pak::pak("pharmaR/riskreports")Risk Report and Metric
code
Stats
R
Reproduce
Since I began working on an internal project that utilizes a validated R environment provided by a third-party vendor, I started considering the need for an open-source image or repository that is validated and can be used by both industry and regulatory authorities. In my search, I discovered that others are already working on this initiative, and I decided to join the R Validation Hub repository working group. This is voluntary work I do in my free time. However, I would appreciate if the group can be sponsored by industry association and this can be part of my job.
Testing the Idea
- Install the package
- Start generating a report
The riskreports package is developed by the R validation hub repo working group.
packageVersion("riskreports")
library(riskreports)
options("riskreports_output_dir" = ".")
pr <- package_report(
package_name = "dplyr",
package_version = "1.1.4",
params = list(
assessment_path = system.file("assessments/dplyr.rds", package = "riskreports")),
quiet = TRUE # To silence quarto output for readability
)Generate a summary report
I would prefer having also a summarize report in the end for the QA to check. I don’t think the QA would check every single validation report for the handreds of packages included in the image.
tmp_packages_file <- tempfile("packages")
repo_packages_url <- "https://raw.githubusercontent.com/pharmaR/pharmapkgs/refs/heads/main/inst/repos/src/contrib/PACKAGES"
download.file(repo_packages_url, tmp_packages_file)
tmp <- read.dcf(tmp_packages_file)
colnames(tmp) [1] "Package" "Version" "Depends"
[4] "Suggests" "License" "MD5sum"
[7] "NeedsCompilation" "DownloadURL" "has_news"
[10] "news_current" "exported_namespace" "has_vignettes"
[13] "export_help" "has_website" "has_maintainer"
[16] "size_codebase" "has_source_control" "has_bug_reports_url"
[19] "downloads_1yr" "reverse_dependencies" "has_examples"
[22] "dependencies" "Imports" "bugs_status"
[25] "LinkingTo" "Enhances" "assess_size_codebase"
[28] "License_restricts_use" "OS_type" "Priority"
[31] "Path" "License_is_FOSS" "Archs" library(dplyr)
Attaching package: 'dplyr'The following objects are masked from 'package:stats':
filter, lagThe following objects are masked from 'package:base':
intersect, setdiff, setequal, unionknitr::kable(t(head(tmp))) %>% kableExtra::kable_classic(.) | Package | A3 | AalenJohansen | AATtools | ABACUS | abasequence | abbreviate |
| Version | 1.0.0 | 1.0 | 0.0.3 | 1.0.0 | 0.1.0 | 0.1 |
| Depends | R (>= 2.15.0), xtable, pbapply | NA | R (>= 3.6.0) | R (>= 3.1.0) | NA | NA |
| Suggests | randomForest, e1071 | knitr, rmarkdown | NA | rmarkdown (>= 1.13), knitr (>= 1.22) | NA | testthat (>= 3.0.0) |
| License | GPL (>= 2) | GPL (>= 2) | GPL-3 | GPL-3 | GPL-3 | GPL-3 |
| MD5sum | 027ebdd8affce8f0effaecfcd5f5ade2 | d7eb2a6275daa6af43bf8a980398b312 | ea8127d953ca6a2f118ea49441772af6 | 50c54c4da09307cb95a70aaaa54b9fbd | 1392d909eb0f65be94fd4160a371ae21 | 37285eddefb6b0fce95783bf21b32999 |
| NeedsCompilation | no | no | no | no | no | no |
| DownloadURL | https://github.com/cran/A3/archive/refs/tags/1.0.0.tar.gz | https://github.com/cran/AalenJohansen/archive/refs/tags/1.0.tar.gz | https://github.com/cran/AATtools/archive/refs/tags/0.0.3.tar.gz | https://github.com/cran/ABACUS/archive/refs/tags/1.0.0.tar.gz | https://github.com/cran/abasequence/archive/refs/tags/0.1.0.tar.gz | https://github.com/cran/abbreviate/archive/refs/tags/0.1.tar.gz |
| has_news | 0 | 0 | 0 | 0 | 0 | 0 |
| news_current | 0 | 0 | 0 | 0 | 0 | 0 |
| exported_namespace | 0.777299861174691 | 0.693596453153698 | 0.386057808916704 | 0.643035173277501 | 0.666185565559974 | 0.731058578630005 |
| has_vignettes | 0 | 1 | 0 | 1 | 0 | 0 |
| export_help | NaN | 1 | 1 | 1 | 1 | 1 |
| has_website | 0 | 0 | 0 | 1 | 0 | 1 |
| has_maintainer | 1 | 1 | 1 | 1 | 1 | 1 |
| size_codebase | 0.29126213592233 | 0.485436893203884 | 0.0949968334388854 | 0.842696629213483 | 0.700934579439252 | 0.746268656716418 |
| has_source_control | 0 | 0 | 0 | 0 | 0 | 1 |
| has_bug_reports_url | 0 | 0 | 1 | 0 | 0 | 0 |
| downloads_1yr | 0.100811068416289 | 0.0360950281781554 | 0.0371777754955325 | 0.0274265707060883 | 0.0283086091857226 | 0.0685081226091708 |
| reverse_dependencies | 0.246376140522644 | 0.246376140522644 | 0.246376140522644 | 0.246376140522644 | 0.246376140522644 | 0.246376140522644 |
| has_examples | 0.923076923076923 | 1 | 1 | 1 | 1 | 1 |
| dependencies | 0.731058578630005 | 0.880797077977882 | 0.5 | 0.731058578630005 | 0.880797077977882 | 0.880797077977882 |
| Imports | NA | NA | magrittr, dplyr, doParallel, foreach | ggplot2 (>= 3.1.0), shiny (>= 1.3.1), | NA | NA |
| bugs_status | NA | NA | 0 | NA | NA | NA |
| LinkingTo | NA | NA | NA | NA | NA | NA |
| Enhances | NA | NA | NA | NA | NA | NA |
| assess_size_codebase | NA | NA | NA | NA | NA | NA |
| License_restricts_use | NA | NA | NA | NA | NA | NA |
| OS_type | NA | NA | NA | NA | NA | NA |
| Priority | NA | NA | NA | NA | NA | NA |
| Path | NA | NA | NA | NA | NA | NA |
| License_is_FOSS | NA | NA | NA | NA | NA | NA |
| Archs | NA | NA | NA | NA | NA | NA |
Testing pharmapkgs
repo <- "C:/Projects/Rlib/pharmapkgs/repos/src/contrib/"
packages <- get_packages(
base_url = system.file("repos", package = "pharmapkgs", mustWork = TRUE)
)
available.packages(repos = repo, fields = risk_fields(repo)) |>
tibble::as_tibble()