Joss-reviews: [PRE REVIEW]: Diff_classifier: Parallelization of multi-particle tracking video analyses
Submitting author: @ccurtis7 (Chad Curtis)
Repository: https://github.com/ccurtis7/diff_classifier
Version: v0.1-alpha
Editor: @cMadan
Reviewers: @stsievert
Author instructions
Thanks for submitting your paper to JOSS @ccurtis7. The JOSS editor (shown at the top of this issue) will work with you on this issue to find a reviewer for your submission before creating the main review issue.
@ccurtis7 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
All 99 comments
Hello human, I'm @whedon, a robot that can help you with some common editorial tasks. @cMadan it looks like you're currently assigned as the editor for this paper :tada:
For a list of things I can do to help you, just type:
@whedon commands
Attempting PDF compilation. Reticulating splines etc...
:wave: @cMadan - the submitting author suggested you as the handling editor.
arfon
on 12 Sep 2018
PDF failed to compile for issue #939 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 17 0 17 0 0 144 0 --:--:-- --:--:-- --:--:-- 145
Error producing PDF.
! Missing $ inserted.
$
l.274
Looks like we failed to compile the PDF
whedon
on 12 Sep 2018
@whedon commands
ccurtis7
on 12 Sep 2018
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
# Compile the paper
@whedon generate pdf
🚧 🚧 🚧 Experimental Whedon features 🚧 🚧 🚧
# Compile the paper from a custom git branch
@whedon generate pdf from branch custom-branch-name
@whedon list reviewers
ccurtis7
on 12 Sep 2018
Here's the current list of reviewers: https://bit.ly/joss-reviewers
whedon
on 12 Sep 2018
@whedon generate pdf
ccurtis7
on 12 Sep 2018
Attempting PDF compilation. Reticulating splines etc...
PDF failed to compile for issue #939 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 17 0 17 0 0 112 0 --:--:-- --:--:-- --:--:-- 112
Error producing PDF.
! Missing $ inserted.
$
l.274
Looks like we failed to compile the PDF
whedon
on 12 Sep 2018
It seems that the test PDF is failing to generate. I looked at a few examples from other JOSS pre-reviews to see if I could track down a solution. I think it has to do with a stray character or figure that is being interpreted incorrectly. I'm not sure exactly what it is, but I suspect it is somewhere in my paper.bib file. I tried removing the abstracts from the paper.bib file to see if I could resolve the error in a new branch joss_review.
@whedon generate pdf from branch joss_review
ccurtis7
on 12 Sep 2018
@whedon generate pdf from branch joss_review
arfon
on 12 Sep 2018
Attempting PDF compilation from custom branch joss_review. Reticulating splines etc...
PDF failed to compile for issue #939 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 17 0 17 0 0 111 0 --:--:-- --:--:-- --:--:-- 111
Error producing PDF.
! Missing $ inserted.
$
l.276
Looks like we failed to compile the PDF
whedon
on 12 Sep 2018
@whedon generate pdf from branch joss_review
ccurtis7
on 12 Sep 2018
Attempting PDF compilation from custom branch joss_review. Reticulating splines etc...
PDF failed to compile for issue #939 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 17 0 17 0 0 143 0 --:--:-- --:--:-- --:--:-- 144
Error producing PDF.
! Missing $ inserted.
$
l.276
Looks like we failed to compile the PDF
whedon
on 12 Sep 2018
@whedon generate pdf from branch joss_review
ccurtis7
on 12 Sep 2018
Attempting PDF compilation from custom branch joss_review. Reticulating splines etc...
PDF failed to compile for issue #939 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 17 0 17 0 0 134 0 --:--:-- --:--:-- --:--:-- 136
Error producing PDF.
! Missing $ inserted.
$
l.276
Looks like we failed to compile the PDF
whedon
on 12 Sep 2018
@whedon generate pdf from branch joss_review
ccurtis7
on 12 Sep 2018
Attempting PDF compilation from custom branch joss_review. Reticulating splines etc...
PDF failed to compile for issue #939 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 17 0 17 0 0 166 0 --:--:-- --:--:-- --:--:-- 165
100 17 0 17 0 0 165 0 --:--:-- --:--:-- --:--:-- 165
Error producing PDF.
! Missing $ inserted.
