Installation OK but failed to build vignettes * creating vignettes ... ERROR Setting r-universe rmarkdown theme... --- re-building ‘anndataR.Rmd’ using rmarkdown Loading required package: BiocStyle Warning: vignette 'usage_python' not found --- finished re-building ‘anndataR.Rmd’ --- re-building ‘usage_python.Rmd’ using rmarkdown Downloading cpython-3.12.14-linux-x86_64-gnu (download) (32.6MiB) Downloaded cpython-3.12.14-linux-x86_64-gnu (download) Downloading scipy (33.7MiB) Downloading pandas (11.8MiB) Downloading networkx (2.0MiB) Downloading matplotlib (9.6MiB) Downloading pillow (6.6MiB) Downloading statsmodels (9.9MiB) Downloading numcodecs (8.7MiB) Downloading scikit-learn (8.7MiB) Downloading h5py (5.2MiB) Downloading kiwisolver (1.4MiB) Downloading pydantic-core (2.0MiB) Downloading fonttools (4.8MiB) Downloading numpy (15.9MiB) Downloading scanpy (2.1MiB) Downloading llvmlite (57.1MiB) Downloading numba (3.7MiB) Downloaded kiwisolver Downloaded pydantic-core Downloaded scanpy Downloaded networkx Downloaded fonttools Downloaded h5py Downloaded pillow Downloaded numba Downloaded numcodecs Downloaded scikit-learn Downloaded matplotlib Downloaded numpy Downloaded statsmodels Downloaded llvmlite Downloaded scipy Downloaded pandas Installed 51 packages in 122ms 0%| | 0.00/23.5M [00:00<?, ?B/s] 17%|█▋ | 4.02M/23.5M [00:00<00:00, 40.4MB/s] 34%|███▍ | 7.98M/23.5M [00:00<00:00, 40.9MB/s] 100%|██████████| 23.5M/23.5M [00:00<00:00, 89.1MB/s] sys:1: UserWarning: Some cells have zero counts /github/home/.cache/R/reticulate/uv/cache/archive-v0/ElWB7s8Sqr7v0luR/lib/python3.12/site-packages/scanpy/preprocessing/_simple.py:378: RuntimeWarning: invalid value encountered in log1p np.log1p(x, out=x) Quitting from usage_python.Rmd:119-127 [load_mudata_example] ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ <error/rlang_error> Error in `py_call_impl()`: ! anndata._io.specs.registry.IORegistryError: No read method registered for IOSpec(encoding_type='AnnData', encoding_version='0.1.0') from <class 'h5py._hl.group.Group'>. You may need to update your installation of anndata. Error raised while reading key 'prot' of <class 'h5py._hl.group.Group'> from /mod Run `reticulate::py_last_error()` for details. --- Backtrace: ▆ 1. └─md$read_h5mu(h5mu_file) 2. └─reticulate:::py_call_impl(callable, call_args$unnamed, call_args$named) ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ Error: processing vignette 'usage_python.Rmd' failed with diagnostics: anndata._io.specs.registry.IORegistryError: No read method registered for IOSpec(encoding_type='AnnData', encoding_version='0.1.0') from <class 'h5py._hl.group.Group'>. You may need to update your installation of anndata. Error raised while reading key 'prot' of <class 'h5py._hl.group.Group'> from /mod Run `reticulate::py_last_error()` for details. --- failed re-building ‘usage_python.Rmd’ --- re-building ‘usage_seurat.Rmd’ using rmarkdown --- finished re-building ‘usage_seurat.Rmd’ --- re-building ‘usage_singlecellexperiment.Rmd’ using rmarkdown --- finished re-building ‘usage_singlecellexperiment.Rmd’ SUMMARY: processing the following file failed: ‘usage_python.Rmd’ Error: Vignette re-building failed. Execution halted If this is expected, consider precomputing your vignettes: https://ropensci.org/blog/2019/12/08/precompute-vignettes/

Check: tests, Result: ERROR Running ‘spelling.R’ Running ‘testthat.R’ [401s/413s] Running the tests in ‘tests/testthat.R’ failed. Last 13 lines of output: In particular, it will write NA_character_ as the string 'NA' in the HDF5 file. Use variable-length strings instead. ── Failure ('test-h5ad-fileclosure.R:23:3'): closing HDF5AnnData file works ──── Expected `{ ... }` not to throw any conditions. Actually got a <simpleWarning> with message: Writing NA_character_ in fixed-length string datasets is fragile and deprecated. In particular, it will write NA_character_ as the string 'NA' in the HDF5 file. Use variable-length strings instead. [ FAIL 3 | WARN 4077 | SKIP 7 | PASS 3669 ] Error: ! Test failures. Execution halted /Users/runner/Library/Caches/org.R-project.R/R/reticulate/uv/python/cpython-3.12.14-macos-aarch64-none/lib/python3.12/multiprocessing/resource_tracker.py:279: 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 '

