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Failure to install - please help! #13

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AtanasDRadkov opened this issue Nov 26, 2023 · 7 comments
Open

Failure to install - please help! #13

AtanasDRadkov opened this issue Nov 26, 2023 · 7 comments

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@AtanasDRadkov
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here is the command that I ran and all of the message that came following that. and also I'm including a list of the exact packages in my conda environment.

packages in my surfmap conda environment:
(surfmap) atanasradkov@Atanass-MBP surfmap_docker % conda list

packages in environment at /Users/atanasradkov/opt/anaconda3/envs/surfmap:

Name Version Build Channel

bzip2 1.0.8 h10d778d_5 conda-forge
ca-certificates 2023.11.17 h8857fd0_0 conda-forge
libexpat 2.5.0 hf0c8a7f_1 conda-forge
libffi 3.4.2 h0d85af4_5 conda-forge
libsqlite 3.44.2 h92b6c6a_0 conda-forge
libzlib 1.2.13 h8a1eda9_5 conda-forge
ncurses 6.4 h93d8f39_2 conda-forge
openssl 3.2.0 hd75f5a5_0 conda-forge
pip 23.3.1 pyhd8ed1ab_0 conda-forge
python 3.12.0 h30d4d87_0_cpython conda-forge
readline 8.2 h9e318b2_1 conda-forge
setuptools 68.2.2 pyhd8ed1ab_0 conda-forge
tk 8.6.13 h1abcd95_1 conda-forge
tzdata 2023c h71feb2d_0 conda-forge
wheel 0.41.3 pyhd8ed1ab_0 conda-forge
xz 5.2.6 h775f41a_0 conda-forge

my command in terminal:
(surfmap) atanasradkov@Atanass-MBP surfmap_docker % python -m pip install -e git+https://github.com/i2bc/[email protected]#egg=surfmap

everything that happened afterwards:
Obtaining surfmap from git+https://github.com/i2bc/[email protected]#egg=surfmap
Cloning https://github.com/i2bc/SURFMAP.git (to revision v2.0.0) to ./src/surfmap
Running command git clone --filter=blob:none --quiet https://github.com/i2bc/SURFMAP.git /Users/atanasradkov/Desktop/Arcadia/developing_coding/ProtCart/surfmap_docker/src/surfmap
Running command git checkout -q f19184f961fcd8ecc12a2a0716125ae8d63c5a05
Resolved https://github.com/i2bc/SURFMAP.git to commit f19184f961fcd8ecc12a2a0716125ae8d63c5a05
Preparing metadata (setup.py) ... done
Collecting freesasa==2.1.0 (from surfmap)
Using cached freesasa-2.1.0.tar.gz (241 kB)
Preparing metadata (setup.py) ... done
Collecting numpy>=1.21.6 (from surfmap)
Using cached numpy-1.26.2-cp312-cp312-macosx_10_9_x86_64.whl.metadata (61 kB)
Collecting pdb2pqr==3.1.0 (from surfmap)
Using cached pdb2pqr-3.1.0-py2.py3-none-any.whl (206 kB)
Collecting requests==2.22.0 (from surfmap)
Using cached requests-2.22.0-py2.py3-none-any.whl (57 kB)
Collecting propka>=3.2 (from pdb2pqr==3.1.0->surfmap)
Using cached propka-3.5.0-py3-none-any.whl (98 kB)
Collecting pandas>=1.0 (from pdb2pqr==3.1.0->surfmap)
Using cached pandas-2.1.3-cp312-cp312-macosx_10_9_x86_64.whl.metadata (18 kB)
Collecting pytest>=5.4.1 (from pdb2pqr==3.1.0->surfmap)
Using cached pytest-7.4.3-py3-none-any.whl.metadata (7.9 kB)
Collecting mmcif-pdbx>=1.1.2 (from pdb2pqr==3.1.0->surfmap)
Using cached mmcif_pdbx-2.0.1-py2.py3-none-any.whl (20 kB)
Collecting chardet<3.1.0,>=3.0.2 (from requests==2.22.0->surfmap)
Using cached chardet-3.0.4-py2.py3-none-any.whl (133 kB)
Collecting idna<2.9,>=2.5 (from requests==2.22.0->surfmap)
Using cached idna-2.8-py2.py3-none-any.whl (58 kB)
Collecting urllib3!=1.25.0,!=1.25.1,<1.26,>=1.21.1 (from requests==2.22.0->surfmap)
Using cached urllib3-1.25.11-py2.py3-none-any.whl (127 kB)
Collecting certifi>=2017.4.17 (from requests==2.22.0->surfmap)
Using cached certifi-2023.11.17-py3-none-any.whl.metadata (2.2 kB)
Collecting python-dateutil>=2.8.2 (from pandas>=1.0->pdb2pqr==3.1.0->surfmap)
Using cached python_dateutil-2.8.2-py2.py3-none-any.whl (247 kB)
Collecting pytz>=2020.1 (from pandas>=1.0->pdb2pqr==3.1.0->surfmap)
Using cached pytz-2023.3.post1-py2.py3-none-any.whl.metadata (22 kB)
Collecting tzdata>=2022.1 (from pandas>=1.0->pdb2pqr==3.1.0->surfmap)
Using cached tzdata-2023.3-py2.py3-none-any.whl (341 kB)
Collecting iniconfig (from pytest>=5.4.1->pdb2pqr==3.1.0->surfmap)
Using cached iniconfig-2.0.0-py3-none-any.whl (5.9 kB)
Collecting packaging (from pytest>=5.4.1->pdb2pqr==3.1.0->surfmap)
Using cached packaging-23.2-py3-none-any.whl.metadata (3.2 kB)
Collecting pluggy<2.0,>=0.12 (from pytest>=5.4.1->pdb2pqr==3.1.0->surfmap)
Using cached pluggy-1.3.0-py3-none-any.whl.metadata (4.3 kB)
Collecting six>=1.5 (from python-dateutil>=2.8.2->pandas>=1.0->pdb2pqr==3.1.0->surfmap)
Using cached six-1.16.0-py2.py3-none-any.whl (11 kB)
Using cached numpy-1.26.2-cp312-cp312-macosx_10_9_x86_64.whl (20.3 MB)
Using cached certifi-2023.11.17-py3-none-any.whl (162 kB)
Using cached pandas-2.1.3-cp312-cp312-macosx_10_9_x86_64.whl (11.4 MB)
Using cached pytest-7.4.3-py3-none-any.whl (325 kB)
Using cached pluggy-1.3.0-py3-none-any.whl (18 kB)
Using cached pytz-2023.3.post1-py2.py3-none-any.whl (502 kB)
Using cached packaging-23.2-py3-none-any.whl (53 kB)
Building wheels for collected packages: freesasa
Building wheel for freesasa (setup.py) ... error
error: subprocess-exited-with-error

