dartR.popgen
Analysing 'SNP' and 'Silicodart' Data Generated by Genome-Wide Restriction Fragment Analysis
Description
Facilitates the analysis of SNP (single nucleotide polymorphism) and silicodart (presence/absence) data. 'dartR.popgen' provides a suit of functions to analyse such data in a population genetics context. It provides several functions to calculate population genetic metrics and to study population structure. Quite a few functions need additional software to be able to run (gl.run.structure(), gl.blast(), gl.LDNe()). You find detailed description in the help pages how to download and link the packages so the function can run the software. 'dartR.popgen' is part of the the 'dartRverse' suit of packages. Gruber et al. (2018) <doi:10.1111/1755-0998.12745>. Mijangos et al. (2022) <doi:10.1111/2041-210X.13918>.
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CRAN Check Status
Show all 14 flavors
| Flavor | Status |
|---|---|
| r-devel-linux-x86_64-debian-clang | OK |
| r-devel-linux-x86_64-debian-gcc | OK |
| r-devel-linux-x86_64-fedora-clang | OK |
| r-devel-linux-x86_64-fedora-gcc | OK |
| r-devel-macos-arm64 | ERROR |
| r-devel-windows-x86_64 | OK |
| r-oldrel-macos-arm64 | ERROR |
| r-oldrel-macos-x86_64 | ERROR |
| r-oldrel-windows-x86_64 | OK |
| r-patched-linux-x86_64 | OK |
| r-release-linux-x86_64 | OK |
| r-release-macos-arm64 | ERROR |
| r-release-macos-x86_64 | ERROR |
| r-release-windows-x86_64 | OK |
Check details (5 non-OK)
package dependencies
Package required but not available: ‘LEA’ See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’ manual.
package dependencies
Package required but not available: ‘LEA’ Package suggested but not available for checking: ‘snpStats’ See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’ manual.
package dependencies
Package required but not available: ‘LEA’ See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’ manual.
package dependencies
Package required but not available: ‘LEA’ Package suggested but not available for checking: ‘snpStats’ See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’ manual.
package dependencies
Package required but not available: ‘LEA’ See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’ manual.
Check History
ERROR 10 OK · 0 NOTE · 2 WARNING · 2 ERROR · 0 FAILURE Mar 16, 2026
whether package can be installed
Found the following significant warnings: Warning: replacing previous import ‘adegenet::glMean’ by ‘dartR.base::glMean’ when loading ‘dartR.popgen’ Warning: replacing previous import ‘adegenet::glSum’ by ‘dartR.base::glSum’ when loading ‘dartR.popgen’ See ‘/home/hornik/tmp/R.check/r-devel-clang/Work/PKGS/dartR.popgen.Rcheck/00install.out’ for details.
package dependencies
Package required but not available: ‘LEA’ See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’ manual.
whether package can be installed
Found the following significant warnings: Warning: replacing previous import ‘adegenet::glMean’ by ‘dartR.base::glMean’ when loading ‘dartR.popgen’ Warning: replacing previous import ‘adegenet::glSum’ by ‘dartR.base::glSum’ when loading ‘dartR.popgen’ See ‘/home/hornik/tmp/R.check/r-release-gcc/Work/PKGS/dartR.popgen.Rcheck/00install.out’ for details.
package dependencies
Package required but not available: ‘LEA’ Package suggested but not available for checking: ‘snpStats’ See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’ manual.
WARNING 12 OK · 0 NOTE · 2 WARNING · 0 ERROR · 0 FAILURE Mar 12, 2026
whether package can be installed
Found the following significant warnings: Warning: replacing previous import ‘adegenet::glMean’ by ‘dartR.base::glMean’ when loading ‘dartR.popgen’ Warning: replacing previous import ‘adegenet::glSum’ by ‘dartR.base::glSum’ when loading ‘dartR.popgen’ See ‘/data/gannet/ripley/R/packages/tests-clang/dartR.popgen.Rcheck/00install.out’ for details.
whether package can be installed
Found the following significant warnings: Warning: replacing previous import ‘adegenet::glMean’ by ‘dartR.base::glMean’ when loading ‘dartR.popgen’ Warning: replacing previous import ‘adegenet::glSum’ by ‘dartR.base::glSum’ when loading ‘dartR.popgen’ See ‘/data/gannet/ripley/R/packages/tests-devel/dartR.popgen.Rcheck/00install.out’ for details.