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ggsc #3136

Closed GuangchuangYu closed 8 months ago

GuangchuangYu commented 10 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 10 months ago

Hi @GuangchuangYu

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: ggsc
Title: Visualizing single cell data
Version: 0.99.1
Authors@R: c(
       person("Guangchuang", "Yu",     email = "guangchuangyu@gmail.com", role = c("aut", "cre", "cph"), comment = c(ORCID = "0000-0002-6485-8781")),
       person("Shuangbin", "Xu",       email = "xshuangbin@163.com",      role = "aut", comment = c(ORCID="0000-0003-3513-5362"))
       )
Description: Useful functions to visualize single cell data.
Imports:
  methods,
  dplyr,
  SingleCellExperiment,
  SummarizedExperiment,
  ggplot2,
  rlang,
  cli,
  scattermore,
  SeuratObject,
  Seurat,
  tidydr,
  tidyr,
  tibble,
  utils,
  yulab.utils
Suggests:
  knitr,
  rmarkdown,
  prettydoc,
  aplot,
  BiocParallel,
  scran,
  scater,
  igraph,
  shadowtext,
  ggnewscale,
  ggforce,
  STexampleData 
biocViews: GeneExpression, SingleCell, Software, Spatial, Transcriptomics,
    Visualization
VignetteBuilder: knitr
ByteCompile: true
License: Artistic-2.0
Encoding: UTF-8
Roxygen: list(markdown = TRUE)
RoxygenNote: 7.2.3
bioc-issue-bot commented 10 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 10 months ago

Dear Package contributor,

This is the automated single package builder at bioconductor.org.

Your package has been built on the Bioconductor Build System.

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.

The following are build products from R CMD build on the Bioconductor Build System: 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/ggsc to trigger a new build. A quick tutorial for setting up remotes and pushing to upstream can be found here.

bioc-issue-bot commented 10 months ago

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

bioc-issue-bot commented 9 months ago

Received a valid push on git.bioconductor.org; starting a build for commit id: 651c4d74849cc6a010ace8aa65a95cfa699300c9

bioc-issue-bot commented 9 months ago

Dear Package contributor,

This is the automated single package builder at bioconductor.org.

Your package has been built on the Bioconductor Build System.

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 Bioconductor Build System: Linux (Ubuntu 22.04.2 LTS): ggsc_0.99.3.tar.gz macOS 12.6.5 Monterey: ggsc_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/ggsc to trigger a new build. A quick tutorial for setting up remotes and pushing to upstream can be found here.

bioc-issue-bot commented 9 months ago

Received a valid push on git.bioconductor.org; starting a build for commit id: 8b38f816137c7cda24611a869809822a5baf4aae

bioc-issue-bot commented 9 months ago

Dear Package contributor,

This is the automated single package builder at bioconductor.org.

Your package has been built on the Bioconductor Build System.

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 Bioconductor Build System: macOS 12.6.5 Monterey: ggsc_0.99.4.tar.gz Linux (Ubuntu 22.04.2 LTS): ggsc_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/ggsc to trigger a new build. A quick tutorial for setting up remotes and pushing to upstream can be found here.

lshep commented 9 months ago

Please correct the Errors, Warnings, and Notes in the build report before a more in depth review will take place. Please also note and correct the message

The legacy packages maptools, rgdal, and rgeos, underpinning the sp package,
which was just loaded, will retire in October 2023.
Please refer to R-spatial evolution reports for details, especially
https://r-spatial.org/r/2023/05/15/evolution4.html.
It may be desirable to make the sf package available;
package maintainers should consider adding sf to Suggests:.
The sp package is now running under evolution status 2
     (status 2 uses the sf package in place of rgdal)
bioc-issue-bot commented 9 months ago

Received a valid push on git.bioconductor.org; starting a build for commit id: 809937ac62c9b6e772ddbcc7e5a36648053de7fc

bioc-issue-bot commented 9 months ago

Dear Package contributor,

This is the automated single package builder at bioconductor.org.

Your package has been built on the Bioconductor Build System.

Congratulations! The package built without errors or warnings on all platforms.

Please see the build report for more details.

The following are build products from R CMD build on the Bioconductor Build System: macOS 12.6.5 Monterey: ggsc_0.99.5.tar.gz Linux (Ubuntu 22.04.2 LTS): ggsc_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/ggsc to trigger a new build. A quick tutorial for setting up remotes and pushing to upstream can be found here.

GuangchuangYu commented 9 months ago

@lshep We have fixed all the issues to satisfy BiocCheck.

Currently, our visualization methods support SingleCellExperiment, SpatialExperiment, and Seurat objects.

For the note you mentioned, we can't do anything about it because it is an issue with the Seurat package.

> asNamespace(ns="Seurat")
The legacy packages maptools, rgdal, and rgeos, underpinning the sp package,
which was just loaded, will retire in October 2023.
Please refer to R-spatial evolution reports for details, especially
https://r-spatial.org/r/2023/05/15/evolution4.html.
It may be desirable to make the sf package available;
package maintainers should consider adding sf to Suggests:.
The sp package is now running under evolution status 2
     (status 2 uses the sf package in place of rgdal)
<environment: namespace:Seurat>
bioc-issue-bot commented 9 months ago

Received a valid push on git.bioconductor.org; starting a build for commit id: df532be6e619e75c686a29b68510161c5f528086

bioc-issue-bot commented 9 months ago

Dear Package contributor,

This is the automated single package builder at bioconductor.org.

