BREW3R.r

[lldelisle]

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[bioc-issue-bot]

Hi @lldelisle

Thanks for submitting your package. We are taking a quick look at it and you will hear back from us soon.

The DESCRIPTION file for this package is:

Package: BREW3R.r
Type: Package
Title: R package associated to BREW3R
Version: 0.99.0
Authors@R: 
    person(given = "Lucille",
 family = "Lopez-Delisle",
 role = c("aut", "cre"),
 email = "[email protected]",
 comment = c(ORCID = "0000-0002-1964-4960"))
Description: This R package provide functions that are used in the BREW3R
    workflow. This mainly contains a function that extend a gtf as GRanges using
    information from another gtf (also as GRanges). The process allows to extend
    gene annotation without increasing the overlap between gene ids.
License: GPL-3
Encoding: UTF-8
LazyData: false
RoxygenNote: 7.3.1
Imports:
    dplyr,
    GenomicRanges,
    methods,
    S4Vectors,
    tidyselect,
    utils
Suggests: 
    testthat (>= 3.0.0),
    IRanges,
    knitr,
    rmarkdown,
    BiocStyle,
    rtracklayer
biocViews:
    GenomeAnnotation
Config/testthat/edition: 3
URL: https://github.com/lldelisle/BREW3R.r
BugReports: https://github.com/lldelisle/BREW3R.r/issues/
VignetteBuilder: knitr

[bioc-issue-bot]

Your package has been added to git.bioconductor.org to continue the pre-review process. A build report will be posted shortly. Please fix any ERROR and WARNING in the build report before a reviewer is assigned or provide a justification on why you feel the ERROR or WARNING should be granted an exception.

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[bioc-issue-bot]

Dear Package contributor,

This is the automated single package builder at bioconductor.org.

Your package has been built on the Bioconductor Single Package Builder.

Congratulations! The package built without errors or warnings on all platforms.

Please see the build report for more details.

The following are build products from R CMD build on the Single Package Builder: Linux (Ubuntu 22.04.3 LTS): BREW3R.r_0.99.0.tar.gz

Links above active for 21 days.

Remember: if you submitted your package after July 7th, 2020, when making changes to your repository push to [email protected]:packages/BREW3R.r to trigger a new build. A quick tutorial for setting up remotes and pushing to upstream can be found here.

[bioc-issue-bot]

A reviewer has been assigned to your package for an indepth review. Please respond accordingly to any further comments from the reviewer.

[LiNk-NY]

Hi @lldelisle

Thank you for your submission. Please see the review below.

Best regards, Marcel

---

BREW3R.r

• Overall, the package looks good. It looks like the range operations rely heavily on the tidyverse which is not really designed for that in mind. Consider using methods in GenomicRanges that may help the code be more robust.

DESCRIPTION

• Looks good.

NAMESPACE

• Minor: Consider using the native pipe over dplyr::'%>%'.

vignettes

• Keep the text at a max 80 character width. IMO, it is easier to review and maintain.
• Avoid mentioning devtools in the vignette. Simply use BiocManager with a username/repo character input.
• Consider adding mustWork = TRUE argument to system.file calls
• Consider providing a verbose = FALSE default to the extend_granges function. Prioritize informative text and remove text e.g., "Extend last exons.", "Extending them.", etc.
• Load GenomicRanges in the vignette and avoid using GenomicRanges:: qualifiers.
• Use runValue on the Rle to extract the character strand value, e.g., runValue(strand(gene_after[1])) and add one to the output i.e., (x == "+") + 1 instead of using if ... else (seen in plotting chunks).

R

• Consider using @importFrom GenomicRanges ... to import functions such as strand, start()<-, etc.
• Consider reducing the cyclomatic complexity of the extend_granges function currently it is at a value of 16: cyclocomp::cyclocomp(extend_granges)
• Have you considered using intra-range methods from GenomicRanges, e.g., flank, resize, shift etc. It seems like those could be useful and robust operations.

tests

Coverage looks good:

covr::package_coverage()
BREW3R.r Coverage: 89.71%
R/extend_granges.R: 76.29%
R/helpers.R: 92.23%

[lldelisle]

Thank you very much for your review. I have started to adress your points in https://github.com/lldelisle/BREW3R.r/pull/1

• For the verbose, I decided to include 3 levels of verbose with default set to 1 with only stats. The problem is that with large gtf the function can be very long, it can be useful to have messages that indicates the progression.
• The cyclomatic complexity seems to be directly linked to the optional messages that display progression. I would prefer to keep these, is it ok for you?

I am trying to strongly reduce the usage of tidyverse in favor of resize etc... but this needs a lot of rethinking.

[LiNk-NY]

Hi Lucille, @lldelisle

Please consider this resource for working with verbosity: https://ropensci.org/blog/2024/02/06/verbosity-control-packages/ Usually, a package-wide option (along with a wrapper function provided by e.g., rlang, cli, futile.logger, etc.) is preferred and as a side-effect, it will cut down on the number of conditional statements.

