Package: ddPCRclust

Version: 1.7.0

Command: /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD check --install=check:ddPCRclust.install-out.txt --library=/Library/Frameworks/R.framework/Versions/Current/Resources/library --no-vignettes --timings ddPCRclust_1.7.0.tar.gz

StartedAt: 2020-01-16 03:31:38 -0500 (Thu, 16 Jan 2020)

EndedAt: 2020-01-16 03:37:26 -0500 (Thu, 16 Jan 2020)

EllapsedTime: 348.3 seconds

RetCode: 0

Status:  OK

CheckDir: ddPCRclust.Rcheck

Warnings: 0

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### Running command:
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###   /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD check --install=check:ddPCRclust.install-out.txt --library=/Library/Frameworks/R.framework/Versions/Current/Resources/library --no-vignettes --timings ddPCRclust_1.7.0.tar.gz
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* using log directory ‘/Users/biocbuild/bbs-3.11-bioc/meat/ddPCRclust.Rcheck’
* using R Under development (unstable) (2019-12-14 r77572)
* using platform: x86_64-apple-darwin15.6.0 (64-bit)
* using session charset: UTF-8
* using option ‘--no-vignettes’
* checking for file ‘ddPCRclust/DESCRIPTION’ ... OK
* this is package ‘ddPCRclust’ version ‘1.7.0’
* 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 for sufficient/correct file permissions ... OK
* checking whether package ‘ddPCRclust’ 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
* 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 sizes of PDF files under ‘inst/doc’ ... OK
* checking files in ‘vignettes’ ... OK
* checking examples ... OK
Examples with CPU (user + system) or elapsed time > 5s
                 user system elapsed
exportPlots    32.065  3.162  33.920
calculateCPDs  23.429  1.488  24.938
exportToExcel  23.495  1.289  24.801
exportToCSV    23.157  1.409  24.569
ddPCRclust     23.122  1.370  24.495
createEnsemble 21.994  0.886  22.882
runSam          9.551  0.714  10.266
runPeaks        9.373  0.068   9.443
* 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 NOTE
See
  ‘/Users/biocbuild/bbs-3.11-bioc/meat/ddPCRclust.Rcheck/00check.log’
for details.

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### Running command:
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###   /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD INSTALL ddPCRclust
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* installing to library ‘/Library/Frameworks/R.framework/Versions/4.0/Resources/library’
* 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
** 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
* DONE (ddPCRclust)

name	user	system	elapsed
calculateCPDs	23.429	1.488	24.938
createEnsemble	21.994	0.886	22.882
ddPCRclust	23.122	1.370	24.495
exportPlots	32.065	3.162	33.920
exportToCSV	23.157	1.409	24.569
exportToExcel	23.495	1.289	24.801
readFiles	0.537	0.019	0.565
readTemplate	0.004	0.001	0.004
runDensity	4.306	0.128	4.434
runPeaks	9.373	0.068	9.443
runSam	9.551	0.714	10.266