× python setup.py bdist_wheel did not run successfully.
│ exit code: 1
╰─> [49 lines of output]
Define environment variable USE_CYTHON to build from Cython source
/Users/atanasradkov/opt/anaconda3/envs/surfmap/lib/python3.12/site-packages/setuptools/init.py:80: _DeprecatedInstaller: setuptools.installer and fetch_build_eggs are deprecated.
!!

          ********************************************************************************
          Requirements should be satisfied by a PEP 517 installer.
          If you are using pip, you can try `pip install --use-pep517`.
          ********************************************************************************
  
  !!
    dist.fetch_build_eggs(dist.setup_requires)
  Traceback (most recent call last):
    File "<string>", line 2, in <module>
    File "<pip-setuptools-caller>", line 34, in <module>
    File "/private/var/folders/ww/lzw7cn4s22d3pm8389qvtw5h0000gn/T/pip-install-e1d0jeji/freesasa_bc2d6c21ed0542b896191bf54d712920/setup.py", line 57, in <module>
      setup(
    File "/Users/atanasradkov/opt/anaconda3/envs/surfmap/lib/python3.12/site-packages/setuptools/__init__.py", line 102, in setup
      _install_setup_requires(attrs)
    File "/Users/atanasradkov/opt/anaconda3/envs/surfmap/lib/python3.12/site-packages/setuptools/__init__.py", line 75, in _install_setup_requires
      _fetch_build_eggs(dist)
    File "/Users/atanasradkov/opt/anaconda3/envs/surfmap/lib/python3.12/site-packages/setuptools/__init__.py", line 80, in _fetch_build_eggs
      dist.fetch_build_eggs(dist.setup_requires)
    File "/Users/atanasradkov/opt/anaconda3/envs/surfmap/lib/python3.12/site-packages/setuptools/dist.py", line 662, in fetch_build_eggs
      return _fetch_build_eggs(self, requires)
             ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
    File "/Users/atanasradkov/opt/anaconda3/envs/surfmap/lib/python3.12/site-packages/setuptools/installer.py", line 38, in _fetch_build_eggs
      resolved_dists = pkg_resources.working_set.resolve(
                       ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
    File "/Users/atanasradkov/opt/anaconda3/envs/surfmap/lib/python3.12/site-packages/pkg_resources/__init__.py", line 829, in resolve
      dist = self._resolve_dist(
             ^^^^^^^^^^^^^^^^^^^
    File "/Users/atanasradkov/opt/anaconda3/envs/surfmap/lib/python3.12/site-packages/pkg_resources/__init__.py", line 865, in _resolve_dist
      dist = best[req.key] = env.best_match(
                             ^^^^^^^^^^^^^^^
    File "/Users/atanasradkov/opt/anaconda3/envs/surfmap/lib/python3.12/site-packages/pkg_resources/__init__.py", line 1135, in best_match
      return self.obtain(req, installer)
             ^^^^^^^^^^^^^^^^^^^^^^^^^^^
    File "/Users/atanasradkov/opt/anaconda3/envs/surfmap/lib/python3.12/site-packages/pkg_resources/__init__.py", line 1147, in obtain
      return installer(requirement)
             ^^^^^^^^^^^^^^^^^^^^^^
    File "/Users/atanasradkov/opt/anaconda3/envs/surfmap/lib/python3.12/site-packages/setuptools/installer.py", line 106, in _fetch_build_egg_no_warn
      wheel.install_as_egg(dist_location)
    File "/Users/atanasradkov/opt/anaconda3/envs/surfmap/lib/python3.12/site-packages/setuptools/wheel.py", line 120, in install_as_egg
      self._install_as_egg(destination_eggdir, zf)
    File "/Users/atanasradkov/opt/anaconda3/envs/surfmap/lib/python3.12/site-packages/setuptools/wheel.py", line 128, in _install_as_egg
      self._convert_metadata(zf, destination_eggdir, dist_info, egg_info)
    File "/Users/atanasradkov/opt/anaconda3/envs/surfmap/lib/python3.12/site-packages/setuptools/wheel.py", line 173, in _convert_metadata
      os.rename(dist_info, egg_info)
  OSError: [Errno 66] Directory not empty: '/private/var/folders/ww/lzw7cn4s22d3pm8389qvtw5h0000gn/T/pip-install-e1d0jeji/freesasa_bc2d6c21ed0542b896191bf54d712920/.eggs/Cython-3.0.5-py3.12-macosx-10.9-x86_64.egg/Cython-3.0.5.dist-info' -> '/private/var/folders/ww/lzw7cn4s22d3pm8389qvtw5h0000gn/T/pip-install-e1d0jeji/freesasa_bc2d6c21ed0542b896191bf54d712920/.eggs/Cython-3.0.5-py3.12-macosx-10.9-x86_64.egg/EGG-INFO'
  [end of output]

note: This error originates from a subprocess, and is likely not a problem with pip.
ERROR: Failed building wheel for freesasa
Running setup.py clean for freesasa
error: subprocess-exited-with-error