Your package has been built on the Bioconductor Build System.

Congratulations! The package built without errors or warnings on all platforms.

Please see the build report for more details.

The following are build products from R CMD build on the Bioconductor Build System: Linux (Ubuntu 22.04.2 LTS): ggsc_0.99.6.tar.gz macOS 12.6.5 Monterey: ggsc_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/ggsc to trigger a new build. A quick tutorial for setting up remotes and pushing to upstream can be found here.

GuangchuangYu commented 9 months ago

@lshep We have fixed all the issues to satisfy BiocCheck.

Currently, our visualization methods support SingleCellExperiment, SpatialExperiment, and Seurat objects.

For the note you mentioned, we can't do anything about it because it is an issue with the Seurat package.

> asNamespace(ns="Seurat")
The legacy packages maptools, rgdal, and rgeos, underpinning the sp package,
which was just loaded, will retire in October 2023.
Please refer to R-spatial evolution reports for details, especially
https://r-spatial.org/r/2023/05/15/evolution4.html.
It may be desirable to make the sf package available;
package maintainers should consider adding sf to Suggests:.
The sp package is now running under evolution status 2
     (status 2 uses the sf package in place of rgdal)
<environment: namespace:Seurat>

The issue will be fixed in the next release of Seurat. Currently, we can ignore this note.

lshep commented 9 months ago

general

docs

vignette

xiangpin commented 9 months ago
lshep commented 9 months ago

Please remember to push updates to git.bioconductor.org to trigger a new build and comment back here with the updates when you are ready for a re-review.

bioc-issue-bot commented 9 months ago

Received a valid push on git.bioconductor.org; starting a build for commit id: bb4f73dba906bcf7b7aa79cdde5a971064513631

bioc-issue-bot commented 9 months ago

Received a valid push on git.bioconductor.org; starting a build for commit id: bc386f1d94f9f747757845a015382150c3158bb0

GuangchuangYu commented 9 months ago
  1. The Makefile is for maintaining the package and it is added in the .Rbuildignore. We have this file in several BioC packages (e.g., clusterProfiler and ggtree) and I think it is fine to have it.
  2. A package level man page is added
  3. vignette have updated as suggested.
  4. We have change to using dgTMatrix instead of dgCMatrix
bioc-issue-bot commented 9 months ago

Dear Package contributor,

This is the automated single package builder at bioconductor.org.

Your package has been built on the Bioconductor Build System.

On one or more platforms, the build results were: "WARNINGS, 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 Bioconductor Build System: Linux (Ubuntu 22.04.2 LTS): ggsc_0.99.7.tar.gz macOS 12.6.5 Monterey: ggsc_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/ggsc to trigger a new build. A quick tutorial for setting up remotes and pushing to upstream can be found here.

bioc-issue-bot commented 9 months ago

Dear Package contributor,

This is the automated single package builder at bioconductor.org.

Your package has been built on the Bioconductor Build System.

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 Bioconductor Build System: macOS 12.6.5 Monterey: ggsc_0.99.8.tar.gz Linux (Ubuntu 22.04.2 LTS): ggsc_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/ggsc to trigger a new build. A quick tutorial for setting up remotes and pushing to upstream can be found here.

bioc-issue-bot commented 9 months ago

Received a valid push on git.bioconductor.org; starting a build for commit id: 30b74d9695f1282865af6e66480717d4dba9bc62

bioc-issue-bot commented 9 months ago

Dear Package contributor,

This is the automated single package builder at bioconductor.org.

Your package has been built on the Bioconductor Build System.

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 Bioconductor Build System: Linux (Ubuntu 22.04.2 LTS): ggsc_0.99.9.tar.gz macOS 12.6.5 Monterey: ggsc_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/ggsc to trigger a new build. A quick tutorial for setting up remotes and pushing to upstream can be found here.

GuangchuangYu commented 9 months ago
  • WARNING: Empty or missing \value sections found in man pages.

@lshep The warning reported by BiocCheck is weird. All the man pages of exported functions have \value session.

We can check the .Rd files in the man folder and all files contain value session except the ggsc-package.Rd and reexports.Rd.

bioc-issue-bot commented 9 months ago

Received a valid push on git.bioconductor.org; starting a build for commit id: f5e1584f2b77f5d6063b0094fcfb81d7be049144

bioc-issue-bot commented 9 months ago

Dear Package contributor,

This is the automated single package builder at bioconductor.org.

Your package has been built on the Bioconductor Build System.

Congratulations! The package built without errors or warnings on all platforms.

Please see the build report for more details.

The following are build products from R CMD build on the Bioconductor Build System: Linux (Ubuntu 22.04.2 LTS): ggsc_0.99.10.tar.gz macOS 12.6.5 Monterey: ggsc_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/ggsc to trigger a new build. A quick tutorial for setting up remotes and pushing to upstream can be found here.

GuangchuangYu commented 9 months ago

@lshep By adding \value session in reexports.Rd, all issues have been solved.

lshep commented 8 months ago

Thank you. everything looks good now. I am happy to accept.

bioc-issue-bot commented 8 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 8 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/GuangchuangYu.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("ggsc"). The package 'landing page' will be created at

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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.