[Bioc-devel] TIMEOUTs on Morelia

[Morgan, Martin]

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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