[PRE REVIEW]: containerit: Generating Dockerfiles for reproducible research with R

[whedon]

Submitting author: @nuest (Daniel Nüst) Repository: https://github.com/o2r-project/containerit/ Version: v0.5.0 Editor: @terrytangyuan Reviewers: @vsoch

Author instructions

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

@nuest if you have any suggestions for potential reviewers then please mention them here in this thread. In addition, this list of people have already agreed to review for JOSS and may be suitable for this submission.

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:

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[whedon]

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

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

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This submission is currently in a pre-review state which means we are waiting for an editor to be assigned and for them to find some reviewers for your submission. This may take anything between a few hours to a couple of weeks. Thanks for your patience :smile_cat:

You can help the editor by looking at this list of potential reviewers to identify individuals who might be able to review your submission (please start at the bottom of the list). Also, feel free to suggest individuals who are not on this list by mentioning their GitHub handles here.

[whedon]

Attempting PDF compilation. Reticulating splines etc...

[whedon]

Failed to discover a valid open source license.

[whedon]

PDF failed to compile for issue #1595 with the following error:

/app/vendor/bundle/ruby/2.4.0/bundler/gems/whedon-5a9319b684e6/lib/whedon.rb:115:in check_fields': Paper YAML header is missing expected fields: authors (RuntimeError) from /app/vendor/bundle/ruby/2.4.0/bundler/gems/whedon-5a9319b684e6/lib/whedon.rb:80:ininitialize' from /app/vendor/bundle/ruby/2.4.0/bundler/gems/whedon-5a9319b684e6/lib/whedon/processor.rb:36:in new' from /app/vendor/bundle/ruby/2.4.0/bundler/gems/whedon-5a9319b684e6/lib/whedon/processor.rb:36:inset_paper' from /app/vendor/bundle/ruby/2.4.0/bundler/gems/whedon-5a9319b684e6/bin/whedon:55: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-5a9319b684e6/bin/whedon:116:in<top (required)>' 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

'

[kyleniemeyer]

Hi @nuest, while we get started handling this submission, please merge the PR I submitted, which fixes the authors field in the paper: https://github.com/o2r-project/containerit/pull/152

[kyleniemeyer]

@arfon whedon didn't find a license, but I can see the GPL-3.0 license in the repository: https://github.com/o2r-project/containerit/blob/master/LICENSE

Any ideas? Just ignore?

[kyleniemeyer]

@lheagy @kthyng can one of you edit this submission? I realize it's a bit outside your domain, but others are a bit overloaded and Karthik (who I'd normally ship R stuff to) is away for a bit.

[arfon]

@arfon whedon didn't find a license, but I can see the GPL-3.0 license in the repository: https://github.com/o2r-project/containerit/blob/master/LICENSE

Any ideas? Just ignore?

Weird, I think this can be safely ignored.

[nuest]

Hi! Thanks for getting things going, and for fixing the error in the paper.md rightaway.

[nuest]

@whedon generate pdf

[whedon]

Attempting PDF compilation. Reticulating splines etc...

[whedon]

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

[nuest]

@whedon generate pdf

[whedon]

Attempting PDF compilation. Reticulating splines etc...

[whedon]

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

[nuest]

PDF generation works, and I added some manual breaks in the contained code snippet so the line does not run off the page:

Now:

[nuest]

Suggested reviewers from the JOSS list:

• @cole-brokamp
• @vsoch
• @jsta
• @adamhsparks

[vsoch]

Yes!

[cole-brokamp]

I'm currently reviewing a singularity compose manuscript by @vsoch but I can't turn this one down either! I would love to review as well if I can!

[kyleniemeyer]

Thanks @vsoch and @cole-brokamp! We're still waiting to get an editor assigned, but I will definitely take you up on the offers to review. @cole-brokamp you can certainly wait until you have completed your other review.

[adamhsparks]

I'm stupidly busy right now, already reviewing for rOpenSci and prepping for some international travel in a few weeks. So sorry, I can't, but it looks like this is already in good hands once an editor is assigned.

On Sat, 27 Jul 2019 at 02:21, Kyle Niemeyer notifications@github.com wrote:

Thanks @vsoch https://github.com/vsoch and @cole-brokamp https://github.com/cole-brokamp! We're still waiting to get an editor assigned, but I will definitely take you up on the offers to review. @cole-brokamp https://github.com/cole-brokamp you can certainly wait until you have completed your other review.

— You are receiving this because you were mentioned. Reply to this email directly, view it on GitHub https://github.com/openjournals/joss-reviews/issues/1595?email_source=notifications&email_token=AAYMIASFTPF2LJV4RUB3A2TQBMQB7A5CNFSM4IG4HUV2YY3PNVWWK3TUL52HS4DFVREXG43VMVBW63LNMVXHJKTDN5WW2ZLOORPWSZGOD25CIJI#issuecomment-515515429, or mute the thread https://github.com/notifications/unsubscribe-auth/AAYMIAQ3VDEY5RZ6NR2OSWTQBMQB7ANCNFSM4IG4HUVQ .

-- Dr Adam H. Sparks http://adamhsparks.netlify.com/ Associate Professor of Field Crops Pathology | Centre for Crop Health | Office C313

Phone (+61) 07 46311948 | Mobile 0415 489 422 | Twitter @adamhsparks https://twitter.com/adamhsparks

Institute for Life Sciences and the Environment | Research and Innovation Division University of Southern Queensland | Toowoomba, Queensland | 4350 | Australia

[nuest]

Thank you @vsoch @cole-brokamp ! I look forward to your feedback.

[terrytangyuan]

@kyleniemeyer I can definitely help with this one as I am wrapping up with one of the other edits. Feel free to assign me if you cannot find anyone else.

[kyleniemeyer]

@terrytangyuan sure, if you're willing to take it!

[kyleniemeyer]

@whedon assign @terrytangyuan as editor

[whedon]

OK, the editor is @terrytangyuan

[kyleniemeyer]

@whedon assign @vsoch @cole-brokamp as reviewer

[whedon]

OK, the reviewer is @vsoch @cole-brokamp

[terrytangyuan]

@whedon assign @cole-brokamp as reviewer

[whedon]

OK, the reviewer is @cole-brokamp

[terrytangyuan]

@whedon assign @vsoch as reviewer

[whedon]

OK, the reviewer is @vsoch

[terrytangyuan]

@whedon start review

[whedon]

OK, I've started the review over in https://github.com/openjournals/joss-reviews/issues/1603. Feel free to close this issue now!

[danielskatz]

👋 @terrytangyuan - you need to @whedon assign X as reviewer -- for the first reviewer @whedon add Y as reviewer -- for additional reviewers

otherwise, only the last assign is stored

[terrytangyuan]

@danielskatz Thanks for the tip! I was wondering why it didn't work and then manually edited the description in the review issue. I'll do that next time.

[danielskatz]

I opened https://github.com/openjournals/whedon-api/issues/63 for this - feel free to make more suggestions as to how this should better work

[lheagy]

Sorry for my late reply, I just returned from 4 days of backpacking and am getting caught up. If you are still in need of an editor here, I am happy to jump in and help, otherwise, @terrytangyuan it looks like you have things in motion!

[kthyng]

Ah, I'm sorry too — I'm traveling and looking through email but missing some things.