Joss-reviews: [PRE REVIEW]: RCaller: A Java package for interfacing R
Submitting author: @jbytecode (Mehmet Hakan Satman)
Repository: https://github.com/jbytecode/rcaller/
Version: v3.0
Editor: @mikldk
Reviewers: @xin-huang, @nthomasCUBE
Managing EiC: Kevin M. Moerman
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Thanks for submitting your paper to JOSS @jbytecode. Currently, there isn't an JOSS editor assigned to your paper.
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Editor instructions
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All 46 comments
Hello human, I'm @whedon, a robot that can help you with some common editorial tasks.
:warning: JOSS reduced service mode :warning:
Due to the challenges of the COVID-19 pandemic, JOSS is currently operating in a "reduced service mode". You can read more about what that means in our blog post.
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:
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PDF failed to compile for issue #2600 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/2600 (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-132474d2711b/lib/whedon/processor.rb:61:infind_paper_paths'
from /app/vendor/bundle/ruby/2.4.0/bundler/gems/whedon-132474d2711b/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-132474d2711b/bin/whedon:119:inload'
from /app/vendor/bundle/ruby/2.4.0/bin/whedon:23:in
whedon
on 26 Aug 2020
Reference check summary:
OK DOIs
- None
MISSING DOIs
- https://doi.org/10.9734/bjmcs/2014/10902 may be missing for title: RCaller: A software library for calling R from Java
- https://doi.org/10.1007/s00180-008-0132-x may be missing for title: How to talk to strangers: ways to leverage connectivity between R, Java and Objective C
- https://doi.org/10.1145/3328433.3328458 may be missing for title: Towards polyglot adapters for the graalvm
INVALID DOIs
- None
@openjournals/dev Can you help trouble shoot the above error? :point_up:
Kevin-Mattheus-Moerman
on 26 Aug 2020
@whedon generate pdf
xuanxu
on 26 Aug 2020
whedon
on 26 Aug 2020
@whedon check references
jbytecode
on 27 Aug 2020
Reference check summary:
OK DOIs
- 10.9734/bjmcs/2014/10902 is OK
- 10.1007/s00180-008-0132-x is OK
- 10.1145/3328433.3328458 is OK
MISSING DOIs
- None
INVALID DOIs
- None
@whedon generate pdf
jbytecode
on 27 Aug 2020
whedon
on 27 Aug 2020
@whedon check repository
arfon
on 28 Aug 2020
Software report (experimental):
github.com/AlDanial/cloc v 1.84 T=0.47 s (243.0 files/s, 23787.0 lines/s)
-------------------------------------------------------------------------------
Language files blank comment code
-------------------------------------------------------------------------------
Java 87 1462 1450 5601
TeX 4 218 14 896
PHP 8 142 271 377
R 2 14 0 187
Maven 1 11 0 166
Markdown 5 55 0 163
INI 3 0 0 13
XML 2 0 0 13
YAML 1 3 0 7
-------------------------------------------------------------------------------
SUM: 113 1905 1735 7423
-------------------------------------------------------------------------------
Statistical information for the repository '2600' was gathered on 2020/08/28.
The following historical commit information, by author, was found:
Author Commits Insertions Deletions % of changes
Alexander Bondarev 4 139 81 0.38
Edinei Piovesan 1 70 9 0.14
Kopilov Aleksandr 7 173 47 0.38
Luke Lai 1 2 1 0.01
Manuel Muradas 3 50 3 0.09
Mehmet Hakan Satman 2 27 1 0.05
Paul Curcean 17 6618 6143 22.19
SKYLAKE-2016\celthan 2 104 4 0.19
hako 11 1945 1420 5.85
jbytecode 39 8914 6442 26.71
kstarosta 2 34 9 0.07
mbatchkarov 4 4598 240 8.41
mhsatman 77 15356 4981 35.37
oem 3 62 6 0.12
stevensotelo 1 12 5 0.03
Below are the number of rows from each author that have survived and are still
intact in the current revision:
Author Rows Stability Age % in comments
Alexander Bondarev 110 79.1 57.6 3.64
Edinei Piovesan 70 100.0 32.4 20.00
Kopilov Aleksandr 157 90.8 2.6 18.47
Manuel Muradas 43 86.0 45.6 6.98
Paul Curcean 1702 25.7 53.2 7.87
SKYLAKE-2016\celthan 104 100.0 44.4 45.19
jbytecode 4124 46.3 63.8 19.88
kstarosta 34 100.0 42.7 17.65
mbatchkarov 2161 47.0 105.0 23.79
stevensotelo 8 66.7 65.0 0.00
since this repo is moved from old code.google.com, I am represented in above table by more than one nicknames, so 'hako', 'jbytecode','Mehmet Hakan Satman', and 'mhsatman' are both I am. fyi.
jbytecode
on 28 Aug 2020
@jbytecode
Some notes to work on for your paper:
- [x] Typo:
persfective->perspective
- [x] We do not accept previously published scholarly works in JOSS. If major changes have been made, or if the focus on the paper is significantly different, exceptions can be made. Therefore, can you please clarify what the difference in focus/content/intent is for the current submission with respect to this paper:
Satman, M. H. (2014). RCaller: A software library for calling r from java.Journal of Advances in Mathematics and Computer Science, 2188–2196. doi:10.9734/bjmcs/2014/10902. Likely you are looking to submit for the new developments from the past 6 years but please formally clarify the difference and list some of these developments please.
