Please update instructions for conda install, numpy=1.18.3 is deprecated

[thierrygrange]

Dear Thorsten The instructions for conda install are not valid anymore, numpy=1.18.3 is deprecated and cannot be installed. Installing 1.18.4 leads to conflict with the other versions, including matplotlib. Not specifying any version works, except for the pip install of plinkio. Currently, a full conda install of read2 fails as indicated in here.

Hopefully, you could figure out one set of library versions that is fully compatible in between them and currently available resources on anaconda.

Best

Thierry

[thierrygrange]

It may be useful for you to have the error issue during the pip install step: pip install plinkio Collecting plinkio Using cached plinkio-0.9.8.tar.gz (34 kB) Preparing metadata (setup.py) ... done Building wheels for collected packages: plinkio Building wheel for plinkio (setup.py) ... error error: subprocess-exited-with-error

× python setup.py bdist_wheel did not run successfully. │ exit code: 1 ╰─> [42 lines of output] Traceback (most recent call last): File "", line 36, in File "", line 34, in File "/tmp/pip-install-upkp6lzh/plinkio_37f71a9c0cec497da726247582180cbf/setup.py", line 101, in entry_points={}, File "/home/paleogenomique/.conda/envs/readv2/lib/python3.7/site-packages/setuptools/init.py", line 153, in setup return distutils.core.setup(**attrs) File "/home/paleogenomique/.conda/envs/readv2/lib/python3.7/distutils/core.py", line 134, in setup ok = dist.parse_command_line() File "/home/paleogenomique/.conda/envs/readv2/lib/python3.7/distutils/dist.py", line 483, in parse_command_line args = self._parse_command_opts(parser, args) File "/home/paleogenomique/.conda/envs/readv2/lib/python3.7/site-packages/setuptools/dist.py", line 1048, in _parse_command_opts nargs = _Distribution._parse_command_opts(self, parser, args) File "/home/paleogenomique/.conda/envs/readv2/lib/python3.7/distutils/dist.py", line 539, in _parse_command_opts cmd_class = self.get_command_class(command) File "/home/paleogenomique/.conda/envs/readv2/lib/python3.7/site-packages/setuptools/dist.py", line 893, in get_command_class self.cmdclass[command] = cmdclass = ep.load() File "/home/paleogenomique/.conda/envs/readv2/lib/python3.7/site-packages/pkg_resources/init.py", line 2465, in load return self.resolve() File "/home/paleogenomique/.conda/envs/readv2/lib/python3.7/site-packages/pkg_resources/init.py", line 2471, in resolve module = import(self.module_name, fromlist=['name'], level=0) File "/home/paleogenomique/.conda/envs/readv2/lib/python3.7/site-packages/wheel/bdist_wheel.py", line 28, in from .metadata import pkginfo_to_metadata File "/home/paleogenomique/.conda/envs/readv2/lib/python3.7/site-packages/wheel/metadata.py", line 16, in from .vendored.packaging.requirements import Requirement File "/home/paleogenomique/.conda/envs/readv2/lib/python3.7/site-packages/wheel/vendored/packaging/requirements.py", line 7, in from ._parser import parse_requirement as _parse_requirement File "/home/paleogenomique/.conda/envs/readv2/lib/python3.7/site-packages/wheel/vendored/packaging/_parser.py", line 10, in from ._tokenizer import DEFAULT_RULES, Tokenizer File "/home/paleogenomique/.conda/envs/readv2/lib/python3.7/site-packages/wheel/vendored/packaging/_tokenizer.py", line 6, in from .specifiers import Specifier File "/home/paleogenomique/.conda/envs/readv2/lib/python3.7/site-packages/wheel/vendored/packaging/specifiers.py", line 16, in from .utils import canonicalize_version File "/home/paleogenomique/.conda/envs/readv2/lib/python3.7/site-packages/wheel/vendored/packaging/utils.py", line 8, in from .tags import Tag, parse_tag File "/home/paleogenomique/.conda/envs/readv2/lib/python3.7/site-packages/wheel/vendored/packaging/tags.py", line 26, in from . import _manylinux, _musllinux File "/home/paleogenomique/.conda/envs/readv2/lib/python3.7/site-packages/wheel/vendored/packaging/_manylinux.py", line 171, in def _get_glibc_version() -> Tuple[int, int]: File "/home/paleogenomique/.conda/envs/readv2/lib/python3.7/functools.py", line 490, in lru_cache raise TypeError('Expected maxsize to be an integer or None') TypeError: Expected maxsize to be an integer or None [end of output]

