{ "_id": "6aedb2959ceaa78f200a1d49", "Package": "GNET2", "Type": "Package", "Title": "Constructing gene regulatory networks from expression data\nthrough functional module inference", "Version": "1.28.0", "Author": "Chen Chen, Jie Hou and Jianlin Cheng", "Maintainer": "Chen Chen ", "Description": "Cluster genes to functional groups with E-M process.\nIteratively perform TF assigning and Gene assigning, until the\nassignment of genes did not change, or max number of iterations\nis reached.", "License": "Apache License 2.0", "Encoding": "UTF-8", "RoxygenNote": "7.1.0", "VignetteBuilder": "knitr", "biocViews": "GeneExpression, Regression, Network, NetworkInference,\nSoftware", "URL": "https://github.com/chrischen1/GNET2", "BugReports": "https://github.com/chrischen1/GNET2/issues", "PackageStatus": "Deprecated", "Config/pak/sysreqs": "cmake libglpk-dev make libicu-dev libuv1-dev\nlibxml2-dev libx11-dev zlib1g-dev", "Repository": "Bioconductor 3.23", "Date/Publication": "2026-04-28 12:49:52 UTC", "RemoteUrl": "https://github.com/bioc/GNET2", "RemoteRef": "RELEASE_3_23", "RemoteSha": "13b58eec1ddb59e2937d77c566e2b53ba4ea52c2", "NeedsCompilation": "yes", "Packaged": { "Date": "2026-11-06 10:47:17 UTC", "User": "root" }, "_user": "bioc-release", "_type": "src", "_file": "GNET2_1.28.0.tar.gz", "_fileid": "https://r2.ropensci.org/9435d372513267fd8ceb10a8dfbf2587a623fbd48cf1504378e6ba59962ce7df", "_filesize": 130846, "_sha256": "9435d372513267fd8ceb10a8dfbf2587a623fbd48cf1504378e6ba59962ce7df", "_expires": "2027-02-14T10:57:23.000Z", "_created": "2026-11-06T10:47:17.000Z", "_published": "2026-11-06T10:57:24.876Z", "_upstream": "https://github.com/bioc/GNET2", "_status": "failure", "_maintainer": { "name": "Chen Chen", "email": "ccm3x@mail.missouri.edu", "login": "chrischen1", "description": "", "uuid": 7677687 }, "_jobs": [ { "job": 127850707804, "time": 173, "config": "bioc-checks", "r": "4.6.2", "check": "ERROR", "artifact": "13496092499" }, { "job": 127850707986, "time": 228, "config": "linux-devel-arm64", "r": "4.7.0", "check": "ERROR", "artifact": "13496133650" }, { "job": 127850708009, "time": 310, "config": "linux-devel-x86_64", "r": "4.7.0", "check": "ERROR", "artifact": "13495464599" }, { "job": 127850708045, "time": 227, "config": "linux-release-arm64", "r": "4.6.2", "check": "ERROR", "artifact": "13495893938" }, { "job": 127850707885, "time": 319, "config": "linux-release-x86_64", "r": "4.6.2", "check": "ERROR", "artifact": "13496103414" }, { "job": 127850708101, "time": 179, "config": "macos-oldrel-arm64", "r": "4.5.3", "check": "ERROR", "artifact": "13496707330" }, { "job": 127850707865, "time": 356, "config": "macos-oldrel-x86_64", "r": "4.5.3", "check": "ERROR", "artifact": "13496143344" }, { "job": 127850707959, "time": 214, "config": "macos-release-arm64", "r": "4.6.2", "check": "ERROR", "artifact": "13495629033" }, { "job": 127850707916, "time": 535, "config": "macos-release-x86_64", "r": "4.6.2", "check": "ERROR", "artifact": "13497430005" }, { "job": 127848837438, "time": 263, "config": "source", "r": "4.6.2", "check": "ERROR", "artifact": "13495678393" }, { "job": 