sa-lee commented 4 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/sa-lee/fluentGenomics

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.

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bioc-issue-bot commented 4 years ago

Hi @sa-lee

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: fluentGenomics
Type: Package
Title: A plyranges and tximeta workflow
Version: 0.99.0
Authors@R: c(
   person(role = c("aut", "cre"), "Stuart", "Lee", email = "lee.s@wehi.edu.au"),
   person(role=c("aut", "ctb"), "Michael", "Love", email = "michaelisaiahlove@gmail.com")
   )
Description: An extended workflow using the plyranges and tximeta
    packages for fluent genomic data analysis. Use tximeta to correctly import 
    RNA-seq transcript  quantifications and summarize them to gene counts for 
    downstream analysis. Use plyranges for clearly expressing operations
    over genomic coordinates and to combine results from differential
    expression and differential accessibility analyses.
License: MIT + file LICENSE
Encoding: UTF-8
LazyData: true
RoxygenNote: 7.0.2
VignetteBuilder:
    knitr,
    rmarkdown
Depends: R (>= 4.0)
Imports:
    plyranges (>= 1.7.7),
    dplyr,
    SummarizedExperiment,
    readr,
    stats,
    utils
Suggests:
    knitr,
    rmarkdown,
    bookdown,
    rappdirs,
    BiocFileCache,
    DESeq2,
    limma,
    ggplot2,
    tidyr,
    tximeta (>= 1.4.2),
    macrophage (>= 1.2.0),
biocViews: Workflow, BasicWorkflow, GeneExpressionWorkflow
Workflow: true
URL: https://github.com/sa-lee/fluentGenomics
BugReports: https://github.com/sa-lee/fluentGenomics/issues

sa-lee commented 4 years ago

cc @mikelove

bioc-issue-bot commented 4 years ago

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.

LiNk-NY commented 4 years ago

Hi Stuart, @sa-lee

Thank you for your submission. Please see the review below. Feel free to comment if you have any questions.

Best, Marcel

fluentGenomics #1350

DESCRIPTION

Looks good.

NAMESPACE

Looks okay although cache functions seem to be helpers rather than main functions.

vignettes/

Formatting looks great! R code could be formatted with 4 spaces but this is a minor detail.
The *.bib and workflow.png files should be in the main vignettes folder. Is there a reason for putting them in /inst/vignettes?
'stable version' should read 'development version' after acceptance and until Bioconductor release.

data/

It would be good if the "peaks" data had a slightly more descriptive name

docs/

Please remove built documentation from the source package (docs folder). This is generated when the package is built.

Other

'pkgdown' files (e.g., _render.R, and _pkgdown.yml) should go in another branch as they are related to the website build and not the Bioconductor software.
WORDLIST file should also be in that branch.
Consolidate LICENSE files, if possible.

bioc-issue-bot commented 4 years ago

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

6261319 consolidate licence a31cbec move vignette content 6fc25fd consolidate licence and version bump 8c50851 remove non package relevant content 572530a update travis

bioc-issue-bot commented 4 years ago

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

88b116a version bump

sa-lee commented 4 years ago

Hi Marcel @LiNk-NY ,

Hi Stuart, @sa-lee

Thank you for your submission. Please see the review below. Feel free to comment if you have any questions.

Best, Marcel

fluentGenomics #1350

DESCRIPTION

Looks good.

NAMESPACE

Looks okay although cache functions seem to be helpers rather than main functions.

I've removed this now.

vignettes/

Formatting looks great! R code could be formatted with 4 spaces but this is a minor detail.

The *.bib and workflow.png files should be in the main vignettes folder. Is there a reason for putting them in /inst/vignettes?

'stable version' should read 'development version' after acceptance and until Bioconductor release.

I've made these changes. I think I originally had this in /inst/vignettes/ cause that's what we did for the workshop.

data/

It would be good if the "peaks" data had a slightly more descriptive name

I think in the context of the vignette this makes sense.

docs/

Please remove built documentation from the source package (docs folder). This is generated when the package is built.

Other

'pkgdown' files (e.g., _render.R, and _pkgdown.yml) should go in another branch as they are related to the website build and not the Bioconductor software.

WORDLIST file should also be in that branch.

Consolidate LICENSE files, if possible.

Done I've moved everything into a separate branch.

Please let me know if there's anything else.

bioc-issue-bot commented 4 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.

sa-lee commented 4 years ago

hi @LiNk-NY Marcel, I think I've made all the changes you suggested. Please let me know if there's anything else.

Thanks, Stuart

LiNk-NY commented 4 years ago

Hi Stuart, @sa-lee I'll have another look at it today. Thanks.

LiNk-NY commented 4 years ago

Hi Stuart, @sa-lee Thanks for making those changes. You probably don't need the Makefile and LICENSE files in there either (since you're the author of the work it's licenced to you automatically AFAIU; do keep License: MIT in the DESCRIPTION). I will accept your package. Best, Marcel

mikelove commented 4 years ago

Woohoo 🎉

bioc-issue-bot commented 4 years ago

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!

sa-lee commented 4 years ago

Thanks @LiNk-NY!

mtmorgan commented 4 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/sa-lee.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("fluentGenomics"). The package 'landing page' will be created at

https://bioconductor.org/packages/fluentGenomics

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 commented 4 years ago

Woohoo 🎉

Bioconductor / Contributions