{ "_id": "6ae5e4438d250e7ad09f419b", "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": "2026-10-31 11:23:33 UTC", "User": "root" }, "_user": "bioc", "_type": "src", "_file": "muscle_3.55.0.tar.gz", "_fileid": "https://r2.ropensci.org/67c1161c39a4eaea6aa440759df6afb003578ed438f5fc006ddc96218f94d4fb", "_filesize": 296786, "_sha256": "67c1161c39a4eaea6aa440759df6afb003578ed438f5fc006ddc96218f94d4fb", "_expires": "2027-02-08T12:51:13.000Z", "_created": "2026-10-31T11:23:33.000Z", "_published": "2026-10-31T12:51:14.955Z", "_upstream": "https://github.com/bioc/muscle", "_status": "failure", "_maintainer": { "name": "Alex T. Kalinka", "email": "alex.t.kalinka@gmail.com", "login": "alextkalinka", "description": "", "uuid": 61851571 }, "_jobs": [ { "job": 124524286040, "time": 145, "config": "bioc-checks", "r": "4.6.1", "check": "ERROR", "artifact": "13040718729" }, { "job": 124524286091, "time": 135, "config": "linux-devel-arm64", "r": "4.7.0", "check": "ERROR", "artifact": "13040534118" }, { "job": 124524286133, "time": 232, "config": "linux-devel-x86_64", "r": "4.7.0", "check": "ERROR", "artifact": "13040294633" }, { "job": 124524286132, "time": 146, "config": "linux-release-arm64", "r": "4.6.1", "check": "ERROR", "artifact": "13041073387" }, { "job": 124524286143, "time": 247, "config": "linux-release-x86_64", "r": "4.6.1", "check": "ERROR", "artifact": "13040429352" }, { "job": 124524286093, "time": 108, "config": "macos-oldrel-arm64", "r": "4.5.3", "check": "ERROR", "artifact": "13043083646" }, { "job": 124524286206, "time": 252, "config": "macos-oldrel-x86_64", "r": "4.5.3", "check": "ERROR", "artifact": "13041307600" }, { "job": 124524286090, "time": 128, "config": "macos-release-arm64", "r": "4.6.2", "check": "ERROR", "artifact": "13042414782" }, { "job": 124524286087, "time": 242, "config": "macos-release-x86_64", "r": "4.6.2", "check": "ERROR", "artifact": "13040798760" }, { "job": 124523362784, "time": 268, "config": "source", "r": "4.6.1", "check": "ERROR", "artifact": "13040362573" }, { "job": 124524286062, "time": 125, "config": "wasm-release", "r": "4.6.0", "check": "OK", "artifact": "13040284399" }, { "job": 124524286148, "time": 352, "config": "windows-devel-arm64", "r": "4.7.0", "check": "ERROR", "artifact": "13041243028" }, { "job": 124524286158, "time": 178, "config": "windows-devel-x86_64", "r": "4.7.0", "check": "ERROR", "artifact": "13040932272" }, { "job": 124524286113, "time": 196, "config": "windows-oldrel-x86_64", "r": "4.5.3", "check": "ERROR", "artifact": "13040347954" }, { "job": 124524286176, "time": 331, "config": "windows-release-arm64", "r": "4.6.2", "check": "ERROR", "artifact": "13040679220" }, { "job": 124524286157, "time": 149, "config": "windows-release-x86_64", "r": "4.6.2", "check": "ERROR", "artifact": "13041332301" } ], "_bioccheck": { "error": 1, "warning": 2, "note": 11 }, "_buildurl": "https://github.com/r-universe/bioc/actions/runs/41196391586", "_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 }, "_distro": "resolute", "_host": "GitHub-Actions", "_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", "repository": "bioc" }, { "branch": "release", "version": "3.54.0", "bioc": "3.23", "repository": "bioc" } ], "_topics": [ "multiplesequencealignment", "alignment", "sequencing", "genetics", "sequencematching", "dataimport", "cpp" ], "_userbio": { "uuid": 2286807, "type": "organization", "name": "Bioconductor", "followers": 481, "description": "Software for the analysis and comprehension of high-throughput genomic data" }, "_downloads": { "count": 970, "source": "https://www.bioconductor.org/packages/stats/bioc/muscle" }, "_mentions": 166, "_searchresults": 105, "_rbuild": "4.6.1", "_assets": [ "extra/citation.cff", "extra/citation.html", "extra/citation.json", "extra/citation.txt", "extra/contents.json", "extra/manual.pdf", "extra/muscle.html", "extra/NEWS.html", "extra/NEWS.txt" ], "_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": 4.3222192947339195, "_indexed": true, "_nocasepkg": "muscle", "_universes": [ "bioc", "alextkalinka" ], "_binaries": [ { "r": "4.7.0", "os": "linux", "version": "3.55.0", "date": "2026-10-31T11:25:43.000Z", "distro": "resolute", "arch": "aarch64", "commit": "2446ca4ab6e585b3aca01b365cfff217f3953ec8", "fileid": "https://r2.ropensci.org/9c729f92476d1a53cf514b75fd005266cec69793e2f49f870c05fc629fcbeff5", "status": "failure", "check": "ERROR", "buildurl": "https://github.com/r-universe/bioc/actions/runs/41196391586" }, { "r": "4.7.0", "os": "linux", "version": "3.55.0", "date": "2026-10-31T11:27:21.000Z", "distro": "resolute", "arch": "x86_64", "commit": "2446ca4ab6e585b3aca01b365cfff217f3953ec8", "fileid": "https://r2.ropensci.org/da4c734688a5ee61c206bc663641334877e73197f5a0817b9e007f764b09171c", "status": "failure", "check": "ERROR", "buildurl": "https://github.com/r-universe/bioc/actions/runs/41196391586" }, { "r": "4.6.1", "os": "linux", "version": "3.55.0", "date": "2026-10-31T11:25:57.000Z", "distro": "resolute", "arch": "aarch64", "commit": "2446ca4ab6e585b3aca01b365cfff217f3953ec8", "fileid": "https://r2.ropensci.org/f2067c00b4a332801b7aec946fcc03a43bb8b0ff548909992ea04c9129822c97", "status": "failure", "check": "ERROR", "buildurl": "https://github.com/r-universe/bioc/actions/runs/41196391586" }, { "r": "4.6.1", "os": "linux", "version": "3.55.0", "date": "2026-10-31T11:27:15.000Z", "distro": "resolute", "arch": "x86_64", "commit": "2446ca4ab6e585b3aca01b365cfff217f3953ec8", "fileid": "https://r2.ropensci.org/057fc498973e3bfeb147d83ef5ed3a40a795d2fa54d9846b072846eca83e6d82", "status": "failure", "check": "ERROR", "buildurl": "https://github.com/r-universe/bioc/actions/runs/41196391586" }, { "r": "4.5.3", "os": "mac", "version": "3.55.0", "date": "2026-10-31T12:49:32.000Z", "arch": "aarch64", "commit": "2446ca4ab6e585b3aca01b365cfff217f3953ec8", "fileid": "https://r2.ropensci.org/03fc8604e690606bf01892dcb42b53ca33fbd5ebbee50aa4c138c20bd3db2315", "status": "failure", "check": "ERROR", "buildurl": "https://github.com/r-universe/bioc/actions/runs/41196391586" }, { "r": "4.5.3", "os": "mac", "version": "3.55.0", "date": "2026-10-31T11:26:37.000Z", "arch": "x86_64", "commit": "2446ca4ab6e585b3aca01b365cfff217f3953ec8", "fileid": "https://r2.ropensci.org/fee3eefdb7de8e08562a8e3bd95c57debf17b