{ "_id": "6a1ad1101d7bb097a09e1e67", "Package": "fmcsR", "Type": "Package", "Title": "Mismatch Tolerant Maximum Common Substructure Searching", "Version": "1.55.0", "Date": "2024-09-26", "Author": "Yan Wang, Tyler Backman, Kevin Horan, Thomas Girke", "Maintainer": "Thomas Girke ", "Description": "The fmcsR package introduces an efficient maximum common\nsubstructure (MCS) algorithms combined with a novel matching\nstrategy that allows for atom and/or bond mismatches in the\nsubstructures shared among two small molecules. The resulting\nflexible MCSs (FMCSs) are often larger than strict MCSs,\nresulting in the identification of more common features in\ntheir source structures, as well as a higher sensitivity in\nfinding compounds with weak structural similarities. The fmcsR\npackage provides several utilities to use the FMCS algorithm\nfor pairwise compound comparisons, structure similarity\nsearching and clustering.", "License": "Artistic-2.0", "LazyLoad": "yes", "URL": "https://github.com/girke-lab/fmcsR", "biocViews": "Cheminformatics, BiomedicalInformatics, Pharmacogenetics,\nPharmacogenomics, MicrotitrePlateAssay, CellBasedAssays,\nVisualization, Infrastructure, DataImport, Clustering,\nProteomics, Metabolomics", "VignetteBuilder": "knitr", "Config/pak/sysreqs": "cmake make libicu-dev libpng-dev librsvg2-dev\nlibuv1-dev", "Repository": "https://bioc.r-universe.dev", "Date/Publication": "2026-04-28 12:36:48 UTC", "RemoteUrl": "https://github.com/bioc/fmcsR", "RemoteRef": "HEAD", "RemoteSha": "f4f7d5d7d65b34acc73030cbe218959967fb4a5b", "NeedsCompilation": "yes", "Packaged": { "Date": "2026-05-30 08:27:50 UTC", "User": "root" }, "MD5sum": "6d7624207b657b1d3fd5605cd19cdfc3", "_user": "bioc", "_type": "src", "_file": "fmcsR_1.55.0.tar.gz", "_fileid": "7c8fb13b656a70244ad02781f1adf4636b68790ba81a29334bc476c7c549ec39", "_filesize": 646278, "_sha256": "7c8fb13b656a70244ad02781f1adf4636b68790ba81a29334bc476c7c549ec39", "_created": "2026-05-30T08:27:50.000Z", "_published": "2026-05-30T11:59:12.324Z", "_jobs": [ { "job": 78636579366, "time": 170, "config": "bioc-checks", "r": "4.6.0", "check": "ERROR", "artifact": "7306842601" }, { "job": 78636579394, "time": 186, "config": "linux-devel-arm64", "r": "4.7.0", "check": "NOTE", "artifact": "7306844111" }, { "job": 78636579374, "time": 250, "config": "linux-devel-x86_64", "r": "4.7.0", "check": "NOTE", "artifact": "7306850556" }, { "job": 78636579378, "time": 187, "config": "linux-release-arm64", "r": "4.6.0", "check": "NOTE", "artifact": "7306844172" }, { "job": 78636579386, "time": 200, "config": "linux-release-x86_64", "r": "4.6.0", "check": "NOTE", "artifact": "7306845645" }, { "job": 78636579417, "time": 129, "config": "macos-oldrel-arm64", "r": "4.5.3", "check": "NOTE", "artifact": "7308007695" }, { "job": 78636579413, "time": 245, "config": "macos-oldrel-x86_64", "r": "4.5.3", "check": "NOTE", "artifact": "7306851063" }, { "job": 78636579409, "time": 107, "config": "macos-release-arm64", "r": "4.6.0", "check": "NOTE", "artifact": "7308005521" }, { "job": 78636579406, "time": 533, "config": "macos-release-x86_64", "r": "4.6.0", "check": "NOTE", "artifact": "7306878051" }, { "job": 78636390586, "time": 222, "config": "source", "r": "4.6.0", "check": "OK", "artifact": "7306826505" }, { "job": 78636579360, "time": 