{ "_id": "6a495bf0f6c47c441949ebc1", "Encoding": "UTF-8", "Package": "bigstatsr", "Type": "Package", "Title": "Statistical Tools for Filebacked Big Matrices", "Version": "1.6.3", "Date": "2025-06-30", "Authors@R": "c(\nperson(\"Florian\", \"Privé\", email = \"florian.prive.21@gmail.com\",\nrole = c(\"aut\", \"cre\")),\nperson(\"Michael\", \"Blum\", role = \"ths\"),\nperson(\"Hugues\", \"Aschard\", email = \"hugues.aschard@pasteur.fr\", role = \"ths\"))", "Description": "Easy-to-use, efficient, flexible and scalable statistical\ntools. Package bigstatsr provides and uses Filebacked Big\nMatrices via memory-mapping. It provides for instance matrix\noperations, Principal Component Analysis, sparse linear\nsupervised models, utility functions and more\n.", "License": "GPL-3", "Language": "en-US", "ByteCompile": "TRUE", "RoxygenNote": "7.3.3", "Roxygen": "list(markdown = TRUE)", "URL": "https://privefl.github.io/bigstatsr/", "BugReports": "https://github.com/privefl/bigstatsr/issues", "Collate": "'AUC.R' 'FBM-attach.R' 'crochet.R' 'FBM.R' 'FBM-code256.R'\n'FBM-copy.R' 'RcppExports.R' 'SVD.R' 'apply-parallelize.R'\n'biglasso.R' 'bigstatsr-package.R' 'colstats.R'\n'crossprodSelf.R' 'mult-mat.R' 'mult-vec.R' 'pcor.R' 'plot.R'\n'predict.R' 'randomSVD.R' 'read-write.R' 'scaling.R'\n'summary.R' 'tcrossprodSelf.R' 'transpose.R' 'univLinReg.R'\n'univLogReg.R' 'utils-assert.R' 'utils.R' 'zzz.R'", "Repository": "https://privefl.r-universe.dev", "Date/Publication": "2026-06-05 05:19:45 UTC", "RemoteUrl": "https://github.com/privefl/bigstatsr", "RemoteRef": "HEAD", "RemoteSha": "99fb318025ca3edff1d0d1639459a1dcb2267c11", "NeedsCompilation": "yes", "Packaged": { "Date": "2026-06-24 03:40:57 UTC", "User": "root" }, "Author": "Florian Privé [aut, cre],\nMichael Blum [ths],\nHugues Aschard [ths]", "Maintainer": "Florian Privé ", "_user": "privefl", "_type": "src", "_file": "bigstatsr_1.6.3.tar.gz", "_fileid": "https://r2.ropensci.org/e1c357ac4d42f7a5f2193c3088c4e7e3c69345aebae5d5d815f8713e08fab550", "_filesize": 1124303, "_sha256": "e1c357ac4d42f7a5f2193c3088c4e7e3c69345aebae5d5d815f8713e08fab550", "_expires": "2026-10-12T19:15:58.000Z", "_created": "2026-06-24T03:40:57.000Z", "_published": "2026-07-04T19:16:00.684Z", "_jobs": [ { "job": 85159690812, "time": 329, "config": "linux-devel-arm64", "r": "4.7.0", "check": "OK", "artifact": "7839634452" }, { "job": 85159690838, "time": 314, "config": "linux-devel-x86_64", "r": "4.7.0", "check": "OK", "artifact": "7839630930" }, { "job": 85159690899, "time": 296, "config": "linux-release-arm64", "r": "4.6.0", "check": "OK", "artifact": "7839628006" }, { "job": 85159690926, "time": 362, "config": "linux-release-x86_64", "r": "4.6.0", "check": "OK", "artifact": "7839640804" }, { "job": 85159690830, "time": 173, "config": "macos-oldrel-arm64", "r": "4.5.3", "check": "OK", "artifact": "7839601883" }, { "job": 85159690855, "time": 388, "config": "macos-oldrel-x86_64", "r": "4.5.3", "check": "OK", "artifact": "7839646130" }, { "job": 85159690836, "time": 243, "config": "macos-release-arm64", "r": "4.6.0", "check": "OK", "artifact": "7839616390" }, { "job": 85159690726, "time": 671, "config": "macos-release-x86_64", "r": "4.6.0", "check": "OK", "artifact": "7839701842" }, { "job": 85159690708, "time": 