Multiple platform build/check report for BioC 3.22 - BUILD results for SpectriPy on lconway

Hostname	OS	Arch (*)	R version	Installed pkgs
nebbiolo2	Linux (Ubuntu 24.04.2 LTS)	x86_64	4.5.1 (2025-06-13) -- "Great Square Root"	4565
palomino8	Windows Server 2022 Datacenter	x64	4.5.1 (2025-06-13 ucrt) -- "Great Square Root"	4505
lconway	macOS 12.7.1 Monterey	x86_64	4.5.1 (2025-06-13) -- "Great Square Root"	4544
kjohnson3	macOS 13.7.1 Ventura	arm64	4.5.1 Patched (2025-06-14 r88325) -- "Great Square Root"	4492
taishan	Linux (openEuler 24.03 LTS)	aarch64	4.5.0 (2025-04-11) -- "How About a Twenty-Six"	4496
Click on any hostname to see more info about the system (e.g. compilers) () as reported by 'uname -p', except on Windows and Mac OS X*

BUILD results for SpectriPy on lconway

To the developers/maintainers of the SpectriPy package:
- Allow up to 24 hours (and sometimes 48 hours) for your latest push to git@git.bioconductor.org:packages/SpectriPy.git to reflect on this report. See Troubleshooting Build Report for more information.
- Use the following Renviron settings to reproduce errors and warnings.
- If 'R CMD check' started to fail recently on the Linux builder(s) over a missing dependency, add the missing dependency to 'Suggests:' in your DESCRIPTION file. See Renviron.bioc for more information.

raw results

Summary

Package: SpectriPy

Version: 0.99.4

Command: /Library/Frameworks/R.framework/Resources/bin/R CMD build --keep-empty-dirs --no-resave-data SpectriPy

StartedAt: 2025-06-20 18:35:36 -0400 (Fri, 20 Jun 2025)

EndedAt: 2025-06-20 18:36:00 -0400 (Fri, 20 Jun 2025)

EllapsedTime: 24.0 seconds

RetCode: 1

Status: ERROR

PackageFile: None

PackageFileSize: NA

Command output

##############################################################################
##############################################################################
###
### 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/RtmpCfjDfm/Rinst2868a0a3ff9/SpectriPy’
      -----------------------------------
ERROR: package installation failed