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### Running command:
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### /home/biocbuild/bbs-3.21-bioc/R/bin/R CMD build --keep-empty-dirs --no-resave-data spatialDE
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* checking for file ‘spatialDE/DESCRIPTION’ ... OK
* preparing ‘spatialDE’:
* checking DESCRIPTION meta-information ... OK
* installing the package to build vignettes
* creating vignettes ... ERROR
--- re-building ‘spatialDE.Rmd’ using rmarkdown
Requirement already satisfied: pip in /home/biocbuild/.cache/R/basilisk/1.19.2/spatialDE/1.13.0/env/lib/python3.12/site-packages (24.3.1)
Collecting pip
Using cached pip-25.0.1-py3-none-any.whl.metadata (3.7 kB)
Collecting wheel
Using cached wheel-0.45.1-py3-none-any.whl.metadata (2.3 kB)
Collecting setuptools
Using cached setuptools-77.0.1-py3-none-any.whl.metadata (6.7 kB)
Using cached pip-25.0.1-py3-none-any.whl (1.8 MB)
Using cached wheel-0.45.1-py3-none-any.whl (72 kB)
Using cached setuptools-77.0.1-py3-none-any.whl (1.3 MB)
Installing collected packages: wheel, setuptools, pip
Attempting uninstall: pip
Found existing installation: pip 24.3.1
Uninstalling pip-24.3.1:
Successfully uninstalled pip-24.3.1
Successfully installed pip-25.0.1 setuptools-77.0.1 wheel-0.45.1
Collecting numpy==1.23.5
Downloading numpy-1.23.5.tar.gz (10.7 MB)
━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━ 10.7/10.7 MB 16.0 MB/s eta 0:00:00
Installing build dependencies: started
Installing build dependencies: finished with status 'done'
Getting requirements to build wheel: started
Getting requirements to build wheel: finished with status 'error'
error: subprocess-exited-with-error
× Getting requirements to build wheel did not run successfully.
│ exit code: 1
╰─> [33 lines of output]
Traceback (most recent call last):
File "/home/biocbuild/.cache/R/basilisk/1.19.2/spatialDE/1.13.0/env/lib/python3.12/site-packages/pip/_vendor/pyproject_hooks/_in_process/_in_process.py", line 389, in <module>
main()
File "/home/biocbuild/.cache/R/basilisk/1.19.2/spatialDE/1.13.0/env/lib/python3.12/site-packages/pip/_vendor/pyproject_hooks/_in_process/_in_process.py", line 373, in main
json_out["return_val"] = hook(**hook_input["kwargs"])
^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File "/home/biocbuild/.cache/R/basilisk/1.19.2/spatialDE/1.13.0/env/lib/python3.12/site-packages/pip/_vendor/pyproject_hooks/_in_process/_in_process.py", line 137, in get_requires_for_build_wheel
backend = _build_backend()
^^^^^^^^^^^^^^^^
File "/home/biocbuild/.cache/R/basilisk/1.19.2/spatialDE/1.13.0/env/lib/python3.12/site-packages/pip/_vendor/pyproject_hooks/_in_process/_in_process.py", line 70, in _build_backend
obj = import_module(mod_path)
^^^^^^^^^^^^^^^^^^^^^^^
File "/home/biocbuild/.pyenv/versions/3.12.9/lib/python3.12/importlib/__init__.py", line 90, in import_module
return _bootstrap._gcd_import(name[level:], package, level)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File "<frozen importlib._bootstrap>", line 1387, in _gcd_import
File "<frozen importlib._bootstrap>", line 1360, in _find_and_load
File "<frozen importlib._bootstrap>", line 1310, in _find_and_load_unlocked
File "<frozen importlib._bootstrap>", line 488, in _call_with_frames_removed
File "<frozen importlib._bootstrap>", line 1387, in _gcd_import
File "<frozen importlib._bootstrap>", line 1360, in _find_and_load
File "<frozen importlib._bootstrap>", line 1331, in _find_and_load_unlocked
File "<frozen importlib._bootstrap>", line 935, in _load_unlocked
File "<frozen importlib._bootstrap_external>", line 999, in exec_module
File "<frozen importlib._bootstrap>", line 488, in _call_with_frames_removed
File "/tmp/pip-build-env-e094c0eh/overlay/lib/python3.12/site-packages/setuptools/__init__.py", line 16, in <module>
import setuptools.version
File "/tmp/pip-build-env-e094c0eh/overlay/lib/python3.12/site-packages/setuptools/version.py", line 1, in <module>
import pkg_resources
File "/tmp/pip-build-env-e094c0eh/overlay/lib/python3.12/site-packages/pkg_resources/__init__.py", line 2172, in <module>
register_finder(pkgutil.ImpImporter, find_on_path)
^^^^^^^^^^^^^^^^^^^
AttributeError: module 'pkgutil' has no attribute 'ImpImporter'. Did you mean: 'zipimporter'?
[end of output]
note: This error originates from a subprocess, and is likely not a problem with pip.
error: subprocess-exited-with-error
× Getting requirements to build wheel did not run successfully.
│ exit code: 1
╰─> See above for output.
note: This error originates from a subprocess, and is likely not a problem with pip.
Quitting from spatialDE.Rmd:122-125 [stabilize]
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
<error/rlang_error>
Error:
! Error installing package(s): "'numpy==1.23.5'", "'scipy==1.9.3'", "'patsy==0.5.3'", "'pandas==1.5.2'", "'SpatialDE==1.1.3'", "'NaiveDE==1.2.0'"
---
Backtrace:
▆
1. └─spatialDE::stabilize(Rep11_MOB_0)
2. └─basilisk::basiliskStart(spatialDE_env, testload = "scipy.optimize")
3. └─basilisk::obtainEnvironmentPath(env)
4. └─basilisk::setupBasiliskEnv(...)
5. └─reticulate::virtualenv_install(...)
6. └─reticulate:::pip_install(...)
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
Error: processing vignette 'spatialDE.Rmd' failed with diagnostics:
Error installing package(s): "'numpy==1.23.5'", "'scipy==1.9.3'", "'patsy==0.5.3'", "'pandas==1.5.2'", "'SpatialDE==1.1.3'", "'NaiveDE==1.2.0'"
--- failed re-building ‘spatialDE.Rmd’
SUMMARY: processing the following file failed:
‘spatialDE.Rmd’
Error: Vignette re-building failed.
Execution halted