{
  "_id": "69e079c9c5259ad4cd8ffaa9",
  "Package": "restez",
  "Type": "Package",
  "Title": "Create and Query a Local Copy of 'GenBank' in R",
  "Version": "2.1.5.9000",
  "Authors@R": "c(\nperson(\ngiven = \"Joel H.\",\nfamily = \"Nitta\",\nrole = c(\"aut\", \"cre\"),\nemail = \"joelnitta@gmail.com\",\ncomment = c(ORCID = \"0000-0003-4719-7472\")),\nperson(\ngiven = \"Dom\",\nfamily = \"Bennett\",\nrole = \"aut\",\nemail = \"dominic.john.bennett@gmail.com\",\ncomment = c(ORCID = \"0000-0003-2722-1359\"))\n)",
  "Maintainer": "Joel H. Nitta <joelnitta@gmail.com>",
  "Description": "Download large sections of 'GenBank'\n<https://www.ncbi.nlm.nih.gov/genbank/> and generate a local\nSQL-based database. A user can then query this database using\n'restez' functions or through 'rentrez'\n<https://CRAN.R-project.org/package=rentrez> wrappers.",
  "URL": "https://github.com/ropensci/restez,\nhttps://docs.ropensci.org/restez/",
  "BugReports": "https://github.com/ropensci/restez/issues",
  "License": "MIT + file LICENSE",
  "Encoding": "UTF-8",
  "LazyData": "true",
  "RoxygenNote": "7.3.2",
  "Roxygen": "list(markdown = TRUE)",
  "Config/pak/sysreqs": "cmake make libicu-dev libuv1-dev libxml2-dev\nlibssl-dev xz-utils",
  "Repository": "https://ropensci.r-universe.dev",
  "Date/Publication": "2025-03-06 23:59:18 UTC",
  "RemoteUrl": "https://github.com/ropensci/restez",
  "RemoteRef": "main",
  "RemoteSha": "2fca23308ad67f064e01cf7e88328a0f98540c28",
  "NeedsCompilation": "no",
  "Packaged": {
    "Date": "2026-04-15 08:26:49 UTC",
    "User": "root"
  },
  "Author": "Joel H. Nitta [aut, cre] (ORCID:\n<https://orcid.org/0000-0003-4719-7472>),\nDom Bennett [aut] (ORCID: <https://orcid.org/0000-0003-2722-1359>)",
  "MD5sum": "56b8fdf3a2e70cae02f05db87278a5e6",
  "_user": "ropensci",
  "_type": "src",
  "_file": "restez_2.1.5.9000.tar.gz",
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  "_created": "2026-04-15T08:26:49.000Z",
  "_published": "2026-04-16T05:55:21.360Z",
  "_distro": "noble",
  "_jobs": [
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  "_buildurl": "https://github.com/r-universe/ropensci/actions/runs/24444179143",
  "_status": "success",
  "_host": "GitHub-Actions",
  "_upstream": "https://github.com/ropensci/restez",
  "_commit": {
    "id": "2fca23308ad67f064e01cf7e88328a0f98540c28",
    "author": "joelnitta <joelnitta@gmail.com>",
    "committer": "joelnitta <joelnitta@gmail.com>",
    "message": "Increment version number to 2.1.5.9000\n",
    "time": 1741305558
  },
  "_maintainer": {
    "name": "Joel H. Nitta",
    "email": "joelnitta@gmail.com",
    "login": "joelnitta",
    "mastodon": "@joelnitta@fosstodon.org",
    "bluesky": "@joelnitta.com",
    "orcid": "0000-0003-4719-7472",
    "uuid": 13459362
  },
  "_registered": true,
  "_dependencies": [
    {
      "package": "R",
      "version": ">= 3.3.0",
      "role": "Depends"
    },
    {
      "package": "utils",
      "role": "Imports"
    },
    {
      "package": "rentrez",
      "role": "Imports"
    },
    {
      "package": "DBI",
      "version": ">= 1.0.0",
      "role": "Imports"
    },
    {
      "package": "curl",
      "role": "Imports"
    },
    {
      "package": "cli",
      "role": "Imports"
    },
    {
      "package": "crayon",
      "role": "Imports"
    },
    {
      "package": "stringi",
      "role": "Imports"
    },
    {
      "package": "duckdb",
      "role": "Imports"
    },
    {
      "package": "fs",
      "role": "Imports"
    },
    {
      "package": "assertthat",
      "role": "Imports"
    },
    {
      "package": "ape",
      "role": "Imports"
    },
    {
      "package": "sessioninfo",
      "role": "Suggests"
    },
    {
      "package": "testthat",
      "role": "Suggests"
    },
    {
      "package": "knitr",
      "role": "Suggests"
    },
    {
      "package": "R.utils",
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    },
    {
      "package": "rmarkdown",
      "role": "Suggests"
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    {
      "package": "mockery",
      "role": "Suggests"
    }
  ],
  "_owner": "ropensci",
  "_selfowned": true,
  "_usedby": 1,
  "_updates": [],
  "_tags": [],
  "_topics": [
    "dna",
    "entrez",
    "genbank",
    "sequence"
  ],
  "_stars": 27,
  "_contributors": [
    {
      "user": "dombennett",
      "count": 221,
      "uuid": 2951559
    },
    {
      "user": "joelnitta",
      "count": 125,
      "uuid": 13459362
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      "uuid": 8360597
