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 <[email protected]> on behalf of Michael Love
<[email protected]>
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 <[email protected]>
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 <[email protected]>
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" <[email protected]>
To: "Hartley, Stephen (NIH/NHGRI) [F]" <[email protected]>
Cc: "bioc-devel" <[email protected]>
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]" <[email protected]>
To: "bioc-devel" <[email protected]>
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
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Hervé Pagès
Program in Computational Biology
Division of Public Health Sciences
Fred Hutchinson Cancer Research Center
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