##############################################################################
##############################################################################
###
### Running command:
###
###   C:\Users\biocbuild\bbs-3.11-bioc\R\bin\R.exe CMD check --force-multiarch --install=check:MethylSeekR.install-out.txt --library=C:\Users\biocbuild\bbs-3.11-bioc\R\library --no-vignettes --timings MethylSeekR_1.28.0.tar.gz
###
##############################################################################
##############################################################################


* using log directory 'C:/Users/biocbuild/bbs-3.11-bioc/meat/MethylSeekR.Rcheck'
* using R version 4.0.3 (2020-10-10)
* using platform: x86_64-w64-mingw32 (64-bit)
* using session charset: ISO8859-1
* using option '--no-vignettes'
* checking for file 'MethylSeekR/DESCRIPTION' ... OK
* checking extension type ... Package
* this is package 'MethylSeekR' version '1.28.0'
* 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 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 R files for non-ASCII characters ... OK
* checking R files for syntax errors ... OK
* loading checks for arch 'i386'
** 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
* loading checks for arch 'x64'
** 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
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 '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 'queryHits'
calculateFDRs : <anonymous>: no visible global function definition for
  'Rle'
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'
plotFinalSegmentation: no visible global function definition for 'Rle'
removeSNPs: no visible global function definition for 'queryHits'
segmentUMRsLMRs : <anonymous>: no visible global function definition
  for 'Rle'
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 'DataFrame'
segmentUMRsLMRs: no visible global function definition for
  'colorRampPalette'
Undefined global functions or variables:
  DataFrame Rle colorRampPalette nrun predict queryHits runValue
  subjectHits
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 ...
** running examples for arch 'i386' ... OK
Examples with CPU (user + system) or elapsed time > 5s
                             user system elapsed
MethylSeekR-package         73.25   4.64   91.66
plotPMDSegmentation         48.22   2.01   50.24
segmentPMDs                 42.74   1.03   43.77
savePMDSegments             40.47   2.05   42.52
plotAlphaDistributionOneChr 12.84   0.27   13.10
calculateFDRs               10.18   0.89   22.95
** running examples for arch 'x64' ... OK
Examples with CPU (user + system) or elapsed time > 5s
                             user system elapsed
MethylSeekR-package         48.34   3.61   66.54
segmentPMDs                 34.67   1.83   36.50
savePMDSegments             32.70   1.87   34.64
plotPMDSegmentation         31.84   1.59   33.46
calculateFDRs                7.91   0.94   20.88
plotAlphaDistributionOneChr  6.49   0.26    6.75
* 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: 3 NOTEs
See
  'C:/Users/biocbuild/bbs-3.11-bioc/meat/MethylSeekR.Rcheck/00check.log'
for details.

##############################################################################
##############################################################################
###
### Running command:
###
###   C:\cygwin\bin\curl.exe -O https://malbec2.bioconductor.org/BBS/3.11/bioc/src/contrib/MethylSeekR_1.28.0.tar.gz && rm -rf MethylSeekR.buildbin-libdir && mkdir MethylSeekR.buildbin-libdir && C:\Users\biocbuild\bbs-3.11-bioc\R\bin\R.exe CMD INSTALL --merge-multiarch --build --library=MethylSeekR.buildbin-libdir MethylSeekR_1.28.0.tar.gz && C:\Users\biocbuild\bbs-3.11-bioc\R\bin\R.exe CMD INSTALL MethylSeekR_1.28.0.zip && rm MethylSeekR_1.28.0.tar.gz MethylSeekR_1.28.0.zip
###
##############################################################################
##############################################################################


  % Total    % Received % Xferd  Average Speed   Time    Time     Time  Current
                                 Dload  Upload   Total   Spent    Left  Speed

  0     0    0     0    0     0      0      0 --:--:-- --:--:-- --:--:--     0
  0     0    0     0    0     0      0      0 --:--:-- --:--:-- --:--:--     0
100 1074k  100 1074k    0     0  13.7M      0 --:--:-- --:--:-- --:--:-- 14.7M

install for i386

* installing *source* package 'MethylSeekR' ...
** using staged installation
** R
** inst
** byte-compile and prepare package for lazy loading
** help
*** installing help indices
  converting help for package 'MethylSeekR'
    finding HTML links ... done
    MethylSeekR-package                     html  
    calculateFDRs                           html  
    plotAlphaDistributionOneChr             html  
    plotFinalSegmentation                   html  
    plotPMDSegmentation                     html  
    readMethylome                           html  
    readSNPTable                            html  
    removeSNPs                              html  
    savePMDSegments                         html  
    saveUMRLMRSegments                      html  
    segmentPMDs                             html  
    segmentUMRsLMRs                         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

install for x64

* installing *source* package 'MethylSeekR' ...
** testing if installed package can be loaded
* MD5 sums
packaged installation of 'MethylSeekR' as MethylSeekR_1.28.0.zip
* DONE (MethylSeekR)
* installing to library 'C:/Users/biocbuild/bbs-3.11-bioc/R/library'
package 'MethylSeekR' successfully unpacked and MD5 sums checked