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      "uuid": 106490
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      "user": "btupper",
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    }
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  "_userbio": {
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    "type": "organization",
    "name": "rOpenSci",
    "description": "Tools and R Packages for Open Science"
  },
  "_downloads": {
    "count": 339,
    "source": "https://cranlogs.r-pkg.org/downloads/total/last-month/restez"
  },
  "_devurl": "https://github.com/ropensci/restez",
  "_pkgdown": "https://docs.ropensci.org/restez",
  "_searchresults": 200,
  "_metadata": {
    "review": {
      "id": 232,
      "status": "reviewed",
      "version": "0.0.0",
      "organization": "rOpenSci Software Review",
      "url": "https://github.com/ropensci/software-review/issues/232"
    },
    "ropensci_category": "data-extraction"
  },
  "_rbuild": "4.5.3",
  "_assets": [
    "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",
    "extra/restez.html",
    "manual.pdf"
  ],
  "_homeurl": "https://github.com/ropensci/restez",
  "_realowner": "ropensci",
  "_cranurl": true,
  "_releases": [
    {
      "version": "1.0.0",
      "date": "2018-11-26"
    },
    {
      "version": "2.1.2",
      "date": "2022-09-05"
    },
    {
      "version": "2.1.3",
      "date": "2022-11-11"
    },
    {
      "version": "2.1.4",
      "date": "2023-10-25"
    },
    {
      "version": "2.1.5",
      "date": "2025-03-07"
    }
  ],
  "_exports": [
    "count_db_ids",
    "db_create",
    "db_delete",
    "db_download",
    "demo_db_create",
    "entrez_fetch",
    "gb_definition_get",
    "gb_extract",
    "gb_fasta_get",
    "gb_organism_get",
    "gb_record_get",
    "gb_sequence_get",
    "gb_version_get",
    "is_in_db",
    "list_db_ids",
    "ncbi_acc_get",
    "restez_connect",
    "restez_disconnect",
    "restez_path_get",
    "restez_path_set",
    "restez_path_unset",
    "restez_ready",
    "restez_status"
  ],
  "_datasets": [
    {
      "name": "record",
      "title": "Example GenBank record",
      "object": "record",
      "class": [
        "character"
      ],
      "fields": [],
      "table": false,
      "tojson": true
    }
  ],
  "_help": [
    {
      "page": "add_rcrd_log",
      "title": "Log files added to the SQL database in the restez path",
      "concept": [
        "private"
      ],
      "topics": [
        "add_rcrd_log"
      ]
    },
    {
      "page": "cat_line",
      "title": "Cat lines",
      "concept": [
        "private"
      ],
      "topics": [
        "cat_line"
      ]
    },
    {
      "page": "char",
      "title": "Print green",
      "concept": [
        "private"
      ],
      "topics": [
        "char"
      ]
    },
    {
      "page": "check_connection",
      "title": "Helper function to test if a stable internet connection can be established.",
      "concept": [
        "private"
      ],
      "topics": [
        "check_connection"
      ]
    },
    {
      "page": "cleanup",
      "title": "Clean up test data",
      "concept": [
        "private"
      ],
      "topics": [
        "cleanup"
      ]
    },
    {
      "page": "connected",
      "title": "Is restez connected?",
      "concept": [
        "private"
      ],
      "topics": [
        "connected"
      ]
    },
    {
      "page": "connection_get",
      "title": "Retrieve restez connection",
      "concept": [
        "private"
      ],
      "topics": [
        "connection_get"
      ]
    },
    {
      "page": "count_db_ids",
      "title": "Return the number of ids",
      "concept": [
        "database"
      ],
      "topics": [
        "count_db_ids"
      ]
    },
    {
      "page": "db_create",
      "title": "Create new NCBI database",
      "concept": [
        "database"
      ],
      "topics": [
        "db_create"
      ]
    },
    {
      "page": "db_delete",
      "title": "Delete database",
      "concept": [
        "database"
      ],
      "topics": [
        "db_delete"
      ]
    },
    {
      "page": "db_download",
      "title": "Download database",
      "concept": [
        "database"
      ],
      "topics": [
        "db_download"
      ]
    },
    {
      "page": "db_download_intern",
      "title": "Download database (internal version)",
      "concept": [
        "private"
      ],
      "topics": [
        "db_download_intern"
      ]
