{ "_id": "6a19823facfb0bcc41df98c3", "Package": "RcwlPipelines", "Title": "Bioinformatics pipelines based on Rcwl", "Version": "1.29.0", "Authors@R": "c(person(given = \"Qiang\", family = \"Hu\",\nrole = c(\"aut\", \"cre\"),\nemail = \"qiang.hu@roswellpark.org\"),\nperson(given = \"Qian\", family = \"Liu\",\nrole = c(\"aut\"),\nemail = \"qian.liu@roswellpark.org\"),\nperson(given = \"Shuang\", family = \"Gao\",\nrole = c(\"aut\"),\nemail = \"shuang.gao@roswellpark.org\"))", "Description": "A collection of Bioinformatics tools and pipelines based\non R and the Common Workflow Language.", "License": "GPL-2", "Encoding": "UTF-8", "VignetteBuilder": "knitr", "RoxygenNote": "7.2.3", "biocViews": "Software, WorkflowStep, Alignment, Preprocessing,\nQualityControl, DNASeq, RNASeq, DataImport, ImmunoOncology", "SystemRequirements": "nodejs", "Config/Bioconductor/UnsupportedPlatforms": "windows", "Config/pak/sysreqs": "cmake libglpk-dev make libgit2-dev libicu-dev\nlibpng-dev libssh2-1-dev libuv1-dev libxml2-dev libssl-dev\npython3 libx11-dev zlib1g-dev", "Repository": "https://bioc.r-universe.dev", "Date/Publication": "2026-04-28 12:49:45 UTC", "RemoteUrl": "https://github.com/bioc/RcwlPipelines", "RemoteRef": "HEAD", "RemoteSha": "37a9fdc7eef5559fdcf588986829c9d9f78f227b", "NeedsCompilation": "no", "Packaged": { "Date": "2026-05-29 10:23:14 UTC", "User": "root" }, "Author": "Qiang Hu [aut, cre],\nQian Liu [aut],\nShuang Gao [aut]", "Maintainer": "Qiang Hu ", "MD5sum": "2d7e4fe5c68d97fcb752d0e0b5f8ae54", "_user": "bioc", "_type": "src", "_file": "RcwlPipelines_1.29.0.tar.gz", "_fileid": "1381f6125d53c9c5dd77c5a518fd7d68d94a915686d1afaa1f26f7c33e389f3d", "_filesize": 116487, "_sha256": "1381f6125d53c9c5dd77c5a518fd7d68d94a915686d1afaa1f26f7c33e389f3d", "_created": "2026-05-29T10:23:14.000Z", "_published": "2026-05-29T12:10:39.844Z", "_jobs": [ { "job": 78482695172, "time": 173, "config": "bioc-checks", "r": "4.6.0", "check": "ERROR", "artifact": "7288541431" }, { "job": 78482695257, "time": 253, "config": "linux-devel-x86_64", "r": "4.7.0", "check": "NOTE", "artifact": "7288564707" }, { "job": 78482695158, "time": 252, "config": "linux-release-x86_64", "r": "4.6.0", "check": "NOTE", "artifact": "7288564476" }, { "job": 78482695157, "time": 132, "config": "macos-oldrel-arm64", "r": "4.5.3", "check": "NOTE", "artifact": "7290300091" }, { "job": 78482695186, "time": 168, "config": "macos-release-arm64", "r": "4.6.0", "check": "NOTE", "artifact": "7290311824" }, { "job": 78482123826, "time": 236, "config": "source", "r": "4.6.0", "check": "OK", "artifact": "7288489689" }, { "job": 78482695275, "time": 151, "config": "wasm-release", "r": "4.6.0", "check": "OK", "artifact": "7288534876" }, { "job": 78482695185, "time": 184, "config": "windows-devel", "r": "4.7.0", "check": "NOTE", "artifact": "7288544768" }, { "job": 78482695174, "time": 180, "config": "windows-oldrel", "r": "4.5.3", "check": "NOTE", "artifact": "7288543764" }, { "job": 78482695212, "time": 159, "config": "windows-release", "r": "4.6.0", "check": "NOTE", "artifact": "7288537548" } ], "_bioccheck": { "error": 1, "warning": 1, "note": 11 }, "_buildurl": "https://github.com/r-universe/bioc/actions/runs/26631756311", "_status": "success", "_host": "GitHub-Actions", "_upstream": "https://github.com/bioc/RcwlPipelines", "_commit": { "id": "37a9fdc7eef5559fdcf588986829c9d9f78f227b", "author": "A Wokaty ", "committer": "A Wokaty ", "message": "bump x.y.z version to odd y following creation of RELEASE_3_23 branch\n", "time": 1777380585 }, "_maintainer": { "name": "Qiang Hu", "email": "qiang.hu@roswellpark.org", "login": "hubentu", "description": "", "uuid": 