Hi Hervé,
Thank you! You saved me.
Best!
Your sincerely,
Jianhong Ou
> On Apr 24, 2020, at 5:59 PM, Hervé Pagès <hpa...@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" <hpa...@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@r-project.org <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
_______________________________________________
Bioc-devel@r-project.org mailing list
https://stat.ethz.ch/mailman/listinfo/bioc-devel
