{
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  "Package": "Rfmalloc",
  "Title": "Out-of-Core Arrays with Pluggable Codecs and Compute Backends",
  "Version": "0.1.0",
  "Authors@R": "c(\nperson(given = \"Sounkou Mahamane\", family = \"Toure\", email = \"sounkoutoure@gmail.com\", role = c(\"aut\", \"cre\")),\nperson(given = \"Kenichi\", family = \"Yasukata\", role = \"cph\", comment = \"fmalloc\"),\nperson(given = \"Wolfram\", family = \"Gloger\", role = \"cph\", comment = \"ptmalloc3\"),\nperson(given = \"Free Software Foundation, Inc.\", role = \"cph\", comment = \"selected GNU C Library support files\")\n)",
  "Description": "Computes on arrays that do not fit in memory. Vectors,\nmatrices and tensors are allocated inside a memory-mapped file\nthrough R's ALTREP interface, backed by a patched copy of the\n'fmalloc' allocator, so available RAM becomes a speed gradient\nrather than a hard limit. Two plugin registries sit on that\nsubstrate: a codec registry deciding how bytes are stored, from\nlossless floating-point and sparse encodings to compressed and\nquantized blocks, and a matrix-multiply backend registry\ndeciding how products are computed, defaulting to whatever\n'BLAS' the R build links against. Matrix products stream in\nbounded panels and release the pages they have consumed, so\noperands larger than memory still multiply. A registered\nbackend may decline any product, in which case the default path\nanswers it, so results never depend on which backend is\nselected. Also provides persistent and scratch runtimes,\ndurable reference-based serialization, explicit vector\nlifecycle management, multiple runtime handles per session, and\nout-of-core reductions and principal components for\ngenomics-scale matrices.",
  "License": "GPL (>= 2)",
  "Encoding": "UTF-8",
  "Roxygen": "list(markdown = TRUE)",
  "RoxygenNote": "7.3.3",
  "SystemRequirements": "GNU make, POSIX threads",
  "URL": "https://github.com/sounkou-bioinfo/Rfmalloc,\nhttps://sounkou-bioinfo.github.io/Rfmalloc/Rfmalloc/",
  "BugReports": "https://github.com/sounkou-bioinfo/Rfmalloc/issues",
  "Config/pak/sysreqs": "make",
  "Repository": "https://rgenomicsetl.r-universe.dev",
  "Date/Publication": "2026-09-09 23:54:20 UTC",
  "RemoteUrl": "https://github.com/RGenomicsETL/Rfmalloc",
  "RemoteRef": "HEAD",
  "RemoteSha": "156efa6ec133a512d8969fded81aaa630ff9ba16",
  "RemoteSubdir": "packages/Rfmalloc",
  "NeedsCompilation": "yes",
  "Packaged": {
    "Date": "2026-10-10 07:35:02 UTC",
    "User": "root"
  },
  "Author": "Sounkou Mahamane Toure [aut, cre],\nKenichi Yasukata [cph] (fmalloc),\nWolfram Gloger [cph] (ptmalloc3),\nFree Software Foundation, Inc. [cph] (selected GNU C Library support\nfiles)",
  "Maintainer": "Sounkou Mahamane Toure <sounkoutoure@gmail.com>",
  "_user": "rgenomicsetl",
  "_type": "src",
  "_file": "Rfmalloc_0.1.0.tar.gz",
  "_fileid": "https://r2.ropensci.org/aa4b849bfaa18980258c9b703b64207b4121954984191723d56ccac36c31cd22",
  "_filesize": 489080,
  "_sha256": "aa4b849bfaa18980258c9b703b64207b4121954984191723d56ccac36c31cd22",
  "_expires": "2027-01-18T07:50:33.000Z",
  "_created": "2026-10-10T07:35:02.000Z",
  "_published": "2026-10-10T07:50:39.366Z",
  "_buildurl": "https://github.com/r-universe/rgenomicsetl/actions/runs/38034772430",
  "_status": "success",
  "_host": "GitHub-Actions",
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  "_commit": {
    "id": "156efa6ec133a512d8969fded81aaa630ff9ba16",
    "author": "sounkou-bioinfo <sounkoutoure@gmail.com>",
    "committer": "sounkou-bioinfo <sounkoutoure@gmail.com>",
