Cannot build 9.7 on Debian Sid
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Luis Finotti
Jan 9, 2023, 2:14:38 PM1/9/23
to Sage Support
My working installation of Sage 9-7 (built from source) on Debian Sid stopped working. I thought it was due to the recent transition to Python 3.11 (or some other change in Sid). So, I tried to build it again from source, but it fails.
Here is the last messages before it stops:
[sagelib-9.7] error: Command "gcc -Wno-unused-result -Wsign-compare -DNDEBUG -g -fwrapv -O3 -Wall -Wno-unused -g -O2 -g -O2 -fPIC -Isage/cpython -I/usr/include/x86_64-linux-gnu/singular -I/usr/include/x86_64-linux-gnu/singular/singular -I/usr/include/singular -I/usr/include/singular/singular -I/home/finotti/src/sage-9.7/local/var/lib/sage/venv-python3.10.5/lib/python3.10/site-packages/cypari2 -Isage/libs/ntl -Isage/rings/finite_rings -I/home/finotti/src/sage-9.7/local/var/lib/sage/venv-python3.10.5/lib/python3.10/site-packages/cysignals -I/home/finotti/src/sage-9.7/src -I/home/finotti/src/sage-9.7/local/var/lib/sage/venv-python3.10.5/lib/python3.10/site-packages/numpy/core/include -I/home/finotti/src/sage-9.7/local/var/lib/sage/venv-python3.10.5/include/python3.10 -I/home/finotti/src/sage-9.7/local/var/lib/sage/venv-python3.10.5/include/python3.10 -c sage/rings/polynomial/multi_polynomial_libsingular.cpp -o build/temp.linux-x86_64-cpython-310/sage/rings/polynomial/multi_polynomial_libsingular.o -std=c++11 -fabi-version=6" failed with exit status 1
[sagelib-9.7] error: subprocess-exited-with-error
[sagelib-9.7]
[sagelib-9.7] × python setup.py develop did not run successfully.
[sagelib-9.7] │ exit code: 1
[sagelib-9.7] ╰─> See above for output.
[sagelib-9.7]
[sagelib-9.7] note: This error originates from a subprocess, and is likely not a problem with pip.
[sagelib-9.7] full command: /home/finotti/src/sage-9.7/local/var/lib/sage/venv-python3.10.5/bin/python3 -c '
[sagelib-9.7] exec(compile('"'"''"'"''"'"'
[sagelib-9.7] # This is <pip-setuptools-caller> -- a caller that pip uses to run setup.py
[sagelib-9.7] #
[sagelib-9.7] # - It imports setuptools before invoking setup.py, to enable projects that directly
[sagelib-9.7] # import from `distutils.core` to work with newer packaging standards.
[sagelib-9.7] # - It provides a clear error message when setuptools is not installed.
[sagelib-9.7] # - It sets `sys.argv[0]` to the underlying `setup.py`, when invoking `setup.py` so
[sagelib-9.7] # setuptools doesn'"'"'t think the script is `-c`. This avoids the following warning:
[sagelib-9.7] # manifest_maker: standard file '"'"'-c'"'"' not found".
[sagelib-9.7] # - It generates a shim setup.py, for handling setup.cfg-only projects.
[sagelib-9.7] import os, sys, tokenize
[sagelib-9.7]
[sagelib-9.7] try:
[sagelib-9.7] import setuptools
[sagelib-9.7] except ImportError as error:
[sagelib-9.7] print(
[sagelib-9.7] "ERROR: Can not execute `setup.py` since setuptools is not available in "
[sagelib-9.7] "the build environment.",
[sagelib-9.7] file=sys.stderr,
[sagelib-9.7] )
[sagelib-9.7] sys.exit(1)
[sagelib-9.7]
[sagelib-9.7] __file__ = %r
[sagelib-9.7] sys.argv[0] = __file__
[sagelib-9.7]
[sagelib-9.7] if os.path.exists(__file__):
[sagelib-9.7] filename = __file__
[sagelib-9.7] with tokenize.open(__file__) as f:
[sagelib-9.7] setup_py_code = f.read()
[sagelib-9.7] else:
[sagelib-9.7] filename = "<auto-generated setuptools caller>"
[sagelib-9.7] setup_py_code = "from setuptools import setup; setup()"
[sagelib-9.7]
[sagelib-9.7] exec(compile(setup_py_code, filename, "exec"))
[sagelib-9.7] '"'"''"'"''"'"' % ('"'"'/home/finotti/src/sage-9.7/src/setup.py'"'"',), "<pip-setuptools-caller>", "exec"))' --no-user-cfg develop --no-deps
[sagelib-9.7] cwd: /home/finotti/src/sage-9.7/src/
[sagelib-9.7] error: subprocess-exited-with-error
[sagelib-9.7]
[sagelib-9.7] × python setup.py develop did not run successfully.
