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### Running command:
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###   /home/biocbuild/bbs-3.19-bioc/R/bin/R CMD check --install=check:segmentSeq.install-out.txt --library=/home/biocbuild/bbs-3.19-bioc/R/site-library --timings segmentSeq_2.37.0.tar.gz
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* using log directory ‘/home/biocbuild/bbs-3.19-bioc/meat/segmentSeq.Rcheck’
* using R Under development (unstable) (2023-10-22 r85388)
* 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 22.04.3 LTS
* using session charset: UTF-8
* checking for file ‘segmentSeq/DESCRIPTION’ ... OK
* checking extension type ... Package
* this is package ‘segmentSeq’ version ‘2.37.0’
* 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 ‘segmentSeq’ can be installed ... WARNING
Found the following significant warnings:
  Warning: Package 'baySeq' is deprecated and will be removed from Bioconductor
See ‘/home/biocbuild/bbs-3.19-bioc/meat/segmentSeq.Rcheck/00install.out’ for details.
* 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 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 ... OK
* checking S3 generic/method consistency ... OK
* checking replacement functions ... OK
* checking foreign function calls ... OK
* checking R code for possible problems ... NOTE
heuristicSeg : <anonymous>: no visible binding for global variable
  ‘sDP’
Undefined global functions or variables:
  sDP
* checking Rd files ... OK
* 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 ... NOTE
Argument items with no description in Rd file 'plotMeth.Rd':
  ‘loci’
* 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 files in ‘vignettes’ ... OK
* checking examples ... OK
Examples with CPU (user + system) or elapsed time > 5s
                      user system elapsed
classifySeg         33.379  0.133  33.514
lociLikelihoods     14.616  0.000  14.618
heuristicSeg        14.549  0.000  14.549
plotGenome           7.788  0.008   7.797
getCounts            5.736  0.012   5.749
alignmentData-class  4.584  0.759   5.345
* checking for unstated dependencies in vignettes ... OK
* checking package vignettes in ‘inst/doc’ ... OK
* checking running R code from vignettes ...
  ‘methylationAnalysis.Rnw’... OK
  ‘segmentSeq.Rnw’... OK
 OK
* checking re-building of vignette outputs ... OK
* checking PDF version of manual ... OK
* DONE

Status: 1 WARNING, 2 NOTEs
See
  ‘/home/biocbuild/bbs-3.19-bioc/meat/segmentSeq.Rcheck/00check.log’
for details.

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### Running command:
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###   /home/biocbuild/bbs-3.19-bioc/R/bin/R CMD INSTALL segmentSeq
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* installing to library ‘/home/biocbuild/bbs-3.19-bioc/R/site-library’
* installing *source* package ‘segmentSeq’ ...
** using staged installation
** R
** data
** inst
** byte-compile and prepare package for lazy loading
Warning message:
Package 'baySeq' is deprecated and will be removed from Bioconductor
  version 3.19 
** help
*** installing help indices
** building package indices
** installing vignettes
** testing if installed package can be loaded from temporary location
Warning: Package 'baySeq' is deprecated and will be removed from Bioconductor
  version 3.19
** testing if installed package can be loaded from final location
Warning: Package 'baySeq' is deprecated and will be removed from Bioconductor
  version 3.19
** testing if installed package keeps a record of temporary installation path
* DONE (segmentSeq)