Closed whedon closed 4 years ago
Hello human, I'm @whedon, a robot that can help you with some common editorial tasks. @ejhigson, @paul-buerkner it looks like you're currently assigned to review this paper :tada:.
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I just finished my review and have the following remaining points:
coef.TEfit
, the example only reads coef(model_fit_by_TEfit)
which is not executable since model_fit_by_TEfit
is not defined. I understand the thought process leading to such examples, but it would be beneficial to have examples that actually run from end to end.@paul-buerkner Thank you for the input.
I've updated the README to include suggested installation instructions.
I may try to publish the package on CRAN at some point. I would want to re-write much of the package first, however, to make improvements to the interface and performance as well as ensure conformity to CRAN guidelines. I will not be able to manage that workload alone for the foreseeable future.
Thanks for pointing that out. I'll make a quick pass through the examples today, although it's still likely that I'll miss things occasionally.
Thanks! Looks good to me.
@paul-buerkner, thanks for reviewing this submission!
@ejhigson, how are things going?
Hi @cMadan - sorry for not being as quick as @paul-buerkner! I am a bit tied up right now but will ensure I review this in the next two weeks
@ejhigson, sounds good, thanks for the update!
@whedon check references
Hi @akcochrane - congratulations on a nice software package! I only have a few minor comments:
Thank you for the input @ejhigson ! I've implemented your suggestions.
Just out of curiosity, is it typical to include instructions for tests to be included in high-level introductory documentation? In my minimal experience tests had struck me as being developer-oriented, but knowing more about user-oriented tests would probably help me write better docs and tests!
Thank you for this @akcochrane! Personally I like to include a line for how to run tests in software install documentation (you can say running tests is optional), but perhaps others have different preferences. If you want to keep the start of the README high-level and concise then I would be happy for you to include the test instructions elsewhere in the documentation instead - up to you.
Although the package seems to generally be working running the examples, I get a "no tests found" error when running the tests with test_package (below). Do you know why this is?
> testthat::test_package('TEfits')
Error: No tests found for TEfits
For reference, here are details of my session:
> sessionInfo()
R version 4.0.2 (2020-06-22)
Platform: x86_64-w64-mingw32/x64 (64-bit)
Running under: Windows 10 x64 (build 18363)
Matrix products: default
locale:
[1] LC_COLLATE=English_United Kingdom.1252
[2] LC_CTYPE=English_United Kingdom.1252
[3] LC_MONETARY=English_United Kingdom.1252
[4] LC_NUMERIC=C
[5] LC_TIME=English_United Kingdom.1252
attached base packages:
[1] stats graphics grDevices utils datasets methods base
other attached packages:
[1] TEfits_00.77.07 testthat_2.3.2
loaded via a namespace (and not attached):
[1] compiler_4.0.2 magrittr_1.5 R6_2.4.1 rlang_0.4.7
Thanks for pointing that out. I'm not super familiar with the intricacies of devtools, but it looks like installing locally (i.e., install('dir')
includes tests but installing from github (i.e., install_github('repo')
can't. In that case, it looks like users might need to download the repo and use devtools::install()
from there.
I'd be happy to hear other suggestions, particularly if there's an option for install_github()
to include tests. I don't see anything in the install_github()
docs that refers to tests, though.
If the above seems like a good way to suggest tests to users then I'll write up some instructions saying, in effect, that users will need to download/clone the repo and install locally.
(EDIT: I've implemented this suggestion near the bottom of the README)
@whedon generate pdf
Installing locally with devtools::install()
from a download of the latest version of master from github makes the test run for me! Please can you note this in the documentation somewhere to avoid confusion for users who want to run the tests? I get some errors when I run the tests though due to "undefined columns selected" - do you get these too/do you know why they are occuring?
> testthat::test_package('TEfits')
Your rate is very close to the boundary. Consider penalizing the likelihood.-- 1. Error: TEfitAll runs with identity link and OLS error function (@test.chec
undefined columns selected
Backtrace:
1. testthat::expect_is(...) tests/testthat/test.check_TEfitAll.R:16:2
4. TEfits::TEfitAll(...) tests/testthat/test.check_TEfitAll.R:17:4
8. base::`[.data.frame`(...)
