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###
### Running command:
###
###   C:\Users\biocbuild\bbs-3.11-bioc\R\bin\R.exe CMD check --force-multiarch --install=check:clippda.install-out.txt --library=C:\Users\biocbuild\bbs-3.11-bioc\R\library --no-vignettes --timings clippda_1.38.0.tar.gz
###
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* using log directory 'C:/Users/biocbuild/bbs-3.11-bioc/meat/clippda.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 'clippda/DESCRIPTION' ... OK
* this is package 'clippda' version '1.38.0'
* checking package namespace information ... NOTE
  Namespaces with empty importFrom:
  'Biobase' 'tools'
* checking package dependencies ... NOTE
Depends: includes the non-default packages:
  'limma', 'statmod', 'rgl', 'lattice', 'scatterplot3d', 'Biobase',
  'tools'
Adding so many packages to the search path is excessive and importing
selectively is preferable.
* 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 'clippda' 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 ... WARNING
Invalid citation information in 'inst/CITATION':
  Error in bibentry(bibtype = entry, textVersion = textVersion, header = header,     footer = footer, ...): argument "textVersion" is missing, with no default
* 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
'library' or 'require' calls to packages already attached by Depends:
  'lattice' 'limma' 'rgl' 'scatterplot3d' 'statmod'
  Please remove these calls from your code.
Packages in Depends field not imported from:
  'lattice' 'rgl'
  These packages need to be imported from (in the NAMESPACE file)
  for when this namespace is loaded but not attached.
* checking S3 generic/method consistency ... OK
* checking replacement functions ... OK
* checking foreign function calls ... OK
* checking R code for possible problems ... NOTE
ZvaluescasesVcontrolsPlots: no visible global function definition for
  'lines'
ZvaluescasesVcontrolsPlots: no visible global function definition for
  'legend'
ZvaluesfrommultinomPlots: no visible global function definition for
  'rmultinom'
ZvaluesfrommultinomPlots: no visible global function definition for
  'density'
ZvaluesfrommultinomPlots: no visible global function definition for
  'lines'
ZvaluesfrommultinomPlots: no visible global function definition for
  'legend'
ZvaluesfrommultinomPlots: no visible global function definition for
  'cloud'
ZvaluesfrommultinomPlots: no visible global function definition for
  'var'
Undefined global functions or variables:
  cloud density legend lines rmultinom var
Consider adding
  importFrom("graphics", "legend", "lines")
  importFrom("stats", "density", "rmultinom", "var")
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 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 ...
** running examples for arch 'i386' ... OK
Examples with CPU (user + system) or elapsed time > 5s
                          user system elapsed
clippda-package          81.62   0.14   81.77
sampleSize               51.51   0.12   51.64
sampleSizeParameters     23.59   0.04   23.64
sample_technicalVariance  6.25   0.02    6.26
** running examples for arch 'x64' ... OK
Examples with CPU (user + system) or elapsed time > 5s
                          user system elapsed
clippda-package          83.18   0.24   83.42
sampleSize               58.37   0.20   58.61
sampleSizeParameters     24.81   0.04   24.86
sample_technicalVariance  6.54   0.03    6.58
replicateCorrelations     4.99   0.05    5.03
* 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, 4 NOTEs
See
  'C:/Users/biocbuild/bbs-3.11-bioc/meat/clippda.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/clippda_1.38.0.tar.gz && rm -rf clippda.buildbin-libdir && mkdir clippda.buildbin-libdir && C:\Users\biocbuild\bbs-3.11-bioc\R\bin\R.exe CMD INSTALL --merge-multiarch --build --library=clippda.buildbin-libdir clippda_1.38.0.tar.gz && C:\Users\biocbuild\bbs-3.11-bioc\R\bin\R.exe CMD INSTALL clippda_1.38.0.zip && rm clippda_1.38.0.tar.gz clippda_1.38.0.zip
###
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  % 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  420k  100  420k    0     0  1697k      0 --:--:-- --:--:-- --:--:-- 1742k

install for i386

* installing *source* package 'clippda' ...
** using staged installation
** R
** data
** inst
** byte-compile and prepare package for lazy loading
** help
*** installing help indices
  converting help for package 'clippda'
    finding HTML links ... done
    ZvaluescasesVcontrolsPlots              html  
    ZvaluesfrommultinomPlots                html  
    aclinicalProteomicsData-class           html  
    aclinicalProteomicsData-methods         html  
    betweensampleVariance-methods           html  
    betweensampleVariance                   html  
    checkNo.replicates                      html  
    clippda-package                         html  
    f                                       html  
    fisherInformation-methods               html  
    fisherInformation                       html  
    liverRawData                            html  
    liver_pheno                             html  
    liverdata                               html  
    mostSimilarTwo                          html  
    negativeIntensitiesCorrection           html  
    phenoDataFrame                          html  
    pheno_urine                             html  
    preProcRepeatedPeakData                 html  
    proteomicsExprsData-methods             html  
    proteomicsExprsData                     html  
    proteomicspData-methods                 html  
    proteomicspData                         html  
    replicateCorrelations-methods           html  
    replicateCorrelations                   html  
    sampleClusteredData                     html  
    sampleSize-methods                      html  
    sampleSize                              html  
    sampleSize3DscatterPlots                html  
    sampleSizeContourPlots                  html  
    sampleSizeParameters-methods            html  
    sampleSizeParameters                    html  
    sample_technicalVariance-methods        html  
    sample_technicalVariance                html  
    show-methods                            html  
    spectrumFilter                          html  
    ztwo                                    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 'clippda' ...
** testing if installed package can be loaded
* MD5 sums
packaged installation of 'clippda' as clippda_1.38.0.zip
* DONE (clippda)
* installing to library 'C:/Users/biocbuild/bbs-3.11-bioc/R/library'
package 'clippda' successfully unpacked and MD5 sums checked