Install error SOLVED by installing zlib and pointing conda to it

[luisalejohurtado]

Hi,

I was following the instructions on and kept running into 'ERROR: Failed building wheel for smudgeplot' after using all install methods (see full error message below).

Collecting smudgeplot==0.5.3b0
  Downloading smudgeplot-0.5.3b0.tar.gz (59 kB)
  Installing build dependencies ... done
  Getting requirements to build wheel ... done
  Preparing metadata (pyproject.toml) ... done
Collecting numpy>=1.20.0 (from smudgeplot==0.5.3b0)
  Using cached numpy-2.4.6-cp314-cp314-manylinux_2_27_x86_64.manylinux_2_28_x86_64.whl.metadata (6.6 kB)
Collecting matplotlib>=3.4.0 (from smudgeplot==0.5.3b0)
  Using cached matplotlib-3.11.0-cp314-cp314-manylinux_2_27_x86_64.manylinux_2_28_x86_64.whl.metadata (80 kB)
Collecting pandas>=1.3.0 (from smudgeplot==0.5.3b0)
  Using cached pandas-3.0.3-cp314-cp314-manylinux_2_24_x86_64.manylinux_2_28_x86_64.whl.metadata (79 kB)
Collecting contourpy>=1.0.1 (from matplotlib>=3.4.0->smudgeplot==0.5.3b0)
  Using cached contourpy-1.3.3-cp314-cp314-manylinux_2_27_x86_64.manylinux_2_28_x86_64.whl.metadata (5.5 kB)
Collecting cycler>=0.10 (from matplotlib>=3.4.0->smudgeplot==0.5.3b0)
  Using cached cycler-0.12.1-py3-none-any.whl.metadata (3.8 kB)
Collecting fonttools>=4.22.0 (from matplotlib>=3.4.0->smudgeplot==0.5.3b0)
  Using cached fonttools-4.63.0-cp314-cp314-manylinux2014_x86_64.manylinux_2_17_x86_64.whl.metadata (118 kB)
Collecting kiwisolver>=1.3.1 (from matplotlib>=3.4.0->smudgeplot==0.5.3b0)
  Using cached kiwisolver-1.5.0-cp314-cp314-manylinux2014_x86_64.manylinux_2_17_x86_64.whl.metadata (5.1 kB)
Requirement already satisfied: packaging>=20.0 in /home/hpc-0411/miniconda3/envs/smudgeplot/lib/python3.14/site-packages (from matplotlib>=3.4.0->smudgeplot==0.5.3b0) (26.2)
Collecting pillow>=9 (from matplotlib>=3.4.0->smudgeplot==0.5.3b0)
  Using cached pillow-12.2.0-cp314-cp314-manylinux_2_27_x86_64.manylinux_2_28_x86_64.whl.metadata (8.8 kB)
Collecting pyparsing>=3 (from matplotlib>=3.4.0->smudgeplot==0.5.3b0)
  Using cached pyparsing-3.3.2-py3-none-any.whl.metadata (5.8 kB)
Collecting python-dateutil>=2.7 (from matplotlib>=3.4.0->smudgeplot==0.5.3b0)
  Using cached python_dateutil-2.9.0.post0-py2.py3-none-any.whl.metadata (8.4 kB)
Collecting six>=1.5 (from python-dateutil>=2.7->matplotlib>=3.4.0->smudgeplot==0.5.3b0)
  Using cached six-1.17.0-py2.py3-none-any.whl.metadata (1.7 kB)
Using cached matplotlib-3.11.0-cp314-cp314-manylinux_2_27_x86_64.manylinux_2_28_x86_64.whl (11.1 MB)
Using cached contourpy-1.3.3-cp314-cp314-manylinux_2_27_x86_64.manylinux_2_28_x86_64.whl (363 kB)
Using cached cycler-0.12.1-py3-none-any.whl (8.3 kB)
Using cached fonttools-4.63.0-cp314-cp314-manylinux2014_x86_64.manylinux_2_17_x86_64.whl (4.9 MB)
Using cached kiwisolver-1.5.0-cp314-cp314-manylinux2014_x86_64.manylinux_2_17_x86_64.whl (1.5 MB)
Using cached numpy-2.4.6-cp314-cp314-manylinux_2_27_x86_64.manylinux_2_28_x86_64.whl (16.6 MB)
Using cached pandas-3.0.3-cp314-cp314-manylinux_2_24_x86_64.manylinux_2_28_x86_64.whl (10.9 MB)
Using cached pillow-12.2.0-cp314-cp314-manylinux_2_27_x86_64.manylinux_2_28_x86_64.whl (7.1 MB)
Using cached pyparsing-3.3.2-py3-none-any.whl (122 kB)
Using cached python_dateutil-2.9.0.post0-py2.py3-none-any.whl (229 kB)
Using cached six-1.17.0-py2.py3-none-any.whl (11 kB)
Building wheels for collected packages: smudgeplot
  Building wheel for smudgeplot (pyproject.toml) ... error
  error: subprocess-exited-with-error
  
