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### Running command:
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###   /home/biocbuild/bbs-3.22-bioc/R/bin/R CMD check --install=check:openPrimeR.install-out.txt --library=/home/biocbuild/bbs-3.22-bioc/R/site-library --timings openPrimeR_1.31.1.tar.gz
###
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* using log directory ‘/home/biocbuild/bbs-3.22-bioc/meat/openPrimeR.Rcheck’
* using R version 4.5.1 Patched (2025-08-23 r88802)
* using platform: x86_64-pc-linux-gnu
* R was compiled by
    gcc (Ubuntu 13.3.0-6ubuntu2~24.04) 13.3.0
    GNU Fortran (Ubuntu 13.3.0-6ubuntu2~24.04) 13.3.0
* running under: Ubuntu 24.04.3 LTS
* using session charset: UTF-8
* 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 for sufficient/correct file permissions ... OK
* checking whether package ‘openPrimeR’ can be installed ... OK
* checking installed package size ... INFO
  installed size is 12.8Mb
  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 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 loading without being on the library search path ... OK
* checking whether 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 ... 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       17.944  1.829  19.311
PrimerDesign 14.147  5.193  12.418
Plots         6.168  1.200   6.492
PrimerEval    5.322  1.832   4.339
* 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 re-building of vignette outputs ... OK
* checking PDF version of manual ... OK
* DONE

Status: 4 NOTEs
See
  ‘/home/biocbuild/bbs-3.22-bioc/meat/openPrimeR.Rcheck/00check.log’
for details.

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###
### Running command:
###
###   /home/biocbuild/bbs-3.22-bioc/R/bin/R CMD INSTALL openPrimeR
###
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* installing to library ‘/home/biocbuild/bbs-3.22-bioc/R/site-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
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 4.5.1 Patched (2025-08-23 r88802) -- "Great Square Root"
Copyright (C) 2025 The R Foundation for Statistical Computing
Platform: x86_64-pc-linux-gnu

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 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 2 | SKIP 8 | PASS 1474 ]

══ Skipped tests (8) ═══════════════════════════════════════════════════════════
• 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'
• empty test (1): 'test_primers.R:29:1'

[ FAIL 0 | WARN 2 | SKIP 8 | PASS 1474 ]
> 
> proc.time()
   user  system elapsed 
 39.664  11.281  41.849