censcyt - Githubissues

retogerber commented 3 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/retogerber/censcyt

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bioc-issue-bot commented 3 years ago

Hi @retogerber

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: censcyt
Version: 0.99.0
Title: Differential abundance analysis with a right censored covariate in high-dimensional cytometry
Description: Methods for differential abundance analysis in high-dimensional cytometry data when a covariate is subject to right censoring (e.g. survival time) based on multiple imputation and generalized linear mixed models.
Authors@R: person("Reto", "Gerber", email = "gerberreto@pm.me", role = c("aut", "cre"), comment = c(ORCID = "0000-0001-5414-8906"))
URL: https://github.com/retogerber/censcyt
BugReports: https://github.com/retogerber/censcyt/issues
License: MIT + file LICENSE
biocViews:
    ImmunoOncology, 
    FlowCytometry, 
    Proteomics, 
    SingleCell, 
    CellBasedAssays, 
    CellBiology, 
    Clustering, 
    FeatureExtraction, 
    Software,
    Survival
Depends: R (>= 4.0)
Imports:
    BiocParallel,
    broom.mixed,
    diffcyt,
    dirmult,
    dplyr, 
    edgeR,
    fitdistrplus,
    lme4, 
    magrittr, 
    MASS,
    methods, 
    mice,
    multcomp, 
    purrr,
    rlang,
    S4Vectors,
    stats, 
    stringr,
    SummarizedExperiment, 
    survival,
    tibble,
    tidyr, 
    utils 
VignetteBuilder: knitr
Suggests:
    BiocStyle,
    knitr,
    rmarkdown,
    testthat,
    ggplot2
RoxygenNote: 7.1.1

bioc-issue-bot commented 3 years ago

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bioc-issue-bot commented 3 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.

On one or more platforms, the build results were: "ERROR, 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. 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/censcyt to trigger a new build. A quick tutorial for setting up remotes and pushing to upstream can be found here.

bioc-issue-bot commented 3 years ago

Received a valid push on git.bioconductor.org; starting a build for commit id: 506cadb0012328bdc2915cc590cea6d99a0b72ee

bioc-issue-bot commented 3 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.

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. 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/censcyt to trigger a new build. A quick tutorial for setting up remotes and pushing to upstream can be found here.

bioc-issue-bot commented 3 years ago

Received a valid push on git.bioconductor.org; starting a build for commit id: 6d205d81402254145dfbd12daa6237610475f030

bioc-issue-bot commented 3 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.

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. 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/censcyt to trigger a new build. A quick tutorial for setting up remotes and pushing to upstream can be found here.

bioc-issue-bot commented 3 years ago

Received a valid push on git.bioconductor.org; starting a build for commit id: c50f19a443fbb8aa78ca212ea879ca44f588832a

bioc-issue-bot commented 3 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.

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 git@git.bioconductor.org:packages/censcyt to trigger a new build. A quick tutorial for setting up remotes and pushing to upstream can be found here.

bioc-issue-bot commented 3 years ago

Received a valid push on git.bioconductor.org; starting a build for commit id: 89d98d8214012130f2ef6e247cf4d284f7099821

bioc-issue-bot commented 3 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/censcyt to trigger a new build. A quick tutorial for setting up remotes and pushing to upstream can be found here.

retogerber commented 3 years ago

Hi @hpages

Thanks for taking the time to review this package. Just a short question: Until when can I expect a feedback? Just asking because I haven't yet gotten any and was wondering if I missed something in the submission process.

Best regards

hpages commented 3 years ago

Hi @retogerber ,

Sorry for the delay. censcyt looks good and is ready for acceptance. Only one minor thing: Is the masking of the createFormula() function from the diffcyt package intended? If yes, then this should be mentioned in the man page with a reference to the original createFormula(). If not, then please rename the function.

Also maybe you could make it easier for the user to compare censcyt with diffcyt by moving the latter from Imports to Depends. This way it will be automatically placed on the search path when the user loads the former, and it will be placed after the former, which is probably what the user would want. This would avoid the current inconvenience that the user explicitly needs to load diffcyt, and also avoid the uncertainty of where diffcyt ends up on the search path, sometimes before censcyt, sometimes after, depending on whether the package is loaded after or before censcyt. Having diffcyt in Depends would make its position on the search list the same for everybody and predictable, and therefore make the potential name conflicts easier to deal with.

Thanks, H.

bioc-issue-bot commented 3 years ago

Received a valid push on git.bioconductor.org; starting a build for commit id: 3b112112bbb8a6a588eff73968461c9fd9e044c6

retogerber commented 3 years ago

Hi @hpages

Thanks for the feedback. Yes the masking of createFormula() is intended since it expands the functionality but is backwards compatible (within diffcyt). Moving diffcyt to Depends indeed solves the issue with inconsistency when loading in different orders. Updated this and pushed to bioconductor.

Thanks again. Best

bioc-issue-bot commented 3 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.

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. 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/censcyt to trigger a new build. A quick tutorial for setting up remotes and pushing to upstream can be found here.

bioc-issue-bot commented 3 years ago

Received a valid push on git.bioconductor.org; starting a build for commit id: 075f634fa9180c95d5c9825721a2ca723573feac

bioc-issue-bot commented 3 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/censcyt to trigger a new build. A quick tutorial for setting up remotes and pushing to upstream can be found here.

hpages commented 3 years ago

Thanks. Package is good to go. Note that it would be great if you could provide a link or reference to diffcyt::createFormula() in your man page for createFormula(). Please consider adding this when you get a chance.

Cheers, H.

bioc-issue-bot commented 3 years ago

Your package has been accepted. It will be added to the Bioconductor nightly builds.

Thank you for contributing to Bioconductor!

retogerber commented 3 years ago

Thanks @hpages! Will add the suggested link to diffcyt::createFormula().

mtmorgan commented 3 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/retogerber.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("censcyt"). The package 'landing page' will be created at

https://bioconductor.org/packages/censcyt

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.

Bioconductor / Contributions

censcyt #1747