  × Building wheel for smudgeplot (pyproject.toml) did not run successfully.
  │ exit code: 1
  ╰─> [104 lines of output]
      running bdist_wheel
      running build
      running build_py
        ERROR: Failed to compile hetmers:
      In file included from /tmp/pip-install-n7j9vkhj/smudgeplot_181dfe8127da4721af43e428d67604bc/src/lib/libfastk.c:12:
      /tmp/pip-install-n7j9vkhj/smudgeplot_181dfe8127da4721af43e428d67604bc/src/lib/gene_core.c:7:10: fatal error: zlib.h: No such file or directory
          7 | #include <zlib.h>
            |          ^~~~~~~~
      compilation terminated.
      
      Compiling hetmers...
        Command: gcc -O3 -Wall -Wextra -Wno-unused-result -fno-strict-aliasing -o /tmp/pip-install-n7j9vkhj/smudgeplot_181dfe8127da4721af43e428d67604bc/src/smudgeplot/bin/hetmers /tmp/pip-install-n7j9vkhj/smudgeplot_181dfe8127da4721af43e428d67604bc/src/lib/PloidyPlot.c /tmp/pip-install-n7j9vkhj/smudgeplot_181dfe8127da4721af43e428d67604bc/src/lib/libfastk.c /tmp/pip-install-n7j9vkhj/smudgeplot_181dfe8127da4721af43e428d67604bc/src/lib/matrix.c -lpthread -lm
      Traceback (most recent call last):
        File "<string>", line 95, in compile_binaries
        File "/home/hpc-0411/miniconda3/envs/smudgeplot/lib/python3.14/subprocess.py", line 578, in run
          raise CalledProcessError(retcode, process.args,
                                   output=stdout, stderr=stderr)
      subprocess.CalledProcessError: Command '['gcc', '-O3', '-Wall', '-Wextra', '-Wno-unused-result', '-fno-strict-aliasing', '-o', '/tmp/pip-install-n7j9vkhj/smudgeplot_181dfe8127da4721af43e428d67604bc/src/smudgeplot/bin/hetmers', '/tmp/pip-install-n7j9vkhj/smudgeplot_181dfe8127da4721af43e428d67604bc/src/lib/PloidyPlot.c', '/tmp/pip-install-n7j9vkhj/smudgeplot_181dfe8127da4721af43e428d67604bc/src/lib/libfastk.c', '/tmp/pip-install-n7j9vkhj/smudgeplot_181dfe8127da4721af43e428d67604bc/src/lib/matrix.c', '-lpthread', '-lm']' returned non-zero exit status 1.
      
      The above exception was the direct cause of the following exception:
      
