Closed Jfortin1 closed 2 years ago
Hi @Jfortin1
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: crisprBowtie
Version: 0.99.0
Date: 2021-12-17
Title: Bowtie-based alignment of CRISPR gRNA spacer sequences
Authors@R: c(
person("Jean-Philippe", "Fortin", email = "fortin946@gmail.com", role = c("aut", "cre")))
Depends:
methods
Imports:
Biostrings,
BSgenome,
crisprBase (>= 0.99.7),
IRanges,
GenomicRanges,
Rbowtie,
S4Vectors,
stats,
stringr,
utils
Suggests:
BiocStyle,
BSgenome.Hsapiens.UCSC.hg38,
knitr,
rmarkdown,
testthat
biocViews: CRISPR, FunctionalGenomics, Alignment
Description: Provides a user-friendly interface to map on-targets and off-targets
of CRISPR gRNA spacer sequences using bowtie. The alignment is fast,
and can be performed using either commonly-used or custom CRISPR nucleases.
The alignment can work with any reference or custom genomes.
License: MIT + file LICENSE
Encoding: UTF-8
RoxygenNote: 7.1.2
VignetteBuilder: knitr
BugReports: https://github.com/Jfortin1/crisprBowtie/issues
URL: https://github.com/Jfortin1/crisprBowtie
A reviewer has been assigned to your package. Learn what to expect during the review process.
IMPORTANT: Please read this documentation for setting up remotes to push to git.bioconductor.org. It is required to push a version bump to git.bioconductor.org to trigger a new build.
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
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. This link will be active for 21 days.
Remember: if you submitted your package after July 7th, 2020,
when making changes to your repository push to
git@git.bioconductor.org:packages/crisprBowtie
to trigger a new build.
A quick tutorial for setting up remotes and pushing to upstream can be found here.
I think there is a formatting error in runBowtie.Rd or its progenitor rmarkdown because in the html I see
link{runCrisprBowtie} to map gRNA spacer sequences.
otherwise this is looking good. Can you look over the generated man pages?
Received a valid push on git.bioconductor.org; starting a build for commit id: ca9683721e8a209265abaf55b8c00ea8ced51986
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. This link will be active for 21 days.
Remember: if you submitted your package after July 7th, 2020,
when making changes to your repository push to
git@git.bioconductor.org:packages/crisprBowtie
to trigger a new build.
A quick tutorial for setting up remotes and pushing to upstream can be found here.
Thank you @vjcitn for the review -- I just pushed a new version with the fixed documentation (changed \code{link{foo}}
to \code{\link{foo}}
).
Your package has been accepted. It will be added to the Bioconductor nightly builds.
Thank you for contributing to Bioconductor!
Reviewers for Bioconductor packages are volunteers from the Bioconductor community. If you are interested in becoming a Bioconductor package reviewer, please see Reviewers Expectations.
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/Jfortin1.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("crisprBowtie")
. The package 'landing page' will be created at
https://bioconductor.org/packages/crisprBowtie
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.
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 Bioconductor Package Naming Policy and acknowledge Bioconductor may retain use of package name.
[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.
[x ] I am familiar with the Bioconductor code of conduct and agree to abide by it.
I am familiar with the essential aspects of Bioconductor software management, including:
For questions/help about the submission process, including questions about the output of the automatic reports generated by the SPB (Single Package Builder), please use the #package-submission channel of our Community Slack. Follow the link on the home page of the Bioconductor website to sign up.