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### Running command:
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###   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
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* 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
Output       10.79   3.51   43.92
PrimerDesign 12.91   0.73   13.89
PrimerEval    6.87   1.02    8.40
Plots         6.50   0.96    7.46
* 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.