{ "_id": "6a494e21f6c47c441949a00d", "Package": "muscle", "Type": "Package", "Title": "Multiple Sequence Alignment with MUSCLE", "Version": "3.55.0", "Date": "2012-10-05", "Author": "Algorithm by Robert C. Edgar. R port by Alex T. Kalinka.", "Maintainer": "Alex T. Kalinka ", "Description": "MUSCLE performs multiple sequence alignments of nucleotide\nor amino acid sequences.", "biocViews": "MultipleSequenceAlignment, Alignment, Sequencing, Genetics,\nSequenceMatching, DataImport", "License": "Unlimited", "URL": "http://www.drive5.com/muscle/", "LazyLoad": "yes", "LazyData": "yes", "NeedsCompilation": "yes", "Config/pak/sysreqs": "zlib1g-dev", "Repository": "https://bioc.r-universe.dev", "Date/Publication": "2026-04-28 12:40:42 UTC", "RemoteUrl": "https://github.com/bioc/muscle", "RemoteRef": "HEAD", "RemoteSha": "2446ca4ab6e585b3aca01b365cfff217f3953ec8", "Packaged": { "Date": "2026-07-03 23:01:18 UTC", "User": "root" }, "_user": "bioc", "_type": "src", "_file": "muscle_3.55.0.tar.gz", "_fileid": "https://r2.ropensci.org/1044cb7840a988b08e5e2921c268cc247aacffc2ce24e35eec14c5c7d0f0101f", "_filesize": 297553, "_sha256": "1044cb7840a988b08e5e2921c268cc247aacffc2ce24e35eec14c5c7d0f0101f", "_expires": "2026-10-12T18:17:03.000Z", "_created": "2026-07-03T23:01:18.000Z", "_published": "2026-07-04T18:17:05.547Z", "_bioccheck": { "error": 1, "warning": 1, "note": 11 }, "_host": "GitHub-Actions", "_buildurl": "https://github.com/r-universe/bioc/actions/runs/28686884468", "_status": "failure", "_upstream": "https://github.com/bioc/muscle", "_commit": { "id": "2446ca4ab6e585b3aca01b365cfff217f3953ec8", "author": "A Wokaty ", "committer": "A Wokaty ", "message": "bump x.y.z version to odd y following creation of RELEASE_3_23 branch\n", "time": 1777380042 }, "_maintainer": { "name": "Alex T. Kalinka", "email": "alex.t.kalinka@gmail.com", "login": "alextkalinka", "description": "", "uuid": 61851571 }, "_distro": "resolute", "_jobs": [ { "job": 85155539571, "time": 165, "config": "bioc-checks", "r": "4.6.1", "check": "ERROR", "artifact": "8075928205" }, { "job": 85155539657, "time": 226, "config": "linux-devel-arm64", "r": "4.7.0", "check": "ERROR", "artifact": "8075937352" }, { "job": 85155539562, "time": 198, "config": "linux-devel-x86_64", "r": "4.7.0", "check": "ERROR", "artifact": "8075932757" }, { "job": 85155539656, "time": 189, "config": "linux-release-arm64", "r": "4.6.1", "check": "ERROR", "artifact": "8075931781" }, { "job": 85155539666, "time": 188, "config": "linux-release-x86_64", "r": "4.6.1", "check": "ERROR", "artifact": "8075931368" }, { "job": 85155539695, "time": 116, "config": "macos-oldrel-arm64", "r": "4.5.3", "check": "ERROR", "artifact": "8075921417" }, { "job": 85155539628, "time": 287, "config": "macos-oldrel-x86_64", "r": "4.5.3", "check": "ERROR", "artifact": "8075945490" }, { "job": 85155539616, "time": 142, "config": "macos-release-arm64", "r": "4.6.1", "check": "ERROR", "artifact": "8075925080" }, { "job": 85155539485, "time": 296, "config": "macos-release-x86_64", "r": "4.6.1", "check": "ERROR", "artifact": "8075946768" }, { "job": 85155539500, "time": 243, "config": "source", "r": "4.6.1", "check": "ERROR", "artifact": "8075904466" }, { "job": 85155539578, "time": 147, "config": "wasm-release", "r": "4.6.0", "check": "OK", "artifact": "8075925555" }, { "job": 85155539641, "time": 208, "config": "windows-devel", "r": "4.7.0", "check": "ERROR", "artifact": "8075934258" }, { "job": 85155539516, "time": 