[Bioc-devel] Build error in tokay2: cannot reserve space for vector

[Martin Morgan]

On 07/09/2018 11:00 AM, Sergio Picart Armada wrote:
> Thank you Morgan,
> 
> I already fixed this by skipping the offending test on win32.
> I fixed the devel version, but the release version has not noticed the 
> version bump (from 1.0.0 to 1.0.1).
> Did I forget anything?

builds are nightly, not on commit. You made your change on

commit 71e725742eafa45a71e49d76441383dda26621c3
Author: Sergi Picart <elpicart using gmail.com>
Date:   Mon Jul 9 12:53:04 2018 +0200

     Version number bump


so the build system has not had a chance to build. Look at the 
'snapshot' date on the build report page for the date that the most 
recent build started.

Martin

> 
> Thank you again,
> 
> On Monday, May 21, 2018 18:58 CEST, Hervé Pagès <hpages using fredhutch.org> 
> wrote:
>> On 05/21/2018 05:50 AM, Martin Morgan wrote:
>> > Remember that 32-bit Windows can only address vectors that are less than
>> > 2^32 - 1 elements long -- it looks like your example is trying to do
>> > more than this, and the solution is to implement a more modest example.
>>
>> 32-bit Windows limits the amount of memory used by a single process to
>> a little bit less than 3GB. So I think you can actually create vectors
>> that have more than 2^32 elements as long as the total memory used by
>> R doesn't exceeds 3GB.
>>
>> One more thing: since this is a 32-bit Windows issue, you should be able
>> to reproduce this locally by starting R in 32-bit mode:
>>
>> R --arch i386
>>
>> Hope this helps,
>>
>> H.
>>
>> >
>> > Martin
>> >
>> > On 05/18/2018 04:05 AM, Sergio Picart Armada wrote:
>> >>
>> >> Dear Bioconductor team,
>> >>
>> >> I'm the maintainer of the FELLA package.
>> >> Lately the check in tokay2 has failed, see
>> >> 
>> https://urldefense.proofpoint.com/v2/url?u=http-3A__bioconductor.org_checkResults_release_bioc-2DLATEST_FELLA_tokay2-2Dchecksrc.html&d=DwIDaQ&c=eRAMFD45gAfqt84VtBcfhQ&r=BK7q3XeAvimeWdGbWY_wJYbW0WYiZvSXAJJKaaPhzWA&m=-81iJhkqlvXvFLUkNuwd1vRA5eMW-Cf9eDiFgGMLDuk&s=e4cRnI7RwkBDHiDNJodfgLbk-BNKmO6OZsD1MoUHxLc&e=
>> >>
>> >> Specifically: Message: At vector.pmt:442 : cannot reserve space for
>> >> vector, Out of memory
>> >> Class:   simpleError/error/conditionIt only happens in tokay2 and I
>> >> cannot reproduce this locally.
>> >> Is this something on the server side or should I take action?
>> >>
>> >> Thank you,
>> >> Sergi
>> >>
>> >>     [[alternative HTML version deleted]]
>> >>
>> >> _______________________________________________
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>> >> 
>> https://urldefense.proofpoint.com/v2/url?u=https-3A__stat.ethz.ch_mailman_listinfo_bioc-2Ddevel&d=DwIDaQ&c=eRAMFD45gAfqt84VtBcfhQ&r=BK7q3XeAvimeWdGbWY_wJYbW0WYiZvSXAJJKaaPhzWA&m=-81iJhkqlvXvFLUkNuwd1vRA5eMW-Cf9eDiFgGMLDuk&s=brMBxrnaU_ShvDUNzFa8pJ08ru-VDl6-q5yWF9aSIQc&e=
>> >>
>> >>
>> >
>> >
>> > This email message may contain legally privileged and/or...{{dropped:2}}
>> >
>> > _______________________________________________
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>> > 
>> https://urldefense.proofpoint.com/v2/url?u=https-3A__stat.ethz.ch_mailman_listinfo_bioc-2Ddevel&d=DwIDaQ&c=eRAMFD45gAfqt84VtBcfhQ&r=BK7q3XeAvimeWdGbWY_wJYbW0WYiZvSXAJJKaaPhzWA&m=-81iJhkqlvXvFLUkNuwd1vRA5eMW-Cf9eDiFgGMLDuk&s=brMBxrnaU_ShvDUNzFa8pJ08ru-VDl6-q5yWF9aSIQc&e=
>> >
>>
>> --
>> 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 using fredhutch.org
>> Phone: (206) 667-5791
>> Fax: (206) 667-1319
> 
> 
> 


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