The packages that were installed by conda when not specifying any library versions: _libgcc_mutex conda-forge/linux-64::_libgcc_mutex-0.1-conda_forge _openmp_mutex conda-forge/linux-64::_openmp_mutex-4.5-2_gnu ca-certificates conda-forge/linux-64::ca-certificates-2024.2.2-hbcca054_0 cycler conda-forge/noarch::cycler-0.11.0-pyhd8ed1ab_0 freetype conda-forge/linux-64::freetype-2.12.1-h267a509_2 icu conda-forge/linux-64::icu-67.1-he1b5a44_0 kiwisolver pkgs/main/linux-64::kiwisolver-1.4.4-py37h6a678d5_0 ld_impl_linux-64 conda-forge/linux-64::ld_impl_linux-64-2.40-h41732ed_0 libblas conda-forge/linux-64::libblas-3.9.0-21_linux64_openblas libcblas conda-forge/linux-64::libcblas-3.9.0-21_linux64_openblas libffi conda-forge/linux-64::libffi-3.4.2-h7f98852_5 libgcc-ng conda-forge/linux-64::libgcc-ng-13.2.0-h807b86a_5 libgfortran-ng conda-forge/linux-64::libgfortran-ng-13.2.0-h69a702a_5 libgfortran5 conda-forge/linux-64::libgfortran5-13.2.0-ha4646dd_5 libgomp conda-forge/linux-64::libgomp-13.2.0-h807b86a_5 liblapack conda-forge/linux-64::liblapack-3.9.0-21_linux64_openblas libnsl conda-forge/linux-64::libnsl-2.0.1-hd590300_0 libopenblas conda-forge/linux-64::libopenblas-0.3.26-pthreads_h413a1c8_0 libpng conda-forge/linux-64::libpng-1.6.43-h2797004_0 libsqlite conda-forge/linux-64::libsqlite-3.45.2-h2797004_0 libstdcxx-ng conda-forge/linux-64::libstdcxx-ng-13.2.0-h7e041cc_5 libzlib conda-forge/linux-64::libzlib-1.2.13-hd590300_5 matplotlib conda-forge/linux-64::matplotlib-3.2.2-1 matplotlib-base conda-forge/linux-64::matplotlib-base-3.2.2-py37h1d35a4c_1 ncurses conda-forge/linux-64::ncurses-6.4.20240210-h59595ed_0 numpy conda-forge/linux-64::numpy-1.21.6-py37h976b520_0 openssl conda-forge/linux-64::openssl-3.2.1-hd590300_1 pandas conda-forge/linux-64::pandas-1.3.5-py37he8f5f7f_0 pip conda-forge/noarch::pip-24.0-pyhd8ed1ab_0 pyparsing conda-forge/noarch::pyparsing-3.1.2-pyhd8ed1ab_0 python conda-forge/linux-64::python-3.7.12-hf930737_100_cpython python-dateutil conda-forge/noarch::python-dateutil-2.9.0-pyhd8ed1ab_0 python_abi conda-forge/linux-64::python_abi-3.7-4_cp37m pytz conda-forge/noarch::pytz-2024.1-pyhd8ed1ab_0 readline conda-forge/linux-64::readline-8.2-h8228510_1 setuptools conda-forge/linux-64::setuptools-59.8.0-py37h89c1867_1 six conda-forge/noarch::six-1.16.0-pyh6c4a22f_0 sqlite conda-forge/linux-64::sqlite-3.45.2-h2c6b66d_0 tk conda-forge/linux-64::tk-8.6.13-noxft_h4845f30_101 tornado conda-forge/linux-64::tornado-6.2-py37h540881e_0 typing_extensions conda-forge/noarch::typing_extensions-4.5.0-pyha770c72_0 wheel conda-forge/noarch::wheel-0.43.0-pyhd8ed1ab_0 xz conda-forge/linux-64::xz-5.2.6-h166bdaf_0

[thierrygrange]

Specifying no version at all of anything, including python, just the latest of python3 worked and the plinkio could be installed by pip conda create -n readv2 python=3 pandas numpy pip matplotlib The problem occurs when specifying python=3.7

[SonofLastPanda]

I received similar errors from the others as well, I am updating the README file. Thank you very much for bringing this to our attention.

[thierrygrange]

Thanks

Best

Thierry

From: Erkin Alacamli @. Sent: Thursday, March 28, 2024 11:18 AM To: GuntherLab/READv2 @.> Cc: GRANGE Thierry @.>; Author @.> Subject: Re: [GuntherLab/READv2] Please update instructions for conda install, numpy=1.18.3 is deprecated (Issue #1)

I received similar errors from the others as well, I am updating the README file. Thank you very much for bringing this to our attention.

— Reply to this email directly, view it on GitHubhttps://github.com/GuntherLab/READv2/issues/1#issuecomment-2024846497, or unsubscribehttps://github.com/notifications/unsubscribe-auth/AKDBI63DPXUTXHD23TXU2O3Y2PN3XAVCNFSM6AAAAABFJBYWNSVHI2DSMVQWIX3LMV43OSLTON2WKQ3PNVWWK3TUHMZDAMRUHA2DMNBZG4. You are receiving this because you authored the thread.Message ID: @.**@.>>