First and foremost, I truly appreciate the time and effort you have taken to review my package, and I am grateful for your valuable feedback. I sincerely apologize for not being able to address your concerns due to the following reasons:
- Example Execution (\dontrun{} → \donttest{})
This package implements the SAHMI algorithm using polars and includes a dataset (4.9M), which makes it impractical to add additional datasets. The algorithm requires at least three FASTQ files, and the absence of such data makes it difficult to provide meaningful runnable examples.
Additionally, the package depends on external command-line tools such as kraken2
and seqkit, as well as packages from Additional_repositories. Since CRAN does
not support install dependencies from Additional_repositories, it is
impossible to provide fully executable examples.
Given these constraints, we believe the use of \dontrun{} is appropriate to
prevent execution failures due to missing data and dependencies.
-
Small Executable Examples The package follows the workflow of the original algorithm, where each step corresponds to a function. While we acknowledge CRAN’s preference for runnable examples, the lack of small, self-contained input data and external dependencies makes this infeasible.
-
Avoiding
install.packages()in Functions, Examples, and Vignettes Theinstall.packages()calls in:R/import-standalone-pkg.RR/import-standalone-polars.R
They were included to ensure a user-friendly experience, as polars is not yet
available on CRAN. Since there are no runnable examples, we believe this
approach remains acceptable, as it simplifies installation for users unfamiliar
with setting up polars. We hope polars will be available on CRAN in the
future, as it is widely used by many users.
Once again, I sincerely appreciate your time, patience, and valuable feedback. I deeply regret any inconvenience caused and will continue working to align the package with CRAN’s best practices.
0 errors | 0 warnings | 1 note
- This is a new release.