| Back to Multiple platform build/check report for BioC 3.19: simplified long |
|
This page was generated on 2024-06-28 17:41 -0400 (Fri, 28 Jun 2024).
| Hostname | OS | Arch (*) | R version | Installed pkgs |
|---|---|---|---|---|
| nebbiolo1 | Linux (Ubuntu 22.04.3 LTS) | x86_64 | 4.4.0 (2024-04-24) -- "Puppy Cup" | 4760 |
| palomino3 | Windows Server 2022 Datacenter | x64 | 4.4.0 (2024-04-24 ucrt) -- "Puppy Cup" | 4494 |
| merida1 | macOS 12.7.4 Monterey | x86_64 | 4.4.0 (2024-04-24) -- "Puppy Cup" | 4508 |
| kjohnson1 | macOS 13.6.6 Ventura | arm64 | 4.4.0 (2024-04-24) -- "Puppy Cup" | 4466 |
| palomino7 | Windows Server 2022 Datacenter | x64 | 4.4.1 (2024-06-14 ucrt) -- "Race for Your Life" | 4362 |
| 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 355/2300 | Hostname | OS / Arch | INSTALL | BUILD | CHECK | BUILD BIN | ||||||||
| circRNAprofiler 1.18.0 (landing page) Simona Aufiero
| nebbiolo1 | Linux (Ubuntu 22.04.3 LTS) / x86_64 | OK | OK | OK |  | ||||||||
| palomino3 | Windows Server 2022 Datacenter / x64 | OK | OK | OK | OK | | ||||||||
| merida1 | macOS 12.7.4 Monterey / x86_64 | OK | OK | OK | OK | | ||||||||
| kjohnson1 | macOS 13.6.6 Ventura / arm64 | OK | OK | OK | OK | | ||||||||
| palomino7 | Windows Server 2022 Datacenter / x64 | OK | OK | ERROR | OK | |||||||||
|
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: 1.18.0 |
| Command: F:\biocbuild\bbs-3.19-bioc\R\bin\R.exe CMD check --no-multiarch --install=check:circRNAprofiler.install-out.txt --library=F:\biocbuild\bbs-3.19-bioc\R\library --no-vignettes --timings circRNAprofiler_1.18.0.tar.gz |
| StartedAt: 2024-06-27 00:05:17 -0400 (Thu, 27 Jun 2024) |
| EndedAt: 2024-06-27 00:22:48 -0400 (Thu, 27 Jun 2024) |
| EllapsedTime: 1050.3 seconds |
| RetCode: 0 |
| Status: OK |
| CheckDir: circRNAprofiler.Rcheck |
| Warnings: 0 |
##############################################################################
##############################################################################
###
### Running command:
###
### F:\biocbuild\bbs-3.19-bioc\R\bin\R.exe CMD check --no-multiarch --install=check:circRNAprofiler.install-out.txt --library=F:\biocbuild\bbs-3.19-bioc\R\library --no-vignettes --timings circRNAprofiler_1.18.0.tar.gz
###
##############################################################################
##############################################################################
* using log directory 'F:/biocbuild/bbs-3.19-bioc/meat/circRNAprofiler.Rcheck'
* using R version 4.4.0 (2024-04-24 ucrt)
* using platform: x86_64-w64-mingw32
* R was compiled by
gcc.exe (GCC) 13.2.0
GNU Fortran (GCC) 13.2.0
* running under: Windows Server 2022 x64 (build 20348)
* using session charset: UTF-8
* using option '--no-vignettes'
* checking for file 'circRNAprofiler/DESCRIPTION' ... OK
* checking extension type ... Package
* this is package 'circRNAprofiler' version '1.18.0'
* 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 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 47.29 3.27 69.85
plotMotifs 24.20 0.61 33.25
mergeMotifs 16.35 0.59 20.79
getMotifs 14.04 0.64 18.81
mergeBSJunctions 5.29 0.44 5.77
getDeseqRes 4.78 0.35 5.14
* 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: 1 NOTE
See
'F:/biocbuild/bbs-3.19-bioc/meat/circRNAprofiler.Rcheck/00check.log'
for details.