× python setup.py clean did not run successfully.
│ exit code: 1
╰─> [49 lines of output]
Define environment variable USE_CYTHON to build from Cython source
/Users/atanasradkov/opt/anaconda3/envs/surfmap/lib/python3.12/site-packages/setuptools/init.py:80: _DeprecatedInstaller: setuptools.installer and fetch_build_eggs are deprecated.
!!

          ********************************************************************************
          Requirements should be satisfied by a PEP 517 installer.
          If you are using pip, you can try `pip install --use-pep517`.
          ********************************************************************************
  
  !!
    dist.fetch_build_eggs(dist.setup_requires)
  Traceback (most recent call last):
    File "<string>", line 2, in <module>
    File "<pip-setuptools-caller>", line 34, in <module>
    File "/private/var/folders/ww/lzw7cn4s22d3pm8389qvtw5h0000gn/T/pip-install-e1d0jeji/freesasa_bc2d6c21ed0542b896191bf54d712920/setup.py", line 57, in <module>
      setup(
    File "/Users/atanasradkov/opt/anaconda3/envs/surfmap/lib/python3.12/site-packages/setuptools/__init__.py", line 102, in setup
      _install_setup_requires(attrs)
    File "/Users/atanasradkov/opt/anaconda3/envs/surfmap/lib/python3.12/site-packages/setuptools/__init__.py", line 75, in _install_setup_requires
      _fetch_build_eggs(dist)
    File "/Users/atanasradkov/opt/anaconda3/envs/surfmap/lib/python3.12/site-packages/setuptools/__init__.py", line 80, in _fetch_build_eggs
      dist.fetch_build_eggs(dist.setup_requires)
    File "/Users/atanasradkov/opt/anaconda3/envs/surfmap/lib/python3.12/site-packages/setuptools/dist.py", line 662, in fetch_build_eggs
      return _fetch_build_eggs(self, requires)
             ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
    File "/Users/atanasradkov/opt/anaconda3/envs/surfmap/lib/python3.12/site-packages/setuptools/installer.py", line 38, in _fetch_build_eggs
      resolved_dists = pkg_resources.working_set.resolve(
                       ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
    File "/Users/atanasradkov/opt/anaconda3/envs/surfmap/lib/python3.12/site-packages/pkg_resources/__init__.py", line 829, in resolve
      dist = self._resolve_dist(
             ^^^^^^^^^^^^^^^^^^^
    File "/Users/atanasradkov/opt/anaconda3/envs/surfmap/lib/python3.12/site-packages/pkg_resources/__init__.py", line 865, in _resolve_dist
      dist = best[req.key] = env.best_match(
                             ^^^^^^^^^^^^^^^
    File "/Users/atanasradkov/opt/anaconda3/envs/surfmap/lib/python3.12/site-packages/pkg_resources/__init__.py", line 1135, in best_match
      return self.obtain(req, installer)
             ^^^^^^^^^^^^^^^^^^^^^^^^^^^
    File "/Users/atanasradkov/opt/anaconda3/envs/surfmap/lib/python3.12/site-packages/pkg_resources/__init__.py", line 1147, in obtain
      return installer(requirement)
             ^^^^^^^^^^^^^^^^^^^^^^
    File "/Users/atanasradkov/opt/anaconda3/envs/surfmap/lib/python3.12/site-packages/setuptools/installer.py", line 106, in _fetch_build_egg_no_warn
      wheel.install_as_egg(dist_location)
    File "/Users/atanasradkov/opt/anaconda3/envs/surfmap/lib/python3.12/site-packages/setuptools/wheel.py", line 120, in install_as_egg
      self._install_as_egg(destination_eggdir, zf)
    File "/Users/atanasradkov/opt/anaconda3/envs/surfmap/lib/python3.12/site-packages/setuptools/wheel.py", line 128, in _install_as_egg
      self._convert_metadata(zf, destination_eggdir, dist_info, egg_info)
    File "/Users/atanasradkov/opt/anaconda3/envs/surfmap/lib/python3.12/site-packages/setuptools/wheel.py", line 173, in _convert_metadata
      os.rename(dist_info, egg_info)
  OSError: [Errno 66] Directory not empty: '/private/var/folders/ww/lzw7cn4s22d3pm8389qvtw5h0000gn/T/pip-install-e1d0jeji/freesasa_bc2d6c21ed0542b896191bf54d712920/.eggs/Cython-3.0.5-py3.12-macosx-10.9-x86_64.egg/Cython-3.0.5.dist-info' -> '/private/var/folders/ww/lzw7cn4s22d3pm8389qvtw5h0000gn/T/pip-install-e1d0jeji/freesasa_bc2d6c21ed0542b896191bf54d712920/.eggs/Cython-3.0.5-py3.12-macosx-10.9-x86_64.egg/EGG-INFO'
  [end of output]

note: This error originates from a subprocess, and is likely not a problem with pip.
ERROR: Failed cleaning build dir for freesasa
Failed to build freesasa
ERROR: Could not build wheels for freesasa, which is required to install pyproject.toml-based projects
@AtanasDRadkov
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Author

I also tried to use pip install --use-pep517 as recommended. here is what happened in that case.

