Back to Mac ARM64 build report for BioC 3.20 |
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This page was generated on 2024-05-13 11:32:01 -0400 (Mon, 13 May 2024).
Hostname | OS | Arch (*) | R version | Installed pkgs |
---|---|---|---|---|
kjohnson1 | macOS 13.6.6 Ventura | arm64 | 4.4.0 Patched (2024-04-24 r86482) -- "Puppy Cup" | 4378 |
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 347/2230 | Hostname | OS / Arch | INSTALL | BUILD | CHECK | BUILD BIN | ||||||||
circRNAprofiler 1.19.0 (landing page) Simona Aufiero
| kjohnson1 | macOS 13.6.6 Ventura / arm64 | OK | OK | OK | OK | ||||||||
To the developers/maintainers of the circRNAprofiler package: - 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: 1.19.0 |
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_1.19.0.tar.gz |
StartedAt: 2024-05-12 08:42:00 -0400 (Sun, 12 May 2024) |
EndedAt: 2024-05-12 08:54:03 -0400 (Sun, 12 May 2024) |
EllapsedTime: 723.1 seconds |
RetCode: 0 |
Status: OK |
CheckDir: circRNAprofiler.Rcheck |
Warnings: 0 |
############################################################################## ############################################################################## ### ### 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_1.19.0.tar.gz ### ############################################################################## ############################################################################## * using log directory ‘/Users/biocbuild/bbs-3.20-bioc-mac-arm64/meat/circRNAprofiler.Rcheck’ * using R version 4.4.0 Patched (2024-04-24 r86482) * using platform: aarch64-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 Ventura 13.6.6 * using session charset: UTF-8 * using option ‘--no-vignettes’ * checking for file ‘circRNAprofiler/DESCRIPTION’ ... OK * checking extension type ... Package * this is package ‘circRNAprofiler’ version ‘1.19.0’ * 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 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 29.301 1.142 34.531 plotMotifs 18.691 0.140 27.724 mergeMotifs 12.394 0.103 16.967 getMotifs 12.006 0.112 16.002 mergeBSJunctions 5.047 0.232 5.466 * 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 ‘/Users/biocbuild/bbs-3.20-bioc-mac-arm64/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/4.4-arm64/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
R version 4.4.0 Patched (2024-04-24 r86482) -- "Puppy Cup" Copyright (C) 2024 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:+:chr11:43704534:43705477trying 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 155.351 4.901 185.837
circRNAprofiler.Rcheck/circRNAprofiler-Ex.timings
name | user | system | elapsed | |
ahChainFiles | 0.212 | 0.007 | 0.220 | |
ahRepeatMasker | 0.002 | 0.002 | 0.005 | |
annotateBSJs | 0.927 | 0.021 | 0.957 | |
annotateRepeats | 2.938 | 0.050 | 3.006 | |
annotateSNPsGWAS | 1.348 | 0.042 | 1.393 | |
attractSpecies | 0.001 | 0.001 | 0.003 | |
backSplicedJunctions | 0.962 | 0.010 | 0.974 | |
checkProjectFolder | 0.002 | 0.000 | 0.002 | |
filterCirc | 0.734 | 0.019 | 0.760 | |
formatGTF | 0.001 | 0.000 | 0.001 | |
getBackSplicedJunctions | 0.000 | 0.000 | 0.001 | |
getCircSeqs | 1.192 | 0.054 | 1.248 | |
getDeseqRes | 4.170 | 0.141 | 4.323 | |
getDetectionTools | 0.002 | 0.000 | 0.003 | |
getEdgerRes | 1.016 | 0.021 | 1.040 | |
getMiRsites | 2.489 | 0.050 | 2.559 | |
getMotifs | 12.006 | 0.112 | 16.002 | |
getRandomBSJunctions | 0.131 | 0.003 | 0.134 | |
getRegexPattern | 0.002 | 0.001 | 0.003 | |
getSeqsAcrossBSJs | 1.027 | 0.032 | 1.066 | |
getSeqsFromGRs | 1.027 | 0.034 | 1.066 | |
gtf | 0.023 | 0.003 | 0.026 | |
gwasTraits | 0.007 | 0.002 | 0.009 | |
importCircExplorer2 | 0.044 | 0.003 | 0.048 | |
importCircMarker | 0.107 | 0.005 | 0.112 | |
importKnife | 0.016 | 0.001 | 0.017 | |
importMapSplice | 0.051 | 0.001 | 0.052 | |
importNCLscan | 0.013 | 0.002 | 0.014 | |
importOther | 0.010 | 0.001 | 0.012 | |
importUroborus | 0.011 | 0.001 | 0.013 | |
initCircRNAprofiler | 0 | 0 | 0 | |
iupac | 0.001 | 0.002 | 0.003 | |
liftBSJcoords | 29.301 | 1.142 | 34.531 | |
memeDB | 0.001 | 0.002 | 0.002 | |
mergeBSJunctions | 5.047 | 0.232 | 5.466 | |
mergeMotifs | 12.394 | 0.103 | 16.967 | |
mergedBSJunctions | 0.671 | 0.007 | 0.796 | |
miRspeciesCodes | 0.003 | 0.003 | 0.006 | |
plotExBetweenBSEs | 1.325 | 0.023 | 1.397 | |
plotExPosition | 1.214 | 0.022 | 1.299 | |
plotHostGenes | 1.224 | 0.018 | 1.402 | |
plotLenBSEs | 1.907 | 0.022 | 2.098 | |
plotLenIntrons | 1.970 | 0.020 | 2.063 | |
plotMiR | 1.075 | 0.036 | 1.186 | |
plotMotifs | 18.691 | 0.140 | 27.724 | |
plotTotExons | 1.186 | 0.023 | 1.247 | |
rearrangeMiRres | 0.992 | 0.039 | 1.052 | |
volcanoPlot | 3.436 | 0.056 | 3.654 | |