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###
### Running command:
###
###   C:\Users\biocbuild\bbs-3.11-bioc\R\bin\R.exe CMD check --force-multiarch --install=check:DEqMS.install-out.txt --library=C:\Users\biocbuild\bbs-3.11-bioc\R\library --no-vignettes --timings DEqMS_1.6.0.tar.gz
###
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* using log directory 'C:/Users/biocbuild/bbs-3.11-bioc/meat/DEqMS.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 'DEqMS/DESCRIPTION' ... OK
* this is package 'DEqMS' version '1.6.0'
* 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 'DEqMS' can be installed ... OK
* checking installed package size ... OK
* checking package directory ... OK
* checking 'build' directory ... OK
* checking DESCRIPTION meta-information ... NOTE
Malformed Title field: should not end in a period.
* 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
Residualplot: no visible global function definition for 'fitted'
Residualplot: no visible global function definition for 'residuals'
VarianceScatterplot: no visible global function definition for 'fitted'
peptideProfilePlot: no visible binding for global variable 'variable'
peptideProfilePlot: no visible binding for global variable 'value'
peptideProfilePlot: no visible binding for global variable 'PSM_id'
peptideProfilePlot: no visible binding for global variable 'Peptide'
spectraCounteBayes: no visible global function definition for 'fitted'
Undefined global functions or variables:
  PSM_id Peptide fitted residuals value variable
Consider adding
  importFrom("stats", "fitted", "residuals")
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
medpolishSummary         75.23   0.14   86.58
farmsSummary             27.98   0.92   28.91
Residualplot             14.68   1.35   18.42
outputResult              8.64   0.26   16.39
VarianceScatterplot       8.52   0.22    8.74
equalMedianNormalization  8.13   0.58    8.70
VarianceBoxplot           8.02   0.28    8.30
medianSummary             7.50   0.20    7.71
spectraCounteBayes        6.66   0.16    6.81
medianSweeping            6.39   0.10    6.48
** running examples for arch 'x64' ... OK
Examples with CPU (user + system) or elapsed time > 5s
                          user system elapsed
medpolishSummary         73.11   0.03   73.14
farmsSummary             24.83   0.48   25.32
Residualplot             12.15   0.87   13.11
spectraCounteBayes        8.14   0.20    8.34
outputResult              7.54   0.30    7.87
VarianceScatterplot       6.85   0.24    7.08
VarianceBoxplot           6.63   0.22    6.85
equalMedianNormalization  6.42   0.28    6.70
medianSweeping            6.22   0.24    6.45
medianSummary             5.78   0.22    6.00
* 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: 2 NOTEs
See
  'C:/Users/biocbuild/bbs-3.11-bioc/meat/DEqMS.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/DEqMS_1.6.0.tar.gz && rm -rf DEqMS.buildbin-libdir && mkdir DEqMS.buildbin-libdir && C:\Users\biocbuild\bbs-3.11-bioc\R\bin\R.exe CMD INSTALL --merge-multiarch --build --library=DEqMS.buildbin-libdir DEqMS_1.6.0.tar.gz && C:\Users\biocbuild\bbs-3.11-bioc\R\bin\R.exe CMD INSTALL DEqMS_1.6.0.zip && rm DEqMS_1.6.0.tar.gz DEqMS_1.6.0.zip
###
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install for i386

* installing *source* package 'DEqMS' ...
** using staged installation
** R
** inst
** byte-compile and prepare package for lazy loading
** help
*** installing help indices
  converting help for package 'DEqMS'
    finding HTML links ... done
    Residualplot                            html  
    VarianceBoxplot                         html  
    VarianceScatterplot                     html  
    equalMedianNormalization                html  
    farmsSummary                            html  
    medianSummary                           html  
    medianSweeping                          html  
    medpolishSummary                        html  
    outputResult                            html  
    peptideProfilePlot                      html  
    spectraCounteBayes                      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 'DEqMS' ...
** testing if installed package can be loaded
* MD5 sums
packaged installation of 'DEqMS' as DEqMS_1.6.0.zip
* DONE (DEqMS)
* installing to library 'C:/Users/biocbuild/bbs-3.11-bioc/R/library'
package 'DEqMS' successfully unpacked and MD5 sums checked