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###
### Running command:
###
###   D:\biocbuild\bbs-3.15-bioc\R\bin\R.exe CMD check --no-multiarch --install=check:frenchFISH.install-out.txt --library=D:\biocbuild\bbs-3.15-bioc\R\library --no-vignettes --timings frenchFISH_1.7.0.tar.gz
###
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* using log directory 'D:/biocbuild/bbs-3.15-bioc/meat/frenchFISH.Rcheck'
* using R Under development (unstable) (2021-11-21 r81221)
* using platform: x86_64-w64-mingw32 (64-bit)
* using session charset: ISO8859-1
* using option '--no-vignettes'
* checking for file 'frenchFISH/DESCRIPTION' ... OK
* checking extension type ... Package
* this is package 'frenchFISH' version '1.7.0'
* 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 whether package 'frenchFISH' 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

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###
### Running command:
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###   D:\biocbuild\bbs-3.15-bioc\R\bin\R.exe CMD INSTALL frenchFISH
###
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* installing to library 'D:/biocbuild/bbs-3.15-bioc/R/library'
* installing *source* package 'frenchFISH' ...
** using staged installation
** R
** inst
** byte-compile and prepare package for lazy loading
** help
*** installing help indices
  converting help for package 'frenchFISH'
    finding HTML links ... done
    areAllNonnegativeIntegers               html  
    checkAutomaticCountsEstimatesArguments
                                            html  
    checkManualCountsEstimatesArguments     html  
    convertFishalyserCsvToCountMatrix       html  
    generatePPdat                           html  
    getAutomaticCountsEstimates             html  
    getAverageVolumeFrac                    html  
    getManualCountsEstimates                html  
    getMaxVolumeFrac                        html  
    getMinVolumeFrac                        html  
    getVsegFrac                             html  
** building package indices
** installing vignettes
** testing if installed package can be loaded from temporary location
** testing if installed package can be loaded from final location
** testing if installed package keeps a record of temporary installation path
* DONE (frenchFISH)
Making 'packages.html' ...Warning in packageDescription(i, lib.loc = lib, fields = "Title", encoding = "UTF-8") :
  DESCRIPTION file of package 'MWASTools' is missing or broken
Warning in packageDescription(i, lib.loc = lib, fields = "Title", encoding = "UTF-8") :
  DESCRIPTION file of package 'OncoSimulR' is missing or broken
 done

R Under development (unstable) (2021-11-21 r81221) -- "Unsuffered Consequences"
Copyright (C) 2021 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(frenchFISH)
> 
> test_check("frenchFISH")

Number of observations  not used in the estimation process:  0
Total number of time observations:  4
Number of events:  7

Convergence code:  0
Convergence attained
Loglikelihood:  -3.083

Estimated coefficients: 
  b0 
0.56 
Full coefficients: 
  b0 
0.56 
attr(,"TypeCoeff")
[1] "Fixed: No  fixed parameters"


Number of observations  not used in the estimation process:  0
Total number of time observations:  4
Number of events:  10

Convergence code:  0
Convergence attained
Loglikelihood:  -3.884

Estimated coefficients: 
   b0 
0.223 
Full coefficients: 
   b0 
0.223 
attr(,"TypeCoeff")
[1] "Fixed: No  fixed parameters"


Number of observations  not used in the estimation process:  0
Total number of time observations:  4
Number of events:  6

Convergence code:  0
Convergence attained
Loglikelihood:  -3.863

Estimated coefficients: 
    b0 
-0.288 
Full coefficients: 
    b0 
-0.288 
attr(,"TypeCoeff")
[1] "Fixed: No  fixed parameters"


Number of observations  not used in the estimation process:  0
Total number of time observations:  2
Number of events:  1

Convergence code:  0
Convergence attained
Loglikelihood:  -1.693

Estimated coefficients: 
    b0 
-0.693 
Full coefficients: 
    b0 
-0.693 
attr(,"TypeCoeff")
[1] "Fixed: No  fixed parameters"

[ FAIL 0 | WARN 0 | SKIP 0 | PASS 48 ]
> 
> proc.time()
   user  system elapsed 
   1.81    0.12    1.92