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octad.db #2391

Closed Lionir closed 2 years ago

Lionir commented 3 years 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]'

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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 3 years ago

Hi @Lionir

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: octad.db
Title: Open Cancer TherApeutic Discovery (OCTAD) database
Version: 0.99.0
Authors@R: 
    c(person(given = "E.",
 family = "Chekalin",
 role = c("aut", "cre"),
 email = "eygen.chekalin@gmail.com"),
 person(given = "B.",
 family = "Zeng",role =c("aut")),
 person(given = "B.",
 family = "Glicksberg",role ="ctb"),
 person(given = "P.",
 family = "Newbury",role ="ctb"),
 person(given = "J.",
 family = "Xing",role ="ctb"),
 person(given = "K.",
 family = "Liu",role ="ctb"),
 person(given = "A.",
 family = "Wen",role ="ctb"),
  person(given = "D.",
 family = "Joseph",role ="ctb"),
 person(given = "B.",
 family = "Chen",
 role ="aut",
 email = "chenbi12@msu.edu")
 )
Description: Open Cancer TherApeutic Discovery (OCTAD) package implies sRGES approach for the drug discovery. The essential idea is to identify drugs that reverse the gene expression signature of a disease by tamping down over-expressed genes and stimulating weakly expressed ones. The following package contains all required precomputed data for whole OCTAD pipeline computation. 
License: Artistic-2.0
Encoding: UTF-8
LazyData: true
Roxygen: list(markdown = TRUE)
RoxygenNote: 7.1.1
Depends: 
    R (>= 4.0)
biocViews: ExperimentData, CancerData, ExperimentHub, SequencingData, ExpressionData
bioc-issue-bot commented 3 years 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.

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bioc-issue-bot commented 3 years ago

Dear Package contributor,

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

Your package has been built on Linux, Mac, and Windows.

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. This link will be 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/octad.db to trigger a new build. A quick tutorial for setting up remotes and pushing to upstream can be found here.

bioc-issue-bot commented 3 years ago

Received a valid push on git.bioconductor.org; starting a build for commit id: 0f941e2aaa3777ba1bb9943b1c3473b4fea881e7

bioc-issue-bot commented 3 years ago

Dear Package contributor,

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

Your package has been built on Linux, Mac, and Windows.

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. This link will be 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/octad.db to trigger a new build. A quick tutorial for setting up remotes and pushing to upstream can be found here.

bioc-issue-bot commented 3 years ago

Received a valid push on git.bioconductor.org; starting a build for commit id: 7747259b374b1dc4ea470e6e62fa215325ac1f48

bioc-issue-bot commented 3 years ago

Dear Package contributor,

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

Your package has been built on Linux, Mac, and Windows.

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. This link will be 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/octad.db to trigger a new build. A quick tutorial for setting up remotes and pushing to upstream can be found here.

bioc-issue-bot commented 3 years ago

Received a valid push on git.bioconductor.org; starting a build for commit id: 330294e9e199d59b2d27eae3a423ec5ba0301455

bioc-issue-bot commented 3 years ago

Dear Package contributor,

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

Your package has been built on Linux, Mac, and Windows.

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. This link will be 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/octad.db to trigger a new build. A quick tutorial for setting up remotes and pushing to upstream can be found here.

bioc-issue-bot commented 3 years ago

Received a valid push on git.bioconductor.org; starting a build for commit id: b5ddc89d887c2b219b21ab9658304b3602b7c012

bioc-issue-bot commented 3 years ago

Dear Package contributor,

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

Your package has been built on Linux, Mac, and Windows.

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. This link will be 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/octad.db to trigger a new build. A quick tutorial for setting up remotes and pushing to upstream can be found here.

bioc-issue-bot commented 3 years ago

Received a valid push on git.bioconductor.org; starting a build for commit id: 748b97946cd6bbee6e53430c8ec0ff14b51ec6f8

bioc-issue-bot commented 3 years ago

Dear Package contributor,

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

Your package has been built on Linux, Mac, and Windows.

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. This link will be 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/octad.db to trigger a new build. A quick tutorial for setting up remotes and pushing to upstream can be found here.

bioc-issue-bot commented 3 years ago

Received a valid push on git.bioconductor.org; starting a build for commit id: 03c50e2db78ef9507a43dcadfee66ba06e4ade2c

bioc-issue-bot commented 3 years ago

Dear Package contributor,

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

Your package has been built on Linux, Mac, and Windows.

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. This link will be 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/octad.db to trigger a new build. A quick tutorial for setting up remotes and pushing to upstream can be found here.

bioc-issue-bot commented 3 years ago

Received a valid push on git.bioconductor.org; starting a build for commit id: 87c9c90bd5364a166c6c55c134e40563b4729822

bioc-issue-bot commented 3 years ago

Dear Package contributor,

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

Your package has been built on Linux, Mac, and Windows.

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. This link will be 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/octad.db to trigger a new build. A quick tutorial for setting up remotes and pushing to upstream can be found here.

bioc-issue-bot commented 3 years ago

Received a valid push on git.bioconductor.org; starting a build for commit id: 2ad1885bc2eef8fc4510094af4d2ff796e40ab22

bioc-issue-bot commented 3 years ago

Dear Package contributor,

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

Your package has been built on Linux, Mac, and Windows.

