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Install pyreadstat package -> " /usr/include/sys/time.h:110:16: error: redefinition of 'struct sigset_t'

  • 1.  Install pyreadstat package -> " /usr/include/sys/time.h:110:16: error: redefinition of 'struct sigset_t'

    Posted Fri September 01, 2023 03:18 AM

    I got following error message when install pyreadstat package. Can AIX expert help to resolve it?

    " /usr/include/sys/time.h:110:16: error: redefinition of 'struct sigset_t'

        110 | typedef struct sigset_t {

            |                ^~~~~~~~

      In file included from /opt/freeware/lib/gcc/powerpc-ibm-aix7.1.0.0/10/include-fixed/stdio.h:503,

                       from /opt/freeware/include/python3.7m/Python.h:25,

                       from pyreadstat/pyreadstat.c:80:

      /opt/freeware/lib/gcc/powerpc-ibm-aix7.1.0.0/10/include-fixed/sys/types.h:345:16: note: originally defined here

        345 | typedef struct sigset_t {

            |                ^~~~~~~~

      In file included from /usr/include/sys/resource.h:57,

                       from /opt/freeware/lib/gcc/powerpc-ibm-aix7.1.0.0/10/include-fixed/sys/wait.h:56,

                       from /opt/freeware/lib/gcc/powerpc-ibm-aix7.1.0.0/10/include-fixed/stdlib.h:391,

                       from /opt/freeware/include/python3.7m/Python.h:34,

                       from pyreadstat/pyreadstat.c:80:

      /usr/include/sys/time.h:126:3: error: conflicting types for 'sigset_t'

        126 | } sigset_t;

            |   ^~~~~~~~

      In file included from /opt/freeware/lib/gcc/powerpc-ibm-aix7.1.0.0/10/include-fixed/stdio.h:503,

                       from /opt/freeware/include/python3.7m/Python.h:25,

                       from pyreadstat/pyreadstat.c:80:

      /opt/freeware/lib/gcc/powerpc-ibm-aix7.1.0.0/10/include-fixed/sys/types.h:361:3: note: previous declaration of 'sigset_t' was here

        361 | } sigset_t;

            |   ^~~~~~~~

      error: command 'gcc' failed with exit status 1 "



    ------------------------------
    Bruce Turgeon
    ------------------------------


  • 2.  RE: Install pyreadstat package -> " /usr/include/sys/time.h:110:16: error: redefinition of 'struct sigset_t'

    Posted Wed September 06, 2023 04:58 AM

    Hi, 
    It looks similar to https://community.ibm.com/community/user/power/discussion/gcc-struct-sigset-t-conflicts-with-aix-systimeh .

    what version of gcc you are using.

    Try to upgrade both gcc and python and see if it's fixing this conflict. 



    ------------------------------
    Ranjit Ranjan
    ------------------------------



  • 3.  RE: Install pyreadstat package -> " /usr/include/sys/time.h:110:16: error: redefinition of 'struct sigset_t'

    Posted Mon September 18, 2023 10:09 AM

    Hi Ranjan,

    We just upgraded from python 3.7 to python 3.9 and got all libraries updated / synced. I then tried the installation again for pyreadstat. But this time I got a different error (see below). I am wondering if this is caused by the setupools version (65.2.0) being too high in python 3.9 eco system? Any suggestion for fixing this?

    Thanks

    Mi

      × pip subprocess to install build dependencies did not run successfully.
      │ exit code: 1
      ╰─> [3 lines of output]
          Looking in links: /usr/opt/sas/python3a
          ERROR: Could not find a version that satisfies the requirement setuptools (from versions: none)
          ERROR: No matching distribution found for setuptools
          [end of output]



    ------------------------------
    Mi Wang
    ------------------------------



  • 4.  RE: Install pyreadstat package -> " /usr/include/sys/time.h:110:16: error: redefinition of 'struct sigset_t'

    Posted Tue September 19, 2023 11:10 AM

    Hi Ranjit,

    Can you please look into this issue? Just as FYI: the previous installation of this package was on Python 3.7 eco system which has a lower version of setuptools and there was no issue with setuptools. Now I have upgraded the environment to Python 3.9 eco system.

