Package: ddPCRclust

Version: 1.3.0

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_1.3.0.tar.gz

StartedAt: 2019-04-09 00:18:45 -0400 (Tue, 09 Apr 2019)

EndedAt: 2019-04-09 00:22:40 -0400 (Tue, 09 Apr 2019)

EllapsedTime: 234.8 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_1.3.0.tar.gz
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* using log directory ‘/Users/biocbuild/bbs-3.9-bioc/meat/ddPCRclust.Rcheck’
* using R Under development (unstable) (2018-11-27 r75683)
* 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 ‘1.3.0’
* 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 or elapsed time > 5s
                 user system elapsed
exportPlots    23.259  1.373  24.037
calculateCPDs  17.752  0.579  18.499
createEnsemble 16.028  0.419  16.565
exportToExcel  15.590  0.454  16.172
ddPCRclust     15.471  0.423  16.038
exportToCSV    15.250  0.492  15.797
runSam          6.964  0.317   7.321
runPeaks        6.426  0.037   6.513
* 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-3.9-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/3.6/Resources/library’
* installing *source* package ‘ddPCRclust’ ...
** 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
Warning: replacing previous import ‘flowCore::plot’ by ‘graphics::plot’ when loading ‘flowDensity’
* DONE (ddPCRclust)

name	user	system	elapsed
calculateCPDs	17.752	0.579	18.499
createEnsemble	16.028	0.419	16.565
ddPCRclust	15.471	0.423	16.038
exportPlots	23.259	1.373	24.037
exportToCSV	15.250	0.492	15.797
exportToExcel	15.590	0.454	16.172
readFiles	0.347	0.008	0.358
readTemplate	0.002	0.000	0.002
runDensity	2.994	0.057	3.065
runPeaks	6.426	0.037	6.513
runSam	6.964	0.317	7.321