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###
### Running command:
###
###   C:\Users\biocbuild\bbs-3.11-bioc\R\bin\R.exe CMD check --force-multiarch --install=check:wavClusteR.install-out.txt --library=C:\Users\biocbuild\bbs-3.11-bioc\R\library --no-vignettes --timings wavClusteR_2.22.0.tar.gz
###
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* using log directory 'C:/Users/biocbuild/bbs-3.11-bioc/meat/wavClusteR.Rcheck'
* using R version 4.0.0 (2020-04-24)
* using platform: x86_64-w64-mingw32 (64-bit)
* using session charset: ISO8859-1
* using option '--no-vignettes'
* checking for file 'wavClusteR/DESCRIPTION' ... OK
* checking extension type ... Package
* this is package 'wavClusteR' version '2.22.0'
* checking package namespace information ... OK
* checking package dependencies ... NOTE
Package which this enhances but not available for checking: 'doMC'
* 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 'wavClusteR' 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
* 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
'library' or 'require' call to 'doMC' in package code.
  Please use :: or requireNamespace() instead.
  See section 'Suggested packages' in the 'Writing R Extensions' manual.
* checking S3 generic/method consistency ... OK
* checking replacement functions ... OK
* checking foreign function calls ... OK
* checking R code for possible problems ... NOTE
annotateClusters: no visible binding for global variable 'Percentage'
annotateClusters: no visible binding for global variable 'Compartment'
estimateFDR: no visible global function definition for 'DNAString'
estimateFDR: no visible global function definition for 'lines'
estimateFDR: no visible global function definition for 'legend'
estimateFDR: no visible global function definition for 'axis'
exportGR: no visible global function definition for 'write.table'
filterClustersCWT: no visible global function definition for
  'DNAString'
filterClustersMRN: no visible global function definition for
  'txtProgressBar'
filterClustersMRN: no visible global function definition for
  'setTxtProgressBar'
getClustersCWT: no visible global function definition for
  'registerDoMC'
getClustersCWT: no visible global function definition for 'seqlevels'
getClustersMRN: no visible global function definition for
  'registerDoMC'
getComplSubst: no visible global function definition for 'DNAStringSet'
getExpInterval: no visible global function definition for 'par'
getExpInterval: no visible global function definition for 'lines'
getExpInterval: no visible global function definition for 'legend'
getExpInterval: no visible global function definition for 'polygon'
getExpInterval: no visible global function definition for 'rect'
getExpInterval: no visible global function definition for 'text'
getLogOdd: no visible global function definition for 'dbinom'
getMetaCoverage: no visible global function definition for 'axis'
getMetaGene: no visible global function definition for 'grid'
getMetaGene: no visible global function definition for 'axis'
getMetaGene: no visible global function definition for 'abline'
getMetaTSS: no visible global function definition for 'grid'
getMetaTSS: no visible global function definition for 'axis'
plotSizeDistribution: no visible global function definition for 'hist'
plotStatistics: no visible binding for global variable 'panel.smooth'
plotStatistics : panelCor: no visible global function definition for
  'par'
plotStatistics : panelCor: no visible global function definition for
  'strwidth'
plotStatistics : panelCor: no visible global function definition for
  'text'
plotStatistics: no visible global function definition for 'pairs'
plotSubstitutions: no visible global function definition for 'par'
plotSubstitutions: no visible global function definition for 'barplot'
processChunk: no visible global function definition for 'extractAt'
processMD: no visible global function definition for 'registerDoMC'
readSortedBam: no visible global function definition for 'scanBamFlag'
readSortedBam : <anonymous>: no visible binding for global variable
  'rname'
readSortedBam : <anonymous>: no visible binding for global variable
  'qwidth'
Undefined global functions or variables:
  Compartment DNAString DNAStringSet Percentage abline axis barplot
  dbinom extractAt grid hist legend lines pairs panel.smooth par
  polygon qwidth rect registerDoMC rname scanBamFlag seqlevels
  setTxtProgressBar strwidth text txtProgressBar write.table
Consider adding
  importFrom("graphics", "abline", "axis", "barplot", "grid", "hist",
             "legend", "lines", "pairs", "panel.smooth", "par",
             "polygon", "rect", "strwidth", "text")
  importFrom("stats", "dbinom")
  importFrom("utils", "setTxtProgressBar", "txtProgressBar",
             "write.table")
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 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 ...
** running examples for arch 'i386' ... OK
Examples with CPU (user + system) or elapsed time > 5s
                 user system elapsed
annotateClusters 8.33   0.89    9.60
getMetaGene      5.25   0.00    5.25
** running examples for arch 'x64' ... OK
Examples with CPU (user + system) or elapsed time > 5s
                 user system elapsed
annotateClusters 5.61   0.08    5.69
* 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/wavClusteR.Rcheck/00check.log'
for details.

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###
### Running command:
###
###   C:\cygwin\bin\curl.exe -O https://malbec2.bioconductor.org/BBS/3.11/bioc/src/contrib/wavClusteR_2.22.0.tar.gz && rm -rf wavClusteR.buildbin-libdir && mkdir wavClusteR.buildbin-libdir && C:\Users\biocbuild\bbs-3.11-bioc\R\bin\R.exe CMD INSTALL --merge-multiarch --build --library=wavClusteR.buildbin-libdir wavClusteR_2.22.0.tar.gz && C:\Users\biocbuild\bbs-3.11-bioc\R\bin\R.exe CMD INSTALL wavClusteR_2.22.0.zip && rm wavClusteR_2.22.0.tar.gz wavClusteR_2.22.0.zip
###
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                                 Dload  Upload   Total   Spent    Left  Speed

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100  143k  100  143k    0     0  1115k      0 --:--:-- --:--:-- --:--:-- 1193k

install for i386

* installing *source* package 'wavClusteR' ...
** using staged installation
** R
** data
** inst
** byte-compile and prepare package for lazy loading
** help
*** installing help indices
  converting help for package 'wavClusteR'
    finding HTML links ... done
    FitMixtureModel                         html  
    annotateClusters                        html  
    estimateFDR                             html  
    exportClusters                          html  
    exportCoverage                          html  
    exportHighConfSub                       html  
    exportSequences                         html  
    filterClusters                          html  
    finding level-2 HTML links ... done

    getAllSub                               html  
    getClusters                             html  
    getExpInterval                          html  
    getHighConfSub                          html  
    getMetaCoverage                         html  
    getMetaGene                             html  
    getMetaTSS                              html  
    model                                   html  
    plotSizeDistribution                    html  
    plotStatistics                          html  
    plotSubstitutions                       html  
    readSortedBam                           html  
    wavClusteR-package                      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 'wavClusteR' ...
** testing if installed package can be loaded
* MD5 sums
packaged installation of 'wavClusteR' as wavClusteR_2.22.0.zip
* DONE (wavClusteR)
* installing to library 'C:/Users/biocbuild/bbs-3.11-bioc/R/library'
package 'wavClusteR' successfully unpacked and MD5 sums checked