    Thanks

    Mi



    ------------------------------
    Mi Wang
    ------------------------------



  • 5.  RE: Install pyreadstat package -> " /usr/include/sys/time.h:110:16: error: redefinition of 'struct sigset_t'

    Posted Tue September 19, 2023 11:14 AM

    Hi Ranjit,

    FYI - the 1st message of this thread was about issue encountered during my previous installation for the pyreadstat package on Python 3.7. As I was having permission issue with the Open Source community, Bruce posted the message for me.

    Thanks

    Mi



    ------------------------------
    Mi Wang
    ------------------------------



  • 6.  RE: Install pyreadstat package -> " /usr/include/sys/time.h:110:16: error: redefinition of 'struct sigset_t'

    Posted Thu September 21, 2023 01:46 AM

    Hi Wang,

    Are you still seeing this issue or is it resolved?

    let us know the output of 'rpm -qa | grep -i python3.9 | grep -I setuptools' .

    I tried to install this pyreadstat  and the above error was not hit. There was some linker error during linking the libraries which can be fixed by exporting below 
    before starting the build.

    export LDFLAGS="-liconv"

    Thanks

    Ranjit



    ------------------------------
    Ranjit Ranjan
    ------------------------------



  • 7.  RE: Install pyreadstat package -> " /usr/include/sys/time.h:110:16: error: redefinition of 'struct sigset_t'

    Posted Mon September 25, 2023 12:04 PM

    Hi Ranjit,

    Yes, I just did the installation and got the same error. Please also find the output for the rpm -qa command:

    Thanks

    Mi

    /tmp: rpm -qa | grep -i python3.9 | grep -i setuptools
    python3.9-setuptools-65.2.0-1.noarch

    Installing build dependencies ... error
      error: subprocess-exited-with-error

     

      × pip subprocess to install build dependencies did not run successfully.
      │ exit code: 1
      ╰─> [3 lines of output]
          Looking in links: /usr/opt/sas/python3a
          ERROR: Could not find a version that satisfies the requirement setuptools (from versions: none)
          ERROR: No matching distribution found for setuptools
          [end of output]



    ------------------------------
    Mi Wang
    ------------------------------



  • 8.  RE: Install pyreadstat package -> " /usr/include/sys/time.h:110:16: error: redefinition of 'struct sigset_t'

    Posted Mon September 25, 2023 02:08 PM
    Edited by Ranjit Ranjan Mon September 25, 2023 02:10 PM

    which command you used to start the installation. Hoping that you are using python3.9. 

    Try to upgrade setup tools to latest once.

    ------------------------------
    Ranjit Ranjan
    ------------------------------



  • 9.  RE: Install pyreadstat package -> " /usr/include/sys/time.h:110:16: error: redefinition of 'struct sigset_t'

    Posted Tue September 26, 2023 02:57 PM

    Hi Ranjit,

    Actually I have already upgraded to the newest setuptools (version 65.5.1). According to another discussion thread, I added '--no-build-isolation' option in my pip installation command and no more setuptools related error. But I got the following new error. Can you please take a look?

    Thanks

    Mi

    Processing ./pyreadstat-1.2.3.tar.gz
      Preparing metadata (pyproject.toml) ... error
      error: subprocess-exited-with-error

     

      × Preparing metadata (pyproject.toml) did not run successfully.
      │ exit code: 1
      ╰─> [13 lines of output]
          Traceback (most recent call last):
            File "/opt/freeware/lib/python3.9/site-packages/pip/_vendor/pep517/in_process/_in_process.py", line 363, in <module>
              main()
            File "/opt/freeware/lib/python3.9/site-packages/pip/_vendor/pep517/in_process/_in_process.py", line 345, in main
              json_out['return_val'] = hook(**hook_input['kwargs'])
            File "/opt/freeware/lib/python3.9/site-packages/pip/_vendor/pep517/in_process/_in_process.py", line 164, in prepare_metadata_for_build_wheel
              return hook(metadata_directory, config_settings)
            File "/opt/freeware/lib/python3.9/site-packages/setuptools/build_meta.py", line 377, in prepare_metadata_for_build_wheel
              self.run_setup()
            File "/opt/freeware/lib/python3.9/site-packages/setuptools/build_meta.py", line 335, in run_setup
              exec(code, locals())
            File "<string>", line 32, in <module>
          Exception: Cython version 3 or newer required
          [end of output]



