Closed seandavi closed 11 months ago
Hi @seandavi
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: MicroBioMap
Type: Package
Title: Access the microbiome compendium from R
Version: 0.99.0
Description: Our dataset includes over 170,000 samples of publicly available
16S rRNA amplicon sequencing data, all processed using the same pipeline
and reference database.
License: MIT + file LICENSE
Depends:
TreeSummarizedExperiment,
ape
Imports:
Matrix,
data.table,
BiocFileCache,
R.utils
Encoding: UTF-8
LazyData: true
Authors@R:
c(person("Sean", "Davis",
role = c("aut", "cre"),
email='seandavi@gmail.com',
comment=c(ORCID='0000-0002-8991-6458')),
person("Richard", "Abdill",
role = c("aut"),
email='rabdill@uchicago.edu',
comment=c(ORCID='0000-0001-9565-5832')),
person("Ran", "Blehkman",
role=c('aut'),
comment=c(ORCID='0000-0003-3218-613X')),
person("Samantha", "Graham", role=c('aut')),
person("Casey", "Greene", role=c("aut"))
)
URL: https://seandavi.github.io/MicroBioMap/
biocViews: Microbiome, Metagenomics
RoxygenNote: 7.2.3
Suggests:
knitr,
rmarkdown,
testthat (>= 3.0.0)
Config/testthat/edition: 3
VignetteBuilder: knitr
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The following are build products from R CMD build on the Bioconductor Build System: Linux (Ubuntu 22.04.2 LTS): MicroBioMap_0.99.1.tar.gz macOS 12.6.5 Monterey: MicroBioMap_0.99.1.tar.gz
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Received a valid push on git.bioconductor.org; starting a build for commit id: 43963664e506173f7083eeba19187290f4afeffd
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Your package has been built on the Bioconductor Build System.
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A quick look through the build reports shows that dependencies are "not available." Not sure what is up, but is this a problem with the builder, as both BiocFileCache and SingleCellExperiemnt are both Bioconductor packages?
I'm going to try and manually kick off a rebuild to see if it was an intermittent issue.
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The following are build products from R CMD build on the Bioconductor Build System: Linux (Ubuntu 22.04.2 LTS): MicroBioMap_0.99.2.tar.gz macOS 12.6.5 Monterey: MicroBioMap_0.99.2.tar.gz
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Received a valid push on git.bioconductor.org; starting a build for commit id: 0f6ff0bd46deea11a55a7b0019e01a899bddc4e9
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The following are build products from R CMD build on the Bioconductor Build System: macOS 12.6.5 Monterey: MicroBioMap_0.99.3.tar.gz Linux (Ubuntu 22.04.2 LTS): MicroBioMap_0.99.3.tar.gz
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Received a valid push on git.bioconductor.org; starting a build for commit id: f8009df17749bd34b96f5b7dd4587eeab7999efb
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The following are build products from R CMD build on the Bioconductor Build System: Linux (Ubuntu 22.04.2 LTS): MicroBioMap_0.99.4.tar.gz macOS 12.6.5 Monterey: MicroBioMap_0.99.4.tar.gz
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I will begin my formal review of this submission soon. In the meantime, please address the R Code issues raised by BiocCheck.
* Checking coding practice ... * NOTE: Avoid 1:...; use seq_len() or seq_along() * NOTE: Avoid 'cat' and 'print' outside of 'show' methods * NOTE: Avoid using '=' for assignment and use '<-' instead
Received a valid push on git.bioconductor.org; starting a build for commit id: f29a058b0c49ec35ce85573641414ebb5baa47d0
Dear Package contributor,
This is the automated single package builder at bioconductor.org.
Your package has been built on the Bioconductor Build System.
Congratulations! The package built without errors or warnings on all platforms.
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The following are build products from R CMD build on the Bioconductor Build System: macOS 12.6.5 Monterey: MicroBioMap_0.99.5.tar.gz Linux (Ubuntu 22.04.2 LTS): MicroBioMap_0.99.5.tar.gz
Links above active for 21 days.
Remember: if you submitted your package after July 7th, 2020,
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I have reviewed MicroBioMap and noted some issues.
snake_case
and camelCase
are present. See Variable Names and Function Names. camelCase
is Bioconductor's standard.get_compendium
. There ought to be more functionality available.[ ] TODO
parts. It would be interesting to demonstrate the identification of an association between some genus and some sample phenotype. Demonstrate its biological usefulness.Received a valid push on git.bioconductor.org; starting a build for commit id: 9795a1868ee2e05a6a77784c5b6910fb0b99f42b
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Received a valid push on git.bioconductor.org; starting a build for commit id: 8c90272eab660ce8ad21654594b1e3499a8f5c76
Dear Package contributor,
This is the automated single package builder at bioconductor.org.
Your package has been built on the Bioconductor Build System.
