Bioconductor Single Package Builder - Build History

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 R CMD BUILD

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* checking for file ‘DuplexDiscovereR/DESCRIPTION’ ... OK
* preparing ‘DuplexDiscovereR’:
* checking DESCRIPTION meta-information ... OK
* installing the package to build vignettes
* creating vignettes ... OK
* checking for LF line-endings in source and make files and shell scripts
* checking for empty or unneeded directories
* looking to see if a ‘data/datalist’ file should be added
* building ‘DuplexDiscovereR_0.99.0.tar.gz’

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 BiocCheckGitClone('DuplexDiscovereR')

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─ BiocCheckVersion: 1.41.2
─ BiocVersion: 3.20
─ Package: DuplexDiscovereR
─ PackageVersion: 0.99.0
─ sourceDir: /Users/pkgbuild/packagebuilder/workers/jobs/3453/DuplexDiscovereR_20240625135205/DuplexDiscovereR
─ platform: unix
─ isTarBall: FALSE

* Checking valid files...
* Checking for stray BiocCheck output folders...
* Checking for inst/doc folders...
* Checking DESCRIPTION...
* Checking if DESCRIPTION is well formatted...
* Checking for valid maintainer...
* Checking CITATION...
    * NOTE: (Optional) CITATION file not found. Only include a CITATION
      file if there is a preprint or publication for this Bioconductor
      package. Note that Bioconductor packages are not required to have
      a CITATION file but it is useful both for users and for tracking
      Bioconductor project-wide metrics. When including a CITATION
      file, add the publication using the 'doi' argument of
      'bibentry()'.

─ BiocCheck results ──
0 ERRORS | 0 WARNINGS | 1 NOTES

For more details, run
    browseVignettes(package = 'BiocCheck')




