STexampleData

[lmweber]

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[bioc-issue-bot]

Hi @lmweber

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: STexampleData
Version: 0.99.0
Title: Collection of spatially resolved transcriptomics datasets in SpatialExperiment 
    Bioconductor format
Description: Collection of spatially resolved transcriptomics datasets in SpatialExperiment 
    Bioconductor format, for use in examples, demonstrations, tutorials, and other 
    purposes. The datasets have been sourced from various publicly available sources, 
    and cover several technological platforms.
Authors@R: person("Lukas M.", "Weber", email = "lukas.weber.edu@gmail.com", 
        role = c("aut", "cre"), comment = c(ORCID = "0000-0002-3282-1730"))
URL: https://github.com/lmweber/STexampleData
BugReports: https://github.com/lmweber/STexampleData/issues
License: MIT + file LICENSE
biocViews:
    ExperimentHub, 
    ExperimentData, 
    ReproducibleResearch, 
    ExpressionData, 
    SingleCellData, 
    Homo_sapiens_Data, 
    Mus_musculus_Data
Depends: 
    ExperimentHub, 
    SpatialExperiment
Imports:
    utils
VignetteBuilder: knitr
Suggests:
    BiocStyle, 
    knitr
RoxygenNote: 7.1.1

[lmweber]

This is an ExperimentHub package. I have contacted the Bioconductor core team and uploaded data files via aws, and data files have now been added to ExperimentHub (EH5443-EH5445). Thank you!

[bioc-issue-bot]

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

[lmweber]

Looks like the error is related to the validity checks for the SpatialExperiment objects.

I will update the objects and get back in touch to upload them again via aws. We are also making some final updates to the SpatialExperiment class package right now, so it might be best if I wait a few days, so I can combine both sets of updates when I re-save the objects - this will minimize the number of times we need to re-upload them.

[Kayla-Morrell]

Hello @lmweber - I'm just checking in to see if there has been any progress with this package. Please keep in mind that the deadline to accept new packages in to the Bioc 3.13 releaese is May 12th. Any packages accepted after this date will be included in the next release.

Best, Kayla

[lmweber]

Thanks for the update. Yes, the error is due to the validity checks in the SpatialExperiment package. We are planning to push a final update to SpatialExperiment tomorrow, so then this error should also resolve here (possibly after a version bump).

If that works and then still leaves time to get it into the current cycle this would be great - but yes, if the review takes longer, then I understand this might mean it gets into the next cycle instead. Thanks!

[bioc-issue-bot]

Received a valid push on git.bioconductor.org; starting a build for commit id: 3a034c163926d32e000ccaf49debde425dfc3b9d

[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/STexampleData 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: 149db681216a9d3b6fc0aa27cfa913d58c83c263

[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/STexampleData 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: 5c19e97ce1f0a54e18544ff2c8250c54466d89fa

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

[lmweber]

Hi @Kayla-Morrell - I have uploaded some updated objects using aws, which should now pass the validity checks with the latest version of the SpatialExperiment structure. This was giving the errors above previously.

Could you please re-link the new objects from aws? The old ones can be deleted. There should be 3 new objects, which I uploaded this afternoon:

• STexampleData/Visium_humanDLPFC.rds
• STexampleData/Visium_mouseCoronal.rds
• STexampleData/seqFISH_mouseEmbryo.rds

Then I will probably need to give it another version bump, and hopefully the checks should pass. Thank you!

[Kayla-Morrell]

@lmweber - I've copied over the new versions of the data so you should be good to do a version bump and hopefully get a clean build.

Best, Kayla

[bioc-issue-bot]

Received a valid push on git.bioconductor.org; starting a build for commit id: 1115c3c94e69751a8fcce64326159df8ab32a5ba

[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/STexampleData 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: 4b75e4dcebb70cee6b2076c4c8850c6d31fbb726

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

[lmweber]

Ok, looks like it is passing now on Linux (malbec2) and Mac (machv2).

On Windows (tokay2) it is still showing the previous error related to validity from the old SpatialExperiment class structure dependency. We pushed the new SpatialExperiment structure 2 days ago - is it possible that this takes a few days to propagate on the Windows builder? If so, I can add additional version bumps over the next few days to restart the builds.

[Kayla-Morrell]

Hmmm, I'm not sure why the news version hasn't propagated yet on the Windows builder. In the mean time I can do an initial review of the package based on the Linux and Mac builders and hopefully with time the Windows builder will catch up.

[lmweber]

Ok, thank you!

[bioc-issue-bot]

Received a valid push on git.bioconductor.org; starting a build for commit id: 574412104cded8c2d1c7f3c0bd989e7b30b2b812

[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/STexampleData 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: 5ce8cd1bea6bafb164e410cbff5113474b7e2e3a

[bioc-issue-bot]

Received a valid push on git.bioconductor.org; starting a build for commit id: f878d6d0df224639ef6b92fbc1b0a690a12dade7

[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.

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

[lmweber]

Oh cool - looks like the Windows builder has caught up and it has passed on all three systems now.

[Kayla-Morrell]

@lmweber - Everything looks good, I have no changes that need to be made. I'm more than happy to accept the package.

Best, Kayla

[bioc-issue-bot]

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

Thank you for contributing to Bioconductor!

[lmweber]

Oh great, thank you very much! That's great that it will be in the next release.

[vjcitn]

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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

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(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("STexampleData"). The package 'landing page' will be created at

https://bioconductor.org/packages/STexampleData

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.