[sagelib-9.7] │ exit code: 1
[sagelib-9.7] ╰─> See above for output.
[sagelib-9.7]
[sagelib-9.7] note: This error originates from a subprocess, and is likely not a problem with pip.
[sagelib-9.7]
[sagelib-9.7] real 12m29.646s
[sagelib-9.7] user 46m59.670s
[sagelib-9.7] sys 1m23.295s
make[4]: *** [Makefile:3115: sagelib-SAGE_VENV-no-deps] Error 1
make[3]: *** [Makefile:3115: /home/finotti/src/sage-9.7/local/var/lib/sage/venv-python3.10.5/var/lib/sage/installed/sagelib-9.7] Error 2
make[2]: *** [Makefile:2647: all-start] Error 2
make[2]: Leaving directory '/home/finotti/src/sage-9.7/build/make'
real 26m21.018s
user 126m3.920s
sys 6m28.588s
***************************************************************
Error building Sage.
The following package(s) may have failed to build (not necessarily
during this run of 'make all-start'):
It is safe to delete any log files and build directories, but they
contain information that is helpful for debugging build problems.
WARNING: If you now run 'make' again, the build directory of the
same version of the package will, by default, be deleted. Set the
environment variable SAGE_KEEP_BUILT_SPKGS=yes to prevent this.
make[1]: *** [Makefile:40: all-start] Error 1
make[1]: Leaving directory '/home/finotti/src/sage-9.7'
make: *** [Makefile:13: all] Error 2
The install.log file is here: https://web.math.utk.edu/~finotti/tmp/install.log
Here is some info on the machine:
System:
Host: finottidell5060 Kernel: 6.1.0-3.slh.1-aptosid-amd64 arch: x86_64
bits: 64 compiler: gcc v: 12.2.0 Desktop: KDE Plasma v: 5.26.5
Distro: aptosid 2013-01 - kde-full - (201305050307) base: Debian
GNU/Linux bookworm/sid
Machine:
Type: Desktop System: Dell product: OptiPlex 5060 v: N/A
serial: <superuser required>
Mobo: Dell model: 0J8G6F v: A02 serial: <superuser required> UEFI: Dell
v: 1.20.0 date: 05/19/2022
Battery:
Device-1: hidpp_battery_0 model: Logitech Wireless Mouse MX Master 3
charge: 50% (should be ignored) status: full
CPU:
Info: 6-core model: Intel Core i7-8700 bits: 64 type: MT MCP
arch: Coffee Lake rev: A cache: L1: 384 KiB L2: 1.5 MiB L3: 12 MiB
Speed (MHz): avg: 1000 high: 3200 min/max: 800/4600 cores: 1: 800 2: 800
3: 800 4: 800 5: 801 6: 3200 7: 800 8: 800 9: 800 10: 800 11: 800 12: 800
bogomips: 76799
Flags: avx avx2 ht lm nx pae sse sse2 sse3 sse4_1 sse4_2 ssse3 vmx
Graphics:
Device-1: Intel CoffeeLake-S GT2 [UHD Graphics 630] vendor: Dell
driver: i915 v: kernel arch: Gen-9.5 bus-ID: 00:02.0
Device-2: Logitech Webcam C270 type: USB driver: snd-usb-audio,uvcvideo
bus-ID: 1-7.4.1:10
Display: x11 server: X.Org v: 1.21.1.6 driver: X: loaded: modesetting
unloaded: fbdev,vesa dri: iris gpu: i915 resolution: 1: 1920x1200~60Hz
2: 1080x1920~60Hz
API: OpenGL v: 4.6 Mesa 22.3.2 renderer: Mesa Intel UHD Graphics 630 (CFL
GT2) direct render: Yes
Network:
Device-1: Intel Ethernet I219-V vendor: Dell driver: e1000e v: kernel
port: N/A bus-ID: 00:1f.6
IF: eno1 state: up speed: 100 Mbps duplex: full mac: 8c:ec:4b:b1:7e:34
Drives:
Local Storage: total: 953.88 GiB used: 721.37 GiB (75.6%)
Info:
Processes: 417 Uptime: 3h 7m Memory: 46.75 GiB used: 8.53 GiB (18.3%)
Init: systemd target: graphical (5) Compilers: gcc: 12.2.0 Packages: 6177
Shell: Bash v: 5.2.15 inxi: 3.3.24
Any help would be greatly appreciated.
