{ "_id": "6a37c33c3efcd9bda442d592", "Package": "Rhisat2", "Type": "Package", "Title": "R Wrapper for HISAT2 Aligner", "Version": "1.28.0", "Authors@R": "c(person(\"Charlotte\", \"Soneson\", role = c(\"aut\", \"cre\"), \nemail = \"charlottesoneson@gmail.com\", comment = c(ORCID = \"0000-0003-3833-2169\")))", "SystemRequirements": "GNU make", "Description": "An R interface to the HISAT2 spliced short-read aligner by\nKim et al. (2015). The package contains wrapper functions to\ncreate a genome index and to perform the read alignment to the\ngenerated index.", "License": "GPL-3", "Encoding": "UTF-8", "RoxygenNote": "7.3.1", "VignetteBuilder": "knitr", "biocViews": "Alignment, Sequencing, SplicedAlignment", "URL": "https://github.com/fmicompbio/Rhisat2", "BugReports": "https://github.com/fmicompbio/Rhisat2/issues", "Archs": "x64", "Config/pak/sysreqs": "libglpk-dev make libbz2-dev libicu-dev liblzma-dev\nlibpng-dev libxml2-dev libssl-dev xz-utils zlib1g-dev", "Repository": "https://bioc-release.r-universe.dev", "Date/Publication": "2026-04-28 12:49:25 UTC", "RemoteUrl": "https://github.com/bioc/Rhisat2", "RemoteRef": "RELEASE_3_23", "RemoteSha": "74b81caf0ed92cd090f17336fa9ce33af16204a1", "NeedsCompilation": "yes", "Packaged": { "Date": "2026-06-21 10:43:31 UTC", "User": "root" }, "Author": "Charlotte Soneson [aut, cre] (ORCID:\n)", "Maintainer": "Charlotte Soneson ", "MD5sum": "903d57d4b8ea9f6a4e450b3200e46d94", "_user": "bioc-release", "_type": "src", "_file": "Rhisat2_1.28.0.tar.gz", "_fileid": "f0da78309dae4a9c135813a6cd7bdde5dcc33f96a59d41bec71a2ba2d50341e7", "_filesize": 7006478, "_sha256": "f0da78309dae4a9c135813a6cd7bdde5dcc33f96a59d41bec71a2ba2d50341e7", "_created": "2026-06-21T10:43:31.000Z", "_published": "2026-06-21T10:55:56.445Z", "_jobs": [ { "job": 82563483265, "time": 303, "config": "bioc-checks", "r": "4.6.0", "check": "NOTE", "artifact": "7774553113" }, { "job": 82563483307, "time": 432, "config": "linux-devel-arm64", "r": "4.7.0", "check": "WARNING", "artifact": "7774567685" }, { "job": 82563483300, "time": 521, "config": "linux-devel-x86_64", "r": "4.7.0", "check": "WARNING", "artifact": "7774576975" }, { "job": 82563483299, "time": 425, "config": "linux-release-arm64", "r": "4.6.0", "check": "WARNING", "artifact": "7774566871" }, { "job": 82563483292, "time": 562, "config": "linux-release-x86_64", "r": "4.6.0", "check": "WARNING", "artifact": "7774581446" }, { "job": 82563483311, "time": 228, "config": "macos-oldrel-arm64", "r": "4.5.3", "check": "WARNING", "artifact": "7774544402" }, { "job": 82563483303, "time": 529, "config": "macos-oldrel-x86_64", "r": "4.5.3", "check": "WARNING", "artifact": "7774578286" }, { "job": 82563483310, "time": 280, "config": "macos-release-arm64", "r": "4.6.0", "check": "WARNING", "artifact": "7774550508" }, { "job": 82563483302, "time": 495, "config": "macos-release-x86_64", "r": "4.6.0", "check": "WARNING", "artifact": "7774574567" }, { "job": 82562965182, "time": 502, "config": "source", "r": "4.6.0", "check": "OK", "artifact": "7774518967" }, { "job": 82563483264, "time": 149, "config": "wasm-release", "r": "4.6.0", "check": "FAIL", "artifact": "" }, { "job": 