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###
### Running command:
###
###   F:\biocbuild\bbs-3.15-bioc\R\bin\R.exe CMD check --no-multiarch --install=check:openPrimeR.install-out.txt --library=F:\biocbuild\bbs-3.15-bioc\R\library --no-vignettes --timings openPrimeR_1.18.0.tar.gz
###
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* using log directory 'F:/biocbuild/bbs-3.15-bioc/meat/openPrimeR.Rcheck'
* using R version 4.2.1 (2022-06-23 ucrt)
* using platform: x86_64-w64-mingw32 (64-bit)
* using session charset: UTF-8
* using option '--no-vignettes'
* checking for file 'openPrimeR/DESCRIPTION' ... OK
* this is package 'openPrimeR' version '1.18.0'
* 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 11.9Mb
  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
PrimerDesign 13.47   0.69   14.19
Output       11.44   0.70   33.84
PrimerEval    6.84   0.20    7.06
Plots         6.65   0.33    6.99
* 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
  'F:/biocbuild/bbs-3.15-bioc/meat/openPrimeR.Rcheck/00check.log'
for details.

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###
### Running command:
###
###   F:\biocbuild\bbs-3.15-bioc\R\bin\R.exe CMD INSTALL openPrimeR
###
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* installing to library 'F:/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
** 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)

R version 4.2.1 (2022-06-23 ucrt) -- "Funny-Looking Kid"
Copyright (C) 2022 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")
!!! Error: Cannot call ghostscript `mgs' (No such file or directory/The system cannot find the file specified)!
pdfcrop: major issue: So far, you have not checked for updates as a MiKTeX user.
!!! Error: Cannot call ghostscript `mgs' (No such file or directory/The system cannot find the file specified)!
pdfcrop: major issue: So far, you have not checked for updates as a MiKTeX user.
!!! Error: Cannot call ghostscript `mgs' (No such file or directory/The system cannot find the file specified)!
pdfcrop: major issue: So far, you have not checked for updates as a MiKTeX user.
!!! Error: Cannot call ghostscript `mgs' (No such file or directory/The system cannot find the file specified)!
pdfcrop: major issue: So far, you have not checked for updates as a MiKTeX user.
!!! Error: Cannot call ghostscript `mgs' (No such file or directory/The system cannot find the file specified)!
pdfcrop: major issue: So far, you have not checked for updates as a MiKTeX user.
[ 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 
  42.29    2.79   54.95