[Bioc-devel] TIMEOUTs on Morelia
Michael Love
michaelisaiahlove at gmail.com
Tue Feb 2 01:16:00 CET 2016
Thanks for the quick fix!
On Feb 1, 2016 6:36 PM, "Hervé Pagès" <hpages at fredhutch.org> wrote:
> Hi all,
>
> The problem was in S4Vectors where I introduced a regression about 10
> days ago. Thanks to Martin for spotting the bug for me. Should be fixed
> in S4Vectors 0.9.27.
>
> Sorry for the inconvenience,
> H.
>
>
> On 02/01/2016 01:02 PM, Morgan, Martin wrote:
>
>> I don't see an error, but on linux under valgrind and current R-devel /
>> bioc packages and especially
>>
>> packageVersion("S4Vectors")
>>>
>> [1] '0.9.26'
>>
>>
>> I see
>>
>> rse[1:2,] # hangs
>>>
>> ==23105== Invalid read of size 4
>> ==23105== at 0xD0B8D4D: int_bsearch (Rle_class.c:606)
>> ==23105== by 0xD0B8C45: find_window_runs2 (Rle_class.c:654)
>> ==23105== by 0xD0B868B: find_runs_of_ranges2 (Rle_class.c:719)
>> ==23105== by 0xD0B6F5A: find_runs_of_ranges (Rle_class.c:837)
>> ==23105== by 0xD0B75CA: _subset_Rle_by_ranges (Rle_class.c:996)
>> ==23105== by 0xD0B7A42: Rle_extract_ranges (Rle_class.c:1018)
>> ==23105== by 0x4F24411: R_doDotCall (dotcode.c:582)
>> ==23105== by 0x4F31621: do_dotcall (dotcode.c:1251)
>> ==23105== by 0x4F6FA8A: Rf_eval (eval.c:713)
>> ==23105== by 0x4F88101: do_begin (eval.c:1806)
>> ==23105== by 0x4F6F8B7: Rf_eval (eval.c:685)
>> ==23105== by 0x4F85303: Rf_applyClosure (eval.c:1134)
>> ==23105== Address 0x80f1760 is 0 bytes after a block of size 0 alloc'd
>> ==23105== at 0x4C2AB80: malloc (in
>> /usr/lib/valgrind/vgpreload_memcheck-amd64-linux.so)
>> ==23105== by 0xD0B8549: find_runs_of_ranges2 (Rle_class.c:704)
>> ==23105== by 0xD0B6F5A: find_runs_of_ranges (Rle_class.c:837)
>> ==23105== by 0xD0B75CA: _subset_Rle_by_ranges (Rle_class.c:996)
>> ==23105== by 0xD0B7A42: Rle_extract_ranges (Rle_class.c:1018)
>> ==23105== by 0x4F24411: R_doDotCall (dotcode.c:582)
>> ==23105== by 0x4F31621: do_dotcall (dotcode.c:1251)
>> ==23105== by 0x4F6FA8A: Rf_eval (eval.c:713)
>> ==23105== by 0x4F88101: do_begin (eval.c:1806)
>> ==23105== by 0x4F6F8B7: Rf_eval (eval.c:685)
>> ==23105== by 0x4F85303: Rf_applyClosure (eval.c:1134)
>> ==23105== by 0x4F6FB9C: Rf_eval (eval.c:732)
>> ==23105==
>> ==23105== Invalid read of size 4
>> ==23105== at 0xD0B8D7D: int_bsearch (Rle_class.c:612)
>> ==23105== by 0xD0B8C45: find_window_runs2 (Rle_class.c:654)
>> ==23105== by 0xD0B868B: find_runs_of_ranges2 (Rle_class.c:719)
>> ==23105== by 0xD0B6F5A: find_runs_of_ranges (Rle_class.c:837)
>> ==23105== by 0xD0B75CA: _subset_Rle_by_ranges (Rle_class.c:996)
>> ==23105== by 0xD0B7A42: Rle_extract_ranges (Rle_class.c:1018)
>> ==23105== by 0x4F24411: R_doDotCall (dotcode.c:582)
>> ==23105== by 0x4F31621: do_dotcall (dotcode.c:1251)
>> ==23105== by 0x4F6FA8A: Rf_eval (eval.c:713)
>> ==23105== by 0x4F88101: do_begin (eval.c:1806)
>> ==23105== by 0x4F6F8B7: Rf_eval (eval.c:685)
>> ==23105== by 0x4F85303: Rf_applyClosure (eval.c:1134)
>> ==23105== Address 0x8ba088c is 4 bytes before a block of size 0 alloc'd
>> ==23105== at 0x4C2AB80: malloc (in
>> /usr/lib/valgrind/vgpreload_memcheck-amd64-linux.so)
>> ==23105== by 0xD0B8549: find_runs_of_ranges2 (Rle_class.c:704)
>> ==23105== by 0xD0B6F5A: find_runs_of_ranges (Rle_class.c:837)
>> ==23105== by 0xD0B75CA: _subset_Rle_by_ranges (Rle_class.c:996)
>> ==23105== by 0xD0B7A42: Rle_extract_ranges (Rle_class.c:1018)
>> ==23105== by 0x4F24411: R_doDotCall (dotcode.c:582)
>> ==23105== by 0x4F31621: do_dotcall (dotcode.c:1251)
>> ==23105== by 0x4F6FA8A: Rf_eval (eval.c:713)
>> ==23105== by 0x4F88101: do_begin (eval.c:1806)
>> ==23105== by 0x4F6F8B7: Rf_eval (eval.c:685)
>> ==23105== by 0x4F85303: Rf_applyClosure (eval.c:1134)
>> ==23105== by 0x4F6FB9C: Rf_eval (eval.c:732)
>> ==23105==
>>
>>
>>
>> ________________________________________
>> From: Bioc-devel <bioc-devel-bounces at r-project.org> on behalf of Michael
>> Love <michaelisaiahlove at gmail.com>
>> Sent: Monday, February 1, 2016 3:35 PM
>> To: Dan Tenenbaum
>> Cc: bioc-devel; Hervé Pagès
>> Subject: Re: [Bioc-devel] TIMEOUTs on Morelia
>>
>> I was able to construct a minimal example where it seems the bug
>> originates
>> from SummarizedExperiment:
>>
>> library(SummarizedExperiment)
>> se <- SummarizedExperiment(matrix(1:6,ncol=2))
>> rse <- as(se, "RangedSummarizedExperiment")
>> rse[1:2,] # hangs
>>
>>
>> On Mon, Feb 1, 2016 at 2:57 PM, Michael Love <michaelisaiahlove at gmail.com
>> >
>> wrote:
>>
>> Thanks Stephen and Dan, sorry I haven't chased this down recently.