Here is the last messages before it stops:
[sagelib-9.7] error: Command "gcc -Wno-unused-result -Wsign-compare -DNDEBUG -g -fwrapv -O3 -Wall -Wno-unused -g -O2 -g -O2 -fPIC -Isage/cpython -I/usr/include/x86_64-linux-gnu/singular -I/usr/include/x86_64-linux-gnu/singular/singular -I/usr/include/singular -I/usr/include/singular/singular -I/home/finotti/src/sage-9.7/local/var/lib/sage/venv-python3.10.5/lib/python3.10/site-packages/cypari2 -Isage/libs/ntl -Isage/rings/finite_rings -I/home/finotti/src/sage-9.7/local/var/lib/sage/venv-python3.10.5/lib/python3.10/site-packages/cysignals -I/home/finotti/src/sage-9.7/src -I/home/finotti/src/sage-9.7/local/var/lib/sage/venv-python3.10.5/lib/python3.10/site-packages/numpy/core/include -I/home/finotti/src/sage-9.7/local/var/lib/sage/venv-python3.10.5/include/python3.10 -I/home/finotti/src/sage-9.7/local/var/lib/sage/venv-python3.10.5/include/python3.10 -c sage/rings/polynomial/multi_polynomial_libsingular.cpp -o build/temp.linux-x86_64-cpython-310/sage/rings/polynomial/multi_polynomial_libsingular.o -std=c++11 -fabi-version=6" failed with exit status 1
[sagelib-9.7] error: subprocess-exited-with-error
[sagelib-9.7]
[sagelib-9.7] × python setup.py develop did not run successfully.
[sagelib-9.7] │ exit code: 1
[sagelib-9.7] ╰─> See above for output.
[sagelib-9.7]
[sagelib-9.7] note: This error originates from a subprocess, and is likely not a problem with pip.
[sagelib-9.7] full command: /home/finotti/src/sage-9.7/local/var/lib/sage/venv-python3.10.5/bin/python3 -c '
[sagelib-9.7] exec(compile('"'"''"'"''"'"'
[sagelib-9.7] # This is <pip-setuptools-caller> -- a caller that pip uses to run setup.py
[sagelib-9.7] #
[sagelib-9.7] # - It imports setuptools before invoking setup.py, to enable projects that directly
[sagelib-9.7] # import from `distutils.core` to work with newer packaging standards.
[sagelib-9.7] # - It provides a clear error message when setuptools is not installed.
[sagelib-9.7] # - It sets `sys.argv[0]` to the underlying `setup.py`, when invoking `setup.py` so
[sagelib-9.7] # setuptools doesn'"'"'t think the script is `-c`. This avoids the following warning:
[sagelib-9.7] # manifest_maker: standard file '"'"'-c'"'"' not found".
[sagelib-9.7] # - It generates a shim setup.py, for handling setup.cfg-only projects.