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. This link will be 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/octad.db to trigger a new build. A quick tutorial for setting up remotes and pushing to upstream can be found here.

bioc-issue-bot commented 3 years ago

Received a valid push on git.bioconductor.org; starting a build for commit id: e1914a4ccabd2306d9ad7fa1a920acd6e1632320

bioc-issue-bot commented 3 years ago

Dear Package contributor,

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

Your package has been built on Linux, Mac, and Windows.

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. This link will be 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/octad.db to trigger a new build. A quick tutorial for setting up remotes and pushing to upstream can be found here.

bioc-issue-bot commented 3 years ago

Received a valid push on git.bioconductor.org; starting a build for commit id: 79b92612cd0f54458b9a13c9d8e20e2639056862

bioc-issue-bot commented 3 years ago

Dear Package contributor,

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

Your package has been built on Linux, Mac, and Windows.

Congratulations! The package built without errors or warnings on all platforms.

Please see the build report for more details. This link will be 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/octad.db to trigger a new build. A quick tutorial for setting up remotes and pushing to upstream can be found here.

Lionir commented 3 years ago

AdditionalPackage: https://github.com/Bin-Chen-Lab/octad

bioc-issue-bot commented 3 years ago

Dear @Lionir ,

The github link provided https://github.com/Bin-Chen-Lab/octad , does not match the capitalization of the github repository: Bin-Chen-Lab/OCTAD. Please update the link for the repository on this issue page.

Lionir commented 3 years ago

AdditionalPackage: https://github.com/Bin-Chen-Lab/OCTAD

bioc-issue-bot commented 3 years ago

Dear @Lionir ,

You (or someone) has already posted a repository with the same name to our tracker.

See https://github.com/Bioconductor/Contributions/issues/

You cannot post the same repository more than once and packages are not allowed to have the same name.

If you would like this repository to be linked to issue number: 2391, Please contact a Bioconductor Core Member. I am closing this issue.

Lionir commented 3 years ago

Hi, For the last submission, I wasn't able to submit the package with the dependency and was instructed to re-submit the package that can be built without dependencies (octad.db) and submit the additional software package (octad). However, after I tried to submit it, the issue was closed. Can you please address it? Thank you in advance.

bioc-issue-bot commented 3 years ago

Dear @Lionir ,

We have reopened the issue to continue the review process. Please remember to push a version bump to git.bioconductor.org to trigger a new build.

lshep commented 3 years ago

Normally you should have submitted under the original open issue. this involves some clean up on our internal system. Please give us a day or two to straighten it out

Lionir commented 3 years ago

Thank you!

lshep commented 3 years ago

@Lionir could you try resubmitting the octad package using the AdditionalPackage line again. I believe we have fixed the issue on our end. Before submitting I would recommend changing the capitalization to be consistent in the DESCRIPTION of the package; R is case sensitive and it does make a difference.

Lionir commented 3 years ago

AdditionalPackage: https://github.com/Bin-Chen-Lab/octad

bioc-issue-bot commented 3 years ago

Hi @Lionir, Thanks for submitting your additional package: https://github.com/Bin-Chen-Lab/octad. We are taking a quick look at it and you will hear back from us soon.

Lionir commented 3 years ago

Hi, any news regarding the moderation of the package?

lshep commented 3 years ago

sorry for delay. we will process "awaiting moderation" packages shortly.

bioc-issue-bot commented 3 years 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 3 years 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 3 years ago

Dear Package contributor,

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

Your package has been built on Linux, Mac, and Windows.

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

bioc-issue-bot commented 3 years ago

Dear Package contributor,

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

Your package has been built on Linux, Mac, and Windows.

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

bioc-issue-bot commented 3 years 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 3 years ago

Dear Package contributor,

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

Your package has been built on Linux, Mac, and Windows.

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

bioc-issue-bot commented 3 years ago

Received a valid push on git.bioconductor.org; starting a build for commit id: c6ff8aa750e89704d88142522a81fde48ff17baa

bioc-issue-bot commented 3 years ago

Dear Package contributor,

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

Your package has been built on Linux, Mac, and Windows.

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

bioc-issue-bot commented 3 years ago

Received a valid push on git.bioconductor.org; starting a build for commit id: 9fc8f3c8f86e460fc00be6ecfaf8b68d2d51efd5

bioc-issue-bot commented 3 years ago

Dear Package contributor,

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

Your package has been built on Linux, Mac, and Windows.

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

Lionir commented 3 years ago

Hi, I am still waiting for the hub team to approve AWS stored data. I sent an e-mail as required, any news regarding this? Thank you!

lshep commented 3 years ago

Could you please re-send the request to hubs@bioconductor.org, we currently do not see any request.

Lionir commented 3 years ago

Thank you. Re-sent the e-mail, can you please check? It was supposed to be from eygen.chekalin@gmail.com. Thank you!

bioc-issue-bot commented 3 years ago

Received a valid push on git.bioconductor.org; starting a build for commit id: bce3d8998c707e23be0025d27d680e6a82a96074