    ------------------------------
    Mi Wang
    ------------------------------



  • 10.  RE: Install pyreadstat package -> " /usr/include/sys/time.h:110:16: error: redefinition of 'struct sigset_t'

    Posted Wed September 27, 2023 02:44 AM
    Edited by Ranjit Ranjan Wed September 27, 2023 02:48 AM

    Hi

    I see below snippet of code in 1.2.3 branch which is raising above exception.

    cyver = int(Cython.__version__.split(".")[0])
    if cyver < 3:
        msg = "Cython version 3 or newer required"
        raise Exception(msg)

    We don't have Cython 3 in AIX Toolbox. 
    So suggestion is to use previous release of pyreadstat 1.2.2.

    Thanks

    Ranjit



    ------------------------------
    Ranjit Ranjan
    ------------------------------



  • 11.  RE: Install pyreadstat package -> " /usr/include/sys/time.h:110:16: error: redefinition of 'struct sigset_t'

    Posted Wed September 27, 2023 10:29 AM

    Hi Ranjit,

    I have tried pyreadstat 1.2.2 and got the following error. Please help.

    Thanks

    Mi

    Preparing metadata (pyproject.toml) ... error
      error: subprocess-exited-with-error

     

      × Preparing metadata (pyproject.toml) did not run successfully.
      │ exit code: 1
      ╰─> [19 lines of output]
          [1/3] Cythonizing pyreadstat/_readstat_parser.pyx
          [2/3] Cythonizing pyreadstat/_readstat_writer.pyx
          [3/3] Cythonizing pyreadstat/pyreadstat.pyx
          running dist_info
          creating /tmp/pip-modern-metadata-v4pvwh5_/pyreadstat.egg-info
          writing /tmp/pip-modern-metadata-v4pvwh5_/pyreadstat.egg-info/PKG-INFO
          writing dependency_links to /tmp/pip-modern-metadata-v4pvwh5_/pyreadstat.egg-info/dependency_links.txt
          writing requirements to /tmp/pip-modern-metadata-v4pvwh5_/pyreadstat.egg-info/requires.txt
          writing top-level names to /tmp/pip-modern-metadata-v4pvwh5_/pyreadstat.egg-info/top_level.txt
          writing manifest file '/tmp/pip-modern-metadata-v4pvwh5_/pyreadstat.egg-info/SOURCES.txt'
          reading manifest file '/tmp/pip-modern-metadata-v4pvwh5_/pyreadstat.egg-info/SOURCES.txt'
          reading manifest template 'MANIFEST.in'
          warning: no files found matching '*.h'
          warning: no files found matching '*.pyx'
          warning: no files found matching '*.pxd'
          adding license file 'LICENSE'
          writing manifest file '/tmp/pip-modern-metadata-v4pvwh5_/pyreadstat.egg-info/SOURCES.txt'
          creating '/tmp/pip-modern-metadata-v4pvwh5_/pyreadstat-1.2.2.dist-info'
          error: invalid command 'bdist_wheel'
          [end of output]



    ------------------------------
    Mi Wang
    ------------------------------



  • 12.  RE: Install pyreadstat package -> " /usr/include/sys/time.h:110:16: error: redefinition of 'struct sigset_t'

    Posted Thu September 28, 2023 02:59 AM

    Looks, Your setup is missing this  https://pypi.org/project/wheel/

    Install this also and try it out again .

    Thanks

    Ranjit



    ------------------------------
    Ranjit Ranjan
    ------------------------------



  • 13.  RE: Install pyreadstat package -> " /usr/include/sys/time.h:110:16: error: redefinition of 'struct sigset_t'

    Posted Fri October 06, 2023 10:25 AM

    Hi Ranjit,

    After installing the wheel package, I have installed pyreadstat package successfully. Jut to let you this related to the installation which is a little bit weird: the pip installation doesn't recognize AIX Toolbox package python3-Cython 0.29.24. So I have to install PYPI package Cython 0.29.36.

    Thanks

    Mi



    ------------------------------
    Mi Wang
    ------------------------------