circRNAprofiler.Rcheck/00install.out
############################################################################## ############################################################################## ### ### Running command: ### ### F:\biocbuild\bbs-3.19-bioc\R\bin\R.exe CMD INSTALL circRNAprofiler ### ############################################################################## ############################################################################## * installing to library 'F:/biocbuild/bbs-3.19-bioc/R/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
R version 4.4.0 (2024-04-24 ucrt) -- "Puppy Cup"
Copyright (C) 2024 The R Foundation for Statistical Computing
Platform: x86_64-w64-mingw32/x64
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
427.53 10.06 460.37
circRNAprofiler.Rcheck/circRNAprofiler-Ex.timings
| name | user | system | elapsed | |
| ahChainFiles | 0.15 | 0.07 | 0.23 | |
| ahRepeatMasker | 0.00 | 0.02 | 0.02 | |
| annotateBSJs | 1.89 | 0.42 | 2.31 | |
| annotateRepeats | 1.25 | 0.39 | 1.65 | |
| annotateSNPsGWAS | 1.01 | 0.39 | 1.42 | |
| attractSpecies | 0.00 | 0.02 | 0.01 | |
| backSplicedJunctions | 0.63 | 0.00 | 0.63 | |
| checkProjectFolder | 0 | 0 | 0 | |
| filterCirc | 1.61 | 0.19 | 1.82 | |
| formatGTF | 0 | 0 | 0 | |
| getBackSplicedJunctions | 0 | 0 | 0 | |
| getCircSeqs | 0.90 | 0.38 | 1.28 | |
| getDeseqRes | 4.78 | 0.35 | 5.14 | |
| getDetectionTools | 0 | 0 | 0 | |
| getEdgerRes | 0.93 | 0.30 | 1.20 | |
| getMiRsites | 1.00 | 0.42 | 1.44 | |
| getMotifs | 14.04 | 0.64 | 18.81 | |
| getRandomBSJunctions | 0.22 | 0.16 | 0.38 | |
| getRegexPattern | 0 | 0 | 0 | |
| getSeqsAcrossBSJs | 0.91 | 0.39 | 1.30 | |
| getSeqsFromGRs | 1.12 | 0.33 | 1.45 | |
| gtf | 0.02 | 0.17 | 0.19 | |
| gwasTraits | 0.02 | 0.00 | 0.01 | |
| importCircExplorer2 | 0.01 | 0.00 | 0.03 | |
| importCircMarker | 0.07 | 0.15 | 0.26 | |
| importKnife | 0.04 | 0.00 | 0.05 | |
| importMapSplice | 0.06 | 0.00 | 0.08 | |
| importNCLscan | 0.01 | 0.00 | 0.03 | |
| importOther | 0.02 | 0.00 | 0.03 | |
| importUroborus | 0.00 | 0.00 | 0.02 | |
| initCircRNAprofiler | 0 | 0 | 0 | |
| iupac | 0 | 0 | 0 | |
| liftBSJcoords | 47.29 | 3.27 | 69.85 | |
| memeDB | 0.02 | 0.00 | 0.01 | |
| mergeBSJunctions | 5.29 | 0.44 | 5.77 | |
| mergeMotifs | 16.35 | 0.59 | 20.79 | |
| mergedBSJunctions | 0.43 | 0.17 | 0.59 | |
| miRspeciesCodes | 0.01 | 0.00 | 0.02 | |
| plotExBetweenBSEs | 1.14 | 0.49 | 1.62 | |
| plotExPosition | 1.13 | 0.36 | 1.49 | |
| plotHostGenes | 1.09 | 0.37 | 1.47 | |
| plotLenBSEs | 2.05 | 0.34 | 2.39 | |
| plotLenIntrons | 2.22 | 0.36 | 2.59 | |
| plotMiR | 1.00 | 0.38 | 1.38 | |
| plotMotifs | 24.20 | 0.61 | 33.25 | |
| plotTotExons | 1.12 | 0.30 | 1.42 | |
| rearrangeMiRres | 0.85 | 0.49 | 1.33 | |
| volcanoPlot | 4.11 | 0.37 | 4.48 | |