Debian 12 (Bookworm) native package

r-cran-bio3d

GNU R package for biological structure analysis

Packages / Debian 12 (Bookworm) / gnu-r / r-cran-bio3d

Package: r-cran-bio3d (2.4-4-1)

Maintainers:

Debian R Packages Maintainers

External Resources:

Homepage: [cran.r-project.org]

GNU R package for biological structure analysis

Other Packages Related to r-cran-bio3d:

dep: [r-base-core] (>= 4.2.1-3)
GNU R core of statistical computation and graphics system
dep: r-api-4.0
Package not available
dep: [r-cran-rcpp]
GNU R package for Seamless R and C++ Integration
dep: [libc6] (>= 2.14)
GNU C Library: Shared libraries
dep: [libgcc-s1] (>= 3.0)
GCC support library
dep: [libstdc++6] (>= 5.2)
GNU Standard C++ Library v3
dep: [zlib1g] (>= 1:1.1.4)
compression library - runtime

rec: [r-cran-testthat] (>= 0.9.1)
GNU R testsuite
rec: [muscle]
Multiple alignment program of protein sequences
rec: [clustalo]
General-purpose multiple sequence alignment program for proteins
rec: [dssp]
protein secondary structure assignment based on 3D structure
rec: [mustang]
multiple structural alignment of proteins

sug: [r-cran-xml]
GNU R package for XML parsing and generation
sug: [r-cran-rcurl]
GNU R General network (HTTP/FTP/...) client interface
sug: [r-cran-lattice]
GNU R package for 'Trellis' graphics
sug: [r-cran-ncdf4]
GNU R interface to Unidata netCDF format data files
sug: [r-cran-igraph]
GNU R network analysis and visualization
sug: [r-cran-bigmemory]
Manage Massive Matrices with Shared Memory and Memory-Mapped Files
sug: [r-cran-knitr]
GNU R package for dynamic report generation using Literate Programming
sug: [r-cran-rmarkdown]
convert R markdown documents into a variety of formats
sug: [r-cran-httr]
GNU R tools for working with URLs and HTTP
sug: [r-bioc-biostrings]
GNU R string objects representing biological sequences

Download r-cran-bio3d

Architecture	Package Size	Installed Size	Files
amd64	2.8 MiB	3.8 MiB	[list of files]
arm64	2.8 MiB	3.9 MiB	[list of files]

Package file paths (89)

