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scaeData #3338

Closed ahmadalajami closed 3 months ago

ahmadalajami commented 3 months ago

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bioc-issue-bot commented 3 months ago

Hi @ahmadalajami

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: scaeData
Type: Package
Title: Data Package for SingleCellAlleleExperiment
Version: 0.99.0
Date: 2024-15-01
Authors@R: 
    c(
    person(given = "Ahmad", family = "Al Ajami", email = "alajami@med.uni-frankfurt.de", role = c("aut", "cre"),
 comment = c(ORCID = "0009-0006-5615-7447")),
    person(given = "Jonas", family = "Schuck", email = "schuck@med.uni-frankfurt.de", role = c("aut"),
 comment = c(ORCID = "0009-0003-5705-4579")),
    person(given = "Federico", family = "Marini", email = "marinif@uni-mainz.de", role = c("aut"),
 comment = c(ORCID = "0000-0003-3252-7758")),
    person(given = "Katharina", family = "Imkeller", email = "imkeller@med.uni-frankfurt.de", role = c("aut"),
 comment = c(ORCID = "0000-0002-5177-0852"))
    )
Description: Contains default datasets used by the Bioconductor package SingleCellAlleleExperiment.
    The raw FASTQ files were sourced from publicly accessible datasets provided by 10x Genomics.
    Subsequently, our scIGD snakemake workflow was employed to process these FASTQ files.
    The resulting output from scIGD constitutes to the contents of this data package.
Depends: R (>= 4.3.0)
Imports: ExperimentHub
Suggests: knitr,
rmarkdown,
markdown,
BiocStyle
biocViews: ExperimentHub, ExperimentData, Homo_sapiens_Data, SingleCellData
License: MIT + file LICENSE
VignetteBuilder: knitr
Encoding: UTF-8
Roxygen: list(markdown = TRUE)
RoxygenNote: 7.3.1
URL: https://github.com/AGImkeller/scaeData
BugReports: https://github.com/AGImkeller/scIGD/issues
ahmadalajami commented 3 months ago

@federicomarini @agimkeller @jonas-schuck

bioc-issue-bot commented 3 months ago

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.

IMPORTANT: Please read this documentation for setting up remotes to push to git.bioconductor.org. All changes should be pushed to git.bioconductor.org moving forward. It is required to push a version bump to git.bioconductor.org to trigger a new build report.

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bioc-issue-bot commented 3 months ago

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

bioc-issue-bot commented 3 months ago

Received a valid push on git.bioconductor.org; starting a build for commit id: 30f96643bd78186a66251a61cd92b59a964a8018

bioc-issue-bot commented 3 months ago

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

bioc-issue-bot commented 3 months ago

Received a valid push on git.bioconductor.org; starting a build for commit id: 2568626f4a45884139d22d2a72129771ea8bbc69

bioc-issue-bot commented 3 months ago

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

bioc-issue-bot commented 3 months ago

A reviewer has been assigned to your package for an indepth review. Please respond accordingly to any further comments from the reviewer.

lshep commented 3 months ago

vignette

pbmc_20k

perhaps it would be best to only execute the pbmc_20k that you use for examples and show but not execute (eval=FALSE) the other sets? Let users download the sets they would like?

- [ ] You don't need to reference github to download the lookup tables that are provided in `inst/extdata`.  You can retrieve those interactively in R through a system.file command combined with read.csv. Something similar to 

lookup = read.csv(system.file("extdata", "pbmc_20k_lookup_table.csv", package="scaeData"))



- [ ] Why is the last section where you run read_allele_counts in an `eval=FALSE` ?  This should be executed.  I see it depends on SingleCellAlleleExperiment -- since these were not submitted as related packages, we can assume it will be accepted and I can test locally / you can ignore the error that will occur that the package cannot be found. 

**man**
- [ ] Please provide a package level man page so when a naive user does `?scaeData` something is displayed. 
federicomarini commented 3 months ago

Thanks for the review comments @lshep !

We will be starting right away to work on them on a specific bioc_review branch!

