{ "_id": "6ada32b92ccc51e6c64e4fb4", "Encoding": "UTF-8", "Package": "opentimsr", "Type": "Package", "Title": "An Open-Source Loader for Bruker's timsTOF Data Files", "Version": "1.2.0", "Date": "2026-09-24", "Authors@R": "c(person(given=\"Michał Piotr\",\nfamily=\"Startek\",\nrole=c(\"aut\",\"cph\"),\nemail=\"michal.startek@mimuw.edu.pl\",\ncomment=c(ORCID=\"0000-0001-5227-3447\")),\nperson(given=\"Mateusz Krzysztof\",\nfamily=\"Łącki\",\nrole=c(\"aut\",\"cre\",\"cph\"),\nemail=\"matteo.lacki@gmail.com\",\ncomment=c(ORCID=\"0000-0001-7415-4748\")),\nperson(given=\"mandreyel\",\nrole=c(\"ctb\",\"cph\"),\ncomment=\"Author and copyright holder of the bundled 'mio' library (https://github.com/mandreyel/mio)\")\n)", "Maintainer": "Mateusz Krzysztof Łącki ", "Description": "Reads raw data from Bruker's timsTOF mass spectrometers,\nstored in analysis.tdf and analysis.tdf_bin files inside .d\nfolders. Frames can be selected by number or by retention time,\nand each peak is reported with its scan, time-of-flight index,\nintensity, mass-to-charge ratio and inverse ion mobility.\nMass-to-charge ratios and ion mobilities are computed with\nbuilt-in open-source calibration, or optionally with Bruker's\nproprietary library. See Łącki et al. (2021)\n.", "License": "MIT + file LICENSE", "Copyright": "See file inst/COPYRIGHTS", "URL": "https://github.com/michalsta/opentims", "BugReports": "https://github.com/michalsta/opentims/issues", "NeedsCompilation": "yes", "SystemRequirements": "C++20, libzstd", "Config/roxygen2/version": "8.1.1", "Packaged": { "Date": "2026-10-22 15:37:13 UTC", "User": "root" }, "Author": "Michał Piotr Startek [aut, cph] (ORCID:\n), Mateusz Krzysztof\nŁącki [aut, cre, cph] (ORCID:\n), mandreyel [ctb, cph]\n(Author and copyright holder of the bundled 'mio' library\n(https://github.com/mandreyel/mio))", "Config/pak/sysreqs": "libzstd-dev", "Repository": "https://cran.r-universe.dev", "Date/Publication": "2026-10-22 10:00:08 UTC", "RemoteUrl": "https://github.com/cran/opentimsr", "RemoteRef": "HEAD", "RemoteSha": "82141cd2b7dc1e77a85c8c0d1f5620266f90bec6", "_user": "cran", "_type": "src", "_file": "opentimsr_1.2.0.tar.gz", "_fileid": "https://r2.ropensci.org/2b3825a048ec9997a4316ffe60c83e4d1948b5031c4ac0322b18282614edb61b", "_filesize": 378448, "_sha256": "2b3825a048ec9997a4316ffe60c83e4d1948b5031c4ac0322b18282614edb61b", "_expires": "2027-01-30T15:58:46.000Z", "_created": "2026-10-22T15:37:13.000Z", "_published": "2026-10-22T15:58:49.050Z", "_upstream": "https://github.com/cran/opentimsr", "_status": "success", "_maintainer": { "name": "Mateusz Krzysztof Łącki", "email": "matteo.lacki@gmail.com", "login": "matteolacki", "description": "No Bio, go Mech.", "uuid": 3964160, "orcid": "0000-0001-7415-4748" }, "_jobs": [ { "job": 119921410762, "time": 147, "config": "linux-devel-arm64", "r": "4.7.0", "check": "OK", "artifact": "12438676247" }, { "job": 119921410571, "time": 120, "config": "linux-devel-x86_64", "r": "4.7.0", "check": "OK", "artifact": "12436824649" }, { "job": 119921410720, "time": 108, "config": "linux-release-arm64", "r": "4.6.1", "check": "OK", "artifact": "12437593115" }, { "job": 119921410451, "time": 279, "config": "linux-release-x86_64", "r": "4.6.1", "check": "OK", "artifact": "12437744453" }, { "job": 119919429137, "time": 215, "config": "source", "r": "4.6.1", "check": "OK", "artifact": "12438640999" }, { "job": 