rfaRm

[LaraSellesVidal]

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

• Repository: https://github.com/LaraSellesVidal/rfaRm

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[bioc-issue-bot]

Hi @LaraSellesVidal

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: rfaRm
Type: Package
Title: An R interface to the Rfam database
Version: 0.99.0
Date: 2020-04-06
Author: Lara Selles Vidal, Rafael Ayala, Guy-Bart Stan, Rodrigo Ledesma-Amaro
Maintainer: Lara Selles Vidal <lara.selles12@imperial.ac.uk>,
  Rafael Ayala <r.ayala14@imperial.ac.uk>
Description: rfaRm provides a client interface to the Rfam database of RNA 
    families. Data that can be retrieved include RNA families, secondary 
    structure images, covariance models, sequences within each family,
    alignments leading to the identification of a family and secondary 
    structures in the dot-bracket format.
License: GPL-3
Depends: R(>= 3.6.3)
Imports: httr, stringi, rsvg, magick, data.table, Biostrings
Suggests: R4RNA, treeio, knitr, BiocStyle, rmarkdown, BiocGenerics
VignetteBuilder: knitr
biocViews: FunctionalGenomics, DataImport, ThirdPartyClient, Visualization,
 MultipleSequenceAlignments
NeedsCompilation: no
Encoding: UTF-8
LazyData: true

[LaraSellesVidal]

Dear BioConductor team,

I have recently pushed some updates to the GitHub repository of this package correcting some mistakes I identified. However, they don't seem to be triggering builds of the package, even though I have included in each update a version bump. I have confirmed that the webhook is setup. Any advice on what could be possibly missing?

Thanks a lot in advance!

[bioc-issue-bot]

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

IMPORTANT: Please read the instructions for setting up a push hook on your repository, or further changes to your repository will NOT trigger a new build.

[mtmorgan]

@LaraSellesVidal the issue needed to be moderated (added to the review queue) before automatically building. If your web-hook is set up correctly, new version bumps should now trigger builds.

[bioc-issue-bot]

Received a valid push; starting a build. Commits are:

b99031b v 0.99.4 3b9738f v 0.99.4

[LaraSellesVidal]

Hi @mtmorgan ,

Thanks a lot for looking into this!

Best wishes,

Lara

[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: "ERROR". 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.

[bioc-issue-bot]

Received a valid push; starting a build. Commits are:

1f85b95 v 0.99.5 BiocCheck warnings

[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.

[LaraSellesVidal]

Hi @mtmorgan @dvantwisk ,

We have now passed BiocCheck without errors or warnings. We have only three remaining notes:

• One of them is about the use of a \dontrun section in one of the manual pages. We included this on purpose to show an example of an error case.
• The other two notes relate to the presence of some lines longer than 80 characters or with indentations not multiple of 4 spaces. We have removed as many as possible of these after seeing the note in the first build report. We believe changing the remaining lines leading to these two notes might make the readability of the code a bit worse

Can we ignore these notes for now, or should we anyway perform the changes required to get a build report free of any notes?

Also, we have observed the single package builder is not currently building on macOS, just on tokay2 (Windows) and malbec2 (ubuntu). Just to confirm, this is the expected behaviour at the moment, right?

Thanks a lot in advance!

Best wishes,

Lara

[dvantwisk]

Hi,

I've reviewed your package and I'm happy to say I don't have anything to add. The package is excellently written as is. I am going to move to accept your package now so it makes it into the next release.

[bioc-issue-bot]

Your package has been accepted. It will be added to the Bioconductor Git repository and nightly builds. Additional information will be posed to this issue in the next several days.

Thank you for contributing to Bioconductor!

[LaraSellesVidal]

Hi @dvantwisk ,

Thanks a lot ! :)

Best wishes,

Lara

[mtmorgan]

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/LaraSellesVidal.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("rfaRm"). The package 'landing page' will be created at

https://bioconductor.org/packages/rfaRm

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.