You can try if 'export MAKE="make -j4"' fixes this
On Thursday, February 8, 2024 at 1:21:32 PM UTC-8 Sai Chandhrasekhar wrote:
> When running python3 -m pip install --no-build-isolation
> sagemath-standard I got this error message:
>
> clang -bundle -undefined dynamic_lookup -g
> -L/Users/user/.sage/sage-10.3.beta7-Darwin-x86_64/local/lib
> -Wl,-rpath,/Users/user/.sage/sage-10.3.beta7-Darwin-x86_64/local/lib
> build/temp.macosx-10.9-universal2-cpython-311/build/cythonized/sage/monoids/free_abelian_monoid_element.o
>
> -lgmp -o build/lib.macosx-10.9-universal2-cpython-311/sage/monoids/
> free_abelian_monoid_element.cpython-311-darwin.so -lpari
>
> error: command '/usr/bin/clang' failed with exit code 1
>
> Exception ignored in: <function Pool.__del__ at 0x11ce2dee0>
>
> Traceback (most recent call last):
>
> File
> "/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/multiprocessing/pool.py",
>
> line 271, in __del__
>
> self._change_notifier.put(None)
>
> File
> "/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/multiprocessing/queues.py",
>
> line 377, in put
>
> self._writer.send_bytes(obj)
>
> File
> "/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/multiprocessing/connection.py",
>
> line 199, in send_bytes
>
> self._send_bytes(m[offset:offset + size])
>
> File
> "/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/multiprocessing/connection.py",
>
> line 410, in _send_bytes
>
> self._send(header + buf)
>
> File
> "/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/multiprocessing/connection.py",
>
> line 367, in _send
>
> n = write(self._handle, buf)
>
> ^^^^^^^^^^^^^^^^^^^^^^^^
>
> OSError: [Errno 9] Bad file descriptor
>
> On Thursday, February 8, 2024 at 1:46:26 PM UTC-6 Sai Chandhrasekhar wrote:
>
>> I was able to get it to work. I found out I added the wrong location to
>> PATH. I fixed it and got the command to work.
>>
>> On Thursday, February 8, 2024 at 1:00:52 PM UTC-6 Sai Chandhrasekhar
>> wrote:
>>
>>> I did get a warning about that and added it to my PATH before running
>>> the command, but I still got the result. I did what you suggested and still
>>> got the same error message.
>>>
>>> On Thursday, February 8, 2024 at 12:27:29 PM UTC-6 Matthias Koeppe wrote:
>>>
>>>> That's great progress.
>>>>
>>>> Did pip issue any warnings when you installed sage_conf?
>>>> In particular, it may have warned that the installation location for
>>>> scripts is not in your PATH.
>>>> If so, you can fix it as follows:
>>>>
>>>> export PATH="$(python3 -c 'import sysconfig;
>>>> print(sysconfig.get_path("scripts", "posix_user"))'):$PATH"
>>>>
>>>> On Thursday, February 8, 2024 at 8:38:27 AM UTC-8 Sai Chandhrasekhar
>>>> wrote:
>>>>
>>>>> I was able to install sage_conf successfully, but when I run, "python3
>>>>> -m pip install $(sage-config SAGE_SPKG_WHEELS)/*.whl sage_setup", I get
>>>>> the
>>>>> following error messages:
>>>>>
>>>>> zsh: command not found: sage-config
>>>>>
>>>>> zsh: no matches found: /*.whl
>>>>>
>>>>> On Wednesday, February 7, 2024 at 3:13:27 PM UTC-6 Matthias Koeppe
>>>>> wrote:
>>>>>
>>>>>> To start from scratch in this mode of installation, you will need to
>>>>>> remove the directory "/Users/user/.sage/sage-10.3.beta7-Darwin-x86_64/"
>>>>>>
>>>>>> On Wednesday, February 7, 2024 at 12:10:21 PM UTC-8 Sai
>>>>>> Chandhrasekhar wrote:
>>>>>>
>>>>>>> I am still getting the same error. In the config.log files, I see
>>>>>>> this: x86_64-apple-darwin13.4.0-clang: command not found. I have tried
>>>>>>> uninstalling and reinstalling Xcode and the Xcode command line tools,
>>>>>>> but I
>>>>>>> still get the same result.
