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[Bioc-devel] Got timeout for machv2 BUILD

9 messages · Stefano de Pretis, Jianhong Ou, Ph.D., Hervé Pagès

Original
Jianhong Ou, Ph.D.
# 
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.ou at 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}}
2 days later
Jianhong Ou, Ph.D.
# 
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.
Stefano de Pretis
# 
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.ou at duke.edu> ha scritto:

  
  


  


      

    

    

      
      

        


  

        

      Hervé Pagès
    

    

      
      #
    

  


  

      
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:

            

      
      
      
    

        

      
      
    

        

  
    

      
      
    

  


  


      

    

    

      
      

        


  

        

      Jianhong Ou, Ph.D.
    

    

      
      #
    

  


  

      
Hi Stefano,

Thank you for your share.

Jianhong.

From: Stefano de Pretis <ste.depo at gmail.com>
Date: Friday, April 17, 2020 at 3:18 PM
To: "Jianhong Ou, Ph.D." <jianhong.ou at duke.edu>
Cc: "bioc-devel at r-project.org" <bioc-devel at 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. <jianhong.ou at duke.edu<mailto:jianhong.ou at 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.

        

      
      
    

  
  


  


      

    

    

      
      

        


  

        

      Jianhong Ou, Ph.D.
    

    

      
      #
    

  


  

      
Hi Herve,

Thank you for your help.

Jianhong.

        
?On 4/17/20, 4:14 PM, "Herv? Pag?s" <hpages at fredhutch.org> 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 at r-project.org <bioc-devel at 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.ou at 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 at 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=
    > 
    
    -- 
    Herv? Pag?s
    
    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 at fredhutch.org
    Phone:  (206) 667-5791
    Fax:    (206) 667-1319

  
  


  


      

    

    
7 days later

    

      
      

        


  

        

      Hervé Pagès
    

    

      
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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?


real	1m33.576s
user	1m26.714s
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:

            

      
      
      
    

        

  
    

      
      
    

  


  


      

    

    

      
      

        


  

        

      Jianhong Ou, Ph.D.
    

    

      
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Hi Herv?,

Thank you! You saved me.

Best!

Your sincerely,

Jianhong Ou

            

      
      
      
    

  
  


  


      

    

    

      
      

        


  

        

      Hervé Pagès
    

    

      
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LOL

        
On 4/24/20 15:00, Jianhong Ou, Ph.D. wrote: