macrophage

[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/macrophage

Confirm the following by editing each check box to '[x]'

• [x] I understand that by submitting my package to Bioconductor, the package source and all review commentary are visible to the general public.

• [x] I have read the Bioconductor Package Submission instructions. My package is consistent with the Bioconductor Package Guidelines.

• [x] I understand that a minimum requirement for package acceptance is to pass R CMD check and R CMD BiocCheck with no ERROR or WARNINGS. Passing these checks does not result in automatic acceptance. The package will then undergo a formal review and recommendations for acceptance regarding other Bioconductor standards will be addressed.

• [x] My package addresses statistical or bioinformatic issues related to the analysis and comprehension of high throughput genomic data.

• [x] I am committed to the long-term maintenance of my package. This includes monitoring the support site for issues that users may have, subscribing to the bioc-devel mailing list to stay aware of developments in the Bioconductor community, responding promptly to requests for updates from the Core team in response to changes in R or underlying software.

I am familiar with the essential aspects of Bioconductor software management, including:

• [x] The 'devel' branch for new packages and features.
• [x] The stable 'release' branch, made available every six months, for bug fixes.
• [x] Bioconductor version control using Git (optionally via GitHub).

For help with submitting your package, please subscribe and post questions to the bioc-devel mailing list.

[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: macrophage
Title: Human macrophage immune response
Version: 0.99.0
Author: Michael Love
Maintainer: Michael Love <michaelisaiahlove@gmail.com>
Description: This package provides the output of running Salmon
  on a set of 24 RNA-seq samples from Alasoo, et al. "Shared genetic 
  effects on chromatin and gene expression indicate a role for enhancer 
  priming in immune response", published in Nature Genetics, January 2018.
  For details on version numbers and how the samples were processed
  see the package vignette.
biocViews: ExperimentData, SequencingData, RNASeqData
License: GPL (>= 2)
Suggests: knitr
VignetteBuilder: knitr
NeedsCompilation: no

[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:

ae0d0a1 move log to txt

[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.

[mikelove]

Question for @Kayla-Morrell

I have a software package which builds on this one as a data package. Should I add the software to this thread or would you prefer I wait and post as a new issue?

[Kayla-Morrell]

Hey @mikelove,

Ultimately it's up to you which way you prefer. I was about to accept the data package because everything looked good but then you would have to wait for it to be officially accepted and then go through a build cycle (without any issues) before the data would be available for the software package.

If it is directly related (depends/imports/etc.) feel free to submit on this thread using AdditionalPackage: with the github repo url. This way the single package builder can find the data package (in it's current state) for the software package. I'll be able to start the review for the software package as soon as there is a clean build.

Best, Kayla

[mikelove]

Thanks for the details. That makes sense (i hadn't thought about the build cycle part)

We're still getting the package in order, so I'll post it as a new issue next week probably. Thanks for clarifying, and thanks for your time during review.

[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!

[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("macrophage"). The package 'landing page' will be created at

https://bioconductor.org/packages/macrophage

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.

[mikelove]

Hi,

I checked out the Bioc git package and then tried to push a change but i get the following:

> git push origin master
fatal: remote error: FATAL: W any packages/macrophage nobody DENIED by fallthru
(or you mis-spelled the reponame)
> git remote -v
origin  https://git.bioconductor.org/packages/macrophage (fetch)
origin  https://git.bioconductor.org/packages/macrophage (push)

This is on a machine where I have other Bioc repositories and no problem pushing. Any ideas why I can't push to Bioc git repo?

Here's the landing page:

http://master.bioconductor.org/packages/3.9/data/experiment/html/macrophage.html

[mtmorgan]

It needs to be checked out with ssh, using git clone git@git.bioconductor.org:packages/macrophage (note :packages versus /packages).

You might have success with renaming the remote, git remote remove origin and updating git remote add origin git@git.bioconductor.org:packages/macrophage.

[mikelove]

Doh, thanks, i was copy pasting without looking.