Closed Jfortin1 closed 7 months 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: crisprShiny
Title: Exploring curated CRISPR gRNAs via Shiny
Version: 0.99.0
Authors@R: c(
person("Jean-Philippe", "Fortin", email = "fortin946@gmail.com", role = c("aut", "cre")),
person("Luke", "Hoberecht", email = "lukehob3@gmail.com", role = c("aut"))
)
Description: Provides means to interactively visualize guide RNAs (gRNAs) in GuideSet objects via Shiny application. This GUI can be self-contained or as a module within a larger Shiny app. The content reflects the annotations present in the passed GuideSet object, and includes intuitive tools to examine, filter, and export gRNAs, thereby making gRNA design more user-friendly.
Bioconductor package crisprDesign via Shiny.
Depends:
R (>= 4.2.0)
Imports:
BiocGenerics,
Biostrings,
BSgenome,
crisprBase,
crisprDesign,
crisprScore,
crisprViz,
DT,
GenomeInfoDb,
htmlwidgets,
methods,
S4Vectors,
shiny,
shinyBS,
shinyjs,
utils,
waiter
Suggests:
BiocStyle,
knitr,
rmarkdown,
shinyFeedback,
testthat (>= 3.0.0)
biocViews:
CRISPR,
FunctionalGenomics,
GeneTarget,
GUI
License: MIT + file LICENSE
Encoding: UTF-8
Roxygen: list(markdown = TRUE)
RoxygenNote: 7.2.3
StagedInstal: no
VignetteBuilder: knitr
BugReports: https://github.com/crisprVerse/crisprShiny/issues
URL: https://github.com/crisprVerse/crisprShiny
Config/testthat/edition: 3
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 the Bioconductor Build System.
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 Bioconductor Build System: macOS 12.6.5 Monterey: crisprShiny_0.99.0.tar.gz Linux (Ubuntu 22.04.2 LTS): crisprShiny_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
git@git.bioconductor.org:packages/crisprShiny
to trigger a new build.
A quick tutorial for setting up remotes and pushing to upstream can be found here.
Hi Jean-Philippe @Jfortin1
Thank you for your submission. Please fix the error and bump the version for another build. See the review below. Best, Marcel
StagedInstal
field from the DESCRIPTION
(see
https://blog.r-project.org/2019/02/14/staged-install/ for details)4.3.0
crisprShiny
?criprShiny
modules is for developer use.styler
or other syntax guide for
arguments and function body delimiters {
..filterTemplate
is not used in the code. Consider removing
it.shiny
package to the Depends
field..renderTssAnnotationTab()
has an "add plot" comment. Please resolve..enzymeAnnotationDataTable
switch
call (interface_tooltips.R
).> covr::package_coverage()
Error: Failure in `/tmp/RtmpgxoZxh/R_LIBS4b94575f2ce6/crisprShiny/crisprShiny-tests/testthat.Rout.fail`
setup.*\\.[rR]$", env = env, wrap = FALSE)
8. │ └─base::lapply(...)
9. │ └─testthat (local) FUN(X[[i]], ...)
10. │ └─testthat::source_file(path, env = env, chdir = chdir, wrap = wrap)
11. │ ├─base::withCallingHandlers(...)
12. │ └─base::eval(exprs, env)
13. │ └─base::eval(exprs, env)
14. │ └─utils::data("txdb_human", package = "crisprDesignData") at crisprShiny-tests/testthat/setup.R:4:0
15. │ └─base::find.package(package, lib.loc, verbose = verbose)
16. │ └─base::stop(packageNotFoundError(bad, lib.loc, sys.call()))
17. └─testthat (local) `<fn>`(`<pckgNtFE>`)
18. └─rlang::abort(...)
which means that crisprDesignData
should be added to the Imports
or
Suggests
.
This issue is being closed because there has been no progress for an extended period of time. You may reopen the issue when you have the time to actively participate in the review / submission process. Please also keep in mind that a package accepted to Bioconductor requires a commitment on your part to ongoing maintenance.
Thank you for your interest in Bioconductor.
Hi @lshep,
I just got back from a 3-month sabbatical and did not have the time to follow up with this package submission. Could we reopen this issue please? We have now finished the review of the package
Dear @Jfortin1 ,
We have reopened the issue to continue the review process. Please remember to push a version bump to git.bioconductor.org to trigger a new build.
