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###
### Running command:
###
###   C:\Users\biocbuild\bbs-3.13-bioc\R\bin\R.exe CMD check --force-multiarch --install=check:exomePeak2.install-out.txt --library=C:\Users\biocbuild\bbs-3.13-bioc\R\library --no-vignettes --timings exomePeak2_1.4.2.tar.gz
###
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* using log directory 'C:/Users/biocbuild/bbs-3.13-bioc/meat/exomePeak2.Rcheck'
* using R version 4.1.1 (2021-08-10)
* using platform: x86_64-w64-mingw32 (64-bit)
* using session charset: ISO8859-1
* using option '--no-vignettes'
* checking for file 'exomePeak2/DESCRIPTION' ... OK
* checking extension type ... Package
* this is package 'exomePeak2' version '1.4.2'
* 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 'exomePeak2' 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 ... OK
* checking S3 generic/method consistency ... OK
* checking replacement functions ... OK
* checking foreign function calls ... OK
* checking R code for possible problems ... NOTE
GLM_inference : <anonymous>: no visible global function definition for
  'median'
Results,SummarizedExomePeak: no visible global function definition for
  'glm_M'
estimateSeqDepth,SummarizedExomePeak : <anonymous>: no visible global
  function definition for 'median'
exomePeakCalling,MeripBamFileList: no visible global function
  definition for 'metadata'
exomePeakCalling,MeripBamFileList: no visible global function
  definition for '%over%'
plotLfcGC,SummarizedExomePeak: no visible binding for global variable
  'GC_idx'
plotLfcGC,SummarizedExomePeak: no visible binding for global variable
  'Log2FC'
plotLfcGC,SummarizedExomePeak: no visible binding for global variable
  'Label'
plotReadsGC,SummarizedExomePeak: no visible binding for global variable
  'GC_cont'
plotReadsGC,SummarizedExomePeak: no visible binding for global variable
  'value'
plotSizeFactors,SummarizedExomePeak: no visible binding for global
  variable 'samples'
plotSizeFactors,SummarizedExomePeak: no visible binding for global
  variable 'size_factors'
plotSizeFactors,SummarizedExomePeak: no visible binding for global
  variable 'Estimation_Methods'
Undefined global functions or variables:
  %over% Estimation_Methods GC_cont GC_idx Label Log2FC glm_M median
  metadata samples size_factors value
Consider adding
  importFrom("stats", "median")
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
exomePeak2                70.53   0.31   71.56
exomePeakCalling-methods  45.06   0.15   45.69
SummarizedExomePeak-class 24.60   1.69   28.12
glmM-methods               6.09   0.00    6.30
** running examples for arch 'x64' ... OK
Examples with CPU (user + system) or elapsed time > 5s
                           user system elapsed
exomePeak2                78.75   0.16   78.91
exomePeakCalling-methods  44.22   0.06   44.28
SummarizedExomePeak-class 26.63   1.06   27.72
glmM-methods               6.03   0.00    6.03
glmDM-methods              5.30   0.00    5.30
* 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 NOTE
See
  'C:/Users/biocbuild/bbs-3.13-bioc/meat/exomePeak2.Rcheck/00check.log'
for details.

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###
### Running command:
###
###   C:\cygwin\bin\curl.exe -O http://155.52.207.165/BBS/3.13/bioc/src/contrib/exomePeak2_1.4.2.tar.gz && rm -rf exomePeak2.buildbin-libdir && mkdir exomePeak2.buildbin-libdir && C:\Users\biocbuild\bbs-3.13-bioc\R\bin\R.exe CMD INSTALL --merge-multiarch --build --library=exomePeak2.buildbin-libdir exomePeak2_1.4.2.tar.gz && C:\Users\biocbuild\bbs-3.13-bioc\R\bin\R.exe CMD INSTALL exomePeak2_1.4.2.zip && rm exomePeak2_1.4.2.tar.gz exomePeak2_1.4.2.zip
###
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  % Total    % Received % Xferd  Average Speed   Time    Time     Time  Current
                                 Dload  Upload   Total   Spent    Left  Speed

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 39 2229k   39  885k    0     0  1975k      0  0:00:01 --:--:--  0:00:01 1977k
100 2229k  100 2229k    0     0  2982k      0 --:--:-- --:--:-- --:--:-- 2981k

install for i386

* installing *source* package 'exomePeak2' ...
** using staged installation
** R
** inst
** byte-compile and prepare package for lazy loading
** help
*** installing help indices
  converting help for package 'exomePeak2'
    finding HTML links ... done
    GC_content_over_grl                     html  
    GCsizeFactors-methods                   html  
    GLM_inference                           html  
    LibraryType-methods                     html  
    MeripBamFileList-class                  html  
    finding level-2 HTML links ... done

    Parameter-methods                       html  
    Results-methods                         html  
    SummarizedExomePeak-class               html  
    call_peaks_with_GLM                     html  
    convertTxDb                             html  
    ctest                                   html  
    decision_deseq2                         html  
    disj_background                         html  
    estimateSeqDepth-methods                html  
    exomePeak2                              html  
    exomePeak2Results-methods               html  
    exomePeakCalling-methods                html  
    exome_bins_from_txdb                    html  
    exonPlot                                html  
    exons_by_unique_gene                    html  
    exportResults-methods                   html  
    flank_on_exons                          html  
    glmDM-methods                           html  
    glmM-methods                            html  
    mclust_bg                               html  
    normalizeGC-methods                     html  
    plotExonLength-methods                  html  
    plotLfcGC-methods                       html  
    plotReadsGC-methods                     html  
    plotSizeFactors-methods                 html  
    quiet                                   html  
    reads_five_POS                          html  
    reads_five_POS_rev                      html  
    reduce_peaks                            html  
    remove_introns                          html  
    replace_bg                              html  
    scanMeripBAM                            html  
    sort_sep                                html  
    split_by_name                           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 'exomePeak2' ...
** testing if installed package can be loaded
* MD5 sums
packaged installation of 'exomePeak2' as exomePeak2_1.4.2.zip
* DONE (exomePeak2)
* installing to library 'C:/Users/biocbuild/bbs-3.13-bioc/R/library'
package 'exomePeak2' successfully unpacked and MD5 sums checked