Debian 12 (Bookworm) native package

r-bioc-variantannotation

BioConductor annotation of genetic variants

Packages / Debian 12 (Bookworm) / gnu-r / r-bioc-variantannotation

Package: r-bioc-variantannotation (1.44.1-1)

Maintainers:

Debian R Packages Maintainers

External Resources:

Homepage: [bioconductor.org]

BioConductor annotation of genetic variants

Other Packages Related to r-bioc-variantannotation:

dep: [r-base-core] (>= 4.2.2.20221110-2)
GNU R core of statistical computation and graphics system
dep: r-api-4.0
Package not available
dep: r-api-bioc-3.16
Package not available
dep: [r-bioc-biocgenerics] (>= 0.37.0)
generic functions for Bioconductor
dep: [r-bioc-matrixgenerics]
S4 Generic Summary Statistic Functions that Operate on Matrix-Like Objects
dep: [r-bioc-genomeinfodb] (>= 1.15.2)
BioConductor utilities for manipulating chromosome identifiers
dep: [r-bioc-genomicranges] (>= 1.41.5)
BioConductor representation and manipulation of genomic intervals
dep: [r-bioc-summarizedexperiment] (>= 1.19.5)
BioConductor assay container
dep: [r-bioc-rsamtools] (>= 1.99.0)
GNU R binary alignment (BAM), variant call (BCF), or tabix file import
dep: [r-cran-dbi]
GNU R package providing a generic database interface
dep: [r-bioc-zlibbioc]
(Virtual) zlibbioc Bioconductor package
dep: [r-bioc-biobase]
base functions for Bioconductor
dep: [r-bioc-s4vectors] (>= 0.27.12)
BioConductor S4 implementation of vectors and lists
dep: [r-bioc-iranges] (>= 2.23.9)
GNU R low-level containers for storing sets of integer ranges
dep: [r-bioc-xvector] (>= 0.29.2)
BioConductor representation and manpulation of external sequences
dep: [r-bioc-biostrings] (>= 2.57.2)
GNU R string objects representing biological sequences
dep: [r-bioc-annotationdbi] (>= 1.27.9)
GNU R Annotation Database Interface for BioConductor
dep: [r-bioc-rtracklayer] (>= 1.39.7)
GNU R interface to genome browsers and their annotation tracks
dep: [r-bioc-bsgenome] (>= 1.47.3)
BioConductor infrastructure for Biostrings-based genome data packages
dep: [r-bioc-genomicfeatures] (>= 1.31.3)
GNU R tools for making and manipulating transcript centric annotations
dep: [r-bioc-rhtslib] (>= 1.99.3)
HTSlib high-throughput sequencing library as GNU R package
dep: [libc6] (>= 2.34)
GNU C Library: Shared libraries
dep: [libcurl4] (>= 7.18.0)
easy-to-use client-side URL transfer library (OpenSSL flavour)

sug: [r-cran-runit]
GNU R package providing unit testing framework
sug: [r-bioc-annotationhub]
GNU R client to access AnnotationHub resources
sug: [r-bioc-snpstats]
BioConductor SnpMatrix and XSnpMatrix classes and methods
sug: [r-cran-ggplot2]
implementation of the Grammar of Graphics
sug: [r-bioc-biocstyle]
standard styles for vignettes and other Bioconductor documents

Download r-bioc-variantannotation

Architecture	Package Size	Installed Size	Files
amd64	3.5 MiB	5.0 MiB	[list of files]
arm64	3.5 MiB	5.0 MiB	[list of files]

Package file paths (73)

