AlphaMissenseR

[mtmorgan]

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[bioc-issue-bot]

Hi @mtmorgan

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: AlphaMissenseR
Title: Accessing AlphaMissense Data Resources in R
Version: 0.99.6
Authors@R: 
    c(person(
        "Martin", "Morgan", role = c("aut", "cre"),
        email = "mtmorgan.bioc@gmail.com",
        comment = c(ORCID = "0000-0002-5874-8148")
    ), person(
        "Chan Zuckerberg Initiative DAF CZF2019-002443",
        role = "fnd"
    ), person(
        "NIH NCI ITCR U24CA180996",
        role = "fnd"
    ))
Description:
    The AlphaMissense publication
    <https://www.science.org/doi/epdf/10.1126/science.adg7492>
    outlines how a variant of AlphaFold / DeepMind was used to predict
    missense variant pathogenicity. Supporting data on Zenodo
    <https://zenodo.org/record/8360242> include, for instance, 71M
    variants across hg19 and hg38 genome builds. The 'AlphaMissense'
    package allows ready access to the data, downloading individual
    files to DuckDB databases for exploration and integration into *R*
    and *Bioconductor* workflows.
License: Artistic-2.0
URL: https://mtmorgan.github.io/AlphaMissenseR/
BugReports: https://github.com/mtmorgan/AlphaMissenseR/issues
Depends:
    dplyr
Imports:
    rjsoncons, jsonlite, DBI, duckdb (>= 0.9.1), rlang,
    curl, BiocFileCache, spdl, memoise, utils,
    whisker
Suggests:
    BiocManager,
    BiocGenerics,
    GenomicRanges,
    GenomeInfoDb,
    AnnotationHub,
    ensembldb,
    methods,
    tidyr,
    knitr,
    rmarkdown,
    testthat (>= 3.0.0)
biocViews: SNP, Annotation, FunctionalGenomics, StructuralPrediction,
    Transcriptomics, VariantAnnotation
Encoding: UTF-8
Roxygen: list(markdown = TRUE)
RoxygenNote: 7.2.3
VignetteBuilder: knitr
Config/testthat/edition: 3

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

Your package has been built on the Bioconductor Build System.

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Or it may mean that there is a problem with the build system itself.

Please see the build report for more details.

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Links above active for 21 days.

Remember: if you submitted your package after July 7th, 2020,
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A quick tutorial for setting up remotes and pushing to upstream can be found here.

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A quick tutorial for setting up remotes and pushing to upstream can be found here.

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Your package has been built on the Bioconductor Build System.

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This may mean there is a problem with the package that you need to fix.
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ERROR before build products produced.

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Remember: if you submitted your package after July 7th, 2020,
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A quick tutorial for setting up remotes and pushing to upstream can be found here.

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A quick tutorial for setting up remotes and pushing to upstream can be found here.

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[LiNk-NY]

Hi Martin, @mtmorgan

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

Best regards,
Marcel

---

AlphaMissenseR #3221

DESCRIPTION && NAMESPACE

• Looks good.

vignettes

• Should sql_template be exported or should the template be copied and
  pasted into the vignette? It is good to avoid using ::: in the vignette.
• Would it make sense to provide a clear_cache wrapper function for
  removing resources that can be identified as incompatible with newer versions
  of DuckDb? It may not be necessary if new users of the package are
  already on newer versions of DuckDb.
• Minor: It would be good to have the file size info shown when downloading.

R

• Consider using BiocBaseUtils for type checking of arguments.
• Looks good.

tests

Consider increasing coverage for some files. Overall, they look good.

> covr::package_coverage()
AlphaMissenseR Coverage: 44.08%
R/AlphaFold.R: 0.00%
R/alphamissense_connection.R: 0.00%
R/am_aa.R: 0.00%
R/zzz.R: 0.00%
R/AlphaMissense.R: 57.69%
R/GenomicRanges.R: 72.22%
R/template.R: 85.71%
R/db.R: 91.58%
R/utilities.R: 91.67%

[bioc-issue-bot]

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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 Build System.

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 Bioconductor Build
System:
Linux (Ubuntu 22.04.2 LTS): AlphaMissenseR_0.99.15.tar.gz
macOS 12.6.5 Monterey: AlphaMissenseR_0.99.15.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
git@git.bioconductor.org:packages/AlphaMissenseR to trigger a new build.
A quick tutorial for setting up remotes and pushing to upstream can be found here.

[mtmorgan]

Thanks Marcel @LiNk-NY

vignettes

• Should sql_template be exported or should the template be copied and
  pasted into the vignette? It is good to avoid using ::: in the vignette.

I include the template directly

• Would it make sense to provide a clear_cache wrapper function for
  removing resources that can be identified as incompatible with newer versions
  of DuckDb? It may not be necessary if new users of the package are
  already on newer versions of DuckDb.

This is really an exceptional situation for very early adopters. The package requires a current version of DuckDB, so it will not create 'old' tables. There's a chance that the finalized DuckDb will change formats (there's only one release left for finalization, according to their plan...) but it's not known what changes will be required then.

• Minor: It would be good to have the file size info shown when downloading.

Done, e.g.,

* [21:56:17][info] retrieving file name 'AlphaMissense_hg38.tsv.gz' (613.2 Mb)

R

• Consider using BiocBaseUtils for type checking of arguments.

Done

tests

Consider increasing coverage for some files. Overall, they look good.

> covr::package_coverage()
AlphaMissenseR Coverage: 44.08%
R/AlphaFold.R: 0.00%
R/alphamissense_connection.R: 0.00%
R/am_aa.R: 0.00%
R/zzz.R: 0.00%
R/AlphaMissense.R: 57.69%
R/GenomicRanges.R: 72.22%
R/template.R: 85.71%
R/db.R: 91.58%
R/utilities.R: 91.67%

I increased test coverage, thanks. Currently

> covr::package_coverage()
AlphaMissenseR Coverage: 65.43%
R/zzz.R: 0.00%
R/AlphaFold.R: 29.73%
R/AlphaMissense.R: 55.56%
R/GenomicRanges.R: 72.22%
R/db.R: 92.63%
R/alphamissense_connection.R: 100.00%
R/am_aa.R: 100.00%
R/template.R: 100.00%
R/utilities.R: 100.00%

R/zzz.R is .onLoad(), so difficult to test directly, but test-zzz.R does make sure that all side effects of .onLoad() are realized (e.g., 'memoizing' key functions).

R/AlphaFold.R is somehow suspect -- there was 30% coverage before I added another test that I expected to result in much higher coverage, but covr reported a decrease...

Examples and vignettes cover more of the package.

Please let me know if there are more changes you would like made.

[LiNk-NY]

Hi Martin, @mtmorgan
Thank you for making those changes.

Coverage looks great:

> covr::package_coverage(type="all")


AlphaMissenseR Coverage: 87.01%
R/zzz.R: 0.00%
R/AlphaMissense.R: 72.22%
R/GenomicRanges.R: 72.22%
R/db.R: 92.63%
R/AlphaFold.R: 97.30%
R/alphamissense_connection.R: 100.00%
R/am_aa.R: 100.00%
R/template.R: 100.00%
R/utilities.R: 100.00%

Your package has been accepted.
Thank you for your contributions!

Best,
Marcel

[bioc-issue-bot]

Your package has been accepted. It will be added to the
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[mtmorgan]

Thanks Marcel for your review and help with this package.

[bioc-issue-bot]

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