Bioconductor / Contributions

Contribute Packages to Bioconductor
135 stars 33 forks source link

MicroBioMap #3100

Closed seandavi closed 11 months ago

seandavi commented 1 year ago

Update the following URL to point to the GitHub repository of the package you wish to submit to Bioconductor

Confirm the following by editing each check box to '[x]'

I am familiar with the essential aspects of Bioconductor software management, including:

For questions/help about the submission process, including questions about the output of the automatic reports generated by the SPB (Single Package Builder), please use the #package-submission channel of our Community Slack. Follow the link on the home page of the Bioconductor website to sign up.

bioc-issue-bot commented 1 year 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
bioc-issue-bot commented 1 year ago

A reviewer has been assigned to your package. Learn what to expect during the review process.

IMPORTANT: Please read this documentation for setting up remotes to push to git.bioconductor.org. It is required to push a version bump to git.bioconductor.org to trigger a new build.

Bioconductor utilized your github ssh-keys for git.bioconductor.org access. To manage keys and future access you may want to active your Bioconductor Git Credentials Account

bioc-issue-bot commented 1 year ago

Dear Package contributor,

This is the automated single package builder at bioconductor.org.

Your package has been built on the Bioconductor Build System.

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 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

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

bioc-issue-bot commented 1 year ago

Received a valid push on git.bioconductor.org; starting a build for commit id: 43963664e506173f7083eeba19187290f4afeffd

bioc-issue-bot commented 1 year ago

Dear Package contributor,

This is the automated single package builder at bioconductor.org.

Your package has been built on the Bioconductor Build System.

On one or more platforms, the build results were: "ERROR, skipped". 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 Bioconductor Build System: 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/MicroBioMap to trigger a new build. A quick tutorial for setting up remotes and pushing to upstream can be found here.

seandavi commented 1 year ago

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?

lshep commented 1 year ago

I'm going to try and manually kick off a rebuild to see if it was an intermittent issue.

bioc-issue-bot commented 1 year ago

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.

Please see the build report for more details.

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

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

bioc-issue-bot commented 1 year ago

Received a valid push on git.bioconductor.org; starting a build for commit id: 0f6ff0bd46deea11a55a7b0019e01a899bddc4e9

bioc-issue-bot commented 1 year ago

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.

Please see the build report for more details.

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

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

bioc-issue-bot commented 1 year ago

Received a valid push on git.bioconductor.org; starting a build for commit id: f8009df17749bd34b96f5b7dd4587eeab7999efb

bioc-issue-bot commented 1 year ago

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.

Please see the build report for more details.

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

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

DarioS commented 1 year ago

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
bioc-issue-bot commented 1 year ago

Received a valid push on git.bioconductor.org; starting a build for commit id: f29a058b0c49ec35ce85573641414ebb5baa47d0

bioc-issue-bot commented 1 year ago

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.

Please see the build report for more details.

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, when making changes to your repository push to git@git.bioconductor.org:packages/MicroBioMap to trigger a new build. A quick tutorial for setting up remotes and pushing to upstream can be found here.

DarioS commented 1 year ago

I have reviewed MicroBioMap and noted some issues.

bioc-issue-bot commented 1 year ago

Received a valid push on git.bioconductor.org; starting a build for commit id: 9795a1868ee2e05a6a77784c5b6910fb0b99f42b

bioc-issue-bot commented 1 year ago

Dear Package contributor,

This is the automated single package builder at bioconductor.org.

Your package has been built on the Bioconductor Build System.

On one or more platforms, the build results were: "ERROR, skipped". 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 Bioconductor Build System: 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/MicroBioMap to trigger a new build. A quick tutorial for setting up remotes and pushing to upstream can be found here.

bioc-issue-bot commented 1 year ago

Received a valid push on git.bioconductor.org; starting a build for commit id: 8c90272eab660ce8ad21654594b1e3499a8f5c76

bioc-issue-bot commented 1 year ago

Dear Package contributor,

This is the automated single package builder at bioconductor.org.

Your package has been built on the Bioconductor Build System.

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 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, when making changes to your repository push to git@git.bioconductor.org:packages/MicroBioMap to trigger a new build. A quick tutorial for setting up remotes and pushing to upstream can be found here.

bioc-issue-bot commented 1 year ago

Received a valid push on git.bioconductor.org; starting a build for commit id: f1fda163075c19f149dce2f0acd34a61f0bb29bc

bioc-issue-bot commented 1 year ago

Received a valid push on git.bioconductor.org; starting a build for commit id: 5a5c9a6e92bed43b0c494111c95d8e8320ddf1f8

bioc-issue-bot commented 1 year ago

Dear Package contributor,

This is the automated single package builder at bioconductor.org.

Your package has been built on the Bioconductor Build System.

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 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

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

bioc-issue-bot commented 1 year ago

Dear Package contributor,

This is the automated single package builder at bioconductor.org.

Your package has been built on the Bioconductor Build System.

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 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

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

bioc-issue-bot commented 1 year ago

Received a valid push on git.bioconductor.org; starting a build for commit id: d52fec2433ff2bdf7466e32ee8e6633506aa2d47

bioc-issue-bot commented 1 year ago

Dear Package contributor,

This is the automated single package builder at bioconductor.org.

Your package has been built on the Bioconductor Build System.

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 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

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

bioc-issue-bot commented 1 year ago

Received a valid push on git.bioconductor.org; starting a build for commit id: f25043b588c914c4791d75b716b1aea0b792451c

bioc-issue-bot commented 1 year ago

Dear Package contributor,

This is the automated single package builder at bioconductor.org.

Your package has been built on the Bioconductor Build System.

On one or more platforms, the build results were: "WARNINGS". 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 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

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

bioc-issue-bot commented 1 year ago

Received a valid push on git.bioconductor.org; starting a build for commit id: 2faa20baea4e54844735b9c6caa20b299e6e6fa7

bioc-issue-bot commented 1 year ago

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.

Please see the build report for more details.

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

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

seandavi commented 1 year ago

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.

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.

— 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: @.***>

bioc-issue-bot commented 1 year ago

Received a valid push on git.bioconductor.org; starting a build for commit id: b78bbd5946d33ea4f4f26581e1984f4e759cfe02

bioc-issue-bot commented 1 year ago

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.

Please see the build report for more details.

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

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

DarioS commented 1 year ago

Are any more commits expected soon? I still see open issues remaining in the tracker.

lshep commented 1 year ago

@seandavi any additional comments in response to @DarioS ?

seandavi commented 1 year ago

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.

lshep commented 1 year ago

Is the package still being worked on @seandavi or is it ready for a review by @DarioS ?

seandavi commented 11 months ago

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.