Package: ddPCRclust

Version: 1.6.0

Command: /home/biocbuild/bbs-3.10-bioc/R/bin/R CMD check --install=check:ddPCRclust.install-out.txt --library=/home/biocbuild/bbs-3.10-bioc/R/library --no-vignettes --timings ddPCRclust_1.6.0.tar.gz

StartedAt: 2020-04-15 05:30:02 -0400 (Wed, 15 Apr 2020)

EndedAt: 2020-04-15 05:33:50 -0400 (Wed, 15 Apr 2020)

EllapsedTime: 227.9 seconds

RetCode: 0

Status:  OK

CheckDir: ddPCRclust.Rcheck

Warnings: 0

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### Running command:
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###   /home/biocbuild/bbs-3.10-bioc/R/bin/R CMD check --install=check:ddPCRclust.install-out.txt --library=/home/biocbuild/bbs-3.10-bioc/R/library --no-vignettes --timings ddPCRclust_1.6.0.tar.gz
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* using log directory ‘/home/biocbuild/bbs-3.10-bioc/meat/ddPCRclust.Rcheck’
* using R version 3.6.3 (2020-02-29)
* using platform: x86_64-pc-linux-gnu (64-bit)
* using session charset: UTF-8
* using option ‘--no-vignettes’
* checking for file ‘ddPCRclust/DESCRIPTION’ ... OK
* this is package ‘ddPCRclust’ version ‘1.6.0’
* 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 files in ‘vignettes’ ... OK
* checking examples ... OK
Examples with CPU or elapsed time > 5s
                 user system elapsed
exportPlots    22.772  0.356  23.360
ddPCRclust     17.704  0.152  18.143
calculateCPDs  16.960  0.188  17.289
exportToExcel  16.640  0.160  16.837
exportToCSV    15.904  0.176  16.120
createEnsemble 15.908  0.024  16.041
runSam          6.440  0.020   6.475
runPeaks        5.240  0.020   5.286
* 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
  ‘/home/biocbuild/bbs-3.10-bioc/meat/ddPCRclust.Rcheck/00check.log’
for details.

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### Running command:
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###   /home/biocbuild/bbs-3.10-bioc/R/bin/R CMD INSTALL ddPCRclust
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* installing to library ‘/home/biocbuild/bbs-3.10-bioc/R/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	16.960	0.188	17.289
createEnsemble	15.908	0.024	16.041
ddPCRclust	17.704	0.152	18.143
exportPlots	22.772	0.356	23.360
exportToCSV	15.904	0.176	16.120
exportToExcel	16.640	0.160	16.837
readFiles	0.400	0.000	0.619
readTemplate	0.000	0.004	0.002
runDensity	3.336	0.004	3.346
runPeaks	5.240	0.020	5.286
runSam	6.440	0.020	6.475