{
  "_id": "6ae76ffa2e87f76f20acd338",
  "Package": "pogos",
  "Title": "PharmacOGenomics Ontology Support",
  "Description": "Provide simple utilities for querying bhklab PharmacoDB,\nmodeling API outputs, and integrating to cell and compound\nontologies.",
  "Version": "1.33.0",
  "Author": "Vince Carey <stvjc@channing.harvard.edu>",
  "Maintainer": "VJ Carey <stvjc@channing.harvard.edu>",
  "License": "Artistic-2.0",
  "LazyLoad": "yes",
  "LazyData": "yes",
  "biocViews": "Pharmacogenomics, PooledScreens, ImmunoOncology",
  "RoxygenNote": "7.3.2",
  "VignetteBuilder": "knitr",
  "Encoding": "UTF-8",
  "Config/pak/sysreqs": "cmake libglpk-dev make libicu-dev libpng-dev\nlibuv1-dev libxml2-dev libssl-dev python3 zlib1g-dev",
  "Repository": "https://bioc.r-universe.dev",
  "Date/Publication": "2026-04-28 12:47:08 UTC",
  "RemoteUrl": "https://github.com/bioc/pogos",
  "RemoteRef": "HEAD",
  "RemoteSha": "b30e57867e6a5fd9c4007b2b2c1cf13e0040b93a",
  "NeedsCompilation": "no",
  "Packaged": {
    "Date": "2026-11-01 14:09:45 UTC",
    "User": "root"
  },
  "_user": "bioc",
  "_type": "src",
  "_file": "pogos_1.33.0.tar.gz",
  "_fileid": "https://r2.ropensci.org/7f0f30cd2fee12033f28a8a348309230ac027036ad3faedd4bdeb859b8e84ebb",
  "_filesize": 1209698,
  "_sha256": "7f0f30cd2fee12033f28a8a348309230ac027036ad3faedd4bdeb859b8e84ebb",
  "_expires": "2027-02-09T16:59:36.000Z",
  "_created": "2026-11-01T14:09:45.000Z",
  "_published": "2026-11-01T16:59:38.647Z",
  "_upstream": "https://github.com/bioc/pogos",
  "_status": "failure",
  "_maintainer": {
    "name": "VJ Carey",
    "email": "stvjc@channing.harvard.edu",
    "login": "vjcitn",
    "description": "Professor of Medicine, Channing Division of Network Medicine, Mass General Brigham, Harvard Medical School.",
    "uuid": 4624066
  },
  "_jobs": [
    {
      "job": 124872620468,
      "time": 191,
      "config": "bioc-checks",
      "r": "4.6.2",
      "check": "ERROR",
      "artifact": "13087019495"
    },
    {
      "job": 124872620458,
      "time": 428,
      "config": "linux-devel-x86_64",
      "r": "4.7.0",
      "check": "WARNING",
      "artifact": "13088105369"
    },
    {
      "job": 124872620521,
      "time": 373,
      "config": "linux-release-x86_64",
      "r": "4.6.2",
      "check": "WARNING",
      "artifact": "13088095288"
    },
    {
      "job": 124872620529,
      "time": 274,
      "config": "macos-oldrel-arm64",
      "r": "4.5.3",
      "check": "WARNING",
      "artifact": "13092855713"
    },
    {
      "job": 124872620373,
      "time": 293,
      "config": "macos-release-arm64",
      "r": "4.6.2",
      "check": "WARNING",
      "artifact": "13092532365"
    },
    {
      "job": 124864078640,
      "time": 323,
      "config": "source",
      "r": "4.6.2",
      "check": "ERROR",
      "artifact": "13086599276"
    },
    {
      "job": 124872620519,
      "time": 140,
      "config": "wasm-release",
      "r": "4.6.0",
      "check": "OK",
      "artifact": "13087807147"
    },
    {
      "job": 124872620477,
      "time": 273,
      "config": "windows-devel-x86_64",
      "r": "4.7.0",
      "check": "WARNING",
      "artifact": "13087226205"
    },
    {
      "job": 124872620482,
