Package: flowStats

Version: 3.42.0

Command: /home/biocbuild/bbs-3.9-bioc/R/bin/R CMD check --install=check:flowStats.install-out.txt --library=/home/biocbuild/bbs-3.9-bioc/R/library --no-vignettes --timings flowStats_3.42.0.tar.gz

StartedAt: 2019-10-16 01:41:56 -0400 (Wed, 16 Oct 2019)

EndedAt: 2019-10-16 01:44:42 -0400 (Wed, 16 Oct 2019)

EllapsedTime: 165.8 seconds

RetCode: 0

Status:  OK

CheckDir: flowStats.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:flowStats.install-out.txt --library=/home/biocbuild/bbs-3.9-bioc/R/library --no-vignettes --timings flowStats_3.42.0.tar.gz
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* using log directory ‘/home/biocbuild/bbs-3.9-bioc/meat/flowStats.Rcheck’
* using R version 3.6.1 (2019-07-05)
* using platform: x86_64-pc-linux-gnu (64-bit)
* using session charset: UTF-8
* using option ‘--no-vignettes’
* checking for file ‘flowStats/DESCRIPTION’ ... OK
* checking extension type ... Package
* this is package ‘flowStats’ version ‘3.42.0’
* package encoding: UTF-8
* 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 ‘flowStats’ 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 ... NOTE
Missing object imported by a ':::' call: ‘flowWorkspace:::.isBooleanGate.graphNEL’
Unexported objects imported by ':::' calls:
  ‘flowCore:::checkClass’ ‘flowCore:::copyFlowSet’
  ‘flowCore:::findTimeChannel’ ‘flowCore:::inPolygon’
  ‘flowViz:::evalError’ ‘flowViz:::plotType’
  ‘flowWorkspace:::.isBoolGate’
  See the note in ?`:::` about the use of this operator.
* checking S3 generic/method consistency ... OK
* checking replacement functions ... OK
* checking foreign function calls ... OK
* checking R code for possible problems ... NOTE
.plotGPAprocess: no visible binding for global variable ‘whichS’
.plotGPAprocess: no visible binding for global variable ‘cluster’
.plotWorkFlow: no visible binding for global variable ‘cluster’
.plotWorkFlow: no visible binding for global variable ‘bogus’
.usingSVD: no visible binding for global variable ‘params’
density1d_simple: no visible binding for global variable ‘y’
normQA: no visible binding for global variable ‘group’
normQA: no visible binding for global variable ‘hasPeak’
Undefined global functions or variables:
  bogus cluster group hasPeak params whichS y
* 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 contents of ‘data’ directory ... OK
* checking data for non-ASCII characters ... OK
* checking data for ASCII and uncompressed saves ... OK
* checking files in ‘vignettes’ ... OK
* checking examples ... OK
Examples with CPU or elapsed time > 5s
            user system elapsed
warpSet   16.344  0.012  16.362
gaussNorm  5.971  0.024   5.994
* checking for unstated dependencies in ‘tests’ ... OK
* checking tests ...
  Running ‘testthat.R’
 OK
* 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: 2 NOTEs
See
  ‘/home/biocbuild/bbs-3.9-bioc/meat/flowStats.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 flowStats
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* installing to library ‘/home/biocbuild/bbs-3.9-bioc/R/library’
* installing *source* package ‘flowStats’ ...
** using staged installation
** R
** data
** byte-compile and prepare package for lazy loading
** help
*** installing help indices
** building package indices
** installing vignettes
** testing if installed package can be loaded from temporary location
** testing if installed package can be loaded from final location
** testing if installed package keeps a record of temporary installation path
* DONE (flowStats)

R version 3.6.1 (2019-07-05) -- "Action of the Toes"
Copyright (C) 2019 The R Foundation for Statistical Computing
Platform: x86_64-pc-linux-gnu (64-bit)

R is free software and comes with ABSOLUTELY NO WARRANTY.
You are welcome to redistribute it under certain conditions.
Type 'license()' or 'licence()' for distribution details.

R is a collaborative project with many contributors.
Type 'contributors()' for more information and
'citation()' on how to cite R or R packages in publications.

Type 'demo()' for some demos, 'help()' for on-line help, or
'help.start()' for an HTML browser interface to help.
Type 'q()' to quit R.

> library(testthat)
> library(flowStats)
Loading required package: flowCore
Loading required package: cluster
Loading required package: flowWorkspace
Loading required package: ncdfFlow
Loading required package: RcppArmadillo
Loading required package: BH
> 
> test_check("flowStats")
══ testthat results  ═══════════════════════════════════════════════════════════
[ OK: 6 | SKIPPED: 0 | WARNINGS: 0 | FAILED: 0 ]
> 
> proc.time()
   user  system elapsed 
  7.158   0.260   7.409 

name	user	system	elapsed
autoGate	2.353	0.052	2.405
binByRef	0.831	0.020	0.851
calcPBChiSquare	0.586	0.020	0.606
calcPearsonChi	1.080	0.024	1.104
curv1Filter-class	0.207	0.000	0.207
curv2Filter-class	0.952	0.028	0.979
curvPeaks	0.507	0.020	0.527
density1d	2.74	0.06	2.80
gate_singlet	0.000	0.000	0.001
gaussNorm	5.971	0.024	5.994
gpaSet	4.377	0.008	4.385
iProcrustes	0.166	0.000	0.166
idFeaturesByBackgating	1.313	0.004	1.317
landmarkMatrix	0.851	0.028	0.880
lymphGate	3.648	0.036	3.683
normalize	0	0	0
overton_like	0.006	0.000	0.006
plotBins	0.767	0.016	0.783
proBin	0.518	0.008	0.527
quadrantGate	0	0	0
rangeGate	2.910	0.012	2.923
warpSet	16.344	0.012	16.362