[REVIEW]: Generating fragment density plots in R/Bioconductor with VplotR

[whedon]

Submitting author: @js2264 (Jacques Serizay)
Repository: https://github.com/js2264/VplotR/
Version: v1.2.0
Editor: @csoneson
Reviewer: @henrykironde, @fgeier
Archive: 10.5281/zenodo.4562440

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Status

Status badge code:

HTML: <a href="https://joss.theoj.org/papers/60a11ae8d7eaafaaf46585e2b22c8556"><img src="https://joss.theoj.org/papers/60a11ae8d7eaafaaf46585e2b22c8556/status.svg"></a>
Markdown: [![status](https://joss.theoj.org/papers/60a11ae8d7eaafaaf46585e2b22c8556/status.svg)](https://joss.theoj.org/papers/60a11ae8d7eaafaaf46585e2b22c8556)

Reviewers and authors:

Please avoid lengthy details of difficulties in the review thread. Instead, please create a new issue in the target repository and link to those issues (especially acceptance-blockers) by leaving comments in the review thread below. (For completists: if the target issue tracker is also on GitHub, linking the review thread in the issue or vice versa will create corresponding breadcrumb trails in the link target.)

Reviewer instructions & questions

@henrykironde & @fgeier, please carry out your review in this issue by updating the checklist below. If you cannot edit the checklist please:

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✨ Please start on your review when you are able, and be sure to complete your review in the next six weeks, at the very latest ✨

Review checklist for @henrykironde

Conflict of interest

• I confirm that I have read the JOSS conflict of interest (COI) policy and that: I have no COIs with reviewing this work or that any perceived COIs have been waived by JOSS for the purpose of this review.

Code of Conduct

• I confirm that I read and will adhere to the JOSS code of conduct.

General checks

• Repository: Is the source code for this software available at the repository url?
• License: Does the repository contain a plain-text LICENSE file with the contents of an OSI approved software license?
• Contribution and authorship: Has the submitting author (@js2264) made major contributions to the software? Does the full list of paper authors seem appropriate and complete?
• Substantial scholarly effort: Does this submission meet the scope eligibility described in the JOSS guidelines

Functionality

• Installation: Does installation proceed as outlined in the documentation?
• Functionality: Have the functional claims of the software been confirmed?
• Performance: If there are any performance claims of the software, have they been confirmed? (If there are no claims, please check off this item.)

Documentation

• A statement of need: Do the authors clearly state what problems the software is designed to solve and who the target audience is?
• Installation instructions: Is there a clearly-stated list of dependencies? Ideally these should be handled with an automated package management solution.
• Example usage: Do the authors include examples of how to use the software (ideally to solve real-world analysis problems).
• Functionality documentation: Is the core functionality of the software documented to a satisfactory level (e.g., API method documentation)?
• Automated tests: Are there automated tests or manual steps described so that the functionality of the software can be verified?
• Community guidelines: Are there clear guidelines for third parties wishing to 1) Contribute to the software 2) Report issues or problems with the software 3) Seek support

Software paper

• Summary: Has a clear description of the high-level functionality and purpose of the software for a diverse, non-specialist audience been provided?
• A statement of need: Do the authors clearly state what problems the software is designed to solve and who the target audience is?
• State of the field: Do the authors describe how this software compares to other commonly-used packages?
• Quality of writing: Is the paper well written (i.e., it does not require editing for structure, language, or writing quality)?
• References: Is the list of references complete, and is everything cited appropriately that should be cited (e.g., papers, datasets, software)? Do references in the text use the proper citation syntax?

Review checklist for @fgeier

Conflict of interest

• I confirm that I have read the JOSS conflict of interest (COI) policy and that: I have no COIs with reviewing this work or that any perceived COIs have been waived by JOSS for the purpose of this review.

Code of Conduct

• I confirm that I read and will adhere to the JOSS code of conduct.

General checks

• Repository: Is the source code for this software available at the repository url?
• License: Does the repository contain a plain-text LICENSE file with the contents of an OSI approved software license?
• Contribution and authorship: Has the submitting author (@js2264) made major contributions to the software? Does the full list of paper authors seem appropriate and complete?
• Substantial scholarly effort: Does this submission meet the scope eligibility described in the JOSS guidelines

Functionality

• Installation: Does installation proceed as outlined in the documentation?
• Functionality: Have the functional claims of the software been confirmed?
• Performance: If there are any performance claims of the software, have they been confirmed? (If there are no claims, please check off this item.)

