Package: flowStats

Version: 3.41.3

Command: /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD check --install=check:flowStats.install-out.txt --library=/Library/Frameworks/R.framework/Versions/Current/Resources/library --no-vignettes --timings flowStats_3.41.3.tar.gz

StartedAt: 2019-04-09 00:55:52 -0400 (Tue, 09 Apr 2019)

EndedAt: 2019-04-09 00:59:12 -0400 (Tue, 09 Apr 2019)

EllapsedTime: 199.6 seconds

RetCode: 0

Status:  OK

CheckDir: flowStats.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:flowStats.install-out.txt --library=/Library/Frameworks/R.framework/Versions/Current/Resources/library --no-vignettes --timings flowStats_3.41.3.tar.gz
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* using log directory ‘/Users/biocbuild/bbs-3.9-bioc/meat/flowStats.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 ‘flowStats/DESCRIPTION’ ... OK
* checking extension type ... Package
* this is package ‘flowStats’ version ‘3.41.3’
* 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 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
warpSet   20.157  4.786  25.111
gaussNorm  7.709  0.525   8.631
lymphGate  4.543  0.303   5.079
* 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
  ‘/Users/biocbuild/bbs-3.9-bioc/meat/flowStats.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 flowStats
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* installing to library ‘/Library/Frameworks/R.framework/Versions/3.6/Resources/library’
* installing *source* package ‘flowStats’ ...
** 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
* DONE (flowStats)

R Under development (unstable) (2018-11-27 r75683) -- "Unsuffered Consequences"
Copyright (C) 2018 The R Foundation for Statistical Computing
Platform: x86_64-apple-darwin15.6.0 (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 FAILED: 0
> 
> proc.time()
   user  system elapsed 
  6.666   0.396   7.086 

name	user	system	elapsed
autoGate	2.278	0.103	2.395
binByRef	1.115	0.090	1.212
calcPBChiSquare	1.151	0.089	1.251
calcPearsonChi	0.982	0.076	1.066
curv1Filter-class	0.312	0.033	0.346
curv2Filter-class	1.621	0.169	1.804
curvPeaks	0.657	0.072	0.733
density1d	3.441	0.398	3.864
gate_singlet	0.000	0.001	0.000
gaussNorm	7.709	0.525	8.631
gpaSet	4.137	0.159	4.387
iProcrustes	0.217	0.003	0.226
idFeaturesByBackgating	1.598	0.012	1.632
landmarkMatrix	0.955	0.116	1.084
lymphGate	4.543	0.303	5.079
normalize	0.001	0.001	0.000
overton_like	0.01	0.00	0.01
plotBins	1.102	0.095	1.225
proBin	0.806	0.059	0.876
quadrantGate	0.000	0.000	0.001
rangeGate	3.665	0.405	4.113
warpSet	20.157	4.786	25.111