Your rate is very close to the boundary. Consider penalizing the likelihood.-- 2. Error: TEfitAll runs with identity link and logcosh error function (@test.
undefined columns selected
Backtrace:
1. testthat::expect_is(...) tests/testthat/test.check_TEfitAll.R:28:2
4. TEfits::TEfitAll(...) tests/testthat/test.check_TEfitAll.R:29:4
8. base::`[.data.frame`(...)
Your rate is very close to the boundary. Consider penalizing the likelihood.-- 3. Error: TEfitAll runs with identity link and bernoulli error function (@tes
undefined columns selected
Backtrace:
1. testthat::expect_is(...) tests/testthat/test.check_TEfitAll.R:41:2
4. TEfits::TEfitAll(...) tests/testthat/test.check_TEfitAll.R:42:4
8. base::`[.data.frame`(...)
-- 4. Error: TEfitAll runs with Weibull link and OLS error function (@test.check
undefined columns selected
Backtrace:
1. testthat::expect_is(...) tests/testthat/test.check_TEfitAll.R:54:2
4. TEfits::TEfitAll(...) tests/testthat/test.check_TEfitAll.R:55:4
8. base::`[.data.frame`(...)
-- 5. Error: TEfitAll runs with Weibull link and bernoulli error function (@test
undefined columns selected
Backtrace:
1. testthat::expect_is(...) tests/testthat/test.check_TEfitAll.R:67:2
4. TEfits::TEfitAll(...) tests/testthat/test.check_TEfitAll.R:68:4
8. base::`[.data.frame`(...)
Warning: model did not converge at tol = 0.05 . Consider respecifying, allowing more runs, or increasing the convergence tolerance.
-- 6. Error: TEfitAll runs with logistic link and OLS error function (@test.chec
undefined columns selected
Backtrace:
1. testthat::expect_is(...) tests/testthat/test.check_TEfitAll.R:80:2
4. TEfits::TEfitAll(...) tests/testthat/test.check_TEfitAll.R:81:4
8. base::`[.data.frame`(...)
Warning: model did not converge at tol = 0.05 . Consider respecifying, allowing more runs, or increasing the convergence tolerance.
-- 7. Error: TEfitAll runs with logistic link and bernoulli error function (@tes
object 'absRat' not found
Backtrace:
1. testthat::expect_is(...) tests/testthat/test.check_TEfitAll.R:93:2
4. TEfits::TEfitAll(...) tests/testthat/test.check_TEfitAll.R:94:4
5. TEfits::TEfit(...)
6. TEfits::tef_tryFits(modList, whichPnames = "null_pNames", whichFun = "null_fun")
7. TEfits::tef_fitErr(...)
8. [ base::eval(...) ] with 1 more call
Your rate is very close to the boundary. Consider penalizing the likelihood.-- 8. Error: TEfitAll runs with d prime link function (@test.check_TEfitAll.R#10
undefined columns selected
Backtrace:
1. testthat::expect_is(...) tests/testthat/test.check_TEfitAll.R:106:2
4. TEfits::TEfitAll(...) tests/testthat/test.check_TEfitAll.R:107:4
8. base::`[.data.frame`(...)