155, "config": "wasm-release", "r": "4.6.0", "check": "OK", "artifact": "7306841183" }, { "job": 78636579424, "time": 166, "config": "windows-devel", "r": "4.7.0", "check": "WARNING", "artifact": "7306842339" }, { "job": 78636579414, "time": 153, "config": "windows-oldrel", "r": "4.5.3", "check": "WARNING", "artifact": "7306841054" }, { "job": 78636579428, "time": 171, "config": "windows-release", "r": "4.6.0", "check": "WARNING", "artifact": "7306842702" } ], "_bioccheck": { "error": 3, "warning": 5, "note": 11 }, "_buildurl": "https://github.com/r-universe/bioc/actions/runs/26679164373", "_status": "success", "_host": "GitHub-Actions", "_upstream": "https://github.com/bioc/fmcsR", "_commit": { "id": "f4f7d5d7d65b34acc73030cbe218959967fb4a5b", "author": "A Wokaty ", "committer": "A Wokaty ", "message": "bump x.y.z version to odd y following creation of RELEASE_3_23 branch\n", "time": 1777379808 }, "_maintainer": { "name": "Thomas Girke", "email": "thomas.girke@ucr.edu", "login": "tgirke", "description": "", "uuid": 1336916 }, "_distro": "noble", "_registered": true, "_dependencies": [ { "package": "R", "version": ">= 2.10.0", "role": "Depends" }, { "package": "ChemmineR", "role": "Depends" }, { "package": "methods", "role": "Depends" }, { "package": "RUnit", "role": "Imports" }, { "package": "methods", "role": "Imports" }, { "package": "ChemmineR", "role": "Imports" }, { "package": "BiocGenerics", "role": "Imports" }, { "package": "parallel", "role": "Imports" }, { "package": "BiocStyle", "role": "Suggests" }, { "package": "knitr", "role": "Suggests" }, { "package": "knitcitations", "role": "Suggests" }, { "package": "knitrBootstrap", "role": "Suggests" }, { "package": "rmarkdown", "role": "Suggests" }, { "package": "codetools", "role": "Suggests" } ], "_owner": "bioc", "_selfowned": true, "_usedby": 1, "_updates": [ { "week": "2025-44", "n": 2 }, { "week": "2026-18", "n": 2 } ], "_tags": [], "_bioc": [ { "branch": "devel", "version": "1.55.0", "bioc": "3.24" }, { "branch": "release", "version": "1.54.0", "bioc": "3.23" } ], "_topics": [ "cheminformatics", "biomedicalinformatics", "pharmacogenetics", "pharmacogenomics", "microtitreplateassay", "cellbasedassays", "visualization", "infrastructure", "dataimport", "clustering", "proteomics", "metabolomics", "cpp" ], "_stars": 6, "_contributors": [ { "user": "khoran", "count": 29, "uuid": 1340344 }, { "user": "tgirke", "count": 8, "uuid": 1336916 }, { "user": "tylerbackman", "count": 1, "uuid": 647482 } ], "_userbio": { "uuid": 2286807, "type": "organization", "name": "Bioconductor", "description": "Software for the analysis and comprehension of high-throughput genomic data" }, "_downloads": { "count": 689, "source": "https://www.bioconductor.org/packages/stats/bioc/fmcsR" }, "_mentions": 4, "_devurl": "https://github.com/girke-lab/fmcsr", "_searchresults": 77, "_rbuild": "4.6.0", "_assets": [ "extra/citation.cff", "extra/citation.html", "extra/citation.json", "extra/citation.txt", "extra/contents.json", "extra/fmcsR.html", "extra/NEWS.html", "extra/NEWS.txt", "extra/readme.html", "extra/readme.md", "manual.pdf" ], "_homeurl": "https://github.com/girke-lab/fmcsr", "_realowner": "bioc", "_cranurl": false, "_exports": [ "coerce", "fmcs", "fmcsBatch", "mcs1", "mcs2", "mcs2sdfset", "plotMCS", "show", "stats" ], "_datasets": [ { "name": "fmcstest", "title": "SD file stored in 