Closed boyiguo1 closed 1 year ago
Hi @boyiguo1
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: escheR
Title: Unified multi-dimensional visualizations with Gestalt principles
Version: 0.99.0
Authors@R: c(
person("Boyi", "Guo",
email = "boyi.guo.work@gmail.com", role = c("aut", "cre"),
comment = c(ORCID = "0000-0003-2950-2349")),
person(c("Stephanie", "C."), "Hicks", role = c("aut"),
email = "shicks19@jhu.edu",
comment = c(ORCID = "0000-0002-7858-0231"))
)
Description: The creation of effective visualizations is a fundamental component
of data analysis. In biomedical research, new challenges are emerging to
visualize multi-dimensional data in a 2D space, but current data
visualization tools have limited capabilities. To address this problem,
we leverage Gestalt principles to improve the design and interpretability
of multi-dimensional data in 2D data visualizations, layering aesthetics
to display multiple variables. The proposed visualization can be applied
to spatially-resolved transcriptomics data, but also broadly to data
visualized in 2D space, such as embedding visualizations. We provide this
open source R package escheR, which is built off of the state-of-the-art
ggplot2 visualization framework and can be seamlessly integrated into
genomics toolboxes and workflows.
License: MIT + file LICENSE
Encoding: UTF-8
Roxygen: list(markdown = TRUE)
RoxygenNote: 7.2.3
biocViews:
Spatial,
SingleCell,
Transcriptomics,
Visualization,
Software
Depends:
ggplot2
Imports:
SpatialExperiment (>= 1.6.1),
spatialLIBD,
rlang,
SummarizedExperiment
BugReports: https://github.com/boyiguo1/escheR/issues
URL: https://github.com/boyiguo1/escheR
Suggests:
STexampleData,
knitr,
rmarkdown
VignetteBuilder: knitr
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.
On one or more platforms, the build results were: "skipped, TIMEOUT". 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. 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/escheR
to trigger a new build.
A quick tutorial for setting up remotes and pushing to upstream can be found here.
Received a valid push on git.bioconductor.org; starting a build for commit id: d282c3f3aa4c55015dd24576e9e643f135a43228
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. 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/escheR
to trigger a new build.
A quick tutorial for setting up remotes and pushing to upstream can be found here.
Received a valid push on git.bioconductor.org; starting a build for commit id: 6b1432abeba54e8e522710658f02ad84bf058da7
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/escheR
to trigger a new build.
A quick tutorial for setting up remotes and pushing to upstream can be found here.
Thank you for submition your package to Bioconductor. The package passed check and build. It is in pretty good shape. However there are several things need to be fixed. Please try to answer the comments line by line when you are ready for a second review. Code: Note: please condsider; Important: must be addressed.
importFrom
instead of import all with import
.
paste
in message()
, message
, stop
::
is not suggested in source code unless you can make sure all the packages are imported. Some people think it is better to keep ::
. However please note that you need to manully double check the import items when you make any change in the DESCRIPTION file during development. My recommendation is to remove one or two repeats to force the dependency check.
1:n
is not suggested in source code. Use seq_along
or seq.int
instead.
add_fill
and add_ground
and add_symbol
theme
in function make_escheR.SpatialExperiment
to a sub_function.dots
to pass parameters to geom_point
in add_symbol
function and add_fill
function and let user to overwrite the defaults.
motivation for submitting to Bioconductor
as part of the abstract/intro of the main vignette.
Received a valid push on git.bioconductor.org; starting a build for commit id: 434f5faae140f57fb2456e67054dc0bbe9190038
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/escheR
to trigger a new build.
A quick tutorial for setting up remotes and pushing to upstream can be found here.
Dear @jianhong,
Thank you very much for your careful review. I have addressed all the important comments and most of the notes. The rest of the unaddressed notes will be considered in the next update of escheR
.
Please find the line-by-line response to your comments at https://github.com/boyiguo1/escheR/issues/4.
My responses are highlighted in
Response: italic font.
Please find all changes to the escheR
package in the recent pull request at https://github.com/boyiguo1/escheR/pull/6.
Again, thank you very much for your review. Please let me know if there is anything else I need to address for this submission.
Sincerely, Boyi
Great Job. Just update your R dependence version from current >=3.6 to >=4.3.0 will be OK for acception. This is required by Bioconductor.
Jianhong.
Received a valid push on git.bioconductor.org; starting a build for commit id: 5982d360b0a69c055c7f67d534fed5802bbe0547
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/escheR
to trigger a new build.
A quick tutorial for setting up remotes and pushing to upstream can be found here.
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.
@jianhong Thank you very much for your feedback!
The default branch of your GitHub repository has been added to Bioconductor's git repository as branch devel.
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/boyiguo1.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("escheR")
. The package 'landing page' will be created at
https://bioconductor.org/packages/escheR
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.