(surfmap) atanasradkov@Atanass-MBP surfmap_docker % python -m pip install --use-pep517 -e git+https://github.com/i2bc/[email protected]#egg=surfmap
Obtaining surfmap from git+https://github.com/i2bc/[email protected]#egg=surfmap
Updating ./src/surfmap clone (to revision v2.0.0)
Running command git fetch -q --tags
Running command git reset --hard -q f19184f961fcd8ecc12a2a0716125ae8d63c5a05
Installing build dependencies ... done
Checking if build backend supports build_editable ... done
Getting requirements to build editable ... done
Preparing editable metadata (pyproject.toml) ... done
Collecting freesasa==2.1.0 (from surfmap)
Using cached freesasa-2.1.0.tar.gz (241 kB)
Installing build dependencies ... done
Getting requirements to build wheel ... done
Installing backend dependencies ... done
Preparing metadata (pyproject.toml) ... done
Collecting numpy>=1.21.6 (from surfmap)
Using cached numpy-1.26.2-cp312-cp312-macosx_10_9_x86_64.whl.metadata (61 kB)
Collecting pdb2pqr==3.1.0 (from surfmap)
Using cached pdb2pqr-3.1.0-py2.py3-none-any.whl (206 kB)
Collecting requests==2.22.0 (from surfmap)
Using cached requests-2.22.0-py2.py3-none-any.whl (57 kB)
Collecting propka>=3.2 (from pdb2pqr==3.1.0->surfmap)
Using cached propka-3.5.0-py3-none-any.whl (98 kB)
Collecting pandas>=1.0 (from pdb2pqr==3.1.0->surfmap)
Using cached pandas-2.1.3-cp312-cp312-macosx_10_9_x86_64.whl.metadata (18 kB)
Collecting pytest>=5.4.1 (from pdb2pqr==3.1.0->surfmap)
Using cached pytest-7.4.3-py3-none-any.whl.metadata (7.9 kB)
Collecting mmcif-pdbx>=1.1.2 (from pdb2pqr==3.1.0->surfmap)
Using cached mmcif_pdbx-2.0.1-py2.py3-none-any.whl (20 kB)
Collecting chardet<3.1.0,>=3.0.2 (from requests==2.22.0->surfmap)
Using cached chardet-3.0.4-py2.py3-none-any.whl (133 kB)
Collecting idna<2.9,>=2.5 (from requests==2.22.0->surfmap)
Using cached idna-2.8-py2.py3-none-any.whl (58 kB)
Collecting urllib3!=1.25.0,!=1.25.1,<1.26,>=1.21.1 (from requests==2.22.0->surfmap)
Using cached urllib3-1.25.11-py2.py3-none-any.whl (127 kB)
Collecting certifi>=2017.4.17 (from requests==2.22.0->surfmap)
Using cached certifi-2023.11.17-py3-none-any.whl.metadata (2.2 kB)
Collecting python-dateutil>=2.8.2 (from pandas>=1.0->pdb2pqr==3.1.0->surfmap)
Using cached python_dateutil-2.8.2-py2.py3-none-any.whl (247 kB)
Collecting pytz>=2020.1 (from pandas>=1.0->pdb2pqr==3.1.0->surfmap)
Using cached pytz-2023.3.post1-py2.py3-none-any.whl.metadata (22 kB)
Collecting tzdata>=2022.1 (from pandas>=1.0->pdb2pqr==3.1.0->surfmap)
Using cached tzdata-2023.3-py2.py3-none-any.whl (341 kB)
Collecting iniconfig (from pytest>=5.4.1->pdb2pqr==3.1.0->surfmap)
Using cached iniconfig-2.0.0-py3-none-any.whl (5.9 kB)
Collecting packaging (from pytest>=5.4.1->pdb2pqr==3.1.0->surfmap)
Using cached packaging-23.2-py3-none-any.whl.metadata (3.2 kB)
Collecting pluggy<2.0,>=0.12 (from pytest>=5.4.1->pdb2pqr==3.1.0->surfmap)
Using cached pluggy-1.3.0-py3-none-any.whl.metadata (4.3 kB)
Collecting six>=1.5 (from python-dateutil>=2.8.2->pandas>=1.0->pdb2pqr==3.1.0->surfmap)
Using cached six-1.16.0-py2.py3-none-any.whl (11 kB)
Using cached numpy-1.26.2-cp312-cp312-macosx_10_9_x86_64.whl (20.3 MB)
Using cached certifi-2023.11.17-py3-none-any.whl (162 kB)
Using cached pandas-2.1.3-cp312-cp312-macosx_10_9_x86_64.whl (11.4 MB)
Using cached pytest-7.4.3-py3-none-any.whl (325 kB)
Using cached pluggy-1.3.0-py3-none-any.whl (18 kB)
Using cached pytz-2023.3.post1-py2.py3-none-any.whl (502 kB)
Using cached packaging-23.2-py3-none-any.whl (53 kB)
Building wheels for collected packages: surfmap, freesasa
Building editable for surfmap (pyproject.toml) ... done
Created wheel for surfmap: filename=surfmap-2.0.0-0.editable-py3-none-any.whl size=4439 sha256=05df30f97e74dbb5be24bfd97dc2d8d4466da3a619c0ada13712ad94e7dda6a8
Stored in directory: /private/var/folders/ww/lzw7cn4s22d3pm8389qvtw5h0000gn/T/pip-ephem-wheel-cache-2dnxgler/wheels/8e/a6/bf/229b26a3bebce1a9c328068768292ff00fbed055af76caedc8
Building wheel for freesasa (pyproject.toml) ... error
error: subprocess-exited-with-error

