HoloFoodR

[TuomasBorman]

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• Repository: https://github.com/EBI-Metagenomics/HoloFoodR

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[bioc-issue-bot]

Hi @TuomasBorman

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: HoloFoodR
Type: Package
Version: 0.99.0
Authors@R:
    c(person(given = "Tuomas", family = "Borman", role = c("aut", "cre"),
   email = "tuomas.v.borman@utu.fi",
   comment = c(ORCID = "0000-0002-8563-8884")),
      person(given = "Leo", family = "Lahti", role = c("aut"),
   email = "leo.lahti@iki.fi",
   comment = c(ORCID = "0000-0001-5537-637X")))
Title: R interface to EBI HoloFood resource
Description:
    Utility package to facilitate integration and analysis of EBI HoloFood data
    in R. This package streamlines access to the resource, allowing for direct
    loading of data into formats optimized for downstream analytics.
biocViews: PackageTypeData, ExperimentData
License: Artistic-2.0 | file LICENSE
Encoding: UTF-8
Depends:
    R(>= 4.4.0),
    TreeSummarizedExperiment,
    MultiAssayExperiment
Imports:
    dplyr,
    httr2,
    jsonlite,
    S4Vectors,
    stats,
    utils
Suggests:
    testthat,
    knitr,
    rmarkdown,
    BiocStyle
URL: https://github.com/EBI-Metagenomics/HoloFoodR
BugReports: https://github.com/EBI-Metagenomics/HoloFoodR/issues
VignetteBuilder: knitr
RoxygenNote: 7.3.0

[lshep]

Just wanted to verify that you want this package to be considered a data experiment package and not a software package?

[TuomasBorman]

This package is related to MGnifyR that is also in Bioc submission #3191 . They should be in same place.

These packages provide linkage between Bioconductor and APIs. They can only search and fetch data. Based on Bioconductor guidelines, software packages can provide access to resources. It also seems that the structure of ExperimentData packages are different: they contain ready datasets stored in ExperimentHub.

Classified as "data package" would be natural (also because the package might be easier to find from there), but I guess this is still "sofware package" based on Bioc guidelines?

[lshep]

Yes in what we have done in the past we would consider it more a software package but it can be listed however you like. If you feel data experiment is a better classification that is fine. Just wanted to check before we add as once it is accepted it will be harder for us to alter.

[lshep]

Please confirm before we advance farther

[TuomasBorman]

Yes, sorry for delay. We had to discuss about this. It seems that all other packages that create R interface to some database are categorized as software. So it is best to follow this convention (and Bioconductor guide).

--> we want to classify HoloFoodR and MGnifyR as software packages

[lshep]

Could you please update your biocViews then to reflect this?

[TuomasBorman]

Updated

[bioc-issue-bot]

Your package has been added to git.bioconductor.org to continue the
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fix any ERROR and WARNING in the build report before a reviewer is
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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: "skipped, 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:
ERROR before build products produced.

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/HoloFoodR to trigger a new build.
A quick tutorial for setting up remotes and pushing to upstream can be found here.

[bioc-issue-bot]

Received a valid push on git.bioconductor.org; starting a build for commit id: e8efb0ea49b857f8e73ae56614e89490f9f777c9

[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 22.04.3 LTS): HoloFoodR_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
git@git.bioconductor.org:packages/HoloFoodR to trigger a new build.
A quick tutorial for setting up remotes and pushing to upstream can be found here.

[bioc-issue-bot]

Received a valid push on git.bioconductor.org; starting a build for commit id: 1180abdf5c97ed06466e8555ebe4eae32689155c

[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 22.04.3 LTS): HoloFoodR_0.99.4.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/HoloFoodR to trigger a new build.
A quick tutorial for setting up remotes and pushing to upstream can be found here.

[bioc-issue-bot]

Received a valid push on git.bioconductor.org; starting a build for commit id: f03e5fec0147a6a3613b3e84debfe8deb59ffccb

[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): HoloFoodR_0.99.5.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/HoloFoodR to trigger a new build.
A quick tutorial for setting up remotes and pushing to upstream can be found here.

[TuomasBorman]

To note:

Examples on getMetaboLights are commented out. The connection fails sometimes which causes build to fail. If I add \dontrun, the build also fails --> "At least 80% of man pages documenting exported objects must have runnable examples."

[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.

[bioc-issue-bot]

Received a valid push on git.bioconductor.org; starting a build for commit id: 08ddb3776ddb8f250b3edfa2cbbf4152391fb119

[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): HoloFoodR_0.99.6.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/HoloFoodR to trigger a new build.
A quick tutorial for setting up remotes and pushing to upstream can be found here.

[TuomasBorman]

Hello! Has this proceeded?

[Kayla-Morrell]

@TuomasBorman - Thank you for submitting to Bioconductor. Please see the initial review of
the package below. The required changes must be made while the suggested
changes do not have to be (though we strongly encourage them). Comment back
here with updates that have been made and when the package is ready for a
re-review.

DESCRIPTION

• SUGGESTION: The Description field in the DESCRIPTION is made up by less than 3 sentences. Please consider expanding this field and structure it as a full paragraph.

NEWS

• REQUIRED: It's good practice to include a NEWS file. However, it doesn't seem to be formatted properly. Please see our documentation for proper formatting of news files - https://contributions.bioconductor.org/news.html.

Data

• REQUIRED: Data included in the 'inst/extdata/' directory needs corresponding documentation. This documentation should be in an 'inst/script/' directory. The scripts in this directory can vary but most importantly they should clearly state how the data was generated and include source information. There should be source URLs and any key information regarding filtering or processing. It can be executable code, sudo code, or a text description. Users should be able to download and roughly reproduce the file or object that is present as data.

Vigenttes

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Man pages

• REQUIRED: Only man pages belong in the 'man/' directory. If the figures are needed they should be moved to an 'inst/figures/' directory and paths should be changed to reflect this.

R code

• SUGGESTION: Avoid redundant 'stop' and 'warn*' in signal conditions.
• SUGGESTION: Avoid 'suppressWarnings'/'*Messages' if possible.

Best,
Kayla