===============================

 R CMD CHECK

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* using log directory ‘/Users/pkgbuild/packagebuilder/workers/jobs/3453/DuplexDiscovereR_20240625135205/DuplexDiscovereR.Rcheck’
* using R version 4.4.1 RC (2024-06-06 r86719)
* using platform: x86_64-apple-darwin20
* 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 ‘DuplexDiscovereR/DESCRIPTION’ ... OK
* this is package ‘DuplexDiscovereR’ version ‘0.99.0’
* 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 ‘DuplexDiscovereR’ can be installed ... OK
* checking installed package size ... OK
* checking package directory ... OK
* checking for future file timestamps ... 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 ... [11s/11s] OK
* checking whether the package can be loaded with stated dependencies ... [10s/11s] OK
* checking whether the package can be unloaded cleanly ... [11s/11s] OK
* checking whether the namespace can be loaded with stated dependencies ... [10s/10s] OK
* checking whether the namespace can be unloaded cleanly ... [10s/10s] OK
* checking loading without being on the library search path ... [10s/10s] OK
* checking use of S3 registration ... 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 ... [35s/35s] NOTE
.DGIdToDuplexId: no visible binding for global variable 'duplex_id'
.DGIdToDuplexId: no visible binding for global variable 'dg_id'
.addDGidsForTmpDGs: no visible global function definition for 'mcols<-'
.addGeneCounts: no visible binding for global variable 'gene_count.A'
.addGeneCounts: no visible binding for global variable 'gene_count.B'
.gv_plotboxes: no visible global function definition for
  '.handleComposite'
DuplexTrack: no visible global function definition for 'GRanges'
DuplexTrack: no visible global function definition for 'IRanges'
DuplexTrack: no visible global function definition for
  'subsetByOverlaps'
DuplexTrack: no visible binding for global variable 'gap'
DuplexTrack: no visible binding for global variable 'in_range'
DuplexTrack: no visible global function definition for 'mcols<-'
DuplexTrack: no visible binding for global variable 'arm'
DuplexTrack: no visible binding for global variable 'full_in_plot'
DuplexTrack: no visible binding for global variable 'pair_arm'
annotateGI: no visible global function definition for
  'findOverlapPairs'
annotateGI: no visible global function definition for 'pintersect'
annotateGI: no visible binding for global variable 'region_id'
annotateGI: no visible binding for global variable 'ambig'
annotateGI: no visible binding for global variable 'overlap_w'
annotateGI: no visible binding for global variable 'feature_id'
annotateGI: no visible binding for global variable 'ambig.A'
annotateGI: no visible binding for global variable 'ambig.B'
annotateGI: no visible binding for global variable 'ambig_list.A'
annotateGI: no visible binding for global variable 'ambig_list.B'
annotateGI: no visible global function definition for 'mcols<-'
assign_name_to_gi: no visible global function definition for 'mcols<-'
calculateLigationPvalues: no visible binding for global variable
  'n_reads'
calculateLigationPvalues: no visible binding for global variable 'AB'
calculateLigationPvalues: no visible binding for global variable 'A'
calculateLigationPvalues: no visible binding for global variable 'B'
calculateLigationPvalues: no visible binding for global variable 'nA'
calculateLigationPvalues: no visible binding for global variable 'nB'
calculateLigationPvalues: no visible binding for global variable 'Pa'
calculateLigationPvalues: no visible binding for global variable 'Pb'
calculateLigationPvalues: no visible binding for global variable
  'p.adj'
clusterDuplexGroups: no visible binding for global variable 'ratio.A'
clusterDuplexGroups: no visible binding for global variable 'ratio.B'
clusterDuplexGroups: no visible binding for global variable 'vert_id1'
clusterDuplexGroups: no visible binding for global variable 'vert_id2'
clusterDuplexGroups: no visible binding for global variable 'weight'
clusterDuplexGroups: no visible global function definition for 'E'
clusterDuplexGroups: no visible binding for global variable 'vert_id'
clusterDuplexGroups: no visible binding for global variable 'dg_id_raw'
clusterDuplexGroups: no visible binding for global variable 'cmp'
clusterDuplexGroups: no visible binding for global variable 'dg_id'
collapseIdenticalReads: no visible binding for global variable 'chromA'
collapseIdenticalReads: no visible binding for global variable
  'strandA'
