##############################################################################
##############################################################################
###
### Running command:
###
###   F:\biocbuild\bbs-3.22-bioc\R\bin\R.exe CMD check --no-multiarch --install=check:openPrimeR.install-out.txt --library=F:\biocbuild\bbs-3.22-bioc\R\library --no-vignettes --timings openPrimeR_1.31.1.tar.gz
###
##############################################################################
##############################################################################


* using log directory 'F:/biocbuild/bbs-3.22-bioc/meat/openPrimeR.Rcheck'
* using R version 4.5.1 (2025-06-13 ucrt)
* using platform: x86_64-w64-mingw32
* R was compiled by
    gcc.exe (GCC) 14.2.0
    GNU Fortran (GCC) 14.2.0
* running under: Windows Server 2022 x64 (build 20348)
* using session charset: UTF-8
* using option '--no-vignettes'
* checking for file 'openPrimeR/DESCRIPTION' ... OK
* this is package 'openPrimeR' version '1.31.1'
* package encoding: UTF-8
* checking package namespace information ... OK
* checking package dependencies ... INFO
Imports includes 25 non-default packages.
Importing from so many packages makes the package vulnerable to any of
them becoming unavailable.  Move as many as possible to Suggests and
use conditionally.
* 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 ... INFO
  installed size is 12.4Mb
  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 code 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 whether startup messages can be suppressed ... 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 ... NOTE
checkRd: (-1) get.primer.binding.idx.Rd:24: Lost braces
    24 | Indices in binding for primer with index code{x} that are allowed.
       |                                              ^
* 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 ... NOTE
Documented arguments not in \usage in Rd file 'align.structures.Rd':
  's1'

Documented arguments not in \usage in Rd file 'build.tool.overview.Rd':
  'AVAILBLE.TOOLS' 'If'

Documented arguments not in \usage in Rd file 'check_restriction_sites_single.Rd':
  'The'

Documented arguments not in \usage in Rd file 'compute.Tm.sets.Rd':
  'primers.rev' 'opti.constraints' 'annealing.temp'

Documented arguments not in \usage in Rd file 'constraints_to_unit.Rd':
  'use.HTML'

Documented arguments not in \usage in Rd file 'create.PCR.table.Rd':
  'format.tyep'

Documented arguments not in \usage in Rd file 'create.k.mers.Rd':
  'seq'

Documented arguments not in \usage in Rd file 'create.primer.ranges.Rd':
  'start.posiion'

Documented arguments not in \usage in Rd file 'create.primers.naive.Rd':
  'updatProgress'

Documented arguments not in \usage in Rd file 'estimate.cvg.Rd':
  'seqs'

Documented arguments not in \usage in Rd file 'evaluate.fw.rev.combinations.Rd':
  'opti.rev.indices'

Documented arguments not in \usage in Rd file 'get.melting.temp.diff.Rd':
  'Tmr.rev'

Documented arguments not in \usage in Rd file 'get.primer.identifier.string.Rd':
  'seq.identifiers'

Documented arguments not in \usage in Rd file 'get_cvg_stats-Primers-method.Rd':
  'primer.df' 'template.df'

Documented arguments not in \usage in Rd file 'optimize.primer.cvg.Rd':
  'template_conc'

Documented arguments not in \usage in Rd file 'plot.filtering.runtime.Rd':
  'filered.stats'

Documented arguments not in \usage in Rd file 'plot_constraint-list-method.Rd':
  'constraint.settings'

Documented arguments not in \usage in Rd file 'plot_constraint_deviation-list-method.Rd':
  'constraint.df'

Documented arguments not in \usage in Rd file 'plot_primer_cvg-Primers-Templates-method.Rd':
  'p.df' 'template.df' 'excluded.seqs'

Documented arguments not in \usage in Rd file 'plot_template_cvg-list-list-method.Rd':
  'colors'

Documented arguments not in \usage in Rd file 'read.sequences.Rd':
  'The'

Documented arguments not in \usage in Rd file 'remove.seqs.by.keyword.Rd':
  'Header'

Documented arguments not in \usage in Rd file 'restriction_hits.Rd':
  'bad.region'

Documented arguments not in \usage in Rd file 'sanitize_path.Rd':
  'sub_char'

Documented arguments not in \usage in Rd file 'solve.ILP.Rd':
  'deltaG.cutoff' 'deltaG.limit'

Documented arguments not in \usage in Rd file 'update.individual.binding.region.Rd':
  'Template'

Documented arguments not in \usage in Rd file 'visualize.all.results.Rd':
  'template_conc'

Documented arguments not in \usage in Rd file 'visualize.filtering.results.Rd':
  'template_conc'

Functions with \usage entries need to have the appropriate \alias
entries, and all their arguments documented.
The \usage entries must correspond to syntactically valid R code.
See chapter 'Writing R documentation files' in the 'Writing R
Extensions' manual.
* 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 13.58   0.64   14.29
Output       10.58   3.27   45.60
Plots         7.31   1.17    8.68
PrimerEval    6.36   0.83    7.17
* checking for unstated dependencies in 'tests' ... OK
* checking tests ...
  Running 'testthat.R'
 OK
* checking for unstated dependencies in vignettes ... OK
* checking package vignettes ... 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
  'F:/biocbuild/bbs-3.22-bioc/meat/openPrimeR.Rcheck/00check.log'
for details.

##############################################################################
##############################################################################
###
### Running command:
###
###   F:\biocbuild\bbs-3.22-bioc\R\bin\R.exe CMD INSTALL openPrimeR
###
##############################################################################
##############################################################################


* installing to library 'F:/biocbuild/bbs-3.22-bioc/R/library'
* installing *source* package 'openPrimeR' ...
** this is package 'openPrimeR' version '1.31.1'
** 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 4.5.1 (2025-06-13 ucrt) -- "Great Square Root"
Copyright (C) 2025 The R Foundation for Statistical Computing
Platform: x86_64-w64-mingw32/x64

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")
pdftex: major issue: User/administrator updates are out-of-sync.
pdfcrop: major issue: User/administrator updates are out-of-sync.
pdftex: major issue: User/administrator updates are out-of-sync.
pdfcrop: major issue: User/administrator updates are out-of-sync.
pdftex: major issue: User/administrator updates are out-of-sync.
pdfcrop: major issue: User/administrator updates are out-of-sync.
pdftex: major issue: User/administrator updates are out-of-sync.
pdfcrop: major issue: User/administrator updates are out-of-sync.
pdftex: major issue: User/administrator updates are out-of-sync.
pdfcrop: major issue: User/administrator updates are out-of-sync.
[ FAIL 0 | WARN 3 | 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 3 | SKIP 9 | PASS 1467 ]
> 
> proc.time()
   user  system elapsed 
  41.21    3.85   57.57