>>>
>>> I have access to a Mac and will look into it now.
>>>
>>> -Mike
>>>
>>> On Mon, Feb 1, 2016 at 1:45 PM, Dan Tenenbaum <dtenenba at fredhutch.org>
>>> wrote:
>>>
>>> Actually, it does seem like there is a more complicated issue going on. I
>>>> will investigate and report back here.
>>>>
>>>> Thanks,
>>>> Dan
>>>>
>>>>
>>>> ----- Original Message -----
>>>>
>>>>> From: "Dan Tenenbaum" <dtenenba at fredhutch.org>
>>>>> To: "Hartley, Stephen (NIH/NHGRI) [F]" <stephen.hartley at nih.gov>
>>>>> Cc: "bioc-devel" <bioc-devel at r-project.org>
>>>>> Sent: Monday, February 1, 2016 10:11:54 AM
>>>>> Subject: Re: [Bioc-devel] TIMEOUTs on Morelia
>>>>>
>>>>
>>>> I think the morelia server was overloaded, so it was restarted
>>>>>
>>>> yesterday around
>>>>
>>>>> 11PM Seattle time, so I hope we will see fewer TIMEOUTs in today's
>>>>> build
>>>>> report.
>>>>> Dan
>>>>>
>>>>>
>>>>> ----- Original Message -----
>>>>>
>>>>>> From: "Hartley, Stephen (NIH/NHGRI) [F]" <stephen.hartley at nih.gov>
>>>>>> To: "bioc-devel" <bioc-devel at r-project.org>
>>>>>> Sent: Monday, February 1, 2016 10:06:11 AM
>>>>>> Subject: [Bioc-devel] TIMEOUTs on Morelia
>>>>>>
>>>>>
>>>>> The current devel build for DESeq2 has status TIMEOUT on Morelia. This
>>>>>>
>>>>> is odd
>>>>
>>>>> since the package builder gives it 40 minutes to complete, and it
>>>>>>
>>>>> finishes in
>>>>
>>>>> less than 5 on zin2 and muscato2.
>>>>>>
>>>>>> A bunch of packages that depend on or suggest DESeq2 also timeout on
>>>>>>
>>>>> Morelia:
>>>>
>>>>> DiffBind, derfinder, DChIPRep, gage, phyloseq, rgsepd, systemPipeR,
>>>>>>
>>>>> and TCC.
>>>>
>>>>> All of them time out after 40 minutes, but take less than 10 minutes
>>>>>>
>>>>> to build
>>>>
>>>>> on zin2 and moscato2.
>>>>>>
>>>>>> So I guess the question is: is it DESeq2, or is something wrong with
>>>>>>
>>>>> the Morelia
>>>>
>>>>> server? I don't have an OSX-mavericks machine to test it all out on.
>>>>>>
>>>>>> Is there any way to get previous daily build reports, or are they
>>>>>>
>>>>> deleted daily?
>>>>
>>>>>
>>>>>> -Steve
>>>>>>
>>>>>> [[alternative HTML version deleted]]
>>>>>>
>>>>>> _______________________________________________
>>>>>> Bioc-devel at r-project.org mailing list
>>>>>> https://stat.ethz.ch/mailman/listinfo/bioc-devel
>>>>>>
>>>>>
>>>>> _______________________________________________
>>>>> Bioc-devel at r-project.org mailing list
>>>>> https://stat.ethz.ch/mailman/listinfo/bioc-devel
>>>>>
>>>>
>>>> _______________________________________________
>>>> Bioc-devel at r-project.org mailing list
>>>> https://stat.ethz.ch/mailman/listinfo/bioc-devel
>>>>
>>>>
>>>
>>>
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>>
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> --
> 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: hpages at fredhutch.org
> Phone: (206) 667-5791
> Fax: (206) 667-1319
>
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