[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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