'SDFset' object", "object": "fmcstest", "file": "fmcstest.rda", "class": [ "SDFset" ], "fields": [], "table": false, "tojson": false } ], "_help": [ { "page": "fmcsR-package", "title": "A FMCS solver package.", "topics": [ "fmcsR-package", "fmcsR" ] }, { "page": "fmcs", "title": "Flexible MCS (FMCS) Finder", "topics": [ "fmcs" ] }, { "page": "fmcsBatch", "title": "FMCS Search Function", "topics": [ "fmcsBatch" ] }, { "page": "fmcstest", "title": "SD file stored in 'SDFset' object", "topics": [ "fmcstest" ] }, { "page": "MCS-class", "title": "Class '\"MCS\"'", "topics": [ "coerce,list,MCS-method", "MCS-class", "mcs1", "mcs1,MCS-method", "mcs2", "mcs2,MCS-method", "show,MCS-method", "stats", "stats,MCS-method", "[[,MCS-method" ] }, { "page": "mcs2sdfset", "title": "Return MCS object as SDFset", "topics": [ "mcs2sdfset" ] }, { "page": "plotMCS", "title": "Plot MCS", "topics": [ "plotMCS" ] } ], "_readme": "https://github.com/bioc/fmcsR/raw/HEAD/README.md", "_rundeps": [ "base64enc", "BH", "BiocGenerics", "bitops", "bslib", "cachem", "ChemmineR", "cli", "cpp11", "crosstalk", "DBI", "digest", "DT", "evaluate", "farver", "fastmap", "fontawesome", "fs", "generics", "ggplot2", "glue", "gridExtra", "gtable", "highr", "htmltools", "htmlwidgets", "isoband", "jquerylib", "jsonlite", "knitr", "labeling", "later", "lazyeval", "lifecycle", "magrittr", "memoise", "mime", "otel", "png", "promises", "R6", "rappdirs", "RColorBrewer", "Rcpp", "RCurl", "rjson", "rlang", "rmarkdown", "rsvg", "RUnit", "S7", "sass", "scales", "stringi", "tinytex", "vctrs", "viridisLite", "withr", "xfun", "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": "fmcsR.Rmd", "filename": "fmcsR.html", "title": "fmcsR: Mismatch Tolerant Maximum Common Substructure Detection for Advanced Compound Similarity Searching", "author": "Authors: Yan Wang, Tyler Backman, Kevin Horan, Thomas Girke", "engine": "knitr::rmarkdown", "headings": [ "Introduction", "Installation", "Quick Overview", "Documentation", "MCS of Two Compounds", "Data Import", "Compute MCS", "Class Usage", "FMCS of Two Compounds", "FMCS Search Functionality", "Clustering with FMCS", "Version Information", "References" ], "created": "2014-04-28 17:30:40", "modified": "2021-01-25 19:58:24", "commits": 14 } ], "_score": 7.044853217267732, "_indexed": true, "_nocasepkg": "fmcsr", "_universes": [ "bioc", "tgirke", "girke-lab" ], "_binaries": [ { "r": "4.7.0", "os": "linux", "version": "1.55.0", "date": "2026-05-30T08:30:37.000Z", "distro": "noble", "arch": "aarch64", "commit": "f4f7d5d7d65b34acc73030cbe218959967fb4a5b", "fileid": "a8378b59c2c52ab2c8a6f8e87a08f919fc48af65b757bc000176d1a62978ddd6", "status": "success", "check": "NOTE", "buildurl": "https://github.com/r-universe/bioc/actions/runs/26679164373" }, { "r": "4.7.0", "os": "linux", "version": "1.55.0", "date": "2026-05-30T08:31:33.000Z", "distro": "noble", "arch": "x86_64", "commit": "f4f7d5d7d65b34acc73030cbe218959967fb4a5b", "fileid": "e9707342abe65d2d5c01094d30cd10c689b4a212130839f3e56e0c65faaa91f8", "status": "success", "check": "NOTE", "buildurl": "https://github.com/r-universe/bioc/actions/runs/26679164373" }, { "r": "4.6.0", "os": "linux", "version": "1.55.0", "date": "2026-05-30T08:30:37.000Z", "distro": "noble", "arch": "aarch64", "commit": "f4f7d5d7d65b34acc73030cbe218959967fb4a5b", "fileid": "ef54c02b889226405