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SpaceMarkers #3196

Closed atuldeshpande closed 5 months ago

atuldeshpande commented 11 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 11 months ago

Hi @atuldeshpande

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:

Type: Package
Package: SpaceMarkers
Title: Spatial Interaction Markers
Version: 0.99.0
Authors@R:c(
    person(given = "Atul", family = "Deshpande", email = "adeshpande@jhu.edu", role = c("aut", "cre"), comment = c(ORCID="0000-0001-5144-6924")),
    person(given = "Ludmila", family = "Danilova", email = "ldanilo1@jhmi.ed", role = "ctb")
  )
Description:Spatial transcriptomic technologies have helped to resolve the connection
  between gene expression and the 2D orientation of tissues relative to each other.
  However, the limited single-cell resolution makes it difficult to highlight the most 
  important molecular interactions in these tissues. SpaceMarkers, R/Bioconductor software,
  can help to find molecular interactions, by identifying genes associated with latent space 
  interactions in spatial transcriptomics.
License: MIT + file LICENSE
Depends: 
    matrixStats,
    matrixTests,
    pracma,
    R (>= 4.3.0),
    rstatix,
    spatstat
biocViews: SingleCell, GeneExpression, Software, Spatial, Transcriptomics
Imports: 
    ape,
    hdf5r,
    jsonlite,
    Matrix,
    qvalue,
    spatstat.explore,
    spatstat.geom,
    stats,
    utils
Suggests:  
    data.table,
    devtools,
    dplyr,
    ggplot2,
    hrbrthemes,
    knitr,
    RColorBrewer,
    cowplot,
    readbitmap,
    rjson,
    rmarkdown,
    testthat (>= 3.0.0),
    viridis,
    AnnotationDbi,
    clusterProfiler,
    enrichplot,
    org.Hs.eg.db
VignetteBuilder: 
    knitr
Config/testthat/edition: 3
Encoding: UTF-8
LazyData: false
Roxygen: list(markdown = TRUE)
RoxygenNote: 7.2.3
lshep commented 11 months ago

You currently download example data for the man example and vignette from github. Downloading from personal github and dropboxes are not allowed. A smaller dataset should be included in the package or the data should be hosted on a trusted public server like zenodo, AWS S3 buckets, Azure Microsoft Data Lakes, etc , minimally an institutional level server. See also ExperimentHub

atuldeshpande commented 11 months ago

Hi @lshep We've updated the package to avoid downloads from the GitHub repository.

bioc-issue-bot commented 11 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 11 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: SpaceMarkers_0.99.1.tar.gz Linux (Ubuntu 22.04.2 LTS): SpaceMarkers_0.99.1.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/SpaceMarkers to trigger a new build. A quick tutorial for setting up remotes and pushing to upstream can be found here.

bioc-issue-bot commented 11 months ago

Received a valid push on git.bioconductor.org; starting a build for commit id: 8c264f2325fbc41b8b713323046ec20d779b7eb9

bioc-issue-bot commented 11 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): SpaceMarkers_0.99.2.tar.gz macOS 12.6.5 Monterey: SpaceMarkers_0.99.2.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/SpaceMarkers to trigger a new build. A quick tutorial for setting up remotes and pushing to upstream can be found here.

bioc-issue-bot commented 11 months ago

Received a valid push on git.bioconductor.org; starting a build for commit id: bd0e0f5549a62f464778adc1d9f528acf6d7392e

bioc-issue-bot commented 11 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): SpaceMarkers_0.99.3.tar.gz macOS 12.6.5 Monterey: SpaceMarkers_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/SpaceMarkers to trigger a new build. A quick tutorial for setting up remotes and pushing to upstream can be found here.

bioc-issue-bot commented 11 months ago

Received a valid push on git.bioconductor.org; starting a build for commit id: d9390cd3cb2a81196aa16f1d3baefac70545f64d

bioc-issue-bot commented 11 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: "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.