119921410538, "time": 140, "config": "wasm-release", "r": "4.6.0", "check": "OK", "artifact": "12437588212" }, { "job": 119921410896, "time": 194, "config": "windows-devel-arm64", "r": "4.7.0", "check": "OK", "artifact": "12437253938" }, { "job": 119921410625, "time": 173, "config": "windows-devel-x86_64", "r": "4.7.0", "check": "OK", "artifact": "12437089122" }, { "job": 119921410409, "time": 228, "config": "windows-release-arm64", "r": "4.6.1", "check": "OK", "artifact": "12438671514" }, { "job": 119921410437, "time": 120, "config": "windows-release-x86_64", "r": "4.6.1", "check": "OK", "artifact": "12438680791" } ], "_buildurl": "https://github.com/r-universe/cran/actions/runs/39805988279", "_commit": { "id": "82141cd2b7dc1e77a85c8c0d1f5620266f90bec6", "author": "Mateusz Krzysztof Łącki ", "committer": "cran-robot ", "message": "version 1.2.0\n", "time": 1792663208 }, "_distro": "resolute", "_host": "GitHub-Actions", "_registered": true, "_dependencies": [ { "package": "R", "version": ">= 4.3.0", "role": "Depends" }, { "package": "Rcpp", "role": "LinkingTo" }, { "package": "Rcpp", "version": ">= 0.12.0", "role": "Imports" }, { "package": "methods", "role": "Imports" }, { "package": "DBI", "role": "Imports" }, { "package": "RSQLite", "role": "Imports" }, { "package": "testthat", "version": ">= 3.0.0", "role": "Suggests" } ], "_owner": "cran", "_selfowned": false, "_usedby": 1, "_updates": [ { "week": "2026-43", "n": 1 } ], "_tags": [ { "name": "1.2.0", "date": "2026-10-22" } ], "_stars": 0, "_contributors": [ { "user": "michalsta", "count": 8, "uuid": 10774916 }, { "user": "matteolacki", "count": 1, "uuid": 3964160 } ], "_userbio": { "uuid": 6899542, "type": "organization", "name": "cran", "followers": 634, "description": "Unofficial read-only mirror of all CRAN R packages" }, "_downloads": { "count": 0, "source": "https://cranlogs.r-pkg.org/downloads/total/last-month/opentimsr" }, "_devurl": "https://github.com/michalsta/opentims", "_searchresults": 14, "_topics": [ "libzstd", "cpp" ], "_rbuild": "4.6.1", "_assets": [ "extra/citation.cff", "extra/citation.html", "extra/citation.json", "extra/citation.txt", "extra/contents.json", "extra/manual.pdf", "extra/opentimsr.html", "LICENSE" ], "_cranurl": false, "_releases": [ { "version": "1.0.2", "date": "2020-12-10" }, { "version": "1.0.3", "date": "2021-01-22" }, { "version": "1.0.4", "date": "2021-02-18" }, { "version": "1.0.5", "date": "2021-03-10" }, { "version": "1.0.7", "date": "2021-07-06" }, { "version": "1.0.11", "date": "2021-12-18" }, { "version": "1.0.12", "date": "2022-03-08" }, { "version": "1.0.13", "date": "2022-03-29" }, { "version": "1.2.0", "date": "2026-10-22" } ], "_exports": [ "CloseTIMS", "download_bruker_proprietary_code", "explore.tdf.tables", "get_separate_frames", "min_max_measurements", "MS1", "OpenTIMS", "opentims_set_threads", "peaks_per_frame_cnts", "query", "query_slice", "retention_times", "rt_query", "setup_bruker_so", "setup_opensource", "table2df", "tables_names", "use_inv_ion_mobility_lookup", "use_mz_lookup" ], "_help": [ { "page": "sub-OpenTIMS-method", "title": "Get some frames of data.", "topics": [ "[,OpenTIMS-method" ] }, { "page": "CloseTIMS", "title": "Close the TIMS data handle and release all resources.", "topics": [ "CloseTIMS" ] }, { "page": "download_bruker_proprietary_code", "title": "Get