{ "_id": "6ac8dd51de46216d5edd894a", "Package": "Rbebelm", "Title": "Native 'BebeLM', 'EmbeddingGemma', and 'ColBERT' CPU Backends\nfor R", "Version": "0.3.6-0.1.0", "Authors@R": "c(\nperson(given = \"Sounkou Mahamane\", family = \"Toure\",\nemail = \"sounkoutoure@gmail.com\", role = c(\"aut\", \"cre\")),\nperson(\"Maxime\", \"Chevalier-Boisvert\", role = \"cph\",\ncomment = \"BebeLM upstream\"),\nperson(\"Hiroaki\", \"Yutani\", role = \"cph\",\ncomment = \"savvy R/Rust interface\"),\nperson(\"llama.cpp contributors\", role = c(\"ctb\", \"cph\"),\ncomment = \"MIT-licensed tokenizer and EmbeddingGemma reference semantics\")\n)", "Description": "Provides focused R interfaces to the pure-Rust 'BebeLM'\nCPU inference library and\na native pure-Rust implementation of the retrieval-trained\n'EmbeddingGemma' encoder\n, and a native\nprofile for LiquidAI's retrieval-trained LFM2.5-'ColBERT' GGUF\nencoder. The package exposes GGUF model loading, tokenizer\naccess, semantic text embeddings, late-interaction token\nvectors and MaxSim scoring, streaming generation events,\npersistent conversation agents, 'BebeLM' tool-call parsing, R\ntool dispatch, and Rust-thread async generation jobs. Loaded\nagents share model weights in process through Rust\nreference-counted handles, and GGUF files are mapped read-only\nso repeated loads of the same file can share physical pages\nthrough the operating-system page cache. Native libraries are\nbuilt as runtime-selected CPU backends so portable R binaries\ncan use scalar code by default and optimized SIMD backends when\navailable.", "License": "GPL (>= 3)", "URL": "https://github.com/sounkou-bioinfo/Rbebelm,\nhttps://sounkou-bioinfo.github.io/Rbebelm", "BugReports": "https://github.com/sounkou-bioinfo/Rbebelm/issues", "Encoding": "UTF-8", "Roxygen": "list(markdown = TRUE)", "SystemRequirements": "Rust toolchain with cargo (>= 1.85), GNU make", "Config/roxygen2/version": "8.0.0", "Config/pak/sysreqs": "make libclang-dev", "Repository": "https://rgenomicsetl.r-universe.dev", "Date/Publication": "2026-08-05 13:38:11 UTC", "RemoteUrl": "https://github.com/RGenomicsETL/Rbebelm", "RemoteRef": "HEAD", "RemoteSha": "507a8877141108070a7d8b66f503844cd324ff53", "NeedsCompilation": "yes", "Packaged": { "Date": "2026-10-09 12:17:00 UTC", "User": "root" }, "Author": "Sounkou Mahamane Toure [aut, cre],\nMaxime Chevalier-Boisvert [cph] (BebeLM upstream),\nHiroaki Yutani [cph] (savvy R/Rust interface),\nllama.cpp contributors [ctb, cph] (MIT-licensed tokenizer and\nEmbeddingGemma reference semantics)", "Maintainer": "Sounkou Mahamane Toure ", "_user": "rgenomicsetl", "_type": "src", "_file": "Rbebelm_0.3.6-0.1.0.tar.gz", "_fileid": "https://r2.ropensci.org/d9cb65848810fd24027977decc6e683b7a211292bbfb9b99a36f1f79d5e9fe97", "_filesize": 369416, "_sha256": "d9cb65848810fd24027977decc6e683b7a211292bbfb9b99a36f1f79d5e9fe97", "_expires": "2027-01-17T12:25:51.000Z", "_created": "2026-10-09T12:17:00.000Z", "_published": "2026-10-09T12:25:53.601Z", "_buildurl": "https://github.com/r-universe/rgenomicsetl/actions/runs/37928699176", "_status": "success", "_host": "GitHub-Actions", "_jobs": [ { "job": 113815181984, "time": 193, "config": "linux-devel-arm64", "r": "4.7.0", "check": "OK", "artifact": "11614923082" }, { "job": 113815182113, "time": 172, "config": "linux-devel-x86_64", "r": "4.7.0", "check": "OK", "artifact": "11615292751" }, { "job": 113815182002, "time": 157, "config": "linux-release-arm64", "r": "4.6.1", "check": "OK", "artifact": "11615372928" }, { "job": 113815182088, "time": 177, "config": "linux-release-x86_64", "r": "4.6.1", "check": "OK", "artifact": "11615202836" }, { "job": 113815182038, "time": 