Dear bioc-devel, one of the requirements for the Bioconductor package is to pass the R CMD BUILD, including some constraints on the time. To accommodate for some specific cases, Bioconductor implements a concept of long tests which are excluded from the build time limit. I wonder if a corresponding concept exists for the vignettes? I do realize the need for time constraints. However, I think it could be of use to supplement a main vignette with supplementary vignettes that could showcase the package use eg. on a larger dataset. Those could have a less strict constraints policy eg. more time to run, more resources like number of cores, RAM etc. Are there any ways to accomplish this? Best Maciek
[Bioc-devel] Supplementing package vignette with workflow vignette
3 messages · migdal migdal, Hervé Pagès
On 16/02/2022 00:35, migdal migdal wrote:
Dear bioc-devel, one of the requirements for the Bioconductor package is to pass the R CMD BUILD, including some constraints on the time. To accommodate for some specific cases, Bioconductor implements a concept of long tests which are excluded from the build time limit. I wonder if a corresponding concept exists for the vignettes? I do realize the need for time constraints. However, I think it could be of use to supplement a main vignette with supplementary vignettes that could showcase the package use eg. on a larger dataset. Those could have a less strict constraints policy eg. more time to run, more resources like number of cores, RAM etc. Are there any ways to accomplish this?
Yes, by creating (and submitting) a workflow package. This is basically a vignette wrapped in its own dedicated package (the package typically contains no R code). List of existing workflow packages: https://bioconductor.org/packages/devel/BiocViews.html#___Workflow Workflow builds (Tuesdays and Fridays): ? https://bioconductor.org/checkResults/3.15/workflows-LATEST/ Timeout limit is 2h for these packages. Cheers, H.
Best Maciek [[alternative HTML version deleted]]
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Herv? Pag?s Bioconductor Core Team hpages.on.github at gmail.com
Awesome, thanks! On Thu, 17 Feb 2022 at 02:29, Herv? Pag?s <hpages.on.github at gmail.com> wrote:
On 16/02/2022 00:35, migdal migdal wrote:
Dear bioc-devel, one of the requirements for the Bioconductor package is to pass the R CMD BUILD, including some constraints on the time. To accommodate for some specific cases, Bioconductor implements a concept of long tests which are excluded from the build time limit. I wonder if a corresponding concept exists for the vignettes? I do realize the need for time constraints. However, I think it could be of use to supplement a main vignette with supplementary vignettes that could showcase the package use eg. on a
larger
dataset. Those could have a less strict constraints policy eg. more time
to
run, more resources like number of cores, RAM etc. Are there any ways to accomplish this?
Yes, by creating (and submitting) a workflow package. This is basically a vignette wrapped in its own dedicated package (the package typically contains no R code). List of existing workflow packages: https://bioconductor.org/packages/devel/BiocViews.html#___Workflow Workflow builds (Tuesdays and Fridays): https://bioconductor.org/checkResults/3.15/workflows-LATEST/ Timeout limit is 2h for these packages. Cheers, H.
Best Maciek
[[alternative HTML version deleted]]
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-- Herv? Pag?s Bioconductor Core Team hpages.on.github at gmail.com