(inactive) inferrnal - wrapper for Infernal RNA sequence analysis programs

[brendanf]

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• Repository: https://github.com/brendanf/inferrnal

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[bioc-issue-bot]

Hi @brendanf

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: inferrnal
Title: Interface to Call Programs from Infernal RNA Covariance Model Package
Version: 0.99.5
Authors@R: 
    person(given = "Brendan",
 family = "Furneaux",
 role = c("aut", "cre"),
 email = "brendan.furneaux@gmail.com",
 comment = c(ORCID = "0000-0003-3522-7363"))
Description: A thin wrapper around the Infernal package to search for matches to
    a covariance model in RNA sequences, or to align RNA sequences to a 
    covariance model. Infernal is not included in the package and needs to be
    installed independently.
License: MIT + file LICENSE
Encoding: UTF-8
LazyData: true
SystemRequirements: Infernal
URL: https://github.com/brendanf/inferrnal
BugReports: https://github.com/brendanf/inferrnal/issues
Imports: 
    assertthat,
    Biostrings,
    S4Vectors,
    methods,
    stats
RoxygenNote: 7.1.0
biocViews:
    SequenceMatching,
    ThirdPartyClient,
    Metagenomics,
    HiddenMarkovModel,
    DNASeq,
    RNASeq,
    Annotation,
    Alignment,
    MultipleSequenceAlignment
Suggests: 
    testthat (>= 2.1.0),
    knitr,
    rmarkdown,
    covr,
    ShortRead
VignetteBuilder: knitr

[bioc-issue-bot]

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[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: "skipped, 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. 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 git@git.bioconductor.org:packages/inferrnal to trigger a new build. A quick tutorial for setting up remotes and pushing to upstream can be found here.

[brendanf]

Because the package interfaces with Infernal, tests and vignette building will fail if Infernal is not present. (This means it cannot work on Windows.) Is there a way to specify the added requirement to the automated build system?

[brendanf]

(Infernal is available as an apt, conda, or homebrew package, as well as binaries for linux and osx).

[Kayla-Morrell]

@brendanf - Sorry for the late reply, here is what can be done for the 2 issues raised.

Windows issue: If you would like to not support Windows (since Infernal is not supported on Windows) you can do so. You should be aware though of the large portion of the Bioconductor community that will not be able to use your package. If this is something you wish to do you can include a .BBSoptions file in the top directory of the package and inside this file should be the following command UnsupportedPlatforms: win. Keep in mind that both the file name and command are case sensitive.

Infernal requirement: The first thing is to be sure that Infernal is listed as a SystemRequirement in the DESCRIPTION file, which you have. The next thing we require is a top level INSTALL file that provides the command for the system requirement to be installed for each platform. Whether that be sudo, pip, brew, we just need instructions for our build system admins to know what commands to run to install the requirement. Once that file is added and pushed they can go ahead and add the requirement.

Hope this helps, let me know if you have any further questions.

Best, Kayla

[brendanf]

@Kayla-Morrell Thanks. If I understand correctly, the INSTALL file is just human-readable?

[Kayla-Morrell]

@brendanf - yes, that's correct.

[brendanf]

OK, I made those changes and pushed to git@git.bioconductor.org:packages/inferrnal.

[Kayla-Morrell]

Great - we will work on getting that added and I'll let you know when it's ready.

[Kayla-Morrell]

@hpages - This is the package that requires the Infernal installed on the builders. Thanks!

[hpages]

@Kayla-Morrell @brendanf I installed Infernal on the Linux and Mac builders, following the instructions in the INSTALL file. Note that this file is useful not only for us, build system maintainers, but also for the users of the inferrnal package. So thanks @brendanf for providing it.

[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: "UNSUPPORTED, skipped, 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. 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 git@git.bioconductor.org:packages/inferrnal to trigger a new build. A quick tutorial for setting up remotes and pushing to upstream can be found here.

[Kayla-Morrell]

@brendanf - Since Infernal was installed on the builders, I went ahead and kicked off a manual build so you could get a proper build report.

Best, Kayla

[brendanf]

I've removed the .Rproj file and subscribed to the mailing list, so it should pass BiocCheckGitClone and BiocCheck without errors next time.

[Kayla-Morrell]

Make sure you push a version bump to ensure a new build is triggered (see here for more help).

[bioc-issue-bot]

Received a valid push on git.bioconductor.org; starting a build for commit id: 9cb9bbce98414713e8ed1b5635ef9664ae6848b5

[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: "skipped, UNSUPPORTED". 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 git@git.bioconductor.org:packages/inferrnal to trigger a new build. A quick tutorial for setting up remotes and pushing to upstream can be found here.