-Marcel

[lldelisle]

Hi @LiNk-NY , Thank you very much for the tip. I have included this, see https://github.com/lldelisle/BREW3R.r/pull/1/commits/661e9bc002fcd6abf5b3e4cdf08e4b3b47a5d425 So I converted my verbose = 1 to rlang::inform, my verbose = 2 to a new function progression_msg and debug to debug_msg. But this did not decreased the cyclomatic complexity as my function progression_msg has a conditional statement inside...

Except from that my PR contains a new version which do not use dplyr anymore. Do you want to review my PR or should I merge it and then you review?

[LiNk-NY]

But this did not decreased the cyclomatic complexity as my function progression_msg has a conditional statement inside...

Hi Lucille, @lldelisle Thank you for making those changes. The improvement can be seen via:

> cyclocomp::cyclocomp(expr=BREW3R.r::extend_granges)
[1] 4

It looks good!

Please merge first and I can follow up with the review.

-Marcel

[lldelisle]

I have merged.

[LiNk-NY]

Hi Lucille, @lldelisle Have you pushed your changes to git.bioconductor.org? Best, Marcel

[LiNk-NY]

Please make sure that the global variables are accounted for. See the NOTE:

* checking R code for possible problems ... NOTE
add_new_exons: no visible binding for global variable ‘transcript_id’
add_new_exons: no visible binding for global variable ‘start’
add_new_exons: no visible binding for global variable
  ‘three_prime_query’
add_new_exons: no visible binding for global variable ‘end’
add_new_exons: no visible binding for global variable ‘exon_number’
adjust_for_collision: no visible binding for global variable
  ‘old_width’
adjust_for_collision: no visible binding for global variable ‘width’
extend_granges: no visible binding for global variable ‘type’
extend_granges: no visible binding for global variable ‘id’
extend_using_overlap: no visible binding for global variable ‘type’
extract_last_exon: no visible binding for global variable ‘type’
filter_new_exons: no visible binding for global variable
  ‘collision_base’
filter_new_exons: no visible binding for global variable ‘start’
filter_new_exons: no visible binding for global variable ‘end’
overlap_different_genes: no visible binding for global variable
  ‘query_gene_id’
overlap_different_genes: no visible binding for global variable
  ‘subject_gene_id’
Undefined global functions or variables:
  collision_base end exon_number id old_width query_gene_id start
  subject_gene_id three_prime_query transcript_id type width
Consider adding
  importFrom("stats", "end", "start")

You can use with() inside of a subset function to avoid the NOTE e.g.,

subset(mtcars, with(mtcars, mpg > 20))

• There are some typos in the argument names. See groupping_variable in the ~extend_last_exon~ extract_last_exon function.

All else looks good. Please bump the version and push to git.bioconductor.org for another build and check. Thanks, -Marcel

[bioc-issue-bot]

Received a valid push on git.bioconductor.org; starting a build for commit id: badb8c774bcd5dbb8b300fb1e42469922fc58484

[bioc-issue-bot]

Dear Package contributor,

This is the automated single package builder at bioconductor.org.

Your package has been built on the Bioconductor Single Package Builder.

Congratulations! The package built without errors or warnings on all platforms.

Please see the build report for more details.

The following are build products from R CMD build on the Single Package Builder: Linux (Ubuntu 22.04.3 LTS): BREW3R.r_0.99.1.tar.gz

Links above active for 21 days.

Remember: if you submitted your package after July 7th, 2020, when making changes to your repository push to [email protected]:packages/BREW3R.r to trigger a new build. A quick tutorial for setting up remotes and pushing to upstream can be found here.

[lldelisle]

Indeed they are all within a subset... Thanks for the typo, I will fix them tomorrow. groupping should be grouping, right? And extend last exon? should be exons?

[LiNk-NY]

groupping should be grouping, right?

Yes

And extend last exon? should be exons?

Sorry, I meant to type extract_last_exon as the name of the function where groupping_variable is an argument. But it does seem like the function should also be plural as the documentation title suggests.

[bioc-issue-bot]

Received a valid push on git.bioconductor.org; starting a build for commit id: df61bd6ed11ea3100a7589a0210c369c6a986bd9

[bioc-issue-bot]

Dear Package contributor,

This is the automated single package builder at bioconductor.org.

Your package has been built on the Bioconductor Single Package Builder.

Congratulations! The package built without errors or warnings on all platforms.

Please see the build report for more details.

The following are build products from R CMD build on the Single Package Builder: Linux (Ubuntu 22.04.3 LTS): BREW3R.r_0.99.2.tar.gz

Links above active for 21 days.

Remember: if you submitted your package after July 7th, 2020, when making changes to your repository push to [email protected]:packages/BREW3R.r to trigger a new build. A quick tutorial for setting up remotes and pushing to upstream can be found here.

[lldelisle]

Hi @LiNk-NY , I fixed the 2 typos and used with in the subset to avoid the NOTE about the undefined variables. Are you happy with my changes. Or do I need to change something else? Thanks

[LiNk-NY]

Hi @lldelisle , Thank you for making those changes. The package has been accepted. Best regards, Marcel

[bioc-issue-bot]

Your package has been accepted. It will be added to the Bioconductor nightly builds.

Thank you for contributing to Bioconductor!

Reviewers for Bioconductor packages are volunteers from the Bioconductor community. If you are interested in becoming a Bioconductor package reviewer, please see Reviewers Expectations.

[lldelisle]

Thanks

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