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### Running command:
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###   /Library/Frameworks/R.framework/Resources/bin/R CMD check --install=check:openPrimeR.install-out.txt --library=/Library/Frameworks/R.framework/Resources/library --no-vignettes --timings openPrimeR_1.22.0.tar.gz
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* using log directory ‘/Users/biocbuild/bbs-3.17-bioc-mac-arm64/meat/openPrimeR.Rcheck’
* using R version 4.3.1 (2023-06-16)
* using platform: aarch64-apple-darwin20 (64-bit)
* R was compiled by
    Apple clang version 14.0.0 (clang-1400.0.29.202)
    GNU Fortran (GCC) 12.2.0
* running under: macOS Monterey 12.6.7
* using session charset: UTF-8
* using option ‘--no-vignettes’
* checking for file ‘openPrimeR/DESCRIPTION’ ... OK
* this is package ‘openPrimeR’ version ‘1.22.0’
* 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 for sufficient/correct file permissions ... OK
* checking whether package ‘openPrimeR’ can be installed ... OK
* checking installed package size ... NOTE
  installed size is 12.1Mb
  sub-directories of 1Mb or more:
    R         1.3Mb
    extdata  10.2Mb
* 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 startup messages can be suppressed ... NOTE
The number of cores for was set to '2' by 'parallel_setup()'.

It looks like this package (or a package it requires) has a startup
message which cannot be suppressed: see ?packageStartupMessage.
* 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       28.803 17.703  62.081
PrimerDesign 17.608  5.693  34.125
PrimerEval    8.134  5.599  14.247
Plots         8.588  4.813  15.841
Settings      0.867  1.411   7.699
* 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
  ‘/Users/biocbuild/bbs-3.17-bioc-mac-arm64/meat/openPrimeR.Rcheck/00check.log’
for details.

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### Running command:
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###   /Library/Frameworks/R.framework/Resources/bin/R CMD INSTALL openPrimeR
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* installing to library ‘/Library/Frameworks/R.framework/Versions/4.3-arm64/Resources/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
The number of cores for was set to '2' by 'parallel_setup()'.
** testing if installed package can be loaded from final location
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 4.3.1 (2023-06-16) -- "Beagle Scouts"
Copyright (C) 2023 The R Foundation for Statistical Computing
Platform: aarch64-apple-darwin20 (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()'.
> #test_package("openPrimeR") 
> test_check("openPrimeR")
[ FAIL 0 | WARN 5 | SKIP 9 | PASS 1467 ]

══ Skipped tests (9) ═══════════════════════════════════════════════════════════
• MAFFT not available. (1): 'test_primer_design.R:125:9'
• OligoArrayAux not available. (5): 'test_con_dimerization.R:7:9',
  'test_con_dimerization.R:42:9', 'test_con_primer_coverage.R:50:9',
  'test_con_primer_coverage.R:77:9', 'test_con_primer_specificity.R:40:9'
• On Bioconductor (1): 'test_primer_design.R:137:5'
• Secondary structure tests require ViennaRNA. (1):
  'test_con_secondary_structure.R:7:9'
• empty test (1): 'test_primers.R:29:1'

[ FAIL 0 | WARN 5 | SKIP 9 | PASS 1467 ]
> 
> proc.time()
   user  system elapsed 
 52.984  16.452 111.188