[R-pkg-team] Bug#947004: S4Vectors Segmentation fault after r-base-core update (Was: Bug#947004: Tests segfaults (since the r-base-core update?))

[Andreas Tille]

Control: tags -1 upstream
Control: forwarded -1 Bioconductor Package Maintainer <maintainer at bioconductor.org>

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
> 
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