      "time": 277,
      "config": "windows-oldrel-x86_64",
      "r": "4.5.3",
      "check": "WARNING",
      "artifact": "13086980941"
    },
    {
      "job": 124872620444,
      "time": 251,
      "config": "windows-release-x86_64",
      "r": "4.6.2",
      "check": "WARNING",
      "artifact": "13086966792"
    }
  ],
  "_bioccheck": {
    "error": 1,
    "warning": 2,
    "note": 10
  },
  "_buildurl": "https://github.com/r-universe/bioc/actions/runs/41310437533",
  "_commit": {
    "id": "b30e57867e6a5fd9c4007b2b2c1cf13e0040b93a",
    "author": "A Wokaty <andres.wokaty@sph.cuny.edu>",
    "committer": "A Wokaty <andres.wokaty@sph.cuny.edu>",
    "message": "bump x.y.z version to odd y following creation of RELEASE_3_23 branch\n",
    "time": 1777380428
  },
  "_distro": "resolute",
  "_host": "GitHub-Actions",
  "_registered": true,
  "_dependencies": [
    {
      "package": "R",
      "version": ">= 3.5.0",
      "role": "Depends"
    },
    {
      "package": "rjson",
      "version": ">= 0.2.15",
      "role": "Depends"
    },
    {
      "package": "httr",
      "version": ">= 1.3.1",
      "role": "Depends"
    },
    {
      "package": "methods",
      "role": "Imports"
    },
    {
      "package": "S4Vectors",
      "role": "Imports"
    },
    {
      "package": "utils",
      "role": "Imports"
    },
    {
      "package": "shiny",
      "role": "Imports"
    },
    {
      "package": "ontoProc",
      "role": "Imports"
    },
    {
      "package": "ggplot2",
      "role": "Imports"
    },
    {
      "package": "graphics",
      "role": "Imports"
    },
    {
      "package": "knitr",
      "role": "Suggests"
    },
    {
      "package": "DT",
      "role": "Suggests"
    },
    {
      "package": "ontologyPlot",
      "role": "Suggests"
    },
    {
      "package": "testthat",
      "role": "Suggests"
    },
    {
      "package": "rmarkdown",
      "role": "Suggests"
    },
    {
      "package": "BiocStyle",
      "role": "Suggests"
    }
  ],
  "_owner": "bioc",
  "_selfowned": true,
  "_usedby": 0,
  "_updates": [
    {
      "week": "2025-44",
      "n": 2
    },
    {
      "week": "2026-18",
      "n": 2
    }
  ],
  "_tags": [],
  "_bioc": [
    {
      "branch": "devel",
      "version": "1.33.0",
      "bioc": "3.24",
      "repository": "bioc"
    },
    {
      "branch": "release",
      "version": "1.32.0",
      "bioc": "3.23",
      "repository": "bioc"
    }
  ],
  "_topics": [
    "pharmacogenomics",
    "pooledscreens",
    "immunooncology"
  ],
  "_userbio": {
    "uuid": 2286807,
    "type": "organization",
    "name": "Bioconductor",
    "followers": 482,
    "description": "Software for the analysis and comprehension of high-throughput genomic data"
  },
  "_downloads": {
    "count": 540,
    "source": "https://www.bioconductor.org/packages/stats/bioc/pogos"
  },
  "_searchresults": 12,
  "_abi": {
    "exports": [
      {
        "key": "pogos::DRProfSet",
        "hash": "6cfbd11a08d79432"
      },
      {
        "key": "pogos::DRProfile",
        "hash": "38f3eb3c7a4e85f8"
      },
      {
        "key": "pogos::DRTraceSet",
        "hash": "0af4c2961939d98d"
      },
      {
        "key": "pogos::generic:getDrugs",
