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###
### Running command:
###
###   D:\biocbuild\bbs-3.15-bioc\R\bin\R.exe CMD check --no-multiarch --install=check:openPrimeR.install-out.txt --library=D:\biocbuild\bbs-3.15-bioc\R\library --no-vignettes --timings openPrimeR_1.17.0.tar.gz
###
##############################################################################
##############################################################################


* using log directory 'D:/biocbuild/bbs-3.15-bioc/meat/openPrimeR.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 'openPrimeR/DESCRIPTION' ... OK
* this is package 'openPrimeR' version '1.17.0'
* 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 ... NOTE
Found the following hidden files and directories:
  .travis.yml
These were most likely included in error. See section 'Package
structure' in the 'Writing R Extensions' manual.
* checking for portable file names ... OK
* checking whether package 'openPrimeR' can be installed ... OK
* checking installed package size ... NOTE
  installed size is 12.3Mb
  sub-directories of 1Mb or more:
    R         1.3Mb
    extdata  10.0Mb
* 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 contents of 'data' directory ... OK
* checking data for non-ASCII characters ... OK
* checking data for ASCII and uncompressed saves ... OK
* checking R/sysdata.rda ... OK
* checking files in 'vignettes' ... OK
* checking examples ... OK
Examples with CPU (user + system) or elapsed time > 5s
             user system elapsed
Output       8.44   2.15   35.39
PrimerDesign 8.20   0.22    8.42
* 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: 2 NOTEs
See
  'D:/biocbuild/bbs-3.15-bioc/meat/openPrimeR.Rcheck/00check.log'
for details.

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###
### Running command:
###
###   D:\biocbuild\bbs-3.15-bioc\R\bin\R.exe CMD INSTALL openPrimeR
###
##############################################################################
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* installing to library 'D:/biocbuild/bbs-3.15-bioc/R/library'
* installing *source* package 'openPrimeR' ...
** using staged installation
** R
** data
** inst
** byte-compile and prepare package for lazy loading
** help
*** installing help indices
  converting help for package 'openPrimeR'
    finding HTML links ... done
    AnalysisStats                           html  
    Data                                    html  
    Input                                   html  
    Output                                  html  
    Plots                                   html  
    PrimerDesign                            html  
    PrimerEval                              html  
    Primers-method                          html  
    Scoring                                 html  
    Settings                                html  
REDIRECT:topic	 Previous alias or file overwritten by alias: D:/biocbuild/bbs-3.15-bioc/R/library/00LOCK-openPrimeR/00new/openPrimeR/help/Settings.html
    Templates-method                        html  
    TemplatesFunctions                      html  
    check_cvg_constraints                   html  
    create_report-Primers-Templates-method
                                            html  
    create_report-list-list-method          html  
    filterLimits-methods                    html  
    filters-methods                         html  
    get_cvg_stats-Primers-method            html  
    get_cvg_stats-list-method               html  
    openPrimeR-package                      html  
    plot_constraint-Primers-method          html  
    plot_constraint-list-method             html  
    plot_constraint_deviation-Primers-method
                                            html  
    plot_constraint_deviation-list-method   html  
    plot_constraint_fulfillment-Primers-method
                                            html  
    plot_constraint_fulfillment-list-method
                                            html  
    plot_cvg_constraints-Primers-method     html  
    plot_cvg_constraints-list-method        html  
    plot_primer_binding_regions-Primers-Templates-method
                                            html  
    plot_primer_binding_regions-list-list-method
                                            html  
    plot_primer_cvg-Primers-Templates-method
                                            html  
    plot_primer_cvg-list-list-method        html  
    plot_template_cvg-Primers-Templates-method
                                            html  
    plot_template_cvg-list-list-method      html  
    runTutorial                             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 (openPrimeR)
Making 'packages.html' ... 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.

> require(testthat)
Loading required package: testthat
> require(openPrimeR)
Loading required package: openPrimeR
There are missing/non-functioning external tools.
To use the full potential of openPrimeR, please make sure
that the required versions of the speciied tools are
 
                installed and that they are functional:
o MELTING (http://www.ebi.ac.uk/biomodels/tools/melting/)
o ViennaRNA (http://www.tbi.univie.ac.at/RNA/)
o OligoArrayAux (http://unafold.rna.albany.edu/OligoArrayAux.php)
o MAFFT (http://mafft.cbrc.jp/alignment/software/)
> #test_package("openPrimeR") 
> test_check("openPrimeR")
[ FAIL 0 | WARN 9 | SKIP 9 | PASS 1467 ]

== Skipped tests ===============================================================
* MAFFT not available. (1)
* OligoArrayAux not available. (5)
* On Bioconductor (1)
* Secondary structure tests require ViennaRNA. (1)
* empty test (1)

[ FAIL 0 | WARN 9 | SKIP 9 | PASS 1467 ]
> 
> proc.time()
   user  system elapsed 
  26.70    1.51   55.09