The following are build products from R CMD build on the Bioconductor Build System: macOS 12.6.5 Monterey: SpaceMarkers_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/SpaceMarkers to trigger a new build. A quick tutorial for setting up remotes and pushing to upstream can be found here.

lshep commented 11 months ago

I'm manually kicking off a rebuild of the package to see if the linux error was a temporary situation.

bioc-issue-bot commented 11 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): SpaceMarkers_0.99.4.tar.gz macOS 12.6.5 Monterey: SpaceMarkers_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/SpaceMarkers to trigger a new build. A quick tutorial for setting up remotes and pushing to upstream can be found here.

bioc-issue-bot commented 11 months ago

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

atuldeshpande commented 10 months ago

Hi @Kayla-Morrell , can you please advise on whether we will need to resubmit the package or if we could continue the review in this thread itself?

Kayla-Morrell commented 10 months ago

@atuldeshpande - Why would you need to resubmit? If you were thinking because of the release, things were a bit busy but now that we are post-release I will be working on reviews again. The review will continue on this thread.

atuldeshpande commented 10 months ago

Thanks! That makes sense.

Kayla-Morrell commented 10 months ago

@atuldeshpande - Thank you for submitting to Bioconductor. Please see the initial review of the package below. 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

DESCRIPTION

NAMESPACE

Data

Vignette

Man pages

Best, Kayla

lshep commented 7 months ago

@atuldeshpande do you plan on pushing updates soon? We like to keep package submissions moving forward

atuldeshpande commented 7 months ago

Hi @lshep yes, we are nearly done with the updates. Will submit the package by this Friday! Sorry did not notice your message sooner.

bioc-issue-bot commented 7 months ago

Received a valid push on git.bioconductor.org; starting a build for commit id: 4109dee17e539a99539b5bdf597768082c947337

bioc-issue-bot commented 7 months ago

Dear Package contributor,

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

Your package has been built on the Bioconductor Single Package Builder.

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.

The following are build products from R CMD build on the Single Package Builder: 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/SpaceMarkers to trigger a new build. A quick tutorial for setting up remotes and pushing to upstream can be found here.

bioc-issue-bot commented 7 months ago

Received a valid push on git.bioconductor.org; starting a build for commit id: 82d676c2ca6b2fd29eb7c8fefce579b785809b86

bioc-issue-bot commented 7 months ago

Dear Package contributor,

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

Your package has been built on the Bioconductor Single Package Builder.

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 Single Package Builder: Linux (Ubuntu 22.04.3 LTS): SpaceMarkers_0.99.6.tar.gz macOS 12.7.1 Monterey: SpaceMarkers_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/SpaceMarkers to trigger a new build. A quick tutorial for setting up remotes and pushing to upstream can be found here.

atuldeshpande commented 7 months ago

Hi @Kayla-Morrell , we have updated the package in response to the review comments. Thanks!

Kayla-Morrell commented 6 months ago

@atuldeshpande - Thank you for making the necessary changes. I have just one requirement that needs to be met before I can accept the package. Please see the requirement below and let me know when the change(s) have been made.

Data

Best, Kayla

atuldeshpande commented 6 months ago

Thanks, will push an update soon!

bioc-issue-bot commented 5 months ago

Received a valid push on git.bioconductor.org; starting a build for commit id: d6108fa7ad7da9eda1bb72321277f0e22608db8f

bioc-issue-bot commented 5 months ago

Dear Package contributor,

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

Your package has been built on the Bioconductor Single Package Builder.

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 Single Package Builder: Linux (Ubuntu 22.04.3 LTS): SpaceMarkers_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/SpaceMarkers to trigger a new build. A quick tutorial for setting up remotes and pushing to upstream can be found here.

bioc-issue-bot commented 5 months ago

Received a valid push on git.bioconductor.org; starting a build for commit id: b03779ada109cf6b2809384dd340f1309fe46055

bioc-issue-bot commented 5 months ago

Dear Package contributor,

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

Your package has been built on the Bioconductor Single Package Builder.

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 Single Package Builder: Linux (Ubuntu 22.04.3 LTS): SpaceMarkers_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/SpaceMarkers to trigger a new build. A quick tutorial for setting up remotes and pushing to upstream can be found here.

Kayla-Morrell commented 5 months ago

@atuldeshpande - Thank you for making that change. I've reviewed everything and it all looks good. I'm more than happy to accept the package.

Best, Kayla

bioc-issue-bot commented 5 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 5 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/atuldeshpande.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("SpaceMarkers"). The package 'landing page' will be created at

https://bioconductor.org/packages/SpaceMarkers

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.