Contributions
Contributions copied to clipboard
Bioconductor
tidyFlowCore
Update the following URL to point to the GitHub repository of the package you wish to submit to Bioconductor
- Repository: https://github.com/keyes-timothy/tidyFlowCore
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:
- [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 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.
Hi @keyes-timothy
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: tidyFlowCore
Type: Package
Title: tidyFlowCore: Bringing flowCore to the tidyverse
Version: 0.99.0
Authors@R:
c(person(given = "Timothy",
family = "Keyes",
role = c("cre"),
email = "[email protected]",
comment = c(ORCID = "0000-0003-0423-9679")),
person(given = "Kara",
family = "Davis",
role = c("rth", "own"),
email = "[email protected]"),
person(given = "Garry",
family = "Nolan",
role = c("rth", "own"),
email = "[email protected]"))
Description: tidyFlowCore bridges the gap between flow cytometry analysis using the
flowCore Bioconductor package and the tidy data principles advocated by the tidyverse. It provides
a suite of dplyr-, ggplot2-, and tidyr-like verbs specifically designed for working with flowFrame
and flowSet objects as if they were tibbles; however, your data remain flowCore
data structures under this layer of abstraction. tidyFlowCore enables
intuitive and streamlined analysis workflows that can leverage both the
Bioconductor and tidyverse ecosystems for cytometry data.
License: MIT + file LICENSE
Encoding: UTF-8
URL: https://github.com/keyes-timothy/tidyFlowCore, https://keyes-timothy.github.io/tidyFlowCore/
BugReports: https://github.com/keyes-timothy/tidyFlowCore/issues
Depends:
R (>= 4.3)
Imports:
Biobase,
dplyr,
flowCore,
ggplot2,
methods,
purrr,
rlang,
stats,
stringr,
tibble,
tidyr
RoxygenNote: 7.3.1
Suggests:
BiocStyle,
HDCytoData,
knitr,
RefManageR,
rmarkdown,
sessioninfo,
testthat (>= 3.0.0)
Config/testthat/edition: 3
biocViews: SingleCell, FlowCytometry
VignetteBuilder: knitr
Your package has been added to git.bioconductor.org to continue the pre-review process. A build report will be posted shortly. Please fix any ERROR and WARNING in the build report before a reviewer is assigned or provide a justification on why you feel the ERROR or WARNING should be granted an exception.
IMPORTANT: Please read this documentation for setting up remotes to push to git.bioconductor.org. All changes should be pushed to git.bioconductor.org moving forward. It is required to push a version bump to git.bioconductor.org to trigger a new build report.
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 the Bioconductor Single Package Builder.
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.
The following are build products from R CMD build on the Single Package Builder: Linux (Ubuntu 22.04.3 LTS): tidyFlowCore_0.99.0.tar.gz
Links above active for 21 days.
Remember: if you submitted your package after July 7th, 2020,
when making changes to your repository push to
[email protected]:packages/tidyFlowCore to trigger a new build.
A quick tutorial for setting up remotes and pushing to upstream can be found here.
A reviewer has been assigned to your package for an indepth review. Please respond accordingly to any further comments from the reviewer.
Received a valid push on git.bioconductor.org; starting a build for commit id: 0ede10bcc13c669fa02bbdedc851e49add9ed342
Dear Package contributor,
This is the automated single package builder at bioconductor.org.
Your package has been built on the Bioconductor Single Package Builder.
Congratulations! The package built without errors or warnings on all platforms.
Please see the build report for more details.
The following are build products from R CMD build on the Single Package Builder: Linux (Ubuntu 22.04.3 LTS): tidyFlowCore_0.99.1.tar.gz
Links above active for 21 days.
Remember: if you submitted your package after July 7th, 2020,
when making changes to your repository push to
[email protected]:packages/tidyFlowCore to trigger a new build.
A quick tutorial for setting up remotes and pushing to upstream can be found here.
The package is well-designed and documentation is clear. It uses many Bioconductor packages. A couple of minor omissions.
- Chunk in vignette generating output should have interpretation afterwards. For example, what does the scatter plot reveal?
-
biocViewsfield of DESCRIPTION file should haveInfrastructurelike other tidy packages already in Bioconductor do.
