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### Running command:
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###   F:\biocbuild\bbs-3.17-bioc\R\bin\R.exe CMD check --no-multiarch --install=check:GUIDEseq.install-out.txt --library=F:\biocbuild\bbs-3.17-bioc\R\library --no-vignettes --timings GUIDEseq_1.30.0.tar.gz
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* using log directory 'F:/biocbuild/bbs-3.17-bioc/meat/GUIDEseq.Rcheck'
* using R version 4.3.1 (2023-06-16 ucrt)
* using platform: x86_64-w64-mingw32 (64-bit)
* R was compiled by
    gcc.exe (GCC) 12.2.0
    GNU Fortran (GCC) 12.2.0
* running under: Windows Server 2022 x64 (build 20348)
* using session charset: UTF-8
* using option '--no-vignettes'
* checking for file 'GUIDEseq/DESCRIPTION' ... OK
* checking extension type ... Package
* this is package 'GUIDEseq' version '1.30.0'
* 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 whether package 'GUIDEseq' can be installed ... OK
* checking installed package size ... NOTE
  installed size is 12.4Mb
  sub-directories of 1Mb or more:
    extdata  12.0Mb
* 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 ... NOTE
':::' call which should be '::': 'CRISPRseek:::translatePattern'
  See the note in ?`:::` about the use of this operator.
* checking S3 generic/method consistency ... OK
* checking replacement functions ... OK
* checking foreign function calls ... OK
* checking R code for possible problems ... NOTE
plotTracks: warning in scale_x_continuous(label =
  xaxis.lab.pos$chromosome, breaks = xaxis.lab.pos$chr.center): partial
  argument match of 'label' to 'labels'
.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 : <anonymous>: no visible binding for global variable
  'pa.f1'
getAlnWithBulge : <anonymous>: 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 sizes of PDF files under 'inst/doc' ... OK
* checking files in 'vignettes' ... OK
* checking examples ... OK
Examples with CPU (user + system) or elapsed time > 5s
                    user system elapsed
PEtagAnalysis      13.07   0.68   14.82
annotateOffTargets  5.85   0.32    6.69
* 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: 4 NOTEs
See
  'F:/biocbuild/bbs-3.17-bioc/meat/GUIDEseq.Rcheck/00check.log'
for details.