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### Running command:
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###   D:\biocbuild\bbs-3.15-bioc\R\bin\R.exe CMD check --no-multiarch --install=check:segmentSeq.install-out.txt --library=D:\biocbuild\bbs-3.15-bioc\R\library --no-vignettes --timings segmentSeq_2.29.1.tar.gz
###
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* using log directory 'D:/biocbuild/bbs-3.15-bioc/meat/segmentSeq.Rcheck'
* using R Under development (unstable) (2021-11-21 r81221)
* using platform: x86_64-w64-mingw32 (64-bit)
* using session charset: ISO8859-1
* using option '--no-vignettes'
* checking for file 'segmentSeq/DESCRIPTION' ... OK
* checking extension type ... Package
* this is package 'segmentSeq' version '2.29.1'
* 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 'segmentSeq' can be installed ... OK
* 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 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 ... 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 files in 'vignettes' ... OK
* checking examples ... OK
Examples with CPU (user + system) or elapsed time > 5s
                    user system elapsed
classifySeg        24.26   0.13   24.39
lociLikelihoods    13.39   0.00   14.89
heuristicSeg       11.00   0.01   11.01
plotGenome          8.39   0.04   10.39
segData-class       4.70   0.02    5.58
normaliseNC         3.83   0.66    5.44
segmentSeq-package  4.28   0.00    5.20
processAD           4.20   0.00    5.67
thresholdFinder     3.22   0.92    5.43
readMeths           3.21   0.69    5.56
* 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 NOTE
See
  'D:/biocbuild/bbs-3.15-bioc/meat/segmentSeq.Rcheck/00check.log'
for details.

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### Running command:
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###   D:\biocbuild\bbs-3.15-bioc\R\bin\R.exe CMD INSTALL segmentSeq
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* installing to library 'D:/biocbuild/bbs-3.15-bioc/R/library'
* installing *source* package 'segmentSeq' ...
** using staged installation
** R
** data
** inst
** byte-compile and prepare package for lazy loading
** help
*** installing help indices
  converting help for package 'segmentSeq'
    finding HTML links ... done
    SL                                      html  
    alignmentClass-class                    html  
    alignmentData-class                     html  
    alignmentMeth-class                     html  
    averageMethylationRegions               html  
    finding level-2 HTML links ... done

    classifySeg                             html  
    findChunks                              html  
    getCounts                               html  
    getOverlaps                             html  
    givenExpression                         html  
    hSL                                     html  
    heuristicSeg                            html  
    lociData-class                          html  
    lociLikelihoods                         html  
    mergeMethSegs                           html  
    methData-class                          html  
    normaliseNC                             html  
    plotGenome                              html  
    plotMeth                                html  
    plotMethDistribution                    html  
    processAD                               html  
    readMethods                             html  
    readMeths                               html  
    segClass-class                          html  
    segData-class                           html  
    segMeth-class                           html  
    segmentSeq-package                      html  
    selectLoci                              html  
    summariseLoci                           html  
    thresholdFinder                         html  
** 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 (segmentSeq)
Making 'packages.html' ...Warning in packageDescription(i, lib.loc = lib, fields = "Title", encoding = "UTF-8") :
  DESCRIPTION file of package 'MouseFM' is missing or broken
Warning in packageDescription(i, lib.loc = lib, fields = "Title", encoding = "UTF-8") :
  DESCRIPTION file of package 'SMAD' is missing or broken
 done