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scanMiR #2067
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Hi @fridoling Thanks for submitting your package. We are taking a quick The DESCRIPTION file for this package is:
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Received a valid push on git.bioconductor.org; starting a build for commit id: 91c37c54fe0d0e31f3ad551705467a21c8b1e08e |
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Hi @hpages, honored to have you as reviewer ;) |
Hi @plger , I would need to be able to take a look at those files in scanMiRData to provide some advice but unfortunately the link you provided doesn't work. Can you fix it? Thanks, |
sorry @hpages , I thought it was public already... now the link should work |
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Hi @plger , scanMiRData_0.99.2.tar.gz is 23M which maybe is a little bit more than what we usually recommend for a data experiment package, so moving the datasets to ExperimentHub would make sense. However it's not crazy big either so we can work with that, at least for now. And since the 3 datasets are serialized instances of a new S4 class that is part of the submission (the KdModelList class), I actually think that it's going to be easier if the datasets live in the data package and not on ExperimentHub. Just in case the design of the S4 class changes during the review process (in which case updating the serialized datasets is going to be easier if they live in the package). So yes, please submit scanMiRData as an additional package. Thanks, |
AdditionalPackage: https://github.com/ETHZ-INS/scanMiRData |
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Received a valid push on git.bioconductor.org; starting a build for commit id: b2c1b7fbf1437c131a55bdcdf91527e2c4064cb1 |
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@hpages we've got a third (and last!) package ( https://github.com/ETHZ-INS/scanMiRApp ) depending on scanMiR. It's the dependency-heavy one, containing wrappers & extras & a shiny app... should we add it here again, or maybe wait for this review to be over and start a fresh new one after? |
Sorry for the delay. If it is a related package that uses scanMiR or scanMirData than I would say it is okay to add it here as an AdditionalPackage. Cheers |
This package is in good shape. I think it would be good to address BiocCheck events:
specifically the unit test suggestion is important; if you don't want to do it please indicate why. |
I also took the liberty of trying out the app. I used the example and was able to generate
Do you want to address these? |
@vjcitn the two scanMiRApp warnings are now fixed. |
Honestly, I dont know if a different maintainer on an additionalpackage would cause an issue; my suspicion is yes we would run into permission issue. The catch with opening a new issue is if these accompanied packages are not accepted yet and in the official Bioconductor repository then the new issue will not be able to find the dependent package so there may be a delay in reviewing the newly opened issue |
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@vjcitn we have added "Alignment" to the biocViews, a NEWS file, and unit tests (> 70% code coverage). We have used 1:... only if ranges are defined by hardcoded digits, so this cannot possibly cause any problems. |
@lshep Thanks for the info. We are not in a hurry, so we can wait for the review of scanMiR to be finished and then open a new issue. |
Your package has been accepted. It will be added to the Thank you for contributing to Bioconductor! Reviewers for Bioconductor packages are volunteers from the Bioconductor |
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The master branch of your GitHub repository has been added to Bioconductor's git repository. To use the git.bioconductor.org repository, we need an 'ssh' key to associate with your github user name. If your GitHub account already has ssh public keys (https://github.com/fridoling.keys is not empty), then no further steps are required. Otherwise, do the following: See further instructions at https://bioconductor.org/developers/how-to/git/ for working with this repository. See especially https://bioconductor.org/developers/how-to/git/new-package-workflow/ to keep your GitHub and Bioconductor repositories in sync. Your package will be included in the next nigthly 'devel' build (check-out from git at about 6 pm Eastern; build completion around 2pm Eastern the next day) at https://bioconductor.org/checkResults/ (Builds sometimes fail, so ensure that the date stamps on the main landing page are consistent with the addition of your package). Once the package builds successfully, you package will be available for download in the 'Devel' version of Bioconductor using https://bioconductor.org/packages/scanMiRData If you have any questions, please contact the bioc-devel mailing list (https://stat.ethz.ch/mailman/listinfo/bioc-devel); this issue will not be monitored further. |
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