rhierbaps

Clustering Genetic Sequence Data Using the HierBAPS Algorithm

v1.1.4 · Nov 18, 2022 · MIT + file LICENSE

Description

Implements the hierarchical Bayesian analysis of populations structure (hierBAPS) algorithm of Cheng et al. (2013) <doi:10.1093/molbev/mst028> for clustering DNA sequences from multiple sequence alignments in FASTA format. The implementation includes improved defaults and plotting capabilities and unlike the original 'MATLAB' version removes singleton SNPs by default.

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Flavor	Status	Time
r-devel-linux-x86_64-debian-clang	NOTE	280.7s
r-devel-linux-x86_64-debian-gcc	NOTE	214.3s
r-devel-linux-x86_64-fedora-clang	OK	440.4s
r-devel-linux-x86_64-fedora-gcc	OK	624s
r-devel-windows-x86_64	OK	381s
r-oldrel-macos-arm64	OK
r-oldrel-macos-x86_64	OK	453s
r-oldrel-windows-x86_64	OK	445s
r-patched-linux-x86_64	OK	266.1s
r-release-linux-x86_64	OK
r-release-macos-arm64	OK	115s
r-release-macos-x86_64	OK	562s
r-release-windows-x86_64	OK	379s

Check details (2 non-OK)

NOTE r-devel-linux-x86_64-debian-clang

CRAN incoming feasibility

Maintainer: ‘Gerry Tonkin-Hill <g.tonkinhill@gmail.com>’

Package CITATION file contains call(s) to old-style personList() or
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Package CITATION file contains call(s) to old-style citEntry().  Please
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NOTE r-devel-linux-x86_64-debian-gcc

CRAN incoming feasibility

Maintainer: ‘Gerry Tonkin-Hill <g.tonkinhill@gmail.com>’

Package CITATION file contains call(s) to old-style personList() or
as.personList().  Please use c() on person objects instead.
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Check History

NOTE 11 OK · 2 NOTE · 0 WARNING · 0 ERROR · 0 FAILURE Jun 9, 2026

NOTE r-devel-linux-x86_64-debian-clang

CRAN incoming feasibility

Maintainer: ‘Gerry Tonkin-Hill <g.tonkinhill@gmail.com>’

Package CITATION file contains call(s) to old-style personList() or
as.personList().  Please use c() on person objects instead.
Package CITATION file contains call(s) to old-style citEntry().  Please
use bibentry() instead.

NOTE r-devel-linux-x86_64-debian-gcc

CRAN incoming feasibility

Maintainer: ‘Gerry Tonkin-Hill <g.tonkinhill@gmail.com>’

Package CITATION file contains call(s) to old-style personList() or
as.personList().  Please use c() on person objects instead.
Package CITATION file contains call(s) to old-style citEntry().  Please
use bibentry() instead.

ERROR 11 OK · 1 NOTE · 0 WARNING · 1 ERROR · 0 FAILURE Jun 8, 2026

NOTE r-devel-linux-x86_64-debian-clang

CRAN incoming feasibility

Maintainer: ‘Gerry Tonkin-Hill <g.tonkinhill@gmail.com>’

Package CITATION file contains call(s) to old-style personList() or
as.personList().  Please use c() on person objects instead.
Package CITATION file contains call(s) to old-style citEntry().  Please
use bibentry() instead.

ERROR r-devel-linux-x86_64-debian-gcc

CRAN incoming feasibility

Maintainer: ‘Gerry Tonkin-Hill <g.tonkinhill@gmail.com>’

Package CITATION file contains call(s) to old-style personList() or
as.personList().  Please use c() on person objects instead.
Package CITATION file contains call(s) to old-style citEntry().  Please
use bibentry() instead.

NOTE 11 OK · 2 NOTE · 0 WARNING · 0 ERROR · 0 FAILURE May 10, 2026

NOTE r-devel-linux-x86_64-debian-clang

CRAN incoming feasibility

Maintainer: ‘Gerry Tonkin-Hill <g.tonkinhill@gmail.com>’

Package CITATION file contains call(s) to old-style personList() or
as.personList().  Please use c() on person objects instead.
Package CITATION file contains call(s) to old-style citEntry().  Please
use bibentry() instead.

NOTE r-devel-linux-x86_64-debian-gcc

CRAN incoming feasibility

Maintainer: ‘Gerry Tonkin-Hill <g.tonkinhill@gmail.com>’

Package CITATION file contains call(s) to old-style personList() or
as.personList().  Please use c() on person objects instead.
Package CITATION file contains call(s) to old-style citEntry().  Please
use bibentry() instead.

ERROR 10 OK · 2 NOTE · 0 WARNING · 1 ERROR · 0 FAILURE May 3, 2026

NOTE r-devel-linux-x86_64-debian-clang

CRAN incoming feasibility

Maintainer: ‘Gerry Tonkin-Hill <g.tonkinhill@gmail.com>’

Package CITATION file contains call(s) to old-style personList() or
as.personList().  Please use c() on person objects instead.
Package CITATION file contains call(s) to old-style citEntry().  Please
use bibentry() instead.

NOTE r-devel-linux-x86_64-debian-gcc

CRAN incoming feasibility

Maintainer: ‘Gerry Tonkin-Hill <g.tonkinhill@gmail.com>’

Package CITATION file contains call(s) to old-style personList() or
as.personList().  Please use c() on person objects instead.
Package CITATION file contains call(s) to old-style citEntry().  Please
use bibentry() instead.

ERROR r-release-linux-x86_64

re-building of vignette outputs

Error(s) in re-building vignettes:
  ...
--- re-building ‘introduction.Rmd’ using rmarkdown

Quitting from introduction.Rmd:39-46 [unnamed-chunk-1]
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
<error/rlang_error>
E
...[truncated]...
nette 'introduction.Rmd' failed with diagnostics:
there is no package called 'ggtree'
--- failed re-building ‘introduction.Rmd’

SUMMARY: processing the following file failed:
  ‘introduction.Rmd’

Error: Vignette re-building failed.
Execution halted

NOTE 12 OK · 2 NOTE · 0 WARNING · 0 ERROR · 0 FAILURE Mar 10, 2026

NOTE r-devel-linux-x86_64-debian-clang

CRAN incoming feasibility

Maintainer: ‘Gerry Tonkin-Hill <g.tonkinhill@gmail.com>’

Package CITATION file contains call(s) to old-style personList() or
as.personList().  Please use c() on person objects instead.
Package CITATION file contains call(s) to old-style citEntry().  Please
use bibentry() instead.

NOTE r-devel-linux-x86_64-debian-gcc

CRAN incoming feasibility

Maintainer: ‘Gerry Tonkin-Hill <g.tonkinhill@gmail.com>’

Package CITATION file contains call(s) to old-style personList() or
as.personList().  Please use c() on person objects instead.
Package CITATION file contains call(s) to old-style citEntry().  Please
use bibentry() instead.

Dependency Network

Version History

6 tracked

new 1.1.4 Mar 10, 2026

updated 1.1.4 ← 1.1.3 diff Nov 17, 2022

updated 1.1.3 ← 1.1.2 diff Dec 10, 2019

updated 1.1.2 ← 1.1.0 diff May 9, 2019

updated 1.1.0 ← 1.0.0 diff Oct 9, 2018

new 1.0.0 Jul 19, 2018