{ "_id": "6a633358d3420cf5dfdb88de", "Package": "BGData", "Version": "2.4.1", "License": "MIT + file LICENSE", "Title": "A Suite of Packages for Analysis of Big Genomic Data", "Description": "An umbrella package providing a phenotype/genotype data\nstructure and scalable and efficient computational methods for\nlarge genomic datasets in combination with several other\npackages: 'BEDMatrix', 'LinkedMatrix', and 'symDMatrix'.", "Authors@R": "c(\nperson(\"Gustavo\", \"de los Campos\", email = \"gustavoc@msu.edu\", role = c(\"aut\")),\nperson(\"Alexander\", \"Grueneberg\", email = \"cran@agrueneberg.info\", role = c(\"aut\", \"cre\")),\nperson(\"Paulino\", \"Perez\", email = \"perpdgo@gmail.com\", role = c(\"ctb\")),\nperson(\"Ana\", \"Vazquez\", email = \"avazquez@epi.msu.edu\", role = c(\"ctb\")))", "URL": "https://github.com/QuantGen/BGData", "BugReports": "https://github.com/QuantGen/BGData/issues", "Repository": "https://quantgen.r-universe.dev", "Date/Publication": "2025-01-20 17:17:46 UTC", "RemoteUrl": "https://github.com/quantgen/bgdata", "RemoteRef": "HEAD", "RemoteSha": "fe7a57779d903f7056d5841482c9afdbeae5744b", "NeedsCompilation": "yes", "Packaged": { "Date": "2026-07-24 07:48:47 UTC", "User": "root" }, "Author": "Gustavo de los Campos [aut],\nAlexander Grueneberg [aut, cre],\nPaulino Perez [ctb],\nAna Vazquez [ctb]", "Maintainer": "Alexander Grueneberg ", "_user": "quantgen", "_type": "src", "_file": "BGData_2.4.1.tar.gz", "_fileid": "https://r2.ropensci.org/dce817d475c3e1651a116d512f466cf0a910c36c9c124e7f1c6e0229218a8c0b", "_filesize": 282579, "_sha256": "dce817d475c3e1651a116d512f466cf0a910c36c9c124e7f1c6e0229218a8c0b", "_expires": "2026-11-01T09:41:42.000Z", "_created": "2026-07-24T07:48:47.000Z", "_published": "2026-07-24T09:41:44.442Z", "_jobs": [ { "job": 89429017600, "time": 118, "config": "linux-devel-arm64", "r": "4.7.0", "check": "ERROR", "artifact": "8590184467" }, { "job": 89429017611, "time": 148, "config": "linux-devel-x86_64", "r": "4.7.0", "check": "ERROR", "artifact": "8590195629" }, { "job": 89429017629, "time": 125, "config": "linux-release-arm64", "r": "4.6.1", "check": "ERROR", "artifact": "8590187048" }, { "job": 89429017594, "time": 141, "config": "linux-release-x86_64", "r": "4.6.1", "check": "ERROR", "artifact": "8590193215" }, { "job": 89429017665, "time": 209, "config": "macos-oldrel-arm64", "r": "4.5.3", "check": "ERROR", "artifact": "8592611120" }, { "job": 89429017637, "time": 213, "config": "macos-oldrel-x86_64", "r": "4.5.3", "check": "ERROR", "artifact": "8592731940" }, { "job": 89429017617, "time": 115, "config": "macos-release-arm64", "r": "4.6.1", "check": "ERROR", "artifact": "8592639868" }, { "job": 89429017639, "time": 183, "config": "macos-release-x86_64", "r": "4.6.1", "check": "ERROR", "artifact": "8592682268" }, { "job": 89428371508, "time": 215, "config": "source", "r": "4.6.1", "check": "OK", "artifact": "8590140627" }, { "job": 89429017529, "time": 115, "config": "wasm-release", "r": "4.6.0", "check": "OK", "artifact": "8590183882" }, { "job": 89429017580, "time": 131, "config": "windows-devel-x86_64", "r": "4.7.0", "check": "ERROR", "artifact": "8590189434" }, { "job": 89429017581, "time": 131, "config": "windows-oldrel-x86_64", "r": "4.5.3", "check": "ERROR", "artifact": "8590189681" }, { "job": 89429017602, "time": 103, "config": "windows-release-x86_64", "r": "4.6.1", "check": "ERROR", "artifact": "8590179034" } ], "_host": "GitHub-Actions", "_buildurl": "https://github.com/r-universe/quantgen/actions/runs/30076507464", "_status": "success", "_upstream": "https://github.com/quantgen/bgdata", "_commit": { "id": "fe7a57779d903f7056d5841482c9afdbeae5744b", "author": "Gustavo