287, "config": "source", "r": "4.6.0", "check": "OK", "artifact": "7839569074" }, { "job": 85159690766, "time": 230, "config": "wasm-release", "r": "4.6.0", "check": "OK", "artifact": "7839613759" }, { "job": 85159690778, "time": 442, "config": "windows-devel", "r": "4.7.0", "check": "OK", "artifact": "7839656682" }, { "job": 85159691050, "time": 361, "config": "windows-oldrel", "r": "4.5.3", "check": "OK", "artifact": "7839640851" }, { "job": 85159690817, "time": 368, "config": "windows-release", "r": "4.6.0", "check": "OK", "artifact": "7839641963" } ], "_host": "GitHub-Actions", "_buildurl": "https://github.com/r-universe/privefl/actions/runs/28073396246", "_status": "success", "_upstream": "https://github.com/privefl/bigstatsr", "_commit": { "id": "99fb318025ca3edff1d0d1639459a1dcb2267c11", "author": "Florian Privé ", "committer": "Florian Privé ", "message": "check ARM\n", "time": 1780636785 }, "_maintainer": { "name": "Florian Privé", "email": "florian.prive.21@gmail.com", "login": "privefl", "bluesky": "@privefl.bsky.social", "description": "Data Scientist at Aíma (2025–)\n\n• Researcher in Statistical Human Genetics (2016–2025)\n \n• ENSIMAG (2013–2016)", "uuid": 11161036 }, "_distro": "resolute", "_registered": true, "_dependencies": [ { "package": "R", "version": ">= 3.4", "role": "Depends" }, { "package": "Rcpp", "role": "LinkingTo" }, { "package": "RcppArmadillo", "role": "LinkingTo" }, { "package": "rmio", "role": "LinkingTo" }, { "package": "bigassertr", "version": ">= 0.1.7", "role": "Imports" }, { "package": "bigparallelr", "version": ">= 0.2.3", "role": "Imports" }, { "package": "cowplot", "role": "Imports" }, { "package": "foreach", "role": "Imports" }, { "package": "ggplot2", "version": ">= 3.0", "role": "Imports" }, { "package": "graphics", "role": "Imports" }, { "package": "methods", "role": "Imports" }, { "package": "ps", "version": ">= 1.4", "role": "Imports" }, { "package": "Rcpp", "role": "Imports" }, { "package": "rmio", "version": ">= 0.4", "role": "Imports" }, { "package": "RSpectra", "role": "Imports" }, { "package": "stats", "role": "Imports" }, { "package": "tibble", "role": "Imports" }, { "package": "utils", "role": "Imports" }, { "package": "bigmemory", "version": ">= 4.5.33", "role": "Suggests" }, { "package": "bigreadr", "version": ">= 0.2", "role": "Suggests" }, { "package": "covr", "role": "Suggests" }, { "package": "data.table", "role": "Suggests" }, { "package": "dplyr", "role": "Suggests" }, { "package": "glmnet", "role": "Suggests" }, { "package": "hexbin", "role": "Suggests" }, { "package": "memuse", "role": "Suggests" }, { "package": "ModelMetrics", "role": "Suggests" }, { "package": "plotly", "role": "Suggests" }, { "package": "ppcor", "role": "Suggests" }, { "package": "RhpcBLASctl", "role": "Suggests" }, { "package": "spelling", "version": ">= 1.2", "role": "Suggests" }, { "package": "testthat", "role": "Suggests" } ], "_owner": "privefl", "_selfowned": true, "_usedby": 45, "_updates": [ { "week": "2025-27", "n": 1 }, { "week": "2025-31", "n": 1 }, { "week": "2026-13", "n": 1 }, { "week": "2026-23", "n": 1 } ], "_tags": [], "_topics": [ "big-data", "large-matrices", "memory-mapped-file", "parallel-computing", "statistical-methods", "openblas", "cpp", "openmp" ], "_stars": 180, "_contributors": [ { "user": "privefl", "count": 944, "uuid": 