>>>>>>>
>>>>>>>
>>>>>>> On Wednesday, February 7, 2024 at 11:06:12 AM UTC-6 Matthias Koeppe
>>>>>>> wrote:
>>>>>>>
>>>>>>>> Thanks for sharing these logs.
>>>>>>>> The key failure is here:
>>>>>>>>
>>>>>>>> configure:3938: x86_64-apple-darwin13.4.0-clang -march=core2
>>>>>>>> -mtune=haswell -mssse3 -ftree-vectorize -fPIC -fstack-protector-strong
>>>>>>>> -O2
>>>>>>>> -pipe -isystem /Users/user/anaconda3/include -D_FORTIFY_SOURCE=2
>>>>>>>> -isystem
>>>>>>>> /Users/user/anaconda3/include
>>>>>>>> -L/Users/user/.sage/sage-10.2-Darwin-x86_64/local/lib
>>>>>>>> -Wl,-ld_classic,-rpath,/Users/user/.sage/sage-10.2-Darwin-x86_64/local/lib
>>>>>>>>
>>>>>>>> -L/Users/user/.sage/sage-10.2-Darwin-x86_64/local/lib
>>>>>>>> -Wl,-ld_classic,-rpath,/Users/user/.sage/sage-10.2-Darwin-x86_64/local/lib
>>>>>>>>
>>>>>>>> -Wl,-headerpad_max_install_names -Wl,-dead_strip_dylibs
>>>>>>>> -Wl,-rpath,/Users/user/anaconda3/lib -L/Users/user/anaconda3/lib
>>>>>>>> conftest.c
>>>>>>>> >&5
>>>>>>>> ld: library not found for -ld_classic
>>>>>>>> clang-16: error: linker command failed with exit code 1 (use -v to
>>>>>>>> see invocation)
>>>>>>>>
>>>>>>>> What's happening here is that a workaround that we use on macOS for
>>>>>>>> compilation with XCode is incompatible with the conda toolchain.
>>>>>>>> I have a fix for this in
>>>>>>>> https://github.com/sagemath/sage/pull/37237
>>>>>>>>
>>>>>>>> For now, if you want to use the installation method using "pip
>>>>>>>> install sage_conf", deactivate conda first.
>>>>>>>> Or alternatively if you want to use conda, use one of the
>>>>>>>> installation methods described in
>>>>>>>> https://doc.sagemath.org/html/en/installation/conda.html
>>>>>>>>
>>>>>>>>
>>>>>>>> On Tuesday, February 6, 2024 at 4:10:53 PM UTC-8 Sai Chandhrasekhar
>>>>>>>> wrote:
>>>>>>>>
>>>>>>>>> I also tried to run the install command again with the --pre flag
>>>>>>>>> and got the same result.
>>>>>>>>>
>>>>>>>>> On Tuesday, February 6, 2024 at 5:54:11 PM UTC-6 Sai
>>>>>>>>> Chandhrasekhar wrote:
>>>>>>>>>
>>>>>>>>>> On Tuesday, February 6, 2024 at 5:14:56 PM UTC-6 Matthias Koeppe
>>>>>>>>>> wrote:
>>>>>>>>>>
>>>>>>>>>>>
>>>>>>>>>>> and
>>>>>>>>>>> /Users/user/.sage/sage-10.2-Darwin-x86_64/local/var/tmp/sage/build/libatomic_ops-7.8.0/src/config.log
>>>>>>>>>>>
>>>>>>>>>>> please
>>>>>>>>>>>
>>>>>>>>>>> On Tuesday, February 6, 2024 at 2:36:21 PM UTC-8 Sai
>>>>>>>>>>> Chandhrasekhar wrote:
>>>>>>>>>>>
>>>>>>>>>>>> On Tuesday, February 6, 2024 at 4:22:59 PM UTC-6 Matthias
>>>>>>>>>>>> Koeppe wrote:
>>>>>>>>>>>>
>>>>>>>>>>>>> Could you post one of these log files please? For example
>>>>>>>>>>>>> info-6.8.log
>>>>>>>>>>>>>
>>>>>>>>>>>>> And could you try "python3 -m pip install --pre sage_conf"
>>>>>>>>>>>>> also?
