Re: [Bioc-devel] Got timeout for machv2 BUILD
Hi Hervé,
Thank you! You saved me.
Best!
Your sincerely,
Jianhong Ou
> On Apr 24, 2020, at 5:59 PM, Hervé Pagès wrote:
>
> Hi Jianhong,
>
> I just updated R from R 4.0 alpha to the final R 4.0.0 on machv2 and the good
> news is that I no longer get a TIMEOUT with this new R:
>
> machv2:meat biocbuild$ time R CMD build motifStack
> * checking for file ‘motifStack/DESCRIPTION’ ... OK
> * preparing ‘motifStack’:
> * checking DESCRIPTION meta-information ... OK
> * installing the package to build vignettes
> * creating vignettes ... OK
> * checking for LF line-endings in source and make files and shell scripts
> * checking for empty or unneeded directories
> * building ‘motifStack_1.31.2.tar.gz’
>
>
> real1m33.576s
> user1m26.714s
> sys0m3.815s
>
> So maybe it was a temporary issue with early Mac builds of R 4.0.
>
> Please keep an eye on tomorrow's report (Saturday) and let me know if the
> TIMEOUT is still there.
>
> Thanks,
> H.
>
>
>> On 4/17/20 13:16, Jianhong Ou, Ph.D. wrote:
>> Hi Herve,
>> Thank you for your help.
>> Jianhong.
>> On 4/17/20, 4:14 PM, "Hervé Pagès" wrote:
>> For some reasons the generation of the plots in the vignette is VERY
>> slow on machv2. 'R CMD build' actually completed... after 6h! This is
>> still under investigation.
>> Best,
>> H.
>> On 4/17/20 12:11, Jianhong Ou, Ph.D. wrote:
>> > Hi,
>> >
>> > I got timeout for my package motifStack in machv2. But I don't know
>> what cuased the issue.
>> >
>> > Any help would be greatly appreciated.
>> >
>> > Jianhong.
>> >
>> > From: Jianhong Ou, Ph.D.
>> > Sent: Wednesday, April 15, 2020 7:53 AM
>> > To: bioc-devel@r-project.org
>> > Subject: Got timeout for machv2 BUILD
>> >
>> > Hi,
>> >
>> > Hope you are doing well.
>> >
>> > I got timeout for my package motifStack in machv2. The ellapsedTime is
>> 2403.0 seconds while in tokay2 is 82.1 seconds and in malbec2 is 126.1
>> seconds. I have limited information how to debug.
>> > Could you share your suggestion? Thank you.
>> >
>> >
>> >
>> > Yours Sincerely,
>> >
>> > Jianhong Ou
>> >
>> > Email: jianhong...@duke.edu
>> > Bioinformatician II
>> > Department of Cell Biology
>> > Duke University School of Medicine
>> > Durham, NC, 27710
>> >
>> > Confidentiality Notice:\ This e-mail message, including
>> ...{{dropped:12}}
>> >
>> > ___
>> > Bioc-devel@r-project.org mailing list
>> >
>> https://urldefense.proofpoint.com/v2/url?u=https-3A__stat.ethz.ch_mailman_listinfo_bioc-2Ddevel&d=DwICAg&c=eRAMFD45gAfqt84VtBcfhQ&r=BK7q3XeAvimeWdGbWY_wJYbW0WYiZvSXAJJKaaPhzWA&m=a83aImZ7c6KpUeEwr7eFpQuhOhlc-gRDnLp6RuQ9Q54&s=_7BtJGe9UeLXCftvPCoyrq3FIKBxCMLUVZwuU9GOx7w&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: hpa...@fredhutch.org
>> Phone: (206) 667-5791
>> Fax:(206) 667-1319
>>
>
> --
> 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] Got timeout for machv2 BUILD
LOL
On 4/24/20 15:00, Jianhong Ou, Ph.D. wrote:
Hi Hervé,
Thank you! You saved me.
Best!
Your sincerely,
Jianhong Ou
On Apr 24, 2020, at 5:59 PM, Hervé Pagès wrote:
Hi Jianhong,
I just updated R from R 4.0 alpha to the final R 4.0.0 on machv2 and the good
news is that I no longer get a TIMEOUT with this new R:
machv2:meat biocbuild$ time R CMD build motifStack
* checking for file ‘motifStack/DESCRIPTION’ ... OK
* preparing ‘motifStack’:
* checking DESCRIPTION meta-information ... OK
* installing the package to build vignettes
* creating vignettes ... OK
* checking for LF line-endings in source and make files and shell scripts
* checking for empty or unneeded directories
* building ‘motifStack_1.31.2.tar.gz’
real1m33.576s
user1m26.714s
sys0m3.815s
So maybe it was a temporary issue with early Mac builds of R 4.0.
