############################################################################## ############################################################################## ### ### Running command: ### ### /home/biocbuild/R/R-4.3.1/bin/R CMD check --install=check:BSgenome.install-out.txt --library=/home/biocbuild/R/R-4.3.1/site-library --no-vignettes --timings BSgenome_1.70.1.tar.gz ### ############################################################################## ############################################################################## * using log directory ‘/home/biocbuild/bbs-3.18-bioc/meat/BSgenome.Rcheck’ * using R version 4.3.1 (2023-06-16) * using platform: aarch64-unknown-linux-gnu (64-bit) * R was compiled by gcc (GCC) 10.3.1 GNU Fortran (GCC) 10.3.1 * running under: openEuler 22.03 (LTS-SP1) * using session charset: UTF-8 * using option ‘--no-vignettes’ * checking for file ‘BSgenome/DESCRIPTION’ ... OK * this is package ‘BSgenome’ version ‘1.70.1’ * 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 8.0Mb sub-directories of 1Mb or more: R 1.7Mb extdata 6.0Mb * 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 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’ ‘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 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: BSgenome-utils > ### Title: BSgenome utilities > ### Aliases: BSgenome-utils vmatchPattern,BSgenome-method > ### vcountPattern,BSgenome-method vmatchPDict,BSgenome-method > ### vcountPDict,BSgenome-method matchPWM,BSgenome-method > ### countPWM,BSgenome-method > ### Keywords: methods utilities > > ### ** Examples > > library(BSgenome.Celegans.UCSC.ce2) > data(HNF4alpha) > > pattern <- consensusString(HNF4alpha) > vmatchPattern(pattern, Celegans, fixed="subject") GRanges object with 123 ranges and 0 metadata columns: seqnames ranges strand [1] chrI 5249651-5249663 + [2] chrI 5858867-5858879 + [3] chrI 6956753-6956765 + [4] chrI 8927423-8927435 + [5] chrI 9260962-9260974 + ... ... ... ... [119] chrX 9436287-9436299 - [120] chrX 10737397-10737409 - [121] chrX 12030747-12030759 - [122] chrX 13784772-13784784 - [123] chrX 16717792-16717804 - ------- seqinfo: 7 sequences (1 circular) from ce2 genome > vcountPattern(pattern, Celegans, fixed="subject") seqname strand count 1 chrI + 7 2 chrI - 7 3 chrII + 12 4 chrII - 8 5 chrIII + 8 6 chrIII - 9 7 chrIV + 15 8 chrIV - 9 9 chrV + 7 10 chrV - 13 11 chrX + 15 12 chrX - 13 13 chrM + 0 14 chrM - 0 > > pdict <- PDict(HNF4alpha) > vmatchPDict(pdict, Celegans) GRanges object with 183 ranges and 1 metadata column: seqnames ranges strand | index | [1] chrI 10714238-10714250 + | 1 [2] chrI 1746247-1746259 + | 33 [3] chrI 11509260-11509272 + | 39 [4] chrI 5249651-5249663 + | 48 [5] chrI 5442409-5442421 + | 64 ... ... ... ... . ... [179] chrX 8554427-8554439 - | 64 [180] chrX 16811413-16811425 - | 69 [181] chrX 8212498-8212510 - | 70 [182] chrX 758648-758660 - | 71 [183] chrX 12553584-12553596 - | 71 ------- seqinfo: 7 sequences (1 circular) from ce2 genome > vcountPDict(pdict, Celegans) DataFrame with 994 rows and 4 columns seqname strand index count 1 chrI + 1 1 2 chrI + 2 0 3 chrI + 3 0 4 chrI + 4 0 5 chrI + 5 0 ... ... ... ... ... 990 chrM - 67 0 991 chrM - 68 0 992 chrM - 69 0 993 chrM - 70 0 994 chrM - 71 0 > > pwm <- PWM(HNF4alpha) > matchPWM(pwm, Celegans) * 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 ERROR, 1 WARNING, 5 NOTEs See ‘/home/biocbuild/bbs-3.18-bioc/meat/BSgenome.Rcheck/00check.log’ for details.