fishpond

[mikelove]

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

• Repository: https://github.com/mikelove/fishpond

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[bioc-issue-bot]

Hi @mikelove

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: fishpond
Title: Fishpond: differential transcript and gene expression
    with inferential replicates
Version: 0.99.5
Author: Anqi Zhu, Avi Srivastava, Joseph Ibrahim, Rob Patro, Michael Love
Maintainer: Michael Love <michaelisaiahlove@gmail.com>
Description: Fishpond contains methods for differential transcript
    and gene expression analysis using inferential replicates for
    uncertainty of abundance quantification, e.g. Gibbs samples
    or bootstrap samples.
Imports:
    graphics,
    stats,
    utils,
    abind,
    samr,
    S4Vectors,
    SummarizedExperiment,
    matrixStats,
    svMisc
Suggests: 
    testthat,
    knitr,
    rmarkdown,
    macrophage,
    tximeta,
    DESeq2,
    apeglm
License: GPL-2
Encoding: UTF-8
URL: https://github.com/mikelove/DESeq2
biocViews: Sequencing, RNASeq, Microbiome,
    GeneExpression, Transcription,
    Normalization, DifferentialExpression, Regression
VignetteBuilder: knitr
LazyData: true
RoxygenNote: 6.1.1

[bioc-issue-bot]

A reviewer has been assigned to your package. Learn what to expect during the review process.

IMPORTANT: Please read the instructions for setting up a push hook on your repository, or further changes to your repository will NOT trigger a new build.

[bioc-issue-bot]

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.

[bioc-issue-bot]

Received a valid push; starting a build. Commits are:

df53617 turning off caching in vignette

[bioc-issue-bot]

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.

[bioc-issue-bot]

Received a valid push; starting a build. Commits are:

5895167 Adding citation to biorxiv preprint

[bioc-issue-bot]

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.

[lshep]

Can you fix the few NOTES on coding style from the report. Else this looks in great shape.

[bioc-issue-bot]

Received a valid push; starting a build. Commits are:

d89abf5 code review

[mikelove]

Thanks @lshep !

I've addressed most of the NOTES on coding style. These are the 3 remaining with some explanation:

* Checking coding practice...
    * NOTE: Avoid 1:...; use seq_len() or seq_along()
      Found in files:
        helper.R (line 159, column 7)
        helper.R (line 166, column 7)

These uses of 1: should be fine, they have a hard coded endpoint (e.g. 1:6) so don't suffer from the 1:0 problem.

    * NOTE: Consider shorter lines; 1 lines (0%) are > 80 characters
      long.
    First 1 lines:
      vignettes/fishpond.Rmd:320 * [Alevin Inf Rep Importer](https://gist.git...

This is a URL in the vignette Rmd.

    * NOTE: Consider multiples of 4 spaces for line indents, 277
      lines(20%) are not.

I use emacs and prefer 2 spaces for line indents. Hopefully this is ok :-)

[bioc-issue-bot]

Your package has been accepted. It will be added to the Bioconductor Git repository and nightly builds. Additional information will be posed to this issue in the next several days.

Thank you for contributing to Bioconductor!

[bioc-issue-bot]

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.

[mtmorgan]

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/mikelove.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("fishpond"). The package 'landing page' will be created at

https://bioconductor.org/packages/fishpond

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.