Control: tags -1 upstream Control: forwarded -1 Bioconductor Package Maintainer <maintai...@bioconductor.org>
Hi, as you can read below the test suite of IRanges in Debian started failing after r-base-core was upgraded. A complete build log can be found here https://ci.debian.net/data/autopkgtest/unstable/amd64/r/r-bioc-iranges/3717079/log.gz which says at the end: ... > IRanges:::.test() firstNA = 0 <=> *no* NA/NaN. firstNA = 0 <=> *no* NA/NaN. firstNA = 0 <=> *no* NA/NaN. firstNA = 0 <=> *no* NA/NaN. *** caught segfault *** address 0x55c0daa0aa60, cause 'invalid permissions' Traceback: 1: FUN(X[[i]], ...) 2: FUN(X[[i]], ...) 3: lapply(as.list(X), match.fun(FUN), ...) 4: lapply(as.list(X), match.fun(FUN), ...) 5: lapply(x, runmed, k = k, endrule = match.arg(endrule), algorithm = algorithm, print.level = print.level) 6: lapply(x, runmed, k = k, endrule = match.arg(endrule), algorithm = algorithm, print.level = print.level) 7: .dotargsAsList("numeric", ...) 8: NumericList(lapply(x, runmed, k = k, endrule = match.arg(endrule), algorithm = algorithm, print.level = print.level), compress = FALSE) 9: runmed(list3, 7) 10: runmed(list3, 7) 11: as.list(runmed(list3, 7)) 12: checkIdentical(as.list(runmed(list3, 7)), lapply(list3, function(x) { y <- runmed(x, 7) if (type != "RleList") y <- as.vector(y) y})) 13: func() 14: system.time(func(), gcFirst = RUnitEnv$.gcBeforeTest) 15: doTryCatch(return(expr), name, parentenv, handler) 16: tryCatchOne(expr, names, parentenv, handlers[[1L]]) 17: tryCatchList(expr, classes, parentenv, handlers) 18: tryCatch(expr, error = function(e) { call <- conditionCall(e) if (!is.null(call)) { if (identical(call[[1L]], quote(doTryCatch))) call <- sys.call(-4L) dcall <- deparse(call)[1L] prefix <- paste("Error in", dcall, ": ") LONG <- 75L sm <- strsplit(conditionMessage(e), "\n")[[1L]] w <- 14L + nchar(dcall, type = "w") + nchar(sm[1L], type = "w") if (is.na(w)) w <- 14L + nchar(dcall, type = "b") + nchar(sm[1L], type = "b") if (w > LONG) prefix <- paste0(prefix, "\n ") } else prefix <- "Error : " msg <- paste0(prefix, conditionMessage(e), "\n") .Internal(seterrmessage(msg[1L])) if (!silent && isTRUE(getOption("show.error.messages"))) { cat(msg, file = outFile) .Internal(printDeferredWarnings()) } invisible(structure(msg, class = "try-error", condition = e))}) 19: try(system.time(func(), gcFirst = RUnitEnv$.gcBeforeTest)) 20: .executeTestCase(funcName, envir = sandbox, setUpFunc = .setUp, tearDownFunc = .tearDown) 21: .sourceTestFile(testFile, testSuite$testFuncRegexp) 22: RUnit::runTestSuite(suite) 23: BiocGenerics:::testPackage("IRanges") 24: IRanges:::.test() An irrecoverable exception occurred. R is aborting now ... Segmentation fault Any idea how to fix this? BTW, there is a similar effect with S4Vectors. May be that's related. Kind regards Andreas. On Thu, Dec 19, 2019 at 11:23:18AM +0100, Sebastien Bacher wrote: > Package: r-bioc-iranges > Version: 2.20.1-1 > > The autopkgtest started failing on a segfault > https://ci.debian.net/packages/r/r-bioc-iranges/unstable/amd64/ > > It seems to have started with the r-base update > -r-base-core 3.6.1-7 > +r-base-core 3.6.1.20191206-1 > > _______________________________________________ > R-pkg-team mailing list > r-pkg-t...@alioth-lists.debian.net > https://alioth-lists.debian.net/cgi-bin/mailman/listinfo/r-pkg-team -- http://fam-tille.de