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###
### Running command:
###
###   C:\Users\biocbuild\bbs-3.12-bioc\R\bin\R.exe CMD check --force-multiarch --install=check:ddPCRclust.install-out.txt --library=C:\Users\biocbuild\bbs-3.12-bioc\R\library --no-vignettes --timings ddPCRclust_1.10.0.tar.gz
###
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* using log directory 'C:/Users/biocbuild/bbs-3.12-bioc/meat/ddPCRclust.Rcheck'
* using R version 4.0.5 (2021-03-31)
* using platform: x86_64-w64-mingw32 (64-bit)
* using session charset: ISO8859-1
* using option '--no-vignettes'
* checking for file 'ddPCRclust/DESCRIPTION' ... OK
* this is package 'ddPCRclust' version '1.10.0'
* 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 'ddPCRclust' can be installed ... WARNING
Found the following significant warnings:
  Rd warning: C:/Users/biocbuild/bbs-3.12-bioc/tmpdir/RtmpSeuDXW/R.INSTALL2bdc61d6260a/ddPCRclust/man/ddPCRclust.Rd:64: file link 'parallel' in package 'parallel' does not exist and so has been treated as a topic
See 'C:/Users/biocbuild/bbs-3.12-bioc/meat/ddPCRclust.Rcheck/00install.out' for details.
* 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
exportPlots: no visible binding for global variable 'Cluster'
Undefined global functions or variables:
  Cluster
* 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 files in 'vignettes' ... OK
* checking examples ...
** running examples for arch 'i386' ... OK
Examples with CPU (user + system) or elapsed time > 5s
                user system elapsed
exportPlots    17.97   1.33   19.30
exportToCSV    14.72   0.08   14.80
ddPCRclust     14.17   0.06   14.23
calculateCPDs  13.95   0.28   14.25
exportToExcel  13.84   0.08   14.06
createEnsemble 13.36   0.05   13.40
runSam          9.28   0.03    9.31
** running examples for arch 'x64' ... OK
Examples with CPU (user + system) or elapsed time > 5s
                user system elapsed
exportPlots    19.34   1.33   20.67
exportToCSV    19.32   0.03   19.34
exportToExcel  19.26   0.07   19.35
ddPCRclust     15.14   0.09   15.23
calculateCPDs  14.47   0.18   14.77
createEnsemble 14.15   0.02   14.17
runSam         10.93   0.03   10.97
runPeaks        7.94   0.00    7.93
* 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, 1 NOTE
See
  'C:/Users/biocbuild/bbs-3.12-bioc/meat/ddPCRclust.Rcheck/00check.log'
for details.

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###
### Running command:
###
###   C:\cygwin\bin\curl.exe -O http://172.29.0.3/BBS/3.12/bioc/src/contrib/ddPCRclust_1.10.0.tar.gz && rm -rf ddPCRclust.buildbin-libdir && mkdir ddPCRclust.buildbin-libdir && C:\Users\biocbuild\bbs-3.12-bioc\R\bin\R.exe CMD INSTALL --merge-multiarch --build --library=ddPCRclust.buildbin-libdir ddPCRclust_1.10.0.tar.gz && C:\Users\biocbuild\bbs-3.12-bioc\R\bin\R.exe CMD INSTALL ddPCRclust_1.10.0.zip && rm ddPCRclust_1.10.0.tar.gz ddPCRclust_1.10.0.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
100  980k  100  980k    0     0  36.3M      0 --:--:-- --:--:-- --:--:-- 38.3M

install for i386

* installing *source* package 'ddPCRclust' ...
** using staged installation
** R
** inst
** byte-compile and prepare package for lazy loading
Warning: replacing previous import 'flowCore::plot' by 'graphics::plot' when loading 'flowDensity'
** help
*** installing help indices
  converting help for package 'ddPCRclust'
    finding HTML links ... done
    calculateCPDs                           html  
    createEnsemble                          html  
    finding level-2 HTML links ... done

    ddPCRclust                              html  
Rd warning: C:/Users/biocbuild/bbs-3.12-bioc/tmpdir/RtmpSeuDXW/R.INSTALL2bdc61d6260a/ddPCRclust/man/ddPCRclust.Rd:64: file link 'parallel' in package 'parallel' does not exist and so has been treated as a topic
    exportPlots                             html  
    exportToCSV                             html  
    exportToExcel                           html  
    readFiles                               html  
    readTemplate                            html  
    runDensity                              html  
    runPeaks                                html  
    runSam                                  html  
    shearCorrection                         html  
** building package indices
** installing vignettes
** testing if installed package can be loaded from temporary location
Warning: replacing previous import 'flowCore::plot' by 'graphics::plot' when loading 'flowDensity'
** testing if installed package can be loaded from final location
Warning: replacing previous import 'flowCore::plot' by 'graphics::plot' when loading 'flowDensity'
** testing if installed package keeps a record of temporary installation path

install for x64

* installing *source* package 'ddPCRclust' ...
** testing if installed package can be loaded
Warning: replacing previous import 'flowCore::plot' by 'graphics::plot' when loading 'flowDensity'
* MD5 sums
packaged installation of 'ddPCRclust' as ddPCRclust_1.10.0.zip
* DONE (ddPCRclust)
* installing to library 'C:/Users/biocbuild/bbs-3.12-bioc/R/library'
package 'ddPCRclust' successfully unpacked and MD5 sums checked