    },
    {
      "page": "db_sqlngths_get",
      "title": "Return the minimum and maximum sequence lengths in db",
      "concept": [
        "private"
      ],
      "topics": [
        "db_sqlngths_get"
      ]
    },
    {
      "page": "db_sqlngths_log",
      "title": "Log the min and max sequence lengths",
      "concept": [
        "private"
      ],
      "topics": [
        "db_sqlngths_log"
      ]
    },
    {
      "page": "demo_db_create",
      "title": "Create demo database",
      "concept": [
        "database"
      ],
      "topics": [
        "demo_db_create"
      ]
    },
    {
      "page": "dir_size",
      "title": "Calculate the size of a directory",
      "concept": [
        "private"
      ],
      "topics": [
        "dir_size"
      ]
    },
    {
      "page": "dwnld_path_get",
      "title": "Get dwnld path",
      "concept": [
        "private"
      ],
      "topics": [
        "dwnld_path_get"
      ]
    },
    {
      "page": "dwnld_rcrd_log",
      "title": "Log a downloaded file in the restez path",
      "concept": [
        "private"
      ],
      "topics": [
        "dwnld_rcrd_log"
      ]
    },
    {
      "page": "entrez_fasta_get",
      "title": "Get Entrez fasta",
      "concept": [
        "private"
      ],
      "topics": [
        "entrez_fasta_get"
      ]
    },
    {
      "page": "entrez_fetch",
      "title": "Entrez fetch",
      "concept": [
        "entrez"
      ],
      "topics": [
        "entrez_fetch"
      ]
    },
    {
      "page": "entrez_gb_get",
      "title": "Get Entrez GenBank record",
      "concept": [
        "private"
      ],
      "topics": [
        "entrez_gb_get"
      ]
    },
    {
      "page": "extract_accession",
      "title": "Extract accession",
      "concept": [
        "private"
      ],
      "topics": [
        "extract_accession"
      ]
    },
    {
      "page": "extract_by_patterns",
      "title": "Extract by keyword",
      "concept": [
        "private"
      ],
      "topics": [
        "extract_by_patterns"
      ]
    },
    {
      "page": "extract_clean_sequence",
      "title": "Extract clean sequence from sequence part",
      "concept": [
        "private"
      ],
      "topics": [
        "extract_clean_sequence"
      ]
    },
    {
      "page": "extract_definition",
      "title": "Extract definition",
      "concept": [
        "private"
      ],
      "topics": [
        "extract_definition"
      ]
    },
    {
      "page": "extract_features",
      "title": "Extract features",
      "concept": [
        "private"
      ],
      "topics": [
        "extract_features"
      ]
    },
    {
      "page": "extract_inforecpart",
      "title": "Extract the information record part",
      "concept": [
        "private"
      ],
      "topics": [
        "extract_inforecpart"
      ]
    },
    {
      "page": "extract_keywords",
      "title": "Extract keywords",
      "concept": [
        "private"
      ],
      "topics": [
        "extract_keywords"
      ]
    },
    {
      "page": "extract_locus",
      "title": "Extract locus",
      "concept": [
        "private"
      ],
      "topics": [
        "extract_locus"
      ]
    },
    {
      "page": "extract_organism",
      "title": "Extract organism",
      "concept": [
        "private"
      ],
      "topics": [
        "extract_organism"
      ]
    },
    {
      "page": "extract_seqrecpart",
      "title": "Extract the sequence record part",
      "concept": [
        "private"
      ],
      "topics": [
        "extract_seqrecpart"
      ]
    },
    {
      "page": "extract_sequence",
      "title": "Extract sequence",
      "concept": [
        "private"
      ],
      "topics": [
        "extract_sequence"
      ]
    },
    {
      "page": "extract_version",
      "title": "Extract version",
      "concept": [
        "private"
      ],
      "topics": [
        "extract_version"
      ]
    },
    {
      "page": "file_download",
      "title": "Download a file",
      "concept": [
        "private"
      ],
      "topics": [
        "file_download"
      ]
    },
    {
      "page": "filename_log",
      "title": "Write filenames to log files",
      "concept": [
        "private"
      ],
      "topics": [
        "filename_log"
      ]
    },
    {
      "page": "flatfile_read",
      "title": "Read flatfile sequence records",
      "concept": [
        "private"
      ],
      "topics": [
        "flatfile_read"
      ]
    },
    {
      "page": "gb_build",