184, "config": "macos-oldrel-arm64", "r": "4.5.3", "check": "NOTE", "artifact": "11615746724" }, { "job": 113815182034, "time": 277, "config": "macos-oldrel-x86_64", "r": "4.5.3", "check": "NOTE", "artifact": "11615008407" }, { "job": 113815182124, "time": 177, "config": "macos-release-arm64", "r": "4.6.1", "check": "OK", "artifact": "11615572285" }, { "job": 113815181971, "time": 443, "config": "macos-release-x86_64", "r": "4.6.1", "check": "OK", "artifact": "11615293489" }, { "job": 113813906282, "time": 213, "config": "source", "r": "4.6.1", "check": "OK", "artifact": "11615751009" }, { "job": 113815181965, "time": 146, "config": "wasm-release", "r": "4.6.0", "check": "OK", "artifact": "11615162917" }, { "job": 113815182099, "time": 295, "config": "windows-devel-arm64", "r": "4.7.0", "check": "OK", "artifact": "11615617132" }, { "job": 113815182014, "time": 236, "config": "windows-devel-x86_64", "r": "4.7.0", "check": "NOTE", "artifact": "11615123173" }, { "job": 113815182040, "time": 219, "config": "windows-oldrel-x86_64", "r": "4.5.3", "check": "NOTE", "artifact": "11614968235" }, { "job": 113815182083, "time": 294, "config": "windows-release-arm64", "r": "4.6.1", "check": "OK", "artifact": "11615308052" }, { "job": 113815182079, "time": 195, "config": "windows-release-x86_64", "r": "4.6.1", "check": "NOTE", "artifact": "11615956290" } ], "_upstream": "https://github.com/RGenomicsETL/Rbebelm", "_commit": { "id": "507a8877141108070a7d8b66f503844cd324ff53", "author": "sounkou-bioinfo ", "committer": "sounkou-bioinfo ", "message": "Use the ARM64 R DLL location\n", "time": 1785937091 }, "_maintainer": { "name": "Sounkou Mahamane Toure", "email": "sounkoutoure@gmail.com", "login": "sounkou-bioinfo", "mastodon": "@bioinfhotep@genomic.social", "description": "Sequences and Consequences.", "uuid": 56392505 }, "_distro": "resolute", "_registered": true, "_dependencies": [ { "package": "S7", "role": "Imports" }, { "package": "yyjsonr", "role": "Imports" }, { "package": "tinytest", "role": "Suggests" }, { "package": "roxygen2", "role": "Suggests" }, { "package": "rmarkdown", "role": "Suggests" }, { "package": "knitr", "role": "Suggests" }, { "package": "pkgdown", "role": "Suggests" } ], "_owner": "rgenomicsetl", "_selfowned": true, "_usedby": 0, "_updates": [ { "week": "2026-23", "n": 32 }, { "week": "2026-24", "n": 12 }, { "week": "2026-28", "n": 16 }, { "week": "2026-29", "n": 6 }, { "week": "2026-30", "n": 1 }, { "week": "2026-32", "n": 4 } ], "_tags": [], "_topics": [ "local-llm", "rust", "simd", "cargo" ], "_stars": 1, "_contributors": [ { "user": "sounkou-bioinfo", "count": 71, "uuid": 56392505 } ], "_userbio": { "uuid": 252609706, "type": "organization", "name": "GenomicsETL", "followers": 10, "description": "Composable genomics in DuckDB, with R, the browser and agents as front ends" }, "_downloads": { "count": 0, "source": "https://cranlogs.r-pkg.org/downloads/total/last-month/Rbebelm" }, "_devurl": "https://github.com/sounkou-bioinfo/rbebelm", "_searchresults": 16, "_cargo": true, "_rbuild": "4.6.1", "_assets": [ "extra/citation.cff", "extra/citation.html", "extra/citation.json", "extra/citation.txt", "extra/contents.json", "extra/manual.pdf", "extra/NEWS.html", "extra/NEWS.txt", "extra/Rbebelm.html", "extra/readme.html", "extra/readme.md" ], "_cranurl": false, "_exports": [ "bebel_agent", "bebel_agent_configure", "bebel_agent_generate", "bebel_agent_generate_async", "bebel_agent_info", "bebel_agent_run", "bebel_append", "bebel_append_system", "bebel_append_tokens", "bebel_append_tool_result", "bebel_append_user", "bebel_assistant_turn", "bebel_assistant_turn_async", "bebel_assistant_turn_tool_stop", "bebel_assistant_turn_tool_stop_async", "bebel_async_cancel", "bebel_async_collect", "bebel_async_events", "bebel_async_poll", "bebel_async_wait", "bebel_benchmark_generation", "bebel_chat", "bebel_chat_async", "bebel_clear", "bebel_detokenize", "bebel_event_handler", "bebel_event_types", "bebel_generate", "bebel_generate_async", "bebel_history", "bebel_model_load", "bebel_parse_tool_call", "bebel_parse_tool_calls", "bebel_token_ids", "bebel_tokenize", "bebel_tool", "bebel_tool_schema_json", "bebel_transcript", "BebelAgent", "BebelAgentConfigureOptions", "BebelAgentOptions", "BebelAgentRef", "BebelAgentRunOptions", "BebelAsyncEventDrainOptions", "BebelAsyncJob", "BebelAsyncJobRef", "BebelAsyncWaitOptions", "BebelGenerationBenchmarkOptions", "BebelGenerationOptions", "BebelModel", "BebelModelLoadOptions", "BebelModelRef", "BebelScalarText", "BebelTokenizeOptions", "BebelToolRef", "BebelToolSpec", "colbert_embedding_ids", "colbert_embedding_vectors", "colbert_embeddings_info", "colbert_encode_document", "colbert_encode_query", "colbert_maxsim", "colbert_model_info", "colbert_model_load", "colbert_rank", "ColbertEmbeddings", "ColbertEmbeddingsRef", "ColbertModel", "ColbertModelLoadOptions", "ColbertModelRef", "embeddinggemma_embed", "embeddinggemma_embed_document", "embeddinggemma_embed_query", "embeddinggemma_model_info", "embeddinggemma_model_load", "embeddinggemma_tokenize", "EmbeddingGemmaLoadOptions", "EmbeddingGemmaModel", "EmbeddingGemmaModelRef", "EmbeddingGemmaOptions", "rbebelm_backend_features", "rbebelm_backend_info", "rbebelm_cpuid_info", "rbebelm_set_backend" ], "_help": [ { "page": "bebel_agent", "title": "Create a persistent BebeLM agent", "topics": [ "bebel_agent" ] }, { "page": "bebel_agent_configure", "title": "Configure a BebeLM agent", "topics": [ "bebel_agent_configure" ] }, { "page": "bebel_agent_generate", "title": "Generate a raw continuation from a BebeLM agent transcript", "topics": [ "bebel_agent_generate" ] }, { "page": "bebel_agent_generate_async", "title": "Start a background raw agent generation job", "topics": [ "bebel_agent_generate_async" ] }, { "page": "bebel_agent_info", "title": "Inspect a BebeLM agent", "topics": [ "bebel_agent_info" ] }, { "page": "bebel_agent_run", "title": "Run a BebeLM agent with R tool dispatch", "topics": [ "bebel_agent_run" ] }, { "page": "bebel_append", "title": "Append raw text to a BebeLM agent transcript", "topics": [ "bebel_append" ] }, { "page": "bebel_append_system", "title": "Append an upstream BebeLM system turn to an agent transcript", "topics": [ "bebel_append_system" ] }, { "page": "bebel_append_tokens", "title": "Append token ids to a BebeLM agent transcript", "topics": [ "bebel_append_tokens" ] }, { "page": "bebel_append_tool_result", "title": "Append a ChatML tool result turn to a BebeLM agent transcript", "topics": [ "bebel_append_tool_result" ] }, { "page": "bebel_append_user", "title": "Append a ChatML user turn to a BebeLM agent transcript", "topics": [ "bebel_append_user" ] }, { "page": "bebel_assistant_turn", "title": "Generate and close an assistant ChatML turn from a BebeLM agent", "topics": [ "bebel_assistant_turn" ] }, { "page": "bebel_assistant_turn_async", "title": "Start a background assistant-turn job", "topics": [ "bebel_assistant_turn_async" ] }, { "page": "bebel_assistant_turn_tool_stop", "title": "Open an assistant turn and stop when a tool call closes", "topics": [ "bebel_assistant_turn_tool_stop" ] }, { "page": "bebel_assistant_turn_tool_stop_async", "title": "Start a background assistant-turn job that stops on tool-call close", "topics": [ "bebel_assistant_turn_tool_stop_async" ] }, { "page": "bebel_async_cancel", "title": "Cancel