Closed Yunuuuu closed 4 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
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.
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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.
Received a valid push on git.bioconductor.org; starting a build for commit id: 2a2b6807b75b07e7eeafb91691c2594bee35719e
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.
Thank you for the review. I have subscribed to the mailing list, but it appears that there is a delay
Received a valid push on git.bioconductor.org; starting a build for commit id: cba6a3e6abfa398178dfe5ba4ddcb7ebbb39ce7a
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.
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: 46bfee4a087b9b0dfa4061470e30b453ffae9529
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.
@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.
inst/extdata
directory
there needs to be documentation of the data included in the inst/script
directory. We don't allow for the data-raw
directory within our packages so I
assume the files here could belong in the inst/script
directory. Documentation
scripts should clearly state how the data within inst/extdata
was generated
and provide source information. It should include source URLs and any key
information regarding filtering or processing. It can be executable code, sudo
code, or text description. Users should be able to download and roughly
reproduce the file or object that is present as data.BiocStyle
package for
formatting.Best, Kayla
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
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.
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.
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
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.
[x] faers_counts() fixed by using internal example data
faers_standardize()
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.
[x] REQUIRED: Avoid '<<-' if possible (found 1 times), R/import-standalone-cli.R line 88 Removed
[] SUGGESTION: For formatting reasons, consider shorter lines. There are 169 lines that are > 80 characters long.
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.
Received a valid push on git.bioconductor.org; starting a build for commit id: f3760851987b116eca67eaf0dd73a214720f34b7
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.
Received a valid push on git.bioconductor.org; starting a build for commit id: 77acb994f3638fa001a7cc2a44d77ce9f28046c4
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.
@Yunuuuu - Thank you for making the necessary changes. I have reviewed everything and I am more than happy to accept the package.
Best, Kayla
Your package has been accepted. It will be added to the Bioconductor nightly builds.
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