== testthat results ===========================================================
[ OK: 45 | SKIPPED: 0 | WARNINGS: 4 | FAILED: 8 ]
1. Error: TEfitAll runs with identity link and OLS error function (@test.check_TEfitAll.R#16)
2. Error: TEfitAll runs with identity link and logcosh error function (@test.check_TEfitAll.R#28)
3. Error: TEfitAll runs with identity link and bernoulli error function (@test.check_TEfitAll.R#41)
4. Error: TEfitAll runs with Weibull link and OLS error function (@test.check_TEfitAll.R#54)
5. Error: TEfitAll runs with Weibull link and bernoulli error function (@test.check_TEfitAll.R#67)
6. Error: TEfitAll runs with logistic link and OLS error function (@test.check_TEfitAll.R#80)
7. Error: TEfitAll runs with logistic link and bernoulli error function (@test.check_TEfitAll.R#93)
8. Error: TEfitAll runs with d prime link function (@test.check_TEfitAll.R#106)
Error: testthat unit tests failed
Here is my session info:
> sessionInfo()
R version 4.0.2 (2020-06-22)
Platform: x86_64-w64-mingw32/x64 (64-bit)
Running under: Windows 10 x64 (build 18363)
Matrix products: default
locale:
[1] LC_COLLATE=English_United Kingdom.1252
[2] LC_CTYPE=English_United Kingdom.1252
[3] LC_MONETARY=English_United Kingdom.1252
[4] LC_NUMERIC=C
[5] LC_TIME=English_United Kingdom.1252
attached base packages:
[1] stats graphics grDevices utils datasets methods base
other attached packages:
[1] TEfits_00.77.07 testthat_2.3.2
loaded via a namespace (and not attached):
[1] ps_1.3.4 fansi_0.4.1 prettyunits_1.1.1 rprojroot_1.3-2
[5] withr_2.2.0 digest_0.6.25 crayon_1.3.4 assertthat_0.2.1
[9] R6_2.4.1 backports_1.1.7 magrittr_1.5 rlang_0.4.7
[13] cli_2.0.2 fs_1.5.0 remotes_2.2.0 callr_3.4.3
[17] ellipsis_0.3.1 desc_1.2.0 devtools_2.3.1 tools_4.0.2
[21] glue_1.4.1 pkgload_1.1.0 compiler_4.0.2 processx_3.4.3
[25] pkgbuild_1.1.0 sessioninfo_1.1.1 memoise_1.1.0 usethis_1.6.1
I included the suggested instructions (to download and run locally) near the end of the README.
Would you mind trying again with the latest version (TEfits_00.77.09)? Thanks!
It appears as though the issue is a R 4.x incompatibility. I'll let you know when that's fixed.
Ok great thank you. The docs look good so once the tests are fixed I am happy to recomend this paper for publication. For reference the error messages I get with v00.77.09 look the same:
> testthat::test_package('TEfits')
-- 1. Error: TEfitAll runs with identity link and OLS error function (@test.chec
undefined columns selected
Backtrace:
1. testthat::expect_is(...) tests/testthat/test.check_TEfitAll.R:16:2
4. TEfits::TEfitAll(...) tests/testthat/test.check_TEfitAll.R:17:4
8. base::`[.data.frame`(...)
-- 2. Error: TEfitAll runs with identity link and logcosh error function (@test.
undefined columns selected
Backtrace:
1. testthat::expect_is(...) tests/testthat/test.check_TEfitAll.R:28:2
4. TEfits::TEfitAll(...) tests/testthat/test.check_TEfitAll.R:29:4
8. base::`[.data.frame`(...)
-- 3. Error: TEfitAll runs with identity link and bernoulli error function (@tes
undefined columns selected
Backtrace:
1. testthat::expect_is(...) tests/testthat/test.check_TEfitAll.R:41:2
4. TEfits::TEfitAll(...) tests/testthat/test.check_TEfitAll.R:42:4
8. base::`[.data.frame`(...)
-- 4. Error: TEfitAll runs with Weibull link and OLS error function (@test.check
undefined columns selected
Backtrace:
1. testthat::expect_is(...) tests/testthat/test.check_TEfitAll.R:54:2
4. TEfits::TEfitAll(...) tests/testthat/test.check_TEfitAll.R:55:4
8. base::`[.data.frame`(...)
-- 5. Error: TEfitAll runs with Weibull link and bernoulli error function (@test.check_TEfitAll.R#67) ---------------------------------------------------------------
undefined columns selected
Backtrace:
1. testthat::expect_is(...) tests/testthat/test.check_TEfitAll.R:67:2
4. TEfits::TEfitAll(...) tests/testthat/test.check_TEfitAll.R:68:4
8. base::`[.data.frame`(...)
-- 6. Error: TEfitAll runs with logistic link and OLS error function (@test.check_TEfitAll.R#80) --------------------------------------------------------------------
undefined columns selected
Backtrace:
1. testthat::expect_is(...) tests/testthat/test.check_TEfitAll.R:80:2
4. TEfits::TEfitAll(...) tests/testthat/test.check_TEfitAll.R:81:4
8. base::`[.data.frame`(...)