b54c6ce31cd5c72c7fefe6c0331658afd9f4376a1b74e6a", "status": "success", "check": "NOTE", "buildurl": "https://github.com/r-universe/bioc/actions/runs/26679164373" }, { "r": "4.6.0", "os": "linux", "version": "1.55.0", "date": "2026-05-30T08:30:49.000Z", "distro": "noble", "arch": "x86_64", "commit": "f4f7d5d7d65b34acc73030cbe218959967fb4a5b", "fileid": "70fa0b7dc989b0973c34e3e7a9c1929862b9beecad66f2c52ffb2d55a5c875e0", "status": "success", "check": "NOTE", "buildurl": "https://github.com/r-universe/bioc/actions/runs/26679164373" }, { "r": "4.5.3", "os": "mac", "version": "1.55.0", "date": "2026-05-30T11:58:11.000Z", "arch": "aarch64", "commit": "f4f7d5d7d65b34acc73030cbe218959967fb4a5b", "fileid": "fae680cf56e03138808bffdd1bb3b262f332044f3746d61d09d46bc00a5c7a46", "status": "success", "check": "NOTE", "buildurl": "https://github.com/r-universe/bioc/actions/runs/26679164373" }, { "r": "4.5.3", "os": "mac", "version": "1.55.0", "date": "2026-05-30T08:31:16.000Z", "arch": "x86_64", "commit": "f4f7d5d7d65b34acc73030cbe218959967fb4a5b", "fileid": "b2cb25eec3983c37fa98b39205af2c5c450968370ed5eeaecbf501e09cd0ef59", "status": "success", "check": "NOTE", "buildurl": "https://github.com/r-universe/bioc/actions/runs/26679164373" }, { "r": "4.6.0", "os": "mac", "version": "1.55.0", "date": "2026-05-30T11:57:51.000Z", "arch": "aarch64", "commit": "f4f7d5d7d65b34acc73030cbe218959967fb4a5b", "fileid": "b90d2246e8ddc7f432d3815a84e2aa43b887b035ef0b5bc9cc446891f7d4427d", "status": "success", "check": "NOTE", "buildurl": "https://github.com/r-universe/bioc/actions/runs/26679164373" }, { "r": "4.6.0", "os": "mac", "version": "1.55.0", "date": "2026-05-30T08:34:21.000Z", "arch": "x86_64", "commit": "f4f7d5d7d65b34acc73030cbe218959967fb4a5b", "fileid": "f4dc90cecf8236489645b8d5930dda0e753c1ff7544bfdc81da6fe4405ece1e7", "status": "success", "check": "NOTE", "buildurl": "https://github.com/r-universe/bioc/actions/runs/26679164373" }, { "r": "4.6.0", "os": "wasm", "version": "1.55.0", "date": "2026-05-30T08:30:48.000Z", "arch": "emscripten", "commit": "f4f7d5d7d65b34acc73030cbe218959967fb4a5b", "fileid": "1f014c6f486825f2c27f0e06da6428b5af256e9b392e2b2ce2b9ed15ed6630df", "status": "success", "buildurl": "https://github.com/r-universe/bioc/actions/runs/26679164373" }, { "r": "4.7.0", "os": "win", "version": "1.55.0", "date": "2026-05-30T08:29:50.000Z", "arch": "x86_64", "commit": "f4f7d5d7d65b34acc73030cbe218959967fb4a5b", "fileid": "d20830119ee94cfefd29f6871a67b820a918468fff6c7bf9591b5005172517f8", "status": "success", "check": "WARNING", "buildurl": "https://github.com/r-universe/bioc/actions/runs/26679164373" }, { "r": "4.5.3", "os": "win", "version": "1.55.0", "date": "2026-05-30T08:29:30.000Z", "arch": "x86_64", "commit": "f4f7d5d7d65b34acc73030cbe218959967fb4a5b", "fileid": "4417f80926c853c6d3a9b07f4ac2bf7e6e534787763afe7ccda06b65e8d3b774", "status": "success", "check": "WARNING", "buildurl": "https://github.com/r-universe/bioc/actions/runs/26679164373" }, { "r": "4.6.0", "os": "win", "version": "1.55.0", "date": "2026-05-30T08:29:41.000Z", "arch": "x86_64", "commit": "f4f7d5d7d65b34acc73030cbe218959967fb4a5b", "fileid": "a708d9ab7eaaeb859d5ddba6b027daf250852f2fa476ab42a2cf15ba0cacdef6", "status": "success", "check": "WARNING", "buildurl": "https://github.com/r-universe/bioc/actions/runs/26679164373" } ] }