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[REVIEW]: surtvep: An R package for estimating time-varying effects #5688

Closed editorialbot closed 2 months ago

editorialbot commented 1 year ago

Submitting author: !--author-handle-->@LingfengLuo0510<!--end-author-handle-- (Lingfeng Luo) Repository: https://github.com/UM-KevinHe/surtvep Branch with paper.md (empty if default branch): JOSS Version: v1.0.0 Editor: !--editor-->@osorensen<!--end-editor-- Reviewers: @adibender, @turgeonmaxime Archive: 10.5281/zenodo.12575049

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Checklists

📝 Checklist for @turgeonmaxime

📝 Checklist for @adibender

editorialbot commented 1 year ago

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editorialbot commented 1 year ago

Checking the BibTeX entries failed with the following error: 

Failed to parse BibTeX on value "title" (NAME) [#<BibTeX::Bibliography data=[8]>, "@", #<BibTeX::Entry >, "%"]
editorialbot commented 1 year ago 
Software report:

github.com/AlDanial/cloc v 1.88  T=0.10 s (720.9 files/s, 190900.9 lines/s)
-------------------------------------------------------------------------------
Language                     files          blank        comment           code
-------------------------------------------------------------------------------
HTML                            31           1137            263           6636
C++                              3            310            446           2410
XML                              2              0            133           1877
R                               14            231           1458           1485
CSS                              3             98             52            442
JavaScript                       3             64             32            256
TeX                              2             29              9            225
Markdown                         4             91              0            215
Rmd                              5            302            617            113
YAML                             3              6              2            109
SVG                              1              0              1             11
C/C++ Header                     1              2              0              5
-------------------------------------------------------------------------------
SUM:                            72           2270           3013          13784
-------------------------------------------------------------------------------

gitinspector failed to run statistical information for the repository
editorialbot commented 1 year ago

Wordcount for paper.md is 1759

editorialbot commented 1 year ago

Failed to discover a valid open source license

editorialbot commented 1 year ago

:point_right::page_facing_up: Download article proof :page_facing_up: View article proof on GitHub :page_facing_up: :point_left:

turgeonmaxime commented 1 year ago

Review checklist for @turgeonmaxime

Conflict of interest

Code of Conduct

General checks

Functionality

Documentation

Software paper

adibender commented 1 year ago

Review checklist for @adibender

Conflict of interest

Code of Conduct

General checks

Functionality

Documentation

Software paper

adibender commented 1 year ago

@osorensen I work in the field and have a package which provides similar functionality. Not sure if this is conflict of interest, but I don't think it will affect review. Just wanted to mention it here

osorensen commented 1 year ago

@adibender, I agree. I see this as a strength rather than a conflict of interest, but thanks for mentioning it.

turgeonmaxime commented 1 year ago

@LingfengLuo0510 I just read the manuscript for the first time, and I have a few questions/comments.

I'm sure I'll have further comments/questions as I keep reviewing the package, but I'll put them in a different comment!

turgeonmaxime commented 1 year ago

Also, I haven't been able to install the package using the instructions in the manuscript. Here is the error message I got.

r$> remotes::install_github('UM-KevinHe/surtvep')
Downloading GitHub repo UM-KevinHe/surtvep@HEAD
── R CMD build ──────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────
   checking for file ‘/private/var/folders/hb/r5l2r5b12gg5y2zxyg4l7nh80000gn/T/Rtmp42cwos/remotes1030ea884ab0/UM-KevinHe-surtvep-31f9fd4/DESC✔  checking for file ‘/private/var/folders/hb/r5l2r5b12gg5y2zxyg4l7nh80000gn/T/Rtmp42cwos/remotes1030ea884ab0/UM-KevinHe-surtvep-31f9fd4/DESCRIPTION’
─  preparing ‘surtvep’:
✔  checking DESCRIPTION meta-information ...
─  cleaning src
─  checking for LF line-endings in source and make files and shell scripts
─  checking for empty or unneeded directories
─  building ‘surtvep_1.0.0.tar.gz’

* installing *source* package ‘surtvep’ ...
** using staged installation
** libs
using C++ compiler: ‘Apple clang version 14.0.3 (clang-1403.0.22.14.1)’
using C++11
using SDK: ‘MacOSX13.3.sdk’
clang++ -arch arm64 -std=gnu++11 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG  -I'/Library/Frameworks/R.framework/Versions/4.3-arm64/Resources/library/Rcpp/include' -I'/Library/Frameworks/R.framework/Versions/4.3-arm64/Resources/library/RcppArmadillo/include' -I/opt/R/arm64/include     -fPIC  -falign-functions=64 -Wall -g -O2  -c PenalizeStopCpp.cpp -o PenalizeStopCpp.o
PenalizeStopCpp.cpp:4:10: fatal error: 'omp.h' file not found
#include <omp.h>
         ^~~~~~~
1 error generated.
make: *** [PenalizeStopCpp.o] Error 1
ERROR: compilation failed for package ‘surtvep’
* removing ‘/Library/Frameworks/R.framework/Versions/4.3-arm64/Resources/library/surtvep’
* restoring previous ‘/Library/Frameworks/R.framework/Versions/4.3-arm64/Resources/library/surtvep’
Warning message:
In i.p(...) :
  installation of package ‘/var/folders/hb/r5l2r5b12gg5y2zxyg4l7nh80000gn/T//Rtmp42cwos/file1030e79df6e36/surtvep_1.0.0.tar.gz’ had non-zero exit status

