CRAN Package Check Results for Package asleep

Last updated on 2026-08-06 23:51:23 CEST.

Flavor	Version	Tinstall	Tcheck	Ttotal	Status	Flags
r-devel-linux-x86_64-debian-gcc	0.1.0	4.43	746.07	750.50	OK
r-devel-linux-x86_64-fedora-clang	0.1.0			97.03	OK
r-devel-linux-x86_64-fedora-gcc	0.1.0			100.22	OK
r-patched-linux-x86_64	0.1.0	5.44	686.34	691.78	OK
r-release-macos-arm64	0.1.0	2.00	170.00	172.00	OK
r-release-macos-x86_64	0.1.0	4.00	110.00	114.00	OK
r-release-windows-x86_64	0.1.0	12.00	974.00	986.00	OK
r-oldrel-macos-arm64	0.1.0	1.00	202.00	203.00	ERROR
r-oldrel-macos-x86_64	0.1.0	4.00	448.00	452.00	OK
r-oldrel-windows-x86_64	0.1.0	13.00	903.00	916.00	OK

Check Details

Version: 0.1.0
Check: tests
Result: ERROR Running ‘testthat.R’ [212s/180s] Running the tests in ‘tests/testthat.R’ failed. Complete output: > # This file is part of the standard setup for testthat. > # It is recommended that you do not modify it. > # > # Where should you do additional test configuration? > # Learn more about the roles of various files in: > # * https://r-pkgs.org/testing-design.html#sec-tests-files-overview > # * https://testthat.r-lib.org/articles/special-files.html > library(testthat) > library(asleep) > > asleep:::cleanup_uv_lock_files( + c(".", tempdir(), dirname(tempdir())) + ) > testthat::test_check("asleep") Downloading uv...Done! Downloading cpython-3.8.20-macos-aarch64-none (download) (16.6MiB) Downloaded cpython-3.8.20-macos-aarch64-none (download) Building antlr4-python3-runtime==4.9.3 Building importlib==1.0.4 Updating https://github.com/muschellij2/asleep.git (HEAD) Downloading transforms3d (1.3MiB) Downloading scikit-learn (7.2MiB) Downloading numba (2.5MiB) Downloading sympy (5.9MiB) Downloading torch (59.3MiB) Downloading statsmodels (9.6MiB) Downloading pandas (10.2MiB) Downloading scipy (27.5MiB) Downloading llvmlite (27.4MiB) Downloading torchvision (1.6MiB) Downloading fonttools (2.6MiB) Downloading numpy (13.2MiB) Downloading networkx (2.0MiB) Downloading matplotlib (7.0MiB) Built importlib==1.0.4 Downloading pillow (3.2MiB) Built antlr4-python3-runtime==4.9.3 Downloaded transforms3d Downloaded torchvision Downloaded fonttools Building pyyaml==6.0.3 Downloaded pillow Downloaded networkx Downloaded numba Downloaded matplotlib Downloaded scikit-learn Downloaded sympy Downloaded statsmodels Downloaded pandas Downloaded numpy Downloaded llvmlite Downloaded scipy Updated https://github.com/muschellij2/asleep.git (4916a50c61dfe513a04ab340da3bfc4bd93dc96d) Building asleep @ git+https://github.com/muschellij2/asleep.git@4916a50c61dfe513a04ab340da3bfc4bd93dc96d Built asleep @ git+https://github.com/muschellij2/asleep.git@4916a50c61dfe513a04ab340da3bfc4bd93dc96d Downloaded torch Built pyyaml==6.0.3 Installed 50 packages in 844ms Checking Data File is:/Volumes/Builds/packages/big-sur-arm64/results/4.5/asleep.Rcheck/asleep/extdata/example_sleep.csv.gz Downloading models if not already present Downloading https://github.com/OxWearables/asleep/releases/download/0.4.12/ssl.joblib.lzma... Saved to /Users/rbuild/Library/Caches/org.R-project.R/R/reticulate/uv/cache/archive-v0/6NMycJb0wWgZYK1y/lib/python3.8/site-packages/asleep/ssl.joblib.lzma Caching ssl-wearables repository... Downloading: "https://github.com/OxWearables/ssl-wearables/zipball/v1.0.0" to /Users/rbuild/Library/Caches/org.R-project.R/R/reticulate/uv/cache/archive-v0/6NMycJb0wWgZYK1y/lib/python3.8/site-packages/asleep/torch_hub_cache/v1.0.0.zip