de los Campos ", "committer": "GitHub ", "message": "Update segments.R", "time": 1737393466 }, "_maintainer": { "name": "Alexander Grueneberg", "email": "cran@agrueneberg.info" }, "_distro": "resolute", "_registered": true, "_dependencies": [ { "package": "R", "version": ">= 3.0.2", "role": "Depends" }, { "package": "BEDMatrix", "version": ">= 1.4.0", "role": "Depends" }, { "package": "LinkedMatrix", "version": ">= 1.3.0", "role": "Depends" }, { "package": "symDMatrix", "version": ">= 2.0.0", "role": "Depends" }, { "package": "methods", "role": "Imports" }, { "package": "parallel", "role": "Imports" }, { "package": "crochet", "version": ">= 2.1.0", "role": "Imports" }, { "package": "bigmemory", "role": "Imports" }, { "package": "synchronicity", "role": "Imports" }, { "package": "ff", "role": "Imports" }, { "package": "bit", "role": "Imports" }, { "package": "data.table", "version": ">= 1.9.6", "role": "Suggests" }, { "package": "lme4", "role": "Suggests" }, { "package": "SKAT", "role": "Suggests" }, { "package": "testthat", "role": "Suggests" } ], "_owner": "quantgen", "_selfowned": true, "_usedby": 0, "_updates": [], "_tags": [], "_topics": [ "genetics", "genomics", "gwas", "r-pkg", "openmp" ], "_stars": 34, "_contributors": [ { "user": "agrueneberg", "count": 852, "uuid": 527708 }, { "user": "gdlc", "count": 155, "uuid": 5049762 } ], "_userbio": { "uuid": 11443138, "type": "organization", "name": "QuantGen", "followers": 30 }, "_downloads": { "count": 318, "source": "https://cranlogs.r-pkg.org/downloads/total/last-month/BGData" }, "_mentions": 3, "_devurl": "https://github.com/quantgen/bgdata", "_searchresults": 66, "_rbuild": "4.6.1", "_assets": [ "extra/BGData.html", "extra/citation.cff", "extra/citation.html", "extra/citation.json", "extra/citation.txt", "extra/contents.json", "extra/NEWS.html", "extra/NEWS.txt", "extra/readme.html", "extra/readme.md", "LICENSE", "manual.pdf" ], "_homeurl": "https://github.com/quantgen/bgdata", "_realowner": "quantgen", "_cranurl": true, "_releases": [ { "version": "1.0.0", "date": "2017-05-11" }, { "version": "2.0.0", "date": "2018-08-24" }, { "version": "2.1.0", "date": "2019-01-25" }, { "version": "2.2.0", "date": "2020-08-02" }, { "version": "2.3.0", "date": "2021-10-05" }, { "version": "2.4.0", "date": "2021-12-08" }, { "version": "2.4.1", "date": "2023-03-22" } ], "_exports": [ "as.BGData", "BGData", "chunkedApply", "chunkedMap", "findRelated", "FWD", "geno", "geno<-", "getG", "getG_symDMatrix", "GWAS", "load.BGData", "map", "map<-", "orderedMerge", "pheno", "pheno<-", "preprocess", "readRAW", "readRAW_big.matrix", "readRAW_matrix", "segments", "summarize" ], "_help": [ { "page": "BGData-package", "title": "A Suite of Packages for Analysis of Big Genomic Data", "topics": [ "BGData-package" ] }, { "page": "as.BGData", "title": "Convert Other Objects to BGData Objects", "topics": [ "as.BGData", "as.BGData.BEDMatrix", "as.BGData.ColumnLinkedMatrix", "as.BGData.RowLinkedMatrix" ] }, { "page": "BGData", "title": "Creates a New BGData Instance", "topics": [ "BGData" ] }, { "page": "BGData-class", "title": "Container for Phenotype and Genotype Data", "topics": [ "BGData-class", "geno,BGData-method", "geno<-,BGData-method", "map,BGData-method", "map<-,BGData-method", "pheno,BGData-method", "pheno<-,BGData-method" ] }, { "page": "chunkedApply", "title": "Applies a Function on Each Row or Column of a File-Backed Matrix", "topics": [ "chunkedApply" ] }, { "page": "chunkedMap", "title": "Applies a Function on Each Chunk of a File-Backed Matrix", "topics": [ "chunkedMap" ] }, { "page": "file-backed-matrices", "title": "File-Backed Matrices", "topics": [ "file-backed-matrices" ] }, { "page": "findRelated", "title": "Find related individuals in a relationship matrix", "topics": [ "findRelated", "findRelated.matrix", "findRelated.symDMatrix" ] }, { "page": "FWD", "title": "Performs Forward Regressions", "topics": [ "FWD" ] }, { "page": "geno", "title": "Getting/Setting Genotypes, Sample Information, and Variant Information", "topics": [ "geno", "geno<-", "map", "map<-", "pheno", "pheno<-" ] }, { "page": "geno-class", "title": "An Abstract S4 Class Union of Matrix-Like Types", "topics": [ "geno-class" ] }, { "page": "getG", "title": "Computes a Genomic Relationship Matrix", "topics": [ "getG" ] }, { "page": "getG_symDMatrix", "title": "Computes a Very Large Genomic Relationship Matrix", "topics": [ "getG_symDMatrix" ] }, { "page": "GWAS", "title": "Performs Single Marker Regressions Using BGData Objects", "topics": [ "GWAS" ] }, { "page": "load.BGData", "title": "Loads BGData (and Other) Objects from .RData Files", "topics": [ "load.BGData" ] }, { "page": "multi-level-parallelism", "title": "Multi-Level Parallelism", "topics": [ "multi-level-parallelism" ] }, { "page": "orderedMerge", "title": "Merge Two Data Frames Keeping the Order of the First", "topics": [ "orderedMerge" ] }, { "page": "preprocess", "title": "Center, scale, and impute data", "topics": [ "preprocess" ] }, { "page": "readRAW", "title": "Creates a BGData Object From a .raw File or a .ped-Like File", "topics": [ "readRAW", "readRAW_big.matrix", "readRAW_matrix" ] }, { "page": "segments", "title": "Find non-overlapping segments based on a summary statistic", "topics": [ "segments" ] }, { "page": "summarize", "title": "Generates Various Summary Statistics", "topics": [ "summarize" ] } ], "_readme": "https://github.com/quantgen/bgdata/raw/HEAD/README.md", "_rundeps": [ "BEDMatrix", "BH", "bigmemory", "bigmemory.sri", "bit", "crochet", "ff", "LinkedMatrix", "Rcpp", "symDMatrix", "synchronicity", "uuid" ], "_sysdeps": [ { "shlib": "libgomp", "package": "libgomp1", "source": "gcc", "version": "16-20260322-1ubuntu1", "name": "openmp", "homepage": "http://gcc.gnu.org/", "description": "GCC OpenMP (GOMP) support library" } ], "_score": 5.527114111639806, "_indexed": true, "_nocasepkg": "bgdata", "_universes": [ "quantgen" ], "_binaries": [ { "r": "4.7.0", "os": "linux", "version": "2.4.1", "date": "2026-07-24T07:50:47.000Z", "distro": "resolute", "arch": "aarch64", "commit": "fe7a57779d903f7056d5841482c9afdbeae5744b", "fileid": "https://r2.ropensci.org/bfd769c4fe71317854aa6932fc8c150b76cf6b2e7e3695a98019d64f32c21308", "status": "failure", "check": "ERROR", "buildurl": "https://github.com/r-universe/quantgen/actions/runs/30076507464" }, { "r": "4.7.0", "os": "linux", "version": "2.4.1", "date": "2026-07-24T07:51:13.000Z", "distro": "resolute", "arch": "x86_64", "commit": "fe7a57779d903f7056d5841482c9afdbeae5744b", "fileid": "https://r2.ropensci.org/e5f88203653ac7a3053ce91d9a2998faba5c0433b4b8a8f02da0df87ab8a5e90", "status": "failure", "check": "ERROR", "buildurl": "https://github.com/r-universe/quantgen/actions/runs/30076507464" }, { "r": "4.6.1", "os": "linux", "version": "2.4.1", "date": "2026-07-24T07:50:55.000Z", "distro": "resolute", "arch": "aarch64", "commit": "fe7a57779d903f7056d5841482c9afdbeae5744b", "fileid": "https://r2.ropensci.org/bc10509953800655579389d8e778a49c69c822a958ecb