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TransOmicsData ExperimentHub package #3270

Closed PYangLab closed 3 months ago

PYangLab 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 @PYangLab

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: TransOmicsData
Title: A collection of trans-omics datasets across various biological systems
Version: 0.99.0
Date: 2023-11-25
Authors@R: c(
    person(given = "Carissa", family = "Chen", email = "carissa.chen@sydney.edu.au", role="aut"),
    person(given = "Di", family = "Xiao", email = "d.xiao@sydney.edu.au", role=c("aut", "cre"))
    )
Description: Contains a collection of trans-omics datasets generated using various sequencing technologies such as RNA-seq, Mass spectrometry and ChIP-seq, from different tissue types and species.
Depends: ExperimentHub
Imports: S4Vectors, utils
License: GPL-3
BugReports: https://support.bioconductor.org/t/TransOmicsData
VignetteBuilder: knitr
Suggests: 
    BiocStyle,
    knitr,
    rmarkdown,
    RefManageR,
    sessioninfo,
    testthat
biocViews: ExperimentHub, MassSpectrometryData, RNASeqData, Tissue, SequencingData
Encoding: UTF-8
LazyData: false
Roxygen: list(markdown = TRUE)
RoxygenNote: 7.3.0
Config/testthat/edition: 3
lshep commented 5 months ago

Note: when I R CMD build your package right now it ERROR with could not find function "listDatasets". You should do a library(TransOmicsData) to load your package before calling your package function in the vignette.

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: "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/TransOmicsData 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: 8abdce65c74a20e066e081c1166368aa40cf891e

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: TransOmicsData_0.99.1.tar.gz Linux (Ubuntu 22.04.2 LTS): TransOmicsData_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/TransOmicsData 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: 971770e591a1d663098f391fa1fed4ccc3c17b8a

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: TransOmicsData_0.99.2.tar.gz Linux (Ubuntu 22.04.2 LTS): TransOmicsData_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/TransOmicsData 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: e186a2e91501624d9dca7952b93a6f20d333c594

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: TransOmicsData_0.99.3.tar.gz Linux (Ubuntu 22.04.2 LTS): TransOmicsData_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/TransOmicsData 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: 5dad7fcb9a666c14cc0d9a7d765fe94e6933ed73

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: macOS 12.7.1 Monterey: TransOmicsData_0.99.4.tar.gz Linux (Ubuntu 22.04.2 LTS): TransOmicsData_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/TransOmicsData to trigger a new build. A quick tutorial for setting up remotes and pushing to upstream can be found here.

carissaynchen commented 5 months ago

Hi Ishep, is the doi issued after publishing the package? I'm not sure how to address the warning about the doi.

lshep commented 5 months ago

yes a doi is issued after acceptance. You can ignore that warning for now

bioc-issue-bot commented 5 months ago

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

carissaynchen commented 4 months ago

Hi @Kayla-Morrell, thank you for reviewing this package. Are there any updates on this package review?

Kayla-Morrell commented 4 months ago

@carissaynchen - 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

Kayla-Morrell commented 3 months ago

@carissaynchen - Thank you for submitting to Bioconductor. Please see the initial review of the package 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 package is ready for a re-review.

General package development

DESCRIPTION

NAMESPACE

CITATION

Vignette

R code

Best, Kayla

bioc-issue-bot commented 3 months ago

Received a valid push on git.bioconductor.org; starting a build for commit id: d8d2437caa5f49cca321d0dc5dc65990884ec35a

bioc-issue-bot commented 3 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): TransOmicsData_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/TransOmicsData to trigger a new build. A quick tutorial for setting up remotes and pushing to upstream can be found here.

carissaynchen commented 3 months ago

Hi Kayla, I have made the changes below:

General package development

  • [X] REQUIRED: File LICENSE is not mentioned in the DESCRIPTION file. Since you are using a standard license you shouldn't need to include the LICENSE file with the package.

