############################################################################## ############################################################################## ### ### Running command: ### ### /home/biocbuild/bbs-3.21-bioc/R/bin/R CMD check --install=check:GUIDEseq.install-out.txt --library=/home/biocbuild/bbs-3.21-bioc/R/site-library --timings GUIDEseq_1.37.0.tar.gz ### ############################################################################## ############################################################################## * using log directory ‘/home/biocbuild/bbs-3.21-bioc/meat/GUIDEseq.Rcheck’ * using R Under development (unstable) (2024-10-21 r87258) * 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 ‘GUIDEseq/DESCRIPTION’ ... OK * checking extension type ... Package * this is package ‘GUIDEseq’ version ‘1.37.0’ * package encoding: UTF-8 * checking package namespace information ... OK * checking package dependencies ...Warning: unable to access index for repository https://CRAN.R-project.org/src/contrib: cannot open URL 'https://CRAN.R-project.org/src/contrib/PACKAGES' INFO Imports includes 25 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 ‘GUIDEseq’ can be installed ... OK * checking installed package size ... INFO installed size is 7.3Mb sub-directories of 1Mb or more: extdata 6.8Mb * 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 .maskSubSeq: no visible global function definition for '.getMatchedInd' .nucleotideSubstitutionMatrix: no visible binding for global variable 'IUPAC_CODE_MAP' .nucleotideSubstitutionMatrix: no visible binding for global variable 'DNA_BASES' GUIDEseqAnalysis: no visible binding for global variable 'offTarget' GUIDEseqAnalysis: no visible binding for global variable 'peak_score' GUIDEseqAnalysis: no visible binding for global variable 'predicted_cleavage_score' GUIDEseqAnalysis: no visible binding for global variable 'gRNA.name' GUIDEseqAnalysis: no visible binding for global variable 'gRNAPlusPAM' GUIDEseqAnalysis: no visible binding for global variable 'offTarget_sequence' GUIDEseqAnalysis: no visible binding for global variable 'guideAlignment2OffTarget' GUIDEseqAnalysis: no visible binding for global variable 'offTargetStrand' GUIDEseqAnalysis: no visible binding for global variable 'mismatch.distance2PAM' GUIDEseqAnalysis: no visible binding for global variable 'n.guide.mismatch' GUIDEseqAnalysis: no visible binding for global variable 'offTarget_Start' GUIDEseqAnalysis: no visible binding for global variable 'offTarget_End' GUIDEseqAnalysis: no visible binding for global variable 'chromosome' GUIDEseqAnalysis: no visible binding for global variable 'gRNA.insertion' GUIDEseqAnalysis: no visible binding for global variable 'gRNA.deletion' GUIDEseqAnalysis: no visible binding for global variable 'pos.insertion' GUIDEseqAnalysis: no visible binding for global variable 'pos.deletion' GUIDEseqAnalysis: no visible binding for global variable 'n.insertion' GUIDEseqAnalysis: no visible binding for global variable 'n.deletion' GUIDEseqAnalysis: no visible binding for global variable 'n.RNA.bulge' GUIDEseqAnalysis: no visible binding for global variable 'n.DNA.bulge' GUIDEseqAnalysis: no visible binding for global variable 'feature' GUIDEseqAnalysis: no visible binding for global variable 'n.distinct.UMIs' annotateOffTargets: no visible binding for global variable 'offTarget_Start' getAlnWithBulge : : no visible binding for global variable 'pa.f1' getAlnWithBulge : : no visible binding for global variable 'pa.r2' getPeaks: no visible binding for global variable 'adjusted.p.value' getPeaks: no visible binding for global variable 'SNratio' getUniqueCleavageEvents: no visible binding for global variable 'width.first' getUniqueCleavageEvents: no visible binding for global variable 'width.last' getUniqueCleavageEvents: no visible binding for global variable 'qwidth.last' getUniqueCleavageEvents: no visible binding for global variable 'strand.last' getUniqueCleavageEvents: no visible binding for global variable 'qwidth.first' getUniqueCleavageEvents: no visible binding for global variable 'strand.first' getUniqueCleavageEvents: no visible binding for global variable 'readName' getUniqueCleavageEvents: no visible binding for global