[PRE REVIEW]: Miet: an R package for region of interest analysis from magnetic reasonance images #1842

whedon · 2019-10-29T12:50:42Z

Submitting author: @benoit-combes (Benoit Combès)
Repository: https://gitlab.inria.fr/miet/miet
Version: 0.1.0
Editor: @arokem
Reviewers: @janfreyberg, @neuroimaginador

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

@benoit-combes 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.

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The text was updated successfully, but these errors were encountered:

whedon · 2019-10-29T12:50:45Z

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:

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

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What happens now?

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whedon · 2019-10-29T12:50:45Z

Attempting PDF compilation. Reticulating splines etc...

whedon · 2019-10-29T12:51:05Z

PDF failed to compile for issue #1842 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/1842 (Errno::ENOENT) from /app/vendor/ruby-2.4.4/lib/ruby/2.4.0/find.rb:43:in collect!'
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-74bc29a6a731/lib/whedon/processor.rb:61:in find_paper_paths'
from /app/vendor/bundle/ruby/2.4.0/bundler/gems/whedon-74bc29a6a731/bin/whedon:50:in prepare' from /app/vendor/bundle/ruby/2.4.0/gems/thor-0.20.3/lib/thor/command.rb:27:in run'
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:in dispatch'
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-74bc29a6a731/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

'

danielskatz · 2019-10-29T12:55:04Z

@whedon generate pdf

whedon · 2019-10-29T12:55:07Z

Attempting PDF compilation. Reticulating splines etc...

whedon · 2019-10-29T12:55:19Z

PDF failed to compile for issue #1842 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/1842 (Errno::ENOENT) from /app/vendor/ruby-2.4.4/lib/ruby/2.4.0/find.rb:43:in collect!'
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-74bc29a6a731/lib/whedon/processor.rb:61:in find_paper_paths'
from /app/vendor/bundle/ruby/2.4.0/bundler/gems/whedon-74bc29a6a731/bin/whedon:50:in prepare' from /app/vendor/bundle/ruby/2.4.0/gems/thor-0.20.3/lib/thor/command.rb:27:in run'
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:in dispatch'
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-74bc29a6a731/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

'

danielskatz · 2019-10-29T12:57:42Z

👋 @arfon - I'm a bit confused about what the error is here - is this related to the figure? Perhaps you can help? (and maybe open a whedon issue related to better error message?)

arfon · 2019-10-29T13:03:19Z

@danielskatz - I think this is because the URL at the top can't be cloned by Git. It needs changing to https://gitlab.inria.fr/miet/miet

danielskatz · 2019-10-29T13:09:22Z

👋 @benoit-combes - Please change the paper.md as @arfon suggests, then enter a new comment here with @whedon generate pdf to try recompiling

arfon · 2019-10-29T13:10:52Z

@whedon generate pdf

whedon · 2019-10-29T13:10:54Z

Attempting PDF compilation. Reticulating splines etc...

arfon · 2019-10-29T13:11:30Z

@danielskatz - just to clarify, the URL for the repo needed editing at the top of the issue (I've done this).

whedon · 2019-10-29T13:11:34Z

👉 Check article proof 📄 👈

danielskatz · 2019-10-29T13:13:38Z

ah, sorry, I thought you meant in the paper.md - How did this wrong URL get in? User error in the submission form?

arfon · 2019-10-29T13:15:53Z

ah, sorry, I thought you meant in the paper.md - How did this wrong URL get in? User error in the submission form?

Yeah, it was an error in the submission form. I've opened an issue to track this (openjournals/whedon#60)

benoit-combes · 2019-10-29T13:57:54Z

May I suggest @neuroimaginador that appears to gather expertise in R, data analysis and neuroimaging (that are relevant for the paper) for reviewing ?

benoit-combes · 2019-10-29T15:11:35Z

@whedon commands

whedon · 2019-10-29T15:11:37Z

Here are some things you can ask me to do:

# List Whedon's capabilities
@whedon commands

# List of editor GitHub usernames
@whedon list editors

# List of reviewers together with programming language preferences and domain expertise
@whedon list reviewers

EDITORIAL TASKS

# Compile the paper
@whedon generate pdf

# Compile the paper from alternative branch
@whedon generate pdf from branch custom-branch-name

# Ask Whedon to check the references for missing DOIs
@whedon check references

benoit-combes · 2019-10-31T13:42:22Z

@whedon list editors

whedon · 2019-10-31T13:42:25Z

Current editors:

@Kevin-Mattheus-Moerman
@VivianePons
@alexhanna
@arfon
@arokem
@brainstorm
@cMadan
@csoneson
@danielskatz
@dfm
@drvinceknight
@gkthiruvathukal
@jedbrown
@karthik
@katyhuff
@kbarnhart
@kthyng
@kyleniemeyer
@labarba
@leouieda
@lheagy
@lpantano
@majensen
@mbobra
@meg-simula
@melissawm
@mgymrek
@mjsottile
@oliviaguest
@poulson
@terrytangyuan
@trallard
@usethedata
@will-rowe
@xuanxu

benoit-combes · 2019-10-31T13:52:27Z

May I suggest @arokem as editor ?
In addition to @neuroimaginador that appears to gather expertise in R, data analysis and neuroimaging (that are relevant for the paper) for reviewer ?

