Closed sa-lee closed 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
cc @mikelove
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.
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
*.bib
and workflow.png
files should be in the main vignettes
folder.
Is there a reason for putting them in /inst/vignettes
?docs
folder).
This is generated when the package is built._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.LICENSE
files, if possible.Received a valid push; starting a build. Commits are:
88b116a version bump
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
andworkflow.png
files should be in the mainvignettes
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.
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.
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
Hi Stuart, @sa-lee I'll have another look at it today. Thanks.
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
Woohoo 🎉
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!
Thanks @LiNk-NY!
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.
Woohoo 🎉
Update the following URL to point to the GitHub repository of the package you wish to submit to Bioconductor
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:
For help with submitting your package, please subscribe and post questions to the bioc-devel mailing list.