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### Running command:
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###   /home/biocbuild/bbs-3.20-bioc/R/bin/R CMD check --install=check:BSgenome.install-out.txt --library=/home/biocbuild/bbs-3.20-bioc/R/site-library --timings BSgenome_1.73.0.tar.gz
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* using log directory ‘/home/biocbuild/bbs-3.20-bioc/meat/BSgenome.Rcheck’
* using R version 4.4.0 RC (2024-04-16 r86468)
* using platform: x86_64-pc-linux-gnu
* R was compiled by
    gcc (Ubuntu 11.4.0-1ubuntu1~22.04) 11.4.0
    GNU Fortran (Ubuntu 11.4.0-1ubuntu1~22.04) 11.4.0
* running under: Ubuntu 22.04.4 LTS
* using session charset: UTF-8
* checking for file ‘BSgenome/DESCRIPTION’ ... OK
* this is package ‘BSgenome’ version ‘1.73.0’
* package encoding: UTF-8
* checking package namespace information ... OK
* checking package dependencies ... NOTE
Depends: includes the non-default packages:
  'BiocGenerics', 'S4Vectors', 'IRanges', 'GenomeInfoDb',
  'GenomicRanges', 'Biostrings', 'BiocIO', 'rtracklayer'
Adding so many packages to the search path is excessive and importing
selectively is preferable.
* 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 ‘BSgenome’ can be installed ... OK
* checking installed package size ... NOTE
  installed size is  7.1Mb
  sub-directories of 1Mb or more:
    R         1.6Mb
    extdata   5.2Mb
* 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 ... NOTE
':::' calls which should be '::':
  ‘S4Vectors:::makeClassinfoRowForCompactPrinting’
  ‘S4Vectors:::makePrettyMatrixForCompactPrinting’
  See the note in ?`:::` about the use of this operator.
Unexported objects imported by ':::' calls:
  ‘rtracklayer:::.DNAString_to_twoBit’ ‘rtracklayer:::.TwoBits_export’
  ‘rtracklayer:::checkArgFormat’ ‘rtracklayer:::twoBitPath’
  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 ... OK
* checking Rd files ... OK
* checking Rd metadata ... OK
* checking Rd cross-references ... OK
* checking for missing documentation entries ... WARNING
Undocumented code objects:
  ‘MaskedBSgenome’ ‘OnDiskLongTable’ ‘OnDiskLongTable_old’
  ‘as.data.frame.BSgenomeViews’ ‘batchsizes’ ‘blocksizes’ ‘breakpoints’
  ‘getBatchesByOverlapsFromOnDiskLongTable’
  ‘getBatchesBySeqnameFromOnDiskLongTable’
  ‘getBatchesFromOnDiskLongTable’ ‘getBatchesFromOnDiskLongTable_old’
  ‘getRowsByIdFromOnDiskLongTable’
  ‘getRowsByIndexFromOnDiskLongTable_old’ ‘getRowsFromOnDiskLongTable’
  ‘saveAsOnDiskLongTable_old’ ‘saveRowidsForOnDiskLongTable_old’
  ‘spatialIndex’ ‘writeOnDiskLongTable’ ‘writeOnDiskLongTableRowids’
Undocumented S4 classes:
  ‘OnDiskLongTable_old’ ‘GRanges_OR_NULL’ ‘MaskedBSgenome’
  ‘OnDiskLongTable’
Undocumented S4 methods:
  generic '[' and siglist 'XStringSet,GRangesList,ANY,ANY'
  generic '[' and siglist 'XStringSet,GenomicRanges,ANY,ANY'
  generic '[[' and siglist 'BSgenome,ANY,ANY'
  generic 'batchsizes' and siglist 'OnDiskLongTable'
  generic 'blocksizes' and siglist 'OnDiskLongTable_old'
  generic 'breakpoints' and siglist 'OnDiskLongTable'
  generic 'breakpoints' and siglist 'OnDiskLongTable_old'
  generic 'coerce' and siglist 'RdsCollection,RdsNamedSequences'
  generic 'dim' and siglist 'OnDiskLongTable'
  generic 'dim' and siglist 'OnDiskLongTable_old'
  generic 'dimnames' and siglist 'OnDiskLongTable'
  generic 'dimnames' and siglist 'OnDiskLongTable_old'
  generic 'dimnames' and siglist 'XtraSNPlocs'
  generic 'extractAt' and siglist 'BSgenome'
  generic 'length' and siglist 'OnDiskNamedSequences'
  generic 'names' and siglist 'FastaNamedSequences'
  generic 'names' and siglist 'TwobitNamedSequences'
  generic 'seqinfo' and siglist 'FastaNamedSequences'
  generic 'seqinfo' and siglist 'RdaNamedSequences'
  generic 'seqinfo' and siglist 'RdsNamedSequences'
  generic 'seqinfo' and siglist 'TwobitNamedSequences'
  generic 'seqnames' and siglist 'OnDiskNamedSequences'
  generic 'show' and siglist 'OnDiskLongTable'
  generic 'show' and siglist 'OnDiskLongTable_old'
  generic 'show' and siglist 'OnDiskNamedSequences'
  generic 'spatialIndex' and siglist 'OnDiskLongTable'
All user-level objects in a package (including S4 classes and methods)
should have documentation entries.
See chapter ‘Writing R documentation files’ in the ‘Writing R
Extensions’ manual.
* checking for code/documentation mismatches ... OK
* checking Rd \usage sections ... OK
* checking Rd contents ... OK
* checking for unstated dependencies in examples ... OK
* checking files in ‘vignettes’ ... OK
* checking examples ... OK
Examples with CPU (user + system) or elapsed time > 5s
                      user system elapsed
SNPlocs-class       38.757  4.690  44.620
BSgenome-utils      19.828  0.412  20.264
BSgenomeViews-class 12.575  1.311  13.914
BSgenome-class      11.217  0.785  12.133
injectSNPs           9.677  2.232  11.948
XtraSNPlocs-class    5.662  0.386   6.056
getSeq-methods       5.534  0.496   6.029
export-methods       4.332  0.724   5.057
* 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 WARNING, 3 NOTEs
See
  ‘/home/biocbuild/bbs-3.20-bioc/meat/BSgenome.Rcheck/00check.log’
for details.