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faers #3227

Closed Yunuuuu closed 4 months ago

Yunuuuu commented 8 months ago

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]'

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.

bioc-issue-bot commented 8 months ago

Hi @Yunuuuu

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: faers
Title: R interface for FDA Adverse Event Reporting System
Version: 0.99.0
Authors@R: 
    person("Yun", "Peng", , "yunyunp96@gmail.com", role = c("aut", "cre"))
Description: FAERS is a database for the spontaneous reporting of adverse events and medication errors involving human drugs and therapeutic biological products. faers is the bridge between FAERS and R.
License: MIT + file LICENSE
Depends: 
    R (>= 3.5.0)
Imports: 
    brio,
    cli,
    curl,
    data.table,
    httr2,
    MCMCpack,
    methods,
    rappdirs,
    rlang (>= 1.1.0),
    rvest,
    utils,
    xml2
Suggests: 
    knitr,
    rmarkdown,
    testthat (>= 3.0.0)
biocViews: Software, DataImport
Encoding: UTF-8
ByteCompile: true
Roxygen: list(markdown = TRUE)
RoxygenNote: 7.2.3
Config/testthat/edition: 3
Config/testthat/parallel: true
VignetteBuilder: knitr
bioc-issue-bot commented 7 months ago

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

bioc-issue-bot commented 7 months ago

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: faers_0.99.0.tar.gz Linux (Ubuntu 22.04.2 LTS): faers_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/faers to trigger a new build. A quick tutorial for setting up remotes and pushing to upstream can be found here.

bioc-issue-bot commented 7 months ago

Received a valid push on git.bioconductor.org; starting a build for commit id: 2a2b6807b75b07e7eeafb91691c2594bee35719e

bioc-issue-bot commented 7 months ago

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: faers_0.99.1.tar.gz Linux (Ubuntu 22.04.2 LTS): faers_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 git@git.bioconductor.org:packages/faers to trigger a new build. A quick tutorial for setting up remotes and pushing to upstream can be found here.

Yunuuuu commented 7 months ago

Thank you for the review. I have subscribed to the mailing list, but it appears that there is a delay

bioc-issue-bot commented 7 months ago

Received a valid push on git.bioconductor.org; starting a build for commit id: cba6a3e6abfa398178dfe5ba4ddcb7ebbb39ce7a

bioc-issue-bot commented 7 months ago

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: macOS 12.7.1 Monterey: faers_0.99.2.tar.gz Linux (Ubuntu 22.04.2 LTS): faers_0.99.2.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/faers to trigger a new build. A quick tutorial for setting up remotes and pushing to upstream can be found here.

bioc-issue-bot commented 6 months ago

A reviewer has been assigned to your package for an indepth review. Please respond accordingly to any further comments from the reviewer.

bioc-issue-bot commented 6 months ago

Received a valid push on git.bioconductor.org; starting a build for commit id: 46bfee4a087b9b0dfa4061470e30b453ffae9529

bioc-issue-bot commented 6 months ago

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 22.04.2 LTS): faers_0.99.3.tar.gz macOS 12.7.1 Monterey: faers_0.99.3.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/faers to trigger a new build. A quick tutorial for setting up remotes and pushing to upstream can be found here.

Kayla-Morrell commented 6 months ago

@Yunuuuu - Thank you for submitting to Bioconductor. Please see the initial review of the package below. The required changes must be made while the suggested changes do not have to be (though we strongly encourage them). Comment back here with updates that have been made and when the package is ready for a re-review.

General package development

DESCRIPTION

NEWS

Data

Vignette

Man pages

R code

Best, Kayla

Yunuuuu commented 5 months ago

Dear @Kayla-Morrell , we extend our sincerest gratitude for your unwavering dedication and valuable time in meticulously evaluating our package. Please find below our responses to your insightful review

General package development

DESCRIPTION

NEWS

We greatly appreciate your valuable suggestion. After reviewing the BioConductor Package development book, we found that employing an md file would be deemed acceptable. Consequently, we have made the choice to augment our project by incorporating a NEWS.md file.

Data

Yes, we have put the code generate data in inst/extdata into data-raw folder, by following your advice, we have moved it into inst/script folder and taken the necessary steps to ensure that the documentation scripts, providing detailed and comprehensive information on how the data within inst/extdata was generated.

Vignette

In the new submission, we have used BiocStyle package to generate html_document document

In the new submission, we added the introduction section in our vignette

Added

Added

Man pages

REQUIRED: There need to be runnable examples for all exported objects. Ideally this means runnable examples within man pages, but we would also take vignette code or tests. It's important to know that these functions indeed work and be able to easily catch when they don't. This applies to the following two functions which have no runnale code, have the tests skipped if there is not a specific directory present, and are not used in the vignette code.

Apologies for the inconvenience caused by the restriction on the faers_standardize function, which internally used MedDRA data to standardize the FAERS database. MedDRA, being a specialized and comprehensive terminology for regulatory information sharing in the field of medical products, plays a vital role in encoding the adverse effects within FAERS.

However, we do not possess the legal rights to distribute the MedDRA data, making it challenging for us to include it within our package. Nevertheless, scholars can easily obtain MedDRA data after appropriate application. As a result, we cannot provide a fully runnable example code involving MedDRA but do lots of tests in local computer.

We appreciate your understanding in this matter and thank you for your comprehension of the limitations surrounding the distribution of MedDRA.

R code

Lots of long lines are running message not the code self which make it challenging to reduce their length.

We have tried to re-style our package with 4 spaces as the indents, but there remains 49 lines, which we are unable to locate the specific locations. We apologize for any inconvenience caused.

bioc-issue-bot commented 5 months ago

Received a valid push on git.bioconductor.org; starting a build for commit id: f3760851987b116eca67eaf0dd73a214720f34b7

bioc-issue-bot commented 5 months ago

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: faers_0.99.4.tar.gz Linux (Ubuntu 22.04.2 LTS): faers_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/faers to trigger a new build. A quick tutorial for setting up remotes and pushing to upstream can be found here.

bioc-issue-bot commented 5 months ago

Received a valid push on git.bioconductor.org; starting a build for commit id: 77acb994f3638fa001a7cc2a44d77ce9f28046c4

bioc-issue-bot commented 5 months ago

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: macOS 12.7.1 Monterey: faers_0.99.5.tar.gz Linux (Ubuntu 22.04.2 LTS): faers_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/faers to trigger a new build. A quick tutorial for setting up remotes and pushing to upstream can be found here.

Kayla-Morrell commented 4 months ago

@Yunuuuu - Thank you for making the necessary changes. I have reviewed everything and I am more than happy to accept the package.

Best, Kayla

bioc-issue-bot commented 4 months ago

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.

lshep commented 4 months ago

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/Yunuuuu.keys is not empty), then no further steps are required. Otherwise, do the following:

  1. Add an SSH key to your github account
  2. Submit your SSH key to Bioconductor

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("faers"). The package 'landing page' will be created at

https://bioconductor.org/packages/faers

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.