############################################################################## ############################################################################## ### ### Running command: ### ### /home/biocbuild/bbs-3.20-bioc/R/bin/R CMD check --install=check:circRNAprofiler.install-out.txt --library=/home/biocbuild/bbs-3.20-bioc/R/site-library --timings circRNAprofiler_1.20.0.tar.gz ### ############################################################################## ############################################################################## * using log directory ‘/media/volume/teran2_disk/biocbuild/bbs-3.20-bioc/meat/circRNAprofiler.Rcheck’ * using R version 4.4.2 (2024-10-31) * using platform: x86_64-pc-linux-gnu * R was compiled by gcc (Ubuntu 13.2.0-23ubuntu4) 13.2.0 GNU Fortran (Ubuntu 13.2.0-23ubuntu4) 13.2.0 * running under: Ubuntu 24.04.1 LTS * using session charset: UTF-8 * 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 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 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 .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 18.026 1.547 24.607 plotMotifs 10.689 0.039 20.517 mergeMotifs 6.536 0.015 11.058 getMotifs 6.303 0.027 11.386 * 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 re-building of vignette outputs ... OK * checking PDF version of manual ... OK * DONE Status: 1 NOTE See ‘/media/volume/teran2_disk/biocbuild/bbs-3.20-bioc/meat/circRNAprofiler.Rcheck/00check.log’ for details.