Debian 13 (Trixie) native package

r-cran-phangorn

GNU R package for phylogenetic analysis

Packages / Debian 13 (Trixie) / gnu-r / r-cran-phangorn

Package: r-cran-phangorn (2.12.1+dfsg-1)

Maintainers:

Debian R Packages Maintainers

External Resources:

Homepage: [cran.r-project.org]

GNU R package for phylogenetic analysis

Other Packages Related to r-cran-phangorn:

dep: r-api-4.0
Package not available
dep: [r-cran-ape] (>= 5.8)
GNU R package for Analyses of Phylogenetics and Evolution
dep: [r-cran-digest]
GNU R package for 'hash digest' of R data structures
dep: [r-cran-fastmatch]
GNU R package for fast match replacement for repeated look-ups
dep: [r-cran-generics]
GNU R common S3 generics not provided by base R methods
dep: [r-cran-igraph] (>= 1.0)
GNU R network analysis and visualization
dep: [r-cran-matrix]
GNU R package of classes for dense and sparse matrices
dep: [r-cran-quadprog]
GNU R package for solving quadratic programming problems
dep: [r-cran-rcpp]
GNU R package for Seamless R and C++ Integration
dep: [libblas3]
Basic Linear Algebra Reference implementations, shared library
dep: libblas.so.3
Package not available
dep: [libc6] (>= 2.29)
GNU C Library: Shared libraries
dep: [libgcc-s1] (>= 3.4)
GCC support library
dep: [libstdc++6] (>= 14)
GNU Standard C++ Library v3

rec: [r-bioc-biostrings]
GNU R string objects representing biological sequences
rec: [r-cran-ggseqlogo]
GNU R ggplot2 extension for publication-ready sequence logos
rec: [r-cran-ggplot2]
implementation of the Grammar of Graphics
rec: [r-cran-knitr]
GNU R package for dynamic report generation using Literate Programming
rec: [r-cran-magick]
advanced graphics and image-processing in GNU R
rec: [r-cran-rgl]
GNU R package for three-dimensional visualisation using OpenGL
rec: [r-cran-rmarkdown]
convert R markdown documents into a variety of formats
rec: [r-cran-seqinr]
GNU R biological sequences retrieval and analysis
rec: [r-cran-testthat] (>= 3.0.0)
GNU R testsuite
rec: [r-cran-tinytest]
Lightweight and Feature Complete Unit Testing Framework
rec: [r-cran-vdiffr]
GNU R visual regression testing and graphical diffing
rec: [r-cran-xtable]
GNU R coerce data to LaTeX and HTML tables

Download r-cran-phangorn

Architecture	Package Size	Installed Size	Files
amd64	1.7 MiB	3.0 MiB	[list of files]
arm64	1.7 MiB	3.0 MiB	[list of files]

Package file paths (142)

Paths come from the repository package-file index for the observed builds. They describe archive/package associations, not every file that will exist on a running system after maintainer scripts, alternatives, generated state, diversions, or installation choices.