× Building wheel for freesasa (pyproject.toml) did not run successfully.
│ exit code: 1
╰─> [48 lines of output]
Define environment variable USE_CYTHON to build from Cython source
running bdist_wheel
running build
running build_ext
building 'freesasa' extension
creating build
creating build/temp.macosx-10.9-x86_64-cpython-312
creating build/temp.macosx-10.9-x86_64-cpython-312/lib
creating build/temp.macosx-10.9-x86_64-cpython-312/lib/src
creating build/temp.macosx-10.9-x86_64-cpython-312/src
clang -fno-strict-overflow -DNDEBUG -O2 -Wall -fPIC -O2 -isystem /Users/atanasradkov/opt/anaconda3/envs/surfmap/include -fPIC -O2 -isystem /Users/atanasradkov/opt/anaconda3/envs/surfmap/include -Ilib/src -I. -I/Users/atanasradkov/opt/anaconda3/envs/surfmap/include/python3.12 -c lib/src/classifier.c -o build/temp.macosx-10.9-x86_64-cpython-312/lib/src/classifier.o -DHAVE_CONFIG_H -std=gnu99
clang -fno-strict-overflow -DNDEBUG -O2 -Wall -fPIC -O2 -isystem /Users/atanasradkov/opt/anaconda3/envs/surfmap/include -fPIC -O2 -isystem /Users/atanasradkov/opt/anaconda3/envs/surfmap/include -Ilib/src -I. -I/Users/atanasradkov/opt/anaconda3/envs/surfmap/include/python3.12 -c lib/src/classifier_naccess.c -o build/temp.macosx-10.9-x86_64-cpython-312/lib/src/classifier_naccess.o -DHAVE_CONFIG_H -std=gnu99
clang -fno-strict-overflow -DNDEBUG -O2 -Wall -fPIC -O2 -isystem /Users/atanasradkov/opt/anaconda3/envs/surfmap/include -fPIC -O2 -isystem /Users/atanasradkov/opt/anaconda3/envs/surfmap/include -Ilib/src -I. -I/Users/atanasradkov/opt/anaconda3/envs/surfmap/include/python3.12 -c lib/src/classifier_oons.c -o build/temp.macosx-10.9-x86_64-cpython-312/lib/src/classifier_oons.o -DHAVE_CONFIG_H -std=gnu99
clang -fno-strict-overflow -DNDEBUG -O2 -Wall -fPIC -O2 -isystem /Users/atanasradkov/opt/anaconda3/envs/surfmap/include -fPIC -O2 -isystem /Users/atanasradkov/opt/anaconda3/envs/surfmap/include -Ilib/src -I. -I/Users/atanasradkov/opt/anaconda3/envs/surfmap/include/python3.12 -c lib/src/classifier_protor.c -o build/temp.macosx-10.9-x86_64-cpython-312/lib/src/classifier_protor.o -DHAVE_CONFIG_H -std=gnu99
clang -fno-strict-overflow -DNDEBUG -O2 -Wall -fPIC -O2 -isystem /Users/atanasradkov/opt/anaconda3/envs/surfmap/include -fPIC -O2 -isystem /Users/atanasradkov/opt/anaconda3/envs/surfmap/include -Ilib/src -I. -I/Users/atanasradkov/opt/anaconda3/envs/surfmap/include/python3.12 -c lib/src/coord.c -o build/temp.macosx-10.9-x86_64-cpython-312/lib/src/coord.o -DHAVE_CONFIG_H -std=gnu99
clang -fno-strict-overflow -DNDEBUG -O2 -Wall -fPIC -O2 -isystem /Users/atanasradkov/opt/anaconda3/envs/surfmap/include -fPIC -O2 -isystem /Users/atanasradkov/opt/anaconda3/envs/surfmap/include -Ilib/src -I. -I/Users/atanasradkov/opt/anaconda3/envs/surfmap/include/python3.12 -c lib/src/freesasa.c -o build/temp.macosx-10.9-x86_64-cpython-312/lib/src/freesasa.o -DHAVE_CONFIG_H -std=gnu99
clang -fno-strict-overflow -DNDEBUG -O2 -Wall -fPIC -O2 -isystem /Users/atanasradkov/opt/anaconda3/envs/surfmap/include -fPIC -O2 -isystem /Users/atanasradkov/opt/anaconda3/envs/surfmap/include -Ilib/src -I. -I/Users/atanasradkov/opt/anaconda3/envs/surfmap/include/python3.12 -c lib/src/lexer.c -o build/temp.macosx-10.9-x86_64-cpython-312/lib/src/lexer.o -DHAVE_CONFIG_H -std=gnu99
lexer.c:1284:17: warning: unused function 'yyunput' [-Wunused-function]
static void yyunput (int c, char * yy_bp , yyscan_t yyscanner)
^
lexer.c:1328:16: warning: function 'input' is not needed and will not be emitted [-Wunneeded-internal-declaration]
static int input (yyscan_t yyscanner)
^
2 warnings generated.
clang -fno-strict-overflow -DNDEBUG -O2 -Wall -fPIC -O2 -isystem /Users/atanasradkov/opt/anaconda3/envs/surfmap/include -fPIC -O2 -isystem /Users/atanasradkov/opt/anaconda3/envs/surfmap/include -Ilib/src -I. -I/Users/atanasradkov/opt/anaconda3/envs/surfmap/include/python3.12 -c lib/src/log.c -o build/temp.macosx-10.9-x86_64-cpython-312/lib/src/log.o -DHAVE_CONFIG_H -std=gnu99
clang -fno-strict-overflow -DNDEBUG -O2 -Wall -fPIC -O2 -isystem /Users/atanasradkov/opt/anaconda3/envs/surfmap/include -fPIC -O2 -isystem /Users/atanasradkov/opt/anaconda3/envs/surfmap/include -Ilib/src -I. -I/Users/atanasradkov/opt/anaconda3/envs/surfmap/include/python3.12 -c lib/src/nb.c -o build/temp.macosx-10.9-x86_64-cpython-312/lib/src/nb.o -DHAVE_CONFIG_H -std=gnu99
