TaxSEA

[feargalr]

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[bioc-issue-bot]

Hi @feargalr

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: TaxSEA
Type: Package
Title: Taxon Set Enrichment Analysis
Version: 0.99.0
Authors@R: c(person("Feargal", "Ryan", 
    email = "[email protected]", 
    role = c("aut", "cre"),comment = c(ORCID = "0000-0002-1565-4598")))
Description: TaxSEA is an R package for Taxon Set Enrichment Analysis, which 
    utilises a Kolmogorov-Smirnov test analyses to 
    investigate differential abundance analysis output for whether there
    are alternations in a-priori defined sets of taxa from five previously 
    published databases (BugSigDB, MiMeDB, GutMGene, mBodyMap and GMRepoV2). 
    TaxSEA takes as input a list of taxonomic identifiers (e.g. species names, 
    NCBI IDs etc.) and a rank (E.g. fold change, correlation coefficient). 
    TaxSEA be applied to any microbiota taxonomic profiling technology 
    (array-based, 16S rRNA gene sequencing, shotgun metagenomics & 
    metatranscriptomics etc.) and enables researchers to rapidly contextualize 
    their findings within the broader literature to accelerate interpretation 
    of results.
License: GPL-3
Encoding: UTF-8
LazyData: false
VignetteBuilder: knitr
RoxygenNote: 7.2.3
biocViews: Microbiome, Metagenomics, Sequencing, GeneSetEnrichment, RNASeq
URL: https://github.com/feargalr/taxsea
BugReports: https://github.com/feargalr/taxsea/issues
Suggests:
    knitr,
    rmarkdown
Imports:
    ggplot2,
    stats,
    utils

[lshep]

Please get rid of the empty export in the namespace

Plesae change the name of the vignette file to something more meaningful than
my-vignette generic names are not recommended to avoid load conflicts. We
recommend the name of the package TaxSEA.Rmd.

[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 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): TaxSEA_0.99.0.tar.gz

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[bioc-issue-bot]

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Please respond accordingly to any further comments from the reviewer.

[feargalr]

Thanks BioC team. A query about one of the warnings. This package is designed to complement several existing BioC packages (e.g. bugsigdbr, ANCOMBC etc.) but it doesn't depend on them as it has other standalone functionality too. However, I get a warning in the check. I wanted to ask how you'd like me to handle that? I could list a package as a dependency, although as an enhance might be more accurate? Thanks!

"WARNING: No Bioconductor dependencies detected. Note that some infrastructure
packages may not have Bioconductor dependencies. For more information, reach
out to the Bioconductor community and/or consider a CRAN submission."