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### Running command:
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###   /home/biocbuild/bbs-3.11-bioc/R/bin/R CMD check --install=check:compartmap.install-out.txt --library=/home/biocbuild/bbs-3.11-bioc/R/library --no-vignettes --timings compartmap_1.6.0.tar.gz
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* using log directory ‘/home/biocbuild/bbs-3.11-bioc/meat/compartmap.Rcheck’
* using R version 4.0.3 (2020-10-10)
* using platform: x86_64-pc-linux-gnu (64-bit)
* using session charset: UTF-8
* using option ‘--no-vignettes’
* checking for file ‘compartmap/DESCRIPTION’ ... OK
* checking extension type ... Package
* this is package ‘compartmap’ version ‘1.6.0’
* package encoding: UTF-8
* 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 ‘compartmap’ 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 ... NOTE
package 'methods' is used but not declared
* checking S3 generic/method consistency ... OK
* checking replacement functions ... OK
* checking foreign function calls ... OK
* checking R code for possible problems ... NOTE
.arraycompartments: no visible global function definition for
  ‘seqlevels’
.createCorMatrix: no visible global function definition for ‘seqlevels’
.createCorMatrix: no visible global function definition for
  ‘seqlevels<-’
.createCorMatrix: no visible global function definition for ‘cor’
.extractAB: no visible global function definition for ‘cor’
.extractAB: no visible global function definition for ‘colSums2’
.fsvd: no visible global function definition for ‘rnorm’
.getFirstPC: no visible global function definition for ‘cor’
.getFirstPCarray: no visible global function definition for ‘rowMeans2’
.getPairedAllChrsArray: no visible global function definition for
  ‘seqlevels’
.removeBadBins: no visible global function definition for ‘colAlls’
.returnBinnedMatrix : bin2D: no visible global function definition for
  ‘median’
.returnBinnedMatrix: no visible global function definition for
  ‘seqlengths’
.returnBinnedMatrix: no visible global function definition for
  ‘standardChromosomes’
.returnBinnedMatrix: no visible global function definition for
  ‘seqlengths<-’
.returnBinnedMatrix: no visible global function definition for
  ‘seqlevels’
.returnBinnedMatrix: no visible global function definition for
  ‘subjectHits’
.run_examples: no visible global function definition for ‘data’
.run_examples: no visible binding for global variable
  ‘bulkATAC_raw_filtered_chr14’
.run_examples: no visible binding for global variable
  ‘filtered.data.chr14’
.run_examples: no visible binding for global variable
  ‘meth_array_450k_chr14’
.run_examples: no visible binding for global variable
  ‘array.data.chr14’
.unitarize: no visible global function definition for ‘median’
getBinMatrix: no visible global function definition for ‘seqlengths’
getBinMatrix: no visible global function definition for ‘IRanges’
getCompartments: no visible global function definition for ‘seqlevels’
getCorMatrix: no visible global function definition for ‘cor’
plotAB: no visible global function definition for ‘barplot’
Undefined global functions or variables:
  IRanges array.data.chr14 barplot bulkATAC_raw_filtered_chr14 colAlls
  colSums2 cor data filtered.data.chr14 median meth_array_450k_chr14
  rnorm rowMeans2 seqlengths seqlengths<- seqlevels seqlevels<-
  standardChromosomes subjectHits
Consider adding
  importFrom("graphics", "barplot")
  importFrom("stats", "cor", "median", "rnorm")
  importFrom("utils", "data")
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 ... WARNING
Codoc mismatches from documentation object 'getABSignal':
getABSignal
  Code: function(x, k = 2, iter = 2, squeeze = FALSE)
  Docs: function(x, k = 5, iter = 2, squeeze = FALSE)
  Mismatches in argument default values:
    Name: 'k' Code: 2 Docs: 5

* 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 installed files from ‘inst/doc’ ... OK
* checking files in ‘vignettes’ ... OK
* checking examples ... OK
Examples with CPU (user + system) or elapsed time > 5s
                  user system elapsed
getATACABsignal 20.028   0.10  20.130
getCompartments 17.463   0.06  17.526
* 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 WARNING, 2 NOTEs
See
  ‘/home/biocbuild/bbs-3.11-bioc/meat/compartmap.Rcheck/00check.log’
for details.

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###
### Running command:
###
###   /home/biocbuild/bbs-3.11-bioc/R/bin/R CMD INSTALL compartmap
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* installing to library ‘/home/biocbuild/bbs-3.11-bioc/R/library’
* installing *source* package ‘compartmap’ ...
** using staged installation
** R
** data
** inst
** byte-compile and prepare package for lazy loading
** help
*** installing help indices
** building package indices
** installing vignettes
   ‘compartmap_vignette.Rmd’ using ‘UTF-8’ 
** 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 (compartmap)