76ab397394d1a9f45b4", "status": "failure", "check": "ERROR", "buildurl": "https://github.com/r-universe/quantgen/actions/runs/30076507464" }, { "r": "4.6.1", "os": "linux", "version": "2.4.1", "date": "2026-07-24T07:51:08.000Z", "distro": "resolute", "arch": "x86_64", "commit": "fe7a57779d903f7056d5841482c9afdbeae5744b", "fileid": "https://r2.ropensci.org/d75d807cc3dc75d1c93eb57eba6c11121b3b3f3b1cdb586aef411144e850fafe", "status": "failure", "check": "ERROR", "buildurl": "https://github.com/r-universe/quantgen/actions/runs/30076507464" }, { "r": "4.5.3", "os": "mac", "version": "2.4.1", "date": "2026-07-24T09:35:35.000Z", "arch": "aarch64", "commit": "fe7a57779d903f7056d5841482c9afdbeae5744b", "fileid": "https://r2.ropensci.org/458d2b1986bc9425d7e178780872c3c7ce6bcc910bd508467794770a5da47c13", "status": "failure", "check": "ERROR", "buildurl": "https://github.com/r-universe/quantgen/actions/runs/30076507464" }, { "r": "4.5.3", "os": "mac", "version": "2.4.1", "date": "2026-07-24T09:40:41.000Z", "arch": "x86_64", "commit": "fe7a57779d903f7056d5841482c9afdbeae5744b", "fileid": "https://r2.ropensci.org/49616df8acfcb001effa0ded89edfadd2991cdddae2e1e0bac664d13b5c7a233", "status": "failure", "check": "ERROR", "buildurl": "https://github.com/r-universe/quantgen/actions/runs/30076507464" }, { "r": "4.6.1", "os": "mac", "version": "2.4.1", "date": "2026-07-24T09:36:57.000Z", "arch": "aarch64", "commit": "fe7a57779d903f7056d5841482c9afdbeae5744b", "fileid": "https://r2.ropensci.org/5b1f0e630400085432a81403c26b9747e6fdb6ebfb8f06e0b60559be65b295f5", "status": "failure", "check": "ERROR", "buildurl": "https://github.com/r-universe/quantgen/actions/runs/30076507464" }, { "r": "4.6.1", "os": "mac", "version": "2.4.1", "date": "2026-07-24T09:38:32.000Z", "arch": "x86_64", "commit": "fe7a57779d903f7056d5841482c9afdbeae5744b", "fileid": "https://r2.ropensci.org/dd496f4d40cc14d5139f6c0e33c453f315dd73662b3635bf02971961f27638e1", "status": "failure", "check": "ERROR", "buildurl": "https://github.com/r-universe/quantgen/actions/runs/30076507464" }, { "r": "4.6.0", "os": "wasm", "version": "2.4.1", "date": "2026-07-24T07:51:01.000Z", "arch": "emscripten", "commit": "fe7a57779d903f7056d5841482c9afdbeae5744b", "fileid": "https://r2.ropensci.org/0cfd57bc70be2e3eab4bdc9d33397fbbd0e6f1e9552ef5af717aed2a036d75a0", "status": "success", "buildurl": "https://github.com/r-universe/quantgen/actions/runs/30076507464" }, { "r": "4.7.0", "os": "win", "version": "2.4.1", "date": "2026-07-24T07:50:41.000Z", "arch": "x86_64", "commit": "fe7a57779d903f7056d5841482c9afdbeae5744b", "fileid": "https://r2.ropensci.org/08dc788f5f7138473c41f0a2c103609cc0572d653d82f83a5f58a7a40d14c3f5", "status": "failure", "check": "ERROR", "buildurl": "https://github.com/r-universe/quantgen/actions/runs/30076507464" }, { "r": "4.5.3", "os": "win", "version": "2.4.1", "date": "2026-07-24T07:50:47.000Z", "arch": "x86_64", "commit": "fe7a57779d903f7056d5841482c9afdbeae5744b", "fileid": "https://r2.ropensci.org/7d4864458fff67a7460392542322c63e8afdf47b4b8d76097801807265ea910a", "status": "failure", "check": "ERROR", "buildurl": "https://github.com/r-universe/quantgen/actions/runs/30076507464" }, { "r": "4.6.1", "os": "win", "version": "2.4.1", "date": "2026-07-24T07:50:12.000Z", "arch": "x86_64", "commit": "fe7a57779d903f7056d5841482c9afdbeae5744b", "fileid": "https://r2.ropensci.org/2eafe4c0a1cb3e9e6b84fd5626cedcaa9a874afaca913504c57ddf10939cccbb", "status": "failure", "check": "ERROR", "buildurl": "https://github.com/r-universe/quantgen/actions/runs/30076507464" } ] }