CRAN Package Check Results for Package ggmlR

Last updated on 2026-07-21 23:58:20 CEST.

Flavor	Version	Tinstall	Tcheck	Ttotal	Status	Flags
r-devel-linux-x86_64-debian-clang	0.8.1	113.17	293.54	406.71	OK
r-devel-linux-x86_64-debian-gcc	0.8.1	80.65	211.26	291.91	OK
r-devel-linux-x86_64-fedora-clang	0.8.1	167.00	473.80	640.80	OK
r-devel-linux-x86_64-fedora-gcc	0.8.1	88.00	200.61	288.61	ERROR
r-devel-windows-x86_64	0.8.1	159.00	391.00	550.00	OK
r-patched-linux-x86_64	0.8.1	124.15	287.41	411.56	OK
r-release-linux-x86_64	0.8.1	114.20	292.63	406.83	OK
r-release-macos-arm64	0.8.1	26.00	83.00	109.00	OK
r-release-macos-x86_64	0.8.1	82.00	379.00	461.00	OK
r-release-windows-x86_64	0.8.1	155.00	472.00	627.00	OK
r-oldrel-macos-arm64	0.8.1	23.00	89.00	112.00	OK
r-oldrel-macos-x86_64	0.8.1	78.00	375.00	453.00	OK
r-oldrel-windows-x86_64	0.8.1	178.00	557.00	735.00	OK

Check Details

Version: 0.8.1
Check: tests
Result: ERROR Running ‘testthat.R’ [46s/49s] Running the tests in ‘tests/testthat.R’ failed. Complete output: > library(testthat) > library(ggmlR) > > if (requireNamespace("mlr3", quietly = TRUE)) library(mlr3) > if (requireNamespace("parsnip", quietly = TRUE)) library(parsnip) > > heavy <- c( + "normalization", + "sequence-ops", + "binary-operations", + "glu", + "nn-sequential", + "matrix-ops", + "callbacks", + "onnx-quant", + "cpu-backend", + "onnx-elementwise", + "onnx-norm", + "onnx-misc", + "onnx-logic", + "onnx-gemm", + "onnx-resize", + "onnx-nn", + "nn-functional", + "activations-extended", + "onnx-ops", + "transformer-ops", + "onnx-shape", + "math-operations", + "activations", + "backend-extended", + "helpers", + "onnx-reduce", + "chain-sequential-batchnorm", + "chain-patterns", + "onnx-chain-quant", + "onnx-chain-qlinearconv", + "onnx-chain-uncovered-ops", + "onnx-chain-transformer", + "onnx-chain-broadcast-strict", + "onnx-chain-maskrcnn-broadcast", + "onnx-chain-erf-gelu", + "onnx-chain-resize-broadcast", + "onnx-chain-constantofshape-int64", + "onnx-chain-roberta-attn", + "onnx-chain-batched-matmul", + "onnx-chain-classify", + "onnx-chain-xcit-dynamic", + "onnx-chain-fpn", + "onnx-chain-pooling", + "onnx-chain-unet", + "onnx-chain-audio", + "onnx-chain-superres", + "onnx-chain-convtranspose", + "onnx-chain-eyelike", + "onnx-chain-decoder", + "onnx-chain-detect", + "onnx-chain-powernorm", + "onnx-chain-bert-mlp", + "onnx-chain-position", + "onnx-chain-attn-mask", + "onnx-chain-postprocess", + "onnx-chain-cast", + "onnx-chain-preprocess", + "model-ops", + "onnx-boundary", + "onnx-edge", + "parsnip", + "parsnip-tidymodels", + "parsnip-broom", + "seed", + "upscale", + "rope-multi", + "mlr3-learner", + "keras-api", + "quants-iq-degenerate", + "getrows-offload-vulkan", + "gpu-linalg" + ) > > # Under the valgrind memtest, running the full light suite (~67 files) blows > # the memory limit: valgrind's shadow memory accumulates across every > # ggml_init / backend buffer and never returns to the OS, so the process grows > # to several GiB and gets SIGKILLed regardless of any single test's size. > # valgrind's purpose here is to catch C-level memory bugs (use-after-free, > # invalid reads/writes) in the ggml bindings — a small core suite that > # exercises context/tensor lifecycle, basic ops and the backend is enough for > # that. So under valgrind we run an explicit whitelist instead of the full set. > valgrind_core <- c( + "tensors", # tensor create/free lifecycle + "context", # ggml_init / ggml_free + "ggml", # core library smoke + "types", # type helpers + "operations-extended", + "tensor-utils", + "backend", # backend init/free + buffers + "memory", + "quants" # quant/dequant round-trips + ) > > # Detect valgrind via several independent signals (any one is