Please keep an eye on tomorrow's report (Saturday) and let me know if the
TIMEOUT is still there.
Thanks,
H.
On 4/17/20 13:16, Jianhong Ou, Ph.D. wrote:
Hi Herve,
Thank you for your help.
Jianhong.
On 4/17/20, 4:14 PM, "Hervé Pagès" wrote:
For some reasons the generation of the plots in the vignette is VERY
slow on machv2. 'R CMD build' actually completed... after 6h! This is
still under investigation.
Best,
H.
On 4/17/20 12:11, Jianhong Ou, Ph.D. wrote:
> Hi,
>
> I got timeout for my package motifStack in machv2. But I don't know what
cuased the issue.
>
> Any help would be greatly appreciated.
>
> Jianhong.
>
> From: Jianhong Ou, Ph.D.
> Sent: Wednesday, April 15, 2020 7:53 AM
> To: bioc-devel@r-project.org
> Subject: Got timeout for machv2 BUILD
>
> Hi,
>
> Hope you are doing well.
>
> I got timeout for my package motifStack in machv2. The ellapsedTime is
2403.0 seconds while in tokay2 is 82.1 seconds and in malbec2 is 126.1 seconds. I
have limited information how to debug.
> Could you share your suggestion? Thank you.
>
>
>
> Yours Sincerely,
>
> Jianhong Ou
>
> Email: jianhong...@duke.edu
> Bioinformatician II
> Department of Cell Biology
> Duke University School of Medicine
> Durham, NC, 27710
>
> Confidentiality Notice:\ This e-mail message, including ...{{dropped:12}}
>
> ___
> Bioc-devel@r-project.org mailing list
>
https://urldefense.proofpoint.com/v2/url?u=https-3A__stat.ethz.ch_mailman_listinfo_bioc-2Ddevel&d=DwICAg&c=eRAMFD45gAfqt84VtBcfhQ&r=BK7q3XeAvimeWdGbWY_wJYbW0WYiZvSXAJJKaaPhzWA&m=a83aImZ7c6KpUeEwr7eFpQuhOhlc-gRDnLp6RuQ9Q54&s=_7BtJGe9UeLXCftvPCoyrq3FIKBxCMLUVZwuU9GOx7w&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: hpa...@fredhutch.org
Phone: (206) 667-5791
Fax:(206) 667-1319
--
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
--
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] Got timeout for machv2 BUILD
Hi Jianhong,
I just updated R from R 4.0 alpha to the final R 4.0.0 on machv2 and the
good news is that I no longer get a TIMEOUT with this new R:
machv2:meat biocbuild$ time R CMD build motifStack
* checking for file ‘motifStack/DESCRIPTION’ ... OK
* preparing ‘motifStack’:
* checking DESCRIPTION meta-information ... OK
* installing the package to build vignettes
* creating vignettes ... OK
* checking for LF line-endings in source and make files and shell scripts
* checking for empty or unneeded directories
* building ‘motifStack_1.31.2.tar.gz’
real1m33.576s
user1m26.714s
sys 0m3.815s
So maybe it was a temporary issue with early Mac builds of R 4.0.
Please keep an eye on tomorrow's report (Saturday) and let me know if
the TIMEOUT is still there.
Thanks,
H.
On 4/17/20 13:16, Jianhong Ou, Ph.D. wrote:
Hi Herve,
Thank you for your help.
Jianhong.
On 4/17/20, 4:14 PM, "Hervé Pagès" wrote:
For some reasons the generation of the plots in the vignette is VERY
slow on machv2. 'R CMD build' actually completed... after 6h! This is
still under investigation.
Best,
H.
On 4/17/20 12:11, Jianhong Ou, Ph.D. wrote:
> Hi,
>
> I got timeout for my package motifStack in machv2. But I don't know what
cuased the issue.
>
> Any help would be greatly appreciated.
>
> Jianhong.
>
> From: Jianhong Ou, Ph.D.
> Sent: Wednesday, April 15, 2020 7:53 AM
> To: bioc-devel@r-project.org
> Subject: Got timeout for machv2 BUILD
>
> Hi,
>
> Hope you are doing well.
>
> I got timeout for my package motifStack in machv2. The ellapsedTime is
2403.0 seconds while in tokay2 is 82.1 seconds and in malbec2 is 126.1 seconds. I
have limited information how to debug.
> Could you share your suggestion? Thank you.
