* using log directory ‘/data/blackswan/ripley/R/packages/tests-devel/rDNAse.Rcheck’ * using R Under development (unstable) (2024-06-27 r86844) * using platform: x86_64-pc-linux-gnu * R was compiled by gcc (GCC) 13.2.1 20240316 (Red Hat 13.2.1-7) GNU Fortran (GCC) 13.2.1 20240316 (Red Hat 13.2.1-7) * running under: Fedora Linux 38 (Workstation Edition) * using session charset: UTF-8 * checking for file ‘rDNAse/DESCRIPTION’ ... OK * checking extension type ... Package * this is package ‘rDNAse’ version ‘1.1-1’ * 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 executable files ... OK * checking for hidden files and directories ... OK * checking for portable file names ... OK * checking for sufficient/correct file permissions ... OK * checking whether package ‘rDNAse’ can be installed ... 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 ... OK * 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 line widths ... 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 LazyData ... NOTE 'LazyData' is specified without a 'data' directory * checking sizes of PDF files under ‘inst/doc’ ... OK * checking installed files from ‘inst/doc’ ... OK * checking files in ‘vignettes’ ... OK * checking examples ... OK * checking examples with --run-donttest ... ERROR Running examples in ‘rDNAse-Ex.R’ failed The error most likely occurred in: > ### Name: parSeqSim > ### Title: Parallellized DNA/RNA Sequence Similarity Calculation based on > ### Sequence Alignment > ### Aliases: parSeqSim > ### Keywords: alignment parallel similarity > > ### ** Examples > > ## No test: > # Be careful when testing this since it involves parallelisation > # and might produce unpredictable results in some environments > > require(Biostrings) Loading required package: Biostrings 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: XVector Loading required package: GenomeInfoDb Attaching package: ‘Biostrings’ The following object is masked from ‘package:base’: strsplit > require(foreach) Loading required package: foreach > require(doParallel) Loading required package: doParallel Loading required package: iterators Loading required package: parallel > > s1 = readFASTA(system.file('dnaseq/hs.fasta', package = 'rDNA'))[[1]] Warning in file(con, "r") : file("") only supports open = "w+" and open = "w+b": using the former Error in readFASTA(system.file("dnaseq/hs.fasta", package = "rDNA")) : no line starting with a > character found Execution halted * checking for unstated dependencies in vignettes ... OK * checking package vignettes ... OK * checking re-building of vignette outputs ... [20s/20s] OK * checking PDF version of manual ... OK * checking for non-standard things in the check directory ... OK * checking for detritus in the temp directory ... OK * checking for new files in some other directories ... OK * DONE Status: 1 ERROR, 1 NOTE See ‘/data/blackswan/ripley/R/packages/tests-devel/rDNAse.Rcheck/00check.log’ for details. Command exited with non-zero status 1 Time 1:07.12, 55.91 + 10.16