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SFEData, SpatialFeatureExperiment, and Voyager
Update the following URL to point to the GitHub repository of the package you wish to submit to Bioconductor
- Repository: https://github.com/pachterlab/SFEData
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Hi @lambdamoses
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: SFEData
Title: Example SpatialFeatureExperiment datasets
Version: 0.99.0
Authors@R:
c(person("Lambda", "Moses", email = "[email protected]",
role = c("aut", "cre"),
comment = c(ORCID = "0000-0002-7092-9427")),
person("Lior", "Pachter", email = "[email protected]",
role = c("aut", "ths"),
comment = c(ORCID = "0000-0002-9164-6231")))
Description:
Example spatial transcriptomics datasets with Simple Feature annotations
as SpatialFeatureExperiment objects. In the first version, the only full
dataset is a mouse skeletal muscle Visium dataset 2 days after notexin
injury from 'Large-scale integration of single-cell transcriptomic data
captures transitional progenitor states in mouse skeletal muscle
regeneration'. More datasets will be added in later versions.
Imports:
AnnotationHub,
ExperimentHub
Suggests:
knitr,
rmarkdown,
SpatialFeatureExperiment,
testthat (>= 3.0.0)
License: GPL-3
Encoding: UTF-8
Roxygen: list(markdown = TRUE)
RoxygenNote: 7.2.0
biocViews:
ExperimentHub,
ExpressionData,
Mus_musculus_Data,
SpatialData,
Tissue,
SingleCellData
VignetteBuilder: knitr
Config/testthat/edition: 3
Will you be following the https://github.com/Bioconductor/Contributions#submitting-related-packages so that SpatialFeatureExperiment is in place for checking SFEData?
I installed SpatialFeatureExperiment from pachterlab repo to check this package and it seemed fine. You will need to submit SpatialFeatureExperiment too, as a related package.
@vjcitn to have the interface for submitting related packages work correctly they can't submit it until the data package is already in review with a 'review in progress' tag (and therefore already initialized in the review process). If it is good please proceed with the 'pre-check passed'
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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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, skipped". 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
[email protected]:packages/SFEData to trigger a new build.
A quick tutorial for setting up remotes and pushing to upstream can be found here.
AdditionalPackage: https://github.com/pachterlab/SpatialFeatureExperiment
Hi @lambdamoses, Thanks for submitting your additional package: https://github.com/pachterlab/SpatialFeatureExperiment. We are taking a quick look at it and you will hear back from us soon.
Hi @lambdamoses, Thanks for submitting your additional package: https://github.com/pachterlab/Voyager. We are taking a quick look at it and you will hear back from us soon.
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.
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.
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, skipped". 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
[email protected]:packages/SpatialFeatureExperiment to trigger a new build.
A quick tutorial for setting up remotes and pushing to upstream can be found here.
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.
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
[email protected]:packages/SpatialFeatureExperiment to trigger a new build.
A quick tutorial for setting up remotes and pushing to upstream can be found here.
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
[email protected]:packages/Voyager to trigger a new build.
A quick tutorial for setting up remotes and pushing to upstream can be found here.
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.
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.
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
[email protected]:packages/SpatialFeatureExperiment to trigger a new build.
A quick tutorial for setting up remotes and pushing to upstream can be found here.
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
[email protected]:packages/SpatialFeatureExperiment to trigger a new build.
A quick tutorial for setting up remotes and pushing to upstream can be found here.
Received a valid push on git.bioconductor.org; starting a build for commit id: 11579860423af00cea4cf7f2f36a5298c659b02d
Received a valid push on git.bioconductor.org; starting a build for commit id: 624514c3976d27cf38c903dd2410d2bbae47f9a3
Received a valid push on git.bioconductor.org; starting a build for commit id: d13cd4cf79d885c6304769e0fd66ae9e55367b00
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
[email protected]:packages/SpatialFeatureExperiment to trigger a new build.
A quick tutorial for setting up remotes and pushing to upstream can be found here.
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
[email protected]:packages/SFEData to trigger a new build.
A quick tutorial for setting up remotes and pushing to upstream can be found here.
Received a valid push on git.bioconductor.org; starting a build for commit id: e05e870d05ceeebf15498c0c27cad69a31419a09
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
[email protected]:packages/Voyager to trigger a new build.
A quick tutorial for setting up remotes and pushing to upstream can be found here.
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
[email protected]:packages/SFEData to trigger a new build.
A quick tutorial for setting up remotes and pushing to upstream can be found here.
Received a valid push on git.bioconductor.org; starting a build for commit id: d219d04006c84d50843413acdc5f2e4e0bcab5f6