Bioconductor / Contributions

Contribute Packages to Bioconductor
131 stars 33 forks source link

MouseAgingData #3293

Closed tram-nguyen-n closed 3 months ago

tram-nguyen-n commented 4 months 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 4 months ago

Hi @tram-nguyen-n

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: MouseAgingData
Title: Multi-omics data access for studies investigating the effects of aging
Version: 0.99.0
Authors@R: c(person("Tram", "Nguyen", role = c("aut", "cre"), 
          email = "Tram_Nguyen@hms.harvard.edu", 
          comment = c(ORCID = "0000-0003-4809-6227")))
Description: This MouseAgingData package provides analysis-ready data resources 
    from different studies focused on aging and rejuvenation in mice. The 
    package currently includes a 10X Genomics single-cell data sets from an 
    aging mouse brain parabiosis transcriptomic study containing 105329 cells 
    and 20905 features (Ximerakis & Holton et al., 2023). The data is provided 
    as a SingleCellExperiment R object and includes a table of raw counts and 
    cell metadata.
URL: https://github.com/ccb-hms/MouseAgingData
BugReports: https://github.com/ccb-hms/MouseAgingData/issues
License: Artistic-2.0
Encoding: UTF-8
Roxygen: list(markdown = TRUE)
RoxygenNote: 7.3.1
Depends:
    R,
    SingleCellExperiment
Imports: 
    BiocGenerics,
    ExperimentHub,
    methods,
    S4Vectors
Suggests: 
    BiocStyle,
    knitr,
    rmarkdown
biocViews: 
    ExperimentData, 
    ExpressionData, 
    SequencingData, 
    RNASeqData, 
    SingleCellData, 
    ExperimentHub, 
    PackageTypeData,
    Mus_musculus_Data
VignetteBuilder: 
    knitr
bioc-issue-bot commented 4 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.

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

bioc-issue-bot commented 4 months ago

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

tram-nguyen-n commented 4 months ago

Hi,

Looking at the latest Build report, it looks like the vignette failed because it cannot access the ExperimentHub data associated with this package yet. Do you have suggestions on how to proceed in this case? Thanks!

lshep commented 4 months ago

R is case sensitive. The issue came because in your metadata data file you specified MouseAgingData/parabiosis_sce.RDS but the file uploaded was MouseAgingData/parabiosis_sce.rds. I have updated the file in Azure and it now should work. Please bump the version on git.bioconductor.org to trigger a new build

bioc-issue-bot commented 4 months ago

Received a valid push on git.bioconductor.org; starting a build for commit id: 845d9af2d0ef8a864d34513913f4dd2208ca29d6

bioc-issue-bot commented 4 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: "WARNINGS, 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): MouseAgingData_0.99.1.tar.gz macOS 12.7.1 Monterey: MouseAgingData_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/MouseAgingData to trigger a new build. A quick tutorial for setting up remotes and pushing to upstream can be found here.

bioc-issue-bot commented 4 months ago

Received a valid push on git.bioconductor.org; starting a build for commit id: 5f0489df0731ee9a52e5265bbbd21dbfe50acc90

bioc-issue-bot commented 4 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: "WARNINGS, 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): MouseAgingData_0.99.2.tar.gz macOS 12.7.1 Monterey: MouseAgingData_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/MouseAgingData to trigger a new build. A quick tutorial for setting up remotes and pushing to upstream can be found here.

bioc-issue-bot commented 4 months ago

Received a valid push on git.bioconductor.org; starting a build for commit id: 78b8f4497f16b5927be04f0ae1cd71541076cdf7

bioc-issue-bot commented 4 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): MouseAgingData_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/MouseAgingData to trigger a new build. A quick tutorial for setting up remotes and pushing to upstream can be found here.

bioc-issue-bot commented 4 months ago

Received a valid push on git.bioconductor.org; starting a build for commit id: 2d2d34167fb7b3bb2689c881035a2c8670144b1c

bioc-issue-bot commented 4 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): MouseAgingData_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/MouseAgingData to trigger a new build. A quick tutorial for setting up remotes and pushing to upstream can be found here.

bioc-issue-bot commented 4 months ago

Received a valid push on git.bioconductor.org; starting a build for commit id: a7765583d8e01be9d37b4665c69a29f32d816d58

bioc-issue-bot commented 4 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): MouseAgingData_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/MouseAgingData to trigger a new build. A quick tutorial for setting up remotes and pushing to upstream can be found here.

