘transcript_id’
.getTranscriptToAnalyze: no visible binding for global variable
  ‘exon_number’
.grCoordsForNegative: no visible binding for global variable
  ‘startUpGR’
.grCoordsForNegative: no visible binding for global variable ‘endUpGR’
.grCoordsForNegative: no visible binding for global variable
  ‘startDownGR’
.grCoordsForNegative: no visible binding for global variable
  ‘endDownGR’
.grCoordsForPositive: no visible binding for global variable
  ‘startUpGR’
.grCoordsForPositive: no visible binding for global variable ‘endUpGR’
.grCoordsForPositive: no visible binding for global variable
  ‘startDownGR’
.grCoordsForPositive: no visible binding for global variable
  ‘endDownGR’
.matchWithKnowRBPs: no visible binding for global variable ‘motif’
.readGTF: no visible binding for global variable ‘type’
.readGTF: no visible binding for global variable ‘seqnames’
.readGTF: no visible binding for global variable ‘strand’
.readGTF: no visible binding for global variable ‘chrom’
.renameRepeats: no visible binding for global variable ‘name’
.renameRepeats: no visible binding for global variable ‘seqnames.1’
.renameRepeats: no visible binding for global variable ‘start.1’
.renameRepeats: no visible binding for global variable ‘end.1’
.renameRepeats: no visible binding for global variable ‘width.1’
.renameRepeats: no visible binding for global variable ‘strand.1’
.renameRepeats: no visible binding for global variable ‘score’
.renameSNPsGWAS: no visible binding for global variable ‘SNPS’
.renameSNPsGWAS: no visible binding for global variable ‘seqnames.1’
.renameSNPsGWAS: no visible binding for global variable ‘start.1’
.renameSNPsGWAS: no visible binding for global variable ‘MAPPED_GENE’
.renameSNPsGWAS: no visible binding for global variable ‘DISEASE.TRAIT’
.renameSNPsGWAS: no visible binding for global variable ‘P.VALUE’
.renameSNPsGWAS: no visible binding for global variable ‘CONTEXT’
.renameSNPsGWAS: no visible binding for global variable
  ‘STRONGEST.SNP.RISK.ALLELE’
.renameSNPsGWAS: no visible binding for global variable ‘PUBMEDID’
.renameSNPsGWAS: no visible binding for global variable ‘STUDY’
.reshapeCounts: no visible binding for global variable ‘motif’
.selectRandomBSEs: no visible binding for global variable ‘type’
.selectRandomBSEs: no visible binding for global variable
  ‘transcript_id’
.selectRandomBSEs: no visible binding for global variable ‘exon_number’
.splitRBPs: no visible binding for global variable ‘motif’
formatGTF: no visible binding for global variable ‘strand’
formatGTF: no visible binding for global variable ‘transcript_id’
formatGTF: no visible binding for global variable ‘start’
formatGTF: no visible binding for global variable ‘exon_number’
formatGTF: no visible binding for global variable ‘chrom’
getBackSplicedJunctions: no visible binding for global variable ‘name’
importCircExplorer2: no visible binding for global variable ‘circType’
importCircExplorer2: no visible binding for global variable ‘geneName’
importCircExplorer2: no visible binding for global variable ‘strand’
importCircExplorer2: no visible binding for global variable ‘chrom’
importCircExplorer2: no visible binding for global variable ‘start’
importCircExplorer2: no visible binding for global variable ‘end’
importCircExplorer2: no visible binding for global variable
  ‘readNumber’
importCircMarker: no visible binding for global variable ‘gene’
importCircMarker: no visible binding for global variable ‘strand’
importCircMarker: no visible binding for global variable ‘chrom’
importCircMarker: no visible binding for global variable ‘start’
importCircMarker: no visible binding for global variable ‘end’
importCircMarker: no visible binding for global variable ‘coverage’
importCircMarker: no visible binding for global variable ‘startUpBSE’
importCircMarker: no visible binding for global variable ‘endDownBSE’
importKnife: no visible binding for global variable ‘gene1_symbol’
importKnife: no visible binding for global variable ‘strand’
importKnife: no visible binding for global variable ‘chr’
importKnife: no visible binding for global variable ‘splice_position1’
importKnife: no visible binding for global variable ‘splice_position2’
importKnife: no visible binding for global variable ‘readNumber’
importKnife: no visible binding for global variable ‘chrom’
importMapSplice: no visible binding for global variable
