############################################################################## ############################################################################## ### ### 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_1.16.0.tar.gz ### ############################################################################## ############################################################################## * using log directory ‘/Users/biocbuild/bbs-3.18-bioc/meat/circRNAprofiler.Rcheck’ * using R version 4.3.3 (2024-02-29) * using platform: x86_64-apple-darwin20 (64-bit) * 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 12.7.1 * using session charset: UTF-8 * using option ‘--no-vignettes’ * checking for file ‘circRNAprofiler/DESCRIPTION’ ... OK * checking extension type ... Package * this is package ‘circRNAprofiler’ version ‘1.16.0’ * 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 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 34.974 3.759 49.025 plotMotifs 35.483 0.298 50.886 mergeMotifs 22.542 0.233 31.688 getMotifs 21.807 0.287 37.923 mergeBSJunctions 9.022 0.680 11.542 getDeseqRes 8.620 0.339 11.143 volcanoPlot 7.487 0.102 8.640 plotLenIntrons 3.733 0.075 5.157 * 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 ... SKIPPED * checking re-building of vignette outputs ... SKIPPED * checking PDF version of manual ... OK * DONE Status: 1 NOTE See ‘/Users/biocbuild/bbs-3.18-bioc/meat/circRNAprofiler.Rcheck/00check.log’ for details.