{ "_id": "6a3b4af15cdecea1d681788c", "Package": "cliqueMS", "Type": "Package", "Title": "Annotation of Isotopes, Adducts and Fragmentation Adducts for\nin-Source LC/MS Metabolomics Data", "Version": "1.14.1", "Date": "2019-23-10", "Authors@R": "c(\nperson(\"Oriol\", \"Senan Campos\", email = \"oriol.senan@praenoscere.com\", role = c(\"aut\",\"cre\")),\nperson(\"Antoni\", \"Aguilar-Mogas\", role = \"aut\"),\nperson(\"Jordi\", \"Capellades\", role = \"aut\"),\nperson(\"Miriam\", \"Navarro\", role = \"aut\"),\nperson(\"Oscar\", \"Yanes\", role = \"aut\"),\nperson(\"Roger\", \"Guimera\", role = \"aut\"),\nperson(\"Marta\", \"Sales-Pardo\", role = \"aut\")\n)", "Description": "Annotates data from liquid chromatography coupled to mass\nspectrometry (LC/MS) metabolomics experiments. Based on a\nnetwork algorithm (O.Senan, A. Aguilar- Mogas, M. Navarro, O.\nYanes, R.Guimerà and M. Sales-Pardo, Bioinformatics, 35(20),\n2019), 'CliqueMS' builds a weighted similarity network where\nnodes are features and edges are weighted according to the\nsimilarity of this features. Then it searches for the most\nplausible division of the similarity network into cliques\n(fully connected components). Finally it annotates metabolites\nwithin each clique, obtaining for each annotated metabolite the\nneutral mass and their features, corresponding to isotopes,\nionization adducts and fragmentation adducts of that\nmetabolite.", "License": "GPL (>= 2)", "URL": "http://cliquems.seeslab.net", "BugReports": "https://github.com/osenan/cliqueMS/issues", "biocViews": "Metabolomics, MassSpectrometry, Network, NetworkInference", "SystemRequirements": "C++11", "Encoding": "UTF-8", "RoxygenNote": "6.1.1", "Collate": "'allGenerics.R' 'allClasses.R' 'buildNetwork.R' 'cliqueMS.R'\n'ex.cliqueGroups.R' 'findAnnotation.R' 'findCliques.R'\n'findIsotopes.R' 'negative.adinfo.R' 'positive.adinfo.R'\n'RcppExports.R'", "VignetteBuilder": "knitr", "Config/pak/sysreqs": "cmake libglpk-dev make libicu-dev libuv1-dev\nlibxml2-dev libnetcdf-dev libssl-dev zlib1g-dev", "Repository": "https://rickhelmus.r-universe.dev", "Date/Publication": "2026-05-07 11:51:36 UTC", "RemoteUrl": "https://github.com/rickhelmus/cliqueMS", "RemoteRef": "HEAD", "RemoteSha": "b06c0fd579ff03972a44561fd19e107bbbea8e6d", "NeedsCompilation": "yes", "Packaged": { "Date": "2026-06-24 02:58:05 UTC", "User": "root" }, "Author": "Oriol Senan Campos [aut, cre],\nAntoni Aguilar-Mogas [aut],\nJordi Capellades [aut],\nMiriam Navarro [aut],\nOscar Yanes [aut],\nRoger Guimera [aut],\nMarta Sales-Pardo [aut]", "Maintainer": "Oriol Senan Campos ", "MD5sum": "8e6b508dbb62f82a0066171ceb400792", "_user": "rickhelmus", "_type": "src", "_file": "cliqueMS_1.14.1.tar.gz", "_fileid": "c16f5a6e076245807698d7db91b7d03d6631c39eb9a97448b0b17d8267a0e051", "_filesize": 700337, "_sha256": "c16f5a6e076245807698d7db91b7d03d6631c39eb9a97448b0b17d8267a0e051", "_created": "2026-06-24T02:58:05.000Z", "_published": "2026-06-24T03:11:45.064Z", "_distro": "resolute", "_jobs": [ { "job": 83108429301, "time": 375, "config": "linux-devel-arm64", "r": "4.7.0", "check": "ERROR", "artifact": "7839099128" }, { "job": 83108429321, "time": 411, "config": "linux-devel-x86_64", "r": "4.7.0", "check": "ERROR", "artifact": "7839107188" }, { "job": 83108429339, "time": 396, "config": "linux-release-arm64", "r": "4.6.0", "check": "ERROR", "artifact": "7839104221" }, { "job": 83108429350, "time": 417, "config": "linux-release-x86_64", "r": "4.6.0", "check": "ERROR", "artifact": "7839108762" }, { "job": 