Hi BioC-devel, I am the author of the Bioconductor package APAlyzer ( https://bioconductor.org/packages/devel/bioc/html/APAlyzer.html). We are trying to release our updated package (version 1.1.2) to Bioconductor. However, the Build Report ( http://bioconductor.org/checkResults/3.11/bioc-LATEST/APAlyzer/) 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
[Bioc-devel] Build timeout in windows only
2 messages · Ruijia Wang, Hervé Pagès
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.
Best,
H.
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]]
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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