82563483286, "time": 519, "config": "windows-devel", "r": "4.7.0", "check": "WARNING", "artifact": "7774576862" }, { "job": 82563483288, "time": 542, "config": "windows-oldrel", "r": "4.5.3", "check": "WARNING", "artifact": "7774579481" }, { "job": 82563483283, "time": 492, "config": "windows-release", "r": "4.6.0", "check": "WARNING", "artifact": "7774574017" } ], "_bioccheck": { "error": 0, "warning": 0, "note": 8 }, "_buildurl": "https://github.com/r-universe/bioc-release/actions/runs/27901664606", "_status": "success", "_host": "GitHub-Actions", "_upstream": "https://github.com/bioc/Rhisat2", "_commit": { "id": "74b81caf0ed92cd090f17336fa9ce33af16204a1", "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": 1777380565 }, "_maintainer": { "name": "Charlotte Soneson", "email": "charlottesoneson@gmail.com", "login": "csoneson", "orcid": "0000-0003-3833-2169", "description": "", "uuid": 5628952 }, "_distro": "noble", "_registered": true, "_dependencies": [ { "package": "R", "version": ">= 4.4.0", "role": "Depends" }, { "package": "txdbmaker", "role": "Imports" }, { "package": "SGSeq", "role": "Imports" }, { "package": "GenomicRanges", "role": "Imports" }, { "package": "methods", "role": "Imports" }, { "package": "utils", "role": "Imports" }, { "package": "testthat", "role": "Suggests" }, { "package": "knitr", "role": "Suggests" }, { "package": "rmarkdown", "role": "Suggests" }, { "package": "BiocStyle", "role": "Suggests" } ], "_owner": "bioc", "_selfowned": false, "_usedby": 1, "_updates": [ { "week": "2025-44", "n": 2 }, { "week": "2026-18", "n": 1 } ], "_tags": [], "_bioc": [ { "branch": "devel", "version": "1.29.0", "bioc": "3.24" }, { "branch": "release", "version": "1.28.0", "bioc": "3.23" } ], "_topics": [ "alignment", "sequencing", "splicedalignment", "cpp" ], "_stars": 3, "_contributors": [ { "user": "csoneson", "count": 164, "uuid": 5628952 }, { "user": "mbstadler", "count": 19, "uuid": 13657342 }, { "user": "jwokaty", "count": 16, "uuid": 1744257 }, { "user": "nturaga", "count": 14, "uuid": 2746443 }, { "user": "hpages", "count": 2, "uuid": 8810451 } ], "_userbio": { "uuid": 2286807, "type": "organization", "name": "Bioconductor", "followers": 440, "description": "Software for the analysis and comprehension of high-throughput genomic data" }, "_devurl": "https://github.com/fmicompbio/rhisat2", "_searchresults": 8, "_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/readme.html", "extra/readme.md", "extra/Rhisat2.html", "LICENSE", "manual.pdf" ], "_homeurl": "https://github.com/fmicompbio/rhisat2", "_realowner": "bioc", "_cranurl": false, "_exports": [ "extract_splice_sites", "hisat2", "hisat2_build", "hisat2_build_usage", "hisat2_usage", "hisat2_version" ], "_help": [ { "page": "extract_splice_sites", "title": "Extract splice sites from annotation", "topics": [ "extract_splice_sites" ] }, { "page": "hisat2", "title": "Align reads with HISAT2", "topics": [ "hisat2" ] }, { "page": "hisat2_build", "title": "Generate HISAT2 index", "topics": [ "hisat2_build" ] }, { "page": "hisat2_build_usage", "title": "Print usage of