$
l.277
Looks like we failed to compile the PDF
whedon
on 12 Sep 2018
@ccurtis7 - I'm trying to debug this myself. The issue seems to be with the YAML header. I'm wondering if there are some hidden characters in there or something...
arfon
on 12 Sep 2018
Thanks @arfon, I couldn't narrow down where the error was.
ccurtis7
on 12 Sep 2018
@ccurtis7 - the issue is with the underscore in the title. Please change:
title: 'diff_classifier: Parallelization of multi-particle tracking videos'
to
title: 'diff\_classifier: Parallelization of multi-particle tracking videos'
Also, I should try and sanitize this kind of input as it's passed to Pandoc. This isn't the first time it's caught us out...
arfon
on 12 Sep 2018
@whedon generate pdf from branch joss_review
ccurtis7
on 12 Sep 2018
Attempting PDF compilation from custom branch joss_review. Reticulating splines etc...
PDF failed to compile for issue #939 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 17 0 17 0 0 27 0 --:--:-- --:--:-- --:--:-- 27
Error producing PDF.
! Missing $ inserted.
$
l.276
Looks like we failed to compile the PDF
whedon
on 12 Sep 2018
@whedon generate pdf from branch joss_review
ccurtis7
on 12 Sep 2018
Attempting PDF compilation from custom branch joss_review. Reticulating splines etc...
PDF failed to compile for issue #939 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
0 0 0 0 0 0 0 0 --:--:-- --:--:-- --:--:-- 0
100 17 0 17 0 0 101 0 --:--:-- --:--:-- --:--:-- 101
Error producing PDF.
! Missing $ inserted.
$
l.276
Looks like we failed to compile the PDF
whedon
on 12 Sep 2018
I'm not sure why it's still not working after I changed the YAML file. I'm unfamiliar with Latek, but I tried checking a complete list of symbols that need to be written as math. Is the colon throwing it as well?
ccurtis7
on 12 Sep 2018
@ccurtis7 - I'm wondering if the new command @whedon generate pdf from branch... is being weird. I can compile your changes on the joss_paper branch locally OK.
Perhaps merge what you have in the joss_paper branch into master and just try @whedon generate pdf?
Sorry for the both here. I've only recently added the ability for Whedon to compile papers from a different branch and it's quite possibly a little buggy...
arfon
on 12 Sep 2018
@whedon generate pdf
ccurtis7
on 12 Sep 2018
Attempting PDF compilation. Reticulating splines etc...
@whedon generate pdf
A few minor edits from @arokem
ccurtis7
on 12 Sep 2018
Attempting PDF compilation. Reticulating splines etc...
Hi @ccurtis7! Do you have any suggestions for potential reviewers?
cMadan
on 17 Sep 2018
Hi @cMadan, looking over the list of reviewers, I think sealhuang or oesteban would be good fits.
ccurtis7
on 17 Sep 2018
@sealhuang @oesteban, would you be available and interested to review this submission?
cMadan
on 19 Sep 2018
I'm on vacation now, and I expect to be pretty swamped for a while when I'm
back. Sorry I have to let this one go.
On Wed, Sep 19, 2018, 03:12 Christopher Madan notifications@github.com
wrote:
@sealhuang https://github.com/sealhuang @oesteban
https://github.com/oesteban, would you be available and interested to
review this submission?—
You are receiving this because you were mentioned.
Reply to this email directly, view it on GitHub
https://github.com/openjournals/joss-reviews/issues/939#issuecomment-422612042,
or mute the thread
https://github.com/notifications/unsubscribe-auth/AAkhxpWv3z5nt70W-8wAKvdyryIZxc0Nks5ucZn7gaJpZM4WlGBz
.
oesteban
on 19 Sep 2018
@oesteban, no problem, thanks for the quick reply!
cMadan
on 19 Sep 2018
Others I think that might be good fits, @stsievert and @vsoch
ccurtis7
on 22 Sep 2018
I'd be happy to review this.
stsievert
on 30 Sep 2018
@stsievert, that would be great, thank you!