    "message": "Keep the shared library the default goal in the statgen Makevars\n",
    "time": 1788998060
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    "name": "Sounkou Mahamane Toure",
    "email": "sounkoutoure@gmail.com",
    "login": "sounkou-bioinfo",
    "mastodon": "@bioinfhotep@genomic.social",
    "description": "Sequences and Consequences.",
    "uuid": 56392505
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      "version": ">= 4.4.0",
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      "package": "methods",
      "role": "Imports"
    },
    {
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      "role": "Suggests"
    },
    {
      "package": "kalis",
      "role": "Suggests"
    },
    {
      "package": "lobstr",
      "role": "Suggests"
    },
    {
      "package": "tinytest",
      "role": "Suggests"
    }
  ],
  "_owner": "rgenomicsetl",
  "_selfowned": true,
  "_usedby": 4,
  "_updates": [
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      "week": "2026-19",
      "n": 50
    },
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    },
    {
      "week": "2026-37",
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  ],
  "_tags": [],
  "_topics": [
    "altrep",
    "blas",
    "genomics",
    "ggml",
    "gguf",
    "llm",
    "llm-inference",
    "malloc",
    "memory-mapped",
    "mmap",
    "out-of-core",
    "quantization",
    "simd",
    "cpp"
  ],
  "_stars": 4,
  "_contributors": [
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      "user": "sounkou-bioinfo",
      "count": 218,
      "uuid": 56392505
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  "_userbio": {
    "uuid": 252609706,
    "type": "organization",
    "name": "GenomicsETL",
    "followers": 10,
    "description": "Composable genomics in DuckDB, with R, the browser and agents as front ends"
  },
  "_downloads": {
    "count": 0,
    "source": "https://cranlogs.r-pkg.org/downloads/total/last-month/Rfmalloc"
  },
  "_devurl": "https://github.com/sounkou-bioinfo/rfmalloc",
  "_searchresults": 43,
  "_rbuild": "4.6.1",
  "_assets": [
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    "extra/citation.html",
    "extra/citation.json",
    "extra/citation.txt",
    "extra/contents.json",
    "extra/manual.pdf",
    "extra/NEWS.html",
    "extra/NEWS.txt",
    "extra/readme.html",
    "extra/readme.md",
    "extra/Rfmalloc.html"
  ],
  "_cranurl": false,
  "_exports": [
    "as_fmalloc_array",
    "as_fmalloc_data_frame",
    "as_fmalloc_matrix",
    "as_fmalloc_tensor",
    "cleanup_fmalloc",
    "colMeans",
    "colSums",
    "create_fmalloc_array",
    "create_fmalloc_data_frame",
    "create_fmalloc_haplotypes",
    "create_fmalloc_matrix",
    "create_fmalloc_tensor",
    "create_fmalloc_vector",
    "destroy_fmalloc_vector",
    "diagnose_fmalloc_runtime",
    "fmalloc_add",
    "fmalloc_bed",
    "fmalloc_bed_standardize",
    "fmalloc_colVars",
    "fmalloc_crossprod_ooc",
    "fmalloc_default_runtime",
    "fmalloc_div",
    "fmalloc_dosage",
    "fmalloc_dosage_standardize",
    "fmalloc_fill",
    "fmalloc_hap_materialize",
    "fmalloc_haplotypes",
    "fmalloc_ld",
    "fmalloc_matmul_backend",
    "fmalloc_matmul_backends",
    "fmalloc_matmul_ooc",
    "fmalloc_mul",
    "fmalloc_pca",
    "fmalloc_rowVars",
    "fmalloc_runtime",
    "fmalloc_runtime_info",
    "fmalloc_set",
    "fmalloc_storage_advise",
    "fmalloc_sub",
    "fmalloc_sync",
    "fmalloc_tcrossprod_ooc",
    "fmalloc_tensor_codecs",
    "fmalloc_tensor_dtype",
    "fmalloc_tensor_materialize",
    "fmalloc_vector_info",
    "fmalloc_vector_length",
    "fmalloc_vector_payload_ptr",