I did notice that the instructions in the README.md file are slightly different, as they point to the branch openmp. When I follow those instructions (i.e. remotes::install_github("UM-KevinHe/surtvep", ref = "openmp")), then the installation proceeds without error.

For reference, here's my session information:

r$> sessionInfo()
R version 4.3.0 (2023-04-21)
Platform: aarch64-apple-darwin20 (64-bit)
Running under: macOS Ventura 13.4.1

Matrix products: default
BLAS:   /Library/Frameworks/R.framework/Versions/4.3-arm64/Resources/lib/libRblas.0.dylib
LAPACK: /Library/Frameworks/R.framework/Versions/4.3-arm64/Resources/lib/libRlapack.dylib;  LAPACK version 3.11.0

locale:
[1] en_CA.UTF-8/en_CA.UTF-8/en_CA.UTF-8/C/en_CA.UTF-8/en_CA.UTF-8

time zone: America/Edmonton
tzcode source: internal

attached base packages:
[1] stats     graphics  grDevices utils     datasets  methods   base

loaded via a namespace (and not attached):
 [1] processx_3.8.2    compiler_4.3.0    R6_2.5.1          rprojroot_2.0.3   cli_3.6.1         prettyunits_1.1.1 tools_4.3.0
 [8] curl_5.0.1        crayon_1.5.2      remotes_2.4.2     desc_1.4.2        callr_3.7.3       ps_1.7.5          pkgbuild_1.4.2
turgeonmaxime commented 1 year ago

@LingfengLuo0510 One more thing: I ran devtools::check() on the openmp branch, and it highlighted many issues with the documentation of your package (among other things). I suggest you ran devtools::check() yourself and fix the warnings, and consider fixing the notes too.

osorensen commented 1 year ago

Thanks a lot for you comments @turgeonmaxime!

editorialbot commented 1 year ago

:point_right::page_facing_up: Download article proof :page_facing_up: View article proof on GitHub :page_facing_up: :point_left:

osorensen commented 1 year ago

@LingfengLuo0510, I just wanted to add to the comments from @turgeonmaxime that although we don't require R package submissions to be on CRAN, they should in general pass R CMD check with no NOTEs, WARNINGs, or ERRORs, unless there are very good arguments for not doing so. However, since this is an R package that needs compilation, I would also strongly recommend uploading it to CRAN, as it makes the installation process much easier for most users.

osorensen commented 1 year ago

@LingfengLuo0510, you're welcome to start addressing the points raised by @turgeonmaxime. Please keep us updated about any progress.

LingfengLuo0510 commented 1 year ago

@osorensen Thanks a lot for the instructions. I am submitting this project to CRAN now. I will update when it is successfully uploaded. @turgeonmaxime The installation issues come from the fact that OpenMP feature is naturally supported in the Mac OS m1 chip system. I am uploading the package to CRAN and trying to fix the issue. I will reply to the points soon. Thanks a lot for the comments!

adibender commented 11 months ago

@LingfengLuo0510 some things that are currently missing from your package:

osorensen commented 11 months ago

Thanks @adibender.

@LingfengLuo0510, any updates on fixing the issues pointed out be @turgeonmaxime or on the CRAN submission?

LingfengLuo0510 commented 11 months ago

Thank you for your comments. The package is currently under CRAN review. I’ve addressed CRAN's feedback and resubmitted the updated package for approval. I will provide an update once the review process is complete.

osorensen commented 10 months ago

@LingfengLuo0510, I notice the package has been on CRAN for a while now. Could you please let us know if there's also been any progress in addressing the points raised by the reviewers?

editorialbot commented 10 months ago

:point_right::page_facing_up: Download article proof :page_facing_up: View article proof on GitHub :page_facing_up: :point_left:

LingfengLuo0510 commented 10 months ago

@editorialbot generate pdf

editorialbot commented 10 months ago

:point_right::page_facing_up: Download article proof :page_facing_up: View article proof on GitHub :page_facing_up: :point_left:

LingfengLuo0510 commented 10 months ago

@turgeonmaxime

Thanks a lot for your comments.

  1. "I noticed that Figure 1 (the function flowchart) doesn't appear in the PDF. In its place, it looks like the caption is repeated twice. Please fix." Fixed. See the revised Figure 1.