11161036 }, { "user": "dramanica", "count": 1, "uuid": 3873428 }, { "user": "jeroen", "count": 1, "uuid": 216319 }, { "user": "katrinleinweber", "count": 1, "uuid": 9948149 } ], "_userbio": { "uuid": 11161036, "type": "user", "name": "Florian Privé", "followers": 312, "description": "Data Scientist at Aíma (2025–)\r\n\r\n• Researcher in Statistical Human Genetics (2016–2025)\r\n \r\n• ENSIMAG (2013–2016)" }, "_downloads": { "count": 6682, "source": "https://cranlogs.r-pkg.org/downloads/total/last-month/bigstatsr" }, "_mentions": 7, "_devurl": "https://github.com/privefl/bigstatsr", "_pkgdown": "https://privefl.github.io/bigstatsr/", "_searchresults": 429, "_rbuild": "4.6.0", "_assets": [ "extra/bigstatsr.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", "manual.pdf" ], "_homeurl": "https://github.com/privefl/bigstatsr", "_realowner": "privefl", "_cranurl": true, "_releases": [ { "version": "0.2.1", "date": "2017-09-02" }, { "version": "0.2.2", "date": "2017-09-02" }, { "version": "0.2.3", "date": "2017-11-30" }, { "version": "0.2.4", "date": "2018-01-31" }, { "version": "0.6.2", "date": "2018-08-17" }, { "version": "0.9.1", "date": "2019-03-04" }, { "version": "1.0.1", "date": "2019-12-20" }, { "version": "1.1.2", "date": "2020-01-19" }, { "version": "1.1.4", "date": "2020-02-01" }, { "version": "1.2.2", "date": "2020-03-09" }, { "version": "1.2.3", "date": "2020-03-12" }, { "version": "1.3.1", "date": "2020-11-06" }, { "version": "1.5.0", "date": "2021-03-29" }, { "version": "1.5.1", "date": "2021-04-05" }, { "version": "1.5.5", "date": "2021-12-01" }, { "version": "1.5.6", "date": "2022-02-03" }, { "version": "1.5.12", "date": "2022-10-14" }, { "version": "1.6.1", "date": "2024-09-09" }, { "version": "1.6.2", "date": "2025-08-01" } ], "_exports": [ "add_code256", "as_FBM", "as_scaling_fun", "asPlotlyText", "AUC", "AUCBoot", "big_apply", "big_attach", "big_attachExtdata", "big_colstats", "big_copy", "big_cor", "big_counts", "big_cprodMat", "big_cprodVec", "big_crossprodSelf", "big_increment", "big_parallelize", "big_prodMat", "big_prodVec", "big_randomSVD", "big_read", "big_scale", "big_spLinReg", "big_spLogReg", "big_SVD", "big_tcrossprodSelf", "big_transpose", "big_univLinReg", "big_univLogReg", "big_write", "block_size", "cols_along", "covar_from_df", "diag", "FBM", "FBM.code256", "get_beta", "nb_cores", "pasteLoc", "pcor", "plot_grid", "plus", "rows_along", "sub_bk", "theme_bigstatsr", "typeof", "without_downcast_warning" ], "_help": [ { "page": "as_scaling_fun", "title": "Scaling function creator", "topics": [ "as_scaling_fun" ] }, { "page": "asPlotlyText", "title": "Plotly text", "topics": [ "asPlotlyText" ] }, { "page": "AUC", "title": "AUC", "topics": [ "AUC", "AUCBoot" ] }, { "page": "big_apply", "title": "Split-Apply-Combine", "topics": [ "big_apply" ] }, { "page": "big_colstats", "title": "Standard univariate statistics", "topics": [ "big_colstats" ] }, { "page": "big_copy", "title": "Copy as a Filebacked Big Matrix", "topics": [ "big_copy" ] }, { "page": "big_cor", "title": "Correlation", "topics": [ "big_cor" ] }, { "page": "big_counts", "title": "Counts for class FBM.code256", "topics": [ "big_counts" ] }, { "page": "big_cprodMat", "title": "Cross-product with a matrix", "topics": [ "big_cprodMat", "crossprod,FBM,matrix-method", "crossprod,matrix,FBM-method", "tcrossprod,FBM,matrix-method", "tcrossprod,matrix,FBM-method" ] }, { "page": "big_cprodVec", "title": "Cross-product with a vector", "topics": [ "big_cprodVec" ] }, { "page": "big_crossprodSelf", "title": "Crossprod", "topics": [ "big_crossprodSelf", "crossprod,FBM,missing-method" ] }, { "page": "big_increment", "title": "Increment an FBM", "topics": [ "big_increment" ] }, { "page": "big_parallelize", "title": "Split-parApply-Combine", "topics": [ "big_parallelize" ] }, { "page": "big_prodMat", "title": "Product with a matrix", "topics": [ "%*%,FBM,matrix-method", "%*%,matrix,FBM-method", "big_prodMat" ] }, { "page": "big_prodVec", "title": "Product with a vector", "topics": [ "big_prodVec" ] }, { "page": "big_randomSVD", "title": "Randomized partial SVD", "topics": [ "big_randomSVD" ] }, { "page": "big_read", "title": "Read a file as FBM", "topics": [ "big_read" ] }, { "page": "big_scale", "title": "Some scaling functions", "topics": [ "big_scale" ] }, { "page": "big_spLinReg", "title": "Sparse linear regression", "topics": [ "big_spLinReg" ] }, { "page": "big_spLogReg", "title": "Sparse logistic regression", "topics": [ "big_spLogReg" ] }, { "page": "big_SVD", "title": "Partial SVD", "topics": [ "big_SVD" ] }, { "page": "big_tcrossprodSelf", "title": "Tcrossprod", "topics": [ "big_tcrossprodSelf", "tcrossprod,FBM,missing-method" ] }, { "page": "big_transpose", "title": "Transpose an FBM", "topics": [ "big_transpose" ] }, { "page": "big_univLinReg", "title": "Column-wise linear regression", "topics": [ "big_univLinReg" ] }, { "page": "big_univLogReg", "title": "Column-wise logistic regression", "topics": [ "big_univLogReg" ] }, { "page": "big_write", "title": "Write an FBM to a file", "topics": [ "big_write" ] }, { "page": "block_size", "title": "Determine a correct value for the block.size parameter", "topics": [ "block_size" ] }, { "page": "covar_from_df", "title": "Numeric matrix from data frame", "topics": [ "covar_from_df" ] }, { "page": "FBM-class", "title": "Class FBM", "topics": [ "as_FBM", "FBM", "FBM-class", "FBM_RC" ] }, { "page": "FBM-methods", "title": "Methods for the FBM class", "topics": [ "diag,FBM-method", "dim,FBM-method", "FBM-methods", "length,FBM-method", "typeof,FBM-method", "[,FBM,ANY,ANY,ANY-method", "[<-,FBM,ANY,ANY,ANY-method" ] }, { "page": "FBM.code256-class", "title": "Class FBM.code256", "topics": [ "add_code256", "FBM.code256", "FBM.code256-class", "FBM.code256_RC" ] }, { "page": "get_beta", "title": "Combine sets of coefficients", "topics": [ "get_beta" ] }, { "page": "pasteLoc", "title": "Get coordinates on plot", "topics": [ "pasteLoc" ] }, { "page": "pcor", "title": "Partial correlation", "topics": [ "pcor" ] }, { "page": "plot.big_sp_list", "title": "Plot method", "topics": [ "plot.big_sp_list" ] }, { "page": "plot.big_SVD", "title": "Plot method", "topics": [ "plot.big_SVD" ] }, { "page": "plot.mhtest", "title": "Plot method", "topics": [ "plot.mhtest" ] }, { "page": "predict.big_sp", "title": "Predict method", "topics": [ "predict.big_sp" ] }, { "page": "predict.big_sp_list", "title": "Predict method", "topics": [ "predict.big_sp_list" ] }, { "page": "predict.big_SVD", "title": "Scores of PCA", "topics": [ "predict.big_SVD" ] }, { "page": "predict.mhtest", "title": "Predict