{ "_id": "6a1ae9ae1d7bb097a09f2c34", "Package": "rfaRm", "Type": "Package", "Title": "An R interface to the Rfam database", "Version": "1.25.0", "Date": "2024-01-25", "Author": "Lara Selles Vidal, Rafael Ayala, Guy-Bart Stan, Rodrigo\nLedesma-Amaro", "Maintainer": "Lara Selles Vidal , Rafael Ayala\n", "Description": "rfaRm provides a client interface to the Rfam database of\nRNA families. Data that can be retrieved include RNA families,\nsecondary structure images, covariance models, sequences within\neach family, alignments leading to the identification of a\nfamily and secondary structures in the dot-bracket format.", "License": "GPL-3", "VignetteBuilder": "knitr", "biocViews": "FunctionalGenomics, DataImport, ThirdPartyClient,\nVisualization, MultipleSequenceAlignment", "NeedsCompilation": "no", "Encoding": "UTF-8", "Config/pak/sysreqs": "libmagick++-dev gsfonts libicu-dev librsvg2-dev\nlibxml2-dev libssl-dev zlib1g-dev", "Repository": "https://bioc.r-universe.dev", "Date/Publication": "2026-04-28 12:52:29 UTC", "RemoteUrl": "https://github.com/bioc/rfaRm", "RemoteRef": "HEAD", "RemoteSha": "f38b5b47045f22f196a678626a349d84d14cdbc7", "Packaged": { "Date": "2026-05-30 09:38:49 UTC", "User": "root" }, "MD5sum": "d2c3ca0895760195e9dc37360ab848dc", "_user": "bioc", "_type": "src", "_file": "rfaRm_1.25.0.tar.gz", "_fileid": "2446207548723d6b923d6689f633942d2e56f16ee566d40930fc67177e19e2fe", "_filesize": 256622, "_sha256": "2446207548723d6b923d6689f633942d2e56f16ee566d40930fc67177e19e2fe", "_created": "2026-05-30T09:38:49.000Z", "_published": "2026-05-30T13:44:14.013Z", "_jobs": [ { "job": 78640189180, "time": 145, "config": "bioc-checks", "r": "4.6.0", "check": "ERROR", "artifact": "7307350807" }, { "job": 78640189181, "time": 332, "config": "linux-devel-x86_64", "r": "4.7.0", "check": "ERROR", "artifact": "7307368144" }, { "job": 78640189190, "time": 317, "config": "linux-release-x86_64", "r": "4.6.0", "check": "ERROR", "artifact": "7307366632" }, { "job": 78640189186, "time": 176, "config": "macos-oldrel-arm64", "r": "4.5.3", "check": "ERROR", "artifact": "7308607202" }, { "job": 78640189184, "time": 173, "config": "macos-release-arm64", "r": "4.6.0", "check": "ERROR", "artifact": "7308606133" }, { "job": 78639546836, "time": 250, "config": "source", "r": "4.6.0", "check": "ERROR", "artifact": "7307239295" }, { "job": 78640189179, "time": 142, "config": "wasm-release", "r": "4.6.0", "check": "OK", "artifact": "7307350479" }, { "job": 78640189204, "time": 176, "config": "windows-devel", "r": "4.7.0", "check": "ERROR", "artifact": "7307352805" }, { "job": 78640189221, "time": 176, "config": "windows-oldrel", "r": "4.5.3", "check": "ERROR", "artifact": "7307352828" }, { "job": 78640189185, "time": 178, "config": "windows-release", "r": "4.6.0", "check": "ERROR", "artifact": "7307352913" } ], "_bioccheck": { "error": 1, "warning": 0, "note": 12 }, "_buildurl": "https://github.com/r-universe/bioc/actions/runs/26676180716", "_status": "failure", "_host": "GitHub-Actions", "_upstream": "https://github.com/bioc/rfaRm", "_commit": { "id": "f38b5b47045f22f196a678626a349d84d14cdbc7", "author": "A Wokaty ", "committer": "A Wokaty ", "message": "bump x.y.z version to odd y following creation of RELEASE_3_23 branch\n", "time": 1777380749 }, "_maintainer": { "name": "Lara Selles Vidal", "email": "rafael.ayala@oist.jp", "login": "larasellesvidal", "description": "", "uuid": 63247480 }, "_distro": "noble", "_registered": true, "_dependencies": [ { "package": "httr", "role": "Imports" }, { "package": "stringi", "role": "Imports" }, { "package": "rsvg", "role": "Imports" }, { "package": "magick", "role": "Imports" }, { "package": "data.table", "role": "Imports" }, { "package": "Biostrings", "role": "Imports" }, { "package": "utils", "role": "Imports" }, { "package": "rvest", "role": "Imports" }, { "package": "xml2", "role": "Imports" }, { "package": "IRanges", "role": "Imports" }, { "package": "S4Vectors", "role": "Imports" }, { "package": "jsonlite", "role": "Imports" }, { "package": "R4RNA", "role": "Suggests" }, { "package": "treeio", "role": "Suggests" }, { "package": "knitr", "role": "Suggests" }, { "package": "BiocStyle", "role": "Suggests" }, { "package": "rmarkdown", "role": "Suggests" }, { "package": "BiocGenerics", "role": "Suggests" }, { "package": "RUnit", "role": "Suggests" } ], "_owner": "bioc", "_selfowned": true, "_usedby": 0, "_updates": [ { "week": "2025-44", "n": 2 }, { "week": "2026-18", "n": 2 } ], "_tags": [], "_bioc": [ { "branch": "devel", "version": "1.25.0", "bioc": "3.24" }, { "branch": "release", "version": "1.23.0", "bioc": "3.23" } ], "_topics": [ "functionalgenomics", "dataimport", "thirdpartyclient", "visualization", "multiplesequencealignment" ], "_userbio": { "uuid": 2286807, "type": "organization", "name": "Bioconductor", "description": "Software for the analysis and comprehension of high-throughput genomic data" }, "_downloads": { "count": 354, "source": "https://www.bioconductor.org/packages/stats/bioc/rfaRm" }, "_mentions": 1, "_searchresults": 1, "_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/rfaRm.html", "manual.pdf" ], "_realowner": "bioc", "_cranurl": false, "_exports": [ "rfamConsensusSecondaryStructure", "rfamCovarianceModel", "rfamFamilyAccessionToID", "rfamFamilyIDToAccession", "rfamFamilySummary", "rfamPDBMapping", "rfamSecondaryStructurePlot", "rfamSecondaryStructureXMLSVG", "rfamSeedAlignment", "rfamSeedTree", "rfamSeedTreeImage", "rfamSequenceRegions", "rfamSequenceSearch", "rfamTextSearchFamilyAccession" ], "_help": [ { "page": "rfamConsensusSecondaryStructure", "title": "Retrieve the secondary structure of an Rfam family", "topics": [ "rfamConsensusSecondaryStructure" ] }, { "page": "rfamCovarianceModel", "title": "Get the covariance model associated to an Rfam family", "topics": [ "rfamCovarianceModel" ] }, { "page": "rfamFamilyAccessionToID", "title": "Convert an Rfam family accession to an Rfam family ID", "topics": [ "rfamFamilyAccessionToID" ] }, { "page": "rfamFamilyIDToAccession", "title": "Convert an Rfam family ID to an Rfam family accession", "topics": [ "rfamFamilyIDToAccession" ] }, { "page": "rfamFamilySummary", "title": "Get a summary describing an Rfam family", "topics": [ "rfamFamilySummary" ] }, { "page": "rfamPDBMapping", "title": "Retrieve PDB entries with the 3D structure of members of an Rfam family", "topics": [ "rfamPDBMapping" ] }, { "page": "rfamSecondaryStructurePlot", "title": "Generate a diagram of the secondary structure of an Rfam family", "topics": [ "rfamSecondaryStructurePlot" ] }, { "page": "rfamSecondaryStructureXMLSVG", "title": "Get an SVG file with a secondary structure representation of an Rfam family", "topics": [ "rfamSecondaryStructureXMLSVG" ] }, { "page": "rfamSeedAlignment", "title": "Retrieve the seed alignment of an Rfam family", "topics": [ "rfamSeedAlignment" ] }, { "page": "rfamSeedTree", "title": "Get the phylogenetic tree of the seed multiple alignment of an Rfam family", "topics": [ "rfamSeedTree" ] }, { "page": "rfamSeedTreeImage", "title": "Get an image of the phylogenetic tree of the seed multiple alignment of an Rfam family", "topics": [ "rfamSeedTreeImage" ] }, { "page": "rfamSequenceRegions", "title": "Retrieve