##############################################################################
##############################################################################
###
### Running command:
###
###   C:\Users\biocbuild\bbs-3.11-bioc\R\bin\R.exe CMD check --force-multiarch --install=check:compartmap.install-out.txt --library=C:\Users\biocbuild\bbs-3.11-bioc\R\library --no-vignettes --timings compartmap_1.6.0.tar.gz
###
##############################################################################
##############################################################################


* using log directory 'C:/Users/biocbuild/bbs-3.11-bioc/meat/compartmap.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 '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 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
* 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
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 ...
** running examples for arch 'i386' ... OK
Examples with CPU (user + system) or elapsed time > 5s
                 user system elapsed
getCompartments 18.53   0.34   18.88
getATACABsignal 15.73   0.23   15.98
plotAB           3.13   0.08    5.38
** running examples for arch 'x64' ... OK
Examples with CPU (user + system) or elapsed time > 5s
                 user system elapsed
getATACABsignal 16.95   0.25   17.20
getCompartments 16.78   0.20   16.99
getABSignal      6.27   0.33    6.60
* 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
  'C:/Users/biocbuild/bbs-3.11-bioc/meat/compartmap.Rcheck/00check.log'
for details.

##############################################################################
##############################################################################
###
### Running command:
###
###   C:\cygwin\bin\curl.exe -O https://malbec2.bioconductor.org/BBS/3.11/bioc/src/contrib/compartmap_1.6.0.tar.gz && rm -rf compartmap.buildbin-libdir && mkdir compartmap.buildbin-libdir && C:\Users\biocbuild\bbs-3.11-bioc\R\bin\R.exe CMD INSTALL --merge-multiarch --build --library=compartmap.buildbin-libdir compartmap_1.6.0.tar.gz && C:\Users\biocbuild\bbs-3.11-bioc\R\bin\R.exe CMD INSTALL compartmap_1.6.0.zip && rm compartmap_1.6.0.tar.gz compartmap_1.6.0.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
100 3082k  100 3082k    0     0  32.6M      0 --:--:-- --:--:-- --:--:-- 35.0M

install for i386

* installing *source* package 'compartmap' ...
** using staged installation
** R
** data
** inst
** byte-compile and prepare package for lazy loading
** help
*** installing help indices
  converting help for package 'compartmap'
    finding HTML links ... done
    array.data.chr14                        html  
    filtered.data.chr14                     html  
    fisherZ                                 html  
    getABSignal                             html  
    getATACABsignal                         html  
    getArrayABsignal                        html  
    getBinMatrix                            html  
    getCompartments                         html  
    getCorMatrix                            html  
    ifisherZ                                html  
    plotAB                                  html  
** 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

install for x64

* installing *source* package 'compartmap' ...
** testing if installed package can be loaded
* MD5 sums
packaged installation of 'compartmap' as compartmap_1.6.0.zip
* DONE (compartmap)
* installing to library 'C:/Users/biocbuild/bbs-3.11-bioc/R/library'
package 'compartmap' successfully unpacked and MD5 sums checked