>>>>>>>>>>>>>
>>>>>>>>>>>>> On Tuesday, February 6, 2024 at 12:15:08 PM UTC-8 Sai
>>>>>>>>>>>>> Chandhrasekhar wrote:
>>>>>>>>>>>>>
>>>>>>>>>>>>>> When I ran python3 -m pip install sage_conf I got this error
>>>>>>>>>>>>>> message:
>>>>>>>>>>>>>>
>>>>>>>>>>>>>> Error building Sage.
>>>>>>>>>>>>>>
>>>>>>>>>>>>>>
>>>>>>>>>>>>>>
>>>>>>>>>>>>>> The following package(s) may have failed to build (not
>>>>>>>>>>>>>> necessarily
>>>>>>>>>>>>>>
>>>>>>>>>>>>>> during this run of 'make all-build'):
>>>>>>>>>>>>>>
>>>>>>>>>>>>>>
>>>>>>>>>>>>>>
>>>>>>>>>>>>>> * package: gf2x-1.3.0
>>>>>>>>>>>>>>
>>>>>>>>>>>>>> last build time: Feb 6 14:07
>>>>>>>>>>>>>>
>>>>>>>>>>>>>> log file:
>>>>>>>>>>>>>> /Users/user/.sage/sage-10.2-Darwin-x86_64/logs/pkgs/gf2x-1.3.0.log
>>>>>>>>>>>>>>
>>>>>>>>>>>>>> build directory:
>>>>>>>>>>>>>> /Users/user/.sage/sage-10.2-Darwin-x86_64/local/var/tmp/sage/build/gf2x-1.3.0
>>>>>>>>>>>>>>
>>>>>>>>>>>>>>
>>>>>>>>>>>>>>
>>>>>>>>>>>>>> * package: cddlib-0.94m
>>>>>>>>>>>>>>
>>>>>>>>>>>>>> last build time: Feb 6 14:07
>>>>>>>>>>>>>>
>>>>>>>>>>>>>> log file:
>>>>>>>>>>>>>> /Users/user/.sage/sage-10.2-Darwin-x86_64/logs/pkgs/cddlib-0.94m.log
>>>>>>>>>>>>>>
>>>>>>>>>>>>>> build directory:
>>>>>>>>>>>>>> /Users/user/.sage/sage-10.2-Darwin-x86_64/local/var/tmp/sage/build/cddlib-0.94m
>>>>>>>>>>>>>>
>>>>>>>>>>>>>>
>>>>>>>>>>>>>>
>>>>>>>>>>>>>> * package: cliquer-1.22
>>>>>>>>>>>>>>
>>>>>>>>>>>>>> last build time: Feb 6 14:07
>>>>>>>>>>>>>>
>>>>>>>>>>>>>> log file:
>>>>>>>>>>>>>> /Users/user/.sage/sage-10.2-Darwin-x86_64/logs/pkgs/cliquer-1.22.log
>>>>>>>>>>>>>>
>>>>>>>>>>>>>> build directory:
>>>>>>>>>>>>>> /Users/user/.sage/sage-10.2-Darwin-x86_64/local/var/tmp/sage/build/cliquer-1.22
>>>>>>>>>>>>>>
>>>>>>>>>>>>>>
>>>>>>>>>>>>>>
>>>>>>>>>>>>>> * package: libatomic_ops-7.8.0
>>>>>>>>>>>>>>
>>>>>>>>>>>>>> last build time: Feb 6 14:07
>>>>>>>>>>>>>>
>>>>>>>>>>>>>> log file:
>>>>>>>>>>>>>> /Users/user/.sage/sage-10.2-Darwin-x86_64/logs/pkgs/libatomic_ops-7.8.0.log
>>>>>>>>>>>>>>
>>>>>>>>>>>>>> build directory:
>>>>>>>>>>>>>> /Users/user/.sage/sage-10.2-Darwin-x86_64/local/var/tmp/sage/build/libatomic_ops-7.8.0
>>>>>>>>>>>>>>
>>>>>>>>>>>>>>
>>>>>>>>>>>>>>
>>>>>>>>>>>>>> * package: m4ri-20200115
