Back to Multiple platform build/check report for BioC 3.18:   simplified   long
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This page was generated on 2024-03-01 11:35:51 -0500 (Fri, 01 Mar 2024).

HostnameOSArch (*)R versionInstalled pkgs
nebbiolo2Linux (Ubuntu 22.04.3 LTS)x86_644.3.2 Patched (2023-11-13 r85521) -- "Eye Holes" 4692
palomino4Windows Server 2022 Datacenterx644.3.2 (2023-10-31 ucrt) -- "Eye Holes" 4445
lconwaymacOS 12.7.1 Montereyx86_644.3.2 Patched (2023-11-01 r85457) -- "Eye Holes" 4466
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 351/2266HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
circRNAprofiler 1.16.0  (landing page)
Simona Aufiero
Snapshot Date: 2024-02-29 14:05:06 -0500 (Thu, 29 Feb 2024)
git_url: https://git.bioconductor.org/packages/circRNAprofiler
git_branch: RELEASE_3_18
git_last_commit: 39fe35b
git_last_commit_date: 2023-10-24 11:15:12 -0500 (Tue, 24 Oct 2023)
nebbiolo2Linux (Ubuntu 22.04.3 LTS) / x86_64  OK    OK    OK  UNNEEDED, same version is already published
palomino4Windows Server 2022 Datacenter / x64  OK    OK    OK    OK  UNNEEDED, same version is already published
lconwaymacOS 12.7.1 Monterey / x86_64  OK    OK    OK    OK  UNNEEDED, same version is already published
kjohnson1macOS 13.6.1 Ventura / arm64see weekly results here

CHECK results for circRNAprofiler on nebbiolo2


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: 1.16.0
Command: /home/biocbuild/bbs-3.18-bioc/R/bin/R CMD check --install=check:circRNAprofiler.install-out.txt --library=/home/biocbuild/bbs-3.18-bioc/R/site-library --timings circRNAprofiler_1.16.0.tar.gz
StartedAt: 2024-02-29 20:57:44 -0500 (Thu, 29 Feb 2024)
EndedAt: 2024-02-29 21:08:12 -0500 (Thu, 29 Feb 2024)
EllapsedTime: 627.6 seconds
RetCode: 0
Status:   OK  
CheckDir: circRNAprofiler.Rcheck
Warnings: 0

Command output

##############################################################################
##############################################################################
###
### Running command:
###
###   /home/biocbuild/bbs-3.18-bioc/R/bin/R CMD check --install=check:circRNAprofiler.install-out.txt --library=/home/biocbuild/bbs-3.18-bioc/R/site-library --timings circRNAprofiler_1.16.0.tar.gz
###
##############################################################################
##############################################################################


* using log directory ‘/home/biocbuild/bbs-3.18-bioc/meat/circRNAprofiler.Rcheck’
* using R version 4.3.2 Patched (2023-11-13 r85521)
* 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 22.04.3 LTS
* using session charset: UTF-8
* checking for file ‘circRNAprofiler/DESCRIPTION’ ... OK
* checking extension type ... Package
* this is package ‘circRNAprofiler’ version ‘1.16.0’
* 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 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 ... NOTE
.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 21.148  2.571  24.271
plotMotifs    14.786  0.681  24.350
mergeMotifs   10.650  0.716  16.404
getMotifs      8.971  0.263  15.362
* 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 ...
  ‘circRNAprofiler.Rmd’ using ‘UTF-8’... OK
 NONE
* checking re-building of vignette outputs ... OK
* checking PDF version of manual ... OK
* DONE

Status: 1 NOTE
See
  ‘/home/biocbuild/bbs-3.18-bioc/meat/circRNAprofiler.Rcheck/00check.log’
for details.



Installation output

circRNAprofiler.Rcheck/00install.out

##############################################################################
##############################################################################
###
### Running command:
###
###   /home/biocbuild/bbs-3.18-bioc/R/bin/R CMD INSTALL circRNAprofiler
###
##############################################################################
##############################################################################


* installing to library ‘/home/biocbuild/bbs-3.18-bioc/R/site-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)

Tests output

circRNAprofiler.Rcheck/tests/testthat.Rout


R version 4.3.2 Patched (2023-11-13 r85521) -- "Eye Holes"
Copyright (C) 2023 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(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'
downloaded 113 KB

trying URL 'https://attract.cnic.es/attract/static/ATtRACT.zip'
downloaded 113 KB

trying URL 'https://attract.cnic.es/attract/static/ATtRACT.zip'
downloaded 113 KB

trying URL 'https://attract.cnic.es/attract/static/ATtRACT.zip'
downloaded 113 KB

trying URL 'https://attract.cnic.es/attract/static/ATtRACT.zip'
downloaded 113 KB

[ FAIL 0 | WARN 1 | SKIP 1 | PASS 255 ]

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

[ FAIL 0 | WARN 1 | SKIP 1 | PASS 255 ]
> 
> proc.time()
   user  system elapsed 
119.668   9.248 153.658 

Example timings

circRNAprofiler.Rcheck/circRNAprofiler-Ex.timings

nameusersystemelapsed
ahChainFiles0.1180.0120.130
ahRepeatMasker0.0020.0000.001
annotateBSJs0.4520.0160.469
annotateRepeats0.8510.0080.860
annotateSNPsGWAS0.6030.0080.612
attractSpecies0.0010.0000.001
backSplicedJunctions0.4610.0080.469
checkProjectFolder0.0020.0000.003
filterCirc0.5180.0040.524
formatGTF0.0010.0000.001
getBackSplicedJunctions0.0000.0010.001
getCircSeqs0.6000.0190.619
getDeseqRes3.9630.2724.235
getDetectionTools0.0020.0000.002
getEdgerRes0.6080.0240.632
getMiRsites0.5990.0080.607
getMotifs 8.971 0.26315.362
getRandomBSJunctions0.1210.0080.129
getRegexPattern0.0020.0000.002
getSeqsAcrossBSJs0.6400.0230.664
getSeqsFromGRs0.7180.0320.750
gtf0.0170.0000.016
gwasTraits0.0050.0000.006
importCircExplorer20.0110.0040.016
importCircMarker0.0940.0080.103
importKnife0.0160.0000.017
importMapSplice0.0530.0000.054
importNCLscan0.0140.0000.014
importOther0.0110.0000.011
importUroborus0.0110.0000.011
initCircRNAprofiler000
iupac0.0010.0000.001
liftBSJcoords21.148 2.57124.271
memeDB0.0010.0000.002
mergeBSJunctions2.7310.1802.911
mergeMotifs10.650 0.71616.404
mergedBSJunctions0.3160.0080.323
miRspeciesCodes0.0020.0000.002
plotExBetweenBSEs0.8990.0640.963
plotExPosition0.8980.0200.918
plotHostGenes0.8450.0520.897
plotLenBSEs2.7590.2883.047
plotLenIntrons1.5930.0681.661
plotMiR0.5860.0320.618
plotMotifs14.786 0.68124.350
plotTotExons0.9550.0561.011
rearrangeMiRres0.6180.0440.662
volcanoPlot3.3510.2673.621