  2. "In Figure 2, the confidence bands don't cover the same range as the curve estimate. Why is that?" The y-axis range in the updated Figure 2 has been expanded to ensure complete coverage of the confidence bands and the curve estimate. See the updates in Figure 2.

  3. "On line 119, you write: "We estimate cancer stage of kidney, lung, and breast." That's incorrect, you're estimating hazard ratios. The cancer stages are part of the data." See the revised text on line 128 for the correct information.

  4. "For the section "Data Example", would it be possible to share your code?" The code for model fitting and plotting can be found in the Repository-joss branch. The name of the file is "GenerateRealDataPlot.R". Access to data can be requested at https://seer.cancer.gov/data/access.html.

  5. "In the manuscript, could you clarify when a user should opt for a penalized approach? Does it depend on the number of covariates, or the number of basis functions?" We have added a detailed paragraph on line 16 to clarify when a user should opt for a penalized approach.

  6. "Also, I haven't been able to install the package using the instructions in the manuscript. Here is the error message I got." The package is now published on CRAN. See line 105.

osorensen commented 9 months ago

👋 @adibender and @turgeonmaxime, could you please consider the author's response to you review issues, and update your checklists accordingly?

turgeonmaxime commented 9 months ago

@osorensen I'll update the checklist by the end of the week, hopefully over the next couple days

turgeonmaxime commented 9 months ago

@LingfengLuo0510 Thank you for addressing my previous comments. I especially appreciate the paragraph starting at line 116, it is really informative.

I had another look at the manuscript. I tried running the code line by line, but there are still some issues:

Finally, in the section "Availability", you wrote "Stable releases of the surtvep package will be made available via the Comprehensive R Archive Network." I think you can switch this to the present tense (i.e. "stable releases are available"), since it's now officially on CRAN!

turgeonmaxime commented 9 months ago

@osorensen I would appreciate your input for some of the points in the checklist:

Apart from that, and provided @LingfengLuo0510 addresses the remaining issues from my previous comment, I'm done with the review.

osorensen commented 9 months ago

Thanks for your review @turgeonmaxime. Here are my answers to your questions, which I hope can guide you on how to proceed further @LingfengLuo0510.

License file: It should by included. @LingfengLuo0510, please add a license file, and then also add the name of the license file to .Rbuildignore, so CRAN doesn't complain.

Testing: For R packages, there should be automated tests. @LingfengLuo0510, I suggest checking out the testthat package to get started. In addition to running on CRAN, the tests should also be part of an automated workflow in the GitHub repository, e.g., using GitHub Actions. You can read more on this in Wickham and Bryan's R packages book.

Contribution: This should be added.

osorensen commented 8 months ago

@LingfengLuo0510, I understand that addressing the review issues might take some time, but please keep us updated on the progress in this thread.

osorensen commented 8 months ago

@LingfengLuo0510, could you please respond here whether you're willing to complete the additional issues raised by the reviewers?

LingfengLuo0510 commented 8 months ago

@osorensen Thanks for asking. I am working on addressing the issues and will provide a detailed update within this week.

LingfengLuo0510 commented 8 months ago

@turgeonmaxime @adibender @osorensen Writing a comprehensive test takes longer than expected. We are still working on it.

We have added License file and Contribution Section. Thanks a lot!

LingfengLuo0510 commented 7 months ago

@turgeonmaxime @adibender @osorensen

In response to the review, we've incorporated testthat into our package and automated testing within our GitHub workflow. This ensures ongoing quality and facilitates future updates. We appreciate the feedback and are committed to continuous improvement. We will continue to update it in the future when adding new features. It is done for now for this paper review. Thanks a lot!

turgeonmaxime commented 7 months ago

@osorensen I've cloned the GH repo for the package and was able to run the tests successfully. With these last updates, I confirm that I've completed my review of this package/software note.

osorensen commented 7 months ago

Thanks @turgeonmaxime

osorensen commented 7 months ago

@adibender, could you please update your checklist based on the latest changes made by the authors?

adibender commented 7 months ago

@adibender, could you please update your checklist based on the latest changes made by the authors?

Hi, yes, will do sometime this week.

adibender commented 6 months ago

@adibender, could you please update your checklist based on the latest changes made by the authors?

Hi, yes, will do sometime this week.

Hi, I'm on it, but it'll take a little longer

osorensen commented 6 months ago

Thanks for the notice, @adibender

osorensen commented 6 months ago

@adibender, just a gentle reminder of this review. Thanks for all your efforts thus far.

osorensen commented 5 months ago

@adibender, could you please take a look at the revised package within the next week?

adibender commented 5 months ago

Hi @osorensen, sorry, the revision came at a bad time. Currently I'm on vacation and will be back on the 09th of April. Will do it until April 15th.

osorensen commented 5 months ago

Thanks for the response, @adibender. I'll set a reminder here in the issue.

osorensen commented 5 months ago

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osorensen commented 5 months ago

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