enough): > # 1. vgpreload_*.so injected into the process (visible in /proc/self/maps) > # 2. the RUNNING_ON_VALGRIND env var some setups export > # 3. R's own valgrind marker in the session (R_CHECK_*/loaded vg libs) > detect_valgrind <- function() { + if (nzchar(Sys.getenv("RUNNING_ON_VALGRIND"))) return(TRUE) + # /proc/self/maps holds vgpreload_core / vgpreload_memcheck under valgrind + m <- tryCatch(readLines("/proc/self/maps", warn = FALSE), + error = function(e) character(0)) + if (any(grepl("valgrind|vgpreload", m, ignore.case = TRUE))) return(TRUE) + # /proc/self/cmdline of the wrapping process: valgrind launches R + s <- tryCatch(readLines("/proc/self/status", warn = FALSE), + error = function(e) character(0)) + ppid <- sub("^PPid:\\s*", "", grep("^PPid:", s, value = TRUE)) + if (length(ppid) == 1L) { + pcmd <- tryCatch( + readChar(file.path("/proc", ppid, "cmdline"), 1e4, useBytes = TRUE), + error = function(e) "") + if (grepl("valgrind", pcmd, ignore.case = TRUE)) return(TRUE) + } + FALSE + } > under_valgrind <- isTRUE(detect_valgrind()) Warning message: In readChar(file.path("/proc", ppid, "cmdline"), 10000, useBytes = TRUE) : truncating string with embedded nuls > message("valgrind detected: ", under_valgrind) valgrind detected: FALSE > > # Disable OpenMP thread pool under valgrind: GOMP_parallel → pthread_create > # allocates 352b TLS per worker thread which valgrind flags as "possibly lost". > # Under valgrind we test correctness, not throughput — 1 thread is sufficient. > if (under_valgrind) { + Sys.setenv(OMP_NUM_THREADS = "1") + } > > on_cran <- !identical(Sys.getenv("NOT_CRAN"), "true") > > test_dir <- if (dir.exists("testthat")) "testthat" else "tests/testthat" > > if (on_cran) { + message("--- RUNNING LIGHT TESTS ONLY ---") + + all_tests <- list.files(test_dir, pattern = "^test-.*\\.R$") + all_names <- sub("^test-(.*)\\.R$", "\\1", all_tests) + + if (under_valgrind) { + message("--- VALGRIND DETECTED: running small core suite only ---") + # Whitelist intersected with what actually exists in the package. + light_tests <- intersect(valgrind_core, all_names) + } else { + light_tests <- setdiff(all_names, heavy) + } + message("Tests to run: ", paste(light_tests, collapse = ", ")) + + if (length(light_tests) == 0) { + # fallback + test_check("ggmlR") + } else { + # testthat applies `filter` as grepl(filter, <test name>) with no anchors, + # so anchor each name with ^...$ to avoid e.g. "backend" also matching + # "backend-buffers"/"backend-extended" (which would re-bloat the set). + filter_regex <- paste0("^(", paste(light_tests, collapse = "|"), ")$") + test_check("ggmlR", filter = filter_regex) + } + } else { + test_check("ggmlR") + } --- RUNNING LIGHT TESTS ONLY --- Tests to run: 5d-ops, ag-device, ag-layers, ag-mha, ag-save, ag-training, autograd-missing, autograd-ops, autograd, backend-buffers, backend, chain-ag-early-stopping, context, conv-transpose-numeric, conv2d-cpu-gpu, conv2d-dw-numeric, conv2d-numeric, convolution-pooling, cpu-features, diagnostics, flash-attn-q4k, flash-attn-quants, functional-shared-layers, ggml, gguf, graph-extended, graph-utils, headers-sync, inplace-ops, logging, memory-extended, memory, meta-backend, misc-ops, mlr3-autograd, new-functions, new-ops-numeric, nn-functional-missing, onnx-activations, onnx-chain-roialign-nms, onnx-chain-scatter-gnn, onnx-helpers, onnx-math, onnx-meta, operations-extended, optimizer, print-methods, q4k-matmul-vulkan, quantization, quantize-fns, quants-missing, quants, reduction-ops, reset, reshape, sc-chunked, sc-knn-gpu, sc-largest-gene, sc-neighbors, sc-normalize-sparse, sc-sce, sc-seurat, sc-umap, scheduler, set-operations, softmax, static-lib, tensor-info, tensor-utils, tensors-extended, tensors, threading, types, version, vulkan-caps, vulkan-push-constants, vulkan-tensor-parallel, vulkan