collapseIdenticalReads: no visible binding for global variable 'startA'
collapseIdenticalReads: no visible binding for global variable 'endA'
collapseIdenticalReads: no visible binding for global variable 'chromB'
collapseIdenticalReads: no visible binding for global variable
  'strandB'
collapseIdenticalReads: no visible binding for global variable 'startB'
collapseIdenticalReads: no visible binding for global variable 'endB'
collapseIdenticalReads: no visible binding for global variable
  'cigar_alnA'
collapseIdenticalReads: no visible binding for global variable
  'cigar_alnB'
collapseIdenticalReads: no visible binding for global variable 'grp'
collapseIdenticalReads: no visible binding for global variable
  'n_reads'
collapseIdenticalReads: no visible binding for global variable
  'read_id'
collapseIdenticalReads: no visible binding for global variable
  'duplex_id'
collapseSimilarChimeras: no visible binding for global variable 'dg_id'
collapseSimilarChimeras: no visible binding for global variable
  'duplex_id'
collapseSimilarChimeras: no visible binding for global variable
  'new_duplex_id'
collapseSimilarChimeras: no visible binding for global variable
  'old_duplex_id'
collapseSimilarChimeras: no visible binding for global variable
  'read_id'
collapse_duplex_groups: no visible binding for global variable
  'n_reads'
collapse_duplex_groups: no visible binding for global variable 'dg_id'
collapse_duplex_groups: no visible binding for global variable
  'seqnames1'
collapse_duplex_groups: no visible binding for global variable 'start1'
collapse_duplex_groups: no visible binding for global variable 'end1'
collapse_duplex_groups: no visible binding for global variable
  'strand1'
collapse_duplex_groups: no visible binding for global variable
  'seqnames2'
collapse_duplex_groups: no visible binding for global variable 'start2'
collapse_duplex_groups: no visible binding for global variable 'end2'
collapse_duplex_groups: no visible binding for global variable
  'strand2'
computeGIPairOverlaps: no visible global function definition for
  'mcols<-'
computeGIPairOverlaps: no visible global function definition for
  'queryHits'
computeGIPairOverlaps: no visible global function definition for
  'subjectHits'
computeGIPairOverlaps: no visible global function definition for
  'punion'
computeGIPairOverlaps: no visible global function definition for
  'pintersect'
computeGIPairOverlaps: no visible binding for global variable 'A_ovl'
computeGIPairOverlaps: no visible binding for global variable 'A_span'
computeGIPairOverlaps: no visible binding for global variable 'B_ovl'
computeGIPairOverlaps: no visible binding for global variable 'B_span'
computeGISelfOverlaps: no visible global function definition for
  'mcols<-'
computeGISelfOverlaps: no visible global function definition for
  'queryHits'
computeGISelfOverlaps: no visible global function definition for
  'subjectHits'
computeGISelfOverlaps: no visible global function definition for
  'punion'
computeGISelfOverlaps: no visible global function definition for
  'pintersect'
computeGISelfOverlaps: no visible binding for global variable 'A_ovl'
computeGISelfOverlaps: no visible binding for global variable 'A_span'
computeGISelfOverlaps: no visible binding for global variable 'B_ovl'
computeGISelfOverlaps: no visible binding for global variable 'B_span'
computeGISelfOverlaps: no visible binding for global variable 'ratio.A'
computeGISelfOverlaps: no visible binding for global variable 'ratio.B'
computeGISelfOverlaps: no visible binding for global variable 'idcol.1'
computeGISelfOverlaps: no visible binding for global variable 'idcol.2'
convert_gi_to_ranges: no visible global function definition for
  'mcols<-'
getSpliceJunctionChimeras: no visible binding for global variable '.'
getSpliceJunctionChimeras: no visible binding for global variable 'x1'
getSpliceJunctionChimeras: no visible binding for global variable 'x2'
getSpliceJunctionChimeras: no visible binding for global variable 'x3'
getSpliceJunctionChimeras: no visible global function definition for
  'queryHits'
get_char_count_cigar: no visible binding for global variable '.'
get_chimeric_junctions_onestrand: no visible global function definition
  for 'GRanges'
makeDfFromGi: no visible global function definition for 'mcols<-'
makeDfFromGi: no visible binding for global variable 'seqnames1'
makeDfFromGi: no visible binding for global variable 'start1'
makeDfFromGi: no visible binding for global variable 'end1'
makeDfFromGi: no visible binding for global variable 'strand1'