Bruker's code needed for running proprietary time of flight to mass over charge and scan to drift time conversion.", "topics": [ "download_bruker_proprietary_code" ] }, { "page": "explore.tdf.tables", "title": "Explore the contentents of the sqlite .tdf database.", "topics": [ "explore.tdf.tables" ] }, { "page": "get_separate_frames", "title": "Get frames as separate data frames.", "topics": [ "get_separate_frames" ] }, { "page": "length-OpenTIMS-method", "title": "Get the overall number of peaks.", "topics": [ "length,OpenTIMS-method" ] }, { "page": "min_max_measurements", "title": "Get border values for measurements.", "topics": [ "min_max_measurements" ] }, { "page": "MS1", "title": "Get MS1 frame numbers.", "topics": [ "MS1" ] }, { "page": "OpenTIMS", "title": "Get OpenTIMS data representation.", "topics": [ "OpenTIMS" ] }, { "page": "opentims_set_threads", "title": "Set the number of threads to be used for data processing by OpenTIMS", "topics": [ "opentims_set_threads" ] }, { "page": "OpenTIMS-class", "title": "TimsTOF data accessor.", "topics": [ "OpenTIMS-class" ] }, { "page": "peaks_per_frame_cnts", "title": "Get the number of peaks per frame.", "topics": [ "peaks_per_frame_cnts" ] }, { "page": "query", "title": "Query for raw data.", "topics": [ "query" ] }, { "page": "query_slice", "title": "Query for raw data.", "topics": [ "query_slice" ] }, { "page": "range-OpenTIMS-method", "title": "Select a range of frames to extract.", "topics": [ "range,OpenTIMS-method" ] }, { "page": "retention_times", "title": "Get the retention time for each frame.", "topics": [ "retention_times" ] }, { "page": "rt_query", "title": "Get the retention time for each frame.", "topics": [ "rt_query" ] }, { "page": "setup_bruker_so", "title": "Dynamically link Bruker's DLL to enable tof-mz and scan-inv_ion_mobility conversion.", "topics": [ "setup_bruker_so" ] }, { "page": "setup_opensource", "title": "Use the built-in open-source tof-to-mz and scan-to-inv_ion_mobility converters.", "topics": [ "setup_opensource" ] }, { "page": "table2df", "title": "Extract tables from sqlite database analysis.tdf.", "topics": [ "table2df" ] }, { "page": "tables_names", "title": "Extract tables from sqlite database analysis.tdf.", "topics": [ "tables_names" ] }, { "page": "use_inv_ion_mobility_lookup", "title": "Use a lookup table for inverse ion mobility conversion with Bruker's library.", "topics": [ "use_inv_ion_mobility_lookup" ] }, { "page": "use_mz_lookup", "title": "Use a lookup table for m/z conversion with Bruker's library.", "topics": [ "use_mz_lookup" ] } ], "_rundeps": [ "bit", "bit64", "blob", "cachem", "cli", "cpp11", "DBI", "fastmap", "glue", "lifecycle", "memoise", "pkgconfig", "Rcpp", "rlang", "RSQLite", "vctrs" ], "_sysdeps": [ { "shlib": "libzstd", "package": "libzstd1", "headers": "libzstd-dev", "source": "libzstd", "version": "1.5.7+dfsg-3", "name": "libzstd", "homepage": "https://github.com/facebook/zstd", "description": "fast lossless compression algorithm" }, { "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": 1.6232492903979003, "_indexed": false, "_nocasepkg": "opentimsr", "_universes": [ "cran", "matteolacki", "michalsta" ], "_indexurl": "https://matteolacki.r-universe.dev/opentimsr", "_binaries": [ { "r": "4.7.0", "os": "linux", "version": "1.2.0", "date": "2026-10-22T15:39:44.000Z", "distro": "resolute", "arch": "aarch64", "commit": "82141cd2b7dc1e77a85c8c0d1f5620266f90bec6", "fileid": "https://r2.ropensci.org/08253c9cbd220b98a1eebf059591ff86aa230ef753e95b6381c9ed66372cfc71", "status": "success", "check": "OK", "buildurl": "https://github.com/r-universe/cran/actions/runs/39805988279" }, { "r": "4.7.0", "os": "linux", "version": "1.2.0", "date": "2026-10-22T15:39:09.000Z", "distro": "resolute", "arch": "x86_64", "commit": "82141cd2b7dc1e77a85c8c0d1f5620266f90bec6", "fileid": "https://r2.ropensci.org/1abf65df3c828cf64c29d0d00d64ae283680a01c29e8ad59a899cab5c02c361f", "status": "success", "check": "OK", "buildurl": "https://github.com/r-universe/cran/actions/runs/39805988279" }, { "r": "4.6.1", "os": "linux", "version": "1.2.0", "date": "2026-10-22T15:39:05.000Z", "distro": "resolute", "arch": "aarch64", "commit": "82141cd2b7dc1e77a85c8c0d1f5620266f90bec6", "fileid": "https://r2.ropensci.org/a47ab3c82ce190c5be2d022f6a1a6be9db02b9a60a5645cbf36eda27fe26fbae", "status": "success", "check": "OK", "buildurl": "https://github.com/r-universe/cran/actions/runs/39805988279" }, { "r": "4.6.1", "os": "linux", "version": "1.2.0", "date": "2026-10-22T15:41:51.000Z", "distro": "resolute", "arch": "x86_64", "commit": "82141cd2b7dc1e77a85c8c0d1f5620266f90bec6", "fileid": "https://r2.ropensci.org/b92f7d18fad4ce754fc36319d0e35a4ff234901dc394ac8461dbfa1232524cd9", "status": "success", "check": "OK", "buildurl": "https://github.com/r-universe/cran/actions/runs/39805988279" }, { "r": "4.6.0", "os": "wasm", "version": "1.2.0", "date": "2026-10-22T15:39:43.000Z", "arch": "emscripten", "commit": "82141cd2b7dc1e77a85c8c0d1f5620266f90bec6", "fileid": "https://r2.ropensci.org/cc8295d1aadfdfb55d1a4d93d427507ed124bbaafd64c4204a83f9445d65c213", "status": "success", "buildurl": "https://github.com/r-universe/cran/actions/runs/39805988279" }, { "r": "4.7.0", "os": "win", "version": "1.2.0", "date": "2026-10-22T15:40:07.000Z", "arch": "aarch64", "commit": "82141cd2b7dc1e77a85c8c0d1f5620266f90bec6", "fileid": "https://r2.ropensci.org/9ce48acf597a5ef96df9a626285ab89e90a3a9cedaa5f6963f0515616ba413bd", "status": "success", "check": "OK", "buildurl": "https://github.com/r-universe/cran/actions/runs/39805988279" }, { "r": "4.7.0", "os": "win", "version": "1.2.0", "date": "2026-10-22T15:38:32.000Z", "arch": "x86_64", "commit": "82141cd2b7dc1e77a85c8c0d1f5620266f90bec6", "fileid": "https://r2.ropensci.org/e794eb2dd397e4cef030c8f04b33e0e4c6e72452bf862e50f07d96c0a7d05881", "status": "success", "check": "OK", "buildurl": "https://github.com/r-universe/cran/actions/runs/39805988279" }, { "r": "4.6.1", "os": "win", "version": "1.2.0", "date": "2026-10-22T15:40:44.000Z", "arch": "aarch64", "commit": "82141cd2b7dc1e77a85c8c0d1f5620266f90bec6", "fileid": "https://r2.ropensci.org/bebeb2fc304aaf5e2061820f47a2638c9b0f8cadb437def6f5dd7a7d32b976f0", "status": "success", "check": "OK", "buildurl": "https://github.com/r-universe/cran/actions/runs/39805988279" }, { "r": "4.6.1", "os": "win", "version": "1.2.0", "date": "2026-10-22T15:38:37.000Z", "arch": "x86_64", "commit": "82141cd2b7dc1e77a85c8c0d1f5620266f90bec6", "fileid": "https://r2.ropensci.org/8ad0d413ff3f2a4050d870b370ae6511e889d93fd3a958b4b6952b404c8cfa05", "status": "success", "check": "OK", "buildurl": "https://github.com/r-universe/cran/actions/runs/39805988279" } ] }