/usr/lib/R/site-library/phangorn/CITATION
/usr/lib/R/site-library/phangorn/data/chloroplast.RData
/usr/lib/R/site-library/phangorn/data/Laurasiatherian.RData
/usr/lib/R/site-library/phangorn/data/mites.RData
/usr/lib/R/site-library/phangorn/data/yeast.RData
/usr/lib/R/site-library/phangorn/DESCRIPTION
/usr/lib/R/site-library/phangorn/doc/AdvancedFeatures.R
/usr/lib/R/site-library/phangorn/doc/AdvancedFeatures.Rmd
/usr/lib/R/site-library/phangorn/doc/Ancestral.R
/usr/lib/R/site-library/phangorn/doc/Ancestral.Rmd
/usr/lib/R/site-library/phangorn/doc/index.html
/usr/lib/R/site-library/phangorn/doc/IntertwiningTreesAndNetworks.R
/usr/lib/R/site-library/phangorn/doc/IntertwiningTreesAndNetworks.Rmd
/usr/lib/R/site-library/phangorn/doc/MLbyHand.R
/usr/lib/R/site-library/phangorn/doc/MLbyHand.Rmd
/usr/lib/R/site-library/phangorn/doc/Morphological.R
/usr/lib/R/site-library/phangorn/doc/Morphological.Rmd
/usr/lib/R/site-library/phangorn/doc/Networx.R
/usr/lib/R/site-library/phangorn/doc/Networx.Rmd
/usr/lib/R/site-library/phangorn/doc/Trees.R
/usr/lib/R/site-library/phangorn/doc/Trees.Rmd
/usr/lib/R/site-library/phangorn/extdata/Blosum62.dat
/usr/lib/R/site-library/phangorn/extdata/cpREV.dat
/usr/lib/R/site-library/phangorn/extdata/Dayhoff.dat
/usr/lib/R/site-library/phangorn/extdata/dayhoff-dcmut.dat
/usr/lib/R/site-library/phangorn/extdata/FLU.dat
/usr/lib/R/site-library/phangorn/extdata/HIVb.dat
/usr/lib/R/site-library/phangorn/extdata/HIVw.dat
/usr/lib/R/site-library/phangorn/extdata/JTT.dat
/usr/lib/R/site-library/phangorn/extdata/jtt-dcmut.dat
/usr/lib/R/site-library/phangorn/extdata/lg.dat
/usr/lib/R/site-library/phangorn/extdata/mites.csv
/usr/lib/R/site-library/phangorn/extdata/mites.nex
/usr/lib/R/site-library/phangorn/extdata/mtArt.dat
/usr/lib/R/site-library/phangorn/extdata/mtmam.dat
/usr/lib/R/site-library/phangorn/extdata/mtREV24.dat
/usr/lib/R/site-library/phangorn/extdata/MtZoa.dat
/usr/lib/R/site-library/phangorn/extdata/RtREV.dat
/usr/lib/R/site-library/phangorn/extdata/trees/H3N2_NA_20.csv
/usr/lib/R/site-library/phangorn/extdata/trees/H3N2_NA_20.fasta
/usr/lib/R/site-library/phangorn/extdata/trees/primates.dna
/usr/lib/R/site-library/phangorn/extdata/trees/RAxML_bestTree.3moles
/usr/lib/R/site-library/phangorn/extdata/trees/RAxML_bestTree.AIs
/usr/lib/R/site-library/phangorn/extdata/trees/RAxML_bestTree.mtG
/usr/lib/R/site-library/phangorn/extdata/trees/RAxML_bestTree.Wang.out
/usr/lib/R/site-library/phangorn/extdata/trees/RAxML_bestTree.YCh
/usr/lib/R/site-library/phangorn/extdata/trees/RAxML_bipartitions.3moles
/usr/lib/R/site-library/phangorn/extdata/trees/RAxML_bipartitions.AIs
/usr/lib/R/site-library/phangorn/extdata/trees/RAxML_bipartitionsBranchLabels.3moles
/usr/lib/R/site-library/phangorn/extdata/trees/RAxML_bipartitionsBranchLabels.AIs
/usr/lib/R/site-library/phangorn/extdata/trees/RAxML_bipartitionsBranchLabels.mtG
/usr/lib/R/site-library/phangorn/extdata/trees/RAxML_bipartitionsBranchLabels.YCh
/usr/lib/R/site-library/phangorn/extdata/trees/RAxML_bipartitions.mtG
/usr/lib/R/site-library/phangorn/extdata/trees/RAxML_bipartitions.woodmouse
/usr/lib/R/site-library/phangorn/extdata/trees/RAxML_bipartitions.YCh
/usr/lib/R/site-library/phangorn/extdata/trees/RAxML_bootstrap.3moles
/usr/lib/R/site-library/phangorn/extdata/trees/RAxML_bootstrap.AIs
/usr/lib/R/site-library/phangorn/extdata/trees/RAxML_bootstrap.mtG
/usr/lib/R/site-library/phangorn/extdata/trees/RAxML_bootstrap.Wang.out
/usr/lib/R/site-library/phangorn/extdata/trees/RAxML_bootstrap.woodmouse
/usr/lib/R/site-library/phangorn/extdata/trees/RAxML_bootstrap.YCh
/usr/lib/R/site-library/phangorn/extdata/trees/RAxML_distances.Wang.nxs
/usr/lib/R/site-library/phangorn/extdata/trees/seqfile.txt
/usr/lib/R/site-library/phangorn/extdata/trees/Splits.txt
/usr/lib/R/site-library/phangorn/extdata/trees/tree.txt
/usr/lib/R/site-library/phangorn/extdata/trees/woodmouse.fasta
/usr/lib/R/site-library/phangorn/extdata/trees/woodmouse.mrbayes.nex.con
/usr/lib/R/site-library/phangorn/extdata/trees/woodmouse.mrbayes.nex.run1.t
