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### Running command:
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###   /Library/Frameworks/R.framework/Resources/bin/R CMD check --install=check:wavClusteR.install-out.txt --library=/Library/Frameworks/R.framework/Resources/library --no-vignettes --timings wavClusteR_2.41.0.tar.gz
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* using log directory ‘/Users/biocbuild/bbs-3.21-bioc/meat/wavClusteR.Rcheck’
* using R Under development (unstable) (2024-11-20 r87352)
* using platform: aarch64-apple-darwin20
* R was compiled by
    Apple clang version 14.0.0 (clang-1400.0.29.202)
    GNU Fortran (GCC) 12.2.0
* running under: macOS Ventura 13.7.1
* using session charset: UTF-8
* using option ‘--no-vignettes’
* checking for file ‘wavClusteR/DESCRIPTION’ ... OK
* checking extension type ... Package
* this is package ‘wavClusteR’ version ‘2.41.0’
* checking package namespace information ... OK
* checking package dependencies ...Warning: unable to access index for repository https://CRAN.R-project.org/src/contrib:
  cannot open URL 'https://CRAN.R-project.org/src/contrib/PACKAGES'
 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 ‘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 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 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’
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 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 ... NOTE
Found the following Rd file(s) with Rd \link{} targets missing package
anchors:
  filterClusters.Rd: coverage
  getClusters.Rd: coverage
Please provide package anchors for all Rd \link{} targets not in the
package itself and the base packages.
* 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
* 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
  ‘/Users/biocbuild/bbs-3.21-bioc/meat/wavClusteR.Rcheck/00check.log’
for details.

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### Running command:
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###   /Library/Frameworks/R.framework/Resources/bin/R CMD INSTALL wavClusteR
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* installing to library ‘/Library/Frameworks/R.framework/Versions/4.5-arm64/Resources/library’
* installing *source* package ‘wavClusteR’ ...
** using staged installation
** R
** data
** 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 (wavClusteR)