makeDfFromGi: no visible binding for global variable 'seqnames2'
makeDfFromGi: no visible binding for global variable 'start2'
makeDfFromGi: no visible binding for global variable 'end2'
makeDfFromGi: no visible binding for global variable 'strand2'
makeDfFromGi: no visible binding for global variable 'width1'
makeDfFromGi: no visible binding for global variable 'width2'
makeGiFromDf: no visible binding for global variable 'chromA'
makeGiFromDf: no visible binding for global variable 'startA'
makeGiFromDf: no visible binding for global variable 'endA'
makeGiFromDf: no visible binding for global variable 'strandA'
makeGiFromDf: no visible binding for global variable 'chromB'
makeGiFromDf: no visible binding for global variable 'startB'
makeGiFromDf: no visible binding for global variable 'endB'
makeGiFromDf: no visible binding for global variable 'strandB'
makeGiFromDf: no visible global function definition for 'GRanges'
makeGiFromDf: no visible global function definition for 'mcols<-'
preproc_chim_junction_out_pe: no visible binding for global variable
  'read_name'
preproc_chim_junction_out_pe: no visible binding for global variable
  'chr_donorA'
preproc_chim_junction_out_pe: no visible binding for global variable
  'chr_acceptorB'
preproc_chim_junction_out_pe: no visible binding for global variable
  'start_alnA'
preproc_chim_junction_out_pe: no visible binding for global variable
  'start_alnB'
preproc_chim_junction_out_pe: no visible binding for global variable
  'strand_donorA'
preproc_chim_junction_out_pe: no visible binding for global variable
  'strand_acceptorB'
preproc_chim_junction_out_pe: no visible binding for global variable
  'cigar_alnA'
preproc_chim_junction_out_pe: no visible binding for global variable
  'cigar_alnB'
preproc_chim_junction_out_pe: no visible binding for global variable
  'brkpt_donorA'
preproc_chim_junction_out_pe: no visible binding for global variable
  'brkpt_acceptorB'
preproc_chim_junction_out_pe: no visible binding for global variable
  'this_chim_aln_score'
preproc_chim_junction_out_pe: no visible binding for global variable
  'num_chim_aln'
preproc_chim_junction_out_pe: no visible binding for global variable
  'cigar_str'
preproc_chim_junction_out_pe: no visible binding for global variable
  'minus_p'
preproc_chim_junction_out_pe: no visible binding for global variable
  'has_p'
preproc_chim_junction_out_pe: no visible binding for global variable
  'n_n'
preproc_chim_junction_out_pe: no visible binding for global variable
  'startA'
preproc_chim_junction_out_pe: no visible binding for global variable
  'n_m'
preproc_chim_junction_out_pe: no visible binding for global variable
  'n_p'
preproc_chim_junction_out_pe: no visible binding for global variable
  'sign_p'
preproc_chim_junction_out_pe: no visible binding for global variable
  'startB'
preproc_chim_junction_out_pe: no visible binding for global variable
  'chromA'
preproc_chim_junction_out_pe: no visible binding for global variable
  'chromB'
preproc_chim_junction_out_pe: no visible binding for global variable
  'strandA'
preproc_chim_junction_out_pe: no visible binding for global variable
  'strandB'
preproc_chim_junction_out_pe: no visible binding for global variable
  'endB'
preproc_chim_junction_out_pe: no visible binding for global variable
  'endA'
preproc_chim_junction_out_pe: no visible binding for global variable
  'lengapsA'
preproc_chim_junction_out_pe: no visible binding for global variable
  'lengapsB'
preproc_chim_junction_out_pe: no visible binding for global variable
  'n_s'
preproc_chim_junction_out_pe: no visible binding for global variable
  'n_i'
preproc_chim_junction_out_pe: no visible binding for global variable
  'ngapsA'
preproc_chim_junction_out_pe: no visible binding for global variable
  'ngapsB'
preproc_chim_junction_out_se: no visible binding for global variable
  'read_name'
preproc_chim_junction_out_se: no visible binding for global variable
  'chr_donorA'
preproc_chim_junction_out_se: no visible binding for global variable
  'chr_acceptorB'
preproc_chim_junction_out_se: no visible binding for global variable
  'start_alnA'
preproc_chim_junction_out_se: no visible binding for global variable
  'start_alnB'
preproc_chim_junction_out_se: no visible binding for global variable
  'strand_donorA'
preproc_chim_junction_out_se: no visible binding for global variable
  'strand_acceptorB'
preproc_chim_junction_out_se: no visible binding for global variable
  'cigar_alnA'
preproc_chim_junction_out_se: no visible binding for global variable