/usr/lib/R/site-library/phangorn/extdata/trees/woodmouse.mrbayes.nex.run2.t
/usr/lib/R/site-library/phangorn/extdata/trees/woodmouse.nxs
/usr/lib/R/site-library/phangorn/extdata/VT.dat
/usr/lib/R/site-library/phangorn/extdata/wag.dat
/usr/lib/R/site-library/phangorn/help/aliases.rds
/usr/lib/R/site-library/phangorn/help/AnIndex
/usr/lib/R/site-library/phangorn/help/figures/logo.png
/usr/lib/R/site-library/phangorn/help/figures/phangorn_sticker.png
/usr/lib/R/site-library/phangorn/help/paths.rds
/usr/lib/R/site-library/phangorn/help/phangorn.rdb
/usr/lib/R/site-library/phangorn/help/phangorn.rdx
/usr/lib/R/site-library/phangorn/html/00Index.html
/usr/lib/R/site-library/phangorn/html/R.css
/usr/lib/R/site-library/phangorn/INDEX
/usr/lib/R/site-library/phangorn/libs/phangorn.so
/usr/lib/R/site-library/phangorn/Meta/data.rds
/usr/lib/R/site-library/phangorn/Meta/features.rds
/usr/lib/R/site-library/phangorn/Meta/hsearch.rds
/usr/lib/R/site-library/phangorn/Meta/links.rds
/usr/lib/R/site-library/phangorn/Meta/nsInfo.rds
/usr/lib/R/site-library/phangorn/Meta/package.rds
/usr/lib/R/site-library/phangorn/Meta/Rd.rds
/usr/lib/R/site-library/phangorn/Meta/vignette.rds
/usr/lib/R/site-library/phangorn/NAMESPACE
/usr/lib/R/site-library/phangorn/NEWS
/usr/lib/R/site-library/phangorn/README
/usr/lib/R/site-library/phangorn/R/phangorn
/usr/lib/R/site-library/phangorn/R/phangorn.rdb
/usr/lib/R/site-library/phangorn/R/phangorn.rdx
/usr/lib/R/site-library/phangorn/R/sysdata.rdb
/usr/lib/R/site-library/phangorn/R/sysdata.rdx
/usr/lib/R/site-library/phangorn/tinytest/test_add_edge_length.R
/usr/lib/R/site-library/phangorn/tinytest/test_ancestral.R
/usr/lib/R/site-library/phangorn/tinytest/test_bootstrap.R
/usr/lib/R/site-library/phangorn/tinytest/test_candidate_tree.R
/usr/lib/R/site-library/phangorn/tinytest/test_Clanistics.R
/usr/lib/R/site-library/phangorn/tinytest/test_codon.R
/usr/lib/R/site-library/phangorn/tinytest/test_distances.R
/usr/lib/R/site-library/phangorn/tinytest/test_dist_tree.R
/usr/lib/R/site-library/phangorn/tinytest/test_hadamard.R
/usr/lib/R/site-library/phangorn/tinytest/test_hash.R
/usr/lib/R/site-library/phangorn/tinytest/test_mast.R
/usr/lib/R/site-library/phangorn/tinytest/test_modelTest.R
/usr/lib/R/site-library/phangorn/tinytest/test_parsimony.R
/usr/lib/R/site-library/phangorn/tinytest/test_phyDat.R
/usr/lib/R/site-library/phangorn/tinytest/test_pmlCluster.R
/usr/lib/R/site-library/phangorn/tinytest/test_pml_generics.R
/usr/lib/R/site-library/phangorn/tinytest/test_pmlMix.R
/usr/lib/R/site-library/phangorn/tinytest/test_pmlPart.R
/usr/lib/R/site-library/phangorn/tinytest/test_pmlPen.R
/usr/lib/R/site-library/phangorn/tinytest/test_pml.R
/usr/lib/R/site-library/phangorn/tinytest/test_readnexus_multi.R
/usr/lib/R/site-library/phangorn/tinytest/test_SH.R
/usr/lib/R/site-library/phangorn/tinytest/test_speciesTree.R
/usr/lib/R/site-library/phangorn/tinytest/test_splits.R
/usr/lib/R/site-library/phangorn/tinytest/test_superTree.R
/usr/lib/R/site-library/phangorn/tinytest/test_treedist.R
/usr/lib/R/site-library/phangorn/tinytest/test_treeManipulation.R
/usr/lib/R/site-library/phangorn/tinytest/test_treeRearrangement.R
/usr/share/doc/r-cran-phangorn/changelog.Debian.gz
/usr/share/doc/r-cran-phangorn/changelog.gz
/usr/share/doc/r-cran-phangorn/copyright
/usr/share/doc/r-cran-phangorn/README.md
/usr/share/doc/r-cran-phangorn/README.test
/usr/share/doc/r-cran-phangorn/run-unit-test
/usr/share/doc/r-cran-phangorn/tests/testthat.R
/usr/share/doc/r-cran-phangorn/tests/testthat/_snaps/plot_ancestral/pie-plots.svg
/usr/share/doc/r-cran-phangorn/tests/testthat/_snaps/plot_networx/plot-networx.svg
/usr/share/doc/r-cran-phangorn/tests/testthat/_snaps/plot_pml/densitree.svg
/usr/share/doc/r-cran-phangorn/tests/testthat/_snaps/plot_pml/plot-pml.svg
/usr/share/doc/r-cran-phangorn/tests/testthat/test_plot_ancestral.R
/usr/share/doc/r-cran-phangorn/tests/testthat/test_plot_networx.R
/usr/share/doc/r-cran-phangorn/tests/testthat/test_plot_pml.R
/usr/share/doc/r-cran-phangorn/tests/tinytest.R

