Contributions G4SNVHunter

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Repository: https://github.com/rongxinzh/G4SNVHunter

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Oct 28 '24 02:10 rongxinzh

Hi @rongxinzh

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: G4SNVHunter
Type: Package
Title: Evaluating SNV-Induced Disruption of G-Quadruplex Structures
Version: 0.99.0
Authors@R: 
    c(
        person("Rongxin", "Zhang", email = "[email protected]", 
        role = c("cre", "aut"),
        comment = c(ORCID = "0000-0002-1643-1185"))
    )
Description: 
    G-quadruplexes (G4s) are unique nucleic acid secondary structures 
    predominantly found in guanine-rich regions and have been shown to be 
    involved in various biological regulatory processes. G4SNVHunter is an R 
    package designed to rapidly identify genomic sequences with G4-forming 
    potential and accurately screen user-provided single nucleotide variants 
    (also applicable to single nucleotide polymorphisms) that may destabilize 
    these G4 structures. This enables users to select key variants for further 
    experimental study, investigating how these mutations may influence 
    biological functions, such as gene regulation, by altering G4 stability.
Encoding: UTF-8
LazyData: false
Depends: R (>= 4.3.0)
Imports:
    Biostrings,
    stats,
    GenomicRanges,
    IRanges,
    Rcpp,
    RcppRoll,
    data.table,
    GenomeInfoDb,
    S4Vectors,
    ggplot2,
    cowplot,
    progress,
    ggseqlogo,
    viridis,
    ggpointdensity
LinkingTo: Rcpp
RoxygenNote: 7.3.2
License: MIT + file LICENSE
Suggests:
    knitr,
    BiocStyle,
    rmarkdown,
    BiocManager,
    BSgenome.Hsapiens.UCSC.hg19,
    DT,
    rtracklayer,
    testthat (>= 3.0.0)
VignetteBuilder: knitr
biocViews: Epigenetics, SNP
News: NEWS.md
URL: https://github.com/rongxinzh/G4SNVHunter
BugReports: https://github.com/rongxinzh/G4SNVHunter/issues
Config/testthat/edition: 3

Oct 28 '24 02:10 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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Nov 22 '24 19:11 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.

On one or more platforms, the build results were: "ERROR". This may mean there is a problem with the package that you need to fix. Or it may mean that there is a problem with the build system itself.

Please see the build report for more details.

The following are build products from R CMD build on the Single Package Builder: Linux (Ubuntu 24.04.1 LTS): G4SNVHunter_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/G4SNVHunter to trigger a new build. A quick tutorial for setting up remotes and pushing to upstream can be found here.

Nov 22 '24 20:11 bioc-issue-bot

Received a valid push on git.bioconductor.org; starting a build for commit id: 1e5ce3c4910b5ffeac1e4c8dba3be9d7aeb3ae84

Nov 23 '24 07:11 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.

On one or more platforms, the build results were: "ERROR". This may mean there is a problem with the package that you need to fix. Or it may mean that there is a problem with the build system itself.

Please see the build report for more details.

The following are build products from R CMD build on the Single Package Builder: Linux (Ubuntu 24.04.1 LTS): G4SNVHunter_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/G4SNVHunter to trigger a new build. A quick tutorial for setting up remotes and pushing to upstream can be found here.

Nov 23 '24 07:11 bioc-issue-bot

Received a valid push on git.bioconductor.org; starting a build for commit id: c88cf825820d58a10abb3628d11f40940f5c0ada

Nov 23 '24 08:11 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 24.04.1 LTS): G4SNVHunter_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/G4SNVHunter to trigger a new build. A quick tutorial for setting up remotes and pushing to upstream can be found here.

Nov 23 '24 08:11 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.

Nov 27 '24 18:11 bioc-issue-bot

Overall, a very good submission and only a few minor changes are needed.

Don't ask the user to install optional packages one-by-one.

You should recommend that the user uses BiocManager::install("G4SNVHunter", dependencies = TRUE).

Section 5.3: Visualize G4Hunter Prediction Results has no biological interpretation of the output. Add a couple of sentences below the plot to help the reader interpret the results. For example, explain why panels B and D are bimodal.
Section 6: Evaluate SNV Effects. The schematic diagram is too small to read. Make it bigger.
For variables such as raw_score_threshold, specify their valid range. Can they be negative? Can they be more than 1?
For a particular package, use either import or importFrom. I see some duplication in the NAMESPACE file.

import(Biostrings)
importFrom(Biostrings,DNAString)
importFrom(Biostrings,DNAStringSet)
importFrom(Biostrings,replaceAt)

No input checking for strands. In function defintion, should be strands = c('b', 'p') and inside function should be strands <- match.arg(strands). See a tutorial.

Dec 04 '24 06:12 DarioS

Received a valid push on git.bioconductor.org; starting a build for commit id: e8722828fe75e0c1252e225be441016ec0f71df5

Dec 08 '24 12:12 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 24.04.1 LTS): G4SNVHunter_0.99.3.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/G4SNVHunter to trigger a new build. A quick tutorial for setting up remotes and pushing to upstream can be found here.

Dec 08 '24 12:12 bioc-issue-bot

Dear @DarioS, thank you very much for taking the time to review our package and providing the valuable comments.

We have reviewed all of your concerns one by one and addressed nearly all of them, except for the last one, as we already have input checking for strands.

Q: Don't ask the user to install optional packages one-by-one. A: Following your suggestion, we have revised this section, removed the part about manual package installation, and recommended users to install using the command BiocManager::install('G4SNVHunter', dependencies = TRUE). Please see section 2 and 3.

Q: Section 5.3: Visualize G4Hunter Prediction Results has no biological interpretation of the output. Add a couple of sentences below the plot to help the reader interpret the results. For example, explain why panels B and D are bimodal. A: We have added an explanation to interpret the biological significance of the figure. Please see section 5.3 for more details.

Q: Section 6: Evaluate SNV Effects. The schematic diagram is too small to read. Make it bigger. A: We have designed a new schematic diagram. It looks clearer and more user-friendly. Please see it in section 6 of the vignette.

Q: For variables such as raw_score_threshold, specify their valid range. Can they be negative? Can they be more than 1? A: We have provided a more stringent definition for the value ranges of the raw_score_threshold, mut_score_threshold, and score_diff_threshold parameters. We have added explanations in the vignette and also enforced these definitions in the code of the filterSNVImpact function.

Q: For a particular package, use either import or importFrom. I see some duplication in the NAMESPACE file. A: Have revised them. Thanks!

Q: No input checking for strands. In function defintion, should be strands = c('b', 'p') and inside function should be strands <- match.arg(strands). See a tutorial. A: We do have input checking for strands. We perform input validation for the strands parameter by calling the validateG4HunterParams function within G4HunterDetect.

Overall, your suggestions have been extremely effective, and we greatly appreciate your contribution as a volunteer to the R open-source community.

Please feel free to let me know if you have any further concerns.

Dec 08 '24 12:12 rongxinzh

All requests have been addressed.

Dec 09 '24 03:12 DarioS

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.

Dec 09 '24 03:12 bioc-issue-bot

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Dec 10 '24 18:12 lshep