TENxVisiumData

[HelenaLC]

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

• Repository: https://github.com/HelenaLC/TENxVisiumData

Confirm the following by editing each check box to '[x]'

• [x] I understand that by submitting my package to Bioconductor, the package source and all review commentary are visible to the general public.

• [x] I have read the Bioconductor Package Submission instructions. My package is consistent with the Bioconductor Package Guidelines.

• [x] I understand that a minimum requirement for package acceptance is to pass R CMD check and R CMD BiocCheck with no ERROR or WARNINGS. Passing these checks does not result in automatic acceptance. The package will then undergo a formal review and recommendations for acceptance regarding other Bioconductor standards will be addressed.

• [x] My package addresses statistical or bioinformatic issues related to the analysis and comprehension of high throughput genomic data.

• [x] I am committed to the long-term maintenance of my package. This includes monitoring the support site for issues that users may have, subscribing to the bioc-devel mailing list to stay aware of developments in the Bioconductor community, responding promptly to requests for updates from the Core team in response to changes in R or underlying software.

• [x] I am familiar with the Bioconductor code of conduct and agree to abide by it.

I am familiar with the essential aspects of Bioconductor software management, including:

• [x] The 'devel' branch for new packages and features.
• [x] The stable 'release' branch, made available every six months, for bug fixes.
• [x] Bioconductor version control using Git (optionally via GitHub).

For help with submitting your package, please subscribe and post questions to the bioc-devel mailing list.

[bioc-issue-bot]

Hi @HelenaLC

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: TENxVisiumData
Version: 0.99.0
Title: Visium spatial gene expression data by 10X Genomics
Description: 
    Collection of Visium spatial gene expression datasets by 10X Genomics, 
    formatted into objects of class SpatialExperiment. 
    Data cover various organisms and tissues, and include: 
    single- and multi-section experiments, as well as single sections 
    subjected to both whole transcriptome and targeted panel analysis. 
    Datasets may be used for testing of and as examples in packages, 
    for tutorials and workflow demonstrations, or similar purposes.
Authors@R: person(
    "Helena L.", "Crowell", 
    email = "helena@crowell.eu", 
    role = c("aut", "cre"), 
    comment = c(ORCID = "0000-0002-4801-1767"))
URL: https://github.com/helenalc/TENxVisiumData
BugReports: https://github.com/helenalc/TENxVisiumData/issues
biocViews: 
    ExperimentHub,
    ExpressionData,
    ExperimentData, 
    Homo_sapiens_Data, 
    Mus_musculus_Data,
    ReproducibleResearch
Depends:
    ExperimentHub,
    SpatialExperiment
Imports:
    utils
Suggests:
    BiocStyle, 
    knitr
VignetteBuilder: 
    knitr
License: MIT + file LICENSE
Encoding: UTF-8
RoxygenNote: 7.1.1

[bioc-issue-bot]

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.

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]

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

[hpages]

Hi @HelenaLC,

Thanks for submitting the TENxVisiumData package.

Please address the errors reported by the Single Package Builder (see "build report" link above).

Thanks, H.

[bioc-issue-bot]

Received a valid push on git.bioconductor.org; starting a build for commit id: 4eb3a2b691ecfc7a98535e62a233ef1174622b23

[bioc-issue-bot]

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

[bioc-issue-bot]

Received a valid push on git.bioconductor.org; starting a build for commit id: 85501602eb9235363c23f88080b03747011d2ba4

[bioc-issue-bot]

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

[HelenaLC]

Okay, so now all is where I was hoping... the current build error is due to the SPE still being under development; once the resent updates go through, the data should be valid. I hope this will happen within the next couple days, or top of next week. Alternatively, I could upload valid data now, which would have to be re-updated afterwards. Happy to do so if this is preferred!

[hpages]

Hi @HelenaLC ,

Looks like a lot of changes got merged to SpatialExperiment in the last couple of days. Do you want to try to bump TENxVisiumData's version and push, so we get a new build report? (If we see an error on Windows only we'll ignore it.)

Thanks, H.

[bioc-issue-bot]

Received a valid push on git.bioconductor.org; starting a build for commit id: c37e9a726cf6e4a005236c97914a0fc24b579464

[bioc-issue-bot]

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

[hpages]

Your NAMESPACE file is empty! Which is the cause of many R CMD check warnings reported by the SPB on Linux and Mac. Please address. (The error on Windows is on our side, so let's ignore it).

Also make sure that you are subscribed to the Bioc-devel mailing list with the same email address that you use in the DESCRIPTION file.

Thanks, H.

[bioc-issue-bot]

Received a valid push on git.bioconductor.org; starting a build for commit id: 13d68bf151b6a58b91f7e36054d3a60b6bd03ca2

[HelenaLC]

My apologies... I am really confused. I had the same DESCRIPTION & zzz.R in another EH package, without any issues. Added the missing imports now, and registered the current email address on the mailing list alongside adding the watch tag on the support site. I get clean R CMD check and BiocCheck reports now locally.

[bioc-issue-bot]

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

[bioc-issue-bot]

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

[hpages]

Looks good. Thanks @HelenaLC !

[bioc-issue-bot]

Your package has been accepted. It will be added to the Bioconductor nightly builds.

Thank you for contributing to Bioconductor!

[vjcitn]

The master branch of your GitHub repository has been added to Bioconductor's git repository.

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/HelenaLC.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("TENxVisiumData"). The package 'landing page' will be created at

https://bioconductor.org/packages/TENxVisiumData

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.