Joss-reviews: [PRE REVIEW]: zalpha: an R package for the identification of regions of the genome under selection

[whedon]

Submitting author: @chorscroft (Clare Horscroft)
Repository: https://github.com/chorscroft/zalpha
Version: v0.2.0
Editor: @lpantano
Reviewers: @juanvillada
Managing EiC: Daniel S. Katz

:warning: JOSS reduced service mode :warning:

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.

Author instructions

Thanks for submitting your paper to JOSS @chorscroft. Currently, there isn't an JOSS editor assigned to your paper.

@chorscroft if you have any suggestions for potential reviewers then please mention them here in this thread (without tagging them with an @). In addition, this list of people have already agreed to review for JOSS and may be suitable for this submission (please start at the bottom of the list).

Editor instructions

The JOSS submission bot @whedon is here to help you find and assign reviewers and start the main review. To find out what @whedon can do for you type:

@whedon commands

[whedon]

Hello human, I'm @whedon, a robot that can help you with some common editorial tasks.

:warning: JOSS reduced service mode :warning:

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.

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]

PDF failed to compile for issue #2560 with the following error:

/app/vendor/ruby-2.4.4/lib/ruby/2.4.0/find.rb:43:in block in find': No such file or directory - tmp/2560 (Errno::ENOENT) from /app/vendor/ruby-2.4.4/lib/ruby/2.4.0/find.rb:43:incollect!'
from /app/vendor/ruby-2.4.4/lib/ruby/2.4.0/find.rb:43:in find' from /app/vendor/bundle/ruby/2.4.0/bundler/gems/whedon-0e09ec0a48e3/lib/whedon/processor.rb:61:infind_paper_paths'
from /app/vendor/bundle/ruby/2.4.0/bundler/gems/whedon-0e09ec0a48e3/bin/whedon:50:in prepare' from /app/vendor/bundle/ruby/2.4.0/gems/thor-0.20.3/lib/thor/command.rb:27:inrun'
from /app/vendor/bundle/ruby/2.4.0/gems/thor-0.20.3/lib/thor/invocation.rb:126:in invoke_command' from /app/vendor/bundle/ruby/2.4.0/gems/thor-0.20.3/lib/thor.rb:387:indispatch'
from /app/vendor/bundle/ruby/2.4.0/gems/thor-0.20.3/lib/thor/base.rb:466:in start' from /app/vendor/bundle/ruby/2.4.0/bundler/gems/whedon-0e09ec0a48e3/bin/whedon:119:in from /app/vendor/bundle/ruby/2.4.0/bin/whedon:23:in load' from /app/vendor/bundle/ruby/2.4.0/bin/whedon:23:in

'

[danielskatz]

@whedon generate pdf

[whedon]

:point_right: Check article proof :page_facing_up: :point_left:

[danielskatz]

@whedon check references

[whedon]

Reference check summary:

OK DOIs

- 10.1534/genetics.115.185900 is OK
- 10.1038/ng1001-217 is OK
- 10.1534/genetics.103.025387 is OK
- 10.1146/annurev-genet-111212-133526 is OK

MISSING DOIs

- None

INVALID DOIs

- None

[danielskatz]

@whedon check repository

[whedon]

Software report (experimental):

github.com/AlDanial/cloc v 1.84  T=0.09 s (501.3 files/s, 86316.9 lines/s)
-------------------------------------------------------------------------------
Language                     files          blank        comment           code
-------------------------------------------------------------------------------
R                               39           1364           1527           4463
Markdown                         5             60              0            158
TeX                              1              0              0             55
Rmd                              1            106            143             44
-------------------------------------------------------------------------------
SUM:                            46           1530           1670           4720
-------------------------------------------------------------------------------


Statistical information for the repository '2560' was gathered on 2020/08/09.
No commited files with the specified extensions were found.

[danielskatz]

👋 @lpantano - would you be able to edit this submission?

[danielskatz]

@whedon invite @lpantano as editor

[whedon]

@lpantano has been invited to edit this submission.

[lpantano]

@whedon assign @lpantano as editor

[whedon]

OK, the editor is @lpantano

[lpantano]

@lshep, @Kayla-Morrell, are you interested in reviewing this software? Some information if you are new to JOSS system: https://joss.readthedocs.io/en/latest/review_criteria.html. Thanks!

[lpantano]

@bernatgel, @naumenko-sa, would you be interested in reviewing this tool?

[lpantano]

@robohyun66, @Nazeeefa, would you be interested in reviewing this tool?

[bernatgel]

@bernatgel, @naumenko-sa, would you be interested in reviewing this tool?

Hi @lpantano, I'm afraid I'll have to decline this. I don't have the expertise to evaluate this software. Thanks for the invitation.

[lshep]

Sorry I never responded. I'm honestly overloaded with work and don't think I have the time to give it a fair review.

[lpantano]

@chorscroft, I am still trying to find reviewers, if you know of any, let me know. Thanks!

[lpantano]

Hey @acolum, @jean997, would you like to review this tool?

[acolum]

Unfortunately, I'm not available to review this tool.

[jean997]

I'm sorry I'm not available either (plus selection isn't really my area of expertise). Looking at the list maybe shaunpwilkinson, giraola, juanvillada, stulacy, r-barnes, vbaliga, CFGrote, or dwinter could be worth a try

[lpantano]

Hey @juanvillada, @vbaliga, would you like to review this tool?

[vbaliga]

I'm sorry to say the content goes beyond my area of expertise, so it's probably best that not I be a reviewer. Thanks for the offer, though

[juanvillada]

Hey @lpantano

Yes, I would like to review this tool. Count me in 👍🏼

[lpantano]

@whedon assign @juanvillada as a reviewer

[whedon]

I'm sorry human, I don't understand that. You can see what commands I support by typing:

@whedon commands

[lpantano]

@whedon assign @juanvillada as reviewer

[whedon]

OK, @juanvillada is now a reviewer

[lpantano]

@dcgerard, would you like to review this tool? link to the guidelines: https://joss.readthedocs.io/en/latest/review_criteria.html

[lpantano]

I will start this review, and continue to look for the second reviewer. This way @juanvillada can start working on this :)

[lpantano]

@whedon start review

[whedon]

OK, I've started the review over in https://github.com/openjournals/joss-reviews/issues/2638.

[lpantano]

Hey @alachins, @FerRacimo would you like to review this tool? link to the guidelines: https://joss.readthedocs.io/en/latest/review_criteria.html