      Traceback (most recent call last):
        File "/home/hpc-0411/miniconda3/envs/smudgeplot/lib/python3.14/site-packages/pip/_vendor/pyproject_hooks/_in_process/_in_process.py", line 389, in <module>
          main()
          ~~~~^^
        File "/home/hpc-0411/miniconda3/envs/smudgeplot/lib/python3.14/site-packages/pip/_vendor/pyproject_hooks/_in_process/_in_process.py", line 373, in main
          json_out["return_val"] = hook(**hook_input["kwargs"])
                                   ~~~~^^^^^^^^^^^^^^^^^^^^^^^^
        File "/home/hpc-0411/miniconda3/envs/smudgeplot/lib/python3.14/site-packages/pip/_vendor/pyproject_hooks/_in_process/_in_process.py", line 280, in build_wheel
          return _build_backend().build_wheel(
                 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~^
              wheel_directory, config_settings, metadata_directory
              ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
          )
          ^
        File "/tmp/pip-build-env-8e_tbv01/overlay/lib/python3.14/site-packages/setuptools/build_meta.py", line 441, in build_wheel
          return _build(['bdist_wheel', '--dist-info-dir', str(metadata_directory)])
        File "/tmp/pip-build-env-8e_tbv01/overlay/lib/python3.14/site-packages/setuptools/build_meta.py", line 429, in _build
          return self._build_with_temp_dir(
                 ~~~~~~~~~~~~~~~~~~~~~~~~~^
              cmd,
              ^^^^
          ...<3 lines>...
              self._arbitrary_args(config_settings),
              ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
          )
          ^
        File "/tmp/pip-build-env-8e_tbv01/overlay/lib/python3.14/site-packages/setuptools/build_meta.py", line 410, in _build_with_temp_dir
          self.run_setup()
          ~~~~~~~~~~~~~~^^
        File "/tmp/pip-build-env-8e_tbv01/overlay/lib/python3.14/site-packages/setuptools/build_meta.py", line 317, in run_setup
          exec(code, locals())
          ~~~~^^^^^^^^^^^^^^^^
        File "<string>", line 139, in <module>
        File "/tmp/pip-build-env-8e_tbv01/overlay/lib/python3.14/site-packages/setuptools/__init__.py", line 117, in setup
          return distutils.core.setup(**attrs)  # type: ignore[return-value]
                 ~~~~~~~~~~~~~~~~~~~~^^^^^^^^^
        File "/tmp/pip-build-env-8e_tbv01/overlay/lib/python3.14/site-packages/setuptools/_distutils/core.py", line 186, in setup
          return run_commands(dist)
        File "/tmp/pip-build-env-8e_tbv01/overlay/lib/python3.14/site-packages/setuptools/_distutils/core.py", line 202, in run_commands
          dist.run_commands()
          ~~~~~~~~~~~~~~~~~^^
        File "/tmp/pip-build-env-8e_tbv01/overlay/lib/python3.14/site-packages/setuptools/_distutils/dist.py", line 1000, in run_commands
          self.run_command(cmd)
          ~~~~~~~~~~~~~~~~^^^^^
        File "/tmp/pip-build-env-8e_tbv01/overlay/lib/python3.14/site-packages/setuptools/dist.py", line 1107, in run_command
          super().run_command(command)
          ~~~~~~~~~~~~~~~~~~~^^^^^^^^^
        File "/tmp/pip-build-env-8e_tbv01/overlay/lib/python3.14/site-packages/setuptools/_distutils/dist.py", line 1019, in run_command
          cmd_obj.run()
          ~~~~~~~~~~~^^
        File "/tmp/pip-build-env-8e_tbv01/overlay/lib/python3.14/site-packages/setuptools/command/bdist_wheel.py", line 370, in run
          self.run_command("build")
          ~~~~~~~~~~~~~~~~^^^^^^^^^
        File "/tmp/pip-build-env-8e_tbv01/overlay/lib/python3.14/site-packages/setuptools/_distutils/cmd.py", line 341, in run_command
          self.distribution.run_command(command)
          ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^^^^^^^^^
        File "/tmp/pip-build-env-8e_tbv01/overlay/lib/python3.14/site-packages/setuptools/dist.py", line 1107, in run_command
          super().run_command(command)
          ~~~~~~~~~~~~~~~~~~~^^^^^^^^^
        File "/tmp/pip-build-env-8e_tbv01/overlay/lib/python3.14/site-packages/setuptools/_distutils/dist.py", line 1019, in run_command
          cmd_obj.run()
          ~~~~~~~~~~~^^
        File "/tmp/pip-build-env-8e_tbv01/overlay/lib/python3.14/site-packages/setuptools/_distutils/command/build.py", line 135, in run
          self.run_command(cmd_name)
          ~~~~~~~~~~~~~~~~^^^^^^^^^^
        File "/tmp/pip-build-env-8e_tbv01/overlay/lib/python3.14/site-packages/setuptools/_distutils/cmd.py", line 341, in run_command
          self.distribution.run_command(command)
          ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^^^^^^^^^
        File "/tmp/pip-build-env-8e_tbv01/overlay/lib/python3.14/site-packages/setuptools/dist.py", line 1107, in run_command
          super().run_command(command)
          ~~~~~~~~~~~~~~~~~~~^^^^^^^^^
        File "/tmp/pip-build-env-8e_tbv01/overlay/lib/python3.14/site-packages/setuptools/_distutils/dist.py", line 1019, in run_command
          cmd_obj.run()
          ~~~~~~~~~~~^^
        File "<string>", line 119, in run
        File "<string>", line 102, in compile_binaries
      CompilationError: Failed to compile hetmers:
      In file included from /tmp/pip-install-n7j9vkhj/smudgeplot_181dfe8127da4721af43e428d67604bc/src/lib/libfastk.c:12:
      /tmp/pip-install-n7j9vkhj/smudgeplot_181dfe8127da4721af43e428d67604bc/src/lib/gene_core.c:7:10: fatal error: zlib.h: No such file or directory
          7 | #include <zlib.h>
            |          ^~~~~~~~
      compilation terminated.
      
      [end of output]
  
  note: This error originates from a subprocess, and is likely not a problem with pip.
  ERROR: Failed building wheel for smudgeplot
Failed to build smudgeplot
error: failed-wheel-build-for-install

× Failed to build installable wheels for some pyproject.toml based projects
╰─> smudgeplot

I ended up finally getting the installation to work with pip install smudgeplot==0.5.3b0 after I running conda install -c conda-forge zlib in my environment and then running export CFLAGS="-I$CONDA_PREFIX/include" and export LDFLAGS="-L$CONDA_PREFIX/lib" before running pip install smudgeplot==0.5.3b0. I'm not sure why or how this work, but I had seen another user report a similar install issue that has since been closed, so I figured it may be helpful to some to know that simply installing zlib may resolve some installation issues.

[KamilSJaron]

Hmm, that's funny. Maybe we should add it to FAQ.