[Bioc-devel] TIMEOUTs on Morelia

Michael Love michaelisaiahlove at gmail.com
Mon Feb 1 21:35:48 CET 2016


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]]
>> >>
>> >> _______________________________________________
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>> >> https://stat.ethz.ch/mailman/listinfo/bioc-devel
>> >
>> > _______________________________________________
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>> > https://stat.ethz.ch/mailman/listinfo/bioc-devel
>>
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>>
>
>

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