pcadapt 3.0 to 4.4.1
CRANTwo releases side by side, the earlier on the left.
- Time between
- 3,388 days12 releases in between
- Advisories, method
Method
Security advisories
Advisories come from the R Consortium advisory database, a community record of security problems in R packages, as OSV publishes it.
- The copy
- The record is read once a day. The data is published under the Apache License 2.0 and is credited on the advisories list.
- Box under the name
- Under the package's name, a box names any advisory that affects the current release, with its fix or that there is none.
- Ranges
- Advisories state ranges, such as from 0.9.12 up to but not including 1.8.8. Each range is checked against every version CRAN has published, using the version rules R itself uses, so a release that came out after the advisory was written is still caught by its range.
- Not the package
- The rating is for the library flaw itself, not for how exposed the R package is, and it is never added up into a figure for the package.
- None knownfor either release
- Exports, method
Method
Code metrics
Code metrics come from reading the released source of each package version. The package is never installed, loaded or run.
- One row a version
- Each analysed version gives one row of figures. The Code, Tests and Documentation sections, the pages of older releases and Release changes all read from those rows.
- CRAN
- CRAN versions are read from the github.com/cran mirror, which holds one commit for each released source file, and every version tag is analysed. Nothing is built, installed or run.
- Release, not repository
- Documentation describes what the analysed release holds: a
README, vignettes, aNEWSfile and the shares read from its help pages. Files kept only in the repository, such as a pkgdown configuration or CI files, are read by the repository scan instead. - Zero
- Zero means the analysis looked and found none.
- 9 removed12 added as well
- Files changed, method
- 330+27,453 −87,260 lines
Record made 29 Oct 2026, 02:43 UTC from data release v2026-10-28, merged 23:10 UTC. Project DOI 10.5281/zenodo.21843040.
https:/
This record reports what R Observatory measured for these two releases. It is not a validation, and it does not say whether either release is fit for your intended use.
- Differs between the two releases
- – not on that release’s record
Release
| Measure | 3.0 | 4.4.1 |
|---|---|---|
| Published | 15 Apr 2016 | 25 Jul 2025 |
| Status | Replaced by 3.0.1 on 14 Jun 2016 | Current release |
| Previous | 2.2, 13 Feb 2016 | 4.4.0, 24 Sep 2024 |
| Releases | – | 20 since 5 Sep 2015 |
| License | GPL (>= 2), OSI approved | GPL (>= 2), OSI approved |
| Maintainer | Keurcien Luu | Florian Privé |
| Download size | 993 KB | 1.6 MB |
| Authors | Keurcien Luu, Michael G.B. Blum, Nicolas Duforet-Frebourg | Keurcien Luu, Michael Blum, Florian Privé, Eric Bazin, Nicolas Duforet-Frebourg |
| Source code | Not kept for this release | https://github.com/bcm-uga/pcadapt |
Advisories
| Measure | 3.0 | 4.4.1 |
|---|---|---|
| This release | None known | None known |
CRAN checks
Method, CRAN checks Method CRAN runs every current package through Checks and health
R CMD check on a set of machines and publishes a result for each one. The health shown on a package page comes from these results alone.
| Measure | 3.0 | 4.4.1 |
|---|---|---|
| Results | Kept only for the current release | 13 OK |
| Release checked | – | 4.4.1 on 13 platforms |
Code
| Measure | 3.0 | 4.4.1 |
|---|---|---|
| Public exports | 11 | 14 |
| Internal functions | 1 | 26 |
| Lines of R code | 696 | 1,297 |
| Lines of compiled code | 60,815, 97.7% of code | 1,252, 40.1% of code |
| Complexity | mean 7.5, highest 30 | mean 3.5, highest 14 |
| Exports changed since 2.2 | 8 added, 11 removed | – |
Exports added (12)
bed2matrixget.pcget.pop.nameshist_plotmanhattan_plotqq_plotread.pcadaptrun.pcadaptscore_plotscree_plotvcf2pcadaptwriteBed
Exports removed (9)
compute.pvalcorpcacreate.pcadaptmanhattan.plottingneutral.plottingpvalqq.plottingread4pcadaptscore.plottingscree.plotting
Most changed files (12 of 330)