>>>>>>>>>>>>>>
>>>>>>>>>>>>>> last build time: Feb 6 14:07
>>>>>>>>>>>>>>
>>>>>>>>>>>>>> log file:
>>>>>>>>>>>>>> /Users/user/.sage/sage-10.2-Darwin-x86_64/logs/pkgs/m4ri-20200115.log
>>>>>>>>>>>>>>
>>>>>>>>>>>>>> build directory:
>>>>>>>>>>>>>> /Users/user/.sage/sage-10.2-Darwin-x86_64/local/var/tmp/sage/build/m4ri-20200115
>>>>>>>>>>>>>>
>>>>>>>>>>>>>>
>>>>>>>>>>>>>>
>>>>>>>>>>>>>> * package: ecm-7.0.5
>>>>>>>>>>>>>>
>>>>>>>>>>>>>> last build time: Feb 6 14:07
>>>>>>>>>>>>>>
>>>>>>>>>>>>>> log file:
>>>>>>>>>>>>>> /Users/user/.sage/sage-10.2-Darwin-x86_64/logs/pkgs/ecm-7.0.5.log
>>>>>>>>>>>>>>
>>>>>>>>>>>>>> build directory:
>>>>>>>>>>>>>> /Users/user/.sage/sage-10.2-Darwin-x86_64/local/var/tmp/sage/build/ecm-7.0.5
>>>>>>>>>>>>>>
>>>>>>>>>>>>>>
>>>>>>>>>>>>>>
>>>>>>>>>>>>>> * package: info-6.8
>>>>>>>>>>>>>>
>>>>>>>>>>>>>> last build time: Feb 6 14:07
>>>>>>>>>>>>>>
>>>>>>>>>>>>>> log file:
>>>>>>>>>>>>>> /Users/user/.sage/sage-10.2-Darwin-x86_64/logs/pkgs/info-6.8.log
>>>>>>>>>>>>>>
>>>>>>>>>>>>>> build directory:
>>>>>>>>>>>>>> /Users/user/.sage/sage-10.2-Darwin-x86_64/local/var/tmp/sage/build/info-6.8
>>>>>>>>>>>>>>
>>>>>>>>>>>>>>
>>>>>>>>>>>>>>
>>>>>>>>>>>>>> * package: pari-2.15.4
>>>>>>>>>>>>>>
>>>>>>>>>>>>>> last build time: Feb 6 14:08
>>>>>>>>>>>>>>
>>>>>>>>>>>>>> log file:
>>>>>>>>>>>>>> /Users/user/.sage/sage-10.2-Darwin-x86_64/logs/pkgs/pari-2.15.4.log
>>>>>>>>>>>>>>
>>>>>>>>>>>>>> build directory:
>>>>>>>>>>>>>> /Users/user/.sage/sage-10.2-Darwin-x86_64/local/var/tmp/sage/build/pari-2.15.4
>>>>>>>>>>>>>>
>>>>>>>>>>>>>>
>>>>>>>>>>>>>> For those packages the following error message was printed
>>>>>>>>>>>>>> earlier:
>>>>>>>>>>>>>>
>>>>>>>>>>>>>> configure: error: C compiler cannot create executables
>>>>>>>>>>>>>>
>>>>>>>>>>>>>> On Tuesday, February 6, 2024 at 2:01:03 PM UTC-6 Matthias
>>>>>>>>>>>>>> Koeppe wrote:
>>>>>>>>>>>>>>
>>>>>>>>>>>>>>> According to your config.log, the run of "configure"
>>>>>>>>>>>>>>> succeeded.
>>>>>>>>>>>>>>> That config.log contains error messages from various
>>>>>>>>>>>>>>> compiler invocations is a normal part of the configure process.
>>>>>>>>>>>>>>>
>>>>>>>>>>>>>>> What is the actual problem that you encountered?