clang -fno-strict-overflow -DNDEBUG -O2 -Wall -fPIC -O2 -isystem /Users/atanasradkov/opt/anaconda3/envs/surfmap/include -fPIC -O2 -isystem /Users/atanasradkov/opt/anaconda3/envs/surfmap/include -Ilib/src -I. -I/Users/atanasradkov/opt/anaconda3/envs/surfmap/include/python3.12 -c lib/src/node.c -o build/temp.macosx-10.9-x86_64-cpython-312/lib/src/node.o -DHAVE_CONFIG_H -std=gnu99
clang -fno-strict-overflow -DNDEBUG -O2 -Wall -fPIC -O2 -isystem /Users/atanasradkov/opt/anaconda3/envs/surfmap/include -fPIC -O2 -isystem /Users/atanasradkov/opt/anaconda3/envs/surfmap/include -Ilib/src -I. -I/Users/atanasradkov/opt/anaconda3/envs/surfmap/include/python3.12 -c lib/src/parser.c -o build/temp.macosx-10.9-x86_64-cpython-312/lib/src/parser.o -DHAVE_CONFIG_H -std=gnu99
parser.c:1039:9: warning: variable 'freesasa_yynerrs' set but not used [-Wunused-but-set-variable]
int yynerrs;
^
lib/src/parser.c:67:25: note: expanded from macro 'yynerrs'
#define yynerrs freesasa_yynerrs
^
1 warning generated.
clang -fno-strict-overflow -DNDEBUG -O2 -Wall -fPIC -O2 -isystem /Users/atanasradkov/opt/anaconda3/envs/surfmap/include -fPIC -O2 -isystem /Users/atanasradkov/opt/anaconda3/envs/surfmap/include -Ilib/src -I. -I/Users/atanasradkov/opt/anaconda3/envs/surfmap/include/python3.12 -c lib/src/pdb.c -o build/temp.macosx-10.9-x86_64-cpython-312/lib/src/pdb.o -DHAVE_CONFIG_H -std=gnu99
clang -fno-strict-overflow -DNDEBUG -O2 -Wall -fPIC -O2 -isystem /Users/atanasradkov/opt/anaconda3/envs/surfmap/include -fPIC -O2 -isystem /Users/atanasradkov/opt/anaconda3/envs/surfmap/include -Ilib/src -I. -I/Users/atanasradkov/opt/anaconda3/envs/surfmap/include/python3.12 -c lib/src/rsa.c -o build/temp.macosx-10.9-x86_64-cpython-312/lib/src/rsa.o -DHAVE_CONFIG_H -std=gnu99
clang -fno-strict-overflow -DNDEBUG -O2 -Wall -fPIC -O2 -isystem /Users/atanasradkov/opt/anaconda3/envs/surfmap/include -fPIC -O2 -isystem /Users/atanasradkov/opt/anaconda3/envs/surfmap/include -Ilib/src -I. -I/Users/atanasradkov/opt/anaconda3/envs/surfmap/include/python3.12 -c lib/src/sasa_lr.c -o build/temp.macosx-10.9-x86_64-cpython-312/lib/src/sasa_lr.o -DHAVE_CONFIG_H -std=gnu99
clang -fno-strict-overflow -DNDEBUG -O2 -Wall -fPIC -O2 -isystem /Users/atanasradkov/opt/anaconda3/envs/surfmap/include -fPIC -O2 -isystem /Users/atanasradkov/opt/anaconda3/envs/surfmap/include -Ilib/src -I. -I/Users/atanasradkov/opt/anaconda3/envs/surfmap/include/python3.12 -c lib/src/sasa_sr.c -o build/temp.macosx-10.9-x86_64-cpython-312/lib/src/sasa_sr.o -DHAVE_CONFIG_H -std=gnu99
clang -fno-strict-overflow -DNDEBUG -O2 -Wall -fPIC -O2 -isystem /Users/atanasradkov/opt/anaconda3/envs/surfmap/include -fPIC -O2 -isystem /Users/atanasradkov/opt/anaconda3/envs/surfmap/include -Ilib/src -I. -I/Users/atanasradkov/opt/anaconda3/envs/surfmap/include/python3.12 -c lib/src/selection.c -o build/temp.macosx-10.9-x86_64-cpython-312/lib/src/selection.o -DHAVE_CONFIG_H -std=gnu99
clang -fno-strict-overflow -DNDEBUG -O2 -Wall -fPIC -O2 -isystem /Users/atanasradkov/opt/anaconda3/envs/surfmap/include -fPIC -O2 -isystem /Users/atanasradkov/opt/anaconda3/envs/surfmap/include -Ilib/src -I. -I/Users/atanasradkov/opt/anaconda3/envs/surfmap/include/python3.12 -c lib/src/structure.c -o build/temp.macosx-10.9-x86_64-cpython-312/lib/src/structure.o -DHAVE_CONFIG_H -std=gnu99
clang -fno-strict-overflow -DNDEBUG -O2 -Wall -fPIC -O2 -isystem /Users/atanasradkov/opt/anaconda3/envs/surfmap/include -fPIC -O2 -isystem /Users/atanasradkov/opt/anaconda3/envs/surfmap/include -Ilib/src -I. -I/Users/atanasradkov/opt/anaconda3/envs/surfmap/include/python3.12 -c lib/src/util.c -o build/temp.macosx-10.9-x86_64-cpython-312/lib/src/util.o -DHAVE_CONFIG_H -std=gnu99
clang -fno-strict-overflow -DNDEBUG -O2 -Wall -fPIC -O2 -isystem /Users/atanasradkov/opt/anaconda3/envs/surfmap/include -fPIC -O2 -isystem /Users/atanasradkov/opt/anaconda3/envs/surfmap/include -Ilib/src -I. -I/Users/atanasradkov/opt/anaconda3/envs/surfmap/include/python3.12 -c src/freesasa.c -o build/temp.macosx-10.9-x86_64-cpython-312/src/freesasa.o -DHAVE_CONFIG_H -std=gnu99
src/freesasa.c:236:12: fatal error: 'longintrepr.h' file not found
#include "longintrepr.h"
^~~~~~~~~~~~~~~
1 error generated.
error: command '/usr/bin/clang' failed with exit code 1
[end of output]

