############################################################################## ############################################################################## ### ### Running command: ### ### /home/biocbuild/R/R/bin/R CMD check --install=check:circRNAprofiler.install-out.txt --library=/home/biocbuild/R/R/site-library --no-vignettes --timings circRNAprofiler_1.21.0.tar.gz ### ############################################################################## ############################################################################## * using log directory ‘/home/biocbuild/bbs-3.21-bioc/meat/circRNAprofiler.Rcheck’ * using R Under development (unstable) (2024-11-24 r87369) * using platform: aarch64-unknown-linux-gnu * R was compiled by aarch64-unknown-linux-gnu-gcc (GCC) 14.2.0 GNU Fortran (GCC) 14.2.0 * running under: openEuler 24.03 (LTS) * using session charset: UTF-8 * using option ‘--no-vignettes’ * checking for file ‘circRNAprofiler/DESCRIPTION’ ... OK * checking extension type ... Package * this is package ‘circRNAprofiler’ version ‘1.21.0’ * package encoding: UTF-8 * checking package namespace information ... OK * checking package dependencies ... INFO Imports includes 23 non-default packages. Importing from so many packages makes the package vulnerable to any of them becoming unavailable. Move as many as possible to Suggests and use conditionally. * 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 ...Warning: program compiled against libxml 212 using older 211 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 ... NOTE Found the following Rd file(s) with Rd \link{} targets missing package anchors: annotateRepeats.Rd: AnnotationHub getCircSeqs.Rd: getBSgenome getSeqsAcrossBSJs.Rd: getBSgenome getSeqsFromGRs.Rd: getBSgenome Please provide package anchors for all Rd \link{} targets not in the package itself and the base packages. * 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 26.518 1.146 32.526 plotMotifs 21.824 0.036 32.979 getMotifs 14.551 0.270 21.023 mergeMotifs 13.723 0.080 19.255 mergeBSJunctions 6.225 0.080 6.321 getDeseqRes 5.217 0.124 5.352 volcanoPlot 5.080 0.032 5.125 * 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: 2 NOTEs See ‘/home/biocbuild/bbs-3.21-bioc/meat/circRNAprofiler.Rcheck/00check.log’ for details.