83108429312, "time": 79, "config": "macos-oldrel-arm64", "r": "4.5.3", "check": "FAIL", "artifact": "" }, { "job": 83108429329, "time": 154, "config": "macos-oldrel-x86_64", "r": "4.5.3", "check": "FAIL", "artifact": "" }, { "job": 83108429265, "time": 237, "config": "macos-release-arm64", "r": "4.6.0", "check": "ERROR", "artifact": "7839082903" }, { "job": 83108429298, "time": 661, "config": "macos-release-x86_64", "r": "4.6.0", "check": "ERROR", "artifact": "7839176010" }, { "job": 83107788226, "time": 374, "config": "source", "r": "4.6.0", "check": "ERROR", "artifact": "7839017126" }, { "job": 83108429244, "time": 225, "config": "wasm-release", "r": "4.6.0", "check": "OK", "artifact": "7839064873" }, { "job": 83108429271, "time": 386, "config": "windows-devel", "r": "4.7.0", "check": "ERROR", "artifact": "7839101565" }, { "job": 83108429266, "time": 119, "config": "windows-oldrel", "r": "4.5.3", "check": "FAIL", "artifact": "" }, { "job": 83108429273, "time": 378, "config": "windows-release", "r": "4.6.0", "check": "ERROR", "artifact": "7839099213" } ], "_buildurl": "https://github.com/r-universe/rickhelmus/actions/runs/28071812404", "_status": "failure", "_host": "GitHub-Actions", "_upstream": "https://github.com/rickhelmus/cliqueMS", "_commit": { "id": "b06c0fd579ff03972a44561fd19e107bbbea8e6d", "author": "rickhelmus ", "committer": "rickhelmus ", "message": "fix: make sure that isoTable is a data.frame if there are no isotope results\n", "time": 1778154696 }, "_maintainer": { "name": "Oriol Senan Campos", "email": "oriol.senan@praenoscere.com", "login": "osenan", "description": "R/Shiny developer at Appsilon. PhD in computational biology at U. Rovira i Virgili, but what I enjoy is programming with paper, pencil and no screen.", "uuid": 35930244 }, "_registered": true, "_dependencies": [ { "package": "R", "version": ">= 3.6.0", "role": "Depends" }, { "package": "Rcpp", "role": "LinkingTo" }, { "package": "BH", "role": "LinkingTo" }, { "package": "RcppArmadillo", "role": "LinkingTo" }, { "package": "Rcpp", "version": ">= 0.12.15", "role": "Imports" }, { "package": "xcms", "version": ">= 3.0.0", "role": "Imports" }, { "package": "MSnbase", "role": "Imports" }, { "package": "igraph", "role": "Imports" }, { "package": "qlcMatrix", "role": "Imports" }, { "package": "matrixStats", "role": "Imports" }, { "package": "methods", "role": "Imports" }, { "package": "knitr", "role": "Suggests" }, { "package": "rmarkdown", "role": "Suggests" }, { "package": "testthat", "role": "Suggests" }, { "package": "CAMERA", "role": "Suggests" } ], "_owner": "rickhelmus", "_selfowned": true, "_usedby": 0, "_updates": [ { "week": "2026-19", "n": 3 } ], "_tags": [], "_bioc": [ { "branch": "devel", "version": "1.27.0", "bioc": "3.24" }, { "branch": "release", "version": "1.26.0", "bioc": "3.23" } ], "_topics": [ "metabolomics", "massspectrometry", "network", "networkinference", "cpp" ], "_stars": 0, "_contributors": [ { "user": "osenan", "count": 38, "uuid": 35930244 }, { "user": "nturaga", "count": 10, "uuid": 2746443 }, { "user": "rickhelmus", "count": 3, "uuid": 37015911 }, { "user": "jwokaty", "count": 3, "uuid": 1744257 }, { "user": "hpages", "count": 2, "uuid": 8810451 } ], "_userbio": { "uuid": 37015911, "type": "user", "name": "rickhelmus", "followers": 24 }, "_downloads": { "count": 27, "source": "https://cranlogs.r-pkg.org/downloads/total/last-month/cliqueMS" }, "_devurl": "https://github.com/osenan/cliquems", "_searchresults": 