############################################################################## ############################################################################## ### ### Running command: ### ### /home/biocbuild/bbs-3.20-bioc/R/bin/R CMD check --install=check:BSgenome.install-out.txt --library=/home/biocbuild/bbs-3.20-bioc/R/site-library --timings BSgenome_1.73.0.tar.gz ### ############################################################################## ############################################################################## * using log directory ‘/home/biocbuild/bbs-3.20-bioc/meat/BSgenome.Rcheck’ * using R version 4.4.1 (2024-06-14) * using platform: x86_64-pc-linux-gnu * R was compiled by gcc (Ubuntu 11.4.0-1ubuntu1~22.04) 11.4.0 GNU Fortran (Ubuntu 11.4.0-1ubuntu1~22.04) 11.4.0 * running under: Ubuntu 22.04.4 LTS * using session charset: UTF-8 * checking for file ‘BSgenome/DESCRIPTION’ ... OK * this is package ‘BSgenome’ version ‘1.73.0’ * 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 ... OK * checking for sufficient/correct file permissions ... OK * checking whether package ‘BSgenome’ can be installed ... OK * checking installed package size ... NOTE installed size is 7.1Mb sub-directories of 1Mb or more: R 1.6Mb extdata 5.2Mb * 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 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’ ‘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 '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 files in ‘vignettes’ ... OK * checking examples ... ERROR Running examples in ‘BSgenome-Ex.R’ failed The error most likely occurred in: > base::assign(".ptime", proc.time(), pos = "CheckExEnv") > ### Name: SNPlocs-class > ### Title: SNPlocs objects > ### Aliases: class:SNPlocs SNPlocs-class SNPlocs class:ODLT_SNPlocs > ### ODLT_SNPlocs-class ODLT_SNPlocs class:OldFashionSNPlocs > ### OldFashionSNPlocs-class OldFashionSNPlocs provider,SNPlocs-method > ### providerVersion,SNPlocs-method releaseDate,SNPlocs-method releaseName > ### releaseName,SNPlocs-method referenceGenome > ### referenceGenome,SNPlocs-method compatibleGenomes > ### compatibleGenomes,SNPlocs-method organism,SNPlocs-method > ### commonName,SNPlocs-method seqinfo,SNPlocs-method > ### seqnames,SNPlocs-method new_ODLT_SNPlocs newSNPlocs > ### show,SNPlocs-method snpcount snpcount,SNPlocs-method > ### snpcount,ODLT_SNPlocs-method snpcount,OldFashionSNPlocs-method > ### snplocs snplocs,SNPlocs-method snplocs,ODLT_SNPlocs-method > ### snplocs,OldFashionSNPlocs-method snpsBySeqname > ### snpsBySeqname,SNPlocs-method snpsBySeqname,ODLT_SNPlocs-method > ### snpsBySeqname,OldFashionSNPlocs-method snpsByOverlaps > ### snpsByOverlaps,SNPlocs-method snpsByOverlaps,ODLT_SNPlocs-method > ### snpsByOverlaps,OldFashionSNPlocs-method snpsById > ### snpsById,SNPlocs-method snpsById,ODLT_SNPlocs-method > ### snpsById,OldFashionSNPlocs-method inferRefAndAltAlleles > ### Keywords: methods classes > > ### ** Examples > > library(SNPlocs.Hsapiens.dbSNP144.GRCh38) Warning: replacing previous import ‘utils::findMatches’ by ‘S4Vectors::findMatches’ when loading ‘SNPlocs.Hsapiens.dbSNP144.GRCh38’ > snps <- SNPlocs.Hsapiens.dbSNP144.GRCh38 > snpcount(snps) 1 2 3 4 5 6 7 8 10352408 11278817 9279095 8909116 8313890 7723096 7317091 7224402 9 10 11 12 13 14 15 16 5748221 6180295 6402437 6203669 4456153 4205104 3796823 4463462 17 18 19 20 21 22 X Y 3802080 3530777 3107971 2979767 1761244 1821463 3979053 192585 MT 1760 > > ## --------------------------------------------------------------------- > ## snpsBySeqname() > ## --------------------------------------------------------------------- > > ## Get all SNPs located on chromosome 22 or MT: > snpsBySeqname(snps, c("22", "MT")) UnstitchedGPos object with 1823223 positions and 2 metadata columns: seqnames pos strand | RefSNP_id alleles_as_ambig | [1] 22 10510770 * | rs71207739 M [2] 22 10510928 * | rs71207740 R [3] 22 10511116 * | rs4022986 R [4] 22 10511641 * | rs71207745 R [5] 22 10516682 * | rs4022528 S ... ... ... ... . ... ... [1823219] MT 16512 * | rs373943637 Y [1823220] MT 16519 * | rs3937033 Y [1823221] MT 16528 * | rs386829315 Y [1823222] MT 16529 * | rs370705831 Y [1823223] MT 16529 * | rs386829316 Y ------- seqinfo: 25 sequences (1 circular) from GRCh38.p2 genome > > ## --------------------------------------------------------------------- > ## snpsByOverlaps() > ## --------------------------------------------------------------------- > > ## Get all SNPs overlapping some genomic region of interest: > snpsByOverlaps(snps, "X:3e6-33e6") UnstitchedGPos object with 956405 positions and 2 metadata columns: seqnames pos strand | RefSNP_id alleles_as_ambig | [1] X 3000004 * | rs369882522 Y [2] X 3000013 * | rs374307143 Y [3] X 3000014 * | rs73437584 R [4] X 3000036 * | rs113897265 R [5] X 3000038 * | rs79982205 M ... ... ... ... . ... ... [956401] X 32999862 * | rs781726587 W [956402] X 32999888 * | rs746298827 R [956403] X 32999892 * | rs188179728 Y [956404] X 32999980 * | rs775781591 R [956405] X 32999998 * | rs193298222 Y ------- seqinfo: 25 sequences (1 circular) from GRCh38.p2 genome > > ## With the regions of interest being all the known CDS for hg38 > ## located on chromosome 22 or MT (except for the chromosome naming > ## convention, hg38 is the same as GRCh38): > library(TxDb.Hsapiens.UCSC.hg38.knownGene) Loading required package: GenomicFeatures Loading required package: AnnotationDbi Loading required package: Biobase Welcome to Bioconductor Vignettes contain introductory material; view with 'browseVignettes()'. To cite Bioconductor, see 'citation("Biobase")', and for packages 'citation("pkgname")'. > txdb <- TxDb.Hsapiens.UCSC.hg38.knownGene > my_cds <- cds(txdb) > seqlevels(my_cds, pruning.mode="coarse") <- c("chr22", "chrM") > seqlevelsStyle(my_cds) # UCSC [1] "UCSC" > seqlevelsStyle(snps) # NCBI [1] "NCBI" > seqlevelsStyle(my_cds) <- seqlevelsStyle(snps) Error in download.file(url, destfile, quiet = TRUE) : cannot open URL 'https://ftp.ncbi.nlm.nih.gov/genomes/all/GCF/000/001/405/GCF_000001405.39_GRCh38.p13/GCF_000001405.39_GRCh38.p13_assembly_report.txt' Calls: seqlevelsStyle<- ... .fetch_assembly_report_from_url -> fetch_table_from_url Execution halted * 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: 1 ERROR, 1 WARNING, 3 NOTEs See ‘/home/biocbuild/bbs-3.20-bioc/meat/BSgenome.Rcheck/00check.log’ for details.