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CHECK report for flowPloidy on malbec2

This page was generated on 2018-10-17 08:29:31 -0400 (Wed, 17 Oct 2018).

Package 512/1561HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
flowPloidy 1.6.0
Tyler Smith
Snapshot Date: 2018-10-15 16:45:08 -0400 (Mon, 15 Oct 2018)
URL: https://git.bioconductor.org/packages/flowPloidy
Branch: RELEASE_3_7
Last Commit: ead8e20
Last Changed Date: 2018-07-30 12:50:33 -0400 (Mon, 30 Jul 2018)
malbec2 Linux (Ubuntu 16.04.1 LTS) / x86_64  OK  OK [ OK ]UNNEEDED, same version exists in internal repository
tokay2 Windows Server 2012 R2 Standard / x64  OK  OK  OK  OK UNNEEDED, same version exists in internal repository
merida2 OS X 10.11.6 El Capitan / x86_64  OK  OK  OK  OK UNNEEDED, same version exists in internal repository

Summary

Package: flowPloidy
Version: 1.6.0
Command: /home/biocbuild/bbs-3.7-bioc/R/bin/R CMD check --install=check:flowPloidy.install-out.txt --library=/home/biocbuild/bbs-3.7-bioc/R/library --no-vignettes --timings flowPloidy_1.6.0.tar.gz
StartedAt: 2018-10-16 00:26:41 -0400 (Tue, 16 Oct 2018)
EndedAt: 2018-10-16 00:27:35 -0400 (Tue, 16 Oct 2018)
EllapsedTime: 53.9 seconds
RetCode: 0
Status:  OK 
CheckDir: flowPloidy.Rcheck
Warnings: 0

Command output

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###
### Running command:
###
###   /home/biocbuild/bbs-3.7-bioc/R/bin/R CMD check --install=check:flowPloidy.install-out.txt --library=/home/biocbuild/bbs-3.7-bioc/R/library --no-vignettes --timings flowPloidy_1.6.0.tar.gz
###
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* using log directory ‘/home/biocbuild/bbs-3.7-bioc/meat/flowPloidy.Rcheck’
* using R version 3.5.1 Patched (2018-07-12 r74967)
* using platform: x86_64-pc-linux-gnu (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 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


Installation output

flowPloidy.Rcheck/00install.out

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###
### Running command:
###
###   /home/biocbuild/bbs-3.7-bioc/R/bin/R CMD INSTALL flowPloidy
###
##############################################################################
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* installing to library ‘/home/biocbuild/bbs-3.7-bioc/R/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)

Tests output

flowPloidy.Rcheck/tests/testthat.Rout


R version 3.5.1 Patched (2018-07-12 r74967) -- "Feather Spray"
Copyright (C) 2018 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(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 | 3334.172| 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 
  2.560   0.080   2.741 

Example timings

flowPloidy.Rcheck/flowPloidy-Ex.timings

nameusersystemelapsed
DebrisModels0.0000.0000.001
FlowHist1.9880.0282.121
FlowStandards0.0760.0000.073
ModelComponent0.0040.0000.003
browseFlowHist1.4960.0001.497
fhAccessors0.0720.0000.070
fhAnalyze0.10.00.1
findPeaks000
pickInit0.1440.0000.144
plotFH0.0720.0000.073
setBins0.2720.0000.270
tabulateFlowHist0.1120.0000.111
updateFlowHist0.1480.0000.149
viewFlowChannels0.020.000.02