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###
### Running command:
###
###   /home/biocbuild/R/R-4.3.1/bin/R CMD check --install=check:BSgenome.install-out.txt --library=/home/biocbuild/R/R-4.3.1/site-library --no-vignettes --timings BSgenome_1.70.1.tar.gz
###
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* using log directory ‘/home/biocbuild/bbs-3.18-bioc/meat/BSgenome.Rcheck’
* using R version 4.3.1 (2023-06-16)
* using platform: aarch64-unknown-linux-gnu (64-bit)
* R was compiled by
    gcc (GCC) 10.3.1
    GNU Fortran (GCC) 10.3.1
* running under: openEuler 22.03 (LTS-SP1)
* using session charset: UTF-8
* using option ‘--no-vignettes’
* checking for file ‘BSgenome/DESCRIPTION’ ... OK
* this is package ‘BSgenome’ version ‘1.70.1’
* 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 ... NOTE
Found the following non-portable file path:
  BSgenome/inst/extdata/GentlemanLab/BSgenome.Gmellonella.NCBI.ASM364042v2-tools/fasta_to_sorted_2bit.R

Tarballs are only required to store paths of up to 100 bytes and cannot
store those of more than 256 bytes, with restrictions including to 100
bytes for the final component.
See section ‘Package structure’ in the ‘Writing R Extensions’ manual.
* checking for sufficient/correct file permissions ... OK
* checking whether package ‘BSgenome’ can be installed ... OK
* checking installed package size ... NOTE
  installed size is  8.0Mb
  sub-directories of 1Mb or more:
    R         1.7Mb
    extdata   6.0Mb
* 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 ... NOTE
Found the following CITATION file in a non-standard place:
  inst/extdata/GentlemanLab/BSgenome.Creinhardtii.JGI.v5.6-tools/CITATION
Most likely ‘inst/CITATION’ should be used instead.
* 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 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’
  ‘forgeMaskedBSgenomeDataPkg’
  ‘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 'forgeMaskedBSgenomeDataPkg' and siglist
    'MaskedBSgenomeDataPkgSeed'
  generic 'forgeMaskedBSgenomeDataPkg' and siglist 'character'
  generic 'forgeMaskedBSgenomeDataPkg' and siglist 'list'
  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 ... ERROR
Running examples in ‘BSgenome-Ex.R’ failed
The error most likely occurred in:

> base::assign(".ptime", proc.time(), pos = "CheckExEnv")
> ### Name: BSgenome-utils
> ### Title: BSgenome utilities
> ### Aliases: BSgenome-utils vmatchPattern,BSgenome-method
> ###   vcountPattern,BSgenome-method vmatchPDict,BSgenome-method
> ###   vcountPDict,BSgenome-method matchPWM,BSgenome-method
> ###   countPWM,BSgenome-method
> ### Keywords: methods utilities
> 
> ### ** Examples
> 
> library(BSgenome.Celegans.UCSC.ce2)
> data(HNF4alpha)
> 
> pattern <- consensusString(HNF4alpha)
> vmatchPattern(pattern, Celegans, fixed="subject")
GRanges object with 123 ranges and 0 metadata columns:
        seqnames            ranges strand
           <Rle>         <IRanges>  <Rle>
    [1]     chrI   5249651-5249663      +
    [2]     chrI   5858867-5858879      +
    [3]     chrI   6956753-6956765      +
    [4]     chrI   8927423-8927435      +
    [5]     chrI   9260962-9260974      +
    ...      ...               ...    ...
  [119]     chrX   9436287-9436299      -
  [120]     chrX 10737397-10737409      -
  [121]     chrX 12030747-12030759      -
  [122]     chrX 13784772-13784784      -
  [123]     chrX 16717792-16717804      -
  -------
  seqinfo: 7 sequences (1 circular) from ce2 genome
> vcountPattern(pattern, Celegans, fixed="subject")
   seqname strand count
1     chrI      +     7
2     chrI      -     7
3    chrII      +    12
4    chrII      -     8
5   chrIII      +     8
6   chrIII      -     9
7    chrIV      +    15
8    chrIV      -     9
9     chrV      +     7
10    chrV      -    13
11    chrX      +    15
12    chrX      -    13
13    chrM      +     0
14    chrM      -     0
> 
> pdict <- PDict(HNF4alpha)
> vmatchPDict(pdict, Celegans)
GRanges object with 183 ranges and 1 metadata column:
        seqnames            ranges strand | index
           <Rle>         <IRanges>  <Rle> | <Rle>
    [1]     chrI 10714238-10714250      + |     1
    [2]     chrI   1746247-1746259      + |    33
    [3]     chrI 11509260-11509272      + |    39
    [4]     chrI   5249651-5249663      + |    48
    [5]     chrI   5442409-5442421      + |    64
    ...      ...               ...    ... .   ...
  [179]     chrX   8554427-8554439      - |    64
  [180]     chrX 16811413-16811425      - |    69
  [181]     chrX   8212498-8212510      - |    70
  [182]     chrX     758648-758660      - |    71
  [183]     chrX 12553584-12553596      - |    71
  -------
  seqinfo: 7 sequences (1 circular) from ce2 genome
> vcountPDict(pdict, Celegans)
DataFrame with 994 rows and 4 columns
    seqname strand     index count
      <Rle>  <Rle> <integer> <Rle>
1      chrI      +         1     1
2      chrI      +         2     0
3      chrI      +         3     0
4      chrI      +         4     0
5      chrI      +         5     0
...     ...    ...       ...   ...
990    chrM      -        67     0
991    chrM      -        68     0
992    chrM      -        69     0
993    chrM      -        70     0
994    chrM      -        71     0
> 
> pwm <- PWM(HNF4alpha)
> matchPWM(pwm, Celegans)
* 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: 1 ERROR, 1 WARNING, 5 NOTEs
See
  ‘/home/biocbuild/bbs-3.18-bioc/meat/BSgenome.Rcheck/00check.log’
for details.

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###
### Running command:
###
###   /home/biocbuild/R/R-4.3.1/bin/R CMD INSTALL BSgenome
###
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* installing to library ‘/home/biocbuild/R/R-4.3.1/site-library’
* installing *source* package ‘BSgenome’ ...
** using staged installation
** R
** 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 (BSgenome)