127850707952, "time": 135, "config": "wasm-release", "r": "4.6.0", "check": "OK", "artifact": "13495598663" }, { "job": 127850707937, "time": 305, "config": "windows-devel-arm64", "r": "4.7.0", "check": "ERROR", "artifact": "13496817487" }, { "job": 127850708118, "time": 257, "config": "windows-devel-x86_64", "r": "4.7.0", "check": "ERROR", "artifact": "13496701990" }, { "job": 127850708018, "time": 211, "config": "windows-oldrel-x86_64", "r": "4.5.3", "check": "ERROR", "artifact": "13495963648" }, { "job": 127850708061, "time": 296, "config": "windows-release-arm64", "r": "4.6.2", "check": "ERROR", "artifact": "13496492336" }, { "job": 127850708064, "time": 218, "config": "windows-release-x86_64", "r": "4.6.2", "check": "ERROR", "artifact": "13495419400" } ], "_bioccheck": { "error": 1, "warning": 3, "note": 10 }, "_buildurl": "https://github.com/r-universe/bioc-release/actions/runs/42204824863", "_commit": { "id": "13b58eec1ddb59e2937d77c566e2b53ba4ea52c2", "author": "A Wokaty ", "committer": "A Wokaty ", "message": "bump x.y.z version to even y prior to creation of RELEASE_3_23 branch\n", "time": 1777380592 }, "_distro": "resolute", "_host": "GitHub-Actions", "_registered": true, "_dependencies": [ { "package": "R", "version": ">= 3.6", "role": "Depends" }, { "package": "Rcpp", "role": "LinkingTo" }, { "package": "ggplot2", "role": "Imports" }, { "package": "xgboost", "role": "Imports" }, { "package": "Rcpp", "role": "Imports" }, { "package": "reshape2", "role": "Imports" }, { "package": "grid", "role": "Imports" }, { "package": "DiagrammeR", "role": "Imports" }, { "package": "methods", "role": "Imports" }, { "package": "stats", "role": "Imports" }, { "package": "matrixStats", "role": "Imports" }, { "package": "graphics", "role": "Imports" }, { "package": "SummarizedExperiment", "role": "Imports" }, { "package": "dplyr", "role": "Imports" }, { "package": "igraph", "role": "Imports" }, { "package": "grDevices", "role": "Imports" }, { "package": "utils", "role": "Imports" }, { "package": "knitr", "role": "Suggests" }, { "package": "rmarkdown", "role": "Suggests" } ], "_owner": "bioc", "_selfowned": false, "_usedby": 0, "_updates": [ { "week": "2026-14", "n": 1 }, { "week": "2026-18", "n": 1 } ], "_tags": [], "_topics": [ "geneexpression", "regression", "network", "networkinference", "software", "cpp" ], "_stars": 2, "_contributors": [ { "user": "chrischen1", "count": 128, "uuid": 7677687 }, { "user": "nturaga", "count": 6, "uuid": 2746443 }, { "user": "jianlin-cheng", "count": 1, "uuid": 20481009 } ], "_userbio": { "uuid": 2286807, "type": "organization", "name": "Bioconductor", "followers": 485, "description": "Software for the analysis and comprehension of high-throughput genomic data" }, "_downloads": { "count": 440, "source": "https://www.bioconductor.org/packages/stats/bioc/GNET2" }, "_mentions": 1, "_devurl": "https://github.com/chrischen1/gnet2", "_searchresults": 8, "_abi": { "exports": [], "imports": [ { "key": "Rcpp::Rcpp_precious_preserve()", "hash": "33a97ea62b293da6" }, { "key": "Rcpp::Rcpp_precious_remove()", "hash": "63d26947ba7e1377" }, { "key": "Rcpp::dataptr()", "hash": "54e69ad2e6668c83" }, { "key": "Rcpp::demangle()", "hash": "b0cfd6754c5ebc4e" }, { "key": "Rcpp::enterRNGScope()", "hash": "a04a299137cef947" }, { "key": "Rcpp::exitRNGScope()", "hash": "a04a299137cef947" }, { "key": "Rcpp::get_cache()", "hash": "1d6d6c9cfafe4068" }, { "key": "Rcpp::rcpp_get_stack_trace()", "hash": "c684a9bbe15cdc52" }, { "key": "Rcpp::rcpp_set_stack_trace()", "hash": "33a97ea62b293da6" } ] }, "_rbuild": "4.6.2", "_assets": [ "extra/citation.cff", "extra/citation.html", "extra/citation.json", "extra/citation.txt", "extra/contents.json", "extra/GNET2.html", "extra/manual.pdf", "extra/NEWS.html", "extra/NEWS.txt", "extra/readme.html", "extra/readme.md" ], "_cranurl": false, "_exports": [ "build_module", "build_moduleR", "build_moduleR_heuristic", "build_split_table", "calc_likelihood_score", "extract_edges", "get_correlation_list", "gnet", "kneepointDetection", "plot_gene_group", "plot_group_correlation", "plot_tree", "save_gnet", "similarity_score" ], "_help": [ { "page": "build_module", "title": "Fit a regression tree.", "topics": [ "build_module" ] }, { "page": "build_moduleR", "title": "Build regression tree.", "topics": [ "build_moduleR" ] }, { "page": "build_moduleR_heuristic", "title": "Build regression tree with splits are detemined by K-means heuristicly.", "topics": [ "build_moduleR_heuristic" ] }, { "page": "build_split_table", "title": "Build split table by K-means heuristicly.", "topics": [ "build_split_table" ] }, { "page": "calc_likelihood_score", "title": "Calculate Gaussian Likelihood score.", "topics": [ "calc_likelihood_score" ] }, { "page": "extract_edges", "title": "Extract the network from the gnet result", "topics": [ "extract_edges" ] }, { "page": "get_correlation_list", "title": "Calculate correlation within each group.", "topics": [ "get_correlation_list" ] }, { "page": "gnet", "title": "Run GNET2", "topics": [ "gnet" ] }, { "page": "kneepointDetection", "title": "Knee point detection.", "topics": [ "kneepointDetection" ] }, { "page": "plot_gene_group", "title": "Plot a module", "topics": [ "plot_gene_group" ] }, { "page": "plot_group_correlation", "title": "Plot the correlation of each group", "topics": [ "plot_group_correlation" ] }, { "page": "plot_tree", "title": "Plot the regression tree.", "topics": [ "plot_tree" ] }, { "page": "save_gnet", "title": "Save the GNET2 results", "topics": [ "save_gnet" ] }, { "page": "similarity_score", "title": "Compute the similarity from a predefined condition group", "topics": [ "similarity_score" ] } ], "_readme": "https://github.com/bioc/GNET2/raw/RELEASE_3_23/README.md", "_rundeps": [ "abind", "base64enc", "Biobase", "BiocGenerics", "bit", "bit64", "bslib", "cachem", "cli", "clipr", "cpp11", "crayon", "data.table", "DelayedArray", "DiagrammeR", "digest", "dplyr", "evaluate", "farver", "fastmap", "fontawesome", "fs", "generics", "GenomicRanges", "ggplot2", "glue", "gtable", "highr", "hms", "htmltools", "htmlwidgets", "igraph", "IRanges", "isoband", "jquerylib", "jsonlite", "knitr", "labeling", "lattice", "lifecycle", "magrittr", "Matrix", "MatrixGenerics", "matrixStats", "memoise", "mime", "pillar", "pkgconfig", "plyr", "prettyunits", "progress", "purrr", "R6", "rappdirs", "RColorBrewer", "Rcpp", "readr", "reshape2", "rlang", "rmarkdown", "rstudioapi", "S4Arrays", "S4Vectors", "S7", "sass", "scales", "Seqinfo", "SparseArray", "stringi", "stringr", "SummarizedExperiment", "tibble", "tidyr", "tidyselect", "tinytex", "tzdb", "utf8", "vctrs", "viridisLite", "visNetwork", "vroom", "withr", "xfun", "xgboost", "XVector", "yaml" ], "_sysdeps": [ { "shlib": "libstdc++", "package": "libstdc++6", "source": "gcc", "version": "16-20260322-1ubuntu1", "name": "c++", "homepage": "http://gcc.gnu.org/", "description": "GNU Standard C++ Library v3" } ], "_score": 2.6020599913279625, "_indexed": false, "_nocasepkg": "gnet2", "_universes": [ "bioc-release" ], "_binaries": [ { "r": "4.7.0", "os": "linux", "version": "1.28.0", "date": "2026-11-06T10:50:02.000Z", "distro": "resolute", "arch": "aarch64", "commit": "13b58eec1ddb59e2937d77c566e2b53ba4ea52c2", "fileid": "https://r2.ropensci.org/f7b48306bc2ee33273903b60a220f1ff3fdaeba89d835fb8b00c36b5649d5ef3", "status": "failure", "check": "ERROR", "buildurl": "https://github.com/r-universe/bioc-release/actions/runs/42204824863" }, { "r": "4.7.0", "os": "linux", "version": "1.28.0", "date": "2026-11-06T10:50:52.000Z", "distro": "resolute", "arch": "x86_64", "commit": "13b58eec1ddb59e2937d77c566e2b53ba4ea52c2", "fileid": "https://r2.ropensci.org/aa152a0e44e26a5cf58cd74e2e86b8e1577fda940182cae07ae88ba7ab326f56", "status": "failure", "check": "ERROR", "buildurl": "https://github.com/r-universe/bioc-release/actions/runs/42204824863" }, { "r": "4.6.2", "os": "linux", "version": "1.28.0", "date": "2026-11-06T10:50:05.000Z", "distro": "resolute", "arch": "aarch64", "commit": "13b58eec1ddb59e2937d77c566e2b53ba4ea52c2", "fileid": "https://r2.ropensci.org/6c283afbd1d5838bc3573dc8e56cbc86dcc59433f55a66f22b7b0a89ad064668", "status": "failure", "check": "ERROR", "buildurl": "https://github.com/r-universe/bioc-release/actions/runs/42204824863" }, { "r": "4.6.2", "os": "linux", "version": "1.28.0", "date": "2026-11-06T10:51:06.000Z", "distro": "resolute", "arch": "x86_64", "commit": "13b58eec1ddb59e2937d77c566e2b53ba4ea52c2", "fileid": "https://r2.ropensci.org/4c5e491e2160fa2483cdec8527b8fb7475b63ab079285f14de9675e943245b7e", "status": "failure", "check": "ERROR", "buildurl": "https://github.com/r-universe/bioc-release/actions/runs/42204824863" }, { "r": "4.5.3", "os": "mac", "version": "1.28.0", "date": "2026-11-06T10:49:20.000Z", "arch": "aarch64", "commit": "13b58eec1ddb59e2937d77c566e2b53ba4ea52c2", "fileid": "https://r2.ropensci.org/31f67764a7996a9c7a68851e2e4f7b5e262201ca6c537a050e5acc1c1d1fc1d1", "status": "failure", "check": "ERROR", "buildurl": "https://github.com/r-universe/bioc-release/actions/runs/42204824863" }, { "r": "4.5.3", "os": "mac", "version": "1.28.0", "date": "2026-11-06T10:50:19.000Z", "arch": "x86_64", "commit": "13b58eec1ddb59e2937d77c566e2b53ba4ea52c2", "fileid": "https://r2.ropensci.org/bab610a4870b44794a54dd8046771cd277bc5cc75e4a1e73ea979dec24c5701b", "status": "failure", "check": "ERROR", "buildurl": "https://