Caching SleepNet repository and weights... Downloading: "https://github.com/OxWearables/asleep/zipball/main" to /Users/rbuild/Library/Caches/org.R-project.R/R/reticulate/uv/cache/archive-v0/6NMycJb0wWgZYK1y/lib/python3.8/site-packages/asleep/torch_hub_cache/main.zip Downloading: "https://github.com/OxWearables/asleep/releases/download/0.4.9/sleepnet_apr_16_2024.mdl" to /Users/rbuild/Library/Caches/org.R-project.R/R/reticulate/uv/cache/archive-v0/6NMycJb0wWgZYK1y/lib/python3.8/site-packages/asleep/torch_hub_cache/checkpoints/sleepnet_apr_16_2024.mdl 0%| | 0.00/232M [00:00<?, ?B/s] 4%|▍ | 9.00M/232M [00:00<00:02, 93.7MB/s] 8%|▊ | 18.0M/232M [00:00<00:04, 48.2MB/s] 10%|█ | 23.8M/232M [00:00<00:06, 36.4MB/s] 13%|█▎ | 30.1M/232M [00:00<00:06, 32.7MB/s] 17%|█▋ | 39.8M/232M [00:00<00:04, 46.2MB/s] 20%|█▉ | 45.5M/232M [00:01<00:05, 37.6MB/s] 22%|██▏ | 50.1M/232M [00:01<00:05, 32.6MB/s] 26%|██▌ | 60.0M/232M [00:01<00:03, 45.8MB/s] 28%|██▊ | 65.8M/232M [00:01<00:04, 35.7MB/s] 30%|███ | 70.4M/232M [00:02<00:05, 30.9MB/s] 35%|███▍ | 80.1M/232M [00:02<00:04, 33.4MB/s] 39%|███▊ | 89.9M/232M [00:02<00:03, 44.4MB/s] 41%|████ | 95.5M/232M [00:02<00:03, 37.9MB/s] 43%|████▎ | 100M/232M [00:02<00:04, 32.4MB/s] 47%|████▋ | 110M/232M [00:03<00:03, 33.9MB/s] 52%|█████▏ | 120M/232M [00:03<00:03, 33.6MB/s] 56%|█████▌ | 130M/232M [00:03<00:03, 35.2MB/s] 60%|██████ | 140M/232M [00:03<00:02, 36.6MB/s] 64%|██████▍ | 149M/232M [00:04<00:01, 43.9MB/s] 66%|██████▌ | 154M/232M [00:04<00:02, 37.9MB/s] 69%|██████▉ | 160M/232M [00:04<00:03, 22.4MB/s] 73%|███████▎ | 170M/232M [00:05<00:02, 31.1MB/s] 75%|███████▌ | 175M/232M [00:05<00:02, 29.3MB/s] 78%|███████▊ | 180M/232M [00:05<00:01, 27.9MB/s] 82%|████████▏ | 190M/232M [00:05<00:01, 31.4MB/s] 86%|████████▌ | 200M/232M [00:05<00:00, 41.8MB/s] 89%|████████▊ | 206M/232M [00:06<00:00, 35.8MB/s] 91%|█████████ | 210M/232M [00:06<00:00, 31.8MB/s] 95%|█████████▍| 220M/232M [00:06<00:00, 33.6MB/s] 98%|█████████▊| 227M/232M [00:06<00:00, 40.1MB/s] 100%|██████████| 232M/232M [00:07<00:00, 21.8MB/s] 100%|██████████| 232M/232M [00:07<00:00, 33.3MB/s]Parsing raw data All models downloaded successfully. Lowpass filter... Skipping lowpass filter: data sample rate 30 too low for cutoff rate 20 Lowpass filter... Done! (0.00s) Gravity calibration... Gravity calibration... Done! (0.04s) Resampling... Resampling... Done! (0.08s) {'WearTime(days)': 0.1666662808564815, 'NonwearTime(days)': 0.0, 'NumNonwearEpisodes': 0} Time shift applied: 0 hours /Users/rbuild/Library/Caches/org.R-project.R/R/reticulate/uv/cache/archive-v0/6NMycJb0wWgZYK1y/lib/python3.8/site-packages/asleep/utils.py:44: UserWarning: Could not infer format, so each element will be parsed individually, falling back to `dateutil`. To ensure parsing is consistent and as-expected, please specify a format. data = pd.read_csv( Raw data file saved to: /Volumes/Temp/tmp/RtmpgHDwFZ/file13fdb6c310387/raw.csv Info data file saved to: /Volumes/Temp/tmp/RtmpgHDwFZ/file13fdb6c310387/info.json time x y z non_wear 0 2000-01-04 20:00:00.000000000 -0.704000 0.413000 -0.540000 False 1 2000-01-04 20:00:00.033333333 -0.720795 0.419000 -0.561667 False 2 2000-01-04 20:00:00.066666666 -0.665154 0.428846 -0.578590 False 3 2000-01-04 20:00:00.100000000 -0.698000 0.434000 -0.525000 False 4 2000-01-04 20:00:00.133333333 -0.674051 0.417308 -0.575385 False Transforming data for model input Data shape for data2model: (480, 3, 900) Data shape for times: (480,) Data shape for nonwear: (480,) Detecting sleep windows args$outdir/Volumes/Temp/tmp/RtmpgHDwFZ/file13fdb6c310387 ssl_sleep_path: /Volumes/Temp/tmp/RtmpgHDwFZ/file13fdb6c310387/ssl_sleep.npy, exists:FALSE data2model array([[[-0.704 , -0.72079488, -0.66515385, ..., -0.69130774, -0.69115383, -0.6903333 ], [ 0.413 , 0.419 , 0.42884615, ..., 0.42430774, 0.42807678, 0.44416667], [-0.54 , -0.56166666, -0.57858971, ..., -0.55976925, -0.59274354, -0.61691666]], [[-0.689 , -0.61469231, -0.58484615, ..., -0.62961541, -0.62735884, -0.62341669], [ 0.469 , 0.42923077, 0.43343586, ..., 0.466 , 0.46 , 0.45547223], [-0.648 , -0.55720514, -0.58207693, ..., -0.57223075, -0.57330765, -0.56950002]], [[-0.625 , -0.62246154, -0.63430771, ..., -0.73707666, -0.73812797, -0.74825001], [ 0.457 , 0.45953846, 0.46923078, ..., 0.18476925, 0.19420501, 0.20291666], [-0.56 , -0.548 , -0.56430771, ..., -0.64523075, -0.6363847 , -0.65150002]], ..., [[-0.032 , -0.032 , -0.032 , ..., -0.032 , -0.032 , -0.032 ], [-0.123 , -0.123 , -0.123 , ..., -0.123 , -0.123 , -0.123 ], [-0.988 , -0.988 , -0.988 , ..., -0.988 , -0.988 , -0.988 ]], [[-0.032 , -0.032 , -0.032 , ..., -0.032 , -0.032 , -0.032 ], [-0.123 , -0.123 , -0.123 , ..., -0.123 , -0.123 , -0.123 ], [-0.988 , -0.988 , -0.988 , ..., -0.988 , -0.988 , -0.988 ]], [[-0.032 , -0.032 , -0.032 , ..., -0.032 , -0.032 , -0.032 ], [-0.123 , -0.123 , -0.123 , ..., -0.123 , -0.123 , -0.123 ], [-0.988 , -0.988 , -0.988 , ..., -0.988 , -0.988 , -0.988 ]]]) non_wear array([False, False, False, False, False, False, False, False, False, False, False, False, False, False, False, False, False, False, False, False, False, False, False, False, False, False, False, False, False, False, False, False, False, False, False, False, False, False, False, False, False, False, False, False, False, False, False, False, False, False, False, False, False, False, False, False, False, False, False, False, False, False, False, False, False, False, False, False, False, False, False, False, False, False, False, False, False, False, False, False, False, False, False, False, False, False, False, False, False, False, False, False, False, False, False, False, False, False, False, False, False, False, False, False, False, False, False, False, False, False, False, False, False, False, False, False, False, False, False, False, False, False, False, False, False, False, False, False, False, False, False, False, False, False, False, False, False, False, False, False, False, False, False, False, False, False, False, False, False, False, False, False, False, False, False, False, False, False, False, False, False, False, False, False, False, False, False, False, False, False, False, False, False, False, False, False, False, False, False, False, False, False, False, False, False, False, False, False, False, False, False, False, False, False, False, False, False, False, False, False, False, False, False, False, False, False, False, False, False, False, False, False, False, False, False, False, False, False, False, False, False, False, False, False, False, False, False, False, False, False, False, False, False, False, False, False, False, False, False, False, False, False, False, False, False, False, False, False, False, False, False, False, False, False, False, False, False, False, False, False, False, False, False, False, False, False, False, False, False, False, False, False, False, False, False, False, False, False