28, "_rbuild": "4.6.0", "_assets": [ "extra/citation.cff", "extra/citation.html", "extra/citation.json", "extra/citation.txt", "extra/cliqueMS.html", "extra/contents.json", "extra/NEWS.html", "extra/NEWS.txt", "extra/readme.html", "extra/readme.md", "manual.pdf" ], "_homeurl": "https://github.com/osenan/cliquems", "_realowner": "bioc", "_cranurl": false, "_releases": [ { "version": "0.2.1", "date": "2018-05-14" }, { "version": "0.2.3", "date": "2018-11-15" }, { "version": "0.2.4", "date": "2019-01-11" }, { "version": "0.3.0", "date": "2019-01-30" }, { "version": "0.3.1", "date": "2019-04-25" } ], "_exports": [ "computeCliques", "createanClique", "createNetwork", "getAnnotation", "getCliques", "getIsolistanClique", "getIsotopes", "getlistofCliques", "getlistofCliques<-", "getNetanClique", "getNetanClique<-", "getPeaklistanClique", "getPeaklistanClique<-", "hasAnnotation", "hasAnnotation<-", "hasCliques", "hasCliques<-", "hasIsotopes", "hasIsotopes<-", "show" ], "_datasets": [ { "name": "ex.cliqueGroups", "title": "Example m/z processed data", "object": "ex.cliqueGroups", "file": "ex.cliqueGroups.RData", "class": [ "anClique" ], "fields": [], "table": false, "tojson": false }, { "name": "negative.adinfo", "title": "Default list of negative charged adducts", "object": "negative.adinfo", "file": "negative.adinfo.RData", "class": [ "data.frame" ], "fields": [ "adduct", "log10freq", "massdiff", "nummol", "charge" ], "rows": 11, "table": true, "tojson": true }, { "name": "positive.adinfo", "title": "Default list of positive charged adducts", "object": "positive.adinfo", "file": "positive.adinfo.RData", "class": [ "data.frame" ], "fields": [ "adduct", "log10freq", "massdiff", "nummol", "charge" ], "rows": 39, "table": true, "tojson": true } ], "_help": [ { "page": "anClique", "title": "'anClique' class constructor", "topics": [ "anClique" ] }, { "page": "anClique-class", "title": "'anClique' S4 class for annotating isotopes and adducts", "topics": [ "anClique-class", "getIsolistanClique", "getIsolistanClique,anClique-method", "getIsolistanClique<-", "getIsolistanClique<-,anClique-method", "getlistofCliques", "getlistofCliques,anClique-method", "getlistofCliques<-", "getlistofCliques<-,anClique-method", "getNetanClique", "getNetanClique,anClique-method", "getNetanClique<-", "getNetanClique<-,anClique-method", "getPeaklistanClique", "getPeaklistanClique,anClique-method", "getPeaklistanClique<-", "getPeaklistanClique<-,anClique-method", "hasAnnotation", "hasAnnotation,anClique-method", "hasAnnotation<-", "hasAnnotation<-,anClique-method", "hasCliques", "hasCliques,anClique-method", "hasCliques<-", "hasCliques<-,anClique-method", "hasIsotopes", "hasIsotopes,anClique-method", "hasIsotopes<-", "hasIsotopes<-,anClique-method", "show,anClique-method" ] }, { "page": "cliqueMS", "title": "'cliqueMS' annotates isotopes and adducts in m/z data", "topics": [ "cliqueMS-package", "cliqueMS" ] }, { "page": "computeCliques", "title": "Computes clique groups from a similarity network", "topics": [ "computeCliques" ] }, { "page": "createanClique", "title": "'createanClique' generic function to create an object of class 'anClique'.", "topics": [ "createanClique", "createanClique,XCMSnExp-method", "createanClique,xcmsSet-method" ] }, { "page": "createNetwork", "title": "Generic function to create a similarity network from processed m/z data", "topics": [ "createNetwork", "createNetwork,XCMSnExp-method", "createNetwork,xcmsSet-method" ] }, { "page": "ex.cliqueGroups", "title": "Example m/z processed data", "topics": [ "ex.cliqueGroups" ] }, { "page": "getAnnotation", "title": "Annotate adducts and fragments", "topics": [ "getAnnotation" ] }, { "page": "getCliques", "title": "Compute clique groups from processed m/z data", "topics": [ "getCliques" ] }, { "page": "getIsotopes", "title": "Annotate isotopes", "topics": [ "getIsotopes" ] }, { "page": "negative.adinfo", "title": "Default list of negative charged adducts", "topics": [ "negative.adinfo" ] }, { "page": "positive.adinfo", "title": "Default list of positive charged adducts", "topics": [ "positive.adinfo" ] } ], "_readme": "https://github.com/rickhelmus/cliqueMS/raw/HEAD/README.md", "_rundeps": [ "abind", "affy", "affyio", "AnnotationFilter", "askpass", "base64enc", "BH", "Biobase", "BiocBaseUtils", "BiocGenerics", "biocmake", "BiocManager", "BiocParallel", "bslib", "cachem", "cli", "clue", "cluster", "codetools", "cpp11", "crayon", "crosstalk", "curl", "data.table", "DBI", "DelayedArray", "digest", "dir.expiry", "docopt", "doParallel", "dplyr", "evaluate", "farver", "fastmap", "filelock", "fontawesome", "foreach", "formatR", "fs", "futile.logger", "futile.options", "generics", "GenomicRanges", "ggplot2", "glue", "gtable", "highr", "hms", "htmltools", "htmlwidgets", "httr", "igraph", "impute", "IRanges", "isoband", "iterators", "jquerylib", "jsonlite", "knitr", "labeling", "lambda.r", "later", "lattice", "lazyeval", "lifecycle", "limma", "magrittr", "MALDIquant", "MASS", "MassSpecWavelet", "Matrix", "MatrixGenerics", "matrixStats", "memoise", "MetaboCoreUtils", "mime", "MsCoreUtils", "MsExperiment", "MsFeatures", "MSnbase", "MultiAssayExperiment", "mzID", "mzR", "ncdf4", "openssl", "otel", "pcaMethods", "pillar", "pkgconfig", "plotly", "plyr", "preprocessCore", "prettyunits", "progress", "promises", "ProtGenerics", "PSMatch", "PTMods", "purrr", "QFeatures", "qlcMatrix", "R6", "rappdirs", "RColorBrewer", "Rcpp", "RcppArmadillo", "reshape2", "Rhdf5lib", "rlang", "rmarkdown", "S4Arrays", "S4Vectors", "S7", "sass", "scales", "Seqinfo", "slam", "snow", "SparseArray", "sparsesvd", "Spectra", "statmod", "stringi", "stringr", "SummarizedExperiment", "sys", "tibble", "tidyr", "tidyselect", "tinytex", "utf8", "vctrs", "viridisLite", "vsn", "withr", "xcms", "xfun", "XML", "XVector", "yaml" ], "_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": 3.7481880270062002, "_indexed": false, "_nocasepkg": "cliquems", "_universes": [ "rickhelmus" ], "_indexurl": "https://bioc.r-universe.dev/cliqueMS", "_binaries": [ { "r": "4.7.0", "os": "linux", "version": "1.14.1", "date": "2026-06-24T03:02:24.000Z", "distro": "resolute", "arch": "aarch64", "commit": "b06c0fd579ff03972a44561fd19e107bbbea8e6d", "fileid": "66972679a1743627124d7d3f36d5591bcbb74f1690b891f2563a1992e634890b", "status": "failure", "check": "ERROR", "buildurl": "https://github.com/r-universe/rickhelmus/actions/runs/28071812404" }, { "r": "4.7.0", "os": "linux", "version": "1.14.1", "date": "2026-06-24T03:02:04.000Z", "distro": "resolute", "arch": "x86_64", "commit": "b06c0fd579ff03972a44561fd19e107bbbea8e6d", "fileid": "0be465d3baad88d1d80a7377878917c946893030e9eea69606f03111e41a0346", "status": "failure", "check": "ERROR", "buildurl": "https://github.com/r-universe/rickhelmus/actions/runs/28071812404" }, { "r": "4.6.0", "os": "linux", "version": "1.14.1", "date": "2026-06-24T03:02:44.000Z", "distro": "resolute", "arch": "aarch64", "commit": "b06c0fd579ff03972a44561fd19e107bbbea8e6d", "fileid": "23d5c70f0252a607fad80195aa39d7732172a432d47ed5cff2bd443fc26b95fd", "status": "failure", "check": "ERROR", "buildurl": "https://github.com/r-universe/rickhelmus/actions/runs/28071812404" }, { "r": "4.6.0", "os": "linux", "version": "1.14.1", "date": "2026-06-24T03:02:12.000Z", "distro": "resolute", "arch": "x86_64", "commit": "b06c0fd579ff03972a44561fd19e107bbbea8e6d", "fileid": "ce677228801a74f5783e6b3ddc6c09a0cf358b4eb685292787cb61940ef50692", "status": "failure", "check": "ERROR", "buildurl": "https://github.com/r-universe/rickhelmus/actions/runs/28071812404" }, { "r": "4.6.0", "os": "mac", "version": "1.14.1", "date": "2026-06-24T03:01:52.000Z", "arch": "aarch64", "commit": "b06c0fd579ff03972a44561fd19e107bbbea8e6d", "fileid": "6729b845a9779db5ae23af731095849697ec2ee0e281f059dbb1c0916956ad13", "status": "failure", "check": "ERROR", "buildurl": "https://github.com/r-universe/rickhelmus/actions/runs/28071812404" }, { "r": "4.6.0", "os": "mac", "version": "1.14.1", "date": "2026-06-24T03:03:39.000Z", "arch": "x86_64", "commit": "b06c0fd579ff03972a44561fd19e107bbbea8e6d", "fileid": "ef50e16eb7385fdcccf10c0331bded64dbd52138056eced6c2daf50da5847c05", "status": "failure", "check": "ERROR", "buildurl": "https://github.com/r-universe/rickhelmus/actions/runs/28071812404" }, { "r": "4.6.0", "os": "wasm", "version": "1.14.1", "date": "2026-06-24T03:02:45.000Z", "arch": "emscripten", "commit": "b06c0fd579ff03972a44561fd19e107bbbea8e6d", "fileid": "e6600815eaacefac1b65d63f357f96cb94c35ff2ef67ceced8392aa107c1a41b", "status": "success", "buildurl": "https://github.com/r-universe/rickhelmus/actions/runs/28071812404" }, { "r": "4.7.0", "os": "win", "version": "1.14.1", "date": "2026-06-24T03:00:38.000Z", "arch": "x86_64", "commit": "b06c0fd579ff03972a44561fd19e107bbbea8e6d", "fileid": "b13ffdcaef3f6cb898a628a27235116cda2f0d32b1faae4d756afbe8aa28890e", "status": "failure", "check": "ERROR", "buildurl": "https://github.com/r-universe/rickhelmus/actions/runs/28071812404" }, { "r": "4.6.0", "os": "win", "version": "1.14.1", "date": "2026-06-24T03:00:46.000Z", "arch": "x86_64", "commit": "b06c0fd579ff03972a44561fd19e107bbbea8e6d", "fileid": "59498c838c9dad39e97ade92a450d123e2914cfb16225a50a5d867208cb9e38c", "status": "failure", "check": "ERROR", "buildurl": "https://github.com/r-universe/rickhelmus/actions/runs/28071812404" }, { "r": "4.5.3", "os": "mac", "version": "1.7.1", "date": "2026-04-20T05:19:31.000Z", "arch": "aarch64", "commit": "cb569e0b78ce0fa4254f1393874762bed08fa855", "fileid": "74b9a64089c984ffbdd630eecff8842bdbed49041a56cc52577172ae8409c5e0", "status": "failure", "check": "ERROR", "buildurl": "https://github.com/r-universe/rickhelmus/actions/runs/24649585437" }, { "r": "4.5.3", "os": "mac", "version": "1.7.1", "date": "2026-04-20T05:21:25.000Z", "arch": "x86_64", "commit": "cb569e0b78ce0fa4254f1393874762bed08fa855", "fileid": "86bee7458f3a199b3a4b8a6bfb7e9be047938153da732278489af4ad286ff2d6", "status": "failure", "check": "ERROR", "buildurl": "https://github.com/r-universe/rickhelmus/actions/runs/24649585437" }, { "r": "4.5.3", "os": "win", "version": "1.7.1", "date": "2026-04-20T05:22:21.000Z", "arch": "x86_64", "commit": "cb569e0b78ce0fa4254f1393874762bed08fa855", "fileid": "ae99325ed4c2bec1aeee3c363f36b879b939fa86c8d1f480884efb157b1c198a", "status": "failure", "check": "ERROR", "buildurl": "https://github.com/r-universe/rickhelmus/actions/runs/24649585437" } ] }