Field source: Debian 13 (Trixie) main amd64 revision trixie-main-amd64:3ab4e811cf4f3e5a335d382c58cc19d85f1abe7a4ef4689160ca1f637fa0e9b3

Use this package

OpenFactory can boot this operating system in a browser VM, or start a build that includes the native package name from this record.

Try Debian 13 (Trixie) in the browser Build an image that includes r-cran-phangorn

Versions, suites, and repositories

Each row is recorded package-index metadata for one version, architecture, suite, and repository. Names, URLs, and sizes are source-reported; a link is a potentially mutable retrieval location, not an OpenFactory redistribution claim or proof that OpenFactory retained the artifact bytes.

Version	Release	Architecture	Repository	Package size	Installed size	Publisher repository artifact
2.12.1+dfsg-1	trixie / main	amd64	Debian 13 · main · amd64	1.7 MiB	3.0 MiB	pool/main/r/r-cran-phangorn/r-cran-phangorn_2.12.1+dfsg-1_amd64.deb
2.12.1+dfsg-1	trixie / main	arm64	Debian 13 · main · arm64	1.7 MiB	3.0 MiB	pool/main/r/r-cran-phangorn/r-cran-phangorn_2.12.1+dfsg-1_arm64.deb

Field source: Debian 13 (Trixie) main amd64 revision trixie-main-amd64:3ab4e811cf4f3e5a335d382c58cc19d85f1abe7a4ef4689160ca1f637fa0e9b3

Checksums and observation dates

For an APT source, signature verification authenticates the repository metadata chain and the Packages index containing this source-reported artifact digest. It does not certify package safety.

2.12.1+dfsg-1 / amd64Observed Sep 1, 2026 to Sep 1, 2026

Verification status: Metadata observed; artifact bytes were not independently fetched or hashed by this catalog import. The digest below is source-reported.

Source-reported sha256: cf325a180367c9859f1190debc34eca882a717f44e954ddce28e904d4e75e1c6

After downloading that exact artifact, compare its bytes with the source-reported expected digest:

printf '%s  %s\n' 'cf325a180367c9859f1190debc34eca882a717f44e954ddce28e904d4e75e1c6' 'r-cran-phangorn_2.12.1+dfsg-1_amd64.deb' | sha256sum --check --strict -

A match establishes equality with the repository metadata value. It does not establish safety or catalog-side artifact retrieval.

Field source: Debian 13 (Trixie) main amd64 revision trixie-main-amd64:3ab4e811cf4f3e5a335d382c58cc19d85f1abe7a4ef4689160ca1f637fa0e9b3

2.12.1+dfsg-1 / arm64Observed Sep 1, 2026 to Sep 1, 2026

Verification status: Metadata observed; artifact bytes were not independently fetched or hashed by this catalog import. The digest below is source-reported.

