Package: flowClean

Version: 1.18.0

Command: C:\Users\biocbuild\bbs-3.7-bioc\R\bin\R.exe CMD check --force-multiarch --install=check:flowClean.install-out.txt --library=C:\Users\biocbuild\bbs-3.7-bioc\R\library --no-vignettes --timings flowClean_1.18.0.tar.gz

StartedAt: 2018-10-17 02:00:36 -0400 (Wed, 17 Oct 2018)

EndedAt: 2018-10-17 02:02:18 -0400 (Wed, 17 Oct 2018)

EllapsedTime: 102.2 seconds

RetCode: 0

Status:  WARNINGS

CheckDir: flowClean.Rcheck

Warnings: 2

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### Running command:
###
###   C:\Users\biocbuild\bbs-3.7-bioc\R\bin\R.exe CMD check --force-multiarch --install=check:flowClean.install-out.txt --library=C:\Users\biocbuild\bbs-3.7-bioc\R\library --no-vignettes --timings flowClean_1.18.0.tar.gz
###
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* using log directory 'C:/Users/biocbuild/bbs-3.7-bioc/meat/flowClean.Rcheck'
* using R version 3.5.1 Patched (2018-07-24 r75005)
* using platform: x86_64-w64-mingw32 (64-bit)
* using session charset: ISO8859-1
* using option '--no-vignettes'
* checking for file 'flowClean/DESCRIPTION' ... OK
* this is package 'flowClean' version '1.18.0'
* 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 'flowClean' 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 ... 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
clean: no visible global function definition for 'runif'
clean: no visible global function definition for 'png'
clean: no visible global function definition for 'dev.off'
diagnosticPlot: no visible global function definition for 'points'
diagnosticPlot: no visible global function definition for 'abline'
makeFCS: no visible global function definition for 'new'
make_pops : <anonymous>: no visible global function definition for
  'quantile'
make_pops : <anonymous>: no visible global function definition for
  'median'
Undefined global functions or variables:
  abline dev.off median new png points quantile runif
Consider adding
  importFrom("grDevices", "dev.off", "png")
  importFrom("graphics", "abline", "points")
  importFrom("methods", "new")
  importFrom("stats", "median", "quantile", "runif")
to your NAMESPACE file (and ensure that your DESCRIPTION Imports field
contains 'methods').
* checking Rd files ... OK
* checking Rd metadata ... OK
* checking Rd cross-references ... OK
* checking for missing documentation entries ... OK
* checking for code/documentation mismatches ... WARNING
Codoc mismatches from documentation object 'clean':
clean
  Code: function(fF, vectMarkers, filePrefixWithDir, ext, binSize =
                 0.01, nCellCutoff = 500, announce = TRUE, cutoff =
                 "median", diagnostic = FALSE, fcMax = 1.3,
                 returnVector = FALSE, nstable = 5)
  Docs: function(fF, vectMarkers, filePrefixWithDir, ext, binSize =
                 0.01, nCellCutoff = 500, announce = TRUE, cutoff =
                 "median", diagnostic = FALSE, fcMax = 1.3)
  Argument names in code not in docs:
    returnVector nstable

* checking Rd \usage sections ... WARNING
Duplicated \argument entries in documentation object 'clean':
  'announce'
Documented arguments not in \usage in documentation object 'clean':
  'returnVector' 'nstable'

Functions with \usage entries need to have the appropriate \alias
entries, and all their arguments documented.
The \usage entries must correspond to syntactically valid R code.
See chapter 'Writing R documentation files' in the 'Writing R
Extensions' manual.
* 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 or elapsed time > 5s
      user system elapsed
clean   13   0.86   14.06
** running examples for arch 'x64' ... OK
Examples with CPU or elapsed time > 5s
       user system elapsed
clean 12.64   0.53   13.17
* 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 WARNINGs, 1 NOTE
See
  'C:/Users/biocbuild/bbs-3.7-bioc/meat/flowClean.Rcheck/00check.log'
for details.

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###
### Running command:
###
###   C:\cygwin\bin\curl.exe -O https://malbec2.bioconductor.org/BBS/3.7/bioc/src/contrib/flowClean_1.18.0.tar.gz && rm -rf flowClean.buildbin-libdir && mkdir flowClean.buildbin-libdir && C:\Users\biocbuild\bbs-3.7-bioc\R\bin\R.exe CMD INSTALL --merge-multiarch --build --library=flowClean.buildbin-libdir flowClean_1.18.0.tar.gz && C:\Users\biocbuild\bbs-3.7-bioc\R\bin\R.exe CMD INSTALL flowClean_1.18.0.zip && rm flowClean_1.18.0.tar.gz flowClean_1.18.0.zip
###
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install for i386

* installing *source* package 'flowClean' ...
** R
** data
** inst
** byte-compile and prepare package for lazy loading
** help
*** installing help indices
  converting help for package 'flowClean'
    finding HTML links ... done
    clean                                   html  
    synPerturbed                            html  
** building package indices
** installing vignettes
** testing if installed package can be loaded
In R CMD INSTALL

install for x64

* installing *source* package 'flowClean' ...
** testing if installed package can be loaded
* MD5 sums
packaged installation of 'flowClean' as flowClean_1.18.0.zip
* DONE (flowClean)
In R CMD INSTALL
In R CMD INSTALL
* installing to library 'C:/Users/biocbuild/bbs-3.7-bioc/R/library'
package 'flowClean' successfully unpacked and MD5 sums checked
In R CMD INSTALL