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### Running command:
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### /Library/Frameworks/R.framework/Resources/bin/R CMD build --keep-empty-dirs --no-resave-data MACSr
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* checking for file ‘MACSr/DESCRIPTION’ ... OK
* preparing ‘MACSr’:
* checking DESCRIPTION meta-information ... OK
* installing the package to build vignettes
* creating vignettes ... ERROR
--- re-building ‘MACSr.Rmd’ using rmarkdown
Collecting package metadata (current_repodata.json): ...working... done
Solving environment: ...working... done
## Package Plan ##
environment location: /private/var/cache/basilisk/1.16.0/MACSr/1.12.0/env_macs
added / updated specs:
- python=3.10
The following NEW packages will be INSTALLED:
bzip2 conda-forge/osx-64::bzip2-1.0.8-h10d778d_5
ca-certificates conda-forge/osx-64::ca-certificates-2024.6.2-h8857fd0_0
libffi conda-forge/osx-64::libffi-3.4.2-h0d85af4_5
libsqlite conda-forge/osx-64::libsqlite-3.46.0-h1b8f9f3_0
libzlib conda-forge/osx-64::libzlib-1.3.1-h87427d6_1
ncurses conda-forge/osx-64::ncurses-6.5-h5846eda_0
openssl conda-forge/osx-64::openssl-3.3.1-h87427d6_0
pip conda-forge/noarch::pip-24.0-pyhd8ed1ab_0
python conda-forge/osx-64::python-3.10.14-h00d2728_0_cpython
readline conda-forge/osx-64::readline-8.2-h9e318b2_1
setuptools conda-forge/noarch::setuptools-70.0.0-pyhd8ed1ab_0
tk conda-forge/osx-64::tk-8.6.13-h1abcd95_1
tzdata conda-forge/noarch::tzdata-2024a-h0c530f3_0
wheel conda-forge/noarch::wheel-0.43.0-pyhd8ed1ab_1
xz conda-forge/osx-64::xz-5.2.6-h775f41a_0
Preparing transaction: ...working... done
Verifying transaction: ...working... done
Executing transaction: ...working... done
Collecting package metadata (current_repodata.json): ...working... done
Solving environment: ...working... done
==> WARNING: A newer version of conda exists. <==
current version: 4.12.0
latest version: 24.5.0
Please update conda by running
$ conda update -n base -c defaults conda
# All requested packages already installed.
Collecting package metadata (current_repodata.json): ...working... done
Solving environment: ...working... done
==> WARNING: A newer version of conda exists. <==
current version: 4.12.0
latest version: 24.5.0
Please update conda by running
$ conda update -n base -c defaults conda
# All requested packages already installed.
Collecting macs3==3.0.0
Using cached MACS3-3.0.0-cp310-cp310-macosx_11_0_x86_64.whl
Collecting numpy>=1.19 (from macs3==3.0.0)
Downloading numpy-2.0.0-cp310-cp310-macosx_10_9_x86_64.whl.metadata (60 kB)
━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━ 60.9/60.9 kB 1.5 MB/s eta 0:00:00
Collecting hmmlearn>=0.3 (from macs3==3.0.0)
Using cached hmmlearn-0.3.2-cp310-cp310-macosx_10_9_x86_64.whl.metadata (2.9 kB)
Collecting cykhash<3.0,>=2.0 (from macs3==3.0.0)
Using cached cykhash-2.0.1-cp310-cp310-macosx_10_9_x86_64.whl
Collecting Cython~=3.0 (from macs3==3.0.0)
Using cached Cython-3.0.10-cp310-cp310-macosx_10_9_x86_64.whl.metadata (3.2 kB)
Collecting scikit-learn!=0.22.0,>=0.16 (from hmmlearn>=0.3->macs3==3.0.0)
Downloading scikit_learn-1.5.0-cp310-cp310-macosx_10_9_x86_64.whl.metadata (11 kB)
Collecting scipy>=0.19 (from hmmlearn>=0.3->macs3==3.0.0)
Downloading scipy-1.13.1-cp310-cp310-macosx_10_9_x86_64.whl.metadata (60 kB)
━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━ 60.6/60.6 kB 2.1 MB/s eta 0:00:00
Collecting joblib>=1.2.0 (from scikit-learn!=0.22.0,>=0.16->hmmlearn>=0.3->macs3==3.0.0)
Using cached joblib-1.4.2-py3-none-any.whl.metadata (5.4 kB)
Collecting threadpoolctl>=3.1.0 (from scikit-learn!=0.22.0,>=0.16->hmmlearn>=0.3->macs3==3.0.0)
Using cached threadpoolctl-3.5.0-py3-none-any.whl.metadata (13 kB)
Using cached Cython-3.0.10-cp310-cp310-macosx_10_9_x86_64.whl (3.1 MB)
Using cached hmmlearn-0.3.2-cp310-cp310-macosx_10_9_x86_64.whl (128 kB)
