############################################################################## ############################################################################## ### ### Running command: ### ### /Library/Frameworks/R.framework/Resources/bin/R CMD check --install=check:BSgenome.install-out.txt --library=/Library/Frameworks/R.framework/Resources/library --no-vignettes --timings BSgenome_1.70.2.tar.gz ### ############################################################################## ############################################################################## * using log directory ‘/Users/biocbuild/bbs-3.18-bioc/meat/BSgenome.Rcheck’ * using R version 4.3.2 Patched (2023-11-01 r85457) * using platform: x86_64-apple-darwin20 (64-bit) * R was compiled by Apple clang version 14.0.3 (clang-1403.0.22.14.1) GNU Fortran (GCC) 12.2.0 * running under: macOS Monterey 12.7.1 * using session charset: UTF-8 * using option ‘--no-vignettes’ * checking for file ‘BSgenome/DESCRIPTION’ ... OK * this is package ‘BSgenome’ version ‘1.70.2’ * package encoding: UTF-8 * checking package namespace information ... OK * checking package dependencies ... NOTE Depends: includes the non-default packages: 'BiocGenerics', 'S4Vectors', 'IRanges', 'GenomeInfoDb', 'GenomicRanges', 'Biostrings', 'BiocIO', 'rtracklayer' Adding so many packages to the search path is excessive and importing selectively is preferable. * 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 ... NOTE Found the following non-portable file path: BSgenome/inst/extdata/GentlemanLab/BSgenome.Gmellonella.NCBI.ASM364042v2-tools/fasta_to_sorted_2bit.R Tarballs are only required to store paths of up to 100 bytes and cannot store those of more than 256 bytes, with restrictions including to 100 bytes for the final component. See section ‘Package structure’ in the ‘Writing R Extensions’ manual. * checking for sufficient/correct file permissions ... OK * checking whether package ‘BSgenome’ can be installed ... OK * checking installed package size ... NOTE installed size is 8.1Mb sub-directories of 1Mb or more: R 2.0Mb extdata 5.9Mb * 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 ... NOTE Found the following CITATION file in a non-standard place: inst/extdata/GentlemanLab/BSgenome.Creinhardtii.JGI.v5.6-tools/CITATION Most likely ‘inst/CITATION’ should be used instead. * checking R 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 dependencies in R code ... NOTE ':::' calls which should be '::': ‘S4Vectors:::makeClassinfoRowForCompactPrinting’ ‘S4Vectors:::makePrettyMatrixForCompactPrinting’ See the note in ?`:::` about the use of this operator. Unexported objects imported by ':::' calls: ‘rtracklayer:::.DNAString_to_twoBit’ ‘rtracklayer:::.TwoBits_export’ ‘rtracklayer:::checkArgFormat’ ‘rtracklayer:::twoBitPath’ See the note in ?`:::` about the use of this operator. * 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 ... OK * checking Rd metadata ... OK * checking Rd cross-references ... OK * checking for missing documentation entries ... WARNING Undocumented code objects: ‘MaskedBSgenome’ ‘OnDiskLongTable’ ‘OnDiskLongTable_old’ ‘as.data.frame.BSgenomeViews’ ‘batchsizes’ ‘blocksizes’ ‘breakpoints’ ‘forgeMaskedBSgenomeDataPkg’ ‘getBatchesByOverlapsFromOnDiskLongTable’ ‘getBatchesBySeqnameFromOnDiskLongTable’ ‘getBatchesFromOnDiskLongTable’ ‘getBatchesFromOnDiskLongTable_old’ ‘getRowsByIdFromOnDiskLongTable’ ‘getRowsByIndexFromOnDiskLongTable_old’ ‘getRowsFromOnDiskLongTable’ ‘saveAsOnDiskLongTable_old’ ‘saveRowidsForOnDiskLongTable_old’ ‘spatialIndex’ ‘writeOnDiskLongTable’ ‘writeOnDiskLongTableRowids’ Undocumented S4 classes: ‘OnDiskLongTable_old’ ‘GRanges_OR_NULL’ ‘MaskedBSgenome’ ‘OnDiskLongTable’ Undocumented S4 methods: generic '[' and siglist 'XStringSet,GRangesList,ANY,ANY' generic '[' and siglist 'XStringSet,GenomicRanges,ANY,ANY' generic '[[' and siglist 'BSgenome,ANY,ANY' generic 'batchsizes' and siglist 'OnDiskLongTable' generic 'blocksizes' and siglist 'OnDiskLongTable_old' generic 'breakpoints' and siglist 'OnDiskLongTable' generic 'breakpoints' and siglist 'OnDiskLongTable_old' generic 'coerce' and siglist 'RdsCollection,RdsNamedSequences' generic 'dim' and siglist 'OnDiskLongTable' generic 'dim' and siglist 'OnDiskLongTable_old' generic 'dimnames' and siglist 'OnDiskLongTable' generic 'dimnames' and siglist 'OnDiskLongTable_old' generic 'dimnames' and siglist 'XtraSNPlocs' generic 'extractAt' and siglist 'BSgenome' generic 'forgeMaskedBSgenomeDataPkg' and siglist 'MaskedBSgenomeDataPkgSeed' generic 'forgeMaskedBSgenomeDataPkg' and siglist 'character' generic 'forgeMaskedBSgenomeDataPkg' and siglist 'list' generic 'length' and siglist 'OnDiskNamedSequences' generic 'names' and siglist 'FastaNamedSequences' generic 'names' and siglist 'TwobitNamedSequences' generic 'seqinfo' and siglist 'FastaNamedSequences' generic 'seqinfo' and siglist 'RdaNamedSequences' generic 'seqinfo' and siglist 'RdsNamedSequences' generic 'seqinfo' and siglist 'TwobitNamedSequences' generic 'seqnames' and siglist 'OnDiskNamedSequences' generic 'show' and siglist 'OnDiskLongTable' generic 'show' and siglist 'OnDiskLongTable_old' generic 'show' and siglist 'OnDiskNamedSequences' generic 'spatialIndex' and siglist 'OnDiskLongTable' All user-level objects in a package (including S4 classes and methods) should have documentation entries. See chapter ‘Writing R documentation files’ in the ‘Writing R Extensions’ manual. * checking for code/documentation mismatches ... OK * checking Rd \usage sections ... OK * checking Rd contents ... OK * checking for unstated dependencies in examples ... OK * checking sizes of PDF files under ‘inst/doc’ ... OK * checking files in ‘vignettes’ ... OK * checking examples ... OK Examples with CPU (user + system) or elapsed time > 5s user system elapsed SNPlocs-class 61.786 3.863 67.640 BSgenomeViews-class 20.198 4.621 30.018 BSgenome-utils 21.209 0.501 21.890 BSgenome-class 14.243 0.627 15.032 XtraSNPlocs-class 7.418 0.541 8.067 getSeq-methods 5.880 0.595 6.566 BSgenomeForge 6.038 0.166 6.287 bsapply 5.385 0.333 5.775 injectSNPs 5.144 0.417 5.641 export-methods 4.141 1.113 5.337 * checking for unstated dependencies in vignettes ... OK * checking package vignettes in ‘inst/doc’ ... OK * checking running R code from vignettes ... SKIPPED * checking re-building of vignette outputs ... SKIPPED * checking PDF version of manual ... OK * DONE Status: 1 WARNING, 5 NOTEs See ‘/Users/biocbuild/bbs-3.18-bioc/meat/BSgenome.Rcheck/00check.log’ for details.