Documentation

• A statement of need: Do the authors clearly state what problems the software is designed to solve and who the target audience is?
• Installation instructions: Is there a clearly-stated list of dependencies? Ideally these should be handled with an automated package management solution.
• Example usage: Do the authors include examples of how to use the software (ideally to solve real-world analysis problems).
• Functionality documentation: Is the core functionality of the software documented to a satisfactory level (e.g., API method documentation)?
• Automated tests: Are there automated tests or manual steps described so that the functionality of the software can be verified?
• Community guidelines: Are there clear guidelines for third parties wishing to 1) Contribute to the software 2) Report issues or problems with the software 3) Seek support

Software paper

• Summary: Has a clear description of the high-level functionality and purpose of the software for a diverse, non-specialist audience been provided?
• A statement of need: Do the authors clearly state what problems the software is designed to solve and who the target audience is?
• State of the field: Do the authors describe how this software compares to other commonly-used packages?
• Quality of writing: Is the paper well written (i.e., it does not require editing for structure, language, or writing quality)?
• References: Is the list of references complete, and is everything cited appropriately that should be cited (e.g., papers, datasets, software)? Do references in the text use the proper citation syntax?

[whedon]

Hello human, I'm @whedon, a robot that can help you with some common editorial tasks. @henrykironde, @fgeier it looks like you're currently assigned to review this paper 🎉.

⚠️ JOSS reduced service mode ⚠️

Due to the challenges of the COVID-19 pandemic, JOSS is currently operating in a "reduced service mode". You can read more about what that means in our blog post.

⭐ Important ⭐

If you haven't already, you should seriously consider unsubscribing from GitHub notifications for this (https://github.com/openjournals/joss-reviews) repository. As a reviewer, you're probably currently watching this repository which means for GitHub's default behaviour you will receive notifications (emails) for all reviews 😿

To fix this do the following two things:

1. Set yourself as 'Not watching' https://github.com/openjournals/joss-reviews:

2. You may also like to change your default settings for this watching repositories in your GitHub profile here: https://github.com/settings/notifications

For a list of things I can do to help you, just type:

@whedon commands

For example, to regenerate the paper pdf after making changes in the paper's md or bib files, type:

@whedon generate pdf

[whedon]

Software report (experimental):

github.com/AlDanial/cloc v 1.88  T=0.09 s (202.9 files/s, 36858.3 lines/s)
-------------------------------------------------------------------------------
Language                     files          blank        comment           code
-------------------------------------------------------------------------------
R                               13            104            913           1792
Rmd                              1             48            119            123
YAML                             2              4              0             87
Markdown                         2             17              0             63
-------------------------------------------------------------------------------
SUM:                            18            173           1032           2065
-------------------------------------------------------------------------------


Statistical information for the repository 'ea33ead25038585c5d89d791' was
gathered on 2021/02/04.
The following historical commit information, by author, was found:

Author                     Commits    Insertions      Deletions    % of changes
js2264                           2           352            352          100.00

Below are the number of rows from each author that have survived and are still
intact in the current revision:

Author                     Rows      Stability          Age       % in comments

[whedon]

PDF failed to compile for issue #3009 with the following error:

Can't find any papers to compile :-(

[csoneson]

👋🏼 @js2264, @henrykironde, @fgeier - this is the review thread for the paper. All of our communications will happen here from now on.

Both reviewers have checklists at the top of this thread. As you go over the submission, please check any items that you feel have been satisfied. There are also links to the JOSS reviewer guidelines.

The JOSS review is different from most other journals. Our goal is to work with the authors to help them meet our criteria instead of merely passing judgment on the submission. As such, the reviewers are encouraged to submit issues directly in the software repository. If you do so, please mention this thread so that a link is created (and I can keep an eye on what is happening). Please also feel free to comment and ask questions in this thread. It is often easier to post comments/questions/suggestions as you come across them instead of waiting until you've reviewed the entire package.

Please feel free to ping me (@csoneson) if you have any questions/concerns.

[csoneson]

@whedon generate pdf from branch JOSS

[whedon]

Attempting PDF compilation from custom branch JOSS. Reticulating splines etc...

[whedon]

👉📄 Download article proof 📄 View article proof on GitHub 📄 👈

[henrykironde]

@js2264, I have made some recommendations as issues on the repo. js2264/VplotR#4. Please let me know if there is something not clear as I continue to review.

[js2264]

@henrykironde I have addressed your initial issues. Please do let me know if you feel like I have not addressed some of them in enough depth!

[js2264]

@csoneson I have merged JOSS branch to master branch. Should I do anything for whedon to know about this change?

[henrykironde]

@whedon generate pdf

[whedon]

👉📄 Download article proof 📄 View article proof on GitHub 📄 👈

[csoneson]

@csoneson I have merged JOSS branch to master branch. Should I do anything for whedon to know about this change?

No, I think this should be all good. And whedon seems to find the paper in the master branch

[js2264]

@henrykironde FYI I have closed the second round of issues you opened. Let me know if anything else needs to be changed!

[henrykironde]

Thanks for the update. I checked the issues and they look good. I am trying to evaluate the paper at the moment. I know the total number of words exceed the maximum (1000) by ~120 words. I will have to get some advice on that. For now, I will go through the writing and get back to the checkboxes.

