crumblr

[GabrielHoffman]

Update the following URL to point to the GitHub repository of
the package you wish to submit to Bioconductor

• Repository: https://github.com/DiseaseNeurogenomics/crumblr

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[bioc-issue-bot]

Hi @GabrielHoffman

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: crumblr
Type: Package
Title: Count ratio uncertainty modeling base linear regression
Version: 0.99.11
Date: 2024-06-14
Authors@R: person("Gabriel", "Hoffman", role=c("aut", "cre"), email="[email protected]")
Description: Crumblr enables analysis of count ratio data using precision weighted linear (mixed) models.  It uses an asymptotic normal approximation of the variance following the centered log ration transform (CLR) that is widely used in compositional data analysis.  Crumblr provides a fast, flexable alternative to GLMs and GLMM's while retaining high power and controlling the false positive rate.  
VignetteBuilder: knitr
License: Artistic-2.0
Encoding: UTF-8
URL: https://DiseaseNeurogenomics.github.io/crumblr
BugReports: https://github.com/DiseaseNeurogenomics/crumblr/issues
Suggests:
    BiocStyle,
    knitr,
    rmarkdown,
    dreamlet,
    muscat,
    ExperimentHub,
    scater,
    HMP,
    BiocGenerics
biocViews: 
    RNASeq,
    GeneExpression,
    DifferentialExpression,
    BatchEffect,
    QualityControl,
    SingleCell,
    Regression,
    Epigenetics,
    FunctionalGenomics,
    Transcriptomics,
    Normalization,
    Preprocessing,
    Software
Depends:
    R (>= 4.2.0),
    ggplot2,
    methods
Imports:
    Rdpack,
    viridis,
    tidytree,
    variancePartition (>= 1.35.3),
    SingleCellExperiment,
    ggtree,
    dplyr,
    stats,
    MASS,
    Rfast
RoxygenNote: 7.3.2
RdMacros: Rdpack
LazyData: false

[GabrielHoffman]

Hi, following up to make sure this doesn't get lost.

Best,
Gabriel

[lshep]

We prefer to have a clean upload to Bioconductor. Please remove pkgdown
directories from default branch until uploaded to Bioconductor.

Please remove comment out code chunks in vignettes.

Could you please provide an abstract/intro section in your vignette that
provides motivation for inclusion in Bioconductor and when appropriate a review
and comparison to existing Bioconductor packages with similar functionality or
scope.

[GabrielHoffman]

Done. I pushed the changes to https://github.com/DiseaseNeurogenomics/crumblr

Best,
Gabriel

[GabrielHoffman]

Following up, since I'd like this be accepted by Bioconductor before I submit my manuscript

Best,
Gabriel

[bioc-issue-bot]

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]

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 24.04.1 LTS): crumblr_0.99.13.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
[email protected]:packages/crumblr to trigger a new build.
A quick tutorial for setting up remotes and pushing to upstream can be found here.

[GabrielHoffman]

I have resolved the issues from the build report, but I can't push it to the Bioconductor git repo. Is this an issue on my end?

crumblr> git remote -v
bioc	[email protected]:packages/crumblr (fetch)
bioc	[email protected]:packages/crumblr (push)
origin	https://github.com/GabrielHoffman/crumblr.git (fetch)
origin	https://github.com/GabrielHoffman/crumblr.git (push)

crumblr> git push bioc
Enumerating objects: 137, done.
Counting objects: 100% (137/137), done.
Delta compression using up to 11 threads
Compressing objects: 100% (80/80), done.
Writing objects: 100% (81/81), 31.81 KiB | 6.36 MiB/s, done.
Total 81 (delta 70), reused 0 (delta 0), pack-reused 0
remote: FATAL: W refs/heads/master packages/crumblr g.hoffman DENIED by fallthru
remote: error: hook declined to update refs/heads/master
To git.bioconductor.org:packages/crumblr
 ! [remote rejected] master -> master (hook declined)
error: failed to push some refs to 'git.bioconductor.org:packages/crumblr

[lshep]

Bioconductor does not have a master branch. See https://contributions.bioconductor.org/git-version-control.html#essential-work-flow 21.5.1 point number 5

[bioc-issue-bot]

Received a valid push on git.bioconductor.org; starting a build for commit id: de95d1b26c5eef78218953a2c7248b1d37b4fa87

[bioc-issue-bot]

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: "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 Single Package Builder:
Linux (Ubuntu 24.04.1 LTS): crumblr_0.99.14.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
[email protected]:packages/crumblr to trigger a new build.
A quick tutorial for setting up remotes and pushing to upstream can be found here.

[bioc-issue-bot]

Received a valid push on git.bioconductor.org; starting a build for commit id: 4d0376e2a052e51f1f44b7e596857c54d435dd89

[bioc-issue-bot]

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 24.04.1 LTS): crumblr_0.99.15.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
[email protected]:packages/crumblr to trigger a new build.
A quick tutorial for setting up remotes and pushing to upstream can be found here.

[bioc-issue-bot]

Received a valid push on git.bioconductor.org; starting a build for commit id: 152385b27e3e9b8c0b6c99747f73ba81cd34074b

[bioc-issue-bot]

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 24.04.1 LTS): crumblr_0.99.16.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
[email protected]:packages/crumblr to trigger a new build.
A quick tutorial for setting up remotes and pushing to upstream can be found here.

[GabrielHoffman]

Can this be accepted to Bioconductor now?

Best,
Gabriel

[bioc-issue-bot]

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