  ‘annotated_gene_acceptor’
importMapSplice: no visible binding for global variable ‘strand’
importMapSplice: no visible binding for global variable ‘chrom’
importMapSplice: no visible binding for global variable
  ‘acceptor_start’
importMapSplice: no visible binding for global variable ‘doner_end’
importMapSplice: no visible binding for global variable ‘coverage’
importMapSplice: no visible binding for global variable ‘gene’
importMapSplice: no visible binding for global variable ‘startUpBSE’
importMapSplice: no visible binding for global variable ‘endDownBSE’
importNCLscan: no visible binding for global variable ‘type’
importNCLscan: no visible binding for global variable ‘gene’
importNCLscan: no visible binding for global variable ‘strand’
importNCLscan: no visible binding for global variable ‘chrom’
importNCLscan: no visible binding for global variable ‘startUpBSE’
importNCLscan: no visible binding for global variable ‘endDownBSE’
importNCLscan: no visible binding for global variable ‘coverage’
importOther: no visible binding for global variable ‘gene’
importOther: no visible binding for global variable ‘strand’
importOther: no visible binding for global variable ‘chrom’
importOther: no visible binding for global variable ‘startUpBSE’
importOther: no visible binding for global variable ‘endDownBSE’
importOther: no visible binding for global variable ‘coverage’
importUroborus: no visible binding for global variable
  ‘Parental_gene_name’
importUroborus: no visible binding for global variable ‘strand’
importUroborus: no visible binding for global variable ‘Chromosome’
importUroborus: no visible binding for global variable
  ‘start_of_junction’
importUroborus: no visible binding for global variable
  ‘end_of_junction’
importUroborus: no visible binding for global variable ‘read_counts’
importUroborus: no visible binding for global variable ‘chrom’
mergeBSJunctions: no visible binding for global variable ‘strand’
mergeBSJunctions: no visible binding for global variable ‘chrom’
mergeBSJunctions: no visible binding for global variable ‘startUpBSE’
mergeBSJunctions: no visible binding for global variable ‘endDownBSE’
mergeBSJunctions: no visible binding for global variable ‘tool’
mergeBSJunctions: no visible binding for global variable ‘mergedTools’
mergeBSJunctions: no visible binding for global variable ‘gene’
mergeMotifs: no visible binding for global variable ‘motif’
Undefined global functions or variables:
  CONTEXT Chromosome DISEASE.TRAIT Gene_name MAPPED_GENE Motif Organism
  P.VALUE PUBMEDID Parental_gene_name SNPS STRONGEST.SNP.RISK.ALLELE
  STUDY acceptor_start annotated_gene_acceptor chr chrom circType
  coverage cwcm doner_end end end.1 endDownBSE endDownGR endDownIntron
  endUpBSE endUpGR endUpIntron end_of_junction exon_number gene
  gene1_symbol geneName gene_name gene_name1 gr gr.1 len lenDownBSE
  lenDownIntron lenUpBSE lenUpIntron meanLengthBSEs meanLengthIntrons
  mergedTools motif name name.1 ncm path readNumber read_counts score
  seqnames seqnames.1 splice_position1 splice_position2 start start.1
  startDownBSE startDownGR startDownIntron startUpBSE startUpGR
  startUpIntron start_of_junction strand strand.1 strand1 tm tool
  transcript_id type width width.1
Consider adding
  importFrom("stats", "end", "start")
to your NAMESPACE file.
* 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 ... OK
Examples with CPU (user + system) or elapsed time > 5s
                   user system elapsed
liftBSJcoords    34.912  3.611  56.078
mergeBSJunctions  9.393  0.519  12.723
getDeseqRes       8.159  0.213   9.390
volcanoPlot       8.055  0.133   9.537
plotMotifs        2.389  0.146 268.929
getMotifs         1.648  0.088 136.572
mergeMotifs       1.617  0.096 135.269
* 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:
  ── Error ('test_getMotifs.R:193:13'): getMotifs() and mergeMotifs() generates the correct data structure
      with circRNA and BSJ seqs ──
  Error in `.getUserDBmotifs(database, species, memeIndexFilePath, reverse, 
      pathToMotifs)`: object 'rbpMotifsFromDBnew' not found
  Backtrace:
      ▆
   1. └─circRNAprofiler::getMotifs(...) at test_getMotifs.R:193:13
   2.   └─circRNAprofiler:::.filterMotifs(...)
   3.     └─circRNAprofiler:::.getUserDBmotifs(...)
   4.       └─base::rbind(motifsFromFileNew[, c(1, 2)], rbpMotifsFromDBnew)
   5.         └─base::rbind(deparse.level, ...)
  