        "hash": "2b995c772450e34e"
      }
    ],
    "imports": []
  },
  "_rbuild": "4.6.2",
  "_assets": [
    "extra/citation.cff",
    "extra/citation.html",
    "extra/citation.json",
    "extra/citation.txt",
    "extra/contents.json",
    "extra/manual.pdf",
    "extra/pogos.html",
    "extra/readme.html",
    "extra/readme.md"
  ],
  "_homeurl": "https://github.com/vjcitn/pogos",
  "_realowner": "bioc",
  "_cranurl": false,
  "_exports": [
    "basicDecoder",
    "compoundsByCell",
    "DRProfSet",
    "DRTraceSet",
    "getDrugs",
    "iriCCLE",
    "plot",
    "rxdbQuery_v1",
    "topEndpoints_v1",
    "traces"
  ],
  "_datasets": [
    {
      "name": "CCLE_drts",
      "title": "compounds_v1: serialization of compounds info from PharmacoDb v1",
      "object": "CCLE_drts",
      "class": [
        "DRTraceSet"
      ],
      "fields": [],
      "table": false,
      "tojson": false
    },
    {
      "name": "cell_lines_v1",
      "title": "compounds_v1: serialization of compounds info from PharmacoDb v1",
      "object": "cell_lines_v1",
      "class": [
        "DFrame"
      ],
      "fields": [],
      "table": false,
      "tojson": false
    },
    {
      "name": "compounds_v1",
      "title": "compounds_v1: serialization of compounds info from PharmacoDb v1",
      "object": "compounds_v1",
      "class": [
        "DFrame"
      ],
      "fields": [],
      "table": false,
      "tojson": false
    },
    {
      "name": "datasets_v1",
      "title": "compounds_v1: serialization of compounds info from PharmacoDb v1",
      "object": "datasets_v1",
      "class": [
        "DFrame"
      ],
      "fields": [],
      "table": false,
      "tojson": false
    },
    {
      "name": "tissues_v1",
      "title": "compounds_v1: serialization of compounds info from PharmacoDb v1",
      "object": "tissues_v1",
      "class": [
        "DFrame"
      ],
      "fields": [],
      "table": false,
      "tojson": false
    }
  ],
  "_help": [
    {
      "page": "sub-DRProfSet-character-ANY-ANY-method",
      "title": "subscripting on DRProfSet extracts a profile for a single drug whose name constitutes the index",
      "topics": [
        "[,DRProfSet,character,ANY,ANY-method"
      ]
    },
    {
      "page": "basicDecoder",
      "title": "convert binary output of GET()$content to list",
      "topics": [
        "basicDecoder"
      ]
    },
    {
      "page": "compounds_v1",
      "title": "compounds_v1: serialization of compounds info from PharmacoDb v1",
      "topics": [
        "CCLE_drts",
        "cell_lines_v1",
        "compounds_v1",
        "datasets_v1",
        "tissues_v1"
      ]
    },
    {
      "page": "compoundsByCell",
      "title": "initial version of compound browser over pharmacoDb cells",
      "topics": [
        "compoundsByCell"
      ]
    },
    {
      "page": "DRProfSet",
      "title": "DRProfSet is a class for managing dose-response information about cell lines from a pharmacogenomics dataset",
      "topics": [
        "DRProfile-class",
        "DRProfSet",
        "DRProfSet-class",
        "getDrugs",
        "getDrugs,DRProfSet-method",
        "plot,DRProfSet,missing-method"
      ]
    },
    {
