Closed TuomasBorman closed 4 days ago
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
Just wanted to verify that you want this package to be considered a data experiment package and not a software package?
This package is related to MGnifyR that is also in Bioc submission https://github.com/Bioconductor/Contributions/issues/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?
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.
Please confirm before we advance farther
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
Could you please update your biocViews then to reflect this?
Updated
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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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
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A quick tutorial for setting up remotes and pushing to upstream can be found here.
Received a valid push on git.bioconductor.org; starting a build for commit id: e8efb0ea49b857f8e73ae56614e89490f9f777c9
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.
Received a valid push on git.bioconductor.org; starting a build for commit id: 1180abdf5c97ed06466e8555ebe4eae32689155c
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.
Received a valid push on git.bioconductor.org; starting a build for commit id: f03e5fec0147a6a3613b3e84debfe8deb59ffccb
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.
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."
A reviewer has been assigned to your package for an indepth review. Please respond accordingly to any further comments from the reviewer.
Received a valid push on git.bioconductor.org; starting a build for commit id: 08ddb3776ddb8f250b3edfa2cbbf4152391fb119
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.
Hello! Has this proceeded?
@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.
Best, Kayla
Received a valid push on git.bioconductor.org; starting a build for commit id: 737983440ce72b6b7af5d16c52c92f991c078a38
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_0.99.7.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.
[x] 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.
[x] SUGGESTION: Avoid redundant 'stop' and 'warn*' in signal conditions.
[x] SUGGESTION: Avoid 'suppressWarnings'/'*Messages' if possible.
[x] 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.
[ ] 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.
--> It seems that NEWS file is parsed correctly
[ ] REQUIRED: All code blocks, except for installation, should be executable and not use 'eval = FALSE'.
--> They are not evaluated because it will take long time to download the data. Instead of loading it from database, the data is already loaded and stored in inst/extdata.
--> They are in man folder because otherwise the figures cannot be included in the manual. (or at least it seems to be the easiest solution). https://ebi-metagenomics.github.io/HoloFoodR/
@TuomasBorman - Thank you for making the necessary changes. My apologies for the NEWS file requirement, you are correct it is formatted properly. Your rational for eval = FALSE in vignette is acceptable. If the figures won't render in the manual than you may move the figures back to the man directory. I am more than happy to accept the package.
Best, Kayla
Your package has been accepted. It will be added to the Bioconductor nightly builds.
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