[Bioc-devel] Build timeout in windows only

Hervé Pagès hp@ge@ @end|ng |rom |redhutch@org
Mon Apr 27 05:55:11 CEST 2020

Hi Ruijia,

The time for 'R CMD check APAlyzer_1.1.2.tar.gz' on the Linux and Mac 
builders are 1220.1 sec and 1441.6 sec, respectively. Keep in mind that 
on Windows it typically takes about twice longer! That's because all 
examples and unit tests are run for the i386 and x64 archs. So my guess 
is that it's very close to the timeout limit of 40 min there. Thus some 
days it might finish in time and some days not.

To address this, try to reduce a little bit the computing time of some 
of the examples ('R CMD check' displays the list of examples that take 
more than 5s) and/or some of the unit tests. You typically do this by 
reducing the size of the data they use.

An alternative it to move the most time consuming tests to the "long 
test" section of your package. See 
https://bioconductor.org/developers/how-to/long-tests/ for how to do this.


On 4/26/20 19:52, Ruijia Wang wrote:
> Hi BioC-devel,
> I am the author of the Bioconductor package APAlyzer (
> https://urldefense.proofpoint.com/v2/url?u=https-3A__bioconductor.org_packages_devel_bioc_html_APAlyzer.html&d=DwICAg&c=eRAMFD45gAfqt84VtBcfhQ&r=BK7q3XeAvimeWdGbWY_wJYbW0WYiZvSXAJJKaaPhzWA&m=31pbyv_7BwBGTMV1Ny46DJOJnIlNGkH4iZ0lKuI_y9c&s=3qgEfx7Kdbx_geHdl4q0xdt7v8UaPdKh1_KI29f2WRc&e= ). We are
> trying to release our updated package (version 1.1.2) to Bioconductor.
> However, the Build Report (
> https://urldefense.proofpoint.com/v2/url?u=http-3A__bioconductor.org_checkResults_3.11_bioc-2DLATEST_APAlyzer_&d=DwICAg&c=eRAMFD45gAfqt84VtBcfhQ&r=BK7q3XeAvimeWdGbWY_wJYbW0WYiZvSXAJJKaaPhzWA&m=31pbyv_7BwBGTMV1Ny46DJOJnIlNGkH4iZ0lKuI_y9c&s=lEmwST7Xeq8hjQzU1Ceg-HgoM5Tl4oLzEZEFlja0DJM&e= )  shows
> there is a TIMEOUT issue in the windows platform only. It's a bit strange
> to me because we have uploaded this version to Bioconductor a few
> weeks ago, and we didn't see this issue until this week.
> I wonder will this TIMEOUT issue affect the release of our package in the
> coming update of Bioconductor? If so, how should we fix this? Thank you
> in advance!
> Best,
> Ruijia
> 	[[alternative HTML version deleted]]
> _______________________________________________
> 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=31pbyv_7BwBGTMV1Ny46DJOJnIlNGkH4iZ0lKuI_y9c&s=-IJF_ge-iTa_woy5JtF5Hczd-x6GmdyB6JDbGw3TXm8&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

More information about the Bioc-devel mailing list