[PRE REVIEW]: The UCSCXenaTools R package: a toolkit for accessing genomics data from UCSC Xena platform, from cancer multi-omics to single-cell RNA-seq

[whedon]

Submitting author: @ShixiangWang (Wang Shixiang) Repository: https://github.com/ropensci/UCSCXenaTools/ Version: v1.2.5 Editor: @arfon Reviewers: @arfon

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

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[whedon]

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

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[whedon]

Attempting PDF compilation. Reticulating splines etc...

[whedon]

PDF failed to compile for issue #1622 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/1622 (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-07bb23bf8f0b/lib/whedon/processor.rb:61:infind_paper_paths' from /app/vendor/bundle/ruby/2.4.0/bundler/gems/whedon-07bb23bf8f0b/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-07bb23bf8f0b/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

'

[labarba]

👋 @ShixiangWang — You provided the archive DOI instead of the repository URL, and our bot cannot build your paper.

Please confirm that this is the correct submission repository: https://github.com/ropensci/UCSCXenaTools/

[ShixiangWang]

@labarba Yes, this is the package repository. I followed the instruction from https://github.com/ropensci/software-review/issues/315#issuecomment-515795175 to submit a Zenodo DOI instead of GitHub repository. I am sorry if this operation was wrong.

[labarba]

@arfon — I'm confused. The author was told to "Submit to JOSS using the Zenodo DOI" after acceptance of his software on rOpenSci. We need the software repo URL, so I think there's some confusion here.

[ShixiangWang]

@labarba Maybe rOpenSci should update the approval comment template.

Could you help me correct the repository URL?

I still see the Zenodo DOI, but I cannot edit it.

[labarba]

@whedon generate pdf

[whedon]

Attempting PDF compilation. Reticulating splines etc...

[whedon]

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

[ShixiangWang]

Amazing!

[arfon]

The author was told to "Submit to JOSS using the Zenodo DOI" after acceptance of his software on rOpenSci. We need the software repo URL, so I think there's some confusion here.

Yes, that's not correct. @ShixiangWang - could you point me to the documentation from rOpenSci that asks for this?

[arfon]

@whedon assign @arfon as editor

[whedon]

OK, the editor is @arfon

[arfon]

@whedon assign @arfon as reviewer

[whedon]

OK, the reviewer is @arfon

[arfon]

@whedon start review

[whedon]

OK, I've started the review over in https://github.com/openjournals/joss-reviews/issues/1627. Feel free to close this issue now!

[ShixiangWang]

@arfon It's from to do list at here https://github.com/ropensci/software-review/issues/315#issuecomment-515795175

[noamross]

Thanks for pointing this out, @ShixiangWang. @arfon, we'll fix this in our templates. Has the submission form changed? I seem to remember that one previously had to put the Zenodo DOI into the form (in addition to the repo URL).

[arfon]

Has the submission form changed?

Nope, it's the same as it's always been. 😁