[PRE REVIEW]: MicrobiomeR: An R Package for Simplified and Standardized Microbiome Analysis Workflows

[whedon]

Submitting author: @grabear (Robert Gilmore) Repository: https://github.com/vallenderlab/MicrobiomeR Version: 0.5.1 Editor: @lpantano Reviewers: @CosteaPaul

Author instructions

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

@grabear 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:

@whedon commands

[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

What happens now?

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]

PDF failed to compile for issue #1288 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/1288 (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-01ece1d1d135/lib/whedon/processor.rb:57:infind_paper_paths' from /app/vendor/bundle/ruby/2.4.0/bundler/gems/whedon-01ece1d1d135/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-01ece1d1d135/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]

👋 @pjotrp - the author requested you (or someone from your group) as editor - ok? Of course, some work is needed on the paper first...

[danielskatz]

👋 @grabear - I don't see the paper part of your submission. Take a look at the author submission guidelines, specifically What should my paper contain? and Example paper and bibliography

[grabear]

Hi, I put the paper in a separate folder under inst/paper/ @danielskatz

[danielskatz]

@whedon generate pdf from inst/paper

[whedon]

Attempting PDF compilation. Reticulating splines etc...

[whedon]

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

[danielskatz]

thanks - I see some issues with the figure, the table, and the references. You can make changes to the paper.md and paper.bib, then use the same command I used (as a new comment here) to regenerate until you are satisfied with the generated proof.

[danielskatz]

In the meantime, @pjotrp and his group can figure out who will edit this, I think.

[grabear]

@danielskatz Thank you! I'll work on it.

[grabear]

@whedon commands

[whedon]

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

[grabear]

@whedon generate pdf from branch joss-review from inst/paper

[whedon]

Attempting PDF compilation from custom branch joss-review from inst/paper . Reticulating splines etc...

[grabear]

@sdhutchins working on tweaking the paper!

[pjotrp]

Yes, I'll ask for an editor.

[lpantano]

@whedon assign @lpantano as editor

[whedon]

OK, the editor is @lpantano

[grabear]

@whedon generate pdf from inst/paper branch joss-review

[whedon]

Attempting PDF compilation. Reticulating splines etc...

[whedon]

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

[lpantano]

Hi @grabear,

let me know when you can figure out the format issue, I will look into possible reviewers in the meantime.

Looking forward to working together in the process.

Cheers

[grabear]

Hello @lpantano! I'll be working on it this afternoon! I just need to play around with whedon a little.

Looking forward to it as well :+1:

[grabear]

@whedon generate pdf from branch joss-review inst/paper

[whedon]

Attempting PDF compilation from custom branch joss-review inst/paper. Reticulating splines etc...

[grabear]

@pjotrp @lpantano @danielskatz Any idea what I should do with @whedon when I'm generating the pdf on a separate branch and in a folder that's not on the top level?

[danielskatz]

👋 @arfon ?

[grabear]

Part of the problem is that I always protect my master and dev-master branches, so it makes it a bit more complicated for me to edit. I can always change the permissions temporarily, but that's not ideal.

[grabear]

@whedon generate pdf from branch joss-review

[whedon]

Attempting PDF compilation from custom branch joss-review. Reticulating splines etc...

[whedon]

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

[lpantano]

sorry @grabear that is not working with two of the conditions (other branch and other location), hopefully, somebody who knows the backend infrastructure can help. I will reach somebody if @arfon doesn't chime in.

At least the figure now. seems right. :)

Thanks!

[grabear]

@lpantano It seems to be working now! It's finding the paper, so no complaints. :)

[grabear]

@whedon generate pdf from branch joss-review

[whedon]

Attempting PDF compilation from custom branch joss-review. Reticulating splines etc...

[whedon]

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

[grabear]

@whedon check references

[whedon]

Attempting to check references...

[whedon]

OK DOIs

- http://doi.org/10.1371/journal.pcbi.1005404 is OK

MISSING DOIs

- https://doi.org/10.1371/journal.pone.0061217 may be missing for title: phyloseq: An R package for reproducible interactive analysis and graphics of microbiome census data
- https://doi.org/10.1038/nmeth.f.303 may be missing for title: QIIME allows analysis of high-throughput community sequencing data.
- https://doi.org/10.1093/nar/gks1219 may be missing for title: The SILVA ribosomal RNA gene database project: improved data processing and web-based tools.
- https://doi.org/10.1093/nar/gkt1209 may be missing for title: The SILVA and “All-species Living Tree Project (LTP)” taxonomic frameworks.

INVALID DOIs

- None

[grabear]

@whedon check references from branch joss-review

[whedon]

Attempting to check references...

[whedon]

OK DOIs

- http://doi.org/10.1371/journal.pcbi.1005404 is OK

MISSING DOIs

- https://doi.org/10.1371/journal.pone.0061217 may be missing for title: phyloseq: An R package for reproducible interactive analysis and graphics of microbiome census data
- https://doi.org/10.1038/nmeth.f.303 may be missing for title: QIIME allows analysis of high-throughput community sequencing data.
- https://doi.org/10.1093/nar/gks1219 may be missing for title: The SILVA ribosomal RNA gene database project: improved data processing and web-based tools.
- https://doi.org/10.1093/nar/gkt1209 may be missing for title: The SILVA and “All-species Living Tree Project (LTP)” taxonomic frameworks.

INVALID DOIs

- None

[grabear]

@whedon generate pdf from branch joss-review

[whedon]

Attempting PDF compilation from custom branch joss-review. Reticulating splines etc...

[whedon]

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

[grabear]

@whedon generate pdf from branch joss-review

[whedon]

Attempting PDF compilation from custom branch joss-review. Reticulating splines etc...

[whedon]

PDF failed to compile for issue #1288 with the following error:

% Total % Received % Xferd Average Speed Time Time Time Current Dload Upload Total Spent Left Speed

0 0 0 0 0 0 0 0 --:--:-- --:--:-- --:--:-- 0 100 16 0 16 0 0 207 0 --:--:-- --:--:-- --:--:-- 207 Error producing PDF. ! Misplaced \noalign. \hline ->\noalign {\ifnum 0=`}\fi \hrule \@height \arrayrulewidth \futurelet... l.386 \hline

Looks like we failed to compile the PDF