, False, False, False, False, False, False, False, False, False, False, False, False, False, False, False, False, False, False, False, False, False, False, False, False, False, False, False, False, False, False, False, False, False, False, False, False, False, False, False, False, False, False, False, False, False, False, False, False, False, False, False, False, False, False, False, False, False, False, False, False, False, False, False, False, False, False, False, False, False, False, False, False, False, False, False, False, False, False, False, False, False, False, False, False, False, False, False, False, False, False, False, False, False, False, False, False, False, False, False, False, False, False, False, False, False, False, False, False, False, False, False, False, False, False, False, False, False, False, False, False, False, False, False, False, False, False, False, False, False, False, False, False, False, False, False, False, False, False, False, False, False, False, False, False, False, False, False, False, False, False, False, False, False, False, False, False, False, False, False, False, False, False, False, False, False, False, False, False, False, False, False, False, False, False, False, False, False, False, False, False, False, False, False, False, False, False, False, False, False, False, False, False, False, False, False, False, False, False, False, False, False, False]) Data2model file saved to: /Volumes/Temp/tmp/RtmpgHDwFZ/file13fdb6c310387/data2model.npy Times file saved to: /Volumes/Temp/tmp/RtmpgHDwFZ/file13fdb6c310387/times.npy Non-wear file saved to: /Volumes/Temp/tmp/RtmpgHDwFZ/file13fdb6c310387/non_wear.npy Downloading https://github.com/OxWearables/asleep/releases/download/0.4.12/ssl.joblib.lzma... prediction set sample count: 480 Using local /Users/rbuild/Library/Caches/org.R-project.R/R/reticulate/uv/cache/archive-v0/6NMycJb0wWgZYK1y/lib/python3.8/site-packages/asleep/torch_hub_cache/OxWearables_ssl-wearables_v1.0.0 0%| | 0/1 [00:00<?, ?it/s] 100%|██████████| 1/1 [00:22<00:00, 22.98s/it]Running SleepNet SleepNet outdir: /Volumes/Temp/tmp/RtmpgHDwFZ/file13fdb6c310387 Upstream ssl model path: /Users/rbuild/Library/Caches/org.R-project.R/R/reticulate/uv/cache/archive-v0/6NMycJb0wWgZYK1y/lib/python3.8/site-packages/asleep/ssl.joblib.lzma, exists: TRUE SleepNet weight URL: https://github.com/OxWearables/asleep/releases/download/0.4.9/sleepnet_apr_16_2024.mdl SleepNet artifact ssl_sleep: /Volumes/Temp/tmp/RtmpgHDwFZ/file13fdb6c310387/ssl_sleep.npy, exists: TRUE SleepNet artifact y_pred: /Volumes/Temp/tmp/RtmpgHDwFZ/file13fdb6c310387/y_pred.npy, exists: FALSE SleepNet artifact pred_prob: /Volumes/Temp/tmp/RtmpgHDwFZ/file13fdb6c310387/pred_prob.npy, exists: FALSE SleepNet artifact x_npy: /Volumes/Temp/tmp/RtmpgHDwFZ/file13fdb6c310387/X.npy, exists: TRUE SleepNet artifact x_npy_gz: /Volumes/Temp/tmp/RtmpgHDwFZ/file13fdb6c310387/X.npy.gz, exists: FALSE SleepNet artifact npid: /Volumes/Temp/tmp/RtmpgHDwFZ/file13fdb6c310387/npid.npy, exists: TRUE (480,) (array([0., 2., 3.]), array([ 79, 45, 356])) pytorch device: mps setting up cnn access local repo /Users/rbuild/Library/Caches/org.R-project.R/R/reticulate/uv/cache/archive-v0/6NMycJb0wWgZYK1y/lib/python3.8/site-packages/asleep/sleepnet.py:207: Hydra14MigrationWarning: The version_base parameter is not specified. Hydra will assume defaults for version 1.1. Hydra 1.4 will remove this compatibility behavior. Before