{ "_id": "6a10aa7dacfb0bcc41cbf087", "Package": "CellMentor", "Type": "Package", "Title": "Supervised Non-negative Matrix Factorization for Dimensional\nReduction in Single-Cell Analysis", "Version": "1.1.2", "Authors@R": "person(\"Ekaterina\", \"Petrenko\", \nemail = \"petrenko.kate@icloud.com\",\nrole = c(\"aut\", \"cre\"),\ncomment = c(ORCID = \"0000-0003-3549-834X\"))", "Description": "Implements supervised cell type-aware non-negative matrix\nfactorization (NMF) for dimensional reduction in single-cell\nRNA sequencing analysis. The package provides methods for\nincorporating cell type information into the dimensionality\nreduction process, enabling improved visualization and\ndownstream analysis of single-cell data while preserving\nbiological structure. CellMentor employs a unique loss function\nthat simultaneously minimizes variation within known cell\npopulations while maximizing distinctions between different\ncell types, enabling effective transfer of learned patterns\nfrom labeled reference datasets to new unlabeled data.", "License": "Apache License (>= 2)", "Encoding": "UTF-8", "Roxygen": "list(markdown = TRUE)", "RoxygenNote": "7.3.2", "VignetteBuilder": "knitr", "biocViews": "Software, SingleCell, Transcriptomics, DimensionReduction", "URL": "https://github.com/petrenkokate/CellMentor", "BugReports": "https://github.com/petrenkokate/CellMentor/issues", "Config/testthat/edition": "3", "Config/pak/sysreqs": "cmake libglpk-dev make libicu-dev libpng-dev\nlibuv1-dev libxml2-dev libssl-dev python3 zlib1g-dev", "Repository": "https://bioc.r-universe.dev", "Date/Publication": "2026-05-22 10:03:17 UTC", "RemoteUrl": "https://github.com/bioc/CellMentor", "RemoteRef": "HEAD", "RemoteSha": "52bfb5db78f2ce67c8e4f619ea1344b44a789d09", "NeedsCompilation": "no", "Packaged": { "Date": "2026-05-22 18:39:09 UTC", "User": "root" }, "Author": "Ekaterina Petrenko [aut, cre] (ORCID:\n)", "Maintainer": "Ekaterina Petrenko ", "MD5sum": "53c3e2709031096ee5f9ffa5faf37e43", "_user": "bioc", "_type": "src", "_file": "CellMentor_1.1.2.tar.gz", "_fileid": "38d21d67bd9481bafa69c13abee2526fcb7089f2260457e293a8d35fb832aa35", "_filesize": 259644, "_sha256": "38d21d67bd9481bafa69c13abee2526fcb7089f2260457e293a8d35fb832aa35", "_created": "2026-05-22T18:39:09.000Z", "_published": "2026-05-22T19:11:57.032Z", "_jobs": [ { "job": 77441410456, "time": 270, "config": "bioc-checks", "r": "4.6.0", "check": "WARNING", "artifact": "7167926527" }, { "job": 77441410485, "time": 737, "config": "linux-devel-x86_64", "r": "4.7.0", "check": "OK", "artifact": "7168072342" }, { "job": 77441410556, "time": 706, "config": "linux-release-x86_64", "r": "4.6.0", "check": "OK", "artifact": "7168062708" }, { "job": 77441410410, "time": 509, "config": "macos-oldrel-arm64", "r": "4.5.3", "check": "OK", "artifact": "7168017436" }, { "job": 77441410409, "time": 388, "config": "macos-release-arm64", "r": "4.6.0", "check": "OK", "artifact": "7167978913" }, { "job": 77440235971, "time": 468, "config": "source", "r": "4.6.0", "check": "OK", "artifact": "7167847224" }, { "job": 77441410444, "time": 214, "config": "wasm-release", "r": "4.6.0", "check": "OK", "artifact": "7167909823" }, { "job": 77441410469, "time": 1906, "config": "windows-devel", "r": "4.7.0", "check": "OK", "artifact": "7168419436" }, { "job": 77441410423, "time": 1557, "config": "windows-oldrel", "r": "4.5.3", "check": "OK", "artifact": "7168314855" }, { "job": 77441410468, "time": 1790, "config": "windows-release", "r": "4.6.0", "check": "OK", "artifact": "7168384368" } ], "_bioccheck": { "error": 0, "warning": 1, "note": 10 }, "_buildurl": "https://github.com/r-universe/bioc/actions/runs/26282330314", "_status": "success", "_host": "GitHub-Actions", "_upstream": "https://github.com/bioc/CellMentor", "_commit": { "id": "52bfb5db78f2ce67c8e4f619ea1344b44a789d09", "author": "Petrenko Kate ", "committer": "Petrenko Kate ", "message": "bug fix: factor-coerce NMI inputs for aricode 1.1.0 in Bioc 3.24\n\ncalculate_performance() in R/helper_functions.R was passing\naricode::NMI() a character vector of cell-type labels and a numeric\nvector of cluster IDs. aricode 1.1.0 (currently shipping in\nBioconductor 3.24) tightened input handling and now routes mixed-type\narguments through sort_pairs(), which calls as.integer() on the\ncharacter argument — turning labels such as \"alpha\" into NA and\naborting with \"NA are not supported.\" Both grid-search\nconfigurations in the vignette therefore failed, cascading to\n\"All parameter configurations failed; cannot select best_params\"\non the Bioconductor build farm.\n\nCoerce both NMI inputs to factor so labels and clusters share a\nwell-defined integer encoding. This restores the vignette and\npreserves the score semantics (NMI is invariant to label coding).\n\nThis is the underlying cause that the previous fix (1.1.1) surfaced\nwith a clearer error message but did not address.\n\nVerified in bioconductor/bioconductor_docker:devel (R 4.6.0 /\nBioc 3.24):\n R CMD build --keep-empty-dirs --no-resave-data --md5 CellMentor\n → creating vignettes ... OK\n R CMD check --no-manual CellMentor_1.1.2.tar.gz\n → Status: OK\n", "time": 1779444197 }, "_maintainer": { "name": "Ekaterina Petrenko", "email": "petrenko.kate@icloud.com", "login": "petrenkokate", "description": "", "uuid": 82456110, "orcid": "0000-0003-3549-834X" }, "_distro": "noble", "_registered": true, "_dependencies": [ { "package": "R", "version": ">= 4.5.0", "role": "Depends" }, { "package": "methods", "role": "Imports" }, { "package": "Matrix", "role": "Imports" }, { "package": "BiocParallel", "role": "Imports" }, { "package": "SingleR", "role": "Imports" }, { "package": "Seurat", "version": ">= 4.0.0", "role": "Imports" }, { "package": "utils", "role": "Imports" }, { "package": "stats", "role": "Imports" }, { "package": "parallel", "role": "Imports" }, { "package": "progress", "role": "Imports" }, { "package": "ggplot2", "role": "Imports" }, { "package": "data.table", "role": "Imports" }, { "package": "magrittr", "role": "Imports" }, { "package": "graphics", "role": 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