One clarification about the unevaluated chunk in the vignette (with read_allele_counts) - We thought that having the function from SingleCellAlleleExperiment in there (and run, i.e. including that as Suggests) would introduce a circular dependency, which we wanted to explicitly avoid. I wanted to apologize for not seeing this one earlier - https://github.com/Bioconductor/Contributions/blob/devel/CONTRIBUTING.md#circular-dependencies.
This seems exactly like our case, so we should (here) Suggest SingleCellAlleleExperiment and there Depend on scaeData?

lshep commented 3 months ago

If this example will be run in the SingleCellAlleleExperiment we can let it go if you want to avoid the dependency. But yes Suggest seems appropriate here since its used in the vignette but the data isn't dependent on a defined class in the Software package; The SingleCellAlleleExperiment will depend on where and how you use the data to define if it should be Suggest, Import, or Depend.

federicomarini commented 3 months ago

If this example will be run in the SingleCellAlleleExperiment we can let it go if you want to avoid the dependency. But yes Suggest seems appropriate here since its used in the vignette but the data isn't dependent on a defined class in the Software package

Fair enough. It does make sense to test it also here, "because why not show the full workflow" at least to read things in fully. The corresponding edits will be done, with SingleCellAlleleExperiment going into "Suggests"

The SingleCellAlleleExperiment will depend on where and how you use the data to define if it should be Suggest, Import, or Depend.

Ok, thanks for clarifying this. In there, read_allele_counts will definitely make use of the data. Probably a "Suggests" entry is too soft, even if we just use it in the examples.

But given scaeData only exports one function (scaeDataGet), I think we can be safe and call it a "Depends", as no masking of the namespaces are expected to happen.

bioc-issue-bot commented 3 months ago

Received a valid push on git.bioconductor.org; starting a build for commit id: b6a053d22fcdd73ffa2f5b5d89aeff9ae86c3215

bioc-issue-bot commented 3 months ago

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

ahmadalajami commented 3 months ago

Thanks a lot for your suggestions, @lshep! Please find below my response:


vignette

[x] Since this line in the vignette seems to download all your data from each of the sets

pbmc_5k <- scaeDataGet("pbmc_5k")
pbmc_10k <- scaeDataGet("pbmc_10k")
pbmc_20k <- scaeDataGet("pbmc_20k")

pbmc_20k

perhaps it would be best to only execute the pbmc_20k that you use for examples and show but not execute (eval=FALSE) the other sets? Let users download the sets they would like?

--> AA: thank you for this suggestion. We split this into two chunks, the first is eval=FALSE and contains the first two datasets. The second chunk, which we want to execute and show as an example, contains the third dataset and is eval=TRUE.

[x] You don't need to reference github to download the lookup tables that are provided in inst/extdata. You can retrieve those interactively in R through a system.file command combined with read.csv. Something similar to

lookup = read.csv(system.file("extdata", "pbmc_20k_lookup_table.csv", package="scaeData"))

--> AA: this is definitely a better way to access the data. We changed this accordingly. Thank you.

[x] Why is the last section where you run read_allele_counts in an eval=FALSE? This should be executed. I see it depends on SingleCellAlleleExperiment -- since these were not submitted as related packages, we can assume it will be accepted and I can test locally / you can ignore the error that will occur that the package cannot be found.

--> AA: upon your suggestion, we added Suggests: SingleCellAlleleExperiment, which as expected, threw an error in the vignette. I am ignoring this per your request.

man

[x] Please provide a package level man page so when a naive user does ?scaeData something is displayed.

--> AA: thank you for reminding us! We have created an scaeData-pkg.R to resolve this.


All changes have been made upon your request. Please note the error the vignette is throwing after adding Suggests: SingleCellAlleleExperiment.

Thanks once again and we are looking forward to your feedback :)

Jonas-Schuck commented 3 months ago

Hello @lshep and thanks for your helpful comments - just a little heads up regarding the local testing of scaeData with the new Suggests:SingleCellAlleleExperiment change, in case you missed the most recent push in SingleCellAlleleExperiment. Please use the most recent version of SingleCellAlleleExperiment 0.99.1, pushed just now, otherwise errors would be expected. Thanks!

lshep commented 3 months ago

Thanks looks good. I'll accept and get it on the builders so SingleCellAlleleExperiment review can progress.
Cheers,

bioc-issue-bot commented 3 months ago

Your package has been accepted. It will be added to the Bioconductor nightly builds.

Thank you for contributing to Bioconductor!

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lshep commented 3 months ago

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federicomarini commented 3 months ago

Thanks @lshep for the timely review! Looking forward to receiving the feedback from the reviewers for the companion package, SingleCellAlleleExperiment!