[js2264]

@henrykironde Let me know if there is anything related to the paper I can do (I can try to shorten it if the length is an issue).
@fgeier sorry to bother with that, any chance I could have an update on the review on your end? Do you have an idea of when you'll be able to start working on it? Thanks!

[csoneson]

👋 @js2264 - please keep in mind that it is only just over a week since this review was opened :) I can also see that @fgeier has indeed started filling the checklist above.
As for the length of the paper, I'd say it's ok.

[henrykironde]

@js2264 thanks for the great science. I have finished the review and the submission meets the criteria for acceptance.

[csoneson]

Thanks @henrykironde!

[js2264]

Thank you very much for your insightful review of the package @henrykironde!

[whedon]

👋 @fgeier, please update us on how your review is going (this is an automated reminder).

[csoneson]

@fgeier - could you give us a quick update about the status of your review? Thanks!

[fgeier]

@csoneson @js2264 Sorry didn't progress yet, but I want to finish by the end of this week. Tell me if you need it quicker

[csoneson]

@whedon generate pdf

[whedon]

👉📄 Download article proof 📄 View article proof on GitHub 📄 👈

[csoneson]

@whedon set 10.5281/zenodo.4562440 as archive

[whedon]

OK. 10.5281/zenodo.4562440 is the archive.

[csoneson]

@whedon set v1.2.0 as version

[whedon]

OK. v1.2.0 is the version.

[csoneson]

Alright, looks good! I'm going to hand over now to the associate editor in chief on rotation this week for the final steps.

[csoneson]

@whedon accept

[whedon]

Attempting dry run of processing paper acceptance...

[whedon]

Reference check summary (note 'MISSING' DOIs are suggestions that need verification):

OK DOIs

- 10.1038/nmeth.2688 is OK
- 10.1186/gb-2010-11-12-r119 is OK
- 10.1101/gr.265934.120 is OK
- 10.1073/pnas.1110731108 is OK
- 10.1101/gr.192294.115 is OK
- 10.1093/nar/gkx1126 is OK
- 10.1093/bioinformatics/btw024 is OK

MISSING DOIs

- None

INVALID DOIs

- None

[whedon]

👋 @openjournals/joss-eics, this paper is ready to be accepted and published.

Check final proof 👉 openjournals/joss-papers#2112

If the paper PDF and Crossref deposit XML look good in openjournals/joss-papers#2112, then you can now move forward with accepting the submission by compiling again with the flag deposit=true e.g.

@whedon accept deposit=true

[kthyng]

@fgeier We need all of the boxes checked to finish up reviews. This is our metric for the review and want them ticked off for the review to be finished.

For

Performance: If there are any performance claims of the software, have they been confirmed? (If there are no claims, please check off this item.)

if there are no claims, you can check this off.

For

State of the field: Do the authors describe how this software compares to other commonly-used packages?

If this is not done in the paper, the author should fix this. If there is no comparable software, that should be stated and then the box can be checked off.

[kthyng]

Looks like everything else is in order to finalize publication (version updated, Zenodo archive looks good, and paper is fine)!

[js2264]

@kthyng @fgeier About other commonly-used packages: I've just added a sentence about 2 tools that already exist. I have not changed the content of the code itself, only paper.md and paper.bib. Should I still re-create the Zenodo archive?

[kthyng]

@js2264 no you don't need to update the archive.

[kthyng]

@whedon generate pdf

[whedon]

👉📄 Download article proof 📄 View article proof on GitHub 📄 👈

[kthyng]

@fgeier It looks like you should be able to finalize your review by checking off the final two boxes now, but either way please let us know.

[fgeier]

@kthyng I check them off. Sorry for the confusion on my side.

[kthyng]

@whedon accept deposit=true

[whedon]

Doing it live! Attempting automated processing of paper acceptance...

[whedon]

🐦🐦🐦 👉 Tweet for this paper 👈 🐦🐦🐦

[whedon]

🚨🚨🚨 THIS IS NOT A DRILL, YOU HAVE JUST ACCEPTED A PAPER INTO JOSS! 🚨🚨🚨

Here's what you must now do:

0. Check final PDF and Crossref metadata that was deposited 👉 Creating pull request for 10.21105.joss.03009 joss-papers#2118
1. Wait a couple of minutes to verify that the paper DOI resolves https://doi.org/10.21105/joss.03009
2. If everything looks good, then close this review issue.
3. Party like you just published a paper! 🎉🌈🦄💃👻🤘

Any issues? Notify your editorial technical team...

[kthyng]

Congrats on your new publication @js2264! Thanks to editor @csoneson and reviewers @henrykironde and @fgeier for your time, hard work, and expertise! 🎉

[whedon]

🎉🎉🎉 Congratulations on your paper acceptance! 🎉🎉🎉

If you would like to include a link to your paper from your README use the following code snippets:

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