hisat2-build", "topics": [ "hisat2_build_usage" ] }, { "page": "hisat2_usage", "title": "Print usage of hisat2", "topics": [ "hisat2_usage" ] }, { "page": "hisat2_version", "title": "Print HISAT2 version", "topics": [ "hisat2_version" ] } ], "_readme": "https://github.com/bioc/Rhisat2/raw/RELEASE_3_23/README.md", "_rundeps": [ "abind", "AnnotationDbi", "askpass", "BH", "Biobase", "BiocFileCache", "BiocGenerics", "BiocIO", "BiocParallel", "biomaRt", "Biostrings", "bit", "bit64", "bitops", "blob", "cachem", "cigarillo", "cli", "codetools", "cpp11", "crayon", "curl", "DBI", "dbplyr", "DelayedArray", "dplyr", "fastmap", "filelock", "formatR", "futile.logger", "futile.options", "generics", "GenomeInfoDb", "GenomicAlignments", "GenomicFeatures", "GenomicRanges", "glue", "hms", "httr", "httr2", "igraph", "IRanges", "jsonlite", "KEGGREST", "lambda.r", "lattice", "lifecycle", "magrittr", "Matrix", "MatrixGenerics", "matrixStats", "memoise", "mime", "openssl", "pillar", "pkgconfig", "png", "prettyunits", "progress", "purrr", "R6", "rappdirs", "RCurl", "restfulr", "Rhtslib", "rjson", "rlang", "Rsamtools", "RSQLite", "rtracklayer", "RUnit", "S4Arrays", "S4Vectors", "Seqinfo", "SGSeq", "snow", "SparseArray", "stringi", "stringr", "SummarizedExperiment", "sys", "tibble", "tidyr", "tidyselect", "txdbmaker", "UCSC.utils", "utf8", "vctrs", "withr", "XML", "xml2", "XVector", "yaml" ], "_sysdeps": [ { "shlib": "libstdc++", "package": "libstdc++6", "source": "gcc", "version": "14.2.0-4ubuntu2~24.04.1", "name": "c++", "homepage": "http://gcc.gnu.org/", "description": "GNU Standard C++ Library v3" } ], "_vignettes": [ { "source": "Rhisat2.Rmd", "filename": "Rhisat2.html", "title": "Aligning reads with Rhisat2", "author": "Charlotte Soneson", "engine": "knitr::rmarkdown", "headings": [ "Installation", "Building a genome index", "Aligning reads to the genome index", "Miscellaneous helper functions", "Session info", "References" ], "created": "2018-10-17 13:28:10", "modified": "2019-02-01 07:32:13", "commits": 8 } ], "_score": 5.556302500767288, "_indexed": false, "_nocasepkg": "rhisat2", "_universes": [ "bioc-release" ], "_indexurl": "https://bioc.r-universe.dev/Rhisat2", "_binaries": [ { "r": "4.7.0", "os": "linux", "version": "1.28.0", "date": "2026-06-21T10:48:49.000Z", "distro": "noble", "arch": "aarch64", "commit": "74b81caf0ed92cd090f17336fa9ce33af16204a1", "fileid": "d2a86a6ba2904adc686e28fd8ddf8860a27355f2b975d3e8516b282fd046a680", "status": "success", "check": "WARNING", "buildurl": "https://github.com/r-universe/bioc-release/actions/runs/27901664606" }, { "r": "4.7.0", "os": "linux", "version": "1.28.0", "date": "2026-06-21T10:49:35.000Z", "distro": "noble", "arch": "x86_64", "commit": "74b81caf0ed92cd090f17336fa9ce33af16204a1", "fileid": "3898dc0ff7472329d2af59399915ecf6ea424ce2f27dc0f3886b6e5d80f9a9e6", "status": "success", "check": "WARNING", "buildurl": "https://github.com/r-universe/bioc-release/actions/runs/27901664606" }, { "r": "4.6.0", "os": "linux", "version": "1.28.0", "date": "2026-06-21T10:48:43.000Z", "distro": "noble", "arch": "aarch64", "commit": "74b81caf0ed92cd090f17336fa9ce33af16