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/VariantAnnotation/CITATION
/usr/lib/R/site-library/VariantAnnotation/DESCRIPTION
/usr/lib/R/site-library/VariantAnnotation/doc/filterVcf.pdf
/usr/lib/R/site-library/VariantAnnotation/doc/filterVcf.R
/usr/lib/R/site-library/VariantAnnotation/doc/filterVcf.Rnw
/usr/lib/R/site-library/VariantAnnotation/doc/index.html
/usr/lib/R/site-library/VariantAnnotation/doc/VariantAnnotation.pdf
/usr/lib/R/site-library/VariantAnnotation/doc/VariantAnnotation.R
/usr/lib/R/site-library/VariantAnnotation/doc/VariantAnnotation.Rnw
/usr/lib/R/site-library/VariantAnnotation/extdata/chr22.vcf.gz
/usr/lib/R/site-library/VariantAnnotation/extdata/chr22.vcf.gz.tbi
/usr/lib/R/site-library/VariantAnnotation/extdata/chr7-sub.vcf.gz
/usr/lib/R/site-library/VariantAnnotation/extdata/chr7-sub.vcf.gz.tbi
/usr/lib/R/site-library/VariantAnnotation/extdata/ex2.vcf
/usr/lib/R/site-library/VariantAnnotation/extdata/gl_chr1.vcf
/usr/lib/R/site-library/VariantAnnotation/extdata/h1187-10k.vcf.gz
/usr/lib/R/site-library/VariantAnnotation/extdata/h1187-10k.vcf.gz.tbi
/usr/lib/R/site-library/VariantAnnotation/extdata/hapmap_exome_chr22.vcf.gz
/usr/lib/R/site-library/VariantAnnotation/extdata/hapmap_exome_chr22.vcf.gz.tbi
/usr/lib/R/site-library/VariantAnnotation/extdata/structural.vcf
/usr/lib/R/site-library/VariantAnnotation/help/aliases.rds
/usr/lib/R/site-library/VariantAnnotation/help/AnIndex
/usr/lib/R/site-library/VariantAnnotation/help/paths.rds
/usr/lib/R/site-library/VariantAnnotation/help/VariantAnnotation.rdb
/usr/lib/R/site-library/VariantAnnotation/help/VariantAnnotation.rdx
/usr/lib/R/site-library/VariantAnnotation/html/00Index.html
/usr/lib/R/site-library/VariantAnnotation/html/R.css
/usr/lib/R/site-library/VariantAnnotation/INDEX
/usr/lib/R/site-library/VariantAnnotation/libs/VariantAnnotation.so
/usr/lib/R/site-library/VariantAnnotation/Meta/features.rds
/usr/lib/R/site-library/VariantAnnotation/Meta/hsearch.rds
/usr/lib/R/site-library/VariantAnnotation/Meta/links.rds
/usr/lib/R/site-library/VariantAnnotation/Meta/nsInfo.rds
/usr/lib/R/site-library/VariantAnnotation/Meta/package.rds
/usr/lib/R/site-library/VariantAnnotation/Meta/Rd.rds
/usr/lib/R/site-library/VariantAnnotation/Meta/vignette.rds
/usr/lib/R/site-library/VariantAnnotation/NAMESPACE
/usr/lib/R/site-library/VariantAnnotation/NEWS
/usr/lib/R/site-library/VariantAnnotation/R/VariantAnnotation
/usr/lib/R/site-library/VariantAnnotation/R/VariantAnnotation.rdb
/usr/lib/R/site-library/VariantAnnotation/R/VariantAnnotation.rdx
/usr/lib/R/site-library/VariantAnnotation/scripts/test_Rplinkseq.R
/usr/lib/R/site-library/VariantAnnotation/unitTests/cases/banded_gvcf.vcf
/usr/lib/R/site-library/VariantAnnotation/unitTests/cases/buffer_realloc.vcf
/usr/lib/R/site-library/VariantAnnotation/unitTests/cases/ex1-seq1-90.vcf
/usr/lib/R/site-library/VariantAnnotation/unitTests/cases/expand.vcf
/usr/lib/R/site-library/VariantAnnotation/unitTests/cases/fewer-FORMAT-than-GENO.vcf
/usr/lib/R/site-library/VariantAnnotation/unitTests/cases/FORMAT_header_no_SAMPLEs.vcf
/usr/lib/R/site-library/VariantAnnotation/unitTests/cases/meta_header.vcf
/usr/lib/R/site-library/VariantAnnotation/unitTests/cases/missing-FORMAT-metadata-elt.vcf
/usr/lib/R/site-library/VariantAnnotation/unitTests/cases/mixedStructural.vcf
/usr/lib/R/site-library/VariantAnnotation/unitTests/cases/multiple_INFO_fields.vcf
/usr/lib/R/site-library/VariantAnnotation/unitTests/cases/negative_FORMAT_Number.vcf
/usr/lib/R/site-library/VariantAnnotation/unitTests/cases/no_FORMAT_column.vcf
/usr/lib/R/site-library/VariantAnnotation/unitTests/cases/no_GENO_row.vcf
/usr/lib/R/site-library/VariantAnnotation/unitTests/cases/no_INFO_header.vcf
/usr/lib/R/site-library/VariantAnnotation/unitTests/cases/unspecified_INFO_FORMAT_fields.vcf
/usr/lib/R/site-library/VariantAnnotation/unitTests/cases/VarScan_header.vcf
/usr/lib/R/site-library/VariantAnnotation/unitTests/test_expand-methods.R
/usr/lib/R/site-library/VariantAnnotation/unitTests/test_filterVcf.R
/usr/lib/R/site-library/VariantAnnotation/unitTests/test_genotypeToSnpMatrix.R
/usr/lib/R/site-library/VariantAnnotation/unitTests/test_isSNV.R
/usr/lib/R/site-library/VariantAnnotation/unitTests/test_readVcf-methods.R
/usr/lib/R/site-library/VariantAnnotation/unitTests/test_ScanVcfParam-class.R
/usr/lib/R/site-library/VariantAnnotation/unitTests/test_scanVcf.R
/usr/lib/R/site-library/VariantAnnotation/unitTests/test_snpSummary.R
/usr/lib/R/site-library/VariantAnnotation/unitTests/test_summarizeVariants-methods.R
/usr/lib/R/site-library/VariantAnnotation/unitTests/test_VCF-class.R
/usr/lib/R/site-library/VariantAnnotation/unitTests/test_vcfFields.R
/usr/lib/R/site-library/VariantAnnotation/unitTests/test_VRanges-class.R
/usr/lib/R/site-library/VariantAnnotation/unitTests/test_writeVcf-methods.R
/usr/share/doc/r-bioc-variantannotation/changelog.Debian.gz
/usr/share/doc/r-bioc-variantannotation/copyright

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

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

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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
1.44.1-1	bookworm / main	amd64	Debian 12 · main · amd64	3.5 MiB	5.0 MiB	pool/main/r/r-bioc-variantannotation/r-bioc-variantannotation_1.44.1-1_amd64.deb
1.44.1-1	bookworm / main	arm64	Debian 12 · main · arm64	3.5 MiB	5.0 MiB	pool/main/r/r-bioc-variantannotation/r-bioc-variantannotation_1.44.1-1_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.

1.44.1-1 / 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: f515726c0cb9580d26ecf5ab42cb9238e7c3861ed320d46d993062ae8ee2f8fa

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

printf '%s  %s\n' 'f515726c0cb9580d26ecf5ab42cb9238e7c3861ed320d46d993062ae8ee2f8fa' 'r-bioc-variantannotation_1.44.1-1_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

1.44.1-1 / 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: 6748cc3b362c162c4d543af69e9cd1b18e7b6119f63ef6d568512b8229c404a7

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

printf '%s  %s\n' '6748cc3b362c162c4d543af69e9cd1b18e7b6119f63ef6d568512b8229c404a7' 'r-bioc-variantannotation_1.44.1-1_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