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sage not installing from source

asked 2021-12-02 02:33:37 +0100

brettpim gravatar image

updated 2021-12-03 20:32:11 +0100

I am running Ubuntu 21.04. I have cloned sagemath's source with git and run ./configure folowed by MAKE='make -j4' make. It terminates with errors. The first error is in cysignals-1.10.3. I can't attach the log files here since I do not have enough points. So I hope these are the relevant things from logs/pkgs/cysignals-1.10.3.log:

Processing /home/brett/Projects/SAGE/sage/local/var/tmp/sage/build/cysignals-1.10.3/src Created temporary directory: /tmp/pip-req-build-reb5uglo DEPRECATION: A future pip version will change local packages to be built in-place without first copying to a temporary directory. We recommend you use --use-feature=in-tree-build to test your packages with this new behavior before it becomes the default. pip 21.3 will remove support for this functionality. You can find discussion regarding this at https://github.com/pypa/pip/issues/7555. Added file:///home/brett/Projects/SAGE/sage/local/var/tmp/sage/build/cysignals-1.10.3/src to build tracker '/tmp/pip-req-tracker-31wllir1' Running setup.py (path:/tmp/pip-req-build-reb5uglo/setup.py) egg_info for package from file:///home/brett/Projects/SAGE/sage/local/var/tmp/sage/build/cysignals-1.10.3/src Created temporary directory: /tmp/pip-pip-egg-info-rmc2dd38 Running command python setup.py egg_info WARNING: Retrying (Retry(total=4, connect=None, read=None, redirect=None, status=None)) after connection broken by 'ConnectTimeoutError(<pip._vendor.urllib3.connection.HTTPSConnection object at 0x7fdd4693a340>, 'Connection to 192.0.2.0 timed out. (connect timeout=15)')': /simple/cython/ WARNING: Retrying (Retry(total=3, connect=None, read=None, redirect=None, status=None)) after connection broken by 'ConnectTimeoutError(<pip._vendor.urllib3.connection.HTTPSConnection object at 0x7fdd4693aa30>, 'Connection to 192.0.2.0 timed out. (connect timeout=15)')': /simple/cython/ WARNING: Retrying (Retry(total=2, connect=None, read=None, redirect=None, status=None)) after connection broken by 'ConnectTimeoutError(<pip._vendor.urllib3.connection.HTTPSConnection object at 0x7fdd4693ab50>, 'Connection to 192.0.2.0 timed out. (connect timeout=15)')': /simple/cython/ WARNING: Retrying (Retry(total=1, connect=None, read=None, redirect=None, status=None)) after connection broken by 'ConnectTimeoutError(<pip._vendor.urllib3.connection.HTTPSConnection object at 0x7fdd4693ac10>, 'Connection to 192.0.2.0 timed out. (connect timeout=15)')': /simple/cython/ WARNING: Retrying (Retry(total=0, connect=None, read=None, redirect=None, status=None)) after connection broken by 'ConnectTimeoutError(<pip._vendor.urllib3.connection.HTTPSConnection object at 0x7fdd4693acd0>, 'Connection to 192.0.2.0 timed out. (connect timeout=15)')': /simple/cython/ ERROR: Could not find a version that satisfies the requirement Cython>=0.28 (from versions: none) ERROR: No matching distribution found for Cython>=0.28 Traceback (most recent call last): File "/home/brett/Projects/SAGE/sage/local/lib/python3.9/site-packages/setuptools/installer.py", line 75, in fetch_build_egg subprocess.check_call(cmd) File "/usr/lib/python3.9/subprocess.py", line 373, in check_call raise CalledProcessError(retcode, cmd) subprocess.CalledProcessError: Command '['/home/brett/Projects/SAGE/sage/local/bin/python3', '-m', 'pip', '--disable-pip-version-check', 'wheel', '--no-deps', '-w', '/tmp/tmpbhnfluj1', '--quiet', 'Cython>=0.28']' returned non-zero exit status 1.

One thing I noticed is that it seems to be looking for cython version >= 0.28. ./configure says

cython-0.29.21: standard, will be installed as an SPKG

but python3 -m pip install cython reports that python v0.29 is installed:

Requirement already satisfied: cython in /home/brett/.local/lib/python3.9/site-packages (0.29.24)

Inside log/pkgs/config.log is says

configure:40443: result: cython-0.29.21: standard, will be installed as an SPKG

The file log/pkgs/cython-0.29.21.log reports no errors. Although it does think at the start that cython is not installed:

Package 'cython' is currently not installed

but the python3 pip command above indicates that it is installed on my system.

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In the file logs/pkgs/config.log, there should be a line starting something like "configure:47094: result: cython-0.29.24:" (search for "cython", might be the first hit). What does the rest of that line say? If it says "standard, will be installed as an SPKG", then what does the cython log file say?

John Palmieri gravatar imageJohn Palmieri ( 2021-12-02 06:37:51 +0100 )edit

I have added that information

brettpim gravatar imagebrettpim ( 2021-12-02 22:05:46 +0100 )edit

Sage should build its own pip and its own cython — that's expected. I don't know what's going wrong here, though.

John Palmieri gravatar imageJohn Palmieri ( 2021-12-03 01:26:32 +0100 )edit

Thanks for letting me know that building its own pip and cython is normal. Is there something I can do to get better information on the error? Do you know what information the process is trying to get from address 192.0.2.0? Are there other venues for getting help with compiling sagemath?

brettpim gravatar imagebrettpim ( 2021-12-03 14:27:04 +0100 )edit

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answered 2021-12-03 20:36:45 +0100

brettpim gravatar image

I was able to successfully compile by running make distclean, tox -r, ./configure and then make without taking advantage of multiprocessrs. I ran tox -r as suggested at ticket 29039 for making sure I was starting "from scratch"

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I'm glad you got it working, although I don't know if tox had anything to do with it.

John Palmieri gravatar imageJohn Palmieri ( 2021-12-03 23:34:05 +0100 )edit

I agree that tox is not relevant.

brettpim gravatar imagebrettpim ( 2021-12-10 17:16:38 +0100 )edit

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Asked: 2021-12-02 02:33:37 +0100

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Last updated: Dec 03 '21