Back to Multiple platform build/check report for BioC 3.21:   simplified   long
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This page was generated on 2025-08-21 11:40 -0400 (Thu, 21 Aug 2025).

HostnameOSArch (*)R versionInstalled pkgs
nebbiolo1Linux (Ubuntu 24.04.3 LTS)x86_644.5.1 (2025-06-13) -- "Great Square Root" 4824
merida1macOS 12.7.5 Montereyx86_644.5.1 RC (2025-06-05 r88288) -- "Great Square Root" 4604
kjohnson1macOS 13.6.6 Venturaarm644.5.1 Patched (2025-06-14 r88325) -- "Great Square Root" 4545
kunpeng2Linux (openEuler 24.03 LTS)aarch64R Under development (unstable) (2025-02-19 r87757) -- "Unsuffered Consequences" 4579
Click on any hostname to see more info about the system (e.g. compilers)      (*) as reported by 'uname -p', except on Windows and Mac OS X

Package 361/2341HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
circRNAprofiler 1.22.1  (landing page)
Simona Aufiero
Snapshot Date: 2025-08-18 13:40 -0400 (Mon, 18 Aug 2025)
git_url: https://git.bioconductor.org/packages/circRNAprofiler
git_branch: RELEASE_3_21
git_last_commit: 9355431
git_last_commit_date: 2025-05-08 03:55:04 -0400 (Thu, 08 May 2025)
nebbiolo1Linux (Ubuntu 24.04.3 LTS) / x86_64  OK    OK    OK  UNNEEDED, same version is already published
merida1macOS 12.7.5 Monterey / x86_64  OK    OK    OK    OK  UNNEEDED, same version is already published
kjohnson1macOS 13.6.6 Ventura / arm64  OK    OK    OK    OK  UNNEEDED, same version is already published
kunpeng2Linux (openEuler 24.03 LTS) / aarch64  OK    OK    OK  


CHECK results for circRNAprofiler on kjohnson1

To the developers/maintainers of the circRNAprofiler package:
- Allow up to 24 hours (and sometimes 48 hours) for your latest push to git@git.bioconductor.org:packages/circRNAprofiler.git to reflect on this report. See Troubleshooting Build Report for more information.
- Use the following Renviron settings to reproduce errors and warnings.
- If 'R CMD check' started to fail recently on the Linux builder(s) over a missing dependency, add the missing dependency to 'Suggests:' in your DESCRIPTION file. See Renviron.bioc for more information.

raw results


Summary

Package: circRNAprofiler
Version: 1.22.1
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_1.22.1.tar.gz
StartedAt: 2025-08-19 16:15:39 -0400 (Tue, 19 Aug 2025)
EndedAt: 2025-08-19 16:26:47 -0400 (Tue, 19 Aug 2025)
EllapsedTime: 667.8 seconds
RetCode: 0
Status:   OK  
CheckDir: circRNAprofiler.Rcheck
Warnings: 0

Command output

##############################################################################
##############################################################################
###
### 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_1.22.1.tar.gz
###
##############################################################################
##############################################################################