[Kayla-Morrell]

@brendanf -

Thank you for submitting to Bioconductor. Please see the initial review of the package below. The required changes must be made while the suggested changes do not have to be (though we strongly encourage them). Comment back here with updates that have been made and when the package is ready for a re-review.

General package development

• [ ] REQUIRED: There seem to be some unnecessary files in your package directory. The LICENSE file is used but the LICENSE.md file doesn't seem to be needed here. Also the same for the README.md and README.Rmd, the .md should stay and the .Rmd file should be removed. What is the purpose of the codecov.yml file?

DESCRIPTION

• [ ] SUGGESTION: The 'Description' field is made up by less than 3 sentences. Please consider expanding this field and structure it as a full paragraph.

• [ ] SUGGESTION: 'LazyData' should be set to 'FALSE'. It is our experience that 'LazyData: TRUE' can slow down the loading of packages, especially those that include data.

• [ ] REQUIRED: I would move 'ShortRead' to 'Imports' because you actually use functionality from the package within the code of inferrnal.

• [ ] REQUIRED: 'utils' should be listed under 'Imports' because you use functionality from it within the code of inferrnal.

Data

• [ ] REQUIRED: There needs to be documentation provided for the files in the 'inst/extdata' directory. The documentation should be in an 'inst/script' directory. The scripts in this directory can vary. Most importantly a related script must be present in this directory documenting very clearly how the data was generated. It should include source urls and any important information regarding filtering or processing. It can be executible code, sudo code, or a text description. A user should be able to download and roughly reproduce the file or object that is present as data.

Vignette

• [ ] REQUIRED: There should be an installation section that demonstrates to the user how to install the package from Bioconductor. The code should look like the following and should include eval = FALSE:

if(!requireNamespace("BiocManager", quietly = TRUE))
    install.packages("BiocManager")
BiocManager::install("inferrnal")

• [ ] SUGGESTION: We strongly encourage the user of table of contents.

• [ ] REQUIRED: The final section of the vignette should be 'Session Information' and should include sessionInfo().

Best, Kayla

[brendanf]

@Kayla-Morrell Thanks for the review. There are a few items that I have questions/comments about:

Including ShortRead in Imports:

The only functionality that requires the ShortRead package is accepting input sequences as objects of class ShortRead. That is there as a convenience for users who already have their sequences in this format. In that case, they obviously have the ShortRead package installed. I would prefer not to require the package for users who are not using it anyway. I can further gate that code using if (!requireNamespace("ShortRead", quietly=TRUE)) stop("Received a ShortRead object but the ShortRead package is unavailable") or something similar. Would that be acceptable?

README.Rmd

This is the source file for README.md. Any changes are made to README.Rmd, which is then rendered to make README.md. README.Rmd is in .Rbuildignore, so it is not included in the built package. Is it really unacceptable to have this file in the git repository?

codecov.yaml

This is settings for automatic calculation of test coverage on Travis, the results of which are included as badges in README.md. Like README.Rmd, it is excluded from the built package using .Rbuildignore.

[Kayla-Morrell]

@brendanf -

For the ShortRead import, it would be fine not to require it but the code you suggested should be implemented.

Thank you for explaining the README.Rmd and codecov.yaml files. These are fine to keep as they are in the .Rbuildignore file.

[Kayla-Morrell]

@brendanf - I was wondering if there has been any progress on the points made in my review. We typically like to see changes within a 2-3 week time frame to be sure the package is actively being worked on.

[brendanf]

@Kayla-Morrell - I had addressed most of your points prior to the holidays, but did not push until just now. I believe the only thing remaining is the data documentation.

[Kayla-Morrell]

@brendanf - It has been over a month now since I last checked in with you. If there are no changes pushed and a new build report produced within in the next couple days I'll be closing this issue for inactivity.

[Kayla-Morrell]

@brendanf - I am closing this package for inactivity. We normally like to see changes to a package within a few weeks to know they are actively being worked on. When you have implemented changes and are ready for a re-review, please comment back here to ask that the issue be reopened.

[bioc-issue-bot]

This issue is being closed because there has been no progress for an extended period of time. You may reopen the issue when you have the time to actively participate in the review / submission process. Please also keep in mind that a package accepted to Bioconductor requires a commitment on your part to ongoing maintenance.

Thank you for your interest in Bioconductor.

[brendanf]

Sorry for the delays! I'm working on revising the article, which will also help in generating the data citations. As you say, I'll reopen when it's ready.