>
>
>
> Yours Sincerely,
>
> Jianhong Ou
>
> Email: jianhong...@duke.edu
> Bioinformatician II
> Department of Cell Biology
> Duke University School of Medicine
> Durham, NC, 27710
>
> Confidentiality Notice:\ This e-mail message, including ...{{dropped:12}}
>
> ___
> Bioc-devel@r-project.org mailing list
>
https://urldefense.proofpoint.com/v2/url?u=https-3A__stat.ethz.ch_mailman_listinfo_bioc-2Ddevel&d=DwICAg&c=eRAMFD45gAfqt84VtBcfhQ&r=BK7q3XeAvimeWdGbWY_wJYbW0WYiZvSXAJJKaaPhzWA&m=a83aImZ7c6KpUeEwr7eFpQuhOhlc-gRDnLp6RuQ9Q54&s=_7BtJGe9UeLXCftvPCoyrq3FIKBxCMLUVZwuU9GOx7w&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: hpa...@fredhutch.org
Phone: (206) 667-5791
Fax:(206) 667-1319
--
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] Got timeout for machv2 BUILD
Hi Herve,
Thank you for your help.
Jianhong.
On 4/17/20, 4:14 PM, "Hervé Pagès" wrote:
For some reasons the generation of the plots in the vignette is VERY
slow on machv2. 'R CMD build' actually completed... after 6h! This is
still under investigation.
Best,
H.
On 4/17/20 12:11, Jianhong Ou, Ph.D. wrote:
> Hi,
>
> I got timeout for my package motifStack in machv2. But I don't know what
cuased the issue.
>
> Any help would be greatly appreciated.
>
> Jianhong.
>
> From: Jianhong Ou, Ph.D.
> Sent: Wednesday, April 15, 2020 7:53 AM
> To: bioc-devel@r-project.org
> Subject: Got timeout for machv2 BUILD
>
> Hi,
>
> Hope you are doing well.
>
> I got timeout for my package motifStack in machv2. The ellapsedTime is
2403.0 seconds while in tokay2 is 82.1 seconds and in malbec2 is 126.1 seconds.
I have limited information how to debug.
> Could you share your suggestion? Thank you.
>
>
>
> Yours Sincerely,
>
> Jianhong Ou
>
> Email: jianhong...@duke.edu
> Bioinformatician II
> Department of Cell Biology
> Duke University School of Medicine
> Durham, NC, 27710
>
> Confidentiality Notice:\ This e-mail message, including ...{{dropped:12}}
>
> ___
> Bioc-devel@r-project.org mailing list
>
https://urldefense.proofpoint.com/v2/url?u=https-3A__stat.ethz.ch_mailman_listinfo_bioc-2Ddevel&d=DwICAg&c=eRAMFD45gAfqt84VtBcfhQ&r=BK7q3XeAvimeWdGbWY_wJYbW0WYiZvSXAJJKaaPhzWA&m=a83aImZ7c6KpUeEwr7eFpQuhOhlc-gRDnLp6RuQ9Q54&s=_7BtJGe9UeLXCftvPCoyrq3FIKBxCMLUVZwuU9GOx7w&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: hpa...@fredhutch.org
Phone: (206) 667-5791
Fax:(206) 667-1319
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Re: [Bioc-devel] Got timeout for machv2 BUILD
Hi Stefano,
Thank you for your share.
Jianhong.
From: Stefano de Pretis
Date: Friday, April 17, 2020 at 3:18 PM
To: "Jianhong Ou, Ph.D."
Cc: "bioc-devel@r-project.org"
Subject: Re: [Bioc-devel] Got timeout for machv2 BUILD
HI,
We solved a similar issue for the INSPEcT package avoiding the parallelization
in the computation of examples and vignettes. In our case it caused the timeout
in the Windows environment.
Best,
Stefano
Il giorno ven 17 apr 2020 alle 21:11 Jianhong Ou, Ph.D.
mailto:jianhong...@duke.edu>> ha scritto:
Hi,
I got timeout for my package motifStack in machv2. But I don't know what cuased
the issue.
Any help would be greatly appreciated.
Jianhong.
From: Jianhong Ou, Ph.D.
Sent: Wednesday, April 15, 2020 7:53 AM
To: bioc-devel@r-project.org<mailto:bioc-devel@r-project.org>
mailto:bioc-devel@r-project.org>>
Subject: Got timeout for machv2 BUILD
Hi,
Hope you are doing well.
I got timeout for my package motifStack in machv2. The ellapsedTime is 2403.0
seconds while in tokay2 is 82.1 seconds and in malbec2 is 126.1 seconds. I have
limited information how to debug.
Could you share your suggestion? Thank you.