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The following are build products from R CMD build on the Bioconductor Build System: Linux (Ubuntu 22.04.2 LTS): MicroBioMap_0.99.7.tar.gz macOS 12.6.5 Monterey: MicroBioMap_0.99.7.tar.gz
Links above active for 21 days.
Remember: if you submitted your package after July 7th, 2020,
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Received a valid push on git.bioconductor.org; starting a build for commit id: f1fda163075c19f149dce2f0acd34a61f0bb29bc
Received a valid push on git.bioconductor.org; starting a build for commit id: 5a5c9a6e92bed43b0c494111c95d8e8320ddf1f8
Dear Package contributor,
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The following are build products from R CMD build on the Bioconductor Build System: Linux (Ubuntu 22.04.2 LTS): MicroBioMap_0.99.8.tar.gz macOS 12.6.5 Monterey: MicroBioMap_0.99.8.tar.gz
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Dear Package contributor,
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Your package has been built on the Bioconductor Build System.
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The following are build products from R CMD build on the Bioconductor Build System: Linux (Ubuntu 22.04.2 LTS): MicroBioMap_0.99.9.tar.gz macOS 12.6.5 Monterey: MicroBioMap_0.99.9.tar.gz
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Received a valid push on git.bioconductor.org; starting a build for commit id: d52fec2433ff2bdf7466e32ee8e6633506aa2d47
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The following are build products from R CMD build on the Bioconductor Build System: Linux (Ubuntu 22.04.2 LTS): MicroBioMap_0.99.10.tar.gz macOS 12.6.5 Monterey: MicroBioMap_0.99.10.tar.gz
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The following are build products from R CMD build on the Bioconductor Build System: Linux (Ubuntu 22.04.2 LTS): MicroBioMap_0.99.11.tar.gz macOS 12.6.5 Monterey: MicroBioMap_0.99.11.tar.gz
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The following are build products from R CMD build on the Bioconductor Build System: Linux (Ubuntu 22.04.2 LTS): MicroBioMap_0.99.12.tar.gz macOS 12.6.5 Monterey: MicroBioMap_0.99.12.tar.gz
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Hi, Dario. Thanks for the thoughtful review. I hope it wasn't too onerous!
On Fri, Sep 8, 2023 at 7:00 AM Dario Strbenac @.***> wrote:
I have reviewed MicroBioMap and noted some issues.
- In biocViews, it ought to have ExperimentData in the list of views.
ExperimentData is not allowed in Software packages.
- Inconsistent variable and function naming. Both snake_case and camelCase are present. See Variable Names https://contributions.bioconductor.org/r-code.html#variable-names and Function Names https://contributions.bioconductor.org/r-code.html#rcode-function-names. camelCase is Bioconductor's standard.
Fixed.
- The package consists of just one exported function, get_compendium. There ought to be more functionality available.
I want to stick to the do one thing and do it well. Access to 170,000 microbiome samples, all homogeneously processed, is quite a bit of functionality, even though it is implemented as a single function. Just a reminder that GEOquery also exposes only one function (not quite true, but basically that is the case). If you have thoughts about improving the data access functionality, please share them.
- Vignette is incomplete. It has some [ ] TODO parts. It would be interesting to demonstrate the identification of an association between some genus and some sample phenotype. Demonstrate its biological usefulness.
The data do not include sample phenotypes just yet. The rationale is that the paper (in preparation) describing these data and analyzing them focuses on regional variation. I'll add some additional documentation and use cases to the vignette(s). These will largely expose functionality from other packages, though. I don't foresee lots of analysis functionality going into MicroBioMap.
Background Text for Pipeline https://github.com/seandavi/MicroBioMap/issues/6 is what I was seeking. This will be important for users to know.
Added these details to the vignette.
— Reply to this email directly, view it on GitHub https://github.com/Bioconductor/Contributions/issues/3100#issuecomment-1711482505, or unsubscribe https://github.com/notifications/unsubscribe-auth/AAAWSE6AFHQDMP4JAGFPHUDXZL3DZANCNFSM6AAAAAA3AI3CC4 . You are receiving this because you were mentioned.Message ID: @.***>
Received a valid push on git.bioconductor.org; starting a build for commit id: b78bbd5946d33ea4f4f26581e1984f4e759cfe02
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The following are build products from R CMD build on the Bioconductor Build System: Linux (Ubuntu 22.04.2 LTS): MicroBioMap_0.99.13.tar.gz macOS 12.6.5 Monterey: MicroBioMap_0.99.13.tar.gz
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Are any more commits expected soon? I still see open issues remaining in the tracker.
@seandavi any additional comments in response to @DarioS ?
I don't have anything else right now, no. I'm fine if you'd rather this just go into devel for the next release cycle.
Is the package still being worked on @seandavi or is it ready for a review by @DarioS ?
Hi, @DarioS and @lshep. Collaborators are still working on components of the package. I'm going to close this for now and will reopen when their contributions are complete.
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