bioc-issue-bot commented 4 months ago

Received a valid push on git.bioconductor.org; starting a build for commit id: 8d3c0ba8ce4eab19cffbdeb920bddff26a6953ba

bioc-issue-bot commented 4 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): MouseAgingData_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/MouseAgingData to trigger a new build. A quick tutorial for setting up remotes and pushing to upstream can be found here.

bioc-issue-bot commented 4 months ago

Received a valid push on git.bioconductor.org; starting a build for commit id: f208bb9e06ff62785084b0aa63efa418a92cdd57

bioc-issue-bot commented 4 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): MouseAgingData_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/MouseAgingData to trigger a new build. A quick tutorial for setting up remotes and pushing to upstream can be found here.

bioc-issue-bot commented 4 months ago

Received a valid push on git.bioconductor.org; starting a build for commit id: 057c8440dd3ab384d95bb090baae666ab56c4150

bioc-issue-bot commented 4 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): MouseAgingData_0.99.9.tar.gz macOS 12.7.1 Monterey: MouseAgingData_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/MouseAgingData to trigger a new build. A quick tutorial for setting up remotes and pushing to upstream can be found here.

bioc-issue-bot commented 4 months ago

Received a valid push on git.bioconductor.org; starting a build for commit id: f0197e5bb0dc457e3e6c26149e1f74497b0d9ff4

bioc-issue-bot commented 4 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/MouseAgingData to trigger a new build. A quick tutorial for setting up remotes and pushing to upstream can be found here.

bioc-issue-bot commented 4 months ago

Received a valid push on git.bioconductor.org; starting a build for commit id: ccdac1cd6b0b5688640abefa8790c76460c98641

bioc-issue-bot commented 4 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): MouseAgingData_0.99.11.tar.gz macOS 12.7.1 Monterey: MouseAgingData_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/MouseAgingData to trigger a new build. A quick tutorial for setting up remotes and pushing to upstream can be found here.

bioc-issue-bot commented 4 months ago

Received a valid push on git.bioconductor.org; starting a build for commit id: ad57ed6b24500c847458487ecf50d84c5ddeeaa0

bioc-issue-bot commented 4 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): MouseAgingData_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/MouseAgingData to trigger a new build. A quick tutorial for setting up remotes and pushing to upstream can be found here.

tram-nguyen-n commented 3 months ago

Hi Bioconductor Team @lshep,

Just wondering if I could get an update on this package and where it's at in the review process please? Thank you!

Kayla-Morrell commented 3 months ago

@tram-nguyen-n - So sorry for the delay, I've been transitioning between jobs. I'll work on getting an initial review posted over the next couple of days.

Best, Kayla

tram-nguyen-n commented 3 months ago

Great, thanks so much for the update @Kayla-Morrell !

tram-nguyen-n commented 3 months ago

Hi @Kayla-Morrell hope you're doing well. Just wanted to check in about the status for this package as we're hoping we'll be able to get it out with the next release. Please let me know if there's anything you need from me. Thank you!

Kayla-Morrell commented 3 months ago

@tram-nguyen-n - I have looked over the package and everything looks good, I have no notes. I'm more than happy to accept the package. Thank you for your patience.

Best, Kayla

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!

Reviewers for Bioconductor packages are volunteers from the Bioconductor community. If you are interested in becoming a Bioconductor package reviewer, please see Reviewers Expectations.

jwokaty commented 3 months ago

The default branch of your GitHub repository has been added to Bioconductor's git repository as branch devel.

To use the git.bioconductor.org repository, we need an 'ssh' key to associate with your github user name. If your GitHub account already has ssh public keys (https://github.com/tram-nguyen-n.keys is not empty), then no further steps are required. Otherwise, do the following:

  1. Add an SSH key to your github account
  2. Submit your SSH key to Bioconductor

See further instructions at

https://bioconductor.org/developers/how-to/git/

for working with this repository. See especially

https://bioconductor.org/developers/how-to/git/new-package-workflow/ https://bioconductor.org/developers/how-to/git/sync-existing-repositories/

to keep your GitHub and Bioconductor repositories in sync.

Your package will be included in the next nigthly 'devel' build (check-out from git at about 6 pm Eastern; build completion around 2pm Eastern the next day) at

https://bioconductor.org/checkResults/

(Builds sometimes fail, so ensure that the date stamps on the main landing page are consistent with the addition of your package). Once the package builds successfully, you package will be available for download in the 'Devel' version of Bioconductor using BiocManager::install("MouseAgingData"). The package 'landing page' will be created at

https://bioconductor.org/packages/MouseAgingData

If you have any questions, please contact the bioc-devel mailing list (https://stat.ethz.ch/mailman/listinfo/bioc-devel); this issue will not be monitored further.