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/bio3d/CITATION
/usr/lib/R/site-library/bio3d/data/Rdata.rdb
/usr/lib/R/site-library/bio3d/data/Rdata.rds
/usr/lib/R/site-library/bio3d/data/Rdata.rdx
/usr/lib/R/site-library/bio3d/demo/md.R
/usr/lib/R/site-library/bio3d/demo/nma.R
/usr/lib/R/site-library/bio3d/demo/pca.R
/usr/lib/R/site-library/bio3d/demo/pdb.R
/usr/lib/R/site-library/bio3d/DESCRIPTION
/usr/lib/R/site-library/bio3d/doc/bio3d_vignettes.html
/usr/lib/R/site-library/bio3d/doc/bio3d_vignettes.Rmd
/usr/lib/R/site-library/bio3d/doc/index.html
/usr/lib/R/site-library/bio3d/examples/1dpx.pdb
/usr/lib/R/site-library/bio3d/examples/1hel.pdb
/usr/lib/R/site-library/bio3d/examples/aspirin.mol2
/usr/lib/R/site-library/bio3d/examples/crambin.inpcrd
/usr/lib/R/site-library/bio3d/examples/crambin.prmtop
/usr/lib/R/site-library/bio3d/examples/hivp.dcd
/usr/lib/R/site-library/bio3d/examples/hivp.pdb
/usr/lib/R/site-library/bio3d/examples/hivp_xray.fa
/usr/lib/R/site-library/bio3d/examples/kif1a.fa
/usr/lib/R/site-library/bio3d/examples/test.pdb
/usr/lib/R/site-library/bio3d/examples/transducin.fa
/usr/lib/R/site-library/bio3d/help/aliases.rds
/usr/lib/R/site-library/bio3d/help/AnIndex
/usr/lib/R/site-library/bio3d/help/bio3d.rdb
/usr/lib/R/site-library/bio3d/help/bio3d.rdx
/usr/lib/R/site-library/bio3d/help/paths.rds
/usr/lib/R/site-library/bio3d/html/00Index.html
/usr/lib/R/site-library/bio3d/html/R.css
/usr/lib/R/site-library/bio3d/INDEX
/usr/lib/R/site-library/bio3d/libs/bio3d.so
/usr/lib/R/site-library/bio3d/matrices/bio3d.mat
/usr/lib/R/site-library/bio3d/matrices/blosum62.mat
/usr/lib/R/site-library/bio3d/matrices/custom.mat
/usr/lib/R/site-library/bio3d/matrices/emboss_properties.mat
/usr/lib/R/site-library/bio3d/matrices/pam30.mat
/usr/lib/R/site-library/bio3d/matrices/properties.mat
/usr/lib/R/site-library/bio3d/matrices/similarity.mat
/usr/lib/R/site-library/bio3d/Meta/data.rds
/usr/lib/R/site-library/bio3d/Meta/demo.rds
/usr/lib/R/site-library/bio3d/Meta/features.rds
/usr/lib/R/site-library/bio3d/Meta/hsearch.rds
/usr/lib/R/site-library/bio3d/Meta/links.rds
/usr/lib/R/site-library/bio3d/Meta/nsInfo.rds
/usr/lib/R/site-library/bio3d/Meta/package.rds
/usr/lib/R/site-library/bio3d/Meta/Rd.rds
/usr/lib/R/site-library/bio3d/Meta/vignette.rds
/usr/lib/R/site-library/bio3d/NAMESPACE
/usr/lib/R/site-library/bio3d/NEWS.md
/usr/lib/R/site-library/bio3d/R/bio3d
/usr/lib/R/site-library/bio3d/R/bio3d.rdb
/usr/lib/R/site-library/bio3d/R/bio3d.rdx
/usr/lib/R/site-library/bio3d/staticdocs/index.r
/usr/share/doc/r-cran-bio3d/changelog.Debian.gz
/usr/share/doc/r-cran-bio3d/copyright
/usr/share/doc/r-cran-bio3d/README.test
/usr/share/doc/r-cran-bio3d/run-unit-test
/usr/share/doc/r-cran-bio3d/tests/testthat.R
/usr/share/doc/r-cran-bio3d/tests/testthat/test-aa2mass.R
/usr/share/doc/r-cran-bio3d/tests/testthat/test-aanma.pdbs.R.gz
/usr/share/doc/r-cran-bio3d/tests/testthat/test-aanma.R.gz
/usr/share/doc/r-cran-bio3d/tests/testthat/test-atom2mass.R
/usr/share/doc/r-cran-bio3d/tests/testthat/test-atom.select.R.gz
/usr/share/doc/r-cran-bio3d/tests/testthat/test-clean.pdb.R
/usr/share/doc/r-cran-bio3d/tests/testthat/test-cmap.R
/usr/share/doc/r-cran-bio3d/tests/testthat/test-cna.R
/usr/share/doc/r-cran-bio3d/tests/testthat/test-core.find.R
/usr/share/doc/r-cran-bio3d/tests/testthat/test-dccm.R
/usr/share/doc/r-cran-bio3d/tests/testthat/test-deformation.R
/usr/share/doc/r-cran-bio3d/tests/testthat/test-dssp.R
/usr/share/doc/r-cran-bio3d/tests/testthat/test-fitting.R.gz
/usr/share/doc/r-cran-bio3d/tests/testthat/test-get.pdb.R
/usr/share/doc/r-cran-bio3d/tests/testthat/test-get.seq.R.gz
/usr/share/doc/r-cran-bio3d/tests/testthat/test-gnm.R
/usr/share/doc/r-cran-bio3d/tests/testthat/test-mol2.R
/usr/share/doc/r-cran-bio3d/tests/testthat/test-nma.pdbs.R.gz
/usr/share/doc/r-cran-bio3d/tests/testthat/test-nma.R.gz
/usr/share/doc/r-cran-bio3d/tests/testthat/test-overlap.R
/usr/share/doc/r-cran-bio3d/tests/testthat/test-pca.R
/usr/share/doc/r-cran-bio3d/tests/testthat/test-pdb.annotate.R
/usr/share/doc/r-cran-bio3d/tests/testthat/test-pdbsplit.R
/usr/share/doc/r-cran-bio3d/tests/testthat/test-read.all.R.gz
/usr/share/doc/r-cran-bio3d/tests/testthat/test-read.cif.R
/usr/share/doc/r-cran-bio3d/tests/testthat/test-read.ncdf.R
/usr/share/doc/r-cran-bio3d/tests/testthat/test-read.pdb.R.gz
/usr/share/doc/r-cran-bio3d/tests/testthat/test-rmsd.R
/usr/share/doc/r-cran-bio3d/tests/testthat/test-seqaln.R
/usr/share/doc/r-cran-bio3d/tests/testthat/test-vector-funs.R

