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### Running command:
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###   /Library/Frameworks/R.framework/Resources/bin/R CMD check --install=check:matchBox.install-out.txt --library=/Library/Frameworks/R.framework/Resources/library --no-vignettes --timings matchBox_1.49.0.tar.gz
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* using log directory ‘/Users/biocbuild/bbs-3.21-bioc/meat/matchBox.Rcheck’
* using R Under development (unstable) (2024-11-20 r87352)
* using platform: x86_64-apple-darwin20
* R was compiled by
    Apple clang version 14.0.0 (clang-1400.0.29.202)
    GNU Fortran (GCC) 12.2.0
* running under: macOS Monterey 12.7.6
* using session charset: UTF-8
* using option ‘--no-vignettes’
* checking for file ‘matchBox/DESCRIPTION’ ... OK
* checking extension type ... Package
* this is package ‘matchBox’ version ‘1.49.0’
* checking package namespace information ... OK
* checking package dependencies ...Warning: unable to access index for repository https://CRAN.R-project.org/src/contrib:
  cannot open URL 'https://CRAN.R-project.org/src/contrib/PACKAGES'
 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 for sufficient/correct file permissions ... OK
* checking whether package ‘matchBox’ 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 code files for non-ASCII characters ... OK
* checking R files for syntax errors ... OK
* 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 ... NOTE
checkRd: (-1) matchBox-package.Rd:26-27: Lost braces
    26 |     {Enables to identify the common set of features across
       |     ^
checkRd: (-1) matchBox-package.Rd:29-30: Lost braces
    29 |     {Enables to merge multiple data.frames based on
       |     ^
checkRd: (-1) matchBox-package.Rd:32-33: Lost braces
    32 |     {Computes the overlap proportion between any pair of ranked
       |     ^
checkRd: (-1) matchBox-package.Rd:35-36: Lost braces
    35 |     {Creates plots of the proportion of overlap along
       |     ^
checkRd: (-1) matchBoxExpression.Rd:29: Lost braces
    29 |     {\code{GENENAME}: Gene name column;}
       |     ^
checkRd: (-1) matchBoxExpression.Rd:31: Lost braces
    31 |     {\code{ENTREZID}: ENTREZ Gene identifier column;}
       |     ^
checkRd: (-1) matchBoxExpression.Rd:33: Lost braces
    33 |     {\code{logFC}: Log2 fold-change column;}
       |     ^
checkRd: (-1) matchBoxExpression.Rd:35: Lost braces
    35 |     {\code{AveExpr}: Average expression (A-value) column;}
       |     ^
checkRd: (-1) matchBoxExpression.Rd:37: Lost braces
    37 |     {\code{t}: moderated t-statistics column;}
       |     ^
checkRd: (-1) matchBoxExpression.Rd:39: Lost braces
    39 |     {\code{P.Value}: P-value column;}
       |     ^
checkRd: (-1) matchBoxExpression.Rd:41: Lost braces
    41 |     {\code{adj.P.Val}: adjusted P-value column;}
       |     ^
checkRd: (-1) matchBoxExpression.Rd:43: Lost braces
    43 |     {\code{B}: B-statitics (log-odds) column;}
       |     ^
* 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 sizes of PDF files under ‘inst/doc’ ... OK
* checking files in ‘vignettes’ ... OK
* checking examples ... OK
* checking for unstated dependencies in vignettes ... OK
* checking package vignettes ... OK
* checking running R code from vignettes ... SKIPPED
* checking re-building of vignette outputs ... SKIPPED
* checking PDF version of manual ... OK
* DONE

Status: 4 NOTEs
See
  ‘/Users/biocbuild/bbs-3.21-bioc/meat/matchBox.Rcheck/00check.log’
for details.

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###
### Running command:
###
###   /Library/Frameworks/R.framework/Resources/bin/R CMD INSTALL matchBox
###
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* installing to library ‘/Library/Frameworks/R.framework/Versions/4.5-x86_64/Resources/library’
* installing *source* package ‘matchBox’ ...
** using staged installation
** R
** data
** inst
** byte-compile and prepare package for lazy loading
** help
*** installing help indices
** 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
* DONE (matchBox)