install error

[linyuiz]

Dear Developers,
I followed the installation instructions at (https://github.com/KamilSJaron/smudgeplot?tab=readme-ov-file#installation), but it failed.

Collecting pytz>=2020.1 (from pandas>=2.2.3->smudgeplot==0.5.1)
  Downloading https://mirrors.ustc.edu.cn/pypi/packages/81/c4/34e93fe5f5429d7570ec1fa436f1986fb1f00c3e0f43a589fe2bbcd22c3f/pytz-2025.2-py2.py3-none-any.whl (509 kB)
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Collecting tzdata>=2022.7 (from pandas>=2.2.3->smudgeplot==0.5.1)
  Downloading https://mirrors.ustc.edu.cn/pypi/packages/5c/23/c7abc0ca0a1526a0774eca151daeb8de62ec457e77262b66b359c3c7679e/tzdata-2025.2-py2.py3-none-any.whl (347 kB)
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Collecting six>=1.5 (from python-dateutil>=2.7->matplotlib>=3.10.0->smudgeplot==0.5.1)
  Downloading https://mirrors.ustc.edu.cn/pypi/packages/b7/ce/149a00dd41f10bc29e5921b496af8b574d8413afcd5e30dfa0ed46c2cc5e/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
  ╰─> [78 lines of output]
      running bdist_wheel
      running build
      running build_py
      running egg_info
      writing src/smudgeplot.egg-info/PKG-INFO
      writing dependency_links to src/smudgeplot.egg-info/dependency_links.txt
      writing entry points to src/smudgeplot.egg-info/entry_points.txt
      writing requirements to src/smudgeplot.egg-info/requires.txt
      writing top-level names to src/smudgeplot.egg-info/top_level.txt
      reading manifest file 'src/smudgeplot.egg-info/SOURCES.txt'
      adding license file 'LICENSE.md'
      writing manifest file 'src/smudgeplot.egg-info/SOURCES.txt'
      installing to build/bdist.linux-x86_64/wheel
      running install
      gcc -O3 -Wall -Wextra -Wno-unused-result -fno-strict-aliasing -o exec/hetmers src/lib/PloidyPlot.c src/lib/libfastk.c src/lib/matrix.c -lpthread -lm
      src/lib/PloidyPlot.c: In function 'in_core_recursion':
      src/lib/PloidyPlot.c:881:17: warning: storing the address of local variable 'bound' in '*parm.bound' [-Wdangling-pointer=]
        881 |     parm->bound = (int64 *) bound;
            |     ~~~~~~~~~~~~^~~~~~~~~~~~~~~~~
      src/lib/PloidyPlot.c:852:10: note: 'bound' declared here
        852 | { uint8 *bound[17];
            |          ^~~~~
      src/lib/PloidyPlot.c:851:60: note: 'parm' declared here
        851 | static void in_core_recursion(uint8 **aptr, int level, TP *parm)
            |                                                        ~~~~^~~~
      In file included from src/lib/libfastk.c:12:
      src/lib/gene_core.c:7:10: fatal error: zlib.h: No such file or directory
          7 | #include <zlib.h>
            |          ^~~~~~~~
      compilation terminated.
      make: *** [Makefile:20: exec/hetmers] Error 1
      Traceback (most recent call last):
        File "/pipeline/zgtools/scripts/software/smudgeplot-0.5.1/env/lib/python3.12/site-packages/pip/_vendor/pyproject_hooks/_in_process/_in_process.py", line 353, in <module>
          main()
        File "/pipeline/zgtools/scripts/software/smudgeplot-0.5.1/env/lib/python3.12/site-packages/pip/_vendor/pyproject_hooks/_in_process/_in_process.py", line 335, in main
          json_out['return_val'] = hook(**hook_input['kwargs'])
                                   ^^^^^^^^^^^^^^^^^^^^^^^^^^^^
        File "/pipeline/zgtools/scripts/software/smudgeplot-0.5.1/env/lib/python3.12/site-packages/pip/_vendor/pyproject_hooks/_in_process/_in_process.py", line 251, in build_wheel
          return _build_backend().build_wheel(wheel_directory, config_settings,
                 ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
        File "/tmp/pip-build-env-_7egwecg/overlay/lib/python3.12/site-packages/setuptools/build_meta.py", line 435, in build_wheel
          return _build(['bdist_wheel', '--dist-info-dir', str(metadata_directory)])
                 ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
        File "/tmp/pip-build-env-_7egwecg/overlay/lib/python3.12/site-packages/setuptools/build_meta.py", line 423, in _build
          return self._build_with_temp_dir(
                 ^^^^^^^^^^^^^^^^^^^^^^^^^^
        File "/tmp/pip-build-env-_7egwecg/overlay/lib/python3.12/site-packages/setuptools/build_meta.py", line 404, in _build_with_temp_dir
          self.run_setup()
        File "/tmp/pip-build-env-_7egwecg/overlay/lib/python3.12/site-packages/setuptools/build_meta.py", line 317, in run_setup
          exec(code, locals())
        File "<string>", line 39, in <module>
        File "/tmp/pip-build-env-_7egwecg/overlay/lib/python3.12/site-packages/setuptools/__init__.py", line 115, in setup
          return distutils.core.setup(**attrs)
                 ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
        File "/tmp/pip-build-env-_7egwecg/overlay/lib/python3.12/site-packages/setuptools/_distutils/core.py", line 186, in setup
          return run_commands(dist)
                 ^^^^^^^^^^^^^^^^^^
        File "/tmp/pip-build-env-_7egwecg/overlay/lib/python3.12/site-packages/setuptools/_distutils/core.py", line 202, in run_commands
          dist.run_commands()
        File "/tmp/pip-build-env-_7egwecg/overlay/lib/python3.12/site-packages/setuptools/_distutils/dist.py", line 1002, in run_commands
          self.run_command(cmd)
        File "/tmp/pip-build-env-_7egwecg/overlay/lib/python3.12/site-packages/setuptools/dist.py", line 1102, in run_command
          super().run_command(command)
        File "/tmp/pip-build-env-_7egwecg/overlay/lib/python3.12/site-packages/setuptools/_distutils/dist.py", line 1021, in run_command
          cmd_obj.run()
        File "/tmp/pip-build-env-_7egwecg/overlay/lib/python3.12/site-packages/setuptools/command/bdist_wheel.py", line 405, in run
          self.run_command("install")
        File "/tmp/pip-build-env-_7egwecg/overlay/lib/python3.12/site-packages/setuptools/_distutils/cmd.py", line 357, in run_command
          self.distribution.run_command(command)
        File "/tmp/pip-build-env-_7egwecg/overlay/lib/python3.12/site-packages/setuptools/dist.py", line 1102, in run_command
          super().run_command(command)
        File "/tmp/pip-build-env-_7egwecg/overlay/lib/python3.12/site-packages/setuptools/_distutils/dist.py", line 1021, in run_command
          cmd_obj.run()
        File "<string>", line 36, in run
        File "<string>", line 30, in compile_and_install_software
        File "/opt/conda/envs/smudgeplot/lib/python3.12/subprocess.py", line 413, in check_call
          raise CalledProcessError(retcode, cmd)
      subprocess.CalledProcessError: Command 'mkdir -p exec && make exec/hetmers exec/extract_kmer_pairs' returned non-zero exit status 2.
      [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: Could not build wheels for smudgeplot, which is required to install pyproject.toml-based projects