    "fmalloc_vector_type",
    "init_fmalloc",
    "is_fmalloc_runtime",
    "is_fmalloc_vector",
    "ld_col",
    "ld_ncol",
    "ld_pair",
    "list_fmalloc_allocations",
    "open_fmalloc",
    "rowMeans",
    "rowSums"
  ],
  "_help": [
    {
      "page": "Rfmalloc-package",
      "title": "Rfmalloc: Memory-Mapped File Allocation for R",
      "topics": [
        "Rfmalloc-package",
        "Rfmalloc"
      ]
    },
    {
      "page": "as_fmalloc_array",
      "title": "Convert a vector to fmalloc array metadata",
      "topics": [
        "as_fmalloc_array"
      ]
    },
    {
      "page": "as_fmalloc_data_frame",
      "title": "Convert to data.frame for fmalloc vectors",
      "topics": [
        "as_fmalloc_data_frame"
      ]
    },
    {
      "page": "as_fmalloc_matrix",
      "title": "Convert a vector to fmalloc matrix metadata",
      "topics": [
        "as_fmalloc_matrix"
      ]
    },
    {
      "page": "cleanup_fmalloc",
      "title": "Clean Up fmalloc",
      "topics": [
        "cleanup_fmalloc"
      ]
    },
    {
      "page": "create_fmalloc_array",
      "title": "Create Array Using fmalloc",
      "topics": [
        "create_fmalloc_array"
      ]
    },
    {
      "page": "create_fmalloc_data_frame",
      "title": "Construct data.frame from fmalloc columns",
      "topics": [
        "create_fmalloc_data_frame"
      ]
    },
    {
      "page": "create_fmalloc_matrix",
      "title": "Create Matrix Using fmalloc",
      "topics": [
        "create_fmalloc_matrix"
      ]
    },
    {
      "page": "create_fmalloc_vector",
      "title": "Create Vector Using fmalloc",
      "topics": [
        "create_fmalloc_vector"
      ]
    },
    {
      "page": "destroy_fmalloc_vector",
      "title": "Explicitly destroy a fmalloc vector",
      "topics": [
        "destroy_fmalloc_vector"
      ]
    },
    {
      "page": "diagnose_fmalloc_runtime",
      "title": "Diagnose fmalloc runtime state",
      "topics": [
        "diagnose_fmalloc_runtime"
      ]
    },
    {
      "page": "fmalloc_api",
      "title": "Public Rfmalloc API helpers",
      "topics": [
        "fmalloc_api",
        "fmalloc_default_runtime",
        "fmalloc_runtime",
        "fmalloc_runtime_info",
        "fmalloc_vector_info",
        "fmalloc_vector_length",
        "fmalloc_vector_payload_ptr",
        "fmalloc_vector_type",
        "is_fmalloc_runtime",
        "is_fmalloc_vector"
      ]
    },
    {
      "page": "fmalloc_backend",
      "title": "Pluggable matrix-multiply backend",
      "topics": [
        "fmalloc_backend",
        "fmalloc_matmul_backend",
        "fmalloc_matmul_backends"
      ]
    },
    {
      "page": "fmalloc_bed",
      "title": "PLINK 1 genotypes as a 2-bit fmalloc tensor",
      "topics": [
        "fmalloc_bed"
      ]
    },
    {
      "page": "fmalloc_bed_standardize",
      "title": "Bake per-variant standardization into a bed tensor",
      "topics": [
        "fmalloc_bed_standardize"
      ]
    },
    {
      "page": "fmalloc_colVars",
      "title": "Column / row variances of an fmalloc matrix",
      "topics": [
        "fmalloc_colVars",
        "fmalloc_rowVars"
      ]
    },
    {
      "page": "fmalloc_dosage",
      "title": "Fractional genotype dosages as a 1-byte fmalloc tensor",
      "topics": [
        "fmalloc_dosage"
      ]
    },
    {
      "page": "fmalloc_dosage_standardize",
      "title": "Bake per-variant standardization into a dosage tensor",
      "topics": [
        "fmalloc_dosage_standardize"
      ]
    },
    {
      "page": "fmalloc_hap_materialize",