Check: tests, Result: ERROR Running ‘spelling.R’ Running ‘testthat.R’ [457s/475s] Running the tests in ‘tests/testthat.R’ failed. Last 13 lines of output: In particular, it will write NA_character_ as the string 'NA' in the HDF5 file. Use variable-length strings instead. ── Failure ('test-h5ad-fileclosure.R:23:3'): closing HDF5AnnData file works ──── Expected `{ ... }` not to throw any conditions. Actually got a <simpleWarning> with message: Writing NA_character_ in fixed-length string datasets is fragile and deprecated. In particular, it will write NA_character_ as the string 'NA' in the HDF5 file. Use variable-length strings instead. [ FAIL 3 | WARN 414 | SKIP 7 | PASS 3669 ] Error: ! Test failures. Execution halted /Users/runner/Library/Caches/org.R-project.R/R/reticulate/uv/python/cpython-3.12.14-macos-aarch64-none/lib/python3.12/multiprocessing/resource_tracker.py:279: 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 '

Check: tests, Result: ERROR Running ‘spelling.R’ Running ‘testthat.R’ [488s/523s] Running the tests in ‘tests/testthat.R’ failed. Last 13 lines of output: Actually got a <simpleWarning> with message: Writing NA_character_ in fixed-length string datasets is fragile and deprecated. In particular, it will write NA_character_ as the string 'NA' in the HDF5 file. Use variable-length strings instead. ── Failure ('test-h5ad-fileclosure.R:23:3'): closing HDF5AnnData file works ──── Expected `{ ... }` not to throw any conditions. Actually got a <simpleWarning> with message: Writing NA_character_ in fixed-length string datasets is fragile and deprecated. In particular, it will write NA_character_ as the string 'NA' in the HDF5 file. Use variable-length strings instead. [ FAIL 3 | WARN 414 | SKIP 7 | PASS 3669 ] Error: ! Test failures. Execution halted

Check: tests, Result: ERROR Running ‘spelling.R’ Running ‘testthat.R’ [545s/540s] Running the tests in ‘tests/testthat.R’ failed. Last 13 lines of output: Actually got a <simpleWarning> with message: Writing NA_character_ in fixed-length string datasets is fragile and deprecated. In particular, it will write NA_character_ as the string 'NA' in the HDF5 file. Use variable-length strings instead. ── Failure ('test-h5ad-fileclosure.R:23:3'): closing HDF5AnnData file works ──── Expected `{ ... }` not to throw any conditions. Actually got a <simpleWarning> with message: Writing NA_character_ in fixed-length string datasets is fragile and deprecated. In particular, it will write NA_character_ as the string 'NA' in the HDF5 file. Use variable-length strings instead. [ FAIL 3 | WARN 414 | SKIP 7 | PASS 3669 ] Error: ! Test failures. Execution halted

Check: tests, Result: ERROR Running 'spelling.R' Running 'testthat.R' [12m] Running the tests in 'tests/testthat.R' failed. Last 13 lines of output: Actually got a <simpleWarning> with message: Writing NA_character_ in fixed-length string datasets is fragile and deprecated. In particular, it will write NA_character_ as the string 'NA' in the HDF5 file. Use variable-length strings instead. ── Failure ('test-h5ad-fileclosure.R:23:3'): closing HDF5AnnData file works ──── Expected `{ ... }` not to throw any conditions. Actually got a <simpleWarning> with message: Writing NA_character_ in fixed-length string datasets is fragile and deprecated. In particular, it will write NA_character_ as the string 'NA' in the HDF5 file. Use variable-length strings instead. [ FAIL 3 | WARN 414 | SKIP 7 | PASS 3669 ] Error: ! Test failures. Execution halted

Check: tests, Result: ERROR Running 'spelling.R' Running 'testthat.R' [13m] Running the tests in 'tests/testthat.R' failed. Last 13 lines of output: Actually got a <simpleWarning> with message: Writing NA_character_ in fixed-length string datasets is fragile and deprecated. In particular, it will write NA_character_ as the string 'NA' in the HDF5 file. Use variable-length strings instead. ── Failure ('test-h5ad-fileclosure.R:23:3'): closing HDF5AnnData file works ──── Expected `{ ... }` not to throw any conditions. Actually got a <simpleWarning> with message: Writing NA_character_ in fixed-length string datasets is fragile and deprecated. In particular, it will write NA_character_ as the string 'NA' in the HDF5 file. Use variable-length strings instead. [ FAIL 3 | WARN 414 | SKIP 7 | PASS 3669 ] Error: ! Test failures. Execution halted