note: This error originates from a subprocess, and is likely not a problem with pip.
ERROR: Failed building wheel for freesasa
Successfully built surfmap
Failed to build freesasa
ERROR: Could not build wheels for freesasa, which is required to install pyproject.toml-based projects

@AtanasDRadkov
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thank you in advance for your time and help!

@nchenche
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Hi,

Thanks for your interest in surfmap.

I think the source of the error may arise from freesasa 2.1.0 that does not seem compatible with python 3.12 version.

To fix your error, I suggest you execute the following instructions:

  1. download the latest archive here
  2. unzip the archive (e.g. unzip SURFMAP-2.0.0.zip)
  3. go to surfmap directory: cd SURFMAP-2.0.0/
  4. edit the setup.py to replace the freesasa version - from 2.1.0 to 2.2.1
    (e.g. sed -i 's/"freesasa==2.1.0"/"freesasa==2.2.1"/' setup.py)
  5. install surfmap (virtual env recommended): pip install -e .

It sould be ok. If not, you could still try your first install process with a lower version of python (e.g. from 3.7 to 3.10 - i guess...).

Please let me know if this resolved the failure.

Thanks,

Nicolas

@AtanasDRadkov
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AtanasDRadkov commented Nov 26, 2023 •
edited
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thank you very much Nicolas!

I was able to install surfmap in the following way:
1-completely removed the requirement to install freesasa==2.2.1 from setup.py
-not sure what's the problem but I could not install surfmap with either version of freesasa in setup.py
2-installed freesasa in my environment with conda install freesasa==2.2.1
3-installed surfmap with pip install -e .

Now I'm running into this error. please see below my command and everything that happened afterwards. is this still a python 3.12 issue? if yes, could you let me know the python version that you know works, and I will just use that python version? thank you Nicolas!

(surfmap) atanasradkov@ surfmap % surfmap -pdb P43235.pdb -tomap stickiness

SURFMAP: Projection of protein surface features on 2D map
Copyright (C) 2021 H. Schweke
Version: 2.0.0

Permission is hereby granted, free of charge, to any person obtaining a copy
of this software and associated documentation files (the "Software"), to deal
in the Software without restriction, including without limitation the rights
to use, copy, modify, merge, publish, distribute, sublicense, and/or sell
copies of the Software, and to permit persons to whom the Software is
furnished to do so, subject to the following conditions:

The above copyright notice and this permission notice shall be included in all
copies or substantial portions of the Software.

THE SOFTWARE IS PROVIDED "AS IS", WITHOUT WARRANTY OF ANY KIND, EXPRESS OR
IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES OF MERCHANTABILITY,
FITNESS FOR A PARTICULAR PURPOSE AND NONINFRINGEMENT. IN NO EVENT SHALL THE
AUTHORS OR COPYRIGHT HOLDERS BE LIABLE FOR ANY CLAIM, DAMAGES OR OTHER
LIABILITY, WHETHER IN AN ACTION OF CONTRACT, TORT OR OTHERWISE, ARISING FROM,
OUT OF OR IN CONNECTION WITH THE SOFTWARE OR THE USE OR OTHER DEALINGS IN THE
SOFTWARE.

SURFMAP relies on the use of MSMS (version 2.6.1) - Copyright (c) M. F. Sanner, 1994.

As a corollary of MSMS's license terms and conditions, by using SURFMAP,
you agree to acknowledge the use of the MSMS software that results in any
published work, including scientific papers, films and videotapes by
citing the following reference:

Sanner, M.F., Spehner, J.-C., and Olson, A.J. (1996) Reduced surface:
an efficient way to compute molecular surfaces. Biopolymers, Vol. 38.,
(3), 305-320.

