Control: tags -1 upstream Control: forwarded -1 Bioconductor Package Maintainer <[email protected]>
Hi, as you can read below S4Vectors segfaults in its test. Here you can find a complete test log https://ci.debian.net/data/autopkgtest/unstable/amd64/r/r-bioc-s4vectors/3725032/log.gz which says in the end: ... > S4Vectors:::.test() *** caught segfault *** address 0x5586e27d4a60, cause 'invalid permissions' Traceback: 1: runmed(y, 7) 2: runmed(y, 7) 3: as.vector(target) 4: mode(target) 5: attr.all.equal(target, current, tolerance = tolerance, scale = scale, ...) 6: all.equal.numeric(as.vector(target), as.vector(current), tolerance = tolerance, ...) 7: checkEqualsNumeric(runmed(y, 7), as.vector(runmed(Rle(y), 7))) 8: func() 9: system.time(func(), gcFirst = RUnitEnv$.gcBeforeTest) 10: doTryCatch(return(expr), name, parentenv, handler) 11: tryCatchOne(expr, names, parentenv, handlers[[1L]]) 12: tryCatchList(expr, classes, parentenv, handlers) 13: tryCatch(expr, error = function(e) { call <- conditionCall(e) if (!is.null(call)) { if (identical(call[[1L]], quote(doTryCatch))) call <- sys.call(-4L) dcall <- deparse(call)[1L] prefix <- paste("Error in", dcall, ": ") LONG <- 75L sm <- strsplit(conditionMessage(e), "\n")[[1L]] w <- 14L + nchar(dcall, type = "w") + nchar(sm[1L], type = "w") if (is.na(w)) w <- 14L + nchar(dcall, type = "b") + nchar(sm[1L], type = "b") if (w > LONG) prefix <- paste0(prefix, "\n ") } else prefix <- "Error : " msg <- paste0(prefix, conditionMessage(e), "\n") .Internal(seterrmessage(msg[1L])) if (!silent && isTRUE(getOption("show.error.messages"))) { cat(msg, file = outFile) .Internal(printDeferredWarnings()) } invisible(structure(msg, class = "try-error", condition = e))}) 14: try(system.time(func(), gcFirst = RUnitEnv$.gcBeforeTest)) 15: .executeTestCase(funcName, envir = sandbox, setUpFunc = .setUp, tearDownFunc = .tearDown) 16: .sourceTestFile(testFile, testSuite$testFuncRegexp) 17: RUnit::runTestSuite(suite) 18: BiocGenerics:::testPackage("S4Vectors") 19: S4Vectors:::.test() An irrecoverable exception occurred. R is aborting now ... Segmentation fault Any idea how to fix this? Kind regards Andreas. On Thu, Dec 19, 2019 at 11:51:03AM +0100, Sebastien Bacher wrote: > Package: r-bioc-s4vectors > Version: 0.24.1-1 > > The autopkgtest started failing on a segfault > https://ci.debian.net/packages/r/r-bioc-s4vectors/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 > [email protected] > https://alioth-lists.debian.net/cgi-bin/mailman/listinfo/r-pkg-team -- http://fam-tille.de
