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### Running command:
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###   /home/biocbuild/R/R-beta-2024-04-15_r86425/bin/R CMD check --install=check:MethylSeekR.install-out.txt --library=/home/biocbuild/R/R-beta-2024-04-15_r86425/site-library --no-vignettes --timings MethylSeekR_1.44.0.tar.gz
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* using log directory ‘/home/biocbuild/bbs-3.19-bioc/meat/MethylSeekR.Rcheck’
* using R version 4.4.0 beta (2024-04-15 r86425)
* using platform: aarch64-unknown-linux-gnu
* 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 ‘MethylSeekR/DESCRIPTION’ ... OK
* checking extension type ... Package
* this is package ‘MethylSeekR’ version ‘1.44.0’
* 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 ‘MethylSeekR’ can be installed ... OK
* checking installed package size ... OK
* checking package directory ... OK
* checking ‘build’ directory ... OK
* checking DESCRIPTION meta-information ... NOTE
Malformed Description field: should contain one or more complete sentences.
Package listed in more than one of Depends, Imports, Suggests, Enhances:
  ‘parallel’
A package should be listed in only one of these fields.
* 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
Namespace in Imports field not imported from: ‘geneplotter’
  All declared Imports should be used.
Package in Depends field not imported from: ‘rtracklayer’
  These packages need to be imported from (in the NAMESPACE file)
  for when this namespace is loaded but not attached.
* checking S3 generic/method consistency ... OK
* checking replacement functions ... OK
* checking foreign function calls ... OK
* checking R code for possible problems ... NOTE
PMDviterbiSegmentation : <anonymous>: no visible global function
  definition for ‘values’
PMDviterbiSegmentation : <anonymous>: no visible global function
  definition for ‘predict’
PMDviterbiSegmentation : <anonymous>: no visible global function
  definition for ‘Rle’
PMDviterbiSegmentation : <anonymous>: no visible global function
  definition for ‘runValue’
calculateAlphaDistr : <anonymous>: no visible global function
  definition for ‘Rle’
calculateFDRs: no visible global function definition for ‘values’
calculateFDRs: no visible global function definition for ‘queryHits’
calculateFDRs: no visible global function definition for ‘values<-’
calculateFDRs : <anonymous>: no visible global function definition for
  ‘Rle’
calculateFDRs : <anonymous>: no visible global function definition for
  ‘values’
calculateFDRs : <anonymous>: no visible global function definition for
  ‘runValue’
createGRangesObjectPMDSegmentation : <anonymous>: no visible global
  function definition for ‘Rle’
createGRangesObjectPMDSegmentation : <anonymous>: no visible global
  function definition for ‘nrun’
createGRangesObjectPMDSegmentation : <anonymous>: no visible global
  function definition for ‘runValue’
plotAlphaDistributionOneChr: no visible global function definition for
  ‘values’
plotFinalSegmentation: no visible global function definition for
  ‘values’
plotFinalSegmentation: no visible global function definition for ‘Rle’
plotPMDSegmentation: no visible global function definition for ‘values’
readMethylome: no visible global function definition for ‘values’
removeSNPs: no visible global function definition for ‘queryHits’
savePMDSegments: no visible global function definition for ‘values’
saveUMRLMRSegments: no visible global function definition for ‘values’
segmentUMRsLMRs: no visible global function definition for ‘values’
segmentUMRsLMRs : <anonymous>: no visible global function definition
  for ‘Rle’
segmentUMRsLMRs : <anonymous>: no visible global function definition
  for ‘values’
segmentUMRsLMRs : <anonymous>: no visible global function definition
  for ‘runValue’
segmentUMRsLMRs: no visible global function definition for ‘queryHits’
segmentUMRsLMRs: no visible global function definition for
  ‘subjectHits’
segmentUMRsLMRs: no visible global function definition for ‘Rle’
segmentUMRsLMRs: no visible global function definition for ‘values<-’
segmentUMRsLMRs: no visible global function definition for ‘DataFrame’
segmentUMRsLMRs: no visible global function definition for
  ‘colorRampPalette’
trainPMDHMM: no visible global function definition for ‘values’
Undefined global functions or variables:
  DataFrame Rle colorRampPalette nrun predict queryHits runValue
  subjectHits values values<-
Consider adding
  importFrom("grDevices", "colorRampPalette")
  importFrom("stats", "predict")
to your NAMESPACE file.
* 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 files in ‘vignettes’ ... OK
* checking examples ... OK
Examples with CPU (user + system) or elapsed time > 5s
                              user system elapsed
MethylSeekR-package         66.444  0.758  80.596
plotPMDSegmentation         42.834  0.060  42.967
savePMDSegments             42.428  0.140  42.645
segmentPMDs                 41.792  0.076  41.947
calculateFDRs               10.633  0.183  23.318
plotAlphaDistributionOneChr  7.671  0.032   7.717
* 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
  ‘/home/biocbuild/bbs-3.19-bioc/meat/MethylSeekR.Rcheck/00check.log’
for details.

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###
### Running command:
###
###   /home/biocbuild/R/R-beta-2024-04-15_r86425/bin/R CMD INSTALL MethylSeekR
###
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* installing to library ‘/home/biocbuild/R/R-beta-2024-04-15_r86425/site-library’
* installing *source* package ‘MethylSeekR’ ...
** 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 (MethylSeekR)