Yours Sincerely,
Jianhong Ou
Email: jianhong...@duke.edu<mailto:jianhong...@duke.edu>
Bioinformatician II
Department of Cell Biology
Duke University School of Medicine
Durham, NC, 27710
Confidentiality Notice:\ This e-mail message, including ...{{dropped:12}}
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Re: [Bioc-devel] Got timeout for machv2 BUILD
For some reasons the generation of the plots in the vignette is VERY
slow on machv2. 'R CMD build' actually completed... after 6h! This is
still under investigation.
Best,
H.
On 4/17/20 12:11, Jianhong Ou, Ph.D. wrote:
Hi,
I got timeout for my package motifStack in machv2. But I don't know what cuased
the issue.
Any help would be greatly appreciated.
Jianhong.
From: Jianhong Ou, Ph.D.
Sent: Wednesday, April 15, 2020 7:53 AM
To: bioc-devel@r-project.org
Subject: Got timeout for machv2 BUILD
Hi,
Hope you are doing well.
I got timeout for my package motifStack in machv2. The ellapsedTime is 2403.0
seconds while in tokay2 is 82.1 seconds and in malbec2 is 126.1 seconds. I have
limited information how to debug.
Could you share your suggestion? Thank you.
Yours Sincerely,
Jianhong Ou
Email: jianhong...@duke.edu
Bioinformatician II
Department of Cell Biology
Duke University School of Medicine
Durham, NC, 27710
Confidentiality Notice:\ This e-mail message, including ...{{dropped:12}}
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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] Got timeout for machv2 BUILD
HI,
We solved a similar issue for the INSPEcT package avoiding the
parallelization in the computation of examples and vignettes. In our case
it caused the timeout in the Windows environment.
Best,
Stefano
Il giorno ven 17 apr 2020 alle 21:11 Jianhong Ou, Ph.D. <
jianhong...@duke.edu> ha scritto:
> Hi,
>
> I got timeout for my package motifStack in machv2. But I don't know what
> cuased the issue.
>
> Any help would be greatly appreciated.
>
> Jianhong.
>
> From: Jianhong Ou, Ph.D.
> Sent: Wednesday, April 15, 2020 7:53 AM
> To: bioc-devel@r-project.org
> Subject: Got timeout for machv2 BUILD
>
> Hi,
>
> Hope you are doing well.
>
> I got timeout for my package motifStack in machv2. The ellapsedTime is
> 2403.0 seconds while in tokay2 is 82.1 seconds and in malbec2 is 126.1
> seconds. I have limited information how to debug.
> Could you share your suggestion? Thank you.
>
>
>
> Yours Sincerely,
>
> Jianhong Ou
>
> Email: jianhong...@duke.edu
> Bioinformatician II
> Department of Cell Biology
> Duke University School of Medicine
> Durham, NC, 27710
>
> Confidentiality Notice:\ This e-mail message, including ...{{dropped:12}}
>
> ___
> Bioc-devel@r-project.org mailing list
> https://stat.ethz.ch/mailman/listinfo/bioc-devel
>
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Re: [Bioc-devel] Got timeout for machv2 BUILD
Hi,
I got timeout for my package motifStack in machv2. But I don't know what cuased
the issue.
Any help would be greatly appreciated.
Jianhong.
From: Jianhong Ou, Ph.D.
Sent: Wednesday, April 15, 2020 7:53 AM
To: bioc-devel@r-project.org
Subject: Got timeout for machv2 BUILD
Hi,
Hope you are doing well.
I got timeout for my package motifStack in machv2. The ellapsedTime is 2403.0
seconds while in tokay2 is 82.1 seconds and in malbec2 is 126.1 seconds. I have
limited information how to debug.
Could you share your suggestion? Thank you.
Yours Sincerely,
Jianhong Ou
Email: jianhong...@duke.edu
Bioinformatician II
Department of Cell Biology
Duke University School of Medicine
Durham, NC, 27710
Confidentiality Notice:\ This e-mail message, including ...{{dropped:12}}
___
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[Bioc-devel] Got timeout for machv2 BUILD
Hi,
Hope you are doing well.
I got timeout for my package motifStack in machv2. The ellapsedTime is 2403.0
seconds while in tokay2 is 82.1 seconds and in malbec2 is 126.1 seconds. I have
limited information how to debug.
Could you share your suggestion? Thank you.
Yours Sincerely,
Jianhong Ou
Email: jianhong...@duke.edu
Bioinformatician II
Department of Cell Biology
Duke University School of Medicine
Durham, NC, 27710
Confidentiality Notice:\ This e-mail message, including ...{{dropped:12}}
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