  [ FAIL 3 | WARN 1 | SKIP 1 | PASS 217 ]
  Error: Test failures
  Execution halted
* checking for unstated dependencies in vignettes ... OK
* checking package vignettes ... OK
* checking running R code from vignettes ... SKIPPED
* checking re-building of vignette outputs ... SKIPPED
* checking PDF version of manual ... OK
* DONE

Status: 1 ERROR, 1 NOTE
See
  ‘/Users/biocbuild/bbs-3.20-bioc/meat/circRNAprofiler.Rcheck/00check.log’
for details.

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###
### Running command:
###
###   /Library/Frameworks/R.framework/Resources/bin/R CMD INSTALL circRNAprofiler
###
##############################################################################
##############################################################################


* installing to library ‘/Library/Frameworks/R.framework/Versions/4.4-x86_64/Resources/library’
* installing *source* package ‘circRNAprofiler’ ...
** 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 (circRNAprofiler)

R version 4.4.2 (2024-10-31) -- "Pile of Leaves"
Copyright (C) 2024 The R Foundation for Statistical Computing
Platform: x86_64-apple-darwin20

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(circRNAprofiler)
> 
> test_check("circRNAprofiler")

Analysing: Ncoa6:-:chr2:155440785:155437860
Analysing: Arhgap5:+:chr12:52516079:52542636
Analysing: Arhgap5:+:chr12:52516079:52542636
Analysing: Pwwp2a:+:chr11:43704534:43705477trying URL 'https://attract.cnic.es/attract/static/ATtRACT.zip'
URL can not be reached:  https://attract.cnic.es/attract/static/ATtRACT.zip .
ATtRACT motif can not be analyzed.trying URL 'https://attract.cnic.es/attract/static/ATtRACT.zip'
URL can not be reached:  https://attract.cnic.es/attract/static/ATtRACT.zip .
ATtRACT motif can not be analyzed.trying URL 'https://attract.cnic.es/attract/static/ATtRACT.zip'
URL can not be reached:  https://attract.cnic.es/attract/static/ATtRACT.zip .
ATtRACT motif can not be analyzed.[ FAIL 3 | WARN 1 | SKIP 1 | PASS 217 ]

══ Skipped tests (1) ═══════════════════════════════════════════════════════════
• empty test (1): 'test_annotateRepeats.R:4:1'

══ Failed tests ════════════════════════════════════════════════════════════════
── Error ('test_getMotifs.R:34:19'): getMotifs() and mergeMotifs() generate the correct data structure
    with GR seqs ──
Error in `.getUserDBmotifs(database, species, memeIndexFilePath, reverse, 
    pathToMotifs)`: object 'rbpMotifsFromDBnew' not found
Backtrace:
    ▆
 1. └─circRNAprofiler::getMotifs(...) at test_getMotifs.R:34:19
 2.   └─circRNAprofiler:::.filterMotifs(...)
 3.     └─circRNAprofiler:::.getUserDBmotifs(...)
 4.       └─base::rbind(motifsFromFileNew[, c(1, 2)], rbpMotifsFromDBnew)
 5.         └─base::rbind(deparse.level, ...)
── Error ('test_getMotifs.R:118:19'): getMotifs() generates a list with the correct
    content with GR seqs ──
Error in `.getUserDBmotifs(database, species, memeIndexFilePath, reverse, 
    pathToMotifs)`: object 'rbpMotifsFromDBnew' not found
Backtrace:
    ▆
 1. └─circRNAprofiler::getMotifs(...) at test_getMotifs.R:118:19
 2.   └─circRNAprofiler:::.filterMotifs(...)
 3.     └─circRNAprofiler:::.getUserDBmotifs(...)
 4.       └─base::rbind(motifsFromFileNew[, c(1, 2)], rbpMotifsFromDBnew)
 5.         └─base::rbind(deparse.level, ...)
── Error ('test_getMotifs.R:193:13'): getMotifs() and mergeMotifs() generates the correct data structure
    with circRNA and BSJ seqs ──
Error in `.getUserDBmotifs(database, species, memeIndexFilePath, reverse, 
    pathToMotifs)`: object 'rbpMotifsFromDBnew' not found
Backtrace:
    ▆
 1. └─circRNAprofiler::getMotifs(...) at test_getMotifs.R:193:13
 2.   └─circRNAprofiler:::.filterMotifs(...)
 3.     └─circRNAprofiler:::.getUserDBmotifs(...)
 4.       └─base::rbind(motifsFromFileNew[, c(1, 2)], rbpMotifsFromDBnew)
 5.         └─base::rbind(deparse.level, ...)

[ FAIL 3 | WARN 1 | SKIP 1 | PASS 217 ]
Error: Test failures
Execution halted