Bioconductor / Contributions

Contribute Packages to Bioconductor
131 stars 33 forks source link

gypsum #3280

Closed LTLA closed 4 months ago

LTLA commented 5 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 5 months ago

Hi @LTLA

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: gypsum
Version: 0.99.0
Date: 2024-01-25
Title: Interface to the gypsum REST API
Description:
    Friendly interface to the gypsum REST API.
    Provides functions for uploads, downloads, and various adminstrative and management tasks.
Authors@R: person("Aaron", "Lun", role=c("aut", "cre"), email="infinite.monkeys.with.keyboards@gmail.com")
License: MIT + file LICENSE
Imports:
    utils,
    tools,
    httr2,
    jsonlite,
    aws.s3,
    parallel,
    filelock
Suggests:
    knitr,
    rmarkdown,
    testthat,
    BiocStyle,
    digest,
    jsonvalidate
RoxygenNote: 7.2.3
VignetteBuilder: knitr
URL: https://github.com/ArtifactDB/gypsum-R
BugReports: https://github.com/ArtifactDB/gypsum-R/issues
biocViews:
    DataImport
bioc-issue-bot commented 5 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 5 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: macOS 12.7.1 Monterey: gypsum_0.99.0.tar.gz Linux (Ubuntu 22.04.2 LTS): gypsum_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/gypsum 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: d394989a56e15deb5af05730e8632569271aa481

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". 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): gypsum_0.99.1.tar.gz macOS 12.7.1 Monterey: gypsum_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/gypsum 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: 993bf9c813ae04c71498cc69a4184178db6167dc

bioc-issue-bot commented 4 months ago

Received a valid push on git.bioconductor.org; starting a build for commit id: 993bf9c813ae04c71498cc69a4184178db6167dc

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: "ABNORMAL". 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/gypsum 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

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/gypsum 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

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". 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): gypsum_0.99.2.tar.gz macOS 12.7.1 Monterey: gypsum_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/gypsum 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.

vjcitn commented 4 months ago

Please add a sentence in the Description field of DESCRIPTION, perhaps mentioning with URL the role of this package in the artifactdb ecosystem. This will scotch one BiocCheck warning. The other one can be ignored.

vjcitn commented 4 months ago

And bump package version.

bioc-issue-bot commented 4 months ago

Received a valid push on git.bioconductor.org; starting a build for commit id: 323cdf5eb73e6250e465d8a37851eadc885a2031

bioc-issue-bot commented 4 months ago

Received a valid push on git.bioconductor.org; starting a build for commit id: 323cdf5eb73e6250e465d8a37851eadc885a2031

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: "ABNORMAL". 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/gypsum 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

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

LTLA commented 4 months ago

Looks like the git clone failed.

vjcitn commented 4 months ago

Your contribution is given as https://github.com/LTLA/gypsum but the changes were made to https://github.com/ArtifactDB/gypsum-R .

vjcitn commented 4 months ago

The third sentence that you added in gypsum-R isn't appreciated. You can just take it out and stay in warning status for BiocCheck, or add something instructive for users.

lshep commented 4 months ago

@LTLA how are you pushing changes? This isn't happening to any other issue but it appears when you push changes you are triggering two events which causes the clone to fail because one has cloned and the other is overwriting it and causes a corrupt state of the clone

bioc-issue-bot commented 4 months ago

Received a valid push on git.bioconductor.org; starting a build for commit id: 160a545dcf2144b5eeb73bacbf4f3538877b17e6

LTLA commented 4 months ago

@lshep Ah, I think I know why. I first push to master, immediately remember that everything got renamed to devel, and then push to devel as well. Hence two pushes in quick succession.

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): gypsum_0.99.3.tar.gz macOS 12.7.1 Monterey: gypsum_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/gypsum 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: 160a545dcf2144b5eeb73bacbf4f3538877b17e6

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". 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): gypsum_0.99.4.tar.gz macOS 12.7.1 Monterey: gypsum_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/gypsum 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

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.

bioc-issue-bot commented 4 months ago

Received a valid push on git.bioconductor.org; starting a build for commit id: 7cc9f362a7b5d7cfea87e314a0478f14b7619a31

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". 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: macOS 12.7.1 Monterey: gypsum_0.99.4.tar.gz Linux (Ubuntu 22.04.3 LTS): gypsum_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/gypsum to trigger a new build. A quick tutorial for setting up remotes and pushing to upstream can be found here.

lshep commented 4 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/LTLA.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("gypsum"). The package 'landing page' will be created at

https://bioconductor.org/packages/gypsum

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.