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AnVILBase #3374

Closed LiNk-NY closed 4 months ago

LiNk-NY commented 7 months ago

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

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bioc-issue-bot commented 7 months ago

Hi @LiNk-NY

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: AnVILBase
Title: Generic functions for interacting with the AnVIL ecosystem
Version: 0.99.22
Authors@R: c(
  person("Marcel", "Ramos", , "marcel.ramos@roswellpark.org",
    c("aut", "cre"), c(ORCID = "0000-0002-3242-0582")),
  person("Martin", "Morgan", , , c("aut", "ctb"),
    c(ORCID = "0000-0002-5874-8148")),
  person("NIH NHGRI U24HG004059", role = "fnd")
  )
Description: Provides generic functions for interacting with the AnVIL
  ecosystem. Packages that use either GCP or Azure in AnVIL are built on top
  of AnVILBase. Extension packages will provide methods for interacting with
  other cloud providers.
License: Artistic-2.0
Imports:
  httr,
  httr2,
  dplyr,
  jsonlite,
  methods,
  tibble
Suggests:
  AnVILAz,
  AnVILGCP,
  BiocStyle,
  knitr,
  rmarkdown,
  testthat (>= 3.0.0),
  tinytest
biocViews: Software, Infrastructure 
URL: https://github.com/Bioconductor/AnVILBase
BugReports: https://github.com/Bioconductor/AnVILBase/issues
VignetteBuilder: knitr
Encoding: UTF-8
Roxygen: list(markdown = TRUE)
RoxygenNote: 7.3.1
Date: 2024-03-23
Config/testthat/edition: 3
Collate: 
    'AnVILBase-generics.R'
    'AnVILBase-methods.R'
    'AnVILBase-package.R'
    'Platform-class.R'
    'Response.R'
    'avdata-generics.R'
    'avdata-methods.R'
    'avnotebooks-generics.R'
    'avnotebooks-methods.R'
    'avtable-generics.R'
    'avtable-methods.R'
    'avworkflow-generics.R'
    'avworkflow-methods.R'
    'avworkspace-generics.R'
    'avworkspace-methods.R'
    'cloud_platform.R'
    'utilities.R'
bioc-issue-bot commented 7 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 7 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): AnVILBase_0.99.22.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/AnVILBase to trigger a new build. A quick tutorial for setting up remotes and pushing to upstream can be found here.

LiNk-NY commented 7 months ago

AdditionalPackage: https://github.com/Bioconductor/AnVILAz

bioc-issue-bot commented 7 months ago

Hi @LiNk-NY, Thanks for submitting your additional package: https://github.com/Bioconductor/AnVILAz. We are taking a quick look at it and you will hear back from us soon.

lshep commented 7 months ago

I can't process AnVILAz because it does not have biocViews in description

LiNk-NY commented 7 months ago

I can't process AnVILAz because it does not have biocViews in description

@lshep Sorry about that. I have added some terms. Thanks!

bioc-issue-bot commented 7 months ago

Additional Package has been approved for building.

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.

bioc-issue-bot commented 7 months ago

Additional Package has been approved for building.

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.

bioc-issue-bot commented 7 months ago

Additional Package has been approved for building.

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.

bioc-issue-bot commented 7 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/AnVILAz to trigger a new build. A quick tutorial for setting up remotes and pushing to upstream can be found here.

bioc-issue-bot commented 7 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/AnVILAz to trigger a new build. A quick tutorial for setting up remotes and pushing to upstream can be found here.

bioc-issue-bot commented 7 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/AnVILAz to trigger a new build. A quick tutorial for setting up remotes and pushing to upstream can be found here.

lshep commented 7 months ago

Sorry @LiNk-NY not sure why this triggered multiple builds

bioc-issue-bot commented 7 months ago

Additional Package has been approved for building.

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.

bioc-issue-bot commented 7 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/AnVILAz to trigger a new build. A quick tutorial for setting up remotes and pushing to upstream can be found here.

bioc-issue-bot commented 7 months ago

Received a valid push on git.bioconductor.org; starting a build for commit id: 44716d23cf801b7594cdec902e1bd85a7a683559

bioc-issue-bot commented 7 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/AnVILAz to trigger a new build. A quick tutorial for setting up remotes and pushing to upstream can be found here.

bioc-issue-bot commented 7 months ago

Received a valid push on git.bioconductor.org; starting a build for commit id: 771d2f65b5959a1fa7809a6d8b105092a9dd2a93

bioc-issue-bot commented 7 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/AnVILAz to trigger a new build. A quick tutorial for setting up remotes and pushing to upstream can be found here.

