Package: flowPloidy

Version: 1.6.0

Command: /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD check --install=check:flowPloidy.install-out.txt --library=/Library/Frameworks/R.framework/Versions/Current/Resources/library --no-vignettes --timings flowPloidy_1.6.0.tar.gz

StartedAt: 2018-10-16 21:24:55 -0400 (Tue, 16 Oct 2018)

EndedAt: 2018-10-16 21:26:06 -0400 (Tue, 16 Oct 2018)

EllapsedTime: 70.8 seconds

RetCode: 0

Status:  OK

CheckDir: flowPloidy.Rcheck

Warnings: 0

##############################################################################
##############################################################################
###
### Running command:
###
###   /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD check --install=check:flowPloidy.install-out.txt --library=/Library/Frameworks/R.framework/Versions/Current/Resources/library --no-vignettes --timings flowPloidy_1.6.0.tar.gz
###
##############################################################################
##############################################################################


* using log directory ‘/Users/biocbuild/bbs-3.7-bioc/meat/flowPloidy.Rcheck’
* using R version 3.5.1 Patched (2018-07-12 r74967)
* using platform: x86_64-apple-darwin15.6.0 (64-bit)
* using session charset: UTF-8
* using option ‘--no-vignettes’
* checking for file ‘flowPloidy/DESCRIPTION’ ... OK
* this is package ‘flowPloidy’ 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 ‘flowPloidy’ 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 ... OK
* 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 sizes of PDF files under ‘inst/doc’ ... OK
* checking files in ‘vignettes’ ... OK
* checking examples ... OK
* 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: OK

##############################################################################
##############################################################################
###
### Running command:
###
###   /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD INSTALL flowPloidy
###
##############################################################################
##############################################################################


* installing to library ‘/Library/Frameworks/R.framework/Versions/3.5/Resources/library’
* installing *source* package ‘flowPloidy’ ...
** R
** inst
** 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 (flowPloidy)

R version 3.5.1 Patched (2018-07-12 r74967) -- "Feather Spray"
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(flowPloidy)
> 
> test_check("flowPloidy")
FlowHist object '188-15.LMD'
channel: FL3.INT.LIN
2 samples
bins: 256
linearity: variable
debris: SC
6 model components: fA1, fA2, brA, fB1, SC, AG
11 parameters: a1, Ma, Sa, a2, d, BRA, b1, Mb, Sb, SCa, Ap
5 special parameters: xx, SCvals, DBvals, TRvals, QDvals
Model fit

Analysis
========

Ratio Peak A / Peak B: 0.727, SE: 0.00039

|       |   counts|    size|   cvs|
|:------|--------:|-------:|-----:|
|Peak A | 1440.229|  99.034| 0.022|
|Peak B | 2827.105| 136.138| 0.020|

RCS: 2.208 
FlowHist object '222.LMD'
channel: FL3.INT.LIN
2 samples
bins: 256
linearity: variable
debris: SC
7 model components: fA1, fA2, brA, fB1, fB2, SC, AG
12 parameters: a1, Ma, Sa, a2, d, BRA, b1, Mb, Sb, b2, SCa, Ap
5 special parameters: xx, SCvals, DBvals, TRvals, QDvals
Model fitting not complete

RCS: NA 
FlowHist object '240+S.LMD'
channel: FL3.INT.LIN
2 samples
bins: 256
linearity: variable
debris: MC
6 model components: fA1, fA2, brA, fB1, MC, AG
12 parameters: a1, Ma, Sa, a2, d, BRA, b1, Mb, Sb, MCa, k, Ap
5 special parameters: xx, MCvals, DBvals, TRvals, QDvals
Model fit

Analysis
========

Ratio Peak A / Peak B: 0.48, SE: 0.00326

|       |   counts|    size|   cvs|
|:------|--------:|-------:|-----:|
|Peak A |  642.085|  77.174| 0.047|
|Peak B | 3334.177| 160.613| 0.078|

RCS: 2.536 
FlowHist object '08.328'
channel: FL2.A
2 samples
bins: 256
linearity: variable
debris: SC
0 model components: 
0 parameters: 
0 special parameters: 
Model fitting not complete

RCS: NA 
══ testthat results  ═══════════════════════════════════════════════════════════
OK: 26 SKIPPED: 0 FAILED: 0
> 
> proc.time()
   user  system elapsed 
  3.555   0.268   3.821 

name	user	system	elapsed
DebrisModels	0.002	0.000	0.002
FlowHist	2.398	0.147	2.564
FlowStandards	0.103	0.005	0.108
ModelComponent	0.005	0.001	0.007
browseFlowHist	1.755	0.084	1.845
fhAccessors	0.094	0.003	0.096
fhAnalyze	0.146	0.006	0.152
findPeaks	0.001	0.000	0.002
pickInit	0.152	0.002	0.160
plotFH	0.086	0.001	0.087
setBins	0.300	0.008	0.309
tabulateFlowHist	0.127	0.002	0.129
updateFlowHist	0.209	0.003	0.212
viewFlowChannels	0.028	0.000	0.029