{ "_id": "6a290247732311cd875911aa", "Package": "fmcsR", "Type": "Package", "Title": "Mismatch Tolerant Maximum Common Substructure Searching", "Version": "1.54.0", "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-release.r-universe.dev", "Date/Publication": "2026-04-28 12:36:48 UTC", "RemoteUrl": "https://github.com/bioc/fmcsR", "RemoteRef": "RELEASE_3_23", "RemoteSha": "3a61bef0284450bcab9c7783c1ba8bb884d76300", "NeedsCompilation": "yes", "Packaged": { "Date": "2026-06-10 06:10:26 UTC", "User": "root" }, "MD5sum": "c2cc4da175003a5637ccfed4567c7650", "_user": "bioc-release", "_type": "src", "_file": "fmcsR_1.54.0.tar.gz", "_fileid": "978a7f71811748c69defeabd53298a7e0c017e7a0bc83a7c741e89374e30051f", "_filesize": 646402, "_sha256": "978a7f71811748c69defeabd53298a7e0c017e7a0bc83a7c741e89374e30051f", "_created": "2026-06-10T06:10:26.000Z", "_published": "2026-06-10T06:20:55.152Z", "_jobs": [ { "job": 80493394563, "time": 170, "config": "bioc-checks", "r": "4.6.0", "check": "ERROR", "artifact": "7527900214" }, { "job": 80493394591, "time": 198, "config": "linux-devel-arm64", "r": "4.7.0", "check": "NOTE", "artifact": "7527907952" }, { "job": 80493394592, "time": 258, "config": "linux-devel-x86_64", "r": "4.7.0", "check": "NOTE", "artifact": "7527922007" }, { "job": 80493394587, "time": 196, "config": "linux-release-arm64", "r": "4.6.0", "check": "NOTE", "artifact": "7527907640" }, { "job": 80493394595, "time": 200, "config": "linux-release-x86_64", "r": "4.6.0", "check": "NOTE", "artifact": "7527907737" }, { "job": 80493394575, "time": 137, "config": "macos-oldrel-arm64", "r": "4.5.3", "check": "NOTE", "artifact": "7527932553" }, { "job": 80493394558, "time": 271, "config": "macos-oldrel-x86_64", "r": "4.5.3", "check": "NOTE", "artifact": "7527965721" }, { "job": 80493394602, "time": 144, "config": "macos-release-arm64", "r": "4.6.0", "check": "NOTE", "artifact": "7527923613" }, { "job": 80493394546, "time": 473, "config": "macos-release-x86_64", "r": "4.6.0", "check": "NOTE", "artifact": "7528003343" }, { "job": 80492953980, "time": 210, "config": "source", "r": "4.6.0", "check": "OK", "artifact": "7527857677" }, { "job": 80493394552, "time": 154, "config": "wasm-release", "r": "4.6.0", "check": "OK", "artifact": "7527896333" }, { "job": 80493394579, "time": 153, "config": "windows-devel", "r": "4.7.0", "check": "WARNING", "artifact": "7527896109" }, { "job": 80493394559, "time": 169, "config": "windows-oldrel", "r": "4.5.3", "check": "WARNING", "artifact": "7527899989" }, { "job": 80493394544, "time": 176, "config": "windows-release", "r": "4.6.0", "check": "WARNING", "artifact": "7527901719" } ], "_bioccheck": { "error": 3, "warning": 5, "note": 11 }, "_buildurl": "https://github.com/r-universe/bioc-release/actions/runs/27256842252", "_status": "success", "_host": "GitHub-Actions", "_upstream": "https://github.com/bioc/fmcsR", "_commit": { "id": "3a61bef0284450bcab9c7783c1ba8bb884d76300", "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": 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": false, "_usedby": 1, "_updates": [ { "week": "2025-44", "n": 2 }, { "week": "2026-18", "n": 1 } ], "_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": 684, "source": "https://www.bioconductor.org/packages/stats/bioc/fmcsR" }, "_mentions": 4, "_devurl": "https://github.com/girke-lab/fmcsr", "_searchresults": 63, "_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/RELEASE_3_23/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": 6.9577030415488315, "_indexed": false, "_nocasepkg": "fmcsr", "_universes": [ "bioc-release" ], "_indexurl": "https://bioc.r-universe.dev/fmcsR", "_binaries": [ { "r": "4.7.0", "os": "linux", "version": "1.54.0", "date": "2026-06-10T06:13:32.000Z", "distro": "noble", "arch": "aarch64", "commit": "3a61bef0284450bcab9c7783c1ba8bb884d76300", "fileid": "8f78950db3ece00dd540ad96b3c24c93ab5a7502f0c72befa340b6cd8a9e3877", "status": "success", "check": "NOTE", "buildurl": "https://github.com/r-universe/bioc-release/actions/runs/27256842252" }, { "r": "4.7.0", "os": "linux", "version": "1.54.0", "date": "2026-06-10T06:14:19.000Z", "distro": "noble", "arch": "x86_64", "commit": "3a61bef0284450bcab9c7783c1ba8bb884d76300", "fileid": "572e02749ee1b705f09926b0501bd69743b50890db97117bb9deedc5aef074a8", "status": "success", "check": "NOTE", "buildurl": "https://github.com/r-universe/bioc-release/actions/runs/27256842252" }, { "r": "4.6.0", "os": "linux", "version": "1.54.0", "date": "2026-06-10T06:13:29.000Z", "distro": "noble", "arch": "aarch64", "commit": "3a61bef0284450bcab9c7783c1ba8bb884d76300", "fileid": "3ef111778c0cc13cf5ddd72ef900fde5b6ad66965a8e424aba432449f88dc09f", "status": "success", "check": "NOTE", "buildurl": "https://github.com/r-universe/bioc-release/actions/runs/27256842252" }, { "r": "4.6.0", "os": "linux", "version": "1.54.0", "date": "2026-06-10T06:13:24.000Z", "distro": "noble", "arch": "x86_64", "commit": "3a61bef0284450bcab9c7783c1ba8bb884d76300", "fileid": "51cb1ac47f7d848746f21098c5fe8d8c86ac0e79b424a6f48ea8438e5e620e56", "status": "success", "check": "NOTE", "buildurl": "https://github.com/r-universe/bioc-release/actions/runs/27256842252" }, { "r": "4.5.3", "os": "mac", "version": "1.54.0", "date": "2026-06-10T06:15:11.000Z", "arch": "aarch64", "commit": "3a61bef0284450bcab9c7783c1ba8bb884d76300", "fileid": "53c62741c87e132193779ec0330520c96dff2f23958a7c97ce048f0e9ce4643f", "status": "success", "check": "NOTE", "buildurl": "https://github.com/r-universe/bioc-release/actions/runs/27256842252" }, { "r": "4.5.3", "os": "mac", "version": "1.54.0", "date": "2026-06-10T06:16:27.000Z", "arch": "x86_64", "commit": "3a61bef0284450bcab9c7783c1ba8bb884d76300", "fileid": "866e0d31b1b9e3925dc4d1b8ef2fbf63198b6f6b354e39c7b219ded79e1d6380", "status": "success", "check": "NOTE", "buildurl": "https://github.com/r-universe/bioc-release/actions/runs/27256842252" }, { "r": "4.6.0", "os": "mac", "version": "1.54.0", "date": "2026-06-10T06:14:34.000Z", "arch": "aarch64", "commit": "3a61bef0284450bcab9c7783c1ba8bb884d76300", "fileid": "8fb6cf2ba1d276fad3642ad31efb71739630537d2bea06fb69f79b39d13ebc6c", "status": "success", "check": "NOTE", "buildurl": "https://github.com/r-universe/bioc-release/actions/runs/27256842252" }, { "r": "4.6.0", "os": "mac", "version": "1.54.0", "date": "2026-06-10T06:17:51.000Z", "arch": "x86_64", "commit": "3a61bef0284450bcab9c7783c1ba8bb884d76300", "fileid": "29743219892384a2273f57c82c882631a13f1680f110348a1f850c41002d23da", "status": "success", "check": "NOTE", "buildurl": "https://github.com/r-universe/bioc-release/actions/runs/27256842252" }, { "r": "4.6.0", "os": "wasm", "version": "1.54.0", "date": "2026-06-10T06:13:24.000Z", "arch": "emscripten", "commit": "3a61bef0284450bcab9c7783c1ba8bb884d76300", "fileid": "b1341b96bc7fd3616f7af486b643f68a7573590e6015f27ce79752c431c841d0", "status": "success", "buildurl": "https://github.com/r-universe/bioc-release/actions/runs/27256842252" }, { "r": "4.7.0", "os": "win", "version": "1.54.0", "date": "2026-06-10T06:12:14.000Z", "arch": "x86_64", "commit": "3a61bef0284450bcab9c7783c1ba8bb884d76300", "fileid": "5f9dc134cb3e0abdc4ba43af2aefc5af9958fa6cd41524f1b9c6aceab84a202d", "status": "success", "check": "WARNING", "buildurl": "https://github.com/r-universe/bioc-release/actions/runs/27256842252" }, { "r": "4.5.3", "os": "win", "version": "1.54.0", "date": "2026-06-10T06:12:24.000Z", "arch": "x86_64", "commit": "3a61bef0284450bcab9c7783c1ba8bb884d76300", "fileid": "86511462d2f7f535b5d1e85e9a4da46c1797996c0c67e54483895e2178079090", "status": "success", "check": "WARNING", "buildurl": "https://github.com/r-universe/bioc-release/actions/runs/27256842252" }, { "r": "4.6.0", "os": "win", "version": "1.54.0", "date": "2026-06-10T06:12:18.000Z", "arch": "x86_64", "commit": "3a61bef0284450bcab9c7783c1ba8bb884d76300", "fileid": "571a8b7b79bb818905a7a2b5cdf76ef3a90336b8bba76d0118cb8ed06189c680", "status": "success", "check": "WARNING", "buildurl": "https://github.com/r-universe/bioc-release/actions/runs/27256842252" } ] }