Package: ddPCRclust

Version: 1.3.0

Command: /home/biocbuild/bbs-3.9-bioc/R/bin/R CMD check --install=check:ddPCRclust.install-out.txt --library=/home/biocbuild/bbs-3.9-bioc/R/library --no-vignettes --timings ddPCRclust_1.3.0.tar.gz

StartedAt: 2019-04-08 23:52:53 -0400 (Mon, 08 Apr 2019)

EndedAt: 2019-04-08 23:56:36 -0400 (Mon, 08 Apr 2019)

EllapsedTime: 222.7 seconds

RetCode: 0

Status:  OK

CheckDir: ddPCRclust.Rcheck

Warnings: 0

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### Running command:
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###   /home/biocbuild/bbs-3.9-bioc/R/bin/R CMD check --install=check:ddPCRclust.install-out.txt --library=/home/biocbuild/bbs-3.9-bioc/R/library --no-vignettes --timings ddPCRclust_1.3.0.tar.gz
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* using log directory ‘/home/biocbuild/bbs-3.9-bioc/meat/ddPCRclust.Rcheck’
* using R Under development (unstable) (2019-03-18 r76245)
* 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 ‘1.3.0’
* 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 files in ‘vignettes’ ... OK
* checking examples ... OK
Examples with CPU or elapsed time > 5s
                 user system elapsed
exportPlots    20.948  0.256  21.319
ddPCRclust     16.365  0.159  16.635
calculateCPDs  15.818  0.220  16.184
createEnsemble 15.771  0.012  15.903
exportToExcel  15.158  0.128  15.308
exportToCSV    14.730  0.131  14.924
runSam          7.344  0.000   7.383
runPeaks        6.326  0.008   6.374
* 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-3.9-bioc/meat/ddPCRclust.Rcheck/00check.log’
for details.

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### Running command:
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###   /home/biocbuild/bbs-3.9-bioc/R/bin/R CMD INSTALL ddPCRclust
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* installing to library ‘/home/biocbuild/bbs-3.9-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	15.818	0.220	16.184
createEnsemble	15.771	0.012	15.903
ddPCRclust	16.365	0.159	16.635
exportPlots	20.948	0.256	21.319
exportToCSV	14.730	0.131	14.924
exportToExcel	15.158	0.128	15.308
readFiles	0.384	0.000	0.426
readTemplate	0.002	0.000	0.002
runDensity	3.268	0.012	3.328
runPeaks	6.326	0.008	6.374
runSam	7.344	0.000	7.383