Source-reported sha256: 81caa9581995bcbeb81ee055346a56d4d273379e2c983a7478c5850798557cfa

After downloading that exact artifact, compare its bytes with the source-reported expected digest:

printf '%s  %s\n' '81caa9581995bcbeb81ee055346a56d4d273379e2c983a7478c5850798557cfa' 'r-cran-phangorn_2.12.1+dfsg-1_arm64.deb' | sha256sum --check --strict -

A match establishes equality with the repository metadata value. It does not establish safety or catalog-side artifact retrieval.

Field source: Debian 13 (Trixie) main arm64 revision trixie-main-arm64:753da751bbc7a679f48bd1b623ffd4479cb6861c426118284c76eb82909e4908

Catalog record completeness

The completeness score measures metadata coverage, not software quality, security, compatibility, or suitability.

Summary and description: 25/25
Artifact path and source digest: 25/25
Dependency metadata: 15/15
Package-file index: 15/15
Homepage: 5/5
License text: 0/5
Source package or maintainer: 10/10

Recorded total: 95/100

Field source: Debian 13 (Trixie) main amd64 revision trixie-main-amd64:3ab4e811cf4f3e5a335d382c58cc19d85f1abe7a4ef4689160ca1f637fa0e9b3, Debian 13 (Trixie) main arm64 revision trixie-main-arm64:753da751bbc7a679f48bd1b623ffd4479cb6861c426118284c76eb82909e4908. The cross-OS mapping is catalog-derived from the source-reported homepage; it does not establish authorship or publisher identity

Sources and provenance

Field-source links above resolve here. Each source entry names the metadata publisher, trust tier, exact snapshot revision, signature result, and observation time; catalog-derived mappings are labeled separately.

Debian 13 (Trixie) main amd64Sep 1, 2026
Authoritative source; repository metadata signature verified, revision trixie-main-amd64:3ab4e811cf4f3e5a335d382c58cc19d85f1abe7a4ef4689160ca1f637fa0e9b3
Signature verification covers the configured repository metadata chain. It does not certify that the package is safe or suitable.
Repository-signature verification record
Signed object
https://deb.debian.org/debian/dists/trixie/InRelease
Signed-object SHA-256
98b25b5cd185c59d34aa6e4c3e9b5b8f01bbe9d104fe2dcfbcd30dc0a14a59ed
Signer fingerprint
4CB50190207B4758A3F73A796ED0E7B82643E131
Keyring revision
debian-archive-keyring.gpg
SHA-256 506b815cbb32d9b6066b4a2aa524071e071761e7e7f68c3ac74f3061ba852017
Tool and policy
gpgv (GnuPG) 2.4.9
openfactory-software-catalog-signature-v1
Verification time
Sep 1, 2026
Signed Release → package-index hash linkage
Path: main/binary-amd64/Packages.xz
Expected SHA-256: 3ab4e811cf4f3e5a335d382c58cc19d85f1abe7a4ef4689160ca1f637fa0e9b3
Observed SHA-256: 3ab4e811cf4f3e5a335d382c58cc19d85f1abe7a4ef4689160ca1f637fa0e9b3
Result: match verified
Debian 13 (Trixie) main arm64Sep 1, 2026
Authoritative source; repository metadata signature verified, revision trixie-main-arm64:753da751bbc7a679f48bd1b623ffd4479cb6861c426118284c76eb82909e4908
Signature verification covers the configured repository metadata chain. It does not certify that the package is safe or suitable.
Repository-signature verification record
Signed object
https://deb.debian.org/debian/dists/trixie/InRelease
Signed-object SHA-256
98b25b5cd185c59d34aa6e4c3e9b5b8f01bbe9d104fe2dcfbcd30dc0a14a59ed
Signer fingerprint
4CB50190207B4758A3F73A796ED0E7B82643E131
Keyring revision
debian-archive-keyring.gpg
SHA-256 506b815cbb32d9b6066b4a2aa524071e071761e7e7f68c3ac74f3061ba852017
Tool and policy
gpgv (GnuPG) 2.4.9
openfactory-software-catalog-signature-v1
Verification time
Sep 1, 2026
Signed Release → package-index hash linkage
Path: main/binary-arm64/Packages.xz
Expected SHA-256: 753da751bbc7a679f48bd1b623ffd4479cb6861c426118284c76eb82909e4908
Observed SHA-256: 753da751bbc7a679f48bd1b623ffd4479cb6861c426118284c76eb82909e4908
Result: match verified