Back to Multiple platform build/check report for BioC 3.20: simplified long |
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This page was generated on 2024-12-23 12:04 -0500 (Mon, 23 Dec 2024).
Hostname | OS | Arch (*) | R version | Installed pkgs |
---|---|---|---|---|
nebbiolo2 | Linux (Ubuntu 24.04.1 LTS) | x86_64 | 4.4.2 (2024-10-31) -- "Pile of Leaves" | 4744 |
palomino8 | Windows Server 2022 Datacenter | x64 | 4.4.2 (2024-10-31 ucrt) -- "Pile of Leaves" | 4487 |
merida1 | macOS 12.7.5 Monterey | x86_64 | 4.4.2 (2024-10-31) -- "Pile of Leaves" | 4515 |
kjohnson1 | macOS 13.6.6 Ventura | arm64 | 4.4.2 (2024-10-31) -- "Pile of Leaves" | 4467 |
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 355/2289 | Hostname | OS / Arch | INSTALL | BUILD | CHECK | BUILD BIN | ||||||||
circRNAprofiler 1.20.0 (landing page) Simona Aufiero
| nebbiolo2 | Linux (Ubuntu 24.04.1 LTS) / x86_64 | OK | OK | OK | |||||||||
palomino8 | Windows Server 2022 Datacenter / x64 | OK | OK | OK | OK | |||||||||
merida1 | macOS 12.7.5 Monterey / x86_64 | OK | OK | OK | OK | |||||||||
kjohnson1 | macOS 13.6.6 Ventura / arm64 | OK | OK | OK | 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: 1.20.0 |
Command: F:\biocbuild\bbs-3.20-bioc\R\bin\R.exe CMD check --no-multiarch --install=check:circRNAprofiler.install-out.txt --library=F:\biocbuild\bbs-3.20-bioc\R\library --no-vignettes --timings circRNAprofiler_1.20.0.tar.gz |
StartedAt: 2024-12-20 00:02:25 -0500 (Fri, 20 Dec 2024) |
EndedAt: 2024-12-20 00:18:28 -0500 (Fri, 20 Dec 2024) |
EllapsedTime: 962.3 seconds |
RetCode: 0 |
Status: OK |
CheckDir: circRNAprofiler.Rcheck |
Warnings: 0 |
############################################################################## ############################################################################## ### ### Running command: ### ### F:\biocbuild\bbs-3.20-bioc\R\bin\R.exe CMD check --no-multiarch --install=check:circRNAprofiler.install-out.txt --library=F:\biocbuild\bbs-3.20-bioc\R\library --no-vignettes --timings circRNAprofiler_1.20.0.tar.gz ### ############################################################################## ############################################################################## * using log directory 'F:/biocbuild/bbs-3.20-bioc/meat/circRNAprofiler.Rcheck' * using R version 4.4.2 (2024-10-31 ucrt) * using platform: x86_64-w64-mingw32 * R was compiled by gcc.exe (GCC) 13.3.0 GNU Fortran (GCC) 13.3.0 * 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 '1.20.0' * 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 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 43.10 2.68 50.22 plotMotifs 24.32 0.44 32.73 getMotifs 14.28 0.42 19.00 mergeMotifs 14.22 0.45 17.70 * 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-3.20-bioc/meat/circRNAprofiler.Rcheck/00check.log' for details.
circRNAprofiler.Rcheck/00install.out
############################################################################## ############################################################################## ### ### Running command: ### ### F:\biocbuild\bbs-3.20-bioc\R\bin\R.exe CMD INSTALL circRNAprofiler ### ############################################################################## ############################################################################## * installing to library 'F:/biocbuild/bbs-3.20-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 4.4.2 (2024-10-31 ucrt) -- "Pile of Leaves" 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 381.23 8.73 414.92
circRNAprofiler.Rcheck/circRNAprofiler-Ex.timings
name | user | system | elapsed | |
ahChainFiles | 0.18 | 0.10 | 0.27 | |
ahRepeatMasker | 0.01 | 0.00 | 0.01 | |
annotateBSJs | 1.74 | 0.24 | 1.97 | |
annotateRepeats | 1.29 | 0.32 | 1.62 | |
annotateSNPsGWAS | 1.10 | 0.27 | 1.36 | |
attractSpecies | 0 | 0 | 0 | |
backSplicedJunctions | 0.65 | 0.00 | 0.65 | |
checkProjectFolder | 0.02 | 0.00 | 0.02 | |
filterCirc | 1.73 | 0.12 | 1.86 | |
formatGTF | 0 | 0 | 0 | |
getBackSplicedJunctions | 0 | 0 | 0 | |
getCircSeqs | 1.07 | 0.32 | 1.39 | |
getDeseqRes | 3.97 | 0.29 | 4.25 | |
getDetectionTools | 0 | 0 | 0 | |
getEdgerRes | 0.73 | 0.17 | 0.91 | |
getMiRsites | 0.75 | 0.39 | 1.14 | |
getMotifs | 14.28 | 0.42 | 19.00 | |
getRandomBSJunctions | 0.14 | 0.08 | 0.22 | |
getRegexPattern | 0.00 | 0.01 | 0.01 | |
getSeqsAcrossBSJs | 1.00 | 0.29 | 1.28 | |
getSeqsFromGRs | 0.92 | 0.29 | 1.22 | |
gtf | 0.01 | 0.14 | 0.15 | |
gwasTraits | 0.02 | 0.00 | 0.02 | |
importCircExplorer2 | 0.03 | 0.00 | 0.03 | |
importCircMarker | 0.12 | 0.15 | 0.37 | |
importKnife | 0.02 | 0.02 | 0.03 | |
importMapSplice | 0.08 | 0.00 | 0.08 | |
importNCLscan | 0.01 | 0.00 | 0.02 | |
importOther | 0.02 | 0.00 | 0.01 | |
importUroborus | 0.01 | 0.00 | 0.02 | |
initCircRNAprofiler | 0 | 0 | 0 | |
iupac | 0 | 0 | 0 | |
liftBSJcoords | 43.10 | 2.68 | 50.22 | |
memeDB | 0 | 0 | 0 | |
mergeBSJunctions | 4.53 | 0.41 | 4.94 | |
mergeMotifs | 14.22 | 0.45 | 17.70 | |
mergedBSJunctions | 0.39 | 0.16 | 0.55 | |
miRspeciesCodes | 0 | 0 | 0 | |
plotExBetweenBSEs | 1.36 | 0.31 | 1.67 | |
plotExPosition | 1.36 | 0.30 | 1.67 | |
plotHostGenes | 1.30 | 0.31 | 1.61 | |
plotLenBSEs | 2.16 | 0.30 | 2.47 | |
plotLenIntrons | 2.28 | 0.26 | 2.58 | |
plotMiR | 1.06 | 0.30 | 1.35 | |
plotMotifs | 24.32 | 0.44 | 32.73 | |
plotTotExons | 1.23 | 0.23 | 1.47 | |
rearrangeMiRres | 0.80 | 0.31 | 1.11 | |
volcanoPlot | 3.61 | 0.27 | 3.88 | |