      "page": "DRTraceSet",
      "title": "DRTraceSet class manages dose-response information for a single cell line, multiple drugs",
      "topics": [
        "DRTraceSet",
        "DRTraceSet-class",
        "plot,DRTraceSet,missing-method"
      ]
    },
    {
      "page": "iriCCLE",
      "title": "obtain an example trace set stored locally, for irinotecan and selected cell lines",
      "topics": [
        "iriCCLE"
      ]
    },
    {
      "page": "rxdbQuery_v1",
      "title": "very simple query formulation, build queries using endpoints of bhklab PharmacoDB API",
      "topics": [
        "rxdbQuery_v1"
      ]
    },
    {
      "page": "topEndpoints_v1",
      "title": "enumerate top level endpoint terms for bhklab PharmacoDB API",
      "topics": [
        "topEndpoints_v1"
      ]
    },
    {
      "page": "traces",
      "title": "trace extractor",
      "topics": [
        "traces"
      ]
    }
  ],
  "_readme": "https://github.com/bioc/pogos/raw/HEAD/README.md",
  "_rundeps": [
    "abind",
    "AnnotationDbi",
    "AnnotationHub",
    "askpass",
    "base64enc",
    "basilisk",
    "BH",
    "Biobase",
    "BiocBaseUtils",
    "BiocFileCache",
    "BiocGenerics",
    "BiocManager",
    "BiocVersion",
    "Biostrings",
    "bit",
    "bit64",
    "blob",
    "bslib",
    "cachem",
    "cli",
    "commonmark",
    "coro",
    "cpp11",
    "crayon",
    "crosstalk",
    "curl",
    "DBI",
    "dbplyr",
    "DelayedArray",
    "digest",
    "dir.expiry",
    "dplyr",
    "DT",
    "ellmer",
    "evaluate",
    "farver",
    "fastmap",
    "filelock",
    "fontawesome",
    "fs",
    "generics",
    "GenomicRanges",
    "ggplot2",
    "glue",
    "graph",
    "gtable",
    "here",
    "highr",
    "htmltools",
    "htmlwidgets",
    "httpuv",
    "httr",
    "httr2",
    "igraph",
    "IRanges",
    "isoband",
    "jquerylib",
    "jsonlite",
    "KEGGREST",
    "knitr",
    "labeling",
    "later",
    "lattice",
    "lazyeval",
    "lifecycle",
    "magrittr",
    "Matrix",
    "MatrixGenerics",
    "matrixStats",
    "memoise",
    "mime",
    "ontologyIndex",
    "ontologyPlot",
    "ontoProc",
    "openssl",
    "otel",
    "paintmap",
    "pillar",
    "pkgconfig",
    "png",
    "promises",
    "purrr",
    "R.methodsS3",
    "R.oo",
    "R.utils",
    "R6",
    "rappdirs",
    "RBGL",
    "RColorBrewer",
    "Rcpp",
    "RcppTOML",
    "reticulate",
    "Rgraphviz",
    "rjson",
    "rlang",
    "rmarkdown",
    "rprojroot",
    "RSQLite",
    "S4Arrays",
    "S4Vectors",
    "S7",
    "sass",
    "scales",
    "Seqinfo",
    "shiny",
    "sourcetools",
    "SparseArray",
    "stringi",
    "stringr",
    "SummarizedExperiment",
    "sys",
    "tibble",
    "tidyr",
    "tidyselect",
    "tinytex",
    "utf8",
    "vctrs",
    "viridisLite",
    "withr",
    "xfun",
    "xtable",
    "XVector",
    "yaml"
  ],
  "_score": 3.079181246047625,
  "_indexed": true,
  "_nocasepkg": "pogos",
  "_universes": [
    "bioc",
    "vjcitn"
  ],
  "_binaries": [
    {
      "r": "4.7.0",
      "os": "linux",
      "version": "1.33.0",
      "date": "2026-11-01T14:33:29.000Z",
      "distro": "resolute",
      "commit": "b30e57867e6a5fd9c4007b2b2c1cf13e0040b93a",