DESCRIPTION

  • [X] SUGGESTION: The Description field in the DESCRIPTION is made up by less than 3 sentences. Please consider expanding this field, and structure it as a full paragraph.
  • [X] SUGGESTION: Consider adding the maintainer's ORCID iD in 'Authors@R' with 'comment=c(ORCID="...")'.
  • [X] SUGGESTION: Provide 'URL' or 'BugReports' field in DESCRIPTION.

NAMESPACE

  • [ ] REQUIRED: Package in Depends field not imported from: 'ExperimentHub'. This package needs to be imported from (in the NAMESPACE file) for when this namespace is loaded but not attached. I have removed the package ExperimentHub from the Depends field as my function does not require the package.

CITATION

  • [ ] SUGGESTION: Include the 'doi' argument in CITATION 'bibentry()'. I will add this when I have been issued a doi.

    Vignette

  • [X] REQUIRED: There should be an 'Installation' section that demonstrates to the user how to install the package from Bioconductor.

R code

  • [X] REQUIRED: In listDatasets, 'read.table()' partial argument match of 'head' to 'header'.
  • [ ] SUGGESTION: For formating reasons, consider shorter lines. There are 5 lines that are > 80 characters long.
  • [ ] SUGGESTION: For formating reasons, consider multiples of 4 spaces for line indents. There are 2 lines that are not.
bioc-issue-bot commented 3 months ago

Received a valid push on git.bioconductor.org; starting a build for commit id: 1a8569ab9a83259f4b42a78c5da718038c9059df

bioc-issue-bot commented 3 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): TransOmicsData_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/TransOmicsData 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 months ago

Received a valid push on git.bioconductor.org; starting a build for commit id: af19e92241d3d50288044f24d1603bc9e7391a50

bioc-issue-bot commented 3 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): TransOmicsData_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/TransOmicsData 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 months ago

Received a valid push on git.bioconductor.org; starting a build for commit id: 3d11c9fb8b2fe78181933e36d908e4b03193cd02

bioc-issue-bot commented 3 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): TransOmicsData_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/TransOmicsData 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 months ago

Received a valid push on git.bioconductor.org; starting a build for commit id: 4e7c6464402914c0b5fd31f4acb401d1ac98952b

bioc-issue-bot commented 3 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): TransOmicsData_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/TransOmicsData 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 months ago

Received a valid push on git.bioconductor.org; starting a build for commit id: d0ee40fe895de4a96a39960d2e73dc9c06abad80

bioc-issue-bot commented 3 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): TransOmicsData_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/TransOmicsData to trigger a new build. A quick tutorial for setting up remotes and pushing to upstream can be found here.

carissaynchen commented 3 months ago

Hi @Kayla-Morrell I've been trying to resolve the error with the bioc-devel subscription, and the maintainer has signed up to the mailing list so I'm not sure why the error is unresolved. Is there a way around this?

lshep commented 3 months ago

Just to be clear here, This assumes that the submitter and the maintainer in the package is registered. The currently listed maintainer and maintainer email is: person(given = "Di", family = "Xiao", email = "d.xiao@sydney.edu.au", role=c("aut", "cre") So it is looking for d.xiao@sydney.edu.au to be registered. Sometime the registration requires confirmation and the confirmation email can end up in the spam folder. I currently do not see this email registered. If you do not see a confirmation email in spam, let us know and we can follow up.

carissaynchen commented 3 months ago

Hi @lshep, could you check again whether d.xiao@sydney.edu.au is registered? we are both receiving the bioc-devel emails now.

lshep commented 3 months ago

yes I can see them

bioc-issue-bot commented 3 months ago

Received a valid push on git.bioconductor.org; starting a build for commit id: dfec4f343f260efdf6bd213c8b7ed61ae2407e9f

bioc-issue-bot commented 3 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): TransOmicsData_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/TransOmicsData to trigger a new build. A quick tutorial for setting up remotes and pushing to upstream can be found here.

Kayla-Morrell commented 3 months ago

@PYangLab - Thank you for making the necessary changes. I have looked everything over and I'm more than happy to accept the package.

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.

lshep 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/PYangLab.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("TransOmicsData"). The package 'landing page' will be created at

https://bioconductor.org/packages/TransOmicsData

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.