############################################################################## ############################################################################## ### ### Running command: ### ### /Library/Frameworks/R.framework/Resources/bin/R CMD build --keep-empty-dirs --no-resave-data SpectriPy ### ############################################################################## ############################################################################## * checking for file ‘SpectriPy/DESCRIPTION’ ... OK * preparing ‘SpectriPy’: * checking DESCRIPTION meta-information ... OK * installing the package to build vignettes ----------------------------------- * installing *source* package ‘SpectriPy’ ... ** this is package ‘SpectriPy’ version ‘0.99.4’ ** using staged installation ** R ** inst ** byte-compile and prepare package for lazy loading ** help *** installing help indices *** copying figures ** building package indices ** installing vignettes ** testing if installed package can be loaded from temporary location Warning: The request to `use_python("/Users/biocbuild/.virtualenvs/r-spectripy/bin/python")` will be ignored because the environment variable RETICULATE_PYTHON is set to "/usr/bin/python3" Using virtual environment 'r-spectripy' ... + /Users/biocbuild/.virtualenvs/r-spectripy/bin/python -m pip install --upgrade --no-user 'matchms==0.30.0' Requirement already satisfied: matchms==0.30.0 in /Users/biocbuild/.virtualenvs/r-spectripy/lib/python3.13/site-packages (0.30.0) Requirement already satisfied: deprecated>=1.2.14 in /Users/biocbuild/.virtualenvs/r-spectripy/lib/python3.13/site-packages (from matchms==0.30.0) (1.2.18) Requirement already satisfied: lxml<6.0.0,>=5.4.0 in /Users/biocbuild/.virtualenvs/r-spectripy/lib/python3.13/site-packages (from matchms==0.30.0) (5.4.0) Requirement already satisfied: matplotlib>=3.7 in /Users/biocbuild/.virtualenvs/r-spectripy/lib/python3.13/site-packages (from matchms==0.30.0) (3.10.3) Requirement already satisfied: networkx<4.0.0,>=3.4.2 in /Users/biocbuild/.virtualenvs/r-spectripy/lib/python3.13/site-packages (from matchms==0.30.0) (3.5) Requirement already satisfied: numba<0.62.0,>=0.61.0 in /Users/biocbuild/.virtualenvs/r-spectripy/lib/python3.13/site-packages (from matchms==0.30.0) (0.61.2) Requirement already satisfied: numpy>=2.0.0 in /Users/biocbuild/.virtualenvs/r-spectripy/lib/python3.13/site-packages (from matchms==0.30.0) (2.2.6) Requirement already satisfied: pandas<3.0.0,>=2.2.3 in /Users/biocbuild/.virtualenvs/r-spectripy/lib/python3.13/site-packages (from matchms==0.30.0) (2.3.0) Requirement already satisfied: pickydict>=0.4.0 in /Users/biocbuild/.virtualenvs/r-spectripy/lib/python3.13/site-packages (from matchms==0.30.0) (0.5.0) Requirement already satisfied: pillow!=9.4.0 in /Users/biocbuild/.virtualenvs/r-spectripy/lib/python3.13/site-packages (from matchms==0.30.0) (11.2.1) Requirement already satisfied: pubchempy in /Users/biocbuild/.virtualenvs/r-spectripy/lib/python3.13/site-packages (from matchms==0.30.0) (1.0.4) Requirement already satisfied: pynndescent>=0.5.13 in /Users/biocbuild/.virtualenvs/r-spectripy/lib/python3.13/site-packages (from matchms==0.30.0) (0.5.13) Requirement already satisfied: pyteomics>=4.6 in /Users/biocbuild/.virtualenvs/r-spectripy/lib/python3.13/site-packages (from matchms==0.30.0) (4.7.5) Requirement already satisfied: pyyaml>=6.0.1 in /Users/biocbuild/.virtualenvs/r-spectripy/lib/python3.13/site-packages (from matchms==0.30.0) (6.0.2) Requirement already satisfied: rdkit<2025.0.0,>=2024.3.5 in /Users/biocbuild/.virtualenvs/r-spectripy/lib/python3.13/site-packages (from matchms==0.30.0) (2024.9.6) Requirement already satisfied: requests>=2.31.0 in /Users/biocbuild/.virtualenvs/r-spectripy/lib/python3.13/site-packages (from matchms==0.30.0) (2.32.4) Requirement already satisfied: scipy<2.0.0,>=1.15.3 in /Users/biocbuild/.virtualenvs/r-spectripy/lib/python3.13/site-packages (from matchms==0.30.0) (1.15.3) Requirement already satisfied: sparsestack>=0.7.0 in /Users/biocbuild/.virtualenvs/r-spectripy/lib/python3.13/site-packages (from matchms==0.30.0) (0.7.0) Requirement already satisfied: tqdm>=4.65.0 in /Users/biocbuild/.virtualenvs/r-spectripy/lib/python3.13/site-packages (from matchms==0.30.0) (4.67.1) Requirement already satisfied: llvmlite<0.45,>=0.44.0dev0 in /Users/biocbuild/.virtualenvs/r-spectripy/lib/python3.13/site-packages (from numba<0.62.0,>=0.61.0->matchms==0.30.0) (0.44.0) Requirement already satisfied: python-dateutil>=2.8.2 in /Users/biocbuild/.virtualenvs/r-spectripy/lib/python3.13/site-packages (from pandas<3.0.0,>=2.2.3->matchms==0.30.0) (2.9.0.post0) Requirement already satisfied: pytz>=2020.1 in /Users/biocbuild/.virtualenvs/r-spectripy/lib/python3.13/site-packages (from pandas<3.0.0,>=2.2.3->matchms==0.30.0) (2025.2) Requirement already satisfied: tzdata>=2022.7 in /Users/biocbuild/.virtualenvs/r-spectripy/lib/python3.13/site-packages (from pandas<3.0.0,>=2.2.3->matchms==0.30.0) (2025.2) Requirement already satisfied: wrapt<2,>=1.10 in /Users/biocbuild/.virtualenvs/r-spectripy/lib/python3.13/site-packages (from deprecated>=1.2.14->matchms==0.30.0) (1.17.2) Requirement already satisfied: contourpy>=1.0.1 in /Users/biocbuild/.virtualenvs/r-spectripy/lib/python3.13/site-packages (from matplotlib>=3.7->matchms==0.30.0) (1.3.2) Requirement already satisfied: cycler>=0.10 in /Users/biocbuild/.virtualenvs/r-spectripy/lib/python3.13/site-packages (from matplotlib>=3.7->matchms==0.30.0) (0.12.1) Requirement already satisfied: fonttools>=4.22.0 in /Users/biocbuild/.virtualenvs/r-spectripy/lib/python3.13/site-packages (from matplotlib>=3.7->matchms==0.30.0) (4.58.4) Requirement already satisfied: kiwisolver>=1.3.1 in /Users/biocbuild/.virtualenvs/r-spectripy/lib/python3.13/site-packages (from matplotlib>=3.7->matchms==0.30.0) (1.4.8) Requirement already satisfied: packaging>=20.0 in /Users/biocbuild/.virtualenvs/r-spectripy/lib/python3.13/site-packages (from matplotlib>=3.7->matchms==0.30.0) (25.0) Requirement already satisfied: pyparsing>=2.3.1 in /Users/biocbuild/.virtualenvs/r-spectripy/lib/python3.13/site-packages (from matplotlib>=3.7->matchms==0.30.0) (3.2.3) Requirement already satisfied: scikit-learn>=0.18 in /Users/biocbuild/.virtualenvs/r-spectripy/lib/python3.13/site-packages (from pynndescent>=0.5.13->matchms==0.30.0) (1.7.0) Requirement already satisfied: joblib>=0.11 in /Users/biocbuild/.virtualenvs/r-spectripy/lib/python3.13/site-packages (from pynndescent>=0.5.13->matchms==0.30.0) (1.5.1) Requirement already satisfied: six>=1.5 in /Users/biocbuild/.virtualenvs/r-spectripy/lib/python3.13/site-packages (from python-dateutil>=2.8.2->pandas<3.0.0,>=2.2.3->matchms==0.30.0) (1.17.0) Requirement already satisfied: charset_normalizer<4,>=2 in /Users/biocbuild/.virtualenvs/r-spectripy/lib/python3.13/site-packages (from requests>=2.31.0->matchms==0.30.0) (3.4.2) Requirement already satisfied: idna<4,>=2.5 in /Users/biocbuild/.virtualenvs/r-spectripy/lib/python3.13/site-packages (from requests>=2.31.0->matchms==0.30.0) (3.10) Requirement already satisfied: urllib3<3,>=1.21.1 in /Users/biocbuild/.virtualenvs/r-spectripy/lib/python3.13/site-packages (from requests>=2.31.0->matchms==0.30.0) (2.5.0) Requirement already satisfied: certifi>=2017.4.17 in /Users/biocbuild/.virtualenvs/r-spectripy/lib/python3.13/site-packages (from requests>=2.31.0->matchms==0.30.0) (2025.6.15) Requirement already satisfied: threadpoolctl>=3.1.0 in /Users/biocbuild/.virtualenvs/r-spectripy/lib/python3.13/site-packages (from scikit-learn>=0.18->pynndescent>=0.5.13->matchms==0.30.0) (3.6.0) Using virtual environment 'r-spectripy' ... + /Users/biocbuild/.virtualenvs/r-spectripy/bin/python -m pip install --upgrade --no-user 'spectrum_utils==0.3.2' Requirement already satisfied: spectrum_utils==0.3.2 in /Users/biocbuild/.virtualenvs/r-spectripy/lib/python3.13/site-packages (0.3.2) Requirement already satisfied: matplotlib in /Users/biocbuild/.virtualenvs/r-spectripy/lib/python3.13/site-packages (from spectrum_utils==0.3.2) (3.10.3) Requirement already satisfied: numba>=0.41 in /Users/biocbuild/.virtualenvs/r-spectripy/lib/python3.13/site-packages (from spectrum_utils==0.3.2) (0.61.2) Requirement already satisfied: numpy in /Users/biocbuild/.virtualenvs/r-spectripy/lib/python3.13/site-packages (from spectrum_utils==0.3.2) (2.2.6) Requirement already satisfied: pyteomics in /Users/biocbuild/.virtualenvs/r-spectripy/lib/python3.13/site-packages (from spectrum_utils==0.3.2) (4.7.5) Requirement already satisfied: llvmlite<0.45,>=0.44.0dev0 in /Users/biocbuild/.virtualenvs/r-spectripy/lib/python3.13/site-packages (from numba>=0.41->spectrum_utils==0.3.2) (0.44.0) Requirement already satisfied: contourpy>=1.0.1 in /Users/biocbuild/.virtualenvs/r-spectripy/lib/python3.13/site-packages (from matplotlib->spectrum_utils==0.3.2) (1.3.2) Requirement already satisfied: cycler>=0.10 in /Users/biocbuild/.virtualenvs/r-spectripy/lib/python3.13/site-packages (from matplotlib->spectrum_utils==0.3.2) (0.12.1) Requirement already satisfied: fonttools>=4.22.0 in /Users/biocbuild/.virtualenvs/r-spectripy/lib/python3.13/site-packages (from matplotlib->spectrum_utils==0.3.2) (4.58.4) Requirement already satisfied: kiwisolver>=1.3.1 in /Users/biocbuild/.virtualenvs/r-spectripy/lib/python3.13/site-packages (from matplotlib->spectrum_utils==0.3.2) (1.4.8) Requirement already satisfied: packaging>=20.0 in /Users/biocbuild/.virtualenvs/r-spectripy/lib/python3.13/site-packages (from matplotlib->spectrum_utils==0.3.2) (25.0) Requirement already satisfied: pillow>=8 in /Users/biocbuild/.virtualenvs/r-spectripy/lib/python3.13/site-packages (from matplotlib->spectrum_utils==0.3.2) (11.2.1) Requirement already satisfied: pyparsing>=2.3.1 in /Users/biocbuild/.virtualenvs/r-spectripy/lib/python3.13/site-packages (from matplotlib->spectrum_utils==0.3.2) (3.2.3) Requirement already satisfied: python-dateutil>=2.7 in /Users/biocbuild/.virtualenvs/r-spectripy/lib/python3.13/site-packages (from matplotlib->spectrum_utils==0.3.2) (2.9.0.post0) Requirement already satisfied: six>=1.5 in /Users/biocbuild/.virtualenvs/r-spectripy/lib/python3.13/site-packages (from python-dateutil>=2.7->matplotlib->spectrum_utils==0.3.2) (1.17.0) Error: package or namespace load failed for ‘SpectriPy’: .onLoad failed in loadNamespace() for 'SpectriPy', details: call: py_module_import(module, convert = convert) error: ModuleNotFoundError: No module named 'matchms' Run `reticulate::py_last_error()` for details. Error: loading failed Execution halted ERROR: loading failed * removing ‘/private/tmp/RtmplxQNRU/Rinst787b2d495586/SpectriPy’ ----------------------------------- ERROR: package installation failed