[Bioc-devel] Got timeout for machv2 BUILD

[Hervé Pagès]

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:
> Hi Herve,
> 
> Thank you for your help.
> 
> Jianhong.
> 
> On 4/17/20, 4:14 PM, "Hervé Pagès" <hpages using 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 using r-project.org <bioc-devel using 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 using 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 using r-project.org mailing list
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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: hpages using 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: hpages using fredhutch.org
Phone:  (206) 667-5791
Fax:    (206) 667-1319