-- 7. Error: TEfitAll runs with logistic link and bernoulli error function (@test.check_TEfitAll.R#93) --------------------------------------------------------------
undefined columns selected
Backtrace:
1. testthat::expect_is(...) tests/testthat/test.check_TEfitAll.R:93:2
4. TEfits::TEfitAll(...) tests/testthat/test.check_TEfitAll.R:94:4
8. base::`[.data.frame`(...)
-- 8. Error: TEfitAll runs with d prime link function (@test.check_TEfitAll.R#106) ----------------------------------------------------------------------------------
undefined columns selected
Backtrace:
1. testthat::expect_is(...) tests/testthat/test.check_TEfitAll.R:106:2
4. TEfits::TEfitAll(...) tests/testthat/test.check_TEfitAll.R:107:4
8. base::`[.data.frame`(...)
== testthat results =================================================================================================================================================
[ OK: 45 | SKIPPED: 0 | WARNINGS: 4 | FAILED: 8 ]
1. Error: TEfitAll runs with identity link and OLS error function (@test.check_TEfitAll.R#16)
2. Error: TEfitAll runs with identity link and logcosh error function (@test.check_TEfitAll.R#28)
3. Error: TEfitAll runs with identity link and bernoulli error function (@test.check_TEfitAll.R#41)
4. Error: TEfitAll runs with Weibull link and OLS error function (@test.check_TEfitAll.R#54)
5. Error: TEfitAll runs with Weibull link and bernoulli error function (@test.check_TEfitAll.R#67)
6. Error: TEfitAll runs with logistic link and OLS error function (@test.check_TEfitAll.R#80)
7. Error: TEfitAll runs with logistic link and bernoulli error function (@test.check_TEfitAll.R#93)
8. Error: TEfitAll runs with d prime link function (@test.check_TEfitAll.R#106)
Error: testthat unit tests failed
Session info:
> sessionInfo()
R version 4.0.2 (2020-06-22)
Platform: x86_64-w64-mingw32/x64 (64-bit)
Running under: Windows 10 x64 (build 18363)
Matrix products: default
locale:
[1] LC_COLLATE=English_United Kingdom.1252 LC_CTYPE=English_United Kingdom.1252 LC_MONETARY=English_United Kingdom.1252 LC_NUMERIC=C
[5] LC_TIME=English_United Kingdom.1252
attached base packages:
[1] stats graphics grDevices utils datasets methods base
other attached packages:
[1] TEfits_00.77.09 testthat_2.3.2
loaded via a namespace (and not attached):
[1] ps_1.3.4 fansi_0.4.1 prettyunits_1.1.1 rprojroot_1.3-2 withr_2.2.0 digest_0.6.25 crayon_1.3.4 assertthat_0.2.1 R6_2.4.1
[10] backports_1.1.7 magrittr_1.5 rlang_0.4.7 cli_2.0.2 fs_1.5.0 remotes_2.2.0 callr_3.4.3 ellipsis_0.3.1 desc_1.2.0
[19] devtools_2.3.1 tools_4.0.2 glue_1.4.1 pkgload_1.1.0 compiler_4.0.2 processx_3.4.3 pkgbuild_1.1.0 sessioninfo_1.1.1 memoise_1.1.0
[28] usethis_1.6.1
``
Evidently I'd accidentally left a necessary dependency on a package that I'd meant to be optional. That bug should be fixed now, and the tests should run.
@akcochrane thank you very much for fixing this! The tests now all pass for me.
I am happy to recommend this paper for publication in JOSS. Congratulations on a nice software package!
@ejhigson, thank you for your thorough review!
@akcochrane, you're almost done! Next step is for me to do some final checks.
@whedon generate pdf
@whedon check references
@whedon check references
@whedon check references
Reference check summary:
OK DOIs
- 10.18637/jss.v067.i01 is OK
- 10.18637/jss.v080.i01 is OK
- 10.1167/17.11.3 is OK
- 10.1007/978-0-387-21706-2 is OK
MISSING DOIs
- None
INVALID DOIs
- 10.1167/jov.0.0.07387 is INVALID
@akcochrane, looks like that ref should have DOI of 10.1167/jov.20.8.16 and no longer "in press" (https://pubmed.ncbi.nlm.nih.gov/32790849/).
