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###
### Running command:
###
###   C:\Users\biocbuild\bbs-3.11-bioc\R\bin\R.exe CMD check --force-multiarch --install=check:matchBox.install-out.txt --library=C:\Users\biocbuild\bbs-3.11-bioc\R\library --no-vignettes --timings matchBox_1.30.0.tar.gz
###
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* using log directory 'C:/Users/biocbuild/bbs-3.11-bioc/meat/matchBox.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 'matchBox/DESCRIPTION' ... OK
* checking extension type ... Package
* this is package 'matchBox' version '1.30.0'
* 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 'matchBox' can be installed ... WARNING
Found the following significant warnings:
  Rd warning: C:/Users/biocbuild/bbs-3.11-bioc/tmpdir/RtmpQLK06Y/R.INSTALL1330681a7ab6/matchBox/man/calcHypPI.Rd:96: file link 'qhyper' in package 'stats' does not exist and so has been treated as a topic
  Rd warning: C:/Users/biocbuild/bbs-3.11-bioc/tmpdir/RtmpQLK06Y/R.INSTALL1330681a7ab6/matchBox/man/plotCat.Rd:125: file link 'rainbow' in package 'grDevices' does not exist and so has been treated as a topic
See 'C:/Users/biocbuild/bbs-3.11-bioc/meat/matchBox.Rcheck/00install.out' for details.
* 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 ... NOTE
There are ::: calls to the package's namespace in its code. A package
  almost never needs to use ::: for its own objects:
  'is.odd'
* checking S3 generic/method consistency ... OK
* checking replacement functions ... OK
* checking foreign function calls ... OK
* checking R code for possible problems ... NOTE
calcHypPI : <anonymous>: no visible global function definition for
  'qhyper'
computeCat: no visible global function definition for 'combn'
medianM: no visible global function definition for 'median'
plotCat: no visible global function definition for 'layout'
plotCat: no visible global function definition for 'rainbow'
plotCat: no visible global function definition for 'par'
plotCat: no visible global function definition for 'colors'
plotCat: no visible global function definition for 'polygon'
plotCat: no visible global function definition for 'points'
plotCat: no visible global function definition for 'mtext'
plotCat: no visible global function definition for 'plot.new'
Undefined global functions or variables:
  colors combn layout median mtext par plot.new points polygon qhyper
  rainbow
Consider adding
  importFrom("grDevices", "colors", "rainbow")
  importFrom("graphics", "layout", "mtext", "par", "plot.new", "points",
             "polygon")
  importFrom("stats", "median", "qhyper")
  importFrom("utils", "combn")
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
** running examples for arch 'x64' ... OK
* 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, 3 NOTEs
See
  'C:/Users/biocbuild/bbs-3.11-bioc/meat/matchBox.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/matchBox_1.30.0.tar.gz && rm -rf matchBox.buildbin-libdir && mkdir matchBox.buildbin-libdir && C:\Users\biocbuild\bbs-3.11-bioc\R\bin\R.exe CMD INSTALL --merge-multiarch --build --library=matchBox.buildbin-libdir matchBox_1.30.0.tar.gz && C:\Users\biocbuild\bbs-3.11-bioc\R\bin\R.exe CMD INSTALL matchBox_1.30.0.zip && rm matchBox_1.30.0.tar.gz matchBox_1.30.0.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  393k  100  393k    0     0  6770k      0 --:--:-- --:--:-- --:--:-- 7575k

install for i386

* installing *source* package 'matchBox' ...
** using staged installation
** R
** data
** inst
** byte-compile and prepare package for lazy loading
** help
*** installing help indices
  converting help for package 'matchBox'
    finding HTML links ... done
    calcHypPI                               html  
Rd warning: C:/Users/biocbuild/bbs-3.11-bioc/tmpdir/RtmpQLK06Y/R.INSTALL1330681a7ab6/matchBox/man/calcHypPI.Rd:96: file link 'qhyper' in package 'stats' does not exist and so has been treated as a topic
    computeCat                              html  
    filterRedundant                         html  
    matchBox-package                        html  
    matchBoxExpression                      html  
    mergeData                               html  
    plotCat                                 html  
Rd warning: C:/Users/biocbuild/bbs-3.11-bioc/tmpdir/RtmpQLK06Y/R.INSTALL1330681a7ab6/matchBox/man/plotCat.Rd:125: file link 'rainbow' in package 'grDevices' does not exist and so has been treated as a topic
** 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 'matchBox' ...
** testing if installed package can be loaded
* MD5 sums
packaged installation of 'matchBox' as matchBox_1.30.0.zip
* DONE (matchBox)
* installing to library 'C:/Users/biocbuild/bbs-3.11-bioc/R/library'
package 'matchBox' successfully unpacked and MD5 sums checked