[Bioc-devel] Got timeout for machv2 BUILD

[Jianhong Ou, Ph.D.]

Hi Hervé,

Thank you! You saved me.

Best!

Your sincerely,

Jianhong Ou

> On Apr 24, 2020, at 5:59 PM, Hervé Pagès <hpages using fredhutch.org> 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’
> 
> 
> 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}}
>>     >
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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