[REVIEW]: biotools: a package for optimization cluster analysis

[whedon]

Submitting author: @arsilva87 (Anderson da Silva)
Repository: https://github.com/arsilva87/biotools
Version: 3.1
Editor: @karthik
Reviewer: @diyadas
Archive: Pending

Status

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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) 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

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

1. Make sure you're logged in to your GitHub account
2. Be sure to accept the invite at this URL: https://github.com/openjournals/joss-reviews/invitations

The reviewer guidelines are available here: https://joss.theoj.org/about#reviewer_guidelines. Any questions/concerns please let @karthik know.

✨ Please try and complete your review in the next two weeks ✨

Review checklist for @diyadas

Conflict of interest

• As the reviewer I confirm that I have read the JOSS conflict of interest policy and that there are no conflicts of interest for me to review this work.

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?
• Version: Does the release version given match the GitHub release (3.1)?
• Authorship: Has the submitting author (@arsilva87) made major contributions to the software? Does the full list of paper authors seem appropriate and complete?

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 function 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

• Authors: Does the paper.md file include a list of authors with their affiliations?
• A statement of need: Do the authors clearly state what problems the software is designed to solve and who the target audience is?
• References: Do all archival references that should have a DOI list one (e.g., papers, datasets, software)?

[whedon]

Hello human, I'm @whedon, a robot that can help you with some common editorial tasks. @diyadas it looks like you're currently assigned as the reviewer for this paper 🎉.

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@whedon commands

[whedon]

Attempting PDF compilation. Reticulating splines etc...

[whedon]

👉 Check article proof 📄 👈

[karthik]

@whedon check references

[whedon]

Attempting to check references...

[whedon]

OK DOIs

- 10.1093/bioinformatics/bts322 is OK
- 10.4155/bfs.13.5 is OK
- 10.1590/S0100-204X2013000600003 is OK
- 10.5897/AJAR2013.7588 is OK
- 10.1590/S0100-204X2007001000008 is OK

MISSING DOIs

- https://doi.org/10.1002/ajpa.1330120224 may be missing for title: Advanced statistical methods in biometric research
- https://doi.org/10.1002/9781118313718.part2 may be missing for title: The relative importance of characters affecting genetic divergence
- https://doi.org/10.3329/bjb.v43i3.21600 may be missing for title: Genetic diversity of chilli (Capsicum annuum L.) genotypes of India based on morpho-chemical traits

INVALID DOIs

- None

[karthik]

@arsilva87 Can you please remove biotools_5.0.tar.gz from the repo?

[arsilva87]

@karthik It was removed.

[karthik]

@arsilva87 Following up from the issue I raised in your repo, the reviewers and I are unable to install your software with reasonable effort. It's because of your dependency on rpanel, which requires a dated Tcltk widget called BWidget. Can you please articulate why you need these dependencies, how you are using them and why you are unable to refactor with modern alternatives? I'm pausing the review until we are able to resolve this.

[arsilva87]

@karthik The problem was solved by removing the dependencies with none or minimal losses, only for a single functionality of the package.

[arsilva87]

@whedon and @karthik Please continue the review.

[diyadas]

The README still directs users to install from CRAN, which I gather has not been updated. Installation proceeds with devtools::install_github - please update the README.

[arsilva87]

@diyadas README file updated.

[labarba]

@karthik — It looks like the author is asking for this review to be re-started. Can you get back in? I'm removing the "paused" label now.

[labarba]

@diyadas — Could you check on the author improvements, continue with your checklist, and report back to us with anything missing? Thank you!

[karthik]

@diyadas Do you need help continuing the review?

[diyadas]

Thanks for your patience. I've opened issues in your repo @arsilva87. I'll be happy to take a look again after they're addressed.

[labarba]

👋 @arsilva87 — Can you give us an update? If you're not close to done, please let me know of a time period to set a reminder for you.

[arsilva87]

@labarba I have updated the repository and worked on the issued pointed out by @diyadas. Thanks.

[labarba]

@karthik — please have a look at the progress here

[arsilva87]

@karthik How is the reviewing progress?

[arfon]

@diyadas & @karthik, many thanks for your efforts thus far. As I have outlined in my email to @arsilva87, this submission still falls well below what is expected of a JOSS submission. As such I am rejecting this submission and invite the author to resubmit if they are able to bring the submission up to standard.

[ooo]

👋 Hey @arfon...

Letting you know, @karthik is currently OOO until Friday, August 30th 2019. ❤️