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: f9079bd894fccfe311ffed6d34c0fe7f198d75ba
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: "WARNINGS, 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 22.04.2 LTS): crisprShiny_0.99.4.tar.gz macOS 12.7.1 Monterey: crisprShiny_0.99.4.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
git@git.bioconductor.org:packages/crisprShiny
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: 46747ab4204dbb7158a3164bfd1380b8c082c6df
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: "WARNINGS, 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 22.04.2 LTS): crisprShiny_0.99.5.tar.gz macOS 12.7.1 Monterey: crisprShiny_0.99.5.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
git@git.bioconductor.org:packages/crisprShiny
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: 39ac5da64cc89fa043c43bae49c028555b17a31f
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: "skipped, 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 22.04.2 LTS): crisprShiny_0.99.6.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
git@git.bioconductor.org:packages/crisprShiny
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: 9de8613f4a074a38f8c3569bc0d23bf7bfe5d175
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: "skipped, 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 22.04.2 LTS): crisprShiny_0.99.7.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
git@git.bioconductor.org:packages/crisprShiny
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: 897b85179a598df1238ffcc1844d3ecca4dd94f9
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: "skipped, 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 22.04.2 LTS): crisprShiny_0.99.8.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
git@git.bioconductor.org:packages/crisprShiny
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: 1a65aa745fe328b06179410750c76784b7900b03
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: "skipped, 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 22.04.2 LTS): crisprShiny_0.99.9.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
git@git.bioconductor.org:packages/crisprShiny
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: 903ea20efdbee7a9dc31629f78ccd42103b3ccaf
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: "WARNINGS". 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: macOS 12.7.1 Monterey: crisprShiny_0.99.10.tar.gz Linux (Ubuntu 22.04.2 LTS): crisprShiny_0.99.10.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
git@git.bioconductor.org:packages/crisprShiny
to trigger a new build.
A quick tutorial for setting up remotes and pushing to upstream can be found here.
Hi @Jfortin1 When ready, please respond to the bullet points in the review. Thanks! -Marcel
Received a valid push on git.bioconductor.org; starting a build for commit id: fa2d3af17ff74712fadfe0b63db3d56073007032
Received a valid push on git.bioconductor.org; starting a build for commit id: 142b565f50ee2ebb066a296353fa6501881d5dfb
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: macOS 12.7.1 Monterey: crisprShiny_0.99.12.tar.gz Linux (Ubuntu 22.04.3 LTS): crisprShiny_0.99.12.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
git@git.bioconductor.org:packages/crisprShiny
to trigger a new build.
A quick tutorial for setting up remotes and pushing to upstream can be found here.
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: "WARNINGS". 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): crisprShiny_0.99.11.tar.gz macOS 12.7.1 Monterey: crisprShiny_0.99.11.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
git@git.bioconductor.org:packages/crisprShiny
to trigger a new build.
A quick tutorial for setting up remotes and pushing to upstream can be found here.
Hi @LiNk-NY, thank you for your review. Here's a response:
> covr::package_coverage()
Error: Failure in `/tmp/RtmpgxoZxh/R_LIBS4b94575f2ce6/crisprShiny/crisprShiny-tests/testthat.Rout.fail`
setup.*\\.[rR]$", env = env, wrap = FALSE)
8. │ └─base::lapply(...)
9. │ └─testthat (local) FUN(X[[i]], ...)
10. │ └─testthat::source_file(path, env = env, chdir = chdir, wrap = wrap)
11. │ ├─base::withCallingHandlers(...)
12. │ └─base::eval(exprs, env)
13. │ └─base::eval(exprs, env)
14. │ └─utils::data("txdb_human", package = "crisprDesignData") at crisprShiny-tests/testthat/setup.R:4:0
15. │ └─base::find.package(package, lib.loc, verbose = verbose)
16. │ └─base::stop(packageNotFoundError(bad, lib.loc, sys.call()))
17. └─testthat (local) `<fn>`(`<pckgNtFE>`)
18. └─rlang::abort(...)
which means that crisprDesignData should be added to the Imports or Suggests. DONE
Hi Jean-Philippe, @Jfortin1
Apologies for the delay in getting back to you. I have taken a second look at the package. It looks good to me. Please be aware that the check on merida is close to timing out. You may want to consider reducing the check timing to avoid a timeout on Mac. Your package has been accepted. Thank you for your contribution.
Best regards, Marcel
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.
@LiNk-NY Thanks Marcel!
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/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("crisprShiny")
. The package 'landing page' will be created at
https://bioconductor.org/packages/crisprShiny
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.