9856666 }, "_distro": "noble", "_registered": true, "_dependencies": [ { "package": "R", "version": ">= 3.6", "role": "Depends" }, { "package": "Rcwl", "role": "Depends" }, { "package": "BiocFileCache", "role": "Depends" }, { "package": "rappdirs", "role": "Imports" }, { "package": "methods", "role": "Imports" }, { "package": "utils", "role": "Imports" }, { "package": "git2r", "role": "Imports" }, { "package": "httr", "role": "Imports" }, { "package": "S4Vectors", "role": "Imports" }, { "package": "testthat", "role": "Suggests" }, { "package": "knitr", "role": "Suggests" }, { "package": "rmarkdown", "role": "Suggests" }, { "package": "BiocStyle", "role": "Suggests" } ], "_owner": "bioc", "_selfowned": true, "_usedby": 1, "_updates": [ { "week": "2025-44", "n": 2 }, { "week": "2026-15", "n": 1 }, { "week": "2026-18", "n": 2 } ], "_tags": [], "_bioc": [ { "branch": "devel", "version": "1.29.0", "bioc": "3.24" }, { "branch": "release", "version": "1.28.0", "bioc": "3.23" } ], "_topics": [ "software", "workflowstep", "alignment", "preprocessing", "qualitycontrol", "dnaseq", "rnaseq", "dataimport", "immunooncology" ], "_userbio": { "uuid": 2286807, "type": "organization", "name": "Bioconductor", "description": "Software for the analysis and comprehension of high-throughput genomic data" }, "_downloads": { "count": 328, "source": "https://www.bioconductor.org/packages/stats/bioc/RcwlPipelines" }, "_searchresults": 29, "_rbuild": "4.6.0", "_assets": [ "extra/citation.cff", "extra/citation.html", "extra/citation.json", "extra/citation.txt", "extra/contents.json", "extra/NEWS.html", "extra/NEWS.txt", "extra/RcwlPipelines.html", "extra/readme.html", "extra/readme.md", "manual.pdf" ], "_realowner": "bioc", "_cranurl": false, "_exports": [ "Command", "Container", "cwlHub", "cwlInstall", "cwlLoad", "cwlSearch", "cwlUpdate", "mcols", "searchContainer", "show", "title", "Type" ], "_help": [ { "page": "cwlHub-class", "title": "cwlHub", "topics": [ "Command", "Container", "cwlHub", "cwlHub-class", "mcols,cwlHub-method", "show,cwlHub-method", "title", "Type", "[,cwlHub,ANY,ANY,ANY-method" ] }, { "page": "cwlInstall", "title": "cwlInstall", "topics": [ "cwlInstall" ] }, { "page": "cwlLoad", "title": "cwlLoad", "topics": [ "cwlLoad" ] }, { "page": "cwlSearch", "title": "cwlSearch", "topics": [ "cwlSearch" ] }, { "page": "cwlUpdate", "title": "cwlUpdate", "topics": [ "cwlUpdate" ] }, { "page": "RcwlPipelines", "title": "RcwlPipelines", "topics": [ "RcwlPipelines" ] }, { "page": "searchContainer", "title": "seawrch containers", "topics": [ "searchContainer" ] } ], "_readme": "https://github.com/bioc/RcwlPipelines/raw/HEAD/README.md", "_rundeps": [ "askpass", "backports", "base64enc", "base64url", "basilisk", "batchtools", "BH", "BiocFileCache", "BiocGenerics", "BiocParallel", "bit", "bit64", "blob", "brew", "bslib", "cachem", "checkmate", "cli", "clipr", "codetools", "commonmark", "cpp11", "crayon", "curl", "data.table", "DBI", "dbplyr", "DiagrammeR", "digest", "dir.expiry", "dplyr", "evaluate", "farver", "fastmap", "filelock", "fontawesome", "formatR", "fs", "futile.logger", "futile.options", "generics", "git2r", "glue", "here", "highr", "hms", "htmltools", "htmlwidgets", "httpuv", "httr", "httr2", "igraph", "jquerylib", "jsonlite", "knitr", "labeling", "lambda.r", "later", "lattice", "lifecycle", "magrittr", "Matrix", "memoise", "mime", "openssl", "otel", "pillar", "pkgconfig", "png", "prettyunits", "progress", "promises", "purrr", "R.methodsS3", "R.oo", "R.utils", "R6", "rappdirs", "RColorBrewer", "Rcpp", "RcppTOML", "Rcwl", "readr", "reticulate", "rlang", "rmarkdown", "rprojroot", "RSQLite", "rstudioapi", "S4Vectors", "sass", "scales", "shiny", "snow", "sourcetools", "stringi", "stringr", "sys", "tibble", "tidyr", "tidyselect", "tinytex", "tzdb", "utf8", "vctrs", "viridisLite", "visNetwork", "vroom", "withr", "xfun", "xtable", "yaml" ], "_vignettes": [ { "source": "RcwlPipelines.Rmd", "filename": "RcwlPipelines.html", "title": "RcwlPipelines: Bioinformatics tools and pipelines based on Rcwl", "author": "Qiang Hu, Qian Liu", "engine": "knitr::rmarkdown", "headings": [ "Installation", "Project resources", "The R recipes and cwl scripts", "Tutorial book", "RcwlPipelines core functions", "cwlUpdate", "cwlSearch", "cwlLoad", "Customize a tool or pipeline", "Run a tool or pipeline", "SessionInfo" ], "created": "2019-03-01 16:03:11", "modified": "2021-02-25 04:03:06", "commits": 17 } ], "_score": 5.1156105116743, "_indexed": true, "_nocasepkg": "rcwlpipelines", "_universes": [ "bioc", "hubentu" ], "_binaries": [ { "r": "4.7.0", "os": "linux", "version": "1.29.0", "date": "2026-05-29T10:26:30.000Z", "distro": "noble", "commit": "37a9fdc7eef5559fdcf588986829c9d9f78f227b", "fileid": "e115619feabaafd560f38efcca05f14b65fefed00113e70833b08baa3eaf4c55", "status": "success", "check": "NOTE", "buildurl": "https://github.com/r-universe/bioc/actions/runs/26631756311" }, { "r": "4.6.0", "os": "linux", "version": "1.29.0", "date": "2026-05-29T10:26:27.000Z", "distro": "noble", "commit": "37a9fdc7eef5559fdcf588986829c9d9f78f227b", "fileid": "dbee0cb88023ece00f162bb46876e634c5ce1baafeeea43eda5f5d92737195b4", "status": "success", "check": "NOTE", "buildurl": "https://github.com/r-universe/bioc/actions/runs/26631756311" }, { "r": "4.5.3", "os": "mac", "version": "1.29.0", "date": "2026-05-29T12:08:41.000Z", "commit": "37a9fdc7eef5559fdcf588986829c9d9f78f227b", "fileid": "ee280652ce6ea7097f3b8fe4d1c485128359cad20ec820c9343390edb04ae5cc", "status": "success", "check": "NOTE", "buildurl": "https://github.com/r-universe/bioc/actions/runs/26631756311" }, { "r": "4.6.0", "os": "mac", "version": "1.29.0", "date": "2026-05-29T12:09:09.000Z", "commit": "37a9fdc7eef5559fdcf588986829c9d9f78f227b", "fileid": "c96aa8ffac90018167715f32e5a9f85a1a070985344fda7063c4c42ce8237ae4", "status": "success", "check": "NOTE", "buildurl": "https://github.com/r-universe/bioc/actions/runs/26631756311" }, { "r": "4.6.0", "os": "wasm", "version": "1.29.0", "date": "2026-05-29T10:26:07.000Z", "commit": "37a9fdc7eef5559fdcf588986829c9d9f78f227b", "fileid": "4749052439f8e99cd55ee7344e39fd61c88373f6b7131ca638819047cdb0174b", "status": "success", "buildurl": "https://github.com/r-universe/bioc/actions/runs/26631756311" }, { "r": "4.7.0", "os": "win", "version": "1.29.0", "date": "2026-05-29T10:25:12.000Z", "commit": "37a9fdc7eef5559fdcf588986829c9d9f78f227b", "fileid": "4a311e05db44337e5e5a9d1549c4c42ddc354e8b195a19544e9cbc2cbcd0f3ef", "status": "success", "check": "NOTE", "buildurl": "https://github.com/r-universe/bioc/actions/runs/26631756311" }, { "r": "4.5.3", "os": "win", "version": "1.29.0", "date": "2026-05-29T10:25:09.000Z", "commit": "37a9fdc7eef5559fdcf588986829c9d9f78f227b", "fileid": "5bdd4723d6314e109d0c139323c971ad321a8bc005303a144a93550eae1450c9", "status": "success", "check": "NOTE", "buildurl": "https://github.com/r-universe/bioc/actions/runs/26631756311" }, { "r": "4.6.0", "os": "win", "version": "1.29.0", "date": "2026-05-29T10:24:48.000Z", "commit": "37a9fdc7eef5559fdcf588986829c9d9f78f227b", "fileid": "3c8e39c5641a4c50eef50aba27578ccc8b97db6d9d72a5fe2a6102dfb2712149", "status": "success", "check": "NOTE", "buildurl": "https://github.com/r-universe/bioc/actions/runs/26631756311" } ] }