      "title": "Read and add .seq files to database",
      "concept": [
        "private"
      ],
      "topics": [
        "gb_build"
      ]
    },
    {
      "page": "gb_definition_get",
      "title": "Get definition from GenBank",
      "concept": [
        "get"
      ],
      "topics": [
        "gb_definition_get"
      ]
    },
    {
      "page": "gb_df_create",
      "title": "Create GenBank data.frame",
      "concept": [
        "private"
      ],
      "topics": [
        "gb_df_create"
      ]
    },
    {
      "page": "gb_df_generate",
      "title": "Generate GenBank records data.frame",
      "concept": [
        "private"
      ],
      "topics": [
        "gb_df_generate"
      ]
    },
    {
      "page": "gb_extract",
      "title": "Extract elements of a GenBank record",
      "concept": [
        "parse"
      ],
      "topics": [
        "gb_extract"
      ]
    },
    {
      "page": "gb_fasta_get",
      "title": "Get fasta from GenBank",
      "concept": [
        "get"
      ],
      "topics": [
        "gb_fasta_get"
      ]
    },
    {
      "page": "gb_organism_get",
      "title": "Get organism from GenBank",
      "concept": [
        "get"
      ],
      "topics": [
        "gb_organism_get"
      ]
    },
    {
      "page": "gb_record_get",
      "title": "Get record from GenBank",
      "concept": [
        "get"
      ],
      "topics": [
        "gb_record_get"
      ]
    },
    {
      "page": "gb_sequence_get",
      "title": "Get sequence from GenBank",
      "concept": [
        "get"
      ],
      "topics": [
        "gb_sequence_get"
      ]
    },
    {
      "page": "gb_sql_add",
      "title": "Add to GenBank SQL database",
      "concept": [
        "private"
      ],
      "topics": [
        "gb_sql_add"
      ]
    },
    {
      "page": "gb_sql_query",
      "title": "Query the GenBank SQL",
      "concept": [
        "private"
      ],
      "topics": [
        "gb_sql_query"
      ]
    },
    {
      "page": "gb_version_get",
      "title": "Get version from GenBank",
      "concept": [
        "get"
      ],
      "topics": [
        "gb_version_get"
      ]
    },
    {
      "page": "gbrelease_check",
      "title": "Check if the last GenBank release number is the latest",
      "concept": [
        "private"
      ],
      "topics": [
        "gbrelease_check"
      ]
    },
    {
      "page": "gbrelease_get",
      "title": "Get the GenBank release number in the restez path",
      "concept": [
        "private"
      ],
      "topics": [
        "gbrelease_get"
      ]
    },
    {
      "page": "gbrelease_log",
      "title": "Log the GenBank release number in the restez path",
      "concept": [
        "private"
      ],
      "topics": [
        "gbrelease_log"
      ]
    },
    {
      "page": "has_data",
      "title": "Does the connected database have data?",
      "concept": [
        "private"
      ],
      "topics": [
        "has_data"
      ]
    },
    {
      "page": "identify_downloadable_files",
      "title": "Identify downloadable files",
      "concept": [
        "private"
      ],
      "topics": [
        "identify_downloadable_files"
      ]
    },
    {
      "page": "is_in_db",
      "title": "Is in db",
      "concept": [
        "database"
      ],
      "topics": [
        "is_in_db"
      ]
    },
    {
      "page": "last_add_get",
      "title": "Return date and time of the last added sequence",
      "concept": [
        "private"
      ],
      "topics": [
        "last_add_get"
      ]
    },
    {
      "page": "last_dwnld_get",
      "title": "Return date and time of the last download",
      "concept": [
        "private"
      ],
      "topics": [
        "last_dwnld_get"
      ]
    },
    {
      "page": "last_entry_get",
      "title": "Return the last entry",
      "concept": [
        "private"
      ],
      "topics": [
        "last_entry_get"
      ]
    },
    {
      "page": "latest_genbank_release",
      "title": "Retrieve latest GenBank release number",
      "concept": [
        "private"
      ],
      "topics": [
        "latest_genbank_release"
      ]
    },
    {
      "page": "latest_genbank_release_notes",
      "title": "Download the latest GenBank Release Notes",
      "concept": [
        "private"
      ],
      "topics": [
        "latest_genbank_release_notes"
      ]
    },
    {
      "page": "list_db_ids",
      "title": "List database IDs",
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