Bug#947004: Tests segfaults (since the r-base-core update?)

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Bug#947004: Tests segfaults (since the r-base-core update?)

Sebastien Bacher-2
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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Bug#947004: S4Vectors Segmentation fault after r-base-core update (Was: Bug#947004: Tests segfaults (since the r-base-core update?))

Andreas Tille-5
Control: tags -1 upstream
Control: forwarded -1 Bioconductor Package Maintainer <[hidden email]>

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
> [hidden email]
> https://alioth-lists.debian.net/cgi-bin/mailman/listinfo/r-pkg-team

--
http://fam-tille.de

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

Hervé Pagès-2
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 <[hidden email]>
>
> 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
>> [hidden email]
>> 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: [hidden email]
Phone:  (206) 667-5791
Fax:    (206) 667-1319