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 <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
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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: 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
--
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
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