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CHECK report for ddPCRclust on malbec1

This page was generated on 2019-04-16 11:53:19 -0400 (Tue, 16 Apr 2019).

Package 375/1649HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
ddPCRclust 1.2.0
Benedikt G. Brink
Snapshot Date: 2019-04-15 17:01:12 -0400 (Mon, 15 Apr 2019)
URL: https://git.bioconductor.org/packages/ddPCRclust
Branch: RELEASE_3_8
Last Commit: 85f5df4
Last Changed Date: 2018-10-30 11:42:08 -0400 (Tue, 30 Oct 2018)
malbec1 Linux (Ubuntu 16.04.6 LTS) / x86_64  OK  OK [ OK ]UNNEEDED, same version exists in internal repository
merida1 OS X 10.11.6 El Capitan / x86_64  OK  OK  OK  OK UNNEEDED, same version exists in internal repository

Summary

Package: ddPCRclust
Version: 1.2.0
Command: /home/biocbuild/bbs-3.8-bioc/R/bin/R CMD check --install=check:ddPCRclust.install-out.txt --library=/home/biocbuild/bbs-3.8-bioc/R/library --no-vignettes --timings ddPCRclust_1.2.0.tar.gz
StartedAt: 2019-04-15 23:20:04 -0400 (Mon, 15 Apr 2019)
EndedAt: 2019-04-15 23:23:58 -0400 (Mon, 15 Apr 2019)
EllapsedTime: 233.8 seconds
RetCode: 0
Status:  OK 
CheckDir: ddPCRclust.Rcheck
Warnings: 0

Command output

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### Running command:
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###   /home/biocbuild/bbs-3.8-bioc/R/bin/R CMD check --install=check:ddPCRclust.install-out.txt --library=/home/biocbuild/bbs-3.8-bioc/R/library --no-vignettes --timings ddPCRclust_1.2.0.tar.gz
###
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* using log directory ‘/home/biocbuild/bbs-3.8-bioc/meat/ddPCRclust.Rcheck’
* using R version 3.5.3 (2019-03-11)
* 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 ‘1.2.0’
* 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    24.324  0.164  24.629
calculateCPDs  17.136  0.144  17.700
exportToCSV    16.916  0.068  17.033
createEnsemble 16.692  0.004  16.830
exportToExcel  16.164  0.052  16.316
ddPCRclust     15.624  0.040  15.757
runSam          8.612  0.004   8.624
runPeaks        6.836  0.004   6.901
* 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-3.8-bioc/meat/ddPCRclust.Rcheck/00check.log’
for details.



Installation output

ddPCRclust.Rcheck/00install.out

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### Running command:
###
###   /home/biocbuild/bbs-3.8-bioc/R/bin/R CMD INSTALL ddPCRclust
###
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* installing to library ‘/home/biocbuild/bbs-3.8-bioc/R/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)

Tests output


Example timings

ddPCRclust.Rcheck/ddPCRclust-Ex.timings

nameusersystemelapsed
calculateCPDs17.136 0.14417.700
createEnsemble16.692 0.00416.830
ddPCRclust15.624 0.04015.757
exportPlots24.324 0.16424.629
exportToCSV16.916 0.06817.033
exportToExcel16.164 0.05216.316
readFiles0.4400.0040.682
readTemplate0.0040.0000.002
runDensity3.6440.0083.669
runPeaks6.8360.0046.901
runSam8.6120.0048.624