  'cigar_alnB'
preproc_chim_junction_out_se: no visible binding for global variable
  'brkpt_donorA'
preproc_chim_junction_out_se: no visible binding for global variable
  'brkpt_acceptorB'
preproc_chim_junction_out_se: no visible binding for global variable
  'this_chim_aln_score'
preproc_chim_junction_out_se: no visible binding for global variable
  'num_chim_aln'
preproc_chim_junction_out_se: no visible binding for global variable
  'startA'
preproc_chim_junction_out_se: no visible binding for global variable
  'startB'
preproc_chim_junction_out_se: no visible binding for global variable
  'chromA'
preproc_chim_junction_out_se: no visible binding for global variable
  'chromB'
preproc_chim_junction_out_se: no visible binding for global variable
  'strandA'
preproc_chim_junction_out_se: no visible binding for global variable
  'strandB'
preproc_chim_junction_out_se: no visible binding for global variable
  'endB'
preproc_chim_junction_out_se: no visible binding for global variable
  'endA'
preproc_chim_junction_out_se: no visible binding for global variable
  'bad_junction'
preproc_chim_junction_out_se: no visible binding for global variable
  'lengapsA'
preproc_chim_junction_out_se: no visible binding for global variable
  'lengapsB'
preproc_generic: no visible binding for global variable 'chromA'
preproc_generic: no visible binding for global variable 'chromB'
preproc_generic: no visible binding for global variable 'strandA'
preproc_generic: no visible binding for global variable 'strandB'
preproc_generic: no visible binding for global variable 'startA'
preproc_generic: no visible binding for global variable 'endB'
preproc_generic: no visible binding for global variable 'endA'
preproc_generic: no visible binding for global variable 'startB'
preproc_generic: no visible binding for global variable 'bad_junction'
preproc_generic: no visible binding for global variable 'readname'
preproc_generic: no visible binding for global variable 'nr'
preproc_generic: no visible binding for global variable 'multimap'
preproc_generic_gi: no visible binding for global variable 'chromA'
preproc_generic_gi: no visible binding for global variable 'chromB'
preproc_generic_gi: no visible binding for global variable 'strandA'
preproc_generic_gi: no visible binding for global variable 'strandB'
preproc_generic_gi: no visible binding for global variable 'startA'
preproc_generic_gi: no visible binding for global variable 'endB'
preproc_generic_gi: no visible binding for global variable 'endA'
preproc_generic_gi: no visible binding for global variable 'startB'
preproc_generic_gi: no visible binding for global variable
  'bad_junction'
preproc_generic_gi: no visible binding for global variable 'readname'
preproc_generic_gi: no visible binding for global variable 'nr'
preproc_generic_gi: no visible binding for global variable 'multimap'
refresh_gi: no visible global function definition for 'mcols<-'
runDuplexDiscoPreproc: no visible binding for global variable
  'multigap'
runDuplexDiscoPreproc: no visible binding for global variable
  'multimap'
runDuplexDiscoPreproc: no visible binding for global variable
  'bad_junction'
runDuplexDiscoPreproc: no visible binding for global variable 'chromA'
runDuplexDiscoPreproc: no visible binding for global variable 'startA'
runDuplexDiscoPreproc: no visible binding for global variable 'endA'
runDuplexDiscoPreproc: no visible binding for global variable 'strandA'
runDuplexDiscoPreproc: no visible binding for global variable 'chromB'
runDuplexDiscoPreproc: no visible binding for global variable 'startB'
runDuplexDiscoPreproc: no visible binding for global variable 'endB'
runDuplexDiscoPreproc: no visible binding for global variable 'strandB'
runDuplexDiscoPreproc: no visible binding for global variable
  'readname'
runDuplexDiscoPreproc: no visible binding for global variable
  'map_type'
runDuplexDiscoPreproc: no visible binding for global variable 'n_reads'
runDuplexDiscoverer: no visible binding for global variable 'map_type'
runDuplexDiscoverer: no visible binding for global variable 'readname'
runDuplexDiscoverer: no visible binding for global variable 'n_reads'
runDuplexDiscoverer: no visible binding for global variable 'read_id'
runDuplexDiscoverer: no visible binding for global variable
  'junction_type'
runDuplexDiscoverer: no visible binding for global variable 'splicejnc'
runDuplexDiscoverer: no visible binding for global variable 'read_type'
runDuplexDiscoverer: no visible binding for global variable 'ratio.A'
