pcadapt 3.0 to 4.4.1
CRANRecord of 3.0Record of 4.4.1Both records side by side
- 3.0 and 4.4.1
- between them
- other releases
- daily mean, in 30-day steps
- after this copy’s series ends on 26 Oct 2026
- Time between
- 3,388 days12 releases 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
- 9 removed12 added
- Dependencies
- 20 changes14 added, 5 removed, 1 bound14 added, 5 removed
- Licence
- SameGPL (>= 2)
- Maintainer
- Changednow Florian Privé
Downloads while newest
Method, downloads Method Download figures count requests logged by each distribution channel. They are not counts of installs or of users, because each channel publishes its own totals and this site reads them.Downloads
| Release | Days newest | Days counted | CRAN downloads | Daily mean |
|---|---|---|---|---|
| 4.4.1 25 Jul 2025 to 28 Oct 2026, still the newest | 461 | 459 | 21,604 | 47 |
| 3.0 15 Apr to 13 Jun 2016 | 60 | 557 | 9 |
Daily mean while newest, 4.4.1 +407% up since 3.0
Counted on the CRAN mirror from each release's day to the day before the next release. This copy's daily series ends on 26 Oct 2026, so a span that runs past it is counted to that day and its daily mean covers the days counted. Other channels repackage on their own schedules, so they are not split by release.
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.
- added
- removed
- bound or field changed
| Package | Field | 3.0 | 4.4.1 | |
|---|---|---|---|---|
| added | bigutilsr | Imports | – | >= 0.3 |
| added | data.table | Imports | – | any version |
| changed | ggplot2 | Imports | any version | >= 3.4 |
| removed | knitr | Suggests | any version | – |
| added | magrittr | Imports | – | any version |
| removed | MASS | Depends | any version | – |
| added | mmapcharr | Imports | – | >= 0.3 |
| added | mmapcharr | LinkingTo | – | any version |
| added | plotly | Suggests | – | any version |
| removed | qvalue | Suggests | any version | – |
| added | Rcpp | Imports | – | >= 0.12.8 |
| added | Rcpp | LinkingTo | – | any version |
| removed | rmarkdown | Suggests | any version | – |
| added | rmio | LinkingTo | – | any version |
| removed | robust | Depends | any version | – |
| added | RSpectra | Imports | – | any version |
| added | shiny | Suggests | – | any version |
| added | spelling | Suggests | – | any version |
| added | testthat | Suggests | – | any version |
| added | vcfR | Suggests | – | any version |
Side by side
| Measure | 3.0 | 4.4.1 | Change |
|---|---|---|---|
| Depends | 2 packages | 0 packages | −2 |
| Imports | 1 package | 7 packages | +6, 1 bound |
| LinkingTo | 0 packages | 3 packages | +3 |
| Suggests | 3 packages | 5 packages | +5 −3 |
Exports
added Added (12)
bed2matrixget.pcget.pop.nameshist_plotmanhattan_plotqq_plotread.pcadaptrun.pcadaptscore_plotscree_plotvcf2pcadaptwriteBed
removed Removed (9)
compute.pvalcorpcacreate.pcadaptmanhattan.plottingneutral.plottingpvalqq.plottingread4pcadaptscore.plottingscree.plotting
Licence and people
Method, licences Method Licence figures come from the Licences
License field of each package's DESCRIPTION file, read the way R itself reads it. No licence file is opened.tools::analyze_license() and R's own licence database, as CRAN's checks read it.| is read, so one string can offer two families.
| Part | 3.0 | 4.4.1 | |
|---|---|---|---|
| changed | Maintainer | Keurcien Luu | Florian Privé |
| added | Person named | – | Eric Bazin |
| added | Person named | – | Florian Privé |
| added | Person named | – | Michael Blum |
| removed | Person named | Michael G.B. Blum | – |
| changed | Keurcien Luu | – | aut |
| changed | Nicolas Duforet-Frebourg | – | ctb |
Side by side
| Measure | 3.0 | 4.4.1 | Change |
|---|---|---|---|
| Licence | GPL (>= 2) | GPL (>= 2) | |
| Maintainer | Keurcien Luu | Florian Privé | changed |
| People named | Keurcien Luu, Michael G.B. Blum, Nicolas Duforet-Frebourg | Keurcien Luu, Michael Blum, Florian Privé, Eric Bazin, Nicolas Duforet-Frebourg | changed |
Code
Method, code Method Code metrics come from reading the released source of each package version. The package is never installed, loaded or run.Code metrics
README, vignettes, a NEWS file 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.
| Measure | 3.0 | 4.4.1 | Change |
|---|---|---|---|
| Lines of R code | 696 | 1,297 | +601 up |
| Lines of compiled code | 60,815 | 1,252 | −59,563 down |
| Files | 231 | 91 | −140 down |
| Public exports | 11 | 14 | +3 up |
| Internal functions | 1 | 26 | +25 up |
| Mean complexity | 7.5 | 3.5 | −4.0 down |
| Highest complexity | 30 | 14 | −16 down |
| Download size | 993 KB | 1.6 MB | +683 KB up |
| Source, unpacked | 3.4 MB | 3.3 MB | −132 KB down |
Side by side
| Measure | 3.0 | 4.4.1 | Change |
|---|---|---|---|
| Lines of R code | 696 | 1,297 | +601 |
| Lines of compiled code | 60,815 | 1,252 | −59,563 |
| Files | 231 | 91 | −140 |
| Public exports | 11 | 14 | +3 |
| Internal functions | 1 | 26 | +25 |
| Mean complexity | 7.5 | 3.5 | −4.0 |
| Highest complexity | 30 | 14 | −16 |
| Download size | 993 KB | 1.6 MB | +683 KB |
| Source, unpacked | 3.4 MB | 3.3 MB | −132 KB |
| Analysed with | rpkg-analyzer 0.5.2 | rpkg-analyzer 0.5.2 |
Documentation
| Measure | 3.0 | 4.4.1 | Change |
|---|---|---|---|
| Arguments documented | 95.5% | 98.7% | +3.2 points up |
| Return value documented | 9.1% | 21.4% | +12.3 points up |
| Lines of documentation | 377 | 573 | +196 up |
| Lines of guides | 379 | 0 | −379 down |
1 other figure of the documentation is the same in both.
Side by side
| Measure | 3.0 | 4.4.1 | Change |
|---|---|---|---|
| Exports documented | 100.0% | 100.0% | |
| Arguments documented | 95.5% | 98.7% | +3.2 points |
| Return value documented | 9.1% | 21.4% | +12.3 points |
| Lines of documentation | 377 | 573 | +196 |
| Lines of guides | 379 | 0 | −379 |
Files changed
- Files changed
- 330over 13 releases
- Lines added
- 27,453
- Lines deleted
- 87,260
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 |
Each release is counted against the release before it, so a line changed twice counts twice.
Unchanged and not compared
Licence is the same in both releases. No advisory is known for either release. Neither release has tests.
Checks, the install tree, dependents and the repository describe the package as it is now, so they are on the package page.