[samebdon]

@linyuiz Can you try

pip install smudgeplot #currently only works for MacOS, for linux please pull the latest version and install yourself currently

instead?

Alternatively have you pulled the most recent update? The subprocess error you got here is no longer part of setup.py

[linyuiz]

@linyuiz Can you try  你能试试

pip install smudgeplot

instead?  吗？

Edit:  编辑： Alternatively have you pulled the most recent update? The subprocess error you got here is no longer part of setup.py或者你已经拉取了最新的更新吗？你在这里得到的子进程错误不再属于 setup.py

@linyuiz Can you try

pip install smudgeplot

instead?

Edit: Alternatively have you pulled the most recent update? The subprocess error you got here is no longer part of setup.py

I successfully installed smudgeplot usingpip install smudgeplot

smudgeplot.py -h
usage: smudgeplot <task> [options] 

tasks: cutoff           Calculate meaningful values for lower kmer histogram cutoff.
       hetmers          Calculate unique kmer pairs from a FastK k-mer database.
       peak_agregation  Agregates smudges using local agregation algorithm.
       plot             Generate 2d histogram; infere ploidy and plot a smudgeplot.
       all              Runs all the steps (with default options)

positional arguments:
  task           Task to execute; for task specific options execute smudgeplot
                 <task> -h

options:
  -h, --help     show this help message and exit
  -v, --version  print the version and exit

I'm trying to test whether it can analyze normally and then give feedback.

