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### Running command:
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###   E:\biocbuild\bbs-3.21-bioc\R\bin\R.exe CMD check --no-multiarch --install=check:bsseq.install-out.txt --library=E:\biocbuild\bbs-3.21-bioc\R\library --no-vignettes --timings bsseq_1.43.0.tar.gz
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* using log directory 'E:/biocbuild/bbs-3.21-bioc/meat/bsseq.Rcheck'
* using R Under development (unstable) (2024-10-26 r87273 ucrt)
* using platform: x86_64-w64-mingw32
* R was compiled by
    gcc.exe (GCC) 13.2.0
    GNU Fortran (GCC) 13.2.0
* running under: Windows Server 2022 x64 (build 20348)
* using session charset: UTF-8
* using option '--no-vignettes'
* checking for file 'bsseq/DESCRIPTION' ... OK
* this is package 'bsseq' version '1.43.0'
* 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 'bsseq' can be installed ... OK
* used C++ compiler: 'G__~1.EXE (GCC) 13.3.0'
* checking installed package size ... OK
* 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 dependencies in R code ... NOTE
Unexported objects imported by ':::' calls:
  'BiocGenerics:::replaceSlots'
  'DelayedArray:::get_verbose_block_processing'
  'DelayedArray:::normarg_grid'
  'GenomicRanges:::.extract_groups_from_GenomicRanges'
  'GenomicRanges:::.get_circle_length'
  'GenomicRanges:::extraColumnSlotNames'
  'IRanges:::.shift_ranges_in_groups_to_first_circle'
  'S4Vectors:::normarg_names' 'S4Vectors:::numeric2integer'
  'S4Vectors:::sapply_isNULL' 'data.table:::funique'
  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 ... NOTE
Found the following Rd file(s) with Rd \link{} targets missing package
anchors:
  BSmooth.Rd: BiocParallelParam-class, SerialParam-class,
    MulticoreParam-class, SnowParam-class, BatchtoolsParam-class,
    getHDF5DumpChunkDim, getHDF5DumpCompressionLevel, HDF5Array-class,
    getAutoRealizationBackend, HDF5Matrix-class, RealizationSink-class
  BSseq-class.Rd: RangedSummarizedExperiment-class,
    setAutoRealizationBackend
  BSseq.Rd: DataFrame-class, GRanges-class, DelayedMatrix-class,
    HDF5Matrix-class
  BSseqStat-class.Rd: DelayedMatrix-class, HDF5Matrix-class
  BSseqTstat-class.Rd: DelayedMatrix-class, HDF5Matrix-class
  findLoci.Rd: BSgenome-class, DNAStringSet-class, GRanges-class
  getCoverage.Rd: DelayedMatrix-class
  getMeth.Rd: DelayedMatrix-class
  read.bismark.Rd: GenomicRanges-class, DataFrame-class,
    BiocParallelParam-class, SerialParam-class, MulticoreParam-class,
    SnowParam-class, BatchtoolsParam-class, getHDF5DumpChunkDim,
    getHDF5DumpCompressionLevel, HDF5Array-class,
    getAutoRealizationBackend, HDF5Matrix-class, RealizationSink-class
Please provide package anchors for all Rd \link{} targets not in the
package itself and the base packages.
* 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 line endings in C/C++/Fortran sources/headers ... OK
* checking compiled code ... NOTE
Note: information on .o files for x64 is not available
File 'E:/biocbuild/bbs-3.21-bioc/R/library/bsseq/libs/x64/bsseq.dll':
  Found '_exit', possibly from '_exit' (C)
  Found 'abort', possibly from 'abort' (C), 'runtime' (Fortran)
  Found 'exit', possibly from 'exit' (C), 'stop' (Fortran)

Compiled code should not call entry points which might terminate R nor
write to stdout/stderr instead of to the console, nor use Fortran I/O
nor system RNGs nor [v]sprintf. The detected symbols are linked into
the code but might come from libraries and not actually be called.

See 'Writing portable packages' in the 'Writing R Extensions' manual.
* checking files in 'vignettes' ... OK
* checking examples ... OK
Examples with CPU (user + system) or elapsed time > 5s
              user system elapsed
getMeth       7.78   1.48    9.31
findLoci      8.18   0.34    8.53
BSmooth.tstat 7.80   0.60    8.85
getCoverage   5.88   0.27    6.17
BSseq-class   5.02   0.19   40.84
read.bismark  1.39   0.05   17.48
* 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 running R code from vignettes ... SKIPPED
* checking re-building of vignette outputs ... SKIPPED
* checking PDF version of manual ... OK
* DONE

Status: 3 NOTEs
See
  'E:/biocbuild/bbs-3.21-bioc/meat/bsseq.Rcheck/00check.log'
for details.