############################################################################## ############################################################################## ### ### Running command: ### ### /home/biocbuild/R/R/bin/R CMD check --install=check:openPrimeR.install-out.txt --library=/home/biocbuild/R/R/site-library --no-vignettes --timings openPrimeR_1.31.1.tar.gz ### ############################################################################## ############################################################################## * using log directory ‘/home/biocbuild/bbs-3.22-bioc/meat/openPrimeR.Rcheck’ * using R version 4.5.0 (2025-04-11) * using platform: aarch64-unknown-linux-gnu * R was compiled by aarch64-unknown-linux-gnu-gcc (GCC) 14.2.0 GNU Fortran (GCC) 14.2.0 * running under: openEuler 24.03 (LTS) * 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 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 PrimerDesign 16.248 4.349 16.749 Output 15.627 1.734 19.202 Plots 8.442 0.945 8.903 PrimerEval 7.553 1.496 6.388 * 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: 4 NOTEs See ‘/home/biocbuild/bbs-3.22-bioc/meat/openPrimeR.Rcheck/00check.log’ for details.