[samebdon]

That is strange your help message looks like the previous version. What is the output of smudgeplot --version? You should be getting 0.5.2 from pip.

Did you have an existing install already or is this in a clean environment?

[linyuiz]

I've downloaded Skylight before and used master.zip, but none of the versions could be installed using the command python install .. This is also the first time I've heard that you can use pip install smudgeplot.

[samebdon]

It looks like you have an existing install, because I don't know how you would install this version from pip. I think your issue will not be fixed by the current zipped release. It should be okay with the up-to-date main branch or installing via pip.

[linyuiz]

I have already run the command up to:

ln -sf $r1 ./used_R1.fastq.gz && \
ln -sf $r2 ./used_R2.fastq.gz && \
FastK -v -t4 -k31 -M300 -T${threads} used_R[12].fastq.gz -NFastK_Table

Now I run:

mkdir -p tmp/matplotlib && export MPLCONFIGDIR=$PWD/tmp/matplotlib
smudgeplot hetmers -L 12 -t $threads -tmp ./tmp -o ./kmerpairs --verbose ./FastK_Table

Error reported:

cat run_02hetmers.sh.err 
Running smudgeplot v0.5.2
Task: hetmers
Calling: hetmers  -o./kmerpairs -e12 -T60 -v -P./tmp ./FastK_Table
sh: 1: /opt/conda/envs/smudgeplot_0.5.1/lib/python3.14/site-packages/smudgeplot/bin/hetmers: Exec format error
ll /opt/conda/envs/smudgeplot_0.5.1/lib/python3.14/site-packages/smudgeplot/bin/hetmers
ls: cannot access '/opt/conda/envs/smudgeplot_0.5.1/lib/python3.14/site-packages/smudgeplot/bin/hetmers': No such file or directory

[samebdon]

Okay thanks, looking into this.

[samebdon]

I haven't managed to recreate this error, are you still having problems? I see in another thread you successfully generated a smudgeplot.

[linyuiz]

I still have this issue, which is a problem with version 0.5.2. My question in another issue was about the results generated using conda's version 0.4.0.

[linyuiz]

In addition, I encountered another issue where I originally intended to obtain the value of L, but now I have no choice but to use -L 12 as a substitute.

smudgeplot cutoff database/FastK_Table.hist L
Running smudgeplot v0.5.2
Task: cutoff
Traceback (most recent call last):
  File "/opt/conda/envs/smudgeplot_0.5.1/bin/smudgeplot", line 7, in <module>
    sys.exit(main())
             ~~~~^^
  File "/opt/conda/envs/smudgeplot_0.5.1/lib/python3.14/site-packages/smudgeplot/cli.py", line 331, in main
    smg.cutoff(args.infile, args.boundary)
    ~~~~~~~~~~^^^^^^^^^^^^^^^^^^^^^^^^^^^^
  File "/opt/conda/envs/smudgeplot_0.5.1/lib/python3.14/site-packages/smudgeplot/smudgeplot.py", line 736, in cutoff
    hist = [int(line.split()[1]) for line in kmer_hist]
                                             ^^^^^^^^^
  File "<frozen codecs>", line 325, in decode
UnicodeDecodeError: 'utf-8' codec can't decode byte 0xff in position 8: invalid start byte

[linyuiz]

I haven't managed to recreate this error, are you still having problems? I see in another thread you successfully generated a smudgeplot.

I generated smudgeplot graphs using version 0.4.0: smudgeplot.py hetmers -L ${L} -t $threads -tmp ./tmp -o ./kmerpairs --verbose database/FastK_Table, because there were issues with hetmers in version 0.5.2. Then I used the 0.5.2 environment to run smudgeplot all, which produced smudgeplot graphs with histograms.

Oh, by the way, can smudgeplot also generate result graphs in SVG format?

[samebdon]

Okay, I think the problem is likely that the precompiled C binaries aren't compatible with your operating system. If you could let me know your operating system and version that would help us look into sorting this out.

It shouldn't be a problem for the python code as you have found out (just hetmers and extract), but for reference sake, you can compile the C libraries yourself from within the downloaded smudgeplot directory using make.

Oh, by the way, can smudgeplot also generate result graphs in SVG format?

Not currently but we can add it in one of the next updates.