Using CPU backend GGML library loaded successfully! GGML version: 0.11.0 Tensor overhead: 448 bytes Saving _problems/test-sc-umap-339.R GGML library loaded successfully! GGML version: 0.11.0 Tensor overhead: 448 bytes Vulkan: NOT AVAILABLE To enable: install libvulkan-dev and glslc, then reinstall ggmlR Ubuntu/Debian: sudo apt install libvulkan-dev glslc [ FAIL 1 | WARN 0 | SKIP 72 | PASS 1537 ] ══ Skipped tests (72) ══════════════════════════════════════════════════════════ • No Vulkan GPU (7): 'test-sc-seurat.R:145:3', 'test-sc-seurat.R:281:3', 'test-sc-seurat.R:309:3', 'test-sc-seurat.R:321:3', 'test-sc-seurat.R:338:3', 'test-sc-seurat.R:359:3', 'test-sc-seurat.R:445:3' • No Vulkan GPU available (7): 'test-conv2d-cpu-gpu.R:55:3', 'test-conv2d-cpu-gpu.R:61:3', 'test-conv2d-cpu-gpu.R:71:3', 'test-conv2d-cpu-gpu.R:78:3', 'test-conv2d-cpu-gpu.R:88:3', 'test-conv2d-cpu-gpu.R:98:3', 'test-conv2d-cpu-gpu.R:108:3' • Overlapping pooling requires specific tensor layout - tested in 2D pooling (1): 'test-convolution-pooling.R:156:3' • Platform-dependent behavior (1): 'test-ggml.R:18:3' • Slow test (6): 'test-quants-missing.R:4:3', 'test-quants-missing.R:17:3', 'test-quants-missing.R:30:3', 'test-quants-missing.R:43:3', 'test-quants-missing.R:56:3', 'test-quants-missing.R:69:3' • Slow test - set GGMLR_SLOW_TESTS=1 to run (6): 'test-quants.R:142:3', 'test-quants.R:168:3', 'test-quants.R:218:3', 'test-quants.R:234:3', 'test-quants.R:250:3', 'test-quants.R:266:3' • Vulkan GPU not available (18): 'test-conv2d-numeric.R:68:3', 'test-flash-attn-q4k.R:42:3', 'test-flash-attn-quants.R:44:7', 'test-flash-attn-quants.R:44:7', 'test-flash-attn-quants.R:44:7', 'test-flash-attn-quants.R:44:7', 'test-flash-attn-quants.R:44:7', 'test-flash-attn-quants.R:44:7', 'test-q4k-matmul-vulkan.R:49:3', 'test-q4k-matmul-vulkan.R:55:3', 'test-q4k-matmul-vulkan.R:62:3', 'test-sc-normalize-sparse.R:77:3', 'test-sc-normalize-sparse.R:95:3', 'test-sc-umap.R:87:3', 'test-sc-umap.R:106:3', 'test-sc-umap.R:179:3', 'test-sc-umap.R:230:3', 'test-sc-umap.R:251:3' • Vulkan not available (15): 'test-scheduler.R:2:3', 'test-scheduler.R:28:3', 'test-scheduler.R:55:3', 'test-scheduler.R:109:3', 'test-scheduler.R:172:3', 'test-scheduler.R:188:3', 'test-scheduler.R:223:3', 'test-vulkan-caps.R:4:3', 'test-vulkan-caps.R:39:3', 'test-vulkan-push-constants.R:11:3', 'test-vulkan-push-constants.R:20:3', 'test-vulkan-push-constants.R:26:3', 'test-vulkan-push-constants.R:36:3', 'test-vulkan-push-constants.R:88:3', 'test-vulkan-push-constants.R:131:3' • Vulkan not available or no devices found (1): 'test-vulkan.R:321:5' • Vulkan not compiled in (1): 'test-vulkan-tensor-parallel.R:10:1' • ggml_flash_attn_back not implemented (TODO in ggml.c) (1): 'test-misc-ops.R:81:3' • ggml_graph_reset requires a backward graph with gradients allocated (1): 'test-graph-utils.R:44:3' • multi-input shared-layer predict not implemented (backend buffer not set) (1): 'test-functional-shared-layers.R:81:3' • no Vulkan GPU (4): 'test-sc-knn-gpu.R:50:3', 'test-sc-knn-gpu.R:76:3', 'test-sc-knn-gpu.R:89:3', 'test-sc-knn-gpu.R:95:3' • src/ directory not found (1): 'test-headers-sync.R:17:3' • src/ggml.h not found (1): 'test-headers-sync.R:42:3' ══ Failed tests ════════════════════════════════════════════════════════════════ ── Failure ('test-sc-umap.R:339:3'): op = 'umap' keeps known clusters separated (quality, not just shape) ── Expected `ss` < `4 * ss_uwot`. Actual comparison: 0.0197 >= 0.0184 Difference: 0.0013 >= 0 [ FAIL 1 | WARN 0 | SKIP 72 | PASS 1537 ] Error: ! Test failures. Execution halted Flavor: r-devel-linux-x86_64-fedora-gcc