| File | Lines added | Lines deleted |
|---|---|---|
src/src_Lapack/clapack.h | 0 | 7,267 |
inst/extdata/missing.bim | 4,000 | 2,000 |
inst/extdata/missing.pcadapt | 4,000 | 2,000 |
inst/extdata/geno3pops.bim | 3,000 | 1,500 |
inst/extdata/geno3pops.pcadapt | 3,000 | 1,500 |
src/src_Lapack/dgesvd.c | 0 | 4,052 |
inst/testdata/novar.bim | 2,000 | 1,000 |
inst/doc/pcadapt.html | 933 | 1,269 |
src/src_Lapack/dgesdd.c | 0 | 1,596 |
inst/extdata/geno3pops.loadings | 0 | 1,500 |
inst/extdata/geno3pops.maf | 0 | 1,500 |
inst/extdata/geno3pops.zscores | 0 | 1,500 |
Tests
Method, Tests Method Test coverage is measured by downloading each CRAN package's current source file, installing its dependencies, building it and running its tests under covr.Test coverage
| Measure | 3.0 | 4.4.1 |
|---|---|---|
| Tests | No | No |
| Test lines per line of code | 0.00 | 0.00 |
| Coverage | Not measured for this release | No tests to run |
| Exports named in tests | 0% | 0% |
| Help pages with running examples | 1 of 10 | 1 of 4 |
Documentation
| Measure | 3.0 | 4.4.1 |
|---|---|---|
| Help pages | 13 | 19 |
| Exports documented | 100% | 100% |
| Exports with examples | 72.7% | 21.4% |
| Arguments documented | 95.5% | 98.7% |
| Return value documented | 9.1% | 21.4% |
| Vignettes | 1 | 0 |
| NEWS | No | Yes, does not mention 4.4.1 |
| Citation file | No | Yes, cites a publication |
| Website | Not kept for this release | No, not declared in DESCRIPTION |
Dependencies
Method, Dependencies Method Dependent packages are other packages that list this one under Reverse dependencies
Depends, Imports or LinkingTo in their DESCRIPTION file. Those fields list the packages a package needs to install, so dependents break if this one is archived or broken.Suggests install and run without it, and use it for tests, examples or an optional feature. They are counted as Suggested by, never among the dependents, and a package that also lists it under one of the three fields is a dependent and is not counted again.
| Measure | 3.0 | 4.4.1 |
|---|---|---|
| Depends | robust, MASS | None |
| Imports | ggplot2 | bigutilsr (>= 0.3), data.table, ggplot2 (>= 3.4), magrittr, mmapcharr (>= 0.3), Rcpp (>= 0.12.8), RSpectra |
| LinkingTo | None | mmapcharr, Rcpp, rmio |
| Suggests | knitr, qvalue, rmarkdown | plotly, shiny, spelling, testthat, vcfR |
| Install tree | Kept only for the current release | 40 packages, 22 with compiled code, 42.9 MB of source tarballs |
| Advisories in the install tree | Kept only for the current release | None known |
Today
| Measure | 3.0 | 4.4.1 |
|---|---|---|
| CRAN downloads, past year | – | 12,300, rank #3,840 |
| Other channels, past year | – | r2u 510, conda-forge 3,234 |
| Reverse dependencies | – | 0 direct, 0 indirect |
| Suggested by | – | 2 |
| Repository | – | 47 stars, 3 open issues |
| Last commit | – | 8 Sep 2026 |
| Task views | – | Anomaly Detection |
Downloads, reverse dependencies and repository activity describe pcadapt today, not 3.0. They are on the 4.4.1 page.
Sources
| Part | 3.0 | 4.4.1 |
|---|---|---|
| Release history | CRAN package versions, 28 Oct 2026 | CRAN package versions, 28 Oct 2026 |
| Advisories | osv-advisories 1.0.0, R version 4.6.1 (2026-06-24), 28 Oct 2026 | osv-advisories 1.0.0, R version 4.6.1 (2026-06-24), 28 Oct 2026 |
| CRAN checks | CRAN check results, Kept only for the current release | CRAN check results, 28 Oct 2026 |
| Tests, documentation, code | rpkg-analyzer 0.5.2, 5 Oct 2026 | rpkg-analyzer 0.5.2, 5 Oct 2026 |
| Coverage | covr, Not measured for this release | covr 3.6.5 on R 4.6.1, run on 4.4.1 |
| Use | CRAN downloads, reverse dependencies, repository, Not shown for this release | – |
| Downloads | – | conda-forge, 30 Sep 2026 |
| Reverse dependencies | – | CRAN package metadata, 28 Oct 2026 |
| Repository | – | github.com/ |
| Task views | – | CRAN Task Views, 28 Oct 2026 |
Daily data releases are kept on GitHub, so the data behind this record can be fetched again from v2026-10-28 (merged 23:10 UTC). Values not kept for a release say so and are never filled in from another release.