method", "topics": [ "predict.mhtest" ] }, { "page": "sub_bk", "title": "Replace extension '.bk'", "topics": [ "sub_bk" ] }, { "page": "summary.big_sp_list", "title": "Summary method", "topics": [ "summary.big_sp_list" ] }, { "page": "theme_bigstatsr", "title": "Theme ggplot2", "topics": [ "theme_bigstatsr" ] }, { "page": "without_downcast_warning", "title": "Temporarily disable downcast warning", "topics": [ "without_downcast_warning" ] } ], "_readme": "https://github.com/privefl/bigstatsr/raw/HEAD/README.md", "_rundeps": [ "bigassertr", "bigparallelr", "bit", "cli", "codetools", "cowplot", "cpp11", "doParallel", "farver", "ff", "flock", "foreach", "ggplot2", "glue", "gtable", "isoband", "iterators", "labeling", "lattice", "lifecycle", "magrittr", "Matrix", "parallelly", "pillar", "pkgconfig", "ps", "R6", "RColorBrewer", "Rcpp", "RcppArmadillo", "RcppEigen", "RhpcBLASctl", "rlang", "rmio", "RSpectra", "S7", "scales", "tibble", "utf8", "vctrs", "viridisLite", "withr" ], "_sysdeps": [ { "shlib": "liblapack", "package": "libopenblas0-pthread", "source": "openblas", "version": "0.3.32+ds-5", "name": "openblas", "homepage": "https://www.openblas.net/", "description": "Optimized BLAS (linear algebra) library (shared lib, pthread)" }, { "shlib": "libblas", "package": "libopenblas0-pthread", "source": "openblas", "version": "0.3.32+ds-5", "name": "openblas", "homepage": "https://www.openblas.net/", "description": "Optimized BLAS (linear algebra) library (shared lib, pthread)" }, { "shlib": "libstdc++", "package": "libstdc++6", "source": "gcc", "version": "16-20260322-1ubuntu1", "name": "c++", "homepage": "http://gcc.gnu.org/", "description": "GNU Standard C++ Library v3" }, { "shlib": "libgomp", "package": "libgomp1", "source": "gcc", "version": "16-20260322-1ubuntu1", "name": "openmp", "homepage": "http://gcc.gnu.org/", "description": "GCC OpenMP (GOMP) support library" } ], "_score": 11.46621932748305, "_indexed": true, "_nocasepkg": "bigstatsr", "_universes": [ "privefl" ], "_binaries": [ { "r": "4.7.0", "os": "linux", "version": "1.6.3", "date": "2026-06-24T03:45:44.000Z", "distro": "resolute", "arch": "aarch64", "commit": "99fb318025ca3edff1d0d1639459a1dcb2267c11", "fileid": "https://r2.ropensci.org/0d713e2cab06540f39eb4d2abec151d7e9ebeaa9b56aa01f8f3e5e4f4476a8f8", "status": "success", "check": "OK", "buildurl": "https://github.com/r-universe/privefl/actions/runs/28073396246" }, { "r": "4.7.0", "os": "linux", "version": "1.6.3", "date": "2026-06-24T03:45:05.000Z", "distro": "resolute", "arch": "x86_64", "commit": "99fb318025ca3edff1d0d1639459a1dcb2267c11", "fileid": "https://r2.ropensci.org/7b4c9e43618d9912b6fdd1b11b1bb8011eb27cbce14bd761e75981b90fc42695", "status": "success", "check": "OK", "buildurl": "https://github.com/r-universe/privefl/actions/runs/28073396246" }, { "r": "4.6.0", "os": "linux", "version": "1.6.3", "date": "2026-06-24T03:45:10.000Z", "distro": "resolute", "arch": "aarch64", "commit": "99fb318025ca3edff1d0d1639459a1dcb2267c11", "fileid": "https://r2.ropensci.org/b108dcbb98af3326889bfeffe80c4c4d984ef5c1290935761f12968a9f493e28", "status": "success", "check": "OK", "buildurl": "https://github.com/r-universe/privefl/actions/runs/28073396246" }, { "r": "4.6.0", "os": "linux", "version": "1.6.3", "date": "2026-06-24T03:45:44.000Z", "distro": "resolute", "arch": "x86_64", "commit": "99fb318025ca3edff1d0d1639459a1dcb2267c11", "fileid": "https://r2.ropensci.org/d20d0ebb0a180f02a14bd357845def82a41c62e13670d1d41b5db89dc2041fde", "status": "success", "check": "OK", "buildurl": "https://github.com/r-universe/privefl/actions/runs/28073396246" }, { "r": "4.5.3", "os": "mac", "version": "1.6.3", "date": "2026-06-24T03:43:48.000Z", "arch": "aarch64", "commit": "99fb318025ca3edff1d0d1639459a1dcb2267c11", "fileid": "https://r2.ropensci.org/76ca0d2d5d8c84e031a36fa47f35fac195469d7186b2a87f0476848c72e1d8d8", "status": "success", "check": "OK", "buildurl": "https://github.com/r-universe/privefl/actions/runs/28073396246" }, { "r": "4.5.3", "os": "mac", "version": "1.6.3", "date": "2026-06-24T03:45:04.000Z", "arch": "x86_64", "commit": "99fb318025ca3edff1d0d1639459a1dcb2267c11", "fileid": "https://r2.ropensci.org/d84c72597ef28b7e100e4cd050a9221dcf8913b52b7f915bc8c7b5e8725e121b", "status": "success", "check": "OK", "buildurl": "https://github.com/r-universe/privefl/actions/runs/28073396246" }, { "r": "4.6.0", "os": "mac", "version": "1.6.3", "date": "2026-06-24T03:44:19.000Z", "arch": "aarch64", "commit": "99fb318025ca3edff1d0d1639459a1dcb2267c11", "fileid": "https://r2.ropensci.org/4713ff2dd8fe82b1f3829bc1bdb7075c0ebe29fc795435b2833ee69457f89963", "status": "success", "check": "OK", "buildurl": "https://github.com/r-universe/privefl/actions/runs/28073396246" }, { "r": "4.6.0", "os": "mac", "version": "1.6.3", "date": "2026-06-24T03:47:02.000Z", "arch": "x86_64", "commit": "99fb318025ca3edff1d0d1639459a1dcb2267c11", "fileid": "https://r2.ropensci.org/8f9e2cd378ba10c695448c25c7fed04a5f29439a8ff2cb8adeb848ee501a7f9f", "status": "success", "check": "OK", "buildurl": "https://github.com/r-universe/privefl/actions/runs/28073396246" }, { "r": "4.6.0", "os": "wasm", "version": "1.6.3", "date": "2026-06-24T03:45:27.000Z", "arch": "emscripten", "commit": "99fb318025ca3edff1d0d1639459a1dcb2267c11", "fileid": "https://r2.ropensci.org/b4c3313eb3d1cea884e8667e31433b2831b341a400ab19c9476609775db32843", "status": "success", "buildurl": "https://github.com/r-universe/privefl/actions/runs/28073396246" }, { "r": "4.7.0", "os": "win", "version": "1.6.3", "date": "2026-06-24T03:45:11.000Z", "arch": "x86_64", "commit": "99fb318025ca3edff1d0d1639459a1dcb2267c11", "fileid": "https://r2.ropensci.org/e88b567c006cdd2093d905287df8eabb0e9928bbc438ec2224c9c9f85e340351", "status": "success", "check": "OK", "buildurl": "https://github.com/r-universe/privefl/actions/runs/28073396246" }, { "r": "4.5.3", "os": "win", "version": "1.6.3", "date": "2026-06-24T03:44:00.000Z", "arch": "x86_64", "commit": "99fb318025ca3edff1d0d1639459a1dcb2267c11", "fileid": "https://r2.ropensci.org/46311bd580e7dbd4a8ea5b85e7fa633b2153da46bfc47ad835b970c912be9747", "status": "success", "check": "OK", "buildurl": "https://github.com/r-universe/privefl/actions/runs/28073396246" }, { "r": "4.6.0", "os": "win", "version": "1.6.3", "date": "2026-06-24T03:43:51.000Z", "arch": "x86_64", "commit": "99fb318025ca3edff1d0d1639459a1dcb2267c11", "fileid": "https://r2.ropensci.org/f707cd5a7d112bc445694cdb2021b7fd7a2fb50aab969cc122040b4bdbfb0eda", "status": "success", "check": "OK", "buildurl": "https://github.com/r-universe/privefl/actions/runs/28073396246" } ] }