Hi, None of our build machines is able to reproduce this sorry:
https://bioconductor.org/checkResults/3.10/bioc-LATEST/S4Vectors/ https://bioconductor.org/checkResults/3.11/bioc-LATEST/S4Vectors/ My own attempt with latest R devel was also unsuccessful: https://github.com/Bioconductor/S4Vectors/issues/57 For me to be able to troubleshoot this, I would need to have access to your setup. How do I do that? Thanks, H. On 12/21/19 23:33, Andreas Tille wrote: > Control: tags -1 upstream > Control: forwarded -1 Bioconductor Package Maintainer > <maintai...@bioconductor.org> > > Hi, > > as you can read below S4Vectors segfaults in its test. Here you can > find a complete test log > > > https://urldefense.proofpoint.com/v2/url?u=https-3A__ci.debian.net_data_autopkgtest_unstable_amd64_r_r-2Dbioc-2Ds4vectors_3725032_log.gz&d=DwIBAg&c=eRAMFD45gAfqt84VtBcfhQ&r=BK7q3XeAvimeWdGbWY_wJYbW0WYiZvSXAJJKaaPhzWA&m=DHL7QJdlJrCrv38t_eLrYpMRBpEuSCg-d7MKzDbJj3U&s=ZjCPkSEcE-UgZ0StnEbjTm8Spw2ogduUSLVi36qppIk&e= > > 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://urldefense.proofpoint.com/v2/url?u=https-3A__ci.debian.net_packages_r_r-2Dbioc-2Ds4vectors_unstable_amd64_&d=DwIBAg&c=eRAMFD45gAfqt84VtBcfhQ&r=BK7q3XeAvimeWdGbWY_wJYbW0WYiZvSXAJJKaaPhzWA&m=DHL7QJdlJrCrv38t_eLrYpMRBpEuSCg-d7MKzDbJj3U&s=RhjsZgmIre-LCJ6W9MTbYT6h-7GoeRVxSNNZRSIYvok&e= >> >> 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://urldefense.proofpoint.com/v2/url?u=https-3A__alioth-2Dlists.debian.net_cgi-2Dbin_mailman_listinfo_r-2Dpkg-2Dteam&d=DwIBAg&c=eRAMFD45gAfqt84VtBcfhQ&r=BK7q3XeAvimeWdGbWY_wJYbW0WYiZvSXAJJKaaPhzWA&m=DHL7QJdlJrCrv38t_eLrYpMRBpEuSCg-d7MKzDbJj3U&s=UGzYFvbWg5wBrN_gos9Ue1RdLwcnqzdBasaqOwTW9Fg&e= > -- Hervé Pagès Program in Computational Biology Division of Public Health Sciences Fred Hutchinson Cancer Research Center 1100 Fairview Ave. N, M1-B514 P.O. Box 19024 Seattle, WA 98109-1024 E-mail: hpa...@fredhutch.org Phone: (206) 667-5791 Fax: (206) 667-1319
