Package: matchBox

Version: 1.24.0

Command: C:\Users\biocbuild\bbs-3.8-bioc\R\bin\R.exe CMD check --force-multiarch --install=check:matchBox.install-out.txt --library=C:\Users\biocbuild\bbs-3.8-bioc\R\library --no-vignettes --timings matchBox_1.24.0.tar.gz

StartedAt: 2019-04-13 03:32:49 -0400 (Sat, 13 Apr 2019)

EndedAt: 2019-04-13 03:34:18 -0400 (Sat, 13 Apr 2019)

EllapsedTime: 89.0 seconds

RetCode: 0

Status:  WARNINGS

CheckDir: matchBox.Rcheck

Warnings: 1

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### Running command:
###
###   C:\Users\biocbuild\bbs-3.8-bioc\R\bin\R.exe CMD check --force-multiarch --install=check:matchBox.install-out.txt --library=C:\Users\biocbuild\bbs-3.8-bioc\R\library --no-vignettes --timings matchBox_1.24.0.tar.gz
###
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* using log directory 'C:/Users/biocbuild/bbs-3.8-bioc/meat/matchBox.Rcheck'
* using R version 3.5.3 (2019-03-11)
* 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 '1.24.0'
* 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 whether package 'matchBox' can be installed ... WARNING
Found the following significant warnings:
  Rd warning: C:/Users/biocbuild/bbs-3.8-bioc/tmpdir/RtmpwH9Xou/R.INSTALLea060f8176d/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-3.8-bioc/tmpdir/RtmpwH9Xou/R.INSTALLea060f8176d/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-3.8-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 'plot'
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 plot.new points polygon
  qhyper rainbow
Consider adding
  importFrom("grDevices", "colors", "rainbow")
  importFrom("graphics", "layout", "mtext", "par", "plot", "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-3.8-bioc/meat/matchBox.Rcheck/00check.log'
for details.

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###
### Running command:
###
###   C:\cygwin\bin\curl.exe -O https://malbec1.bioconductor.org/BBS/3.8/bioc/src/contrib/matchBox_1.24.0.tar.gz && rm -rf matchBox.buildbin-libdir && mkdir matchBox.buildbin-libdir && C:\Users\biocbuild\bbs-3.8-bioc\R\bin\R.exe CMD INSTALL --merge-multiarch --build --library=matchBox.buildbin-libdir matchBox_1.24.0.tar.gz && C:\Users\biocbuild\bbs-3.8-bioc\R\bin\R.exe CMD INSTALL matchBox_1.24.0.zip && rm matchBox_1.24.0.tar.gz matchBox_1.24.0.zip
###
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install for i386

* installing *source* package 'matchBox' ...
** 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-3.8-bioc/tmpdir/RtmpwH9Xou/R.INSTALLea060f8176d/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-3.8-bioc/tmpdir/RtmpwH9Xou/R.INSTALLea060f8176d/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
In R CMD INSTALL

install for x64

* installing *source* package 'matchBox' ...
** testing if installed package can be loaded
* MD5 sums
packaged installation of 'matchBox' as matchBox_1.24.0.zip
* DONE (matchBox)
In R CMD INSTALL
In R CMD INSTALL
* installing to library 'C:/Users/biocbuild/bbs-3.8-bioc/R/library'
package 'matchBox' successfully unpacked and MD5 sums checked
In R CMD INSTALL