upgrading to Hydra 1.4, set version_base="1.3" and test your application. See https://hydra.cc/docs/upgrades/1.3_to_1.4/prepare_for_1_4/ for preparation instructions. initialize(config_path="conf") Loading local weight from /Users/rbuild/Library/Caches/org.R-project.R/R/reticulate/uv/cache/archive-v0/6NMycJb0wWgZYK1y/lib/python3.8/site-packages/asleep/torch_hub_cache/checkpoints/sleepnet_apr_16_2024.mdl /Users/rbuild/Library/Caches/org.R-project.R/R/reticulate/uv/cache/archive-v0/6NMycJb0wWgZYK1y/lib/python3.8/site-packages/asleep/torch_hub_cache/OxWearables_asleep_main/hubconf.py:22: FutureWarning: You are using `torch.load` with `weights_only=False` (the current default value), which uses the default pickle module implicitly. It is possible to construct malicious pickle data which will execute arbitrary code during unpickling (See https://github.com/pytorch/pytorch/blob/main/SECURITY.md#untrusted-models for more details). In a future release, the default value for `weights_only` will be flipped to `True`. This limits the functions that could be executed during unpickling. Arbitrary objects will no longer be allowed to be loaded via this mode unless they are explicitly allowlisted by the user via `torch.serialization.add_safe_globals`. We recommend you start setting `weights_only=True` for any use case where you don't have full control of the loaded file. Please open an issue on GitHub for any issues related to this experimental feature. state_dict = torch.load(local_weight_path, Saving _problems/test-asleep-20.R Lowpass filter... Skipping lowpass filter: data sample rate 30 too low for cutoff rate 20 Lowpass filter... Done! (0.00s) Gravity calibration... Gravity calibration... Done! (0.03s) Resampling... /Users/rbuild/Library/Caches/org.R-project.R/R/reticulate/uv/cache/archive-v0/6NMycJb0wWgZYK1y/lib/python3.8/site-packages/asleep/utils.py:44: UserWarning: Could not infer format, so each element will be parsed individually, falling back to `dateutil`. To ensure parsing is consistent and as-expected, please specify a format. data = pd.read_csv( [ FAIL 1 | WARN 0 | SKIP 0 | PASS 67 ] ══ Failed tests ════════════════════════════════════════════════════════════════ ── Error ('test-asleep.R:20:5'): asleep model works ──────────────────────────── <python.builtin.RuntimeError/python.builtin.Exception/python.builtin.BaseException/python.builtin.object/error/condition> Error in `py_call_impl(callable, call_args$unnamed, call_args$named)`: RuntimeError: MPS backend out of memory (MPS allocated: 8.00 MB, other allocations: 272.00 KB, max allowed: 1.70 GB). Tried to allocate 256 bytes on shared pool. Use PYTORCH_MPS_HIGH_WATERMARK_RATIO=0.0 to disable upper limit for memory allocations (may cause system failure). Run `reticulate::py_last_error()` for details. Backtrace: ▆ 1. └─asleep::asleep(file = file, verbose = 2L, force_download = TRUE) at test-asleep.R:20:5 2. └─reticulate (local) start_sleep_net(...) 3. └─reticulate:::py_call_impl(callable, call_args$unnamed, call_args$named) [ FAIL 1 | WARN 0 | SKIP 0 | PASS 67 ] Error: ! Test failures. Execution halted /Users/rbuild/Library/Caches/org.R-project.R/R/reticulate/uv/python/cpython-3.8.20-macos-aarch64-none/lib/python3.8/multiprocessing/resource_tracker.py:216: UserWarning: resource_tracker: There appear to be 1 leaked semaphore objects to clean up at shutdown warnings.warn('resource_tracker: There appear to be %d ' Flavor: r-oldrel-macos-arm64