bioc-issue-bot commented 7 months ago

Received a valid push on git.bioconductor.org; starting a build for commit id: 1a99b84b87fe5eb4a7fd08426e6b1f5a4d950f78

bioc-issue-bot commented 7 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): AnVILAz_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/AnVILAz to trigger a new build. A quick tutorial for setting up remotes and pushing to upstream can be found here.

bioc-issue-bot commented 7 months ago

Received a valid push on git.bioconductor.org; starting a build for commit id: c6c16a01c53417e572ef2da86e8b7adc73efa671

bioc-issue-bot commented 7 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): AnVILAz_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/AnVILAz to trigger a new build. A quick tutorial for setting up remotes and pushing to upstream can be found here.

bioc-issue-bot commented 7 months ago

Received a valid push on git.bioconductor.org; starting a build for commit id: cb949c78779e1da8d90494916542ce0263b6becd

bioc-issue-bot commented 7 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): AnVILAz_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/AnVILAz to trigger a new build. A quick tutorial for setting up remotes and pushing to upstream can be found here.

bioc-issue-bot commented 7 months ago

Received a valid push on git.bioconductor.org; starting a build for commit id: 8fc38e87d1ef1b14f4fc77e8fe73ab21a27ac58f

bioc-issue-bot commented 7 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): AnVILAz_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/AnVILAz to trigger a new build. A quick tutorial for setting up remotes and pushing to upstream can be found here.

bioc-issue-bot commented 7 months ago

Additional Package has been approved for building.

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.

bioc-issue-bot commented 7 months ago

Additional Package has been approved for building.

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.

bioc-issue-bot commented 7 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): AnVILAz_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/AnVILAz to trigger a new build. A quick tutorial for setting up remotes and pushing to upstream can be found here.

bioc-issue-bot commented 7 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): AnVILAz_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/AnVILAz to trigger a new build. A quick tutorial for setting up remotes and pushing to upstream can be found here.

LiNk-NY commented 7 months ago

AdditionalPackage: https://github.com/Bioconductor/AnVILGCP

bioc-issue-bot commented 7 months ago

Hi @LiNk-NY, Thanks for submitting your additional package: https://github.com/Bioconductor/AnVILGCP. We are taking a quick look at it and you will hear back from us soon.

LiNk-NY commented 7 months ago

Hi @lshep Can AnVILGCP be run through the SPB? Thank you.

lshep commented 7 months ago

DataStorageAndAnalysis is not a valid biocViews term and causing issues when processing

LiNk-NY commented 7 months ago

@lshep Sorry about that. I fixed it.

bioc-issue-bot commented 7 months ago

Additional Package has been approved for building.

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.

bioc-issue-bot commented 7 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): AnVILGCP_0.99.23.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/AnVILGCP to trigger a new build. A quick tutorial for setting up remotes and pushing to upstream can be found here.

bioc-issue-bot commented 7 months ago

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

LiNk-NY commented 5 months ago

Hi Kayla, @Kayla-Morrell

I hope you are doing well. The review has been pending for a bit. I am sure you are busy with other things.

Should someone else be assigned, Lori? @lshep

Thank you.

Best regards, Marcel

Kayla-Morrell commented 5 months ago

@LiNk-NY - Sorry for the delay. The review of the packages are below. The required changes must be made while the suggested changes do not have to be (though we strongly encourage them). Comment back here with updates that have been made and when the packages are ready for a re-review.

AnVILBase

AnVILAz

AnVILGCP

Best, Kayla

bioc-issue-bot commented 5 months ago

Received a valid push on git.bioconductor.org; starting a build for commit id: 3c57a767877b07a456a77ffd1cda1dba74a3d254

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: Linux (Ubuntu 22.04.3 LTS): AnVILBase_0.99.24.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/AnVILBase to trigger a new build. A quick tutorial for setting up remotes and pushing to upstream can be found here.

bioc-issue-bot commented 5 months ago

Received a valid push on git.bioconductor.org; starting a build for commit id: 30bef519210585f342d571a2ca0076c2f20fc64b

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.

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

bioc-issue-bot commented 5 months ago

Received a valid push on git.bioconductor.org; starting a build for commit id: a88d198b8e6611a1e1de48351cf2458403f49453

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: "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): AnVILGCP_0.99.24.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/AnVILGCP to trigger a new build. A quick tutorial for setting up remotes and pushing to upstream can be found here.

bioc-issue-bot commented 5 months ago

Received a valid push on git.bioconductor.org; starting a build for commit id: 54a94e7ad9674b60b3f27ca260b77933bcc8547d

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: "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): AnVILGCP_0.99.25.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/AnVILGCP to trigger a new build. A quick tutorial for setting up remotes and pushing to upstream can be found here.