[R-pkg-team] Bug#947001: IRanges segfaults after R was upgraded in Debian (Was: Bug#947001: Tests segfaults (since the r-base-core update?))

Andreas Tille andreas at an3as.eu
Sun Dec 22 07:29:23 GMT 2019


Control: tags -1 upstream
Control: forwarded -1 Bioconductor Package Maintainer <maintainer at 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
> 
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> R-pkg-team at alioth-lists.debian.net
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