variable 'seqnames.last' getUniqueCleavageEvents: no visible binding for global variable 'seqnames.first' getUniqueCleavageEvents: no visible binding for global variable 'start.last' getUniqueCleavageEvents: no visible binding for global variable 'end.first' getUniqueCleavageEvents: no visible binding for global variable 'UMI' getUniqueCleavageEvents: no visible binding for global variable 'start.first' getUniqueCleavageEvents: no visible binding for global variable 'end.last' offTargetAnalysisOfPeakRegions: no visible binding for global variable 'thePeak' offTargetAnalysisOfPeakRegions: no visible binding for global variable 'gRNAPlusPAM' offTargetAnalysisOfPeakRegions: no visible binding for global variable 'offTarget' plotAlignedOfftargets: no visible binding for global variable 'total.mismatch.bulge' plotAlignedOfftargets: no visible binding for global variable 'RIR' plotAlignedOfftargets: no visible binding for global variable 'guideAlignment2OffTarget' plotAlignedOfftargets: no visible binding for global variable 'DNA.bulge' plotAlignedOfftargets: no visible binding for global variable 'y' plotAlignedOfftargets: no visible binding for global variable 'h' plotAlignedOfftargets: no visible binding for global variable 'IR' plotHeatmapOfftargets: no visible binding for global variable 'total.mismatch.bulge' plotHeatmapOfftargets: no visible binding for global variable 'Offtargets' plotHeatmapOfftargets: no visible binding for global variable 'IR' plotHeatmapOfftargets: no visible binding for global variable 'Ontarget' plotHeatmapOfftargets: no visible binding for global variable 'IR.max' plotHeatmapOfftargets: no visible binding for global variable 'Samples' plotHeatmapOfftargets: no visible global function definition for 'guides' plotHeatmapOfftargets: no visible global function definition for 'guide_legend' plotHeatmapOfftargets: no visible global function definition for 'unit' plotTracks: no visible binding for global variable 'total.mismatch.bulge' plotTracks: no visible binding for global variable 'n.PAM.mismatch' plotTracks: no visible binding for global variable 'offTargetStrand' plotTracks: no visible binding for global variable 'offTarget_Start' plotTracks: no visible binding for global variable 'offTarget_End' plotTracks: no visible binding for global variable 'n.distinct.UMIs' plotTracks: no visible binding for global variable 'predicted_cleavage_score' plotTracks: no visible global function definition for 'geom_smooth' plotTracks: no visible binding for global variable 'chromosome' plotTracks: no visible binding for global variable 'chr.max' plotTracks: no visible binding for global variable 'chr.offset' plotTracks: no visible binding for global variable '.' plotTracks: no visible binding for global variable 'cum.cleavage.position' Undefined global functions or variables: . .getMatchedInd DNA.bulge DNA_BASES IR IR.max IUPAC_CODE_MAP Offtargets Ontarget RIR SNratio Samples UMI adjusted.p.value chr.max chr.offset chromosome cum.cleavage.position end.first end.last feature gRNA.deletion gRNA.insertion gRNA.name gRNAPlusPAM geom_smooth guideAlignment2OffTarget guide_legend guides h mismatch.distance2PAM n.DNA.bulge n.PAM.mismatch n.RNA.bulge n.deletion n.distinct.UMIs n.guide.mismatch n.insertion offTarget offTargetStrand offTarget_End offTarget_Start offTarget_sequence pa.f1 pa.r2 peak_score pos.deletion pos.insertion predicted_cleavage_score qwidth.first qwidth.last readName seqnames.first seqnames.last start.first start.last strand.first strand.last thePeak total.mismatch.bulge unit width.first width.last y * checking Rd files ... NOTE prepare_Rd: annotateOffTargets.Rd:35-37: Dropping empty section \details prepare_Rd: annotateOffTargets.Rd:63-65: Dropping empty section \references prepare_Rd: createBarcodeFasta.Rd:56-58: Dropping empty section \references prepare_Rd: getUsedBarcodes.Rd:53-55: Dropping empty section \references checkRd: (-1) mergePlusMinusPeaks.Rd:72: Escaped LaTeX specials: \_ * 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 PEtagAnalysis 13.984 0.857 14.844 annotateOffTargets 4.825 0.172 5.002 * 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: 2 NOTEs See ‘/home/biocbuild/bbs-3.21-bioc/meat/GUIDEseq.Rcheck/00check.log’ for details.