059666b99d63e907bfa8d8fe236", "status": "failure", "check": "ERROR", "buildurl": "https://github.com/r-universe/bioc/actions/runs/41196391586" }, { "r": "4.6.2", "os": "mac", "version": "3.55.0", "date": "2026-10-31T12:49:54.000Z", "arch": "aarch64", "commit": "2446ca4ab6e585b3aca01b365cfff217f3953ec8", "fileid": "https://r2.ropensci.org/d0143ecc94aab429499ac2205b4166b52198235f472497f2ec528721a3be9e29", "status": "failure", "check": "ERROR", "buildurl": "https://github.com/r-universe/bioc/actions/runs/41196391586" }, { "r": "4.6.2", "os": "mac", "version": "3.55.0", "date": "2026-10-31T11:26:45.000Z", "arch": "x86_64", "commit": "2446ca4ab6e585b3aca01b365cfff217f3953ec8", "fileid": "https://r2.ropensci.org/938438d8359eac224ea3af065af223a6bd1f0b85b4d465d4c3f22f4e5c52120f", "status": "failure", "check": "ERROR", "buildurl": "https://github.com/r-universe/bioc/actions/runs/41196391586" }, { "r": "4.6.0", "os": "wasm", "version": "3.55.0", "date": "2026-10-31T11:25:48.000Z", "arch": "emscripten", "commit": "2446ca4ab6e585b3aca01b365cfff217f3953ec8", "fileid": "https://r2.ropensci.org/a65ca418d00c7468747100d466a8c6aa1a2028ebe5cd3778422ef1b88df27575", "status": "success", "buildurl": "https://github.com/r-universe/bioc/actions/runs/41196391586" }, { "r": "4.7.0", "os": "win", "version": "3.55.0", "date": "2026-10-31T11:27:39.000Z", "arch": "aarch64", "commit": "2446ca4ab6e585b3aca01b365cfff217f3953ec8", "fileid": "https://r2.ropensci.org/74c713723f500ccb5927b3664bea3d619d7dcd59b1b801537ac48831f9fe43ef", "status": "failure", "check": "ERROR", "buildurl": "https://github.com/r-universe/bioc/actions/runs/41196391586" }, { "r": "4.7.0", "os": "win", "version": "3.55.0", "date": "2026-10-31T11:25:02.000Z", "arch": "x86_64", "commit": "2446ca4ab6e585b3aca01b365cfff217f3953ec8", "fileid": "https://r2.ropensci.org/793ad66f48f3e20eac21af7ef7a416890c6987f5af22dacfe2ab6422a8fc4f2f", "status": "failure", "check": "ERROR", "buildurl": "https://github.com/r-universe/bioc/actions/runs/41196391586" }, { "r": "4.5.3", "os": "win", "version": "3.55.0", "date": "2026-10-31T11:25:17.000Z", "arch": "x86_64", "commit": "2446ca4ab6e585b3aca01b365cfff217f3953ec8", "fileid": "https://r2.ropensci.org/9609dae45dd7c30defe7551f665653c50151d75ef31783168af8942b8aa194aa", "status": "failure", "check": "ERROR", "buildurl": "https://github.com/r-universe/bioc/actions/runs/41196391586" }, { "r": "4.6.2", "os": "win", "version": "3.55.0", "date": "2026-10-31T11:27:29.000Z", "arch": "aarch64", "commit": "2446ca4ab6e585b3aca01b365cfff217f3953ec8", "fileid": "https://r2.ropensci.org/fe56c5b2c482b48bc8a766a4d0de8c6a7d39a98b8a1f4e63442249142c2e7379", "status": "failure", "check": "ERROR", "buildurl": "https://github.com/r-universe/bioc/actions/runs/41196391586" }, { "r": "4.6.2", "os": "win", "version": "3.55.0", "date": "2026-10-31T11:25:06.000Z", "arch": "x86_64", "commit": "2446ca4ab6e585b3aca01b365cfff217f3953ec8", "fileid": "https://r2.ropensci.org/f2a8838d0c2eee34b3eb8a9387b0457fb850974ef1e6f189831f73f60a17988f", "status": "failure", "check": "ERROR", "buildurl": "https://github.com/r-universe/bioc/actions/runs/41196391586" } ] }