MSMS is free for academic use. For commercial use please contact
M. F. Sanner at [email protected].

If you use SURFMAP for your research, please cite the following
papers:
- Hugo Schweke, Marie-Hélène Mucchielli, Nicolas Chevrollier,
Simon Gosset, Anne Lopes (2021) SURFMAP: a software for mapping
in two dimensions protein surface features. bioRxiv
2021.10.15.464543; doi: https://doi.org/10.1101/2021.10.15.464543

- Sanner, M.F., Spehner, J.-C., and Olson, A.J. (1996) Reduced 
  surface: an efficient way to compute molecular surfaces. 
  Biopolymers, Vol. 38., (3), 305-320.

SURFACE MAPPING OF THE STICKINESS PROPERTY
Step 1: computing a shell around the protein surface
Traceback (most recent call last):
File "/Users/atanasradkov/opt/anaconda3/envs/surfmap/bin/surfmap", line 33, in
sys.exit(load_entry_point('surfmap', 'console_scripts', 'surfmap')())
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File "/Users/atanasradkov/Desktop/Arcadia/developing_coding/ProtCart/surfmap/SURFMAP200/surfmap/bin/surfmap.py", line 63, in main
surfmap_local(params=params)
File "/Users/atanasradkov/Desktop/Arcadia/developing_coding/ProtCart/surfmap/SURFMAP200/surfmap/bin/surfmap.py", line 18, in surfmap_local
surfmap_from_pdb(params=params)
File "/Users/atanasradkov/Desktop/Arcadia/developing_coding/ProtCart/surfmap/SURFMAP200/surfmap/lib/core.py", line 160, in surfmap_from_pdb
csv_coords, shell = run_compute_shell(pdb_filename=params.pdbarg, out_dir=outdir_shell, extra_radius=extra_radius)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File "/Users/atanasradkov/Desktop/Arcadia/developing_coding/ProtCart/surfmap/SURFMAP200/surfmap/tools/compute_shell.py", line 108, in run
status = subprocess.run(cmd_msms, capture_output=True)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File "/Users/atanasradkov/opt/anaconda3/envs/surfmap/lib/python3.12/subprocess.py", line 548, in run
with Popen(*popenargs, **kwargs) as process:
^^^^^^^^^^^^^^^^^^^^^^^^^^^
File "/Users/atanasradkov/opt/anaconda3/envs/surfmap/lib/python3.12/subprocess.py", line 1026, in init
self._execute_child(args, executable, preexec_fn, close_fds,
File "/Users/atanasradkov/opt/anaconda3/envs/surfmap/lib/python3.12/subprocess.py", line 1950, in _execute_child
raise child_exception_type(errno_num, err_msg, err_filename)
OSError: [Errno 8] Exec format error: '/Users/atanasradkov/Desktop/Arcadia/developing_coding/ProtCart/surfmap/SURFMAP200/surfmap/utils/MSMS/msms'

@nchenche
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Hi,

The msms executable does not seem to work:
OSError: [Errno 8] Exec format error: '/Users/atanasradkov/Desktop/Arcadia/developing_coding/ProtCart/surfmap/SURFMAP200/surfmap/utils/MSMS/**msms**'

Are you on a macOS system?

The first solution i would recommend is to use the docker image of surfmap:

  1. install docker on your machine
  2. run your command as following surfmap -pdb P43235.pdb -tomap stickiness --docker

This should work,

Nicolas

@AtanasDRadkov
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hi Nicolas! Thank you so much for your help!

I think I have Docker set up correctly. Now I'm getting this error (please see below). I may need to look into Docker a bit more to make sure I have it set up correctly. I don't have much experience using Docker. Feel free to close this issue because I might not be able to return to this for some time.

Thank you again for all your time and help!

This is the error:

(surfmap) atanasradkov@Atanass-MacBook-Pro surfmap % surfmap -pdb P43235.pdb -tomap stickiness --docker
Traceback (most recent call last):
  File "/Users/atanasradkov/opt/anaconda3/envs/surfmap/lib/python3.12/importlib/metadata/__init__.py", line 397, in from_name
    return next(cls.discover(name=name))
           ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
StopIteration

During handling of the above exception, another exception occurred:

Traceback (most recent call last):
  File "/Users/atanasradkov/opt/anaconda3/envs/surfmap/bin/surfmap", line 33, in <module>
    sys.exit(load_entry_point('surfmap', 'console_scripts', 'surfmap')())
             ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
  File "/Users/atanasradkov/opt/anaconda3/envs/surfmap/bin/surfmap", line 22, in importlib_load_entry_point
    for entry_point in distribution(dist_name).entry_points
                       ^^^^^^^^^^^^^^^^^^^^^^^
  File "/Users/atanasradkov/opt/anaconda3/envs/surfmap/lib/python3.12/importlib/metadata/__init__.py", line 861, in distribution
    return Distribution.from_name(distribution_name)
           ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
  File "/Users/atanasradkov/opt/anaconda3/envs/surfmap/lib/python3.12/importlib/metadata/__init__.py", line 399, in from_name
    raise PackageNotFoundError(name)
importlib.metadata.PackageNotFoundError: No package metadata was found for surfmap

@nchenche
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Dear Atanas,

I am afraid this has nothing to do with docker. I suspect a strange behaviour causes from the use of anaconda (don't know what exactly).

I suggest you use an other virtual environment manager (venv, virtualenv, ....) and also you should try with another python version (3.10 should be ok, without using conda to install it if possible).

Sorry for the failures.

N.

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