all sequence regions belonging to an Rfam family", "topics": [ "rfamSequenceRegions" ] }, { "page": "rfamSequenceSearch", "title": "Performs a sequence search of the Rfam database", "topics": [ "rfamSequenceSearch" ] }, { "page": "rfamTextSearchFamilyAccession", "title": "Search the Rfam database by a given keyword", "topics": [ "rfamTextSearchFamilyAccession" ] } ], "_rundeps": [ "askpass", "BiocGenerics", "Biostrings", "cli", "crayon", "curl", "data.table", "generics", "glue", "httr", "IRanges", "jsonlite", "lifecycle", "magick", "magrittr", "mime", "openssl", "pillar", "pkgconfig", "R6", "Rcpp", "rlang", "rsvg", "rvest", "S4Vectors", "selectr", "Seqinfo", "stringi", "stringr", "sys", "tibble", "utf8", "vctrs", "xml2", "XVector" ], "_score": 2.3010299956639813, "_indexed": true, "_nocasepkg": "rfarm", "_universes": [ "bioc", "larasellesvidal" ], "_binaries": [ { "r": "4.7.0", "os": "linux", "version": "1.25.0", "date": "2026-05-30T09:58:53.000Z", "distro": "noble", "commit": "f38b5b47045f22f196a678626a349d84d14cdbc7", "fileid": "f6fe2fb579c45e81bbb35f1fac0a10cbc619de019475f83edd22c31194abf7ca", "status": "failure", "check": "ERROR", "buildurl": "https://github.com/r-universe/bioc/actions/runs/26676180716" }, { "r": "4.6.0", "os": "linux", "version": "1.25.0", "date": "2026-05-30T09:58:47.000Z", "distro": "noble", "commit": "f38b5b47045f22f196a678626a349d84d14cdbc7", "fileid": "49d3e3b5f282e1fc854082de4c7ddf46a89b52389f0ca96d9b960918ad87d8f2", "status": "failure", "check": "ERROR", "buildurl": "https://github.com/r-universe/bioc/actions/runs/26676180716" }, { "r": "4.5.3", "os": "mac", "version": "1.25.0", "date": "2026-05-30T13:42:33.000Z", "commit": "f38b5b47045f22f196a678626a349d84d14cdbc7", "fileid": "251e34679715ac0af48dc6a766eccae5fb17190c5304dcdccf60c4a4c7b1a362", "status": "failure", "check": "ERROR", "buildurl": "https://github.com/r-universe/bioc/actions/runs/26676180716" }, { "r": "4.6.0", "os": "mac", "version": "1.25.0", "date": "2026-05-30T13:42:12.000Z", "commit": "f38b5b47045f22f196a678626a349d84d14cdbc7", "fileid": "072b4e573b9278302ebabad727d51e9f88a42a94bc45beedd3a52bca13a63faa", "status": "failure", "check": "ERROR", "buildurl": "https://github.com/r-universe/bioc/actions/runs/26676180716" }, { "r": "4.6.0", "os": "wasm", "version": "1.25.0", "date": "2026-05-30T09:57:48.000Z", "commit": "f38b5b47045f22f196a678626a349d84d14cdbc7", "fileid": "082c0037d7eec37bafd6ae32b4c3fa57f8129202b1ddf6a46042eaa0f3e9da4b", "status": "success", "buildurl": "https://github.com/r-universe/bioc/actions/runs/26676180716" }, { "r": "4.7.0", "os": "win", "version": "1.25.0", "date": "2026-05-30T09:56:17.000Z", "commit": "f38b5b47045f22f196a678626a349d84d14cdbc7", "fileid": "9162e1272167e0bae5e64d28a36943e6f7472114daa9b818eb92297a704f697e", "status": "failure", "check": "ERROR", "buildurl": "https://github.com/r-universe/bioc/actions/runs/26676180716" }, { "r": "4.5.3", "os": "win", "version": "1.25.0", "date": "2026-05-30T09:56:23.000Z", "commit": "f38b5b47045f22f196a678626a349d84d14cdbc7", "fileid": "3cbb98bfcf99e2909db0b5f74e43f21dc464ea6fdc4c0a05051174b3b97389ce", "status": "failure", "check": "ERROR", "buildurl": "https://github.com/r-universe/bioc/actions/runs/26676180716" }, { "r": "4.6.0", "os": "win", "version": "1.25.0", "date": "2026-05-30T09:56:11.000Z", "commit": "f38b5b47045f22f196a678626a349d84d14cdbc7", "fileid": "f70ad602dc013e76de1d9d4b1f9edbf865990bb2cb40daa5c36bf395f488abd3", "status": "failure", "check": "ERROR", "buildurl": "https://github.com/r-universe/bioc/actions/runs/26676180716" } ] }