Kevin-Mattheus-Moerman
on 2 Sep 2020
@mikldk @kakiac could one of you edit this submission?
Kevin-Mattheus-Moerman
on 2 Sep 2020
@Kevin-Mattheus-Moerman Dear editor, new features such as support for DataFrames, R Start-up options, Java Scripting API (JSR 223), performance improvements, and minor API changes are not included in the paper you mentioned above. I will highlight the differences. Thanks.
jbytecode
on 2 Sep 2020
@whedon generate pdf
jbytecode
on 2 Sep 2020
whedon
on 2 Sep 2020
@mikldk @kakiac could one of you edit this submission?
I am rather busy at the moment, so I prefer if @kakearney could handle this interesting submission. But if they cannot, I will be happy to.
mikldk
on 4 Sep 2020
@kakearney is not an editor. Maybe you meant @kakiac ?
danielskatz
on 8 Sep 2020
👋 @kakiac - can you edit this submission?
danielskatz
on 8 Sep 2020
@mikldk - I'm going to assign this to you, based on your semi-willingness and the fact that @kakiac also has another request right now. Thanks!
danielskatz
on 8 Sep 2020
@whedon assign @mikldk as editor
danielskatz
on 8 Sep 2020
OK, the editor is @mikldk
whedon
on 8 Sep 2020
@jbytecode Can you please explain/clarify why the other (major) committers are not co-authors (maybe they declined?)?
mikldk
on 10 Sep 2020
@mikldk the most active contributor, Paul, is not interested in the project any more, so I didn't offer him to join. Should I offer them to participate?
jbytecode
on 10 Sep 2020
@jbytecode Yes, please ask all who contributed one way or another.
mikldk
on 10 Sep 2020
Dear editor @mikldk, I have just opened an issue in RCaller repo and I invited them to participate. fyi.
update: @Kopilov is now a co-author
update: 5 commiters responded, a committer joined to the paper. @Kopilov is the new co-author and he is the owner of project RCallerService which is a project built on top of the RCaller.
update: Simon Carter joined us as a new contributor today (September, 15th), made minor contributions, asked him to join manuscript, he is fine being in the Acknowledgement section.
jbytecode
on 10 Sep 2020
@whedon generate pdf
jbytecode
on 11 Sep 2020
:point_right::page_facing_up: Download article proof :page_facing_up: View article proof on GitHub :page_facing_up: :point_left:
whedon
on 11 Sep 2020
@whedon generate pdf
jbytecode
on 14 Sep 2020
:point_right::page_facing_up: Download article proof :page_facing_up: View article proof on GitHub :page_facing_up: :point_left:
whedon
on 14 Sep 2020
Dear editor @mikldk , after asking all contributors to join manuscript 11 days ago, one of the major contributor @Kopilov joined, other major contributor is no longer interested in the project and has no response. The third major one and some of other minor contributors are happy being in the Acknowledgement section, some of them also have no response. Any actions needed?
jbytecode
on 21 Sep 2020
@jbytecode Thanks. Do you have any suggested reviewers?
mikldk
on 23 Sep 2020
No, but if you don't have time, I can choose a few suitable reviewers from the list for you.
jbytecode
on 23 Sep 2020
pragyansmita, nthomasCUBE, xin-huang, marcoapintoo, tylerwmarrs have both Java and R in their preferred programming language column.
jbytecode
on 24 Sep 2020
@marcoapintoo, @tylerwmarrs: Would you be interested in reviewing this submission to The Journal of Open Source Software? Reviews are open and based on a checklist. The reviewer guidelines are available here: https://joss.readthedocs.io/en/latest/reviewer_guidelines.html. If you have any questions or concerns please let me know.
mikldk
on 25 Sep 2020
@nthomasCUBE, @xin-huang: Would you be interested in reviewing this submission to The Journal of Open Source Software? Reviews are open and based on a checklist. The reviewer guidelines are available here: https://joss.readthedocs.io/en/latest/reviewer_guidelines.html. If you have any questions or concerns please let me know.
mikldk
on 29 Sep 2020
Hi @mikldk, I am happy to help
xin-huang
on 29 Sep 2020
Hi, me too
nthomasCUBE
on 30 Sep 2020
@whedon add @xin-huang as reviewer
mikldk
on 6 Oct 2020
OK, @xin-huang is now a reviewer
whedon
on 6 Oct 2020
@whedon add @nthomasCUBE as reviewer
mikldk
on 6 Oct 2020
OK, @nthomasCUBE is now a reviewer
whedon
on 6 Oct 2020
@whedon start review
mikldk
on 6 Oct 2020
OK, I've started the review over in https://github.com/openjournals/joss-reviews/issues/2722.
whedon
on 6 Oct 2020
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Most helpful comment
@mikldk - I'm going to assign this to you, based on your semi-willingness and the fact that @kakiac also has another request right now. Thanks!