Package: flowPloidy

Version: 1.8.0

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_1.8.0.tar.gz

StartedAt: 2019-04-15 23:59:06 -0400 (Mon, 15 Apr 2019)

EndedAt: 2019-04-16 00:00:28 -0400 (Tue, 16 Apr 2019)

EllapsedTime: 81.8 seconds

RetCode: 0

Status:  OK

CheckDir: flowPloidy.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:flowPloidy.install-out.txt --library=/Library/Frameworks/R.framework/Versions/Current/Resources/library --no-vignettes --timings flowPloidy_1.8.0.tar.gz
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* using log directory ‘/Users/biocbuild/bbs-3.8-bioc/meat/flowPloidy.Rcheck’
* using R version 3.5.3 (2019-03-11)
* 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 ‘1.8.0’
* 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

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### Running command:
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###   /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD INSTALL flowPloidy
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* 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 3.5.3 (2019-03-11) -- "Great Truth"
Copyright (C) 2019 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
7 model components: a1, a2, a_s, b1, b_s, SC, AG
12 parameters: a1P, a_mean, a_stddev, a2P, linearity, a_sP, b1P, b_mean, b_stddev, b_sP, SCaP, AP
5 special parameters: xx, SCvals, DBvals, TRvals, QDvals
Model fit

Analysis
========

Counts
------
 a1_count  a2_count a_s_count  b1_count b_s_count 
  1442.99    336.58      0.00   2820.64    405.87 

Peak Sizes
----------
a_mean b_mean 
 99.04 136.12 

CVs
---
a_CV b_CV 
 2.2  2.0 

RCS: 1.589 
FlowHist object '222.LMD'
channel: FL3.INT.LIN
2 samples
bins: 256
linearity: variable
debris: SC
8 model components: a1, a2, a_s, b1, b2, b_s, SC, AG
13 parameters: a1P, a_mean, a_stddev, a2P, linearity, a_sP, b1P, b_mean, b_stddev, b2P, b_sP, SCaP, 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
7 model components: a1, a2, a_s, b1, b_s, MC, AG
13 parameters: a1P, a_mean, a_stddev, a2P, linearity, a_sP, b1P, b_mean, b_stddev, b_sP, MCaP, k, AP
5 special parameters: xx, MCvals, DBvals, TRvals, QDvals
Model fit

Analysis
========

Counts
------
 a1_count  a2_count a_s_count  b1_count b_s_count 
   664.23      0.00    195.73   3269.65      0.00 

Peak Sizes
----------
a_mean b_mean 
 77.10 160.79 

CVs
---
a_CV b_CV 
 4.8  7.7 

RCS: 2.22 
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 
  4.283   0.313   4.600 

name	user	system	elapsed
DebrisModels	0	0	0
FlowHist	3.321	0.180	3.536
FlowStandards	0.167	0.008	0.176
ModelComponent	0.003	0.001	0.004
browseFlowHist	2.644	0.101	2.753
fhAccessors	0.180	0.004	0.185
fhAnalyze	0.280	0.008	0.289
findPeaks	0	0	0
pickInit	0.271	0.005	0.277
plotFH	0.203	0.004	0.208
setBins	0.398	0.010	0.411
tabulateFlowHist	0.343	0.015	0.361
updateFlowHist	0.400	0.010	0.413
viewFlowChannels	0.027	0.001	0.028