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CHECK report for flowPloidy on tokay1

This page was generated on 2019-04-13 11:27:11 -0400 (Sat, 13 Apr 2019).

Package 541/1649HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
flowPloidy 1.8.0
Tyler Smith
Snapshot Date: 2019-04-12 17:01:30 -0400 (Fri, 12 Apr 2019)
URL: https://git.bioconductor.org/packages/flowPloidy
Branch: RELEASE_3_8
Last Commit: 3c5dcce
Last Changed Date: 2018-10-30 11:42:02 -0400 (Tue, 30 Oct 2018)
malbec1 Linux (Ubuntu 16.04.6 LTS) / x86_64  OK  OK  OK UNNEEDED, same version exists in internal repository
tokay1 Windows Server 2012 R2 Standard / x64  OK  OK [ OK ] OK UNNEEDED, same version exists in internal repository
merida1 OS X 10.11.6 El Capitan / x86_64  OK  OK  OK  OK UNNEEDED, same version exists in internal repository

Summary

Package: flowPloidy
Version: 1.8.0
Command: C:\Users\biocbuild\bbs-3.8-bioc\R\bin\R.exe CMD check --force-multiarch --install=check:flowPloidy.install-out.txt --library=C:\Users\biocbuild\bbs-3.8-bioc\R\library --no-vignettes --timings flowPloidy_1.8.0.tar.gz
StartedAt: 2019-04-13 02:17:53 -0400 (Sat, 13 Apr 2019)
EndedAt: 2019-04-13 02:20:27 -0400 (Sat, 13 Apr 2019)
EllapsedTime: 154.0 seconds
RetCode: 0
Status:  OK  
CheckDir: flowPloidy.Rcheck
Warnings: 0

Command output

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###
### Running command:
###
###   C:\Users\biocbuild\bbs-3.8-bioc\R\bin\R.exe CMD check --force-multiarch --install=check:flowPloidy.install-out.txt --library=C:\Users\biocbuild\bbs-3.8-bioc\R\library --no-vignettes --timings flowPloidy_1.8.0.tar.gz
###
##############################################################################
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* using log directory 'C:/Users/biocbuild/bbs-3.8-bioc/meat/flowPloidy.Rcheck'
* using R version 3.5.3 (2019-03-11)
* using platform: x86_64-w64-mingw32 (64-bit)
* using session charset: ISO8859-1
* 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 ...Warning: unable to access index for repository https://CRAN.R-project.org/src/contrib:
  cannot open URL 'https://CRAN.R-project.org/src/contrib/PACKAGES'
 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 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
* loading checks for arch 'i386'
** 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
* loading checks for arch 'x64'
** 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 ...
** running examples for arch 'i386' ... OK
** running examples for arch 'x64' ... OK
* checking for unstated dependencies in 'tests' ... OK
* checking tests ...
** running tests for arch 'i386' ...
  Running 'testthat.R'
 OK
** running tests for arch 'x64' ...
  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:
###
###   C:\cygwin\bin\curl.exe -O https://malbec1.bioconductor.org/BBS/3.8/bioc/src/contrib/flowPloidy_1.8.0.tar.gz && rm -rf flowPloidy.buildbin-libdir && mkdir flowPloidy.buildbin-libdir && C:\Users\biocbuild\bbs-3.8-bioc\R\bin\R.exe CMD INSTALL --merge-multiarch --build --library=flowPloidy.buildbin-libdir flowPloidy_1.8.0.tar.gz && C:\Users\biocbuild\bbs-3.8-bioc\R\bin\R.exe CMD INSTALL flowPloidy_1.8.0.zip && rm flowPloidy_1.8.0.tar.gz flowPloidy_1.8.0.zip
###
##############################################################################
##############################################################################


  % Total    % Received % Xferd  Average Speed   Time    Time     Time  Current
                                 Dload  Upload   Total   Spent    Left  Speed

  0     0    0     0    0     0      0      0 --:--:-- --:--:-- --:--:--     0
100 1125k  100 1125k    0     0  20.3M      0 --:--:-- --:--:-- --:--:-- 21.5M

install for i386

* installing *source* package 'flowPloidy' ...
** R
** inst
** byte-compile and prepare package for lazy loading
** help
*** installing help indices
  converting help for package 'flowPloidy'
    finding HTML links ... done
    DebrisModels                            html  
    FlowHist                                html  
    finding level-2 HTML links ... done

    FlowStandards                           html  
    ModelComponent                          html  
    browseFlowHist                          html  
    fhAccessors                             html  
    fhAnalyze                               html  
    fhDoCV                                  html  
    fhDoCounts                              html  
    fhDoNLS                                 html  
    fhDoRCS                                 html  
    fhModels                                html  
    fhStart                                 html  
    findPeaks                               html  
    flowPloidy                              html  
    gauss                                   html  
    pickInit                                html  
    plot.FlowHist                           html  
    plotFH                                  html  
    resetFlowHist                           html  
    setBins                                 html  
    setGate                                 html  
    tabulateFlowHist                        html  
    updateFlowHist                          html  
    viewFlowChannels                        html  
** building package indices
** installing vignettes
** testing if installed package can be loaded
In R CMD INSTALL

install for x64

* installing *source* package 'flowPloidy' ...
** testing if installed package can be loaded
* MD5 sums
packaged installation of 'flowPloidy' as flowPloidy_1.8.0.zip
* DONE (flowPloidy)
In R CMD INSTALL
In R CMD INSTALL
* installing to library 'C:/Users/biocbuild/bbs-3.8-bioc/R/library'
package 'flowPloidy' successfully unpacked and MD5 sums checked
In R CMD INSTALL

Tests output

flowPloidy.Rcheck/tests_i386/testthat.Rout


R version 3.5.3 (2019-03-11) -- "Great Truth"
Copyright (C) 2019 The R Foundation for Statistical Computing
Platform: i386-w64-mingw32/i386 (32-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    195.72   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 
   2.79    0.28    3.11 

flowPloidy.Rcheck/tests_x64/testthat.Rout


R version 3.5.3 (2019-03-11) -- "Great Truth"
Copyright (C) 2019 The R Foundation for Statistical Computing
Platform: x86_64-w64-mingw32/x64 (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 
   2.98    0.15    3.64 

Example timings

flowPloidy.Rcheck/examples_i386/flowPloidy-Ex.timings

nameusersystemelapsed
DebrisModels000
FlowHist3.110.033.14
FlowStandards0.250.000.25
ModelComponent000
browseFlowHist3.000.013.01
fhAccessors0.220.000.22
fhAnalyze0.330.000.32
findPeaks000
pickInit0.240.000.23
plotFH0.180.000.19
setBins0.470.020.48
tabulateFlowHist0.290.000.30
updateFlowHist0.440.000.44
viewFlowChannels0.030.000.03

flowPloidy.Rcheck/examples_x64/flowPloidy-Ex.timings

nameusersystemelapsed
DebrisModels000
FlowHist303
FlowStandards0.150.020.18
ModelComponent000
browseFlowHist2.660.002.65
fhAccessors0.360.000.36
fhAnalyze0.260.000.27
findPeaks000
pickInit0.210.000.20
plotFH0.170.000.17
setBins0.250.000.25
tabulateFlowHist0.280.000.28
updateFlowHist0.360.000.36
viewFlowChannels0.010.000.02