198, "config": "windows-oldrel", "r": "4.5.3", "check": "ERROR", "artifact": "8075932678" }, { "job": 85155539511, "time": 206, "config": "windows-release", "r": "4.6.1", "check": "ERROR", "artifact": "8075933869" } ], "_registered": true, "_dependencies": [ { "package": "Biostrings", "role": "Depends" } ], "_owner": "bioc", "_selfowned": true, "_usedby": 0, "_updates": [ { "week": "2025-44", "n": 2 }, { "week": "2026-18", "n": 2 } ], "_tags": [], "_bioc": [ { "branch": "devel", "version": "3.55.0", "bioc": "3.24" }, { "branch": "release", "version": "3.54.0", "bioc": "3.23" } ], "_topics": [ "multiplesequencealignment", "alignment", "sequencing", "genetics", "sequencematching", "dataimport", "cpp" ], "_userbio": { "uuid": 2286807, "type": "organization", "name": "Bioconductor", "followers": 445, "description": "Software for the analysis and comprehension of high-throughput genomic data" }, "_mentions": 166, "_searchresults": 108, "_rbuild": "4.6.1", "_assets": [ "extra/citation.cff", "extra/citation.html", "extra/citation.json", "extra/citation.txt", "extra/contents.json", "extra/muscle.html", "extra/NEWS.html", "extra/NEWS.txt", "manual.pdf" ], "_realowner": "bioc", "_cranurl": false, "_releases": [ { "version": "3.8.31-0", "date": "2012-10-15" }, { "version": "3.8.31-1", "date": "2013-03-29" }, { "version": "3.8.31-2", "date": "2014-05-07" }, { "version": "3.8.31-3", "date": "2014-07-04" }, { "version": "3.8.31-4", "date": "2014-07-07" } ], "_exports": [ ".muscleR", "muscle" ], "_datasets": [ { "name": "umax", "title": "Unaligned MAX sequences", "object": "umax", "class": [ "DNAStringSet" ], "fields": [], "table": false, "tojson": false } ], "_help": [ { "page": "muscle-package", "title": "Multiple Sequence Alignment", "topics": [ "muscle-package" ] }, { "page": "muscle", "title": "Multiple Sequence Alignment", "topics": [ "muscle" ] }, { "page": "umax", "title": "Unaligned MAX sequences", "topics": [ "umax" ] } ], "_rundeps": [ "BiocGenerics", "Biostrings", "crayon", "generics", "IRanges", "S4Vectors", "Seqinfo", "XVector" ], "_sysdeps": [ { "shlib": "libstdc++", "package": "libstdc++6", "source": "gcc", "version": "16-20260322-1ubuntu1", "name": "c++", "homepage": "http://gcc.gnu.org/", "description": "GNU Standard C++ Library v3" } ], "_score": 4.334453751150931, "_indexed": true, "_nocasepkg": "muscle", "_universes": [ "bioc", "alextkalinka" ], "_binaries": [ { "r": "4.7.0", "os": "linux", "version": "3.55.0", "date": "2026-07-03T23:04:53.000Z", "distro": "resolute", "arch": "aarch64", "commit": "2446ca4ab6e585b3aca01b365cfff217f3953ec8", "fileid": "https://r2.ropensci.org/4304565d74dab4f99cef72a88933cd4ab7c888e85feb3880f52f5df1b693ee11", "status": "failure", "check": "ERROR", "buildurl": "https://github.com/r-universe/bioc/actions/runs/28686884468" }, { "r": "4.7.0", "os": "linux", "version": "3.55.0", "date": "2026-07-03T23:04:06.000Z", "distro": "resolute", "arch": "x86_64", "commit": "2446ca4ab6e585b3aca01b365cfff217f3953ec8", "fileid": "https://r2.ropensci.org/63e216db2a0cf7aa79efe8f0af27ce3fe5666d684d06a79a696a3be849338a92", "status": "failure", "check": "ERROR", "buildurl": "https://github.com/r-universe/bioc/actions/runs/28686884468" }, { "r": "4.6.1", "os": "linux", "version": "3.55.0", "date": "2026-07-03T23:04:14.000Z", "distro": "resolute", "arch": "aarch64", "commit": "2446ca4ab6e585b3aca01b365cfff217f3953ec8", "fileid": "https://r2.ropensci.org/e7b9c38eba35bcfbb48842af1e4b281c058cd7f355820d0e9bfcc6c669147643", "status": "failure", "check": "ERROR", "buildurl": "https://github.com/r-universe/bioc/actions/runs/28686884468" }, { "r": "4.6.1", "os": "linux", "version": "3.55.0", "date": "2026-07-03T23:03:58.000Z", "distro": "resolute", "arch": "x86_64", "commit": "2446ca4ab6e585b3aca01b365cfff217f3953ec8", "fileid": "https://r2.ropensci.org/f0ac50714c9d3a492483752639867c052868ed90b5f5874395e0a4806d04629c", "status": "failure", "check": "ERROR", "buildurl": "https://github.com/r-universe/bioc/actions/runs/28686884468" }, { "r": "4.5.3", "os": "mac", "version": "3.55.0", "date": "2026-07-03T23:03:07.000Z", "arch": "aarch64", "commit": "2446ca4ab6e585b3aca01b365cfff217f3953ec8", "fileid": "https://r2.ropensci.org/117fd764877ee032a8b184b461c99577b5b8bec1f7e615e03a1b6889658b29e4", "status": "failure", "check": "ERROR", "buildurl": "https://github.com/r-universe/bioc/actions/runs/28686884468" }, { "r": "4.5.3", "os": "mac", "version": "3.55.0", "date": "2026-07-03T23:04:56.000Z", "arch": "x86_64", "commit": "2446ca4ab6e585b3aca01b365cfff217f3953ec8", "fileid": "https://r2.ropensci.org/348bfc8d10e4c23009fb3f81161cc3121a9c837dc85ba208ba760d314cece3da", "status": "failure", "check": "ERROR", "buildurl": "https://github.com/r-universe/bioc/actions/runs/28686884468" }, { "r": "4.6.1", "os": "mac", "version": "3.55.0", "date": "2026-07-03T23:03:22.000Z", "arch": "aarch64", "commit": "2446ca4ab6e585b3aca01b365cfff217f3953ec8", "fileid": "https://r2.ropensci.org/c6c2128ad63dd44658e7f291d056fd8c32b632fa3b00c1cb36558bdb4ee034de", "status": "failure", "check": "ERROR", "buildurl": "https://github.com/r-universe/bioc/actions/runs/28686884468" }, { "r": "4.6.1", "os": "mac", "version": "3.55.0", "date": "2026-07-03T23:04:20.000Z", "arch": "x86_64", "commit": "2446ca4ab6e585b3aca01b365cfff217f3953ec8", "fileid": "https://r2.ropensci.org/cb93b28f90281a2907e8dc2b68bd443f79f806f63e4facb887fbc86559ca81c2", "status": "failure", "check": "ERROR", "buildurl": "https://github.com/r-universe/bioc/actions/runs/28686884468" }, { "r": "4.6.0", "os": "wasm", "version": "3.55.0", "date": "2026-07-03T23:03:41.000Z", "arch": "emscripten", "commit": "2446ca4ab6e585b3aca01b365cfff217f3953ec8", "fileid": "https://r2.ropensci.org/be310fa29baa7b2bae9f43b2454c1c97daebc8d26814efecbe573052f66a105a", "status": "success", "buildurl": "https://github.com/r-universe/bioc/actions/runs/28686884468" }, { "r": "4.7.0", "os": "win", "version": "3.55.0", "date": "2026-07-03T23:03:02.000Z", "arch": "x86_64", "commit": "2446ca4ab6e585b3aca01b365cfff217f3953ec8", "fileid": "https://r2.ropensci.org/548a3e036731004e307414ede9a72bfe343c1e315ad79d543da4541a266c949d", "status": "failure", "check": "ERROR", "buildurl": "https://github.com/r-universe/bioc/actions/runs/28686884468" }, { "r": "4.5.3", "os": "win", "version": "3.55.0", "date": "2026-07-03T23:02:48.000Z", "arch": "x86_64", "commit": "2446ca4ab6e585b3aca01b365cfff217f3953ec8", "fileid": "https://r2.ropensci.org/64793676289c617fa678e6387b68765f9112f614a241b4e912a14bed6e00913d", "status": "failure", "check": "ERROR", "buildurl": "https://github.com/r-universe/bioc/actions/runs/28686884468" }, { "r": "4.6.1", "os": "win", "version": "3.55.0", "date": "2026-07-03T23:02:52.000Z", "arch": "x86_64", "commit": "2446ca4ab6e585b3aca01b365cfff217f3953ec8", "fileid": "https://r2.ropensci.org/9b051e8c9df73f27e5540f97364ae62e3e732a2d673cbda0f36b0f95620f584b", "status": "failure", "check": "ERROR", "buildurl": "https://github.com/r-universe/bioc/actions/runs/28686884468" } ] }