arokem · 2019-10-31T14:16:05Z

Yes. I can edit this.

arokem · 2019-10-31T14:16:21Z

@whedon assign arokem as editor

whedon · 2019-10-31T14:16:26Z

OK, the editor is arokem

arokem · 2019-10-31T14:17:22Z

👋 @neuroimaginador : would you be willing to review this paper for JOSS?

arfon · 2019-10-31T14:47:34Z

@arokem @brechmos (who's here at STScI) might be a good additional reviewer.

arokem · 2019-10-31T15:03:38Z

@brechmos : would you be willing to review this paper for JOSS?

…

On Thu, Oct 31, 2019 at 7:47 AM Arfon Smith ***@***.***> wrote: @arokem <https://github.com/arokem> @brechmos <https://github.com/brechmos> (who's here at STScI) might be a good additional reviewer. — You are receiving this because you were mentioned. Reply to this email directly, view it on GitHub <#1842?email_source=notifications&email_token=AAA46NXVLT6JYNXQRAERDZDQRLVY3A5CNFSM4JGIBTKKYY3PNVWWK3TUL52HS4DFVREXG43VMVBW63LNMVXHJKTDN5WW2ZLOORPWSZGOECYBOPA#issuecomment-548411196>, or unsubscribe <https://github.com/notifications/unsubscribe-auth/AAA46NRSLTMWCII2PAIKZA3QRLVY3ANCNFSM4JGIBTKA> .

arokem · 2019-10-31T17:56:01Z

👋 @janfreyberg : would you be willing to review this paper for JOSS? You are one of the only people among our reviewer pool who are neuro-savvy and also R-literate, so it would be a great help.

janfreyberg · 2019-10-31T20:38:29Z

@arokem yes, of course!

arokem · 2019-10-31T20:40:00Z

Wonderful. Thank you! I will assign you first, and then stand by until I find another reviewer and kick off the review for this.

arokem · 2019-10-31T20:40:12Z

@whedon assign @janfreyberg as reviewer

whedon · 2019-10-31T20:40:16Z

OK, the reviewer is @janfreyberg

neuroimaginador · 2019-11-02T15:07:34Z

Hello, I'd like to review this work!! El jue., 31 oct. 2019 15:17, Ariel Rokem <[email protected]> escribió:

…

👋 @neuroimaginador <https://github.com/neuroimaginador> : would you be willing to review this paper for JOSS? — You are receiving this because you were mentioned. Reply to this email directly, view it on GitHub <#1842?email_source=notifications&email_token=AH6U472UD4VIWXARMAYNRYLQRLSHNA5CNFSM4JGIBTKKYY3PNVWWK3TUL52HS4DFVREXG43VMVBW63LNMVXHJKTDN5WW2ZLOORPWSZGOECX56KI#issuecomment-548396841>, or unsubscribe <https://github.com/notifications/unsubscribe-auth/AH6U47YVKKVDSZNFMHJUEITQRLSHNANCNFSM4JGIBTKA> .

arokem · 2019-11-02T17:11:45Z

Thanks @neuroimaginador ! You are on!

arokem · 2019-11-02T17:11:57Z

@whedon add @neuroimaginador as reviewer

whedon · 2019-11-02T17:12:01Z

OK, @neuroimaginador is now a reviewer

arokem · 2019-11-02T17:12:56Z

@whedon start review

whedon · 2019-11-02T17:13:00Z

OK, I've started the review over in #1862. Feel free to close this issue now!

arokem · 2019-11-02T17:14:09Z

Alright, @janfreyberg and @neuroimaginador, please head over to #1862 for your reviewer check-lists. Feel free to tag me into issues, if you have any questions, as you work through this. I'll close this now. Thanks again!

whedon added the pre-review label Oct 29, 2019

arfon mentioned this issue Oct 29, 2019

Whedon should return a better error when it can't git clone openjournals/whedon#60

Open

whedon added R TeX labels Oct 29, 2019

whedon assigned arokem Oct 31, 2019

whedon assigned arokem and janfreyberg and unassigned arokem Oct 31, 2019

whedon assigned arokem, janfreyberg and neuroimaginador and unassigned arokem and janfreyberg Nov 2, 2019

arokem closed this as completed Nov 2, 2019

[PRE REVIEW]: Miet: an R package for region of interest analysis from magnetic reasonance images #1842

[PRE REVIEW]: Miet: an R package for region of interest analysis from magnetic reasonance images #1842

Comments

whedon commented Oct 29, 2019 • edited Loading

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whedon commented Oct 29, 2019 •

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