Package: flowCHIC

Version: 1.12.0

Command: rm -rf flowCHIC.buildbin-libdir flowCHIC.Rcheck && mkdir flowCHIC.buildbin-libdir flowCHIC.Rcheck && C:\Users\biocbuild\bbs-3.6-bioc\R\bin\R.exe CMD INSTALL --build --merge-multiarch --library=flowCHIC.buildbin-libdir flowCHIC_1.12.0.tar.gz >flowCHIC.Rcheck\00install.out 2>&1 && cp flowCHIC.Rcheck\00install.out flowCHIC-install.out && C:\Users\biocbuild\bbs-3.6-bioc\R\bin\R.exe CMD check --library=flowCHIC.buildbin-libdir --install="check:flowCHIC-install.out" --force-multiarch --no-vignettes --timings flowCHIC_1.12.0.tar.gz

StartedAt: 2018-04-11 23:59:48 -0400 (Wed, 11 Apr 2018)

EndedAt: 2018-04-12 00:02:46 -0400 (Thu, 12 Apr 2018)

EllapsedTime: 178.6 seconds

RetCode: 0

Status:  OK

CheckDir: flowCHIC.Rcheck

Warnings: 0

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### Running command:
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###   rm -rf flowCHIC.buildbin-libdir flowCHIC.Rcheck && mkdir flowCHIC.buildbin-libdir flowCHIC.Rcheck && C:\Users\biocbuild\bbs-3.6-bioc\R\bin\R.exe CMD INSTALL --build --merge-multiarch --library=flowCHIC.buildbin-libdir flowCHIC_1.12.0.tar.gz >flowCHIC.Rcheck\00install.out 2>&1 && cp flowCHIC.Rcheck\00install.out flowCHIC-install.out  &&  C:\Users\biocbuild\bbs-3.6-bioc\R\bin\R.exe CMD check --library=flowCHIC.buildbin-libdir --install="check:flowCHIC-install.out" --force-multiarch --no-vignettes --timings flowCHIC_1.12.0.tar.gz
###
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* using log directory 'C:/Users/biocbuild/bbs-3.6-bioc/meat/flowCHIC.Rcheck'
* using R version 3.4.4 (2018-03-15)
* using platform: x86_64-w64-mingw32 (64-bit)
* using session charset: ISO8859-1
* using option '--no-vignettes'
* checking for file 'flowCHIC/DESCRIPTION' ... OK
* checking extension type ... Package
* this is package 'flowCHIC' version '1.12.0'
* package encoding: UTF-8
* 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 'flowCHIC' can be installed ... OK
* checking installed package size ... NOTE
  installed size is  6.2Mb
  sub-directories of 1Mb or more:
    extdata   5.7Mb
* checking package directory ... OK
* checking 'build' directory ... OK
* checking DESCRIPTION meta-information ... NOTE
Malformed Description field: should contain one or more complete sentences.
* 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
** checking loading without being on the library search path ... 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 loading without being on the library search path ... 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
fcs_to_img,character: warning in hexbin(x, y, xbin = 128): partial
  argument match of 'xbin' to 'xbins'
img_sub,character: warning in hexbin(x, y, xbin = xbin): partial
  argument match of 'xbin' to 'xbins'
fcs_to_img,character: no visible global function definition for 'png'
fcs_to_img,character: no visible binding for global variable 'count'
fcs_to_img,character: no visible global function definition for
  'dev.off'
img_sub,character: no visible global function definition for 'png'
img_sub,character: no visible binding for global variable 'count'
img_sub,character: no visible global function definition for 'dev.off'
plot_nmds,data.frame-data.frame: no visible global function definition
  for 'as.dist'
plot_nmds,data.frame-data.frame: no visible global function definition
  for 'par'
plot_nmds,data.frame-data.frame: no visible global function definition
  for 'plot'
plot_nmds,data.frame-data.frame: no visible global function definition
  for 'hclust'
plot_nmds,data.frame-data.frame: no visible global function definition
  for 'points'
plot_nmds,data.frame-data.frame: no visible global function definition
  for 'text'
plot_nmds,data.frame-data.frame: no visible global function definition
  for 'legend'
Undefined global functions or variables:
  as.dist count dev.off hclust legend par plot png points text
Consider adding
  importFrom("grDevices", "dev.off", "png")
  importFrom("graphics", "legend", "par", "plot", "points", "text")
  importFrom("stats", "as.dist", "hclust")
to your NAMESPACE file.
* checking Rd files ... OK
* checking Rd metadata ... OK
* checking Rd cross-references ... NOTE
Package unavailable to check Rd xrefs: 'flowCyBar'
* 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 installed files from 'inst/doc' ... OK
* checking files in 'vignettes' ... OK
* checking examples ...
** running examples for arch 'i386' ... OK
Examples with CPU or elapsed time > 5s
                        user system elapsed
calculate_overlaps_xor 11.13   2.28   13.57
plot_nmds               5.34   0.86    6.28
** running examples for arch 'x64' ... OK
Examples with CPU or elapsed time > 5s
                        user system elapsed
calculate_overlaps_xor 11.48   1.81   13.96
plot_nmds               5.69   0.87    6.62
* 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: 4 NOTEs
See
  'C:/Users/biocbuild/bbs-3.6-bioc/meat/flowCHIC.Rcheck/00check.log'
for details.

install for i386

* installing *source* package 'flowCHIC' ...
** R
** data
** inst
** preparing package for lazy loading
** help
*** installing help indices
  converting help for package 'flowCHIC'
    finding HTML links ... done
    Results_overlaps                        html  
    Results_overlaps_incol                  html  
    Results_overlaps_mix                    html  
    Results_xor                             html  
    Results_xor_incol                       html  
    Results_xor_mix                         html  
    abiotic_incol                           html  
    calculate_overlaps_xor                  html  
    fcs_to_img                              html  
    flowCHIC_package                        html  
    img_sub                                 html  
    plot_nmds                               html  
** building package indices
** installing vignettes
** testing if installed package can be loaded
In R CMD INSTALL

install for x64

* installing *source* package 'flowCHIC' ...
** testing if installed package can be loaded
* MD5 sums
packaged installation of 'flowCHIC' as flowCHIC_1.12.0.zip
* DONE (flowCHIC)
In R CMD INSTALL
In R CMD INSTALL