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###
### Running command:
###
###   C:\Users\biocbuild\bbs-3.13-bioc\R\bin\R.exe CMD check --force-multiarch --install=check:flowCHIC.install-out.txt --library=C:\Users\biocbuild\bbs-3.13-bioc\R\library --no-vignettes --timings flowCHIC_1.26.0.tar.gz
###
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* using log directory 'C:/Users/biocbuild/bbs-3.13-bioc/meat/flowCHIC.Rcheck'
* using R version 4.1.1 (2021-08-10)
* 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 '1.26.0'
* 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  6.0Mb
  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
* 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
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 '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 png points text
Consider adding
  importFrom("grDevices", "dev.off", "png")
  importFrom("graphics", "legend", "par", "points", "text")
  importFrom("stats", "as.dist", "hclust")
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
Examples with CPU (user + system) or elapsed time > 5s
                       user system elapsed
calculate_overlaps_xor 8.16   2.37   11.00
plot_nmds              4.72   1.05    5.78
** running examples for arch 'x64' ... OK
Examples with CPU (user + system) or elapsed time > 5s
                       user system elapsed
calculate_overlaps_xor 7.56   2.09    9.70
plot_nmds              5.47   1.08    6.58
* 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: 3 NOTEs
See
  'C:/Users/biocbuild/bbs-3.13-bioc/meat/flowCHIC.Rcheck/00check.log'
for details.

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###
### Running command:
###
###   C:\cygwin\bin\curl.exe -O http://155.52.207.165/BBS/3.13/bioc/src/contrib/flowCHIC_1.26.0.tar.gz && rm -rf flowCHIC.buildbin-libdir && mkdir flowCHIC.buildbin-libdir && C:\Users\biocbuild\bbs-3.13-bioc\R\bin\R.exe CMD INSTALL --merge-multiarch --build --library=flowCHIC.buildbin-libdir flowCHIC_1.26.0.tar.gz && C:\Users\biocbuild\bbs-3.13-bioc\R\bin\R.exe CMD INSTALL flowCHIC_1.26.0.zip && rm flowCHIC_1.26.0.tar.gz flowCHIC_1.26.0.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
 17 3126k   17  536k    0     0  1142k      0  0:00:02 --:--:--  0:00:02 1141k
 86 3126k   86 2710k    0     0  1857k      0  0:00:01  0:00:01 --:--:-- 1857k
100 3126k  100 3126k    0     0  1932k      0  0:00:01  0:00:01 --:--:-- 1932k

install for i386

* installing *source* package 'flowCHIC' ...
** using staged installation
** R
** data
** inst
** byte-compile and prepare 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 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 'flowCHIC' ...
** testing if installed package can be loaded
* MD5 sums
packaged installation of 'flowCHIC' as flowCHIC_1.26.0.zip
* DONE (flowCHIC)
* installing to library 'C:/Users/biocbuild/bbs-3.13-bioc/R/library'
package 'flowCHIC' successfully unpacked and MD5 sums checked