############################################################################## ############################################################################## ### ### Running command: ### ### /Library/Frameworks/R.framework/Resources/bin/R CMD check --install=check:amplican.install-out.txt --library=/Library/Frameworks/R.framework/Resources/library --no-vignettes --timings amplican_1.29.0.tar.gz ### ############################################################################## ############################################################################## * using log directory ‘/Users/biocbuild/bbs-3.21-bioc/meat/amplican.Rcheck’ * using R Under development (unstable) (2024-11-20 r87352) * using platform: x86_64-apple-darwin20 * R was compiled by Apple clang version 14.0.0 (clang-1400.0.29.202) GNU Fortran (GCC) 12.2.0 * running under: macOS Monterey 12.7.6 * using session charset: UTF-8 * using option ‘--no-vignettes’ * checking for file ‘amplican/DESCRIPTION’ ... OK * checking extension type ... Package * this is package ‘amplican’ version ‘1.29.0’ * package encoding: UTF-8 * checking package namespace information ... OK * checking package dependencies ...Warning: unable to access index for repository https://CRAN.R-project.org/src/contrib: cannot open URL 'https://CRAN.R-project.org/src/contrib/PACKAGES' OK * checking if this is a source package ... OK * checking if there is a namespace ... OK * checking for hidden files and directories ... OK * checking for portable file names ... OK * checking for sufficient/correct file permissions ... OK * checking whether package ‘amplican’ can be installed ... OK * used C++ compiler: ‘Apple clang version 14.0.0 (clang-1400.0.29.202)’ * used SDK: ‘MacOSX11.3.sdk’ * checking installed package size ... OK * 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 ... NOTE There are ::: calls to the package's namespace in its code. A package almost never needs to use ::: for its own objects: ‘get_seq’ * 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) amplicanAlign.Rd:64: Lost braces in \itemize; meant \describe ? checkRd: (-1) amplicanAlign.Rd:65-68: Lost braces in \itemize; meant \describe ? checkRd: (-1) amplicanAlign.Rd:69: Lost braces in \itemize; meant \describe ? checkRd: (-1) amplicanAlign.Rd:70: Lost braces in \itemize; meant \describe ? checkRd: (-1) amplicanPipeline.Rd:58-59: Lost braces in \itemize; meant \describe ? checkRd: (-1) amplicanPipeline.Rd:60-70: Lost braces in \itemize; meant \describe ? checkRd: (-1) amplicanPipeline.Rd:71: Lost braces in \itemize; meant \describe ? checkRd: (-1) amplicanPipeline.Rd:72-73: Lost braces in \itemize; meant \describe ? checkRd: (-1) amplicanPipeline.Rd:106: Lost braces in \itemize; meant \describe ? checkRd: (-1) amplicanPipeline.Rd:107-110: Lost braces in \itemize; meant \describe ? checkRd: (-1) amplicanPipeline.Rd:111: Lost braces in \itemize; meant \describe ? checkRd: (-1) amplicanPipeline.Rd:112: Lost braces in \itemize; meant \describe ? checkRd: (-1) amplicanPipelineConservative.Rd:58-59: Lost braces in \itemize; meant \describe ? checkRd: (-1) amplicanPipelineConservative.Rd:60-70: Lost braces in \itemize; meant \describe ? checkRd: (-1) amplicanPipelineConservative.Rd:71: Lost braces in \itemize; meant \describe ? checkRd: (-1) amplicanPipelineConservative.Rd:72-73: Lost braces in \itemize; meant \describe ? checkRd: (-1) amplicanPipelineConservative.Rd:106: Lost braces in \itemize; meant \describe ? checkRd: (-1) amplicanPipelineConservative.Rd:107-110: Lost braces in \itemize; meant \describe ? checkRd: (-1) amplicanPipelineConservative.Rd:111: Lost braces in \itemize; meant \describe ? checkRd: (-1) amplicanPipelineConservative.Rd:112: Lost braces in \itemize; meant \describe ? checkRd: (-1) amplicanSummarize.Rd:26-27: Lost braces in \itemize; meant \describe ? checkRd: (-1) amplicanSummarize.Rd:28-29: Lost braces in \itemize; meant \describe ? checkRd: (-1) makeAlignment.Rd:52: Lost braces in \itemize; meant \describe ? checkRd: (-1) makeAlignment.Rd:53-56: Lost braces in \itemize; meant \describe ? checkRd: (-1) makeAlignment.Rd:57: Lost braces in \itemize; meant \describe ? checkRd: (-1) makeAlignment.Rd:58: Lost braces in \itemize; meant \describe ? checkRd: (-1) plot_variants.Rd:74-75: Lost braces in \itemize; meant \describe ? checkRd: (-1) plot_variants.Rd:76: Lost braces in \itemize; meant \describe ? checkRd: (-1) plot_variants.Rd:77-78: Lost braces in \itemize; meant \describe ? * checking Rd metadata ... OK * checking Rd cross-references ... NOTE Found the following Rd file(s) with Rd \link{} targets missing package anchors: AlignmentsExperimentSet-class.Rd: PairwiseAlignmentsSingleSubject, GRanges amplicanAlign.Rd: nucleotideSubstitutionMatrix amplicanMap.Rd: GRanges amplicanPipeline.Rd: nucleotideSubstitutionMatrix amplicanPipelineConservative.Rd: nucleotideSubstitutionMatrix cigarsToEvents.Rd: GRanges cumsumw.Rd: IRanges defGR.Rd: IRanges, GRanges extractEvents.Rd: GRanges findPD.Rd: GRanges fwdReads-set.Rd: PairwiseAlignmentsSingleSubject fwdReadsType-set.Rd: PairwiseAlignmentsSingleSubject getEventInfo.Rd: PairwiseAlignmentsSingleSubject, GRanges getEvents.Rd: pairwiseAlignment, GRanges makeAlignment.Rd: nucleotideSubstitutionMatrix pairToEvents.Rd: GRanges readCounts-set.Rd: PairwiseAlignmentsSingleSubject rveReads-set.Rd: PairwiseAlignmentsSingleSubject rveReadsType-set.Rd: PairwiseAlignmentsSingleSubject unassignedData-set.Rd: PairwiseAlignmentsSingleSubject upperGroups.Rd: IRanges Please provide package anchors for all Rd \link{} targets not in the package itself and the base packages. * 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 'getEventInfo.Rd': ‘ampl_len’ 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 line endings in C/C++/Fortran sources/headers ... OK * checking compiled code ... NOTE Note: information on .o files is not available * checking files in ‘vignettes’ ... OK * checking examples ... OK Examples with CPU (user + system) or elapsed time > 5s user system elapsed amplicanAlign 5.591 0.679 6.304 amplicanPipeline 5.410 0.396 5.820 * 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: 5 NOTEs See ‘/Users/biocbuild/bbs-3.21-bioc/meat/amplican.Rcheck/00check.log’ for details.