* using log directory ‘/Users/biocbuild/bbs-3.21-bioc/meat/circRNAprofiler.Rcheck’
* using R version 4.5.1 Patched (2025-06-14 r88325)
* using platform: aarch64-apple-darwin20
* R was compiled by
    Apple clang version 16.0.0 (clang-1600.0.26.6)
    GNU Fortran (GCC) 14.2.0
* running under: macOS Ventura 13.7.5
* using session charset: UTF-8
* using option ‘--no-vignettes’
* checking for file ‘circRNAprofiler/DESCRIPTION’ ... OK
* checking extension type ... Package
* this is package ‘circRNAprofiler’ version ‘1.22.1’
* package encoding: UTF-8
* checking package namespace information ... OK
* checking package dependencies ... INFO
Imports includes 23 non-default packages.
Importing from so many packages makes the package vulnerable to any of
them becoming unavailable.  Move as many as possible to Suggests and
use conditionally.
* 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 ... NOTE
Found the following Rd file(s) with Rd \link{} targets missing package
anchors:
  annotateRepeats.Rd: AnnotationHub
  getCircSeqs.Rd: getBSgenome
  getSeqsAcrossBSJs.Rd: getBSgenome
  getSeqsFromGRs.Rd: getBSgenome
Please provide package anchors for all Rd \link{} targets not in the
package itself and the base packages.
* 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 33.917  1.378  38.487
plotMotifs    18.085  0.127  25.390
mergeMotifs   11.853  0.116  15.406
getMotifs     11.194  0.152  15.203
getDeseqRes    4.906  0.110   5.029
* checking for unstated dependencies in ‘tests’ ... OK
* checking tests ...
  Running ‘testthat.R’
 OK
* 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: 2 NOTEs
See
  ‘/Users/biocbuild/bbs-3.21-bioc/meat/circRNAprofiler.Rcheck/00check.log’
for details.


Installation output

circRNAprofiler.Rcheck/00install.out

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


* installing to library ‘/Library/Frameworks/R.framework/Versions/4.5-arm64/Resources/library’
* installing *source* package ‘circRNAprofiler’ ...
** this is package ‘circRNAprofiler’ version ‘1.22.1’
** 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)

Tests output

circRNAprofiler.Rcheck/tests/testthat.Rout


R version 4.5.1 Patched (2025-06-14 r88325) -- "Great Square Root"
Copyright (C) 2025 The R Foundation for Statistical Computing
Platform: aarch64-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:+:chr11:43704534:43705477[ FAIL 0 | WARN 1 | SKIP 1 | PASS 217 ]

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

[ FAIL 0 | WARN 1 | SKIP 1 | PASS 217 ]
> 
> proc.time()
   user  system elapsed 
140.089   5.267 146.527 

Example timings

circRNAprofiler.Rcheck/circRNAprofiler-Ex.timings

nameusersystemelapsed
ahChainFiles0.1900.0110.221
ahRepeatMasker0.0020.0030.005
annotateBSJs0.7260.0170.743
annotateRepeats1.2060.0421.257
annotateSNPsGWAS1.0160.0351.055
attractSpecies0.0010.0020.003
backSplicedJunctions0.8760.0110.886
checkProjectFolder0.0020.0010.003
filterCirc0.6460.0090.657
formatGTF0.0010.0010.001
getBackSplicedJunctions0.0010.0000.001
getCircSeqs0.9640.0301.002
getDeseqRes4.9060.1105.029
getDetectionTools0.0030.0000.003
getEdgerRes0.9280.0170.948
getMiRsites0.9880.0331.036
getMotifs11.194 0.15215.203
getRandomBSJunctions0.1130.0060.119
getRegexPattern0.0020.0020.003
getSeqsAcrossBSJs1.0670.0331.108
getSeqsFromGRs1.0620.0351.098
gtf0.0240.0040.027
gwasTraits0.0070.0020.010
importCircExplorer20.0220.0010.024
importCircMarker0.1080.0060.114
importKnife0.0150.0010.016
importMapSplice0.0450.0010.046
importNCLscan0.0120.0010.014
importOther0.0100.0010.012
importUroborus0.0110.0020.013
initCircRNAprofiler000
iupac0.0010.0030.003
liftBSJcoords33.917 1.37838.487
memeDB0.0010.0020.003
mergeBSJunctions4.6790.2474.930
mergeMotifs11.853 0.11615.406
mergedBSJunctions0.5590.0120.573
miRspeciesCodes0.0020.0020.005
plotExBetweenBSEs1.1960.0191.220
plotExPosition1.0400.0151.056
plotHostGenes1.1280.0131.146
plotLenBSEs1.7010.0241.734
plotLenIntrons2.0080.0232.039
plotMiR0.9760.0311.009
plotMotifs18.085 0.12725.390
plotTotExons1.0410.0171.084
rearrangeMiRres1.0120.0291.058
volcanoPlot3.5860.0583.654