Message-ID: <0678ee5f-8500-0b5c-0bab-b687c2dcc295@fredhutch.org>
Date: 2020-04-24T21:59:23Z
From: Hervé Pagès
Subject: [Bioc-devel] Got timeout for machv2 BUILD
In-Reply-To: <4E76D844-5BF6-4121-8340-D8FE162B9D20@duke.edu>
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, "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
>
>
--
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