a BebeLM async job", "topics": [ "bebel_async_cancel" ] }, { "page": "bebel_async_collect", "title": "Collect a BebeLM async job result", "topics": [ "bebel_async_collect" ] }, { "page": "bebel_async_events", "title": "Drain queued BebeLM async job events", "topics": [ "bebel_async_events" ] }, { "page": "bebel_async_poll", "title": "Poll a BebeLM async job", "topics": [ "bebel_async_poll" ] }, { "page": "bebel_async_wait", "title": "Wait for a BebeLM async job", "topics": [ "bebel_async_wait" ] }, { "page": "bebel_benchmark_generation", "title": "Benchmark async BebeLM generation throughput", "topics": [ "bebel_benchmark_generation" ] }, { "page": "bebel_chat", "title": "Generate a single ChatML assistant reply", "topics": [ "bebel_chat" ] }, { "page": "bebel_chat_async", "title": "Start a background ChatML assistant reply job", "topics": [ "bebel_chat_async" ] }, { "page": "bebel_clear", "title": "Clear a BebeLM agent transcript and caches", "topics": [ "bebel_clear" ] }, { "page": "bebel_detokenize", "title": "Decode BebeLM token ids", "topics": [ "bebel_detokenize" ] }, { "page": "bebel_event_handler", "title": "Build a BebeLM generation event handler", "topics": [ "bebel_event_handler" ] }, { "page": "bebel_event_types", "title": "Return BebeLM stream event types.", "topics": [ "bebel_event_types" ] }, { "page": "bebel_generate", "title": "Generate a raw continuation from a prompt", "topics": [ "bebel_generate" ] }, { "page": "bebel_generate_async", "title": "Start a background raw generation job", "topics": [ "bebel_generate_async" ] }, { "page": "bebel_history", "title": "Return a BebeLM agent token transcript", "topics": [ "bebel_history" ] }, { "page": "bebel_model_load", "title": "Load a BebeLM GGUF model", "topics": [ "bebel_model_load" ] }, { "page": "bebel_parse_tool_call", "title": "Parse a single BebeLM tool call block", "topics": [ "bebel_parse_tool_call" ] }, { "page": "bebel_parse_tool_calls", "title": "Parse BebeLM tool calls", "topics": [ "bebel_parse_tool_calls" ] }, { "page": "bebel_token_ids", "title": "Return BebeLM tokenizer special token ids.", "topics": [ "bebel_token_ids" ] }, { "page": "bebel_tokenize", "title": "Tokenize text with a BebeLM model tokenizer", "topics": [ "bebel_tokenize" ] }, { "page": "bebel_tool", "title": "Define a BebeLM R tool", "topics": [ "bebel_tool" ] }, { "page": "bebel_tool_schema_json", "title": "Render a BebeLM tool schema", "topics": [ "bebel_tool_schema_json" ] }, { "page": "bebel_transcript", "title": "Decode a BebeLM agent transcript", "topics": [ "bebel_transcript" ] }, { "page": "BebelAgent", "title": "Persistent BebeLM conversation agent with transcript and decode caches.", "topics": [ "BebelAgent" ] }, { "page": "BebelAgentConfigureOptions", "title": "Agent configuration update", "topics": [ "BebelAgentConfigureOptions" ] }, { "page": "BebelAgentOptions", "title": "Agent construction options", "topics": [ "BebelAgentOptions" ] }, { "page": "BebelAgentRef", "title": "BebeLM agent reference", "topics": [ "BebelAgentRef" ] }, { "page": "BebelAgentRunOptions", "title": "Agent run options", "topics": [ "BebelAgentRunOptions" ] }, { "page": "BebelAsyncEventDrainOptions", "title": "Async event drain options", "topics": [ "BebelAsyncEventDrainOptions" ] }, { "page": "BebelAsyncJob", "title": "Background BebeLM generation job.", "topics": [ "BebelAsyncJob" ] }, { "page": "BebelAsyncJobRef", "title": "BebeLM async job reference", "topics": [ "BebelAsyncJobRef" ] }, { "page": "BebelAsyncWaitOptions", "title": "Async wait options", "topics": [ "BebelAsyncWaitOptions" ] }, { "page": "BebelGenerationBenchmarkOptions", "title": "Generation benchmark options", "topics": [ "BebelGenerationBenchmarkOptions" ] }, { "page": "BebelGenerationOptions", "title": "Generation options", "topics": [ "BebelGenerationOptions" ] }, { "page": "BebelModel", "title": "Loaded BebeLM GGUF generation model.", "topics": [ "BebelModel" ] }, { "page": "BebelModelLoadOptions", "title": "Model loading options", "topics": [ "BebelModelLoadOptions" ] }, { "page": "BebelModelRef", "title": "BebeLM model reference", "topics": [ "BebelModelRef" ] }, { "page": "BebelScalarText", "title": "Scalar non-empty text", "topics": [ "BebelScalarText" ] }, { "page": "BebelTokenizeOptions", "title": "Tokenizer options", "topics": [ "BebelTokenizeOptions" ] }, { "page": "BebelToolRef", "title": "BebeLM tool reference", "topics": [ "BebelToolRef" ] }, { "page": "BebelToolSpec", "title": "R tool exposed to BebeLM", "topics": [ "BebelToolSpec" ] }, { "page": "colbert_embedding_ids", "title": "Return model-input ids aligned to ColBERT token vectors", "topics": [ "colbert_embedding_ids" ] }, { "page": "colbert_embedding_vectors", "title": "Materialize ColBERT token vectors", "topics": [ "colbert_embedding_vectors" ] }, { "page": "colbert_embeddings_info", "title": "Inspect ColBERT token vectors", "topics": [ "colbert_embeddings_info" ] }, { "page": "colbert_encode_document", "title": "Encode a retrieval document with ColBERT", "topics": [ "colbert_encode_document" ] }, { "page": "colbert_encode_query", "title": "Encode a retrieval query with ColBERT", "topics": [ "colbert_encode_query" ] }, { "page": "colbert_maxsim", "title": "Score a query and document with ColBERT MaxSim", "topics": [ "colbert_maxsim" ] }, { "page": "colbert_model_info", "title": "Inspect a ColBERT model", "topics": [ "colbert_model_info" ] }, { "page": "colbert_model_load", "title": "Load a native LFM2.5-ColBERT GGUF model", "topics": [ "colbert_model_load" ] }, { "page": "colbert_rank", "title": "Rank documents with ColBERT MaxSim", "topics": [ "colbert_rank" ] }, { "page": "ColbertEmbeddings", "title": "One query or document's L2-normalized ColBERT token vectors.", "topics": [ "ColbertEmbeddings" ] }, { "page": "ColbertEmbeddingsRef", "title": "ColBERT token-vector reference", "topics": [ "ColbertEmbeddingsRef" ] }, { "page": "ColbertModel", "title": "Loaded LFM2.5-ColBERT GGUF model.", "topics": [ "ColbertModel" ] }, { "page": "ColbertModelLoadOptions", "title": "ColBERT loading options", "topics": [ "ColbertModelLoadOptions" ] }, { "page": "ColbertModelRef", "title": "ColBERT model reference", "topics": [ "ColbertModelRef" ] }, { "page": "embeddinggemma_embed", "title": "Generate EmbeddingGemma text embeddings", "topics": [ "embeddinggemma_embed" ] }, { "page": "embeddinggemma_embed_document", "title": "Encode retrieval documents with EmbeddingGemma", "topics": [ "embeddinggemma_embed_document" ] }, { "page": "embeddinggemma_embed_query", "title": "Encode retrieval queries with EmbeddingGemma", "topics": [ "embeddinggemma_embed_query" ] }, { "page": "embeddinggemma_model_info", "title": "Inspect an EmbeddingGemma model", "topics": [ "embeddinggemma_model_info" ] }, { "page": "embeddinggemma_model_load", "title": "Load an EmbeddingGemma GGUF model", "topics": [ "embeddinggemma_model_load" ] }, { "page": "embeddinggemma_tokenize", "title": "Tokenize EmbeddingGemma model input", "topics": [ "embeddinggemma_tokenize" ] }, { "page": "EmbeddingGemmaLoadOptions", "title": "EmbeddingGemma loading options", "topics": [ "EmbeddingGemmaLoadOptions" ] }, { "page": "EmbeddingGemmaModel", "title": "Loaded EmbeddingGemma GGUF model.", "topics": [ "EmbeddingGemmaModel" ] }, { "page": "EmbeddingGemmaModelRef", 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