Package: faissR
Type: Package
Title: FAISS-Backed Nearest Neighbours, Graph Clustering, kNN Models,
        and k-Means
Version: 0.99.14
Authors@R: person(given = "Stefano",
    family = "Cacciatore",
    role = c("aut", "cre"),
    email = "tkcaccia@gmail.com",
    comment = c(ORCID = "0000-0001-7052-7156"))
Description: Native nearest-neighbour search, graph construction, graph
        clustering, k-nearest neighbour prediction, and k-means helpers
        for large dimensionality reduction workflows in high-throughput
        biological data analysis, including single-cell, flow
        cytometry, imaging, and mass spectrometry applications. The
        package requires the FAISS C++ library for all builds,
        including CPU-only indexes, and can optionally use FAISS GPU
        indexes with NVIDIA cuVS integration or direct RAPIDS cuVS/CUDA
        indexes on NVIDIA machines. CPU-only systems do not need NVIDIA
        libraries, but NVIDIA CUDA/cuVS libraries are mandatory when a
        GPU-enabled build is explicitly requested. Supervised kNN
        models use knn(Xtrain, Ytrain) and predict(), or knn(Xtrain,
        Ytrain, Xtest) for immediate prediction. Class probabilities
        are returned through predict(type = "prob") for kNN
        classification models.
License: MIT + file LICENSE
URL: https://github.com/tkcaccia/faissR
BugReports: https://github.com/tkcaccia/faissR/issues
OS_type: unix
biocViews: Software, Infrastructure, GPU, SingleCell, FlowCytometry,
        MassSpectrometry, ImagingMassSpectrometry, Proteomics,
        Clustering, DimensionReduction, Classification
Encoding: UTF-8
Imports: methods, Rcpp
Suggests: BiocStyle, knitr, Matrix, float, rmarkdown, testthat, withr
LinkingTo: Rcpp
SystemRequirements: C++20, Fortran, FAISS C++ development library
        (Debian/Ubuntu: libfaiss-dev), OpenMP runtime on macOS when
        FAISS headers include omp.h (for example Homebrew libomp).
        Optional GPU libraries are documented in the installation guide
        and are used only when a GPU-enabled build is explicitly
        requested.
Config/Bioconductor/UnsupportedPlatforms: mac
VignetteBuilder: knitr
Config/roxygen2/version: 8.0.0
Config/testthat/edition: 3
Config/pak/sysreqs: libfaiss-dev
Repository: https://biocstaging.r-universe.dev
Date/Publication: 2026-07-10 12:21:49 UTC
RemoteUrl: https://github.com/BiocStaging/faissR
RemoteRef: HEAD
RemoteSha: 9f626aa0ea2a37188e15753a47d21dde64154815
NeedsCompilation: yes
Packaged: 2026-07-10 13:05:24 UTC; root
Author: Stefano Cacciatore [aut, cre] (ORCID:
    <https://orcid.org/0000-0001-7052-7156>)
Maintainer: Stefano Cacciatore <tkcaccia@gmail.com>