Hello, I am trying to package this python application, ChimeraX; however, I keep getting a numpy error when I attempt to run it. Please see code and then error message below. I have tried everything that I can think of to solve the problem. The libfortran file in question lives in the numpy.lib folder in ChimeraX.
{ stdenv, gzip, lib, buildFHSEnv }:
let
pname = "chimerax";
version = "1.7.1"; # Adjust to the correct version
chimerax = stdenv.mkDerivation rec {
inherit pname version;
# src = fetchzip {
# url = "https://www.cgl.ucsf.edu/chimerax/cgi-bin/secure/chimerax-get.py?file=1.7/linux/ChimeraX-${version}.tar.gz";
# sha256 = "sha256-h8mMdDOAyTlH8q9OiXM5iDAEg/LqClKLkm/COdigJS0=";
# };
src = ./ChimeraX-1.7.1.tar.gz;
dontBuild = true;
buildInputs = [ gzip ];
unpackPhase = ''
gunzip -c $src > ${pname}.tar
tar -xf ${pname}.tar
'';
installPhase = ''
mv ${pname}-${version} $out
chmod +x $out/bin/ChimeraX
'';
};
in
buildFHSEnv {
name = pname;
targetPkgs = pkgs: [
chimerax
# pkgs.python311Packages.pip
# pkgs.python311Packages.virtualenv
# pkgs.libgcc
# pkgs.gcc
# pkgs.pkg-config
# pkgs.cmake
# pkgs.libffi.dev
# pkgs.binutils
# pkgs.coreutils
# pkgs.expat
# pkgs.libz
# pkgs.glib.dev
];
# multiPkgs = pkgs: with pkgs; [
# gcc
# libgcc
# binutils
# coreutils
# ];
profile = ''
export PYTHONPATH=/nix/store/rap39wzrgbbahpizxz6ydxja30zx7q0b-python3-3.11.9/lib/python3.11/site-packages:/nix/store/ylvsb39l0wq5q6xdphrq35an6dxqhjw9-python3.11-numpy-1.26.4/lib/python3.11/site-packages:/nix/store/7hnr99nxrd2aw6lghybqdmkckq60j6l9-python3-3.11.9/lib/python3.11/site-packages
export LIBRARY_PATH=/usr/lib:/usr/lib64:$LIBRARY_PATH
export PATH=/usr/bin/gcc:$PATH
'';
# runScript = "ChimeraX";
runScript = "ChimeraX";
meta = with lib; {
description = "ChimeraX - next-generation molecular visualization program";
homepage = "https://www.cgl.ucsf.edu/chimerax/";
platforms = platforms.linux;
};
}
Error message below:
NOTE: Traceback (most recent call last):
File
“/nix/store/jpggf201nxv2lx7imcsawpghz1w5gm73-chimerax-1.7.1/lib/python3.11/site-
packages/numpy/core/init.py”, line 23, in
from . import multiarray
File
“/nix/store/jpggf201nxv2lx7imcsawpghz1w5gm73-chimerax-1.7.1/lib/python3.11/site-
packages/numpy/core/multiarray.py”, line 10, in
from . import overrides
File
“/nix/store/jpggf201nxv2lx7imcsawpghz1w5gm73-chimerax-1.7.1/lib/python3.11/site-
packages/numpy/core/overrides.py”, line 8, in
from numpy.core._multiarray_umath import (
ImportError: libgfortran-040039e1.so.5.0.0: cannot open shared object file: No
such file or directoryDuring handling of the above exception, another exception occurred:
Traceback (most recent call last):
File “”, line 198, in _run_module_as_main
File “”, line 88, in _run_code
File
“/nix/store/jpggf201nxv2lx7imcsawpghz1w5gm73-chimerax-1.7.1/lib/python3.11/site-
packages/chimerax/core/main.py”, line 1069, in
exit_code = init(sys.argv)
^^^^^^^^^^^^^^
File
“/nix/store/jpggf201nxv2lx7imcsawpghz1w5gm73-chimerax-1.7.1/lib/python3.11/site-
packages/chimerax/core/main.py”, line 568, in init
sess = session.Session(app_name,
^^^^^^^^^^^^^^^^^^^^^^^^^
File
“/nix/store/jpggf201nxv2lx7imcsawpghz1w5gm73-chimerax-1.7.1/lib/python3.11/site-
packages/chimerax/core/session.py”, line 490, in init
from chimerax.graphics.gsession import register_graphics_session_save
File
“/nix/store/jpggf201nxv2lx7imcsawpghz1w5gm73-chimerax-1.7.1/lib/python3.11/site-
packages/chimerax/graphics/init.py”, line 48, in
from .opengl import Texture, Lighting, Material
File
“/nix/store/jpggf201nxv2lx7imcsawpghz1w5gm73-chimerax-1.7.1/lib/python3.11/site-
packages/chimerax/graphics/opengl.py”, line 2596, in
from numpy import uint8, uint32, float32
File
“/nix/store/jpggf201nxv2lx7imcsawpghz1w5gm73-chimerax-1.7.1/lib/python3.11/site-
packages/numpy/init.py”, line 139, in
from . import core
File
“/nix/store/jpggf201nxv2lx7imcsawpghz1w5gm73-chimerax-1.7.1/lib/python3.11/site-
packages/numpy/core/init.py”, line 49, in
raise ImportError(msg)
ImportError:IMPORTANT: PLEASE READ THIS FOR ADVICE ON HOW TO SOLVE THIS ISSUE!
Importing the numpy C-extensions failed. This error can happen for
many reasons, often due to issues with your setup or how NumPy was
installed.We have compiled some common reasons and troubleshooting tips at:
https://numpy.org/devdocs/user/troubleshooting-importerror.htmlPlease note and check the following:
- The Python version is: Python3.11 from “/usr/bin/ChimeraX”
- The NumPy version is: “1.25.1”
and make sure that they are the versions you expect.
Please carefully study the documentation linked above for further help.Original error was: libgfortran-040039e1.so.5.0.0: cannot open shared object
file: No such file or directoryBUG: ImportError:
IMPORTANT: PLEASE READ THIS FOR ADVICE ON HOW TO SOLVE THIS ISSUE!
Importing the numpy C-extensions failed. This error can happen for
many reasons, often due to issues with your setup or how NumPy was
installed.We have compiled some common reasons and troubleshooting tips at:
Troubleshooting — NumPy v2.1.dev0 Manual
Please note and check the following:
- The Python version is: Python3.11 from “/usr/bin/ChimeraX”
- The NumPy version is: “1.25.1”
and make sure that they are the versions you expect.
Please carefully study the documentation linked above for further help.Original error was: libgfortran-040039e1.so.5.0.0: cannot open shared object
file: No such file or directoryFile
“/nix/store/jpggf201nxv2lx7imcsawpghz1w5gm73-chimerax-1.7.1/lib/python3.11/site-
packages/numpy/core/init.py”, line 49, in
raise ImportError(msg)See log for complete Python traceback.