Bioconductor / Contributions

Contribute Packages to Bioconductor
131 stars 33 forks source link

scMitoMut: single cell mitochondrial mutation calling tool #3095

Closed wenjie1991 closed 4 months ago

wenjie1991 commented 1 year 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 1 year ago

Hi @wenjie1991

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: scMitoMut
Title: Single-cell Mitochondrial Mutation Analysis Tool
Version: 0.99.0
Authors@R: 
    person("Wenjie", "SUN", , "sunwjie@gmail.com", role = c("aut", "cre"),
    comment = c(ORCID = "https://orcid.org/0000-0002-3100-2346"))
Description: This package is for analysing mitochondrial mutations using single cell omics
    data such as scRNASeq and scATACSeq. It provides functions for mutation
    filtering and visualization.
License: MIT + file LICENSE
Encoding: UTF-8
Depends: R (>= 4.1.0)
Imports: 
    data.table,
    Rcpp,
    magrittr,
    plyr,
    stringr,
    utils,
    stats,
    methods,
    ggplot2,
    pheatmap,
    zlibbioc,
    RColorBrewer,
    rhdf5,
    readr,
    parallel,
    grDevices
LinkingTo:
    Rcpp,
    RcppArmadillo
Roxygen: list(markdown = TRUE)
RoxygenNote: 7.2.3
Suggests: testthat (>= 3.0.0), BiocStyle, knitr, rmarkdown, magick, VGAM
Config/testthat/edition: 3
VignetteBuilder: knitr
NeedsCompilation: yes
biocViews: Preprocessing, Sequencing
bioc-issue-bot commented 11 months ago

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.

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: "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): scMitoMut_0.99.1.tar.gz macOS 12.6.5 Monterey: scMitoMut_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/scMitoMut to trigger a new build. A quick tutorial for setting up remotes and pushing to upstream can be found here.

ococrook commented 10 months ago

Hi, sorry for the delay in the review! This will be completed in the next dew days!

wenjie1991 commented 10 months ago

Hi Oliver, no need to worry. There's no rush.

On Tue, Sep 5, 2023 at 2:27 PM Oliver M. Crook @.***> wrote:

Hi, sorry for the delay in the review! This will be completed in the next dew days!

— Reply to this email directly, view it on GitHub https://github.com/Bioconductor/Contributions/issues/3095#issuecomment-1706526320, or unsubscribe https://github.com/notifications/unsubscribe-auth/ABSL7VREZA4P7363MLEVAVLXY4LCPANCNFSM6AAAAAA24QPF5Y . You are receiving this because you were mentioned.Message ID: @.***>

ococrook commented 10 months ago

Looks good! Thanks for the submission, just a couple of things, but the package is great otherwise

wenjie1991 commented 10 months ago

Thank you for reviewing the submission. I'm glad to hear that overall, the package looks great. I appreciate your feedback and would be happy to address any concerns or make necessary adjustments.

lshep commented 9 months ago

@wenjie1991 the deadline for new submission acceptance for the Bioc 3.18 release is this week. Please pushed changes addressing the above issues.

wenjie1991 commented 9 months ago

Hello @lshep, Thank you for the reminder. I'm currently jammed by other tasks and will resume the submission process next week. If it's not feasible to release with Bioc 3.18, I am also comfortable waiting until 3.20 ;-)

wenjie1991 commented 9 months ago

Hi @ococrook,

Thank you for your comments once again. I have made some changes:

bioc-issue-bot commented 9 months ago

Received a valid push on git.bioconductor.org; starting a build for commit id: 0c57b0ac24b071a4726c0124f2bf43bb9a3f47f9

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: scMitoMut_0.99.2.tar.gz Linux (Ubuntu 22.04.2 LTS): scMitoMut_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/scMitoMut to trigger a new build. A quick tutorial for setting up remotes and pushing to upstream can be found here.

ococrook commented 8 months ago

Thanks!

Final comment is that the README.md should indicate its a bioconductor package, how to make issues and how to contribute to the package (if you're open to that).

Then we can move to accept tha package.

best wishes, Olly

bioc-issue-bot commented 8 months ago

Received a valid push on git.bioconductor.org; starting a build for commit id: 59fbac3988a8c506be7b420193d1b9a462725d67

bioc-issue-bot commented 8 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: macOS 12.7.1 Monterey: scMitoMut_0.99.3.tar.gz Linux (Ubuntu 22.04.2 LTS): scMitoMut_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/scMitoMut to trigger a new build. A quick tutorial for setting up remotes and pushing to upstream can be found here.

wenjie1991 commented 8 months ago

@ococrook Thank you for your suggestions; they prompted me to consider aspects I hadn't previously thought of.

The following changes have been implemented:

  1. A GitHub issue link has been added to the DESCRIPTION file.
  2. An announcement that scMitoMut is an R/Bioconductor package has been included in the README.
  3. A contribution section has been created to explicitly encourage contributions from the community.

Wenjie

bioc-issue-bot commented 8 months ago

Received a valid push on git.bioconductor.org; starting a build for commit id: cc019a914aa1d43c01444cb24a2a619a4d261776

bioc-issue-bot commented 8 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 22.04.2 LTS): scMitoMut_0.99.4.tar.gz macOS 12.7.1 Monterey: scMitoMut_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/scMitoMut to trigger a new build. A quick tutorial for setting up remotes and pushing to upstream can be found here.

ococrook commented 6 months ago

Sorry for the delay can you add that the bioconductor install instructions to the .readme ?

bioc-issue-bot commented 6 months ago

Received a valid push on git.bioconductor.org; starting a build for commit id: a3894b7c8f2232ee5a0d4e552c07460675aedc1f

bioc-issue-bot commented 6 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: Linux (Ubuntu 22.04.2 LTS): scMitoMut_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/scMitoMut to trigger a new build. A quick tutorial for setting up remotes and pushing to upstream can be found here.

wenjie1991 commented 6 months ago

The bioconductor install instructions have been added to the readme.

Surprisingly, the updated package got error in macOS platform. I guess it is not scMitoMut package issue for the Error in the Bioconductor Single Package Builder report above. Since the error is about the dependencies in macOS platform and scMitoMut package has passed the biocCheck in Github Action. I will bump version and try it again in another day.

wenjie1991 commented 6 months ago

The error may stem from the absence of a binary package for R-devel on the macOS platform, as described here: https://contributions.bioconductor.org/troubleshooting-build-report.html#cran-binaries-not-available-for-r-4.0

Anyway, I am not sure.

lshep commented 6 months ago

yes this is true. some mac binaries are not available yet as they have not been made for r-devel yet. We can ignore the mac error for now.

bioc-issue-bot commented 6 months ago

Received a valid push on git.bioconductor.org; starting a build for commit id: 8ef0b148eef40fb108bf923b39a8b8d79f424243

bioc-issue-bot commented 6 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 22.04.2 LTS): scMitoMut_0.99.6.tar.gz macOS 12.7.1 Monterey: scMitoMut_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/scMitoMut to trigger a new build. A quick tutorial for setting up remotes and pushing to upstream can be found here.

bioc-issue-bot commented 4 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 4 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/wenjie1991.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("scMitoMut"). The package 'landing page' will be created at

https://bioconductor.org/packages/scMitoMut

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.