############################################################################## ############################################################################## ### ### Running command: ### ### /home/biocbuild/R/R/bin/R CMD check --install=check:gDNAx.install-out.txt --library=/home/biocbuild/R/R/site-library --no-vignettes --timings gDNAx_1.3.0.tar.gz ### ############################################################################## ############################################################################## * using log directory ‘/home/biocbuild/bbs-3.20-bioc/meat/gDNAx.Rcheck’ * using R version 4.4.1 (2024-06-14) * using platform: aarch64-unknown-linux-gnu * R was compiled by gcc (GCC) 12.2.1 20220819 (openEuler 12.2.1-14) 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 ‘gDNAx/DESCRIPTION’ ... OK * checking extension type ... Package * this is package ‘gDNAx’ version ‘1.3.0’ * package encoding: UTF-8 * checking package namespace information ... OK * checking package dependencies ... 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 ‘gDNAx’ can be installed ... OK * 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 loading without being on the library search path ... OK * checking dependencies in R code ... NOTE Unexported objects imported by ':::' calls: ‘GenomicAlignments:::.make_GAlignmentPairs_from_GAlignments’ ‘GenomicAlignments:::.normargParam’ ‘S4Vectors:::makePowersOfTwo’ 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 ... OK * 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 ‘gDNAx-Ex.R’ failed The error most likely occurred in: > base::assign(".ptime", proc.time(), pos = "CheckExEnv") > ### Name: filterBAMtx > ### Title: Filter alignments in a BAM file using a transcriptome > ### Aliases: filterBAMtx filterBAMtxFlag testBAMtxFlag > > ### ** Examples > > library(gDNAinRNAseqData) > > library(TxDb.Hsapiens.UCSC.hg38.knownGene) Loading required package: GenomicFeatures Loading required package: BiocGenerics Attaching package: ‘BiocGenerics’ The following objects are masked from ‘package:stats’: IQR, mad, sd, var, xtabs The following objects are masked from ‘package:base’: Filter, Find, Map, Position, Reduce, anyDuplicated, aperm, append, as.data.frame, basename, cbind, colnames, dirname, do.call, duplicated, eval, evalq, get, grep, grepl, intersect, is.unsorted, lapply, mapply, match, mget, order, paste, pmax, pmax.int, pmin, pmin.int, rank, rbind, rownames, sapply, setdiff, table, tapply, union, unique, unsplit, which.max, which.min Loading required package: S4Vectors Loading required package: stats4 Attaching package: ‘S4Vectors’ The following object is masked from ‘package:utils’: findMatches The following objects are masked from ‘package:base’: I, expand.grid, unname Loading required package: IRanges Loading required package: GenomeInfoDb Loading required package: GenomicRanges 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 > > # Getting the 'gDNAx' object > bamfiles <- LiYu22subsetBAMfiles() see ?gDNAinRNAseqData and browseVignettes('gDNAinRNAseqData') for documentation loading from cache require(“Rsamtools”) see ?gDNAinRNAseqData and browseVignettes('gDNAinRNAseqData') for documentation loading from cache see ?gDNAinRNAseqData and browseVignettes('gDNAinRNAseqData') for documentation loading from cache see ?gDNAinRNAseqData and browseVignettes('gDNAinRNAseqData') for documentation loading from cache see ?gDNAinRNAseqData and browseVignettes('gDNAinRNAseqData') for documentation loading from cache see ?gDNAinRNAseqData and browseVignettes('gDNAinRNAseqData') for documentation loading from cache see ?gDNAinRNAseqData and browseVignettes('gDNAinRNAseqData') for documentation loading from cache see ?gDNAinRNAseqData and browseVignettes('gDNAinRNAseqData') for documentation loading from cache see ?gDNAinRNAseqData and browseVignettes('gDNAinRNAseqData') for documentation loading from cache > bamfiles <- bamfiles[c(1,7)] # using a subset of samples > gdnax <- gDNAdx(bamfiles, txdb, singleEnd=FALSE, strandMode=NA) ℹ Library layout: paired-end, 2 (2x50nt). ℹ Fetching gene-level annotations for hg38 ℹ Fetching RepeatMasker annotations for hg38 Warning: download failed web resource path: ‘https://annotationhub.bioconductor.org/fetch/118079’ local file path: ‘/home/biocbuild/.cache/R/AnnotationHub/file229d093e4fdf11’ reason: Internal Server Error (HTTP 500). Warning: bfcdownload() failed rid: BFC37 file: ‘https://annotationhub.bioconductor.org/fetch/118079’ reason: download failed Warning: download failed hub path: ‘https://annotationhub.bioconductor.org/fetch/118079’ cache resource: ‘AH111333 : 118079’ reason: download failed; see warnings() Error: failed to load resource name: AH111333 title: UCSC RepeatMasker annotations (Oct2022) for Human (hg38) reason: 1 resources failed to download Execution halted * checking for unstated dependencies in ‘tests’ ... OK * checking tests ... Running ‘runTests.R’ ERROR Running the tests in ‘tests/runTests.R’ failed. Last 13 lines of output: gDNAx RUnit Tests - 7 test functions, 1 error, 0 failures ERROR in test_gDNAdx: Error : failed to load resource name: AH111333 title: UCSC RepeatMasker annotations (Oct2022) for Human (hg38) reason: 1 resources failed to download Test files with failing tests test_dx.R test_gDNAdx Error in BiocGenerics:::testPackage("gDNAx") : unit tests failed for package gDNAx Execution halted * 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: 2 ERRORs, 1 NOTE See ‘/home/biocbuild/bbs-3.20-bioc/meat/gDNAx.Rcheck/00check.log’ for details.