netZooR

[marouenbg]

Update the following URL to point to the GitHub repository of the package you wish to submit to Bioconductor

• Repository: https://github.com/netZoo/netZooR

Confirm the following by editing each check box to '[x]'

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• [x ] My package addresses statistical or bioinformatic issues related to the analysis and comprehension of high throughput genomic data.

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[vjcitn]

Your package is in the devel branch of Bioconductor which only builds against R4.2 at this time. To use netZooR with a different version of R, please install netZooR based on a compatible source version of your package that is, for example, in github. You can use devtools::install_github to accomplish this if working from github; other approaches are available depending on how the source is managed.

[marouenbg]

Hi @vjcitn , When do you think it will be on the base branch and how can I install R4.2 on my computer? Thank you

[vjcitn]

I want to make sure it is understood that you can use the package in R 4.1 if you install it from github. If you want to install it with the Bioconductor devel branch software, which is likely to be unstable, you can install R 4.2 using instructions at the bottom of https://bioconductor.org/developers/how-to/useDevel/

[violafanfani]

Hi @vjcitn, thanks a lot for helping. We encountered this issue as we are trying to prepare the conda recipe so that we can add netzooR to the bioconda channel as bioconductor-netzoor. If I understand correctly, to have a stable recipe (stable R version + stable version of dependencies) we should wait for netzoor to be on the base branch of bioconductor and In the meantime we could prepare a recipe from the github version. Is that correct?

[marouenbg]

Hi @lshep , I've been trying to push new commits to git@git.bioconductor.org:packages/netZooR.git but the push does not trigger tests, are there any issues in the testing machines currently?

[lshep]

Once the package has been accepted it is on the daily builder and does not build through the SPB submission here.
You will have to wait for the daily build report found: http://bioconductor.org/checkResults/ This page also list the schedule of each type of package.
The daily builder does a git pull of all Bioconductor package once a day and performs the install/build/check. Depending on the time of your push it may take up to 48 hours to appear on the daily build report.

Please also always remember to do a version bump with changes. Changes will not propagate if there is not a version bump in the description.

[marouenbg]

Great, thank you!

[marouenbg]

@lshep Is there a buildignore for bioconductor? Like a .biocignore, I am running large tests on my self hosted server and I don't want to include them in bioc build.

[lshep]

bioconductor should respect the traditional .buildignore if its included

[marouenbg]

Hi @lshep , I have updated my package netZooR and the tests ok in http://bioconductor.org/checkResults/ But the develop landing page http://bioconductor.org/packages/3.16/bioc/html/netZooR.html still lists version 1.1 although I bumped the description file to 1.1.15. How often does this page gets updated?

Thank you so much for answering all my questions!

[lshep]

They regenerate once per day after the builds complete and propagate. It looks like today's run was just finishing up and the new version is clean and propagating so I expect the landing page to be updated later today over the next few hours.

[marouenbg]

makes sense, thank you!