corearray / pygds Goto Github PK
View Code? Open in Web Editor NEWPython Interface to CoreArray Genomic Data Structure (GDS) Files (pre-release version)
License: GNU General Public License v3.0
Python Interface to CoreArray Genomic Data Structure (GDS) Files (pre-release version)
License: GNU General Public License v3.0
(This message has also been posted as an issue on the gdsfmt repo)
Hello Dr. Zheng,
I was wondering if pygds is still being supported and if it’s compatible with the GDS file format and with modern versions of python, numpy, and gcc? I’ve been experiencing issues installing pygds. In particular, using the command ’pip install git+git://github.com/CoreArray/pygds.git' generates the following error:
src/PyCoreArray.cpp: In function ‘bool pygds_init()’:
src/PyCoreArray.cpp:899:25: error: ‘NUMPY_IMPORT_ARRAY_RETVAL’ was not declared in this scope
899 | if (init() == NUMPY_IMPORT_ARRAY_RETVAL) return false;
| ^~~~~~~~~~~~~~~~~~~~~~~~~
error: command '/usr/lib64/ccache/gcc' failed with exit code 1
----------------------------------------
ERROR: Command errored out with exit status 1: /usr/bin/python3 -u -c 'import sys, setuptools, tokenize; sys.argv[0] = '"'"'/tmp/pip-req-build-ffkgdaz9/setup.py'"'"'; file='"'"'/tmp/pip-req-build-ffkgdaz9/setup.py'"'"';f=getattr(tokenize, '"'"'open'"'"', open)(file);code=f.read().replace('"'"'\r\n'"'"', '"'"'\n'"'"');f.close();exec(compile(code, file, '"'"'exec'"'"'))' install --record /tmp/pip-record-btac33gq/install-record.txt --single-version-externally-managed --user --prefix= --compile --install-headers /home/kyle/.local/include/python3.9/pygds Check the logs for full command output.
Is there any chance you know what may cause this?
Specifications:
OS: Mac 10.15.7
Python: 3.8.5
numpy: 1.21.2
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