[Bioc-devel] TIMEOUTs on Morelia
Hervé Pagès
hpages at fredhutch.org
Tue Feb 2 00:36:38 CET 2016
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
>>>
>>
>>
>
> [[alternative HTML version deleted]]
>
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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
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