      "fileid": "https://r2.ropensci.org/a8b4a100fe1cde060f2d7bfb8e7ad77ae0d0ad5064ce60270ecfc2a1ca9bb626",
      "status": "success",
      "check": "WARNING",
      "buildurl": "https://github.com/r-universe/bioc/actions/runs/41310437533"
    },
    {
      "r": "4.6.2",
      "os": "linux",
      "version": "1.33.0",
      "date": "2026-11-01T14:33:11.000Z",
      "distro": "resolute",
      "commit": "b30e57867e6a5fd9c4007b2b2c1cf13e0040b93a",
      "fileid": "https://r2.ropensci.org/fbc5f86ea797d3414eea4385ad643e148b5c9588118fd8e1064dea6f45372e53",
      "status": "success",
      "check": "WARNING",
      "buildurl": "https://github.com/r-universe/bioc/actions/runs/41310437533"
    },
    {
      "r": "4.5.3",
      "os": "mac",
      "version": "1.33.0",
      "date": "2026-11-01T16:56:21.000Z",
      "commit": "b30e57867e6a5fd9c4007b2b2c1cf13e0040b93a",
      "fileid": "https://r2.ropensci.org/af8ed5d8d948db6ab4e5227dbd793c09ad0fea6fe258ff15934b9581d6f477e7",
      "status": "success",
      "check": "WARNING",
      "buildurl": "https://github.com/r-universe/bioc/actions/runs/41310437533"
    },
    {
      "r": "4.6.2",
      "os": "mac",
      "version": "1.33.0",
      "date": "2026-11-01T16:56:01.000Z",
      "commit": "b30e57867e6a5fd9c4007b2b2c1cf13e0040b93a",
      "fileid": "https://r2.ropensci.org/c9651f8b859dad5b0faf61e75f093932595d33ac6e88711b018dc327ada69a52",
      "status": "success",
      "check": "WARNING",
      "buildurl": "https://github.com/r-universe/bioc/actions/runs/41310437533"
    },
    {
      "r": "4.6.0",
      "os": "wasm",
      "version": "1.33.0",
      "date": "2026-11-01T14:31:46.000Z",
      "commit": "b30e57867e6a5fd9c4007b2b2c1cf13e0040b93a",
      "fileid": "https://r2.ropensci.org/f42bd088f0f3e1c3fae5b8639b20789aa7c229bf7f8fd8a5ff5e47622cc52abe",
      "status": "success",
      "buildurl": "https://github.com/r-universe/bioc/actions/runs/41310437533"
    },
    {
      "r": "4.7.0",
      "os": "win",
      "version": "1.33.0",
      "date": "2026-11-01T14:11:55.000Z",
      "commit": "b30e57867e6a5fd9c4007b2b2c1cf13e0040b93a",
      "fileid": "https://r2.ropensci.org/300c06e96ba6c64c16a6677a76e866ff9f8551063751215d9896fd575e49acb1",
      "status": "success",
      "check": "WARNING",
      "buildurl": "https://github.com/r-universe/bioc/actions/runs/41310437533"
    },
    {
      "r": "4.5.3",
      "os": "win",
      "version": "1.33.0",
      "date": "2026-11-01T14:12:10.000Z",
      "commit": "b30e57867e6a5fd9c4007b2b2c1cf13e0040b93a",
      "fileid": "https://r2.ropensci.org/5fa191edebb02caaf3f8523670f9f6cbbe1d739424180be49a9fee45325b4bae",
      "status": "success",
      "check": "WARNING",
      "buildurl": "https://github.com/r-universe/bioc/actions/runs/41310437533"
    },
    {
      "r": "4.6.2",
      "os": "win",
      "version": "1.33.0",
      "date": "2026-11-01T14:11:39.000Z",
      "commit": "b30e57867e6a5fd9c4007b2b2c1cf13e0040b93a",
      "fileid": "https://r2.ropensci.org/f5b50bcbdf965fae33b4e5b7fad572021dee887cf9ecacc06a455787aa86efbf",
      "status": "success",
      "check": "WARNING",
      "buildurl": "https://github.com/r-universe/bioc/actions/runs/41310437533"
    }
  ]
}