[Bioc-devel] Got timeout for machv2 BUILD

[Hervé Pagès]

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 <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}}
>>>      >
>>>      > _______________________________________________
>>>      > Bioc-devel using 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: 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

-- 
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