I'll go ahead and start the review process now.
cMadan
on 30 Sep 2018
@whedon assign @stsievert as reviewer
cMadan
on 30 Sep 2018
OK, the reviewer is @stsievert
whedon
on 30 Sep 2018
@whedon start review
cMadan
on 30 Sep 2018
OK, I've started the review over in https://github.com/openjournals/joss-reviews/issues/989. Feel free to close this issue now!
whedon
on 30 Sep 2018
@whedon generate pdf
ccurtis7
on 9 Apr 2019
Attempting PDF compilation. Reticulating splines etc...
PDF failed to compile for issue #939 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 17 0 17 0 0 388 0 --:--:-- --:--:-- --:--:-- 395
Error producing PDF.
! Missing $ inserted.
$
l.356 T
Looks like we failed to compile the PDF
whedon
on 9 Apr 2019
@whedon generate pdf
ccurtis7
on 9 Apr 2019
Attempting PDF compilation. Reticulating splines etc...
PDF failed to compile for issue #939 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 17 0 17 0 0 251 0 --:--:-- --:--:-- --:--:-- 253
Error producing PDF.
! Missing $ inserted.
$
l.354 T
Looks like we failed to compile the PDF
whedon
on 9 Apr 2019
@whedon generate pdf
ccurtis7
on 9 Apr 2019
Attempting PDF compilation. Reticulating splines etc...
@whedon generate pdf
ccurtis7
on 9 Apr 2019
Attempting PDF compilation. Reticulating splines etc...
PDF failed to compile for issue #939 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 17 0 17 0 0 164 0 --:--:-- --:--:-- --:--:-- 166
pandoc-citeproc: reference Pulford:2005 not found
pandoc-citeproc: reference Chenouard:2014 not found
pandoc-citeproc: reference Tineves:2017 not found
pandoc-citeproc: reference Wang:2015 not found
pandoc-citeproc: reference cloudknot not found
pandoc-citeproc: reference zenodo not found
Error producing PDF.
! Missing $ inserted.
$
l.356 T
Looks like we failed to compile the PDF
whedon
on 9 Apr 2019
@whedon generate pdf
ccurtis7
on 9 Apr 2019
Attempting PDF compilation. Reticulating splines etc...
PDF failed to compile for issue #939 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 17 0 17 0 0 349 0 --:--:-- --:--:-- --:--:-- 354
Error producing PDF.
! Missing { inserted.
$
l.357 T
Looks like we failed to compile the PDF
whedon
on 9 Apr 2019
@whedon generate pdf
ccurtis7
on 9 Apr 2019
Attempting PDF compilation. Reticulating splines etc...
@whedon generate pdf
ccurtis7
on 9 Apr 2019
Attempting PDF compilation. Reticulating splines etc...
@whedon generate pdf
ccurtis7
on 9 Apr 2019
Attempting PDF compilation. Reticulating splines etc...
PDF failed to compile for issue #939 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 17 0 17 0 0 179 0 --:--:-- --:--:-- --:--:-- 180
Error producing PDF.
! Missing { inserted.
$
l.356 T
Looks like we failed to compile the PDF
whedon
on 9 Apr 2019
@whedon generate pdf
ccurtis7
on 9 Apr 2019
Attempting PDF compilation. Reticulating splines etc...
PDF failed to compile for issue #939 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 17 0 17 0 0 299 0 --:--:-- --:--:-- --:--:-- 303
Error producing PDF.
! Missing $ inserted.
$
l.356 T
Looks like we failed to compile the PDF
whedon
on 9 Apr 2019
@whedon generate pdf
ccurtis7
on 9 Apr 2019
Attempting PDF compilation. Reticulating splines etc...
@whedon generate pdf
ccurtis7
on 9 Apr 2019
Attempting PDF compilation. Reticulating splines etc...
@whedon generate pdf
ccurtis7
on 9 Apr 2019
Attempting PDF compilation. Reticulating splines etc...
@whedon generate pdf
ccurtis7
on 9 Apr 2019
Attempting PDF compilation. Reticulating splines etc...
@whedon generate pdf
ccurtis7
on 9 Apr 2019
Attempting PDF compilation. Reticulating splines etc...
@whedon generate pdf
ccurtis7
on 9 Apr 2019
Attempting PDF compilation. Reticulating splines etc...
Related issues
whedon
·
9Comments
whedon
·
12Comments
whedon
·
12Comments
whedon
·
12Comments
whedon
·
10Comments
Most helpful comment
:point_right: Check article proof :page_facing_up: :point_left: