{ "_id": "6a50c97d89c83ec243a30c38", "Package": "Rpgen", "Title": "Vendored 'PLINK 2' pgenlib with a C-Callable Genotype Reader API", "Version": "0.1.0", "Authors@R": "c(\nperson(given = \"Sounkou Mahamane\", family = \"Toure\", email = \"sounkoutoure@gmail.com\", role = c(\"aut\", \"cre\")),\nperson(given = \"Christopher\", family = \"Chang\", role = \"cph\", comment = \"Author of the vendored pgenlib library and plink2 program\"),\nperson(given = \"Shaun\", family = \"Purcell\", role = \"cph\", comment = \"Co-author of the vendored plink2 program (VcfToPgen import closure)\"),\nperson(given = \"Eric\", family = \"Biggers\", role = \"cph\", comment = \"Author of included libdeflate library\"),\nperson(given = \"Yann Collet\", family = \"\", role = \"cph\", comment = \"Author of included Zstd library\"),\nperson(given = \"Meta Platforms, Inc.\", role = \"cph\", comment = \"Zstd library\"),\nperson(given = \"Evan\", family = \"Nemerson\", role = \"cph\", comment = \"Author of included SIMDe library\"),\nperson(given = \"Mutsuo\", family = \"Saito\", role = \"cph\", comment = \"Co-author of included SFMT library\"),\nperson(given = \"Makoto\", family = \"Matsumoto\", role = \"cph\", comment = \"Co-author of included SFMT library\")\n)", "Description": "Vendors the read subset of 'PLINK 2's pgenlib library\n(), the same subset the\nCRAN package 'pgenlibr' vendors and builds, as a static library\nand exposes it through 'R_RegisterCCallable' C-callable entry\npoints. Also vendors plink2's own import closure ('VcfToPgen',\n'BcfToPgen', 'OxBgenToPgen', 'OxGenToPgen',\n'OxHapslegendToPgen', 'Plink1DosageToPgen') so a VCF, BCF,\nBGEN, Oxford .gen, Oxford .haps/.legend, or legacy PLINK 1\n--import-dosage file can be converted to a '.pgen' and read\nback through this package's own reader, without a separate\n'htslib'-based parser. This is a carrier package: it has no\nhigh-level R modeling API of its own beyond a milestone smoke\ntest that opens a '.pgen' file and reports its sample and\nvariant counts. Other R packages link to it ('LinkingTo') to\nread 'PLINK 2' genotype files natively from their own C or C++\ncode, which 'pgenlibr' does not expose, since it only offers an\nR-level interface.", "License": "GPL-3", "Encoding": "UTF-8", "Remotes": [ "sounkou-bioinfo/Rfmalloc/packages/Rfmalloc" ], "Roxygen": "list(markdown = TRUE)", "RoxygenNote": "7.3.3", "URL": "https://github.com/sounkou-bioinfo/Rfmalloc,\nhttps://sounkou-bioinfo.github.io/Rfmalloc/Rpgen/", "BugReports": "https://github.com/sounkou-bioinfo/Rfmalloc/issues", "Config/pak/sysreqs": "make", "Repository": "https://sounkou-bioinfo.r-universe.dev", "Date/Publication": "2026-07-10 06:12:39 UTC", "RemoteUrl": "https://github.com/sounkou-bioinfo/Rfmalloc", "RemoteRef": "HEAD", "RemoteSha": "921d01f6786a2db38d90a2629c39f56a244b7875", "RemoteSubdir": "packages/Rpgen", "NeedsCompilation": "yes", "Packaged": { "Date": "2026-07-10 10:09:41 UTC", "User": "root" }, "Author": "Sounkou Mahamane Toure [aut, cre],\nChristopher Chang [cph] (Author of the vendored pgenlib library and\nplink2 program),\nShaun Purcell [cph] (Co-author of the vendored plink2 program\n(VcfToPgen import closure)),\nEric Biggers [cph] (Author of included libdeflate library),\nYann Collet [cph] (Author of included Zstd library),\nMeta Platforms, Inc. [cph] (Zstd library),\nEvan Nemerson [cph] (Author of included SIMDe library),\nMutsuo Saito [cph] (Co-author of included SFMT library),\nMakoto Matsumoto [cph] (Co-author of included SFMT library)", "Maintainer": "Sounkou Mahamane Toure ", "_user": "sounkou-bioinfo", "_type": "src", "_file": "Rpgen_0.1.0.tar.gz", "_fileid": "https://r2.ropensci.org/002cca3fad4ce8b879201bdcaa0af33b662ccd74774872359602b6be6e3271fc", "_filesize": 2152202, "_sha256": "002cca3fad4ce8b879201bdcaa0af33b662ccd74774872359602b6be6e3271fc", "_expires": "2026-10-18T10:29:15.000Z", "_created": "2026-07-10T10:09:41.000Z", "_published": "2026-07-10T10:29:17.566Z", "_jobs": [ { "job": 86338120112, "time": 193, "config": "linux-devel-arm64", "r": "4.7.0", "check": "OK", "artifact": "8224615343" }, { "job": 86338120203, "time": 152, "config": "linux-devel-x86_64", "r": "4.7.0", "check": "OK", "artifact": "8224599222" }, { "job": 86338120113, "time": 161, "config": "linux-release-arm64", "r": "4.6.1", "check": "OK", "artifact": "8224604442" }, { "job": 86338120141, "time": 191, "config": "linux-release-x86_64", "r": "4.6.1", "check": "OK", "artifact": "8224615802" }, { "job": 86338120189, "time": 145, "config": "macos-oldrel-arm64", "r": "4.5.3", "check": "OK", "artifact": "8224843044" }, { "job": 86338120116, "time": 264, "config": "macos-oldrel-x86_64", "r": "4.5.3", "check": "OK", "artifact": "8224883378" }, { "job": 86338120137, "time": 139, "config": "macos-release-arm64", "r": "4.6.1", "check": "OK", "artifact": "8224799540" }, { "job": 86338120159, "time": 218, "config": "macos-release-x86_64", "r": "4.6.1", "check": "OK", "artifact": "8224930395" }, { "job": 86337449375, "time": 220, "config": "source", "r": "4.6.1", "check": "OK", "artifact": "8224538470" }, { "job": 86338120013, "time": 110, "config": "wasm-release", "r": "4.6.0", "check": "FAIL", "artifact": "" }, { "job": 86338120091, "time": 205, "config": "windows-devel", "r": "4.7.0", "check": "OK", "artifact": "8224618519" }, { "job": 86338120156, "time": 175, "config": "windows-oldrel", "r": "4.5.3", "check": "OK", "artifact": "8224606880" }, { "job": 86338120219, "time": 187, "config": "windows-release", "r": "4.6.1", "check": "OK", "artifact": "8224612529" } ], "_host": "GitHub-Actions", "_buildurl": "https://github.com/r-universe/sounkou-bioinfo/actions/runs/29085272650", "_status": "success", "_upstream": "https://github.com/sounkou-bioinfo/Rfmalloc", "_commit": { "id": "921d01f6786a2db38d90a2629c39f56a244b7875", "author": "sounkou-bioinfo ", "committer": "sounkou-bioinfo ", "message": "Rggml: opt-in GGML_VK_ALLOW_128_PUSH for 128-byte-push-constant GPUs\n\nUpstream ggml refuses any Vulkan device with maxPushConstantsSize < 256 B,\nrejecting the whole device at init. In this 5D fork that 256 B is needed by\nexactly one op - the 5D non-contiguous tensor copy, already guarded at its\ndispatch in ggml-vulkan-elemwise.cpp - while vk_mat_mat_push_constants is\n68 B and every <=4D op fits in 128 B. A GPU reached only through a D3D12\ntranslation layer (Mesa dzn under WSL - the sole Vulkan path to the GPU\nthere) exposes just 128 B push constants, a D3D12 root-signature limit, so\na real GPU is rejected though it can run GEMM and all <=4D ops.\n\nGGML_VK_ALLOW_128_PUSH=1 opts in to devices with >= 128 B push constants:\nmatmul and <=4D ops run; the 5D-copy path still errors at its own dispatch.\nOff by default, so default behaviour is byte-for-byte upstream's (the error\nmessage now also points at the flag when the device has >= 128 B). Extends\nthe existing patches/ggml-vulkan_ggml-vulkan-misc.cpp.patch (regenerated;\nvendorggml.R drift guard green) exactly like the GGML_VK_ALLOW_CPU gate.\n\nVerified on an RTX 5050 via dzn (GGML_VK_DEVICE=0): flag unset -> device\nrejected with the guidance message; GGML_VK_ALLOW_128_PUSH=1 -> vulkan\nmul_mat runs, fp32-correct, 2-2.6x OpenBLAS through 4096^3 (6144^3 hits a\ndzn large-dispatch correctness cliff - a dzn limit, not this gate).\n\nShips with the public rggml_mul_mat(A, B, backend) so callers reach the\nvulkan GEMM without the RC_*_test_* symbol; RfmallocStatgen's coloc GEMM\ndispatches through it.\n", "time": 1783663959 }, "_maintainer": { "name": "Sounkou Mahamane Toure", "email": "sounkoutoure@gmail.com", "login": "sounkou-bioinfo", "mastodon": "@bioinfhotep@genomic.social", "description": "Sequences and Consequences.", "uuid": 56392505 }, "_distro": "resolute", "_registered": true, "_dependencies": [ { "package": "R", "version": ">= 4.4.0", "role": "Depends" }, { 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