204a1", "fileid": "c0756439d127956e728e769f2c105466f29aa537e510a89fbd07ccc207ed0362", "status": "success", "check": "WARNING", "buildurl": "https://github.com/r-universe/bioc-release/actions/runs/27901664606" }, { "r": "4.6.0", "os": "linux", "version": "1.28.0", "date": "2026-06-21T10:49:58.000Z", "distro": "noble", "arch": "x86_64", "commit": "74b81caf0ed92cd090f17336fa9ce33af16204a1", "fileid": "71b5886d438e2a9211ce1bcb0c40122ca39f3447918fd2f9f7ab80bbc66f8981", "status": "success", "check": "WARNING", "buildurl": "https://github.com/r-universe/bioc-release/actions/runs/27901664606" }, { "r": "4.5.3", "os": "mac", "version": "1.28.0", "date": "2026-06-21T10:47:19.000Z", "arch": "aarch64", "commit": "74b81caf0ed92cd090f17336fa9ce33af16204a1", "fileid": "9d7ca54fdfa41971700582e50321a00faf2f60c15c16577f62ac9b85f76153f5", "status": "success", "check": "WARNING", "buildurl": "https://github.com/r-universe/bioc-release/actions/runs/27901664606" }, { "r": "4.5.3", "os": "mac", "version": "1.28.0", "date": "2026-06-21T10:48:42.000Z", "arch": "x86_64", "commit": "74b81caf0ed92cd090f17336fa9ce33af16204a1", "fileid": "365d00240648ac72dc18e80de61acbb92928a2d0abbcfb6a6213b02857b41cbc", "status": "success", "check": "WARNING", "buildurl": "https://github.com/r-universe/bioc-release/actions/runs/27901664606" }, { "r": "4.6.0", "os": "mac", "version": "1.28.0", "date": "2026-06-21T10:47:34.000Z", "arch": "aarch64", "commit": "74b81caf0ed92cd090f17336fa9ce33af16204a1", "fileid": "b57b89a137a96b8a03bd3fd57a5edac00b71d7be20ca9837f17977430552ea67", "status": "success", "check": "WARNING", "buildurl": "https://github.com/r-universe/bioc-release/actions/runs/27901664606" }, { "r": "4.6.0", "os": "mac", "version": "1.28.0", "date": "2026-06-21T10:48:38.000Z", "arch": "x86_64", "commit": "74b81caf0ed92cd090f17336fa9ce33af16204a1", "fileid": "0f56b8e0bda3f0b66d647c051b6b0a66a43c1b44120f558c6a24e1e37e1543b9", "status": "success", "check": "WARNING", "buildurl": "https://github.com/r-universe/bioc-release/actions/runs/27901664606" }, { "r": "4.7.0", "os": "win", "version": "1.28.0", "date": "2026-06-21T10:47:50.000Z", "arch": "x86_64", "commit": "74b81caf0ed92cd090f17336fa9ce33af16204a1", "fileid": "5cd8ce459fb71d988b9ecf2c7b06f17275b76e5762caa48d7b3ac9a480a3e1ac", "status": "success", "check": "WARNING", "buildurl": "https://github.com/r-universe/bioc-release/actions/runs/27901664606" }, { "r": "4.5.3", "os": "win", "version": "1.28.0", "date": "2026-06-21T10:47:53.000Z", "arch": "x86_64", "commit": "74b81caf0ed92cd090f17336fa9ce33af16204a1", "fileid": "a64f4b5768bae3f48830975509e129a75e88b98b20b8bfd16cf5c969676c2dd8", "status": "success", "check": "WARNING", "buildurl": "https://github.com/r-universe/bioc-release/actions/runs/27901664606" }, { "r": "4.6.0", "os": "win", "version": "1.28.0", "date": "2026-06-21T10:47:26.000Z", "arch": "x86_64", "commit": "74b81caf0ed92cd090f17336fa9ce33af16204a1", "fileid": "9e16d034cd96fe8718acfb61c654d91d5f043241ffe47b6599c681d390882106", "status": "success", "check": "WARNING", "buildurl": "https://github.com/r-universe/bioc-release/actions/runs/27901664606" } ] }