| Back to Multiple platform build/check report for BioC 3.21: simplified long |
|
This page was generated on 2025-01-04 11:43 -0500 (Sat, 04 Jan 2025).
| Hostname | OS | Arch (*) | R version | Installed pkgs |
|---|---|---|---|---|
| nebbiolo1 | Linux (Ubuntu 24.04.1 LTS) | x86_64 | R Under development (unstable) (2024-10-21 r87258) -- "Unsuffered Consequences" | 4756 |
| palomino7 | Windows Server 2022 Datacenter | x64 | R Under development (unstable) (2024-10-26 r87273 ucrt) -- "Unsuffered Consequences" | 4475 |
| lconway | macOS 12.7.1 Monterey | x86_64 | R Under development (unstable) (2024-11-20 r87352) -- "Unsuffered Consequences" | 4435 |
| kjohnson3 | macOS 13.7.1 Ventura | arm64 | R Under development (unstable) (2024-11-20 r87352) -- "Unsuffered Consequences" | 4390 |
| kunpeng2 | Linux (openEuler 22.03 LTS-SP1) | aarch64 | R Under development (unstable) (2024-11-24 r87369) -- "Unsuffered Consequences" | 4383 |
| 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 349/2275 | Hostname | OS / Arch | INSTALL | BUILD | CHECK | BUILD BIN | ||||||||
| circRNAprofiler 1.21.0 (landing page) Simona Aufiero
| nebbiolo1 | Linux (Ubuntu 24.04.1 LTS) / x86_64 | OK | OK | ERROR | |||||||||
| palomino7 | Windows Server 2022 Datacenter / x64 | OK | OK | ERROR | OK | |||||||||
| lconway | macOS 12.7.1 Monterey / x86_64 | OK | OK | ERROR | OK | |||||||||
| kjohnson3 | macOS 13.7.1 Ventura / arm64 | OK | OK | ERROR | OK | |||||||||
| kunpeng2 | Linux (openEuler 22.03 LTS-SP1) / aarch64 | OK | OK | ERROR | ||||||||||
|
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. |
| Package: circRNAprofiler |
| Version: 1.21.0 |
| 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_1.21.0.tar.gz |
| StartedAt: 2025-01-03 19:34:58 -0500 (Fri, 03 Jan 2025) |
| EndedAt: 2025-01-03 20:00:24 -0500 (Fri, 03 Jan 2025) |
| EllapsedTime: 1526.1 seconds |
| RetCode: 1 |
| Status: ERROR |
| CheckDir: circRNAprofiler.Rcheck |
| Warnings: NA |
##############################################################################
##############################################################################
###
### 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_1.21.0.tar.gz
###
##############################################################################
##############################################################################
* using log directory ‘/Users/biocbuild/bbs-3.21-bioc/meat/circRNAprofiler.Rcheck’
* using R Under development (unstable) (2024-11-20 r87352)
* 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 ‘1.21.0’
* 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 23.287 2.247 26.660
getDeseqRes 6.423 0.154 6.642
plotMotifs 1.471 0.088 267.428
getMotifs 1.215 0.065 135.390
mergeMotifs 1.157 0.067 137.544
* 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, 2 NOTEs
See
‘/Users/biocbuild/bbs-3.21-bioc/meat/circRNAprofiler.Rcheck/00check.log’
for details.
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-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)
circRNAprofiler.Rcheck/tests/testthat.Rout.fail
R Under development (unstable) (2024-11-20 r87352) -- "Unsuffered Consequences"
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
circRNAprofiler.Rcheck/circRNAprofiler-Ex.timings
| name | user | system | elapsed | |
| ahChainFiles | 0.190 | 0.010 | 0.201 | |
| ahRepeatMasker | 0.002 | 0.002 | 0.004 | |
| annotateBSJs | 0.760 | 0.030 | 0.796 | |
| annotateRepeats | 1.490 | 0.061 | 1.567 | |
| annotateSNPsGWAS | 1.118 | 0.053 | 1.184 | |
| attractSpecies | 0.001 | 0.002 | 0.003 | |
| backSplicedJunctions | 0.972 | 0.016 | 1.001 | |
| checkProjectFolder | 0.002 | 0.000 | 0.003 | |
| filterCirc | 0.756 | 0.018 | 0.781 | |
| formatGTF | 0.001 | 0.000 | 0.000 | |
| getBackSplicedJunctions | 0.001 | 0.001 | 0.001 | |
| getCircSeqs | 1.033 | 0.044 | 1.087 | |
| getDeseqRes | 6.423 | 0.154 | 6.642 | |
| getDetectionTools | 0.001 | 0.001 | 0.002 | |
| getEdgerRes | 0.891 | 0.015 | 0.913 | |
| getMiRsites | 1.044 | 0.045 | 1.098 | |
| getMotifs | 1.215 | 0.065 | 135.390 | |
| getRandomBSJunctions | 0.131 | 0.004 | 0.136 | |
| getRegexPattern | 0.002 | 0.001 | 0.004 | |
| getSeqsAcrossBSJs | 1.084 | 0.045 | 1.143 | |
| getSeqsFromGRs | 1.128 | 0.045 | 1.184 | |
| gtf | 0.020 | 0.002 | 0.023 | |
| gwasTraits | 0.005 | 0.002 | 0.008 | |
| importCircExplorer2 | 0.023 | 0.001 | 0.025 | |
| importCircMarker | 0.108 | 0.008 | 0.118 | |
| importKnife | 0.013 | 0.001 | 0.015 | |
| importMapSplice | 0.055 | 0.001 | 0.057 | |
| importNCLscan | 0.014 | 0.002 | 0.016 | |
| importOther | 0.011 | 0.002 | 0.012 | |
| importUroborus | 0.011 | 0.001 | 0.013 | |
| initCircRNAprofiler | 0 | 0 | 0 | |
| iupac | 0.000 | 0.001 | 0.002 | |
| liftBSJcoords | 23.287 | 2.247 | 26.660 | |
| memeDB | 0.001 | 0.002 | 0.002 | |
| mergeBSJunctions | 4.506 | 0.419 | 4.963 | |
| mergeMotifs | 1.157 | 0.067 | 137.544 | |
| mergedBSJunctions | 0.583 | 0.009 | 0.596 | |
| miRspeciesCodes | 0.002 | 0.005 | 0.007 | |
| plotExBetweenBSEs | 1.176 | 0.020 | 1.203 | |
| plotExPosition | 1.104 | 0.030 | 1.139 | |
| plotHostGenes | 1.087 | 0.017 | 1.111 | |
| plotLenBSEs | 1.899 | 0.022 | 1.932 | |
| plotLenIntrons | 2.054 | 0.024 | 2.089 | |
| plotMiR | 0.949 | 0.040 | 0.994 | |
| plotMotifs | 1.471 | 0.088 | 267.428 | |
| plotTotExons | 1.082 | 0.028 | 1.121 | |
| rearrangeMiRres | 0.896 | 0.032 | 0.931 | |
| volcanoPlot | 3.498 | 0.083 | 3.594 | |