github.com/r-universe/bioc-release/actions/runs/42204824863" }, { "r": "4.6.2", "os": "mac", "version": "1.28.0", "date": "2026-11-06T10:49:32.000Z", "arch": "aarch64", "commit": "13b58eec1ddb59e2937d77c566e2b53ba4ea52c2", "fileid": "https://r2.ropensci.org/e3196682c364ab886fd838659e3839b33793760a49c73d2473e9547b619e2988", "status": "failure", "check": "ERROR", "buildurl": "https://github.com/r-universe/bioc-release/actions/runs/42204824863" }, { "r": "4.6.2", "os": "mac", "version": "1.28.0", "date": "2026-11-06T10:52:02.000Z", "arch": "x86_64", "commit": "13b58eec1ddb59e2937d77c566e2b53ba4ea52c2", "fileid": "https://r2.ropensci.org/80f84d1a7441261252205aa59d059be46e931a11e88b6a756d9c1cd0f8a3ee9d", "status": "failure", "check": "ERROR", "buildurl": "https://github.com/r-universe/bioc-release/actions/runs/42204824863" }, { "r": "4.6.0", "os": "wasm", "version": "1.28.0", "date": "2026-11-06T10:50:08.000Z", "arch": "emscripten", "commit": "13b58eec1ddb59e2937d77c566e2b53ba4ea52c2", "fileid": "https://r2.ropensci.org/fff8bb2e8f288e37001fefb6727a325c274adaef3f8d28afd6d8734f34552332", "status": "success", "buildurl": "https://github.com/r-universe/bioc-release/actions/runs/42204824863" }, { "r": "4.7.0", "os": "win", "version": "1.28.0", "date": "2026-11-06T10:50:53.000Z", "arch": "aarch64", "commit": "13b58eec1ddb59e2937d77c566e2b53ba4ea52c2", "fileid": "https://r2.ropensci.org/52d0239797c273a1b87e02cce0e13feca787255133a2a22cc39d724ec7195ade", "status": "failure", "check": "ERROR", "buildurl": "https://github.com/r-universe/bioc-release/actions/runs/42204824863" }, { "r": "4.7.0", "os": "win", "version": "1.28.0", "date": "2026-11-06T10:48:58.000Z", "arch": "x86_64", "commit": "13b58eec1ddb59e2937d77c566e2b53ba4ea52c2", "fileid": "https://r2.ropensci.org/40ad6b4919eb6c4170889339279d43dbb4a03ab4103bf78ad81f35476f24875a", "status": "failure", "check": "ERROR", "buildurl": "https://github.com/r-universe/bioc-release/actions/runs/42204824863" }, { "r": "4.5.3", "os": "win", "version": "1.28.0", "date": "2026-11-06T10:48:55.000Z", "arch": "x86_64", "commit": "13b58eec1ddb59e2937d77c566e2b53ba4ea52c2", "fileid": "https://r2.ropensci.org/5c3f6e3485f6ba9a8eef0db9dbd1910b3bb55b5ea06415c4d4c38b6260671474", "status": "failure", "check": "ERROR", "buildurl": "https://github.com/r-universe/bioc-release/actions/runs/42204824863" }, { "r": "4.6.2", "os": "win", "version": "1.28.0", "date": "2026-11-06T10:50:55.000Z", "arch": "aarch64", "commit": "13b58eec1ddb59e2937d77c566e2b53ba4ea52c2", "fileid": "https://r2.ropensci.org/db4c030dde0a0b7c53519fcb759dcebb59fc982e550015cd6ecb15ae70057d2e", "status": "failure", "check": "ERROR", "buildurl": "https://github.com/r-universe/bioc-release/actions/runs/42204824863" }, { "r": "4.6.2", "os": "win", "version": "1.28.0", "date": "2026-11-06T10:48:59.000Z", "arch": "x86_64", "commit": "13b58eec1ddb59e2937d77c566e2b53ba4ea52c2", "fileid": "https://r2.ropensci.org/df84a8810c649f1f1cdfc3a1d65102c3f1dc7cf7d6d66d3a8073800401e72120", "status": "failure", "check": "ERROR", "buildurl": "https://github.com/r-universe/bioc-release/actions/runs/42204824863" } ] }