runDuplexDiscoverer: no visible binding for global variable 'ratio.B'
runDuplexDiscoverer: no visible binding for global variable 'dg_id'
runDuplexDiscoverer: no visible binding for global variable
  'n_reads_dg'
runDuplexDiscoverer: no visible binding for global variable 'duplex_id'
set_hg19_seqlengths: no visible binding for global variable
  'hg38_seqlengths'
set_hg19_seqlengths: no visible global function definition for
  'seqlengths<-'
set_hg38_seqlengths: no visible global function definition for
  'seqlengths<-'
subset_gi: no visible binding for global variable 'gi_trans'
subset_gi: no visible global function definition for 'mcols<-'
writeGiToSAMfile: no visible global function definition for
  'seqlengths'
writeGiToSAMfile: no visible global function definition for 'mcols<-'
writeGiToSAMfile: no visible global function definition for 'distance'
writeGiToSAMfile: no visible binding for global variable 'rname'
writeGiToSAMfile: no visible binding for global variable 'col2'
writeGiToSAMfile: no visible binding for global variable 'seqnames1'
writeGiToSAMfile: no visible binding for global variable 'start1'
writeGiToSAMfile: no visible binding for global variable 'col5'
writeGiToSAMfile: no visible binding for global variable 'artCIGAR'
writeGiToSAMfile: no visible binding for global variable 'col7'
writeGiToSAMfile: no visible binding for global variable 'col8'
writeGiToSAMfile: no visible binding for global variable 'col9'
writeGiToSAMfile: no visible binding for global variable 'artSEQ'
writeGiToSAMfile: no visible binding for global variable 'col11'
writeGiToSAMfile: no visible binding for global variable 'tag'
writeGiToSAMfile: no visible binding for global variable 'col1read1'
writeGiToSAMfile: no visible binding for global variable 'artCIGAR1'
writeGiToSAMfile: no visible binding for global variable 'seq_anchor1'
writeGiToSAMfile: no visible binding for global variable 'col1read2'
writeGiToSAMfile: no visible binding for global variable 'seqnames2'
writeGiToSAMfile: no visible binding for global variable 'start2'
writeGiToSAMfile: no visible binding for global variable 'artCIGAR2'
writeGiToSAMfile: no visible binding for global variable 'seq_anchor2'
drawGD,DuplexTrack: no visible global function definition for 'mcols<-'
drawGD,DuplexTrack: no visible binding for global variable 'rDens'
drawGD,DuplexTrack: no visible global function definition for
  '.getBiotypeColor'
drawGD,DuplexTrack: no visible binding for global variable 'gap'
drawGD,DuplexTrack: no visible binding for global variable 'has_A'
drawGD,DuplexTrack: no visible binding for global variable 'has_B'
drawGD,DuplexTrack: no visible binding for global variable 'grpvar'
drawGD,DuplexTrack: no visible binding for global variable 'arc_max_y'
drawGD,DuplexTrack: no visible binding for global variable 'grp'
Undefined global functions or variables:
  . .getBiotypeColor .handleComposite A AB A_ovl A_span B B_ovl B_span
  E GRanges IRanges Pa Pb ambig ambig.A ambig.B ambig_list.A
  ambig_list.B arc_max_y arm artCIGAR artCIGAR1 artCIGAR2 artSEQ
  bad_junction brkpt_acceptorB brkpt_donorA chr_acceptorB chr_donorA
  chromA chromB cigar_alnA cigar_alnB cigar_str cmp col11 col1read1
  col1read2 col2 col5 col7 col8 col9 dg_id dg_id_raw distance duplex_id
  end1 end2 endA endB feature_id findOverlapPairs full_in_plot gap
  gene_count.A gene_count.B gi_trans grp grpvar has_A has_B has_p
  hg38_seqlengths idcol.1 idcol.2 in_range junction_type lengapsA
  lengapsB map_type mcols<- minus_p multigap multimap nA nB n_i n_m n_n
  n_p n_reads n_reads_dg n_s new_duplex_id ngapsA ngapsB nr
  num_chim_aln old_duplex_id overlap_w p.adj pair_arm pintersect punion
  queryHits rDens ratio.A ratio.B read_id read_name read_type readname
  region_id rname seq_anchor1 seq_anchor2 seqlengths seqlengths<-
  seqnames1 seqnames2 sign_p splicejnc start1 start2 startA startB
  start_alnA start_alnB strand1 strand2 strandA strandB
  strand_acceptorB strand_donorA subjectHits subsetByOverlaps tag
  this_chim_aln_score vert_id vert_id1 vert_id2 weight width1 width2 x1
  x2 x3
* checking Rd files ... [0s/0s] OK
* checking Rd metadata ... OK
* checking Rd line widths ... 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 ... [4s/4s] OK
* checking data for ASCII and uncompressed saves ... OK
* checking files in ‘vignettes’ ... OK
* checking examples ... [40s/40s] OK
* checking for unstated dependencies in ‘tests’ ... OK
* checking tests ...
  Running ‘testthat.R’ [25s/25s]
 [25s/25s] 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 ... [4s/4s] OK
* DONE

