mrbakhsh commented 1 year ago

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mrbakhsh commented 1 year ago

Hi @lshep. Yes, of course. I've already implemented all the necessary changes and plan to submit the updates by the end of this week.

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The following are build products from R CMD build on the Single Package Builder: macOS 12.7.1 Monterey: DeProViR_0.99.19.tar.gz Linux (Ubuntu 22.04.2 LTS): DeProViR_0.99.19.tar.gz

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mrbakhsh commented 1 year ago

Hi @hpages, I have pushed the following updates. Thank you!

R code

[X] Please consistently use camelCase style when naming your functions Answer:

[1] "encodeHostSeq"             "encodeViralSeq"           
[3] "gloveImport"                  "loadPreTrainedModel"      
[5] "loadTrainingSet"            "performancePlots"
[7] "modelTraining"               "predInteractions"

[X] The man page for one of the 2 main functions in the package (ModelTraining()) has no example, and the code chunk in the vignette where the function is used is not evaluated. Answer: I have included eval=TRUE for the modelTraining() function in the vignette to enable the evaluation of the code chunk in the vignette.

Man page

[X] Use <- consistently everywhere for assignment. Answer:


pred_label <- seq(0,1, length.out = 100)
truth_label <- rep(c(0,1), each = 50)
perf <- performancePlots(pred_label,
                     truth_label,
                     tpath = tempdir())



- [X] Use proper indentation for multiple-line expressions, to make the code easier to read.
**Answer:** I have modified the examples in the man page to include correct indentation.

- [X] Either move the details to the Details section and keep the Description section short, or remove the Details section
**Answer:** I removed the @details section from the man page.

mrbakhsh commented 11 months ago

Hi @hpages, I pushed the requested changes last month and would appreciate your feedback. Thank you, and I am looking forward to hearing from you.

lshep commented 11 months ago

I'm very sorry for the delay; it should not be taking this long. I will check in with @hpages if he plans to revisit this review soon or reassign the reviewer if necessary

mrbakhsh commented 11 months ago

Hi @lshep, thanks a lot for your help and for the follow-up.

hpages commented 11 months ago

Hi @mrbakhsh, sorry for the delay. I'll take another look at the package in the next couple of days. Thanks for your patience.

mrbakhsh commented 10 months ago

Hi @hpages, sure, that would be great. Thank you

hpages commented 10 months ago

Hi @mrbakhsh,

Thanks for all the changes and improvements and sorry again for the delay. Package looks good and is almost ready for acceptance. Note that you still have a few places where the code is not properly indented, e.g. here:

testing_set <- data.table::fread(
system.file("extdata", "test_Set", "test_set_unknownInteraction.csv",
package = "DeProViR"))

As mentioned before, this makes your code unnecessarily hard to read.

Please make sure to format/indent all your code properly.

Thanks again, H.

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hpages commented 10 months ago

@mrbakhsh I get clean R CMD check and BiocCheck() results on my Linux laptop (Ubuntu 23.10) so I'm not sure what's happening with the SPB. Can you bump the version one more time? I know you already bumped twice in the last couple of days, sorry for that. Hopefully third time's the charm... :crossed_fingers: Thanks!

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hpages commented 10 months ago

Thank you. So at least now the package is all green on nebbiolo1. I'm investigating the vignette error on merida1. I'll let you know what I find.

matineh-procogia commented 10 months ago

@hpages Thanks much for following up. There was a small issue with my author list names in the description, but after fixing that, I'm not encountering any errors in my Mac environment using R cmd build or R cmd check.

hpages commented 10 months ago

I can't reproduce the vignette error on merida1. Let's ignore it.

This has not changed:

testing_set <- data.table::fread(
system.file("extdata", "test_Set", "test_set_unknownInteraction.csv",
package = "DeProViR"))

Still not properly indented/formatted! :confused:

Again please check all your code and make sure it is properly indented/formatted.

Note that things like this are not properly indented/formatted either:

embeddings_index <-
gloveImport(url_path = "https://nlp.stanford.edu/data")

Finally: any reason why gloveImport() reprocess the cached file each time it's called? This processing is expensive and takes a significant amount of time. Why not process glove.6B.zip once for all and cache the result instead (the result is an environment that you can save to disk with saveRDS()).

Thanks, H.

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mrbakhsh commented 9 months ago

Hi @hpages, apologies for the delay. I have already fixed the indentation in the man files. Thank you.

hpages commented 9 months ago

Thanks for formatting the code. That makes it a lot easier to read and understand.

The package is good to go. Hopefully you will consider revisiting the caching approach in gloveImport() at some point (see my previous comment about this). It is not great software design to recompute the same thing over and over again, especially when this computation is expensive.

Thanks for your contribution to Bioconductor.

Best, H.

bioc-issue-bot commented 9 months ago

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lshep commented 9 months ago

The default branch of your GitHub repository has been added to Bioconductor's git repository as branch devel.

To use the git.bioconductor.org repository, we need an 'ssh' key to associate with your github user name. If your GitHub account already has ssh public keys (https://github.com/mrbakhsh.keys is not empty), then no further steps are required. Otherwise, do the following:

See further instructions at

https://bioconductor.org/developers/how-to/git/

for working with this repository. See especially

https://bioconductor.org/developers/how-to/git/new-package-workflow/ https://bioconductor.org/developers/how-to/git/sync-existing-repositories/

to keep your GitHub and Bioconductor repositories in sync.

Your package will be included in the next nigthly 'devel' build (check-out from git at about 6 pm Eastern; build completion around 2pm Eastern the next day) at

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(Builds sometimes fail, so ensure that the date stamps on the main landing page are consistent with the addition of your package). Once the package builds successfully, you package will be available for download in the 'Devel' version of Bioconductor using BiocManager::install("DeProViR"). The package 'landing page' will be created at

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Bioconductor / Contributions

DeProViR #3148

R code

Man page