      "title": "Adapt a bit-packed haplotype store to a 0/1 matrix",
      "topics": [
        "fmalloc_hap_materialize"
      ]
    },
    {
      "page": "fmalloc_haplotypes",
      "title": "Phased haplotypes as a 1-bit fmalloc store",
      "topics": [
        "create_fmalloc_haplotypes",
        "dim.fmalloc_haplotypes",
        "fmalloc_haplotypes",
        "print.fmalloc_haplotypes"
      ]
    },
    {
      "page": "fmalloc_insitu",
      "title": "In-place (by-reference) mutation of fmalloc vectors",
      "topics": [
        "fmalloc_add",
        "fmalloc_div",
        "fmalloc_fill",
        "fmalloc_insitu",
        "fmalloc_mul",
        "fmalloc_set",
        "fmalloc_sub"
      ]
    },
    {
      "page": "fmalloc_ld",
      "title": "Banded LD (correlation) matrix as a compressed fmalloc store",
      "topics": [
        "dim.fmalloc_ld",
        "fmalloc_ld",
        "print.fmalloc_ld"
      ]
    },
    {
      "page": "fmalloc_linalg",
      "title": "Matrix algebra for fmalloc-backed vectors and matrices",
      "topics": [
        "%*%.fmalloc",
        "crossprod.fmalloc",
        "fmalloc_linalg",
        "matrixOps.fmalloc",
        "tcrossprod.fmalloc"
      ]
    },
    {
      "page": "fmalloc_matmul_ooc",
      "title": "Out-of-core matrix product for fmalloc matrices larger than RAM",
      "topics": [
        "fmalloc_crossprod_ooc",
        "fmalloc_matmul_ooc",
        "fmalloc_tcrossprod_ooc"
      ]
    },
    {
      "page": "fmalloc_pca",
      "title": "Out-of-core PCA / truncated SVD for fmalloc matrices",
      "topics": [
        "fmalloc_pca"
      ]
    },
    {
      "page": "fmalloc_reduction_methods",
      "title": "Matrix reduction helpers for fmalloc-backed matrices",
      "topics": [
        "colMeans",
        "colSums",
        "fmalloc_reduction_methods",
        "rowMeans",
        "rowSums"
      ]
    },
    {
      "page": "fmalloc_storage_advise",
      "title": "Give the pager an access hint for typed storage",
      "topics": [
        "fmalloc_storage_advise"
      ]
    },
    {
      "page": "fmalloc_sync",
      "title": "Flush an fmalloc runtime's backing store to disk",
      "topics": [
        "fmalloc_sync"
      ]
    },
    {
      "page": "fmalloc_tensor",
      "title": "Typed fmalloc tensors",
      "topics": [
        "%*%.fmalloc_tensor",
        "as_fmalloc_tensor",
        "create_fmalloc_tensor",
        "crossprod.fmalloc_tensor",
        "dim.fmalloc_tensor",
        "fmalloc_tensor",
        "fmalloc_tensor_codecs",
        "fmalloc_tensor_dtype",
        "fmalloc_tensor_materialize",
        "matrixOps.fmalloc_tensor",
        "print.fmalloc_tensor",
        "tcrossprod.fmalloc_tensor"
      ]
    },
    {
      "page": "init_fmalloc",
      "title": "Initialize fmalloc",
      "topics": [
        "init_fmalloc"
      ]
    },
    {
      "page": "ld_col",
      "title": "Neighbour run of one column of a banded LD store",
      "topics": [
        "ld_col"
      ]
    },
    {
      "page": "ld_ncol",
      "title": "Number of variants in a banded LD store",
      "topics": [
        "ld_ncol"
      ]
    },
    {
      "page": "ld_pair",
      "title": "Correlation between two variants of a banded LD store",
      "topics": [
        "ld_pair"
      ]
    },
    {
      "page": "list_fmalloc_allocations",
      "title": "List Persistent fmalloc Allocations",
      "topics": [
        "list_fmalloc_allocations"
      ]
    },
    {
      "page": "open_fmalloc",
      "title": "Open an fmalloc Runtime",
      "topics": [
        "open_fmalloc"
      ]
    }
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