After that, there are a few last things to take care of:
You may find this helpful: https://guides.github.com/activities/citable-code/
@whedon generate pdf
Thank you all for your attentive help during this review process!
version tag: v00.77.12
Zenodo archived doi: 10.5281/zenodo.3992314
@whedon set 10.5281/zenodo.3992314 as archive
OK. 10.5281/zenodo.3992314 is the archive.
@akcochrane I see it is in Zenodo as well, but did you mean for the version number to have to zeros before the decimal place?
@cMadan Yes, that was my intention. Would it be better for me to remove them?
@akcochrane, I'm fine with it, just thought it was a bit unconventional and thought I'd check it's not a typo.
@cMadan No, it was not a typo.
@whedon set v00.77.12 as version
OK. v00.77.12 is the version.
@whedon accept
Attempting dry run of processing paper acceptance...
Reference check summary:
OK DOIs
- 10.18637/jss.v067.i01 is OK
- 10.18637/jss.v080.i01 is OK
- 10.1167/17.11.3 is OK
- 10.1007/978-0-387-21706-2 is OK
- 10.1167/jov.20.8.16 is OK
MISSING DOIs
- None
INVALID DOIs
- None
PDF failed to compile for issue #2535 with the following error:
/app/vendor/bundle/ruby/2.4.0/bundler/gems/whedon-0e09ec0a48e3/lib/whedon/bibtex_parser.rb:45:in block in generate_citations': undefined method
key' for #<BibTeX::Preamble " \newcommand{\noop}[1]{} "> (NoMethodError)
from /app/vendor/bundle/ruby/2.4.0/gems/bibtex-ruby-5.1.4/lib/bibtex/bibliography.rb:149:in each' from /app/vendor/bundle/ruby/2.4.0/gems/bibtex-ruby-5.1.4/lib/bibtex/bibliography.rb:149:in
each'
from /app/vendor/bundle/ruby/2.4.0/bundler/gems/whedon-0e09ec0a48e3/lib/whedon/bibtex_parser.rb:41:in generate_citations' from /app/vendor/bundle/ruby/2.4.0/bundler/gems/whedon-0e09ec0a48e3/lib/whedon/compilers.rb:245:in
crossref_from_markdown'
from /app/vendor/bundle/ruby/2.4.0/bundler/gems/whedon-0e09ec0a48e3/lib/whedon/compilers.rb:21:in generate_crossref' from /app/vendor/bundle/ruby/2.4.0/bundler/gems/whedon-0e09ec0a48e3/lib/whedon/processor.rb:95:in
compile'
from /app/vendor/bundle/ruby/2.4.0/bundler/gems/whedon-0e09ec0a48e3/bin/whedon:82:in compile' 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-0e09ec0a48e3/bin/whedon:119: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
@arfon, can you look into this?
@whedon accept
Attempting dry run of processing paper acceptance...
Reference check summary:
OK DOIs
- 10.18637/jss.v067.i01 is OK
- 10.18637/jss.v080.i01 is OK
- 10.1167/17.11.3 is OK
- 10.1007/978-0-387-21706-2 is OK
- 10.1167/jov.20.8.16 is OK
MISSING DOIs
- None
INVALID DOIs
- None
:wave: @openjournals/joss-eics, this paper is ready to be accepted and published.
Check final proof :point_right: https://github.com/openjournals/joss-papers/pull/1652
If the paper PDF and Crossref deposit XML look good in https://github.com/openjournals/joss-papers/pull/1652, then you can now move forward with accepting the submission by compiling again with the flag deposit=true
e.g.
@whedon accept deposit=true
@cMadan - fixed.
Submitting author: @akcochrane (Aaron Cochrane) Repository: https://github.com/akcochrane/TEfits Version: v00.77.12 Editor: @cMadan Reviewer: @ejhigson, @paul-buerkner Archive: 10.5281/zenodo.3992314
: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.
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