Downloading numpy-2.0.0-cp310-cp310-macosx_10_9_x86_64.whl (21.2 MB)
━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━ 21.2/21.2 MB 31.2 MB/s eta 0:00:00
Downloading scikit_learn-1.5.0-cp310-cp310-macosx_10_9_x86_64.whl (12.1 MB)
━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━ 12.1/12.1 MB 27.6 MB/s eta 0:00:00
Downloading scipy-1.13.1-cp310-cp310-macosx_10_9_x86_64.whl (39.3 MB)
━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━ 39.3/39.3 MB 27.5 MB/s eta 0:00:00
Using cached joblib-1.4.2-py3-none-any.whl (301 kB)
Using cached threadpoolctl-3.5.0-py3-none-any.whl (18 kB)
Installing collected packages: cykhash, threadpoolctl, numpy, joblib, Cython, scipy, scikit-learn, hmmlearn, macs3
Successfully installed Cython-3.0.10 cykhash-2.0.1 hmmlearn-0.3.2 joblib-1.4.2 macs3-3.0.0 numpy-2.0.0 scikit-learn-1.5.0 scipy-1.13.1 threadpoolctl-3.5.0
A module that was compiled using NumPy 1.x cannot be run in
NumPy 2.0.0 as it may crash. To support both 1.x and 2.x
versions of NumPy, modules must be compiled with NumPy 2.0.
Some module may need to rebuild instead e.g. with 'pybind11>=2.12'.
If you are a user of the module, the easiest solution will be to
downgrade to 'numpy<2' or try to upgrade the affected module.
We expect that some modules will need time to support NumPy 2.
Traceback (most recent call last): File "/Library/Frameworks/R.framework/Versions/4.4-x86_64/Resources/library/reticulate/python/rpytools/loader.py", line 122, in _find_and_load_hook
return _run_hook(name, _hook)
File "/Library/Frameworks/R.framework/Versions/4.4-x86_64/Resources/library/reticulate/python/rpytools/loader.py", line 96, in _run_hook
module = hook()
File "/Library/Frameworks/R.framework/Versions/4.4-x86_64/Resources/library/reticulate/python/rpytools/loader.py", line 120, in _hook
return _find_and_load(name, import_)
File "/private/var/cache/basilisk/1.16.0/MACSr/1.12.0/env_macs/lib/python3.10/site-packages/MACS3/Commands/callpeak_cmd.py", line 23, in <module>
from MACS3.Utilities.OptValidator import opt_validate_callpeak
File "/Library/Frameworks/R.framework/Versions/4.4-x86_64/Resources/library/reticulate/python/rpytools/loader.py", line 122, in _find_and_load_hook
return _run_hook(name, _hook)
File "/Library/Frameworks/R.framework/Versions/4.4-x86_64/Resources/library/reticulate/python/rpytools/loader.py", line 96, in _run_hook
module = hook()
File "/Library/Frameworks/R.framework/Versions/4.4-x86_64/Resources/library/reticulate/python/rpytools/loader.py", line 120, in _hook
return _find_and_load(name, import_)
File "/private/var/cache/basilisk/1.16.0/MACSr/1.12.0/env_macs/lib/python3.10/site-packages/MACS3/Utilities/OptValidator.py", line 24, in <module>
from MACS3.IO.Parser import BEDParser, ELANDResultParser, ELANDMultiParser, \
File "/Library/Frameworks/R.framework/Versions/4.4-x86_64/Resources/library/reticulate/python/rpytools/loader.py", line 122, in _find_and_load_hook
return _run_hook(name, _hook)
File "/Library/Frameworks/R.framework/Versions/4.4-x86_64/Resources/library/reticulate/python/rpytools/loader.py", line 96, in _run_hook
module = hook()
File "/Library/Frameworks/R.framework/Versions/4.4-x86_64/Resources/library/reticulate/python/rpytools/loader.py", line 120, in _hook
return _find_and_load(name, import_)
Quitting from lines 88-94 [unnamed-chunk-3] (MACSr.Rmd)
Error: processing vignette 'MACSr.Rmd' failed with diagnostics:
ImportError: numpy.core.multiarray failed to import (auto-generated because you didn't call 'numpy.import_array()' after cimporting numpy; use '<void>numpy._import_array' to disable if you are certain you don't need it).
Run `reticulate::py_last_error()` for details.
--- failed re-building ‘MACSr.Rmd’
SUMMARY: processing the following file failed:
‘MACSr.Rmd’
Error: Vignette re-building failed.
Execution halted