>>>>>>>>>>>>>>>
>>>>>>>>>>>>>>>
>>>>>>>>>>>>>>> On Monday, February 5, 2024 at 2:58:36 PM UTC-8 Sai
>>>>>>>>>>>>>>> Chandhrasekhar wrote:
>>>>>>>>>>>>>>>
>>>>>>>>>>>>>>>> On Monday, February 5, 2024 at 4:48:08 PM UTC-6 Dima
>>>>>>>>>>>>>>>> Pasechnik wrote:
>>>>>>>>>>>>>>>>
>>>>>>>>>>>>>>>>>
>>>>>>>>>>>>>>>>>
>>>>>>>>>>>>>>>>> On 5 February 2024 21:58:54 GMT, "dan...@gmail.com" <
>>>>>>>>>>>>>>>>> dan...@gmail.com> wrote:
>>>>>>>>>>>>>>>>> >You could just use Sage_macOS
>>>>>>>>>>>>>>>>> ><
>>>>>>>>>>>>>>>>> https://github.com/3-manifolds/Sage_macOS/releases/tag/v2.2.0>,
>>>>>>>>>>>>>>>>>
>>>>>>>>>>>>>>>>> quick and
>>>>>>>>>>>>>>>>> >easy!
>>>>>>>>>>>>>>>>>
>>>>>>>>>>>>>>>>> for Sage development, you need a source install.
>>>>>>>>>>>>>>>>>
>>>>>>>>>>>>>>>>> >
>>>>>>>>>>>>>>>>> >On Monday, February 5, 2024 at 3:49:02 PM UTC-6 Matthias
>>>>>>>>>>>>>>>>> Koeppe wrote:
>>>>>>>>>>>>>>>>> >
>>>>>>>>>>>>>>>>> >> We would need to see the full logs
>>>>>>>>>>>>>>>>> >>
>>>>>>>>>>>>>>>>> >> On Monday, February 5, 2024 at 1:26:31 PM UTC-8 Sai
>>>>>>>>>>>>>>>>> Chandhrasekhar wrote:
>>>>>>>>>>>>>>>>> >>
>>>>>>>>>>>>>>>>> >>> Hello,
>>>>>>>>>>>>>>>>> >>>
>>>>>>>>>>>>>>>>> >>> When I tried to run python3 -m pip install sage_conf,
>>>>>>>>>>>>>>>>> I got this error
>>>>>>>>>>>>>>>>> >>> message from config.log. I tried to change to GCC but
>>>>>>>>>>>>>>>>> then I got a message
>>>>>>>>>>>>>>>>> >>> that Sage cannot be built on macOS with GNU's gcc. Any
>>>>>>>>>>>>>>>>> suggestions on what
>>>>>>>>>>>>>>>>> >>> to do would be appreciated.
>>>>>>>>>>>>>>>>> >>> configure:6595: x86_64-apple-darwin13.4.0-clang -V >&5
>>>>>>>>>>>>>>>>> >>> clang-16: error: argument to '-V' is missing (expected
>>>>>>>>>>>>>>>>> 1 value)
>>>>>>>>>>>>>>>>> >>> clang-16: error: no input files
>>>>>>>>>>>>>>>>> >>> configure:6606: $? = 1
>>>>>>>>>>>>>>>>> >>> configure:6595: x86_64-apple-darwin13.4.0-clang
>>>>>>>>>>>>>>>>> -qversion >&5
>>>>>>>>>>>>>>>>> >>> clang-16: error: unknown argument '-qversion'; did you
>>>>>>>>>>>>>>>>> mean '--version'?
>>>>>>>>>>>>>>>>> >>> clang-16: error: no input files
>>>>>>>>>>>>>>>>> >>> configure:6606: $? = 1
>>>>>>>>>>>>>>>>> >>> configure:6595: x86_64-apple-darwin13.4.0-clang
>>>>>>>>>>>>>>>>> -version >&5
>>>>>>>>>>>>>>>>> >>> clang-16: error: unknown argument '-version'; did you
>>>>>>>>>>>>>>>>> mean '--version'?
>>>>>>>>>>>>>>>>> >>> clang-16: error: no input files
>>>>>>>>>>>>>>>>> >>>
>>>>>>>>>>>>>>>>> >>
>>>>>>>>>>>>>>>>> >
>>>>>>>>>>>>>>>>>
>>>>>>>>>>>>>>>>
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