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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