SFEData, SpatialFeatureExperiment, and Voyager

lambdamoses commented 2 years ago

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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bioc-issue-bot commented 2 years ago

Received a valid push on git.bioconductor.org; starting a build for commit id: 6bdb6bdb0335a78caf76483c683af3a1586750af

bioc-issue-bot commented 2 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/SpatialFeatureExperiment to trigger a new build. A quick tutorial for setting up remotes and pushing to upstream can be found here.

Kayla-Morrell commented 2 years ago

@lambdamoses - Thank you for making the necessary changes to SpatialFeatureExperiment. Everything looks good. I wanted to check in to let you know that I'm finishing up my initial review of Voyager and should have it posted by the end of the week. Thank you for your patience during the review process.

Best, Kayla

Kayla-Morrell commented 2 years ago

@lambdamoses - Below is my initial review of Voyager. Again, 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

[ ] REQUIRED: In the README file the installation instructions should also include Bioconductor installation instructions.

DESCRIPTION

[ ] SUGGESTION: It is encouraged to include the BugReports: field with a relevant link to GitHub for reporting Issues.

Data

[ ] REQUIRED: The inst/testdata should be changed to inst/extdata and the data-raw directory should become inst/script since it seems that this file documents the creation of the data file.

Vignette

[ ] SUGGESTION: I would rename the vignette file to something more meaningful then 'overview'.
[ ] REQUIRED: There needs to be a vignette present within the package. Perhaps you have a subset of the larger vignette within the package and direct users to the more indepth one if they want to learn more.

Man pages

[ ] SUGGESTION: It is encouraged to include a package man page with an overview of the package and links to the main functions. Users should be able to have a relevant page display with ?Voyager.

Unit tests

[ ] REQUIRED: What is the purpose of the _snaps/plot directory?

R code

[ ] SUGGESTION: For formatting reasons, consider shorter lines. There are 87 lines that are > 80 characters long.
[ ] SUGGESTION: For formatting reasons, consider mulitples of 4 spaces for line indents. There are 1225 lines that are not.

Best, Kayla

bioc-issue-bot commented 2 years ago

Received a valid push on git.bioconductor.org; starting a build for commit id: 63e3717efbc24a29a4fc63605c6c06ad87a25544

bioc-issue-bot commented 2 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/SpatialFeatureExperiment to trigger a new build. A quick tutorial for setting up remotes and pushing to upstream can be found here.

bioc-issue-bot commented 2 years ago

Received a valid push on git.bioconductor.org; starting a build for commit id: e9f80f80a7c3cca4f073dcc4675d6d4cb01a276d

bioc-issue-bot commented 2 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/Voyager to trigger a new build. A quick tutorial for setting up remotes and pushing to upstream can be found here.

lambdamoses commented 2 years ago

I have written some new functionalities for both SFE and Voyager in addition to addressing the reviews.

General package development

[x] REQUIRED: In the README file the installation instructions should also include Bioconductor installation instructions.

DESCRIPTION

[x] SUGGESTION: It is encouraged to include the BugReports: field with a relevant link to GitHub for reporting Issues.

Data

[x] REQUIRED: The inst/testdata should be changed to inst/extdata and the data-raw directory should become inst/script since it seems that this file documents the creation of the data file.

Vignette

[ ] SUGGESTION: I would rename the vignette file to something more meaningful then 'overview'.

[x] REQUIRED: There needs to be a vignette present within the package. Perhaps you have a subset of the larger vignette within the package and direct users to the more indepth one if they want to learn more.

I have written a shorter vignette, though I no longer link to SFEWorkshop because the user interface has changed. I'll link to a new website later.

Man pages

[ ] SUGGESTION: It is encouraged to include a package man page with an overview of the package and links to the main functions. Users should be able to have a relevant page display with ?Voyager.

I don't really find that necessary since I myself rarely look at package man pages and go straight to the vignette or package website instead for overviews of packages I use.

Unit tests

[x] REQUIRED: What is the purpose of the _snaps/plot directory?

To unit test plotting functions. This directory contains SVG snapshots of plots as how they should look like, and the unit tests, using vdiffr::expect_doppelganger, compare the plot generated when the unit tests are run to the snapshots. If they don't match, then I can check the differences with a shiny app to see if the plotting functions have really been broken. However, expect_doppelganger tests are skipped on CRAN style checks by default since they're fragile as there may be inconsequential differences unnoticeable by eye from different systems, especially the ones involving geom_sf which depend on the system dependencies like GEOS. These tests are helpful locally.

R code

[x] SUGGESTION: For formatting reasons, consider shorter lines. There are 87 lines that are > 80 characters long.

[x] SUGGESTION: For formatting reasons, consider mulitples of 4 spaces for line indents. There are 1225 lines that are not.

Best, Kayla

Kayla-Morrell commented 2 years ago

@lambdamoses - Thank you for making the necessary changes. I have reviewed them and everything looks good. I am more than happy to accept the packages.

Best, Kayla

bioc-issue-bot commented 2 years ago

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lshep commented 2 years ago

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/lambdamoses.keys is not empty), then no further steps are required. Otherwise, do the following:

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

https://bioconductor.org/packages/SFEData

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.

lshep commented 2 years ago

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/lambdamoses.keys is not empty), then no further steps are required. Otherwise, do the following:

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

https://bioconductor.org/packages/SpatialFeatureExperiment

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.

lshep commented 2 years ago

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/lambdamoses.keys is not empty), then no further steps are required. Otherwise, do the following:

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

https://bioconductor.org/packages/Voyager

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.

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