Field source: Debian 12 (Bookworm) main amd64 revision bookworm-main-amd64:9e0b5aabb2465b3d2e7a7fe27f9913846277833f7a2826e7767acccff5b588c5

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 12 (Bookworm) in the browser Build an image that includes r-cran-bio3d

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
2.4-4-1	bookworm / main	amd64	Debian 12 · main · amd64	2.8 MiB	3.8 MiB	pool/main/r/r-cran-bio3d/r-cran-bio3d_2.4-4-1_amd64.deb
2.4-4-1	bookworm / main	arm64	Debian 12 · main · arm64	2.8 MiB	3.9 MiB	pool/main/r/r-cran-bio3d/r-cran-bio3d_2.4-4-1_arm64.deb

Field source: Debian 12 (Bookworm) main amd64 revision bookworm-main-amd64:9e0b5aabb2465b3d2e7a7fe27f9913846277833f7a2826e7767acccff5b588c5

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.

2.4-4-1 / 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: d8783c500111645e0a4e02170859e3494bebf9666a698c07b5be5a20ab011234

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

printf '%s  %s\n' 'd8783c500111645e0a4e02170859e3494bebf9666a698c07b5be5a20ab011234' 'r-cran-bio3d_2.4-4-1_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 12 (Bookworm) main amd64 revision bookworm-main-amd64:9e0b5aabb2465b3d2e7a7fe27f9913846277833f7a2826e7767acccff5b588c5

2.4-4-1 / 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: 79276f29e498c55af73333fc859bfc201c067b6bfd75b6f2408a11a64e3d24f6

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

printf '%s  %s\n' '79276f29e498c55af73333fc859bfc201c067b6bfd75b6f2408a11a64e3d24f6' 'r-cran-bio3d_2.4-4-1_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 12 (Bookworm) main arm64 revision bookworm-main-arm64:2ddb1737692e8c45c53e8d57c0ce4cd21c78c5703b830c3226b1423566a06c00

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 12 (Bookworm) main amd64 revision bookworm-main-amd64:9e0b5aabb2465b3d2e7a7fe27f9913846277833f7a2826e7767acccff5b588c5, Debian 12 (Bookworm) main arm64 revision bookworm-main-arm64:2ddb1737692e8c45c53e8d57c0ce4cd21c78c5703b830c3226b1423566a06c00. 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 12 (Bookworm) main amd64Sep 1, 2026
Authoritative source; repository metadata signature verified, revision bookworm-main-amd64:9e0b5aabb2465b3d2e7a7fe27f9913846277833f7a2826e7767acccff5b588c5
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/bookworm/InRelease
Signed-object SHA-256
77737fa4b34f2693e982cc9ee35736816c35a7778fc2d326cc1bbf5b301fe1aa
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: 9e0b5aabb2465b3d2e7a7fe27f9913846277833f7a2826e7767acccff5b588c5
Observed SHA-256: 9e0b5aabb2465b3d2e7a7fe27f9913846277833f7a2826e7767acccff5b588c5
Result: match verified
Debian 12 (Bookworm) main arm64Sep 1, 2026
Authoritative source; repository metadata signature verified, revision bookworm-main-arm64:2ddb1737692e8c45c53e8d57c0ce4cd21c78c5703b830c3226b1423566a06c00
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/bookworm/InRelease
Signed-object SHA-256
77737fa4b34f2693e982cc9ee35736816c35a7778fc2d326cc1bbf5b301fe1aa
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: 2ddb1737692e8c45c53e8d57c0ce4cd21c78c5703b830c3226b1423566a06c00
Observed SHA-256: 2ddb1737692e8c45c53e8d57c0ce4cd21c78c5703b830c3226b1423566a06c00
Result: match verified