Closed ahmadalajami closed 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
@federicomarini @agimkeller @jonas-schuck
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Dear Package contributor,
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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
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Received a valid push on git.bioconductor.org; starting a build for commit id: 2568626f4a45884139d22d2a72129771ea8bbc69
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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
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vignette
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?
- [ ] 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.
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
?
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.
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.
Received a valid push on git.bioconductor.org; starting a build for commit id: b6a053d22fcdd73ffa2f5b5d89aeff9ae86c3215
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.
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 :)
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!
Thanks looks good. I'll accept and get it on the builders so SingleCellAlleleExperiment review can progress.
Cheers,
Your package has been accepted. It will be added to the Bioconductor nightly builds.
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Thanks @lshep for the timely review!
Looking forward to receiving the feedback from the reviewers for the companion package, SingleCellAlleleExperiment
!
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