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### Running command:
###
###   /home/biocbuild/bbs-3.12-bioc/R/bin/R CMD check --install=check:openPrimeR.install-out.txt --library=/home/biocbuild/bbs-3.12-bioc/R/library --no-vignettes --timings openPrimeR_1.12.1.tar.gz
###
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* using log directory ‘/home/biocbuild/bbs-3.12-bioc/meat/openPrimeR.Rcheck’
* using R version 4.0.5 (2021-03-31)
* using platform: x86_64-pc-linux-gnu (64-bit)
* using session charset: UTF-8
* using option ‘--no-vignettes’
* checking for file ‘openPrimeR/DESCRIPTION’ ... OK
* this is package ‘openPrimeR’ version ‘1.12.1’
* 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 for sufficient/correct file permissions ... 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  10.3Mb
* 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 ... NOTE
Warning in check.tool.function() :
  ViennaRNA had version < 2.4.1. Disabling ViennaRNA.

A namespace must be able to be loaded with just the base namespace
loaded: otherwise if the namespace gets loaded by a saved object, the
session will be unable to start.

Probably some imports need to be declared in the NAMESPACE file.
* 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
PrimerDesign 20.972 16.768  32.713
Output       22.476  5.436  31.370
Plots        10.736  3.932  13.861
PrimerEval    9.192  4.252   9.484
Settings      0.472  9.004  10.701
* 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: 3 NOTEs
See
  ‘/home/biocbuild/bbs-3.12-bioc/meat/openPrimeR.Rcheck/00check.log’
for details.

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### Running command:
###
###   /home/biocbuild/bbs-3.12-bioc/R/bin/R CMD INSTALL openPrimeR
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* installing to library ‘/home/biocbuild/bbs-3.12-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
** building package indices
** installing vignettes
** testing if installed package can be loaded from temporary location
Warning in check.tool.function() :
  ViennaRNA had version < 2.4.1. Disabling ViennaRNA.
Warning in check.tool.function() :
  ViennaRNA had version < 2.4.1. Disabling ViennaRNA.
The number of cores for was set to '2' by 'parallel_setup()'.
** testing if installed package can be loaded from final location
Warning in check.tool.function() :
  ViennaRNA had version < 2.4.1. Disabling ViennaRNA.
Warning in check.tool.function() :
  ViennaRNA had version < 2.4.1. Disabling ViennaRNA.
The number of cores for was set to '2' by 'parallel_setup()'.
** testing if installed package keeps a record of temporary installation path
* DONE (openPrimeR)

R version 4.0.5 (2021-03-31) -- "Shake and Throw"
Copyright (C) 2021 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.

> 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/)
The number of cores for was set to '2' by 'parallel_setup()'.
Warning messages:
1: In check.tool.function() :
  ViennaRNA had version < 2.4.1. Disabling ViennaRNA.
2: In check.tool.function() :
  ViennaRNA had version < 2.4.1. Disabling ViennaRNA.
> #test_package("openPrimeR") 
> test_check("openPrimeR")
══ Skipped tests ═══════════════════════════════════════════════════════════════
• MAFFT not available. (1)
• OligoArrayAux not available. (5)
• On Bioconductor (1)
• Secondary structure tests require ViennaRNA. (1)

[ FAIL 0 | WARN 55 | SKIP 8 | PASS 1467 ]
> 
> proc.time()
   user  system elapsed 
 63.232  42.704 109.402