Status: 1 NOTE
See
  ‘/Users/pkgbuild/packagebuilder/workers/jobs/3453/DuplexDiscovereR_20240625135205/DuplexDiscovereR.Rcheck/00check.log’
for details.





===============================

 BiocCheck('DuplexDiscovereR_0.99.0.tar.gz')

===============================

─ BiocCheckVersion: 1.41.2
─ BiocVersion: 3.20
─ Package: DuplexDiscovereR
─ PackageVersion: 0.99.0
─ sourceDir: /var/folders/db/d7_0z9ss4n3692ppdmx9hlgr0000gv/T//RtmplDLegW/file44232efa42b8/DuplexDiscovereR
─ installDir: /var/folders/db/d7_0z9ss4n3692ppdmx9hlgr0000gv/T//RtmplDLegW/file442338b46798
─ BiocCheckDir: /Users/pkgbuild/packagebuilder/workers/jobs/3453/DuplexDiscovereR_20240625135205/DuplexDiscovereR.BiocCheck
─ platform: unix
─ isTarBall: TRUE

* Installing package...
* Checking for deprecated package usage...
* Checking for remote package usage...
* Checking for 'LazyData: true' usage...
* Checking version number...
* Checking for version number mismatch...
* Checking new package version number...
* Checking R version dependency...
* Checking package size...
* Checking individual file sizes...
* Checking biocViews...
* Checking that biocViews are present...
* Checking package type based on biocViews...
    Software
* Checking for non-trivial biocViews...
* Checking that biocViews come from the same category...
* Checking biocViews validity...
* Checking for recommended biocViews...
    * NOTE: Consider adding these automatically suggested biocViews:
      Alignment, Classification, HiC
Search 'biocViews' at https://contributions.bioconductor.org
* Checking build system compatibility...
* Checking for blank lines in DESCRIPTION...
* Checking if DESCRIPTION is well formatted...
* Checking for proper Description: field...
* Checking for whitespace in DESCRIPTION field names...
* Checking that Package field matches directory/tarball name...
* Checking for Version: field...
* Checking for valid maintainer...
* Checking License: for restrictive use...
* Checking for recommended DESCRIPTION fields...
* Checking for Bioconductor software dependencies...
    Bioconductor dependencies found in Imports & Depends (31%).
* Checking for pinned package versions in DESCRIPTION...
* Checking .Rbuildignore...
* Checking for stray BiocCheck output folders...
* Checking vignette directory...
* Checking whether vignette is built with 'R CMD build'...
* Checking package installation calls in R code...
* Checking for library/require of DuplexDiscovereR...
* Checking coding practice...
* Checking parsed R code in R directory, examples, vignettes...
* Checking function lengths...
    * NOTE: The recommended function length is 50 lines or less. There
      are 16 functions greater than 50 lines.
* Checking man page documentation...
    * NOTE: Usage of dontrun{} / donttest{} tags found in man page
      examples. 2% of man pages use at least one of these tags.
    * NOTE: Use donttest{} instead of dontrun{}.
* Checking package NEWS...
* Checking unit tests...
* Checking skip_on_bioc() in tests...
* Checking formatting of DESCRIPTION, NAMESPACE, man pages, R source,
  and vignette source...
    * NOTE: Consider shorter lines; 347 lines (8%) are > 80 characters
      long.
    * NOTE: Consider multiples of 4 spaces for line indents; 25 lines
      (1%) are not.
    See https://contributions.bioconductor.org/r-code.html
    See styler package: https://cran.r-project.org/package=styler as
      described in the BiocCheck vignette.
* Checking if package already exists in CRAN...
* Checking if new package already exists in Bioconductor...
* Checking for bioc-devel mailing list subscription...
    Maintainer is subscribed to bioc-devel.
* Checking for support site registration...
    Maintainer is registered at support site.
    Package is in the Support Site Watched Tags.

─ BiocCheck results ──
0 ERRORS | 0 WARNINGS | 6 NOTES

See the DuplexDiscovereR.BiocCheck folder and run
    browseVignettes(package = 'BiocCheck')
for details.

===============================

 R CMD BUILD

===============================

>>>>>>> 
>>>>>>> INSTALLATION WITH 'R CMD INSTALL --preclean --no-multiarch --library=libdir DuplexDiscovereR_0.99.0.tar.gz'
>>>>>>> 

* installing *source* package ‘DuplexDiscovereR’ ...
** using staged installation
** R
** data
** inst
** byte-compile and prepare package for lazy loading
** help
*** installing help indices
** building package indices
** installing vignettes
** testing if installed package can be loaded from temporary location
** testing if installed package can be loaded from final location
** testing if installed package keeps a record of temporary installation path
* DONE (DuplexDiscovereR)