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

2018-05-18 Thread Sergio Picart Armada 

Dear Bioconductor team, 

I'm the maintainer of the FELLA package. 
Lately the check in tokay2 has failed, see 
http://bioconductor.org/checkResults/release/bioc-LATEST/FELLA/tokay2-checksrc.html
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
 

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

2018-05-21 Thread Martin Morgan 
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.


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 
http://bioconductor.org/checkResults/release/bioc-LATEST/FELLA/tokay2-checksrc.html
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
  


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

2018-05-21 Thread Hervé Pagès 

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

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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
P.O. Box 19024
Seattle, WA 98109-1024

E-mail: hpa...@fredhutch.org
Phone:  (206) 667-5791
Fax:(206) 667-1319

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

2018-07-09 Thread Sergio Picart Armada 


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?

Thank you again, 

On Monday, May 21, 2018 18:58 CEST, Hervé Pagès  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]]
>>
>> ___
>> Bioc-devel@r-project.org mailing list
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>>
>>
>
>
> This email message may contain legally privileged and/or...{{dropped:2}}
>
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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
P.O. Box 19024
Seattle, WA 98109-1024

E-mail: hpa...@fredhutch.org
Phone: (206) 667-5791
Fax: (206) 667-1319


 

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

2018-07-09 Thread 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 
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  
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]]
>>
>> ___
>> Bioc-devel@r-project.org mailing list
>> 
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>>
>>
>
>
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>
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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
P.O. Box 19024
Seattle, WA 98109-1024

E-mail: hpa...@fredhutch.org
Phone: (206) 667-5791
Fax: (206) 667-1319







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