magrene

[almeidasilvaf]

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

• Repository: https://github.com/almeidasilvaf/magrene

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[bioc-issue-bot]

Hi @almeidasilvaf

Thanks for submitting your package. We are taking a quick look at it and you will hear back from us soon.

The DESCRIPTION file for this package is:

Package: magrene
Title: Motif Analysis In Gene Regulatory Networks
Version: 0.99.0
Date: 2022-01-21
Authors@R: 
    c(
    person(given = "Fabrício",
 family = "Almeida-Silva",
 role = c("aut", "cre"),
 email = "[email protected]",
 comment = c(ORCID = "0000-0002-5314-2964")),
    person(given = "Yves",
 family = "Van de Peer",
 role = "aut",
 comment = c(ORCID = "0000-0003-4327-3730"))
    )
Description: magrene allows the identification and analysis of graph motifs 
    in (duplicated) gene regulatory networks (GRNs), including lambda, 
    V, PPI V, delta, and  bifan motifs. GRNs can be tested for motif 
    enrichment by comparing motif frequencies to a null distribution 
    generated from degree-preserving simulated GRNs. Motif frequencies 
    can be analyzed in the context of gene duplications to explore the 
    impact of small-scale and whole-genome duplications on gene 
    regulatory networks. Finally, users can calculate interaction similarity
    for gene pairs based on the Sorensen-Dice similarity index.
License: GPL-3
URL: https://github.com/almeidasilvaf/magrene
BugReports: https://support.bioconductor.org/t/magrene
biocViews: Software,
    MotifDiscovery,
    NetworkEnrichment,
    SystemsBiology,
    GraphAndNetwork
Encoding: UTF-8
Roxygen: list(markdown = TRUE)
RoxygenNote: 7.2.0
Imports:
    utils,
    stats,
    BiocParallel
Suggests: 
    BiocStyle,
    covr,
    knitr,
    rmarkdown,
    ggplot2,
    sessioninfo,
    testthat (>= 3.0.0)
Config/testthat/edition: 3
VignetteBuilder: knitr
Depends: 
    R (>= 4.2.0)
LazyData: false

[bioc-issue-bot]

A reviewer has been assigned to your package. Learn what to expect during the review process.

IMPORTANT: Please read this documentation for setting up remotes to push to git.bioconductor.org. It is required to push a version bump to git.bioconductor.org to trigger a new build.

Bioconductor utilized your github ssh-keys for git.bioconductor.org access. To manage keys and future access you may want to active your Bioconductor Git Credentials Account

[bioc-issue-bot]

Dear Package contributor,

This is the automated single package builder at bioconductor.org.

Your package has been built on Linux, Mac, and Windows.

On one or more platforms, the build results were: "ABNORMAL". This may mean there is a problem with the package that you need to fix. Or it may mean that there is a problem with the build system itself.

Please see the build report for more details. This link will be active for 21 days.

Remember: if you submitted your package after July 7th, 2020, when making changes to your repository push to [email protected]:packages/magrene to trigger a new build. A quick tutorial for setting up remotes and pushing to upstream can be found here.

[almeidasilvaf]

Hi, @vjcitn

I think there is a problem with the build system. I've never seen this "ABNORMAL" thing before, and the build report is empty.

As I would have to push a version bump just to trigger another build, I added more 3 unit tests to increase the test coverage, but when I tried to push to the Bioc repo, I got a "permission denied" error.

Upon inspection, I noticed that this package was not added to Bioc Git Credentials. I only have access to the following packages:

BioNERO cageminer cogeqc syntenet

Is there something you can do on your end? Perhaps force trigger a build?

[lshep]

It doesn't look like this was moderated properly. Give me a few minutes to straighten it out.

[bioc-issue-bot]

A reviewer has been assigned to your package. Learn what to expect during the review process.

IMPORTANT: Please read this documentation for setting up remotes to push to git.bioconductor.org. It is required to push a version bump to git.bioconductor.org to trigger a new build.

Bioconductor utilized your github ssh-keys for git.bioconductor.org access. To manage keys and future access you may want to active your Bioconductor Git Credentials Account

[lshep]

It should be all set. A new build has already been kicked off for you and should post in a few minutes

[bioc-issue-bot]

Dear Package contributor,

This is the automated single package builder at bioconductor.org.

Your package has been built on Linux, Mac, and Windows.

Congratulations! The package built without errors or warnings on all platforms.

Please see the build report for more details. This link will be active for 21 days.

Remember: if you submitted your package after July 7th, 2020, when making changes to your repository push to [email protected]:packages/magrene to trigger a new build. A quick tutorial for setting up remotes and pushing to upstream can be found here.

[almeidasilvaf]

Thanks a million, @lshep! ;)

[almeidasilvaf]

Hi, @vjcitn

It's been more than one month since the package built successfully. Any news on this package?

Best, Fabricio

[bioc-issue-bot]

Your package has been accepted. It will be added to the Bioconductor nightly builds.

Thank you for contributing to Bioconductor!

Reviewers for Bioconductor packages are volunteers from the Bioconductor community. If you are interested in becoming a Bioconductor package reviewer, please see Reviewers Expectations.

[lshep]

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/almeidasilvaf.keys is not empty), then no further steps are required. Otherwise, do the following:

1. Add an SSH key to your github account
2. Submit your SSH key to Bioconductor

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/ https://bioconductor.org/developers/how-to/git/sync-existing-repositories/

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 BiocManager::install("magrene"). The package 'landing page' will be created at

https://bioconductor.org/packages/magrene

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.