StrucGAP

Structural and site-specific Glycoproteomics Analysis Platform

StrucGAP is a modular toolkit for downstream analysis of glycoproteomics data. It includes support for preprocessing, glycan structure analysis, quantification, network visualization, functional annotation, and more.

View the documentation for more information.

Installation

pip install strucgap

Troubleshooting

StrucGAP works successfully on Python 3.7, 3.8, 3.9, 3.10,
but for stability we recommend Python 3.9 or 3.10.

Most errors are caused by incompatible versions of NumPy and pandas.

• For Python 3.7 and 3.8 → use NumPy 1.18.1
• For Python 3.9 and 3.10 → use NumPy 1.26.4
• For all Python versions → use pandas 1.3.5

Q1: ModuleNotFoundError: No module named 'statsmodels'

A1:

pip install statsmodels

Q2: ImportError: Missing optional dependency 'openpyxl'

A2:

pip install openpyxl

Q3: TypeError: loop of ufunc does not support argument 0 of type float which has no callable log2 method

A3:

pip install numpy==1.26.4
pip install pandas==1.3.5

Q4: ModuleNotFoundError: No module named 'importlib.metadata'

Cause: This package is included in the Python standard library only since version 3.8.

A4:

pip install importlib-metadata==6.7.0

Q5: During installation, I see errors mentioning Rust or Cargo. Do StrucGAP or gseapy depend on Rust?

Cause: Neither StrucGAP nor gseapy requires Rust directly. However, in some environments pip may try to compile dependencies from source (instead of using pre-built wheels). When that happens, Rust may be required if the dependency’s source build involves it.

A5: Alternatively, ensure that your environment has access to the official Python package index (PyPI) so wheels can be downloaded.
If compilation still occurs, you may need to install Rust temporarily, but this is not normally required.

Q6: TypeError: loop of ufunc does not support argument 0 of type float which has no callable log2 method

A6:

pip install pandas==1.3.5

Q7: ERROR: Cannot uninstall 'llvmlite'. It is a distutils installed project and thus we cannot accurately determine which files belong to it which would lead to only a partial uninstall when execute pip install strucgap.

A7:

pip install --ignore-installed llvmlite

Q8: OSError: no library called "cairo-2" was found no library called "cairo" was found no library called "libcairo-2" was found cannot load library 'libcairo.so.2': error 0x7e. Additionally, ctypes.util.find_library() did not manage to locate a library called 'libcairo.so.2' cannot load library 'libcairo.2.dylib': error 0x7e. Additionally, ctypes.util.find_library() did not manage to locate a library called 'libcairo.2.dylib' cannot load library 'libcairo-2.dll': error 0x7e. Additionally, ctypes.util.find_library() did not manage to locate a library called 'libcairo-2.dll' when execute pip install strucgap.

A8:

conda install -c conda-forge cairo

If your problem is not listed here, please open a GitHub Issue with your error message and environment details (Python version, OS, and package versions).