[sagelib-9.7] import os, sys, tokenize
[sagelib-9.7]
[sagelib-9.7] try:
[sagelib-9.7] import setuptools
[sagelib-9.7] except ImportError as error:
[sagelib-9.7] print(
[sagelib-9.7] "ERROR: Can not execute `setup.py` since setuptools is not available in "
[sagelib-9.7] "the build environment.",
[sagelib-9.7] file=sys.stderr,
[sagelib-9.7] )
[sagelib-9.7] sys.exit(1)
[sagelib-9.7]
[sagelib-9.7] __file__ = %r
[sagelib-9.7] sys.argv[0] = __file__
[sagelib-9.7]
[sagelib-9.7] if os.path.exists(__file__):
[sagelib-9.7] filename = __file__
[sagelib-9.7] with tokenize.open(__file__) as f:
[sagelib-9.7] setup_py_code = f.read()
[sagelib-9.7] else:
[sagelib-9.7] filename = "<auto-generated setuptools caller>"
[sagelib-9.7] setup_py_code = "from setuptools import setup; setup()"
[sagelib-9.7]
[sagelib-9.7] exec(compile(setup_py_code, filename, "exec"))
[sagelib-9.7] '"'"''"'"''"'"' % ('"'"'/home/finotti/src/sage-9.7/src/setup.py'"'"',), "<pip-setuptools-caller>", "exec"))' --no-user-cfg develop --no-deps
[sagelib-9.7] cwd: /home/finotti/src/sage-9.7/src/
[sagelib-9.7] error: subprocess-exited-with-error
[sagelib-9.7]
[sagelib-9.7] × python setup.py develop did not run successfully.
[sagelib-9.7] │ exit code: 1
[sagelib-9.7] ╰─> See above for output.
[sagelib-9.7]
[sagelib-9.7] note: This error originates from a subprocess, and is likely not a problem with pip.
[sagelib-9.7]
[sagelib-9.7] real 12m29.646s
[sagelib-9.7] user 46m59.670s
[sagelib-9.7] sys 1m23.295s
make[4]: *** [Makefile:3115: sagelib-SAGE_VENV-no-deps] Error 1
make[3]: *** [Makefile:3115: /home/finotti/src/sage-9.7/local/var/lib/sage/venv-python3.10.5/var/lib/sage/installed/sagelib-9.7] Error 2
make[2]: *** [Makefile:2647: all-start] Error 2
make[2]: Leaving directory '/home/finotti/src/sage-9.7/build/make'
real 26m21.018s
user 126m3.920s
sys 6m28.588s
***************************************************************
Error building Sage.
The following package(s) may have failed to build (not necessarily
during this run of 'make all-start'):
It is safe to delete any log files and build directories, but they
contain information that is helpful for debugging build problems.
WARNING: If you now run 'make' again, the build directory of the
same version of the package will, by default, be deleted. Set the
environment variable SAGE_KEEP_BUILT_SPKGS=yes to prevent this.
make[1]: *** [Makefile:40: all-start] Error 1
make[1]: Leaving directory '/home/finotti/src/sage-9.7'
make: *** [Makefile:13: all] Error 2
The install.log file is here: https://web.math.utk.edu/~finotti/tmp/install.log
Here is some info on the machine:
System:
Host: finottidell5060 Kernel: 6.1.0-3.slh.1-aptosid-amd64 arch: x86_64
bits: 64 compiler: gcc v: 12.2.0 Desktop: KDE Plasma v: 5.26.5
Distro: aptosid 2013-01 - kde-full - (201305050307) base: Debian
GNU/Linux bookworm/sid
Machine:
Type: Desktop System: Dell product: OptiPlex 5060 v: N/A
serial: <superuser required>
Mobo: Dell model: 0J8G6F v: A02 serial: <superuser required> UEFI: Dell
v: 1.20.0 date: 05/19/2022
Battery:
Device-1: hidpp_battery_0 model: Logitech Wireless Mouse MX Master 3
charge: 50% (should be ignored) status: full
CPU:
Info: 6-core model: Intel Core i7-8700 bits: 64 type: MT MCP
arch: Coffee Lake rev: A cache: L1: 384 KiB L2: 1.5 MiB L3: 12 MiB
Speed (MHz): avg: 1000 high: 3200 min/max: 800/4600 cores: 1: 800 2: 800
3: 800 4: 800 5: 801 6: 3200 7: 800 8: 800 9: 800 10: 800 11: 800 12: 800
bogomips: 76799
Flags: avx avx2 ht lm nx pae sse sse2 sse3 sse4_1 sse4_2 ssse3 vmx
Graphics:
Device-1: Intel CoffeeLake-S GT2 [UHD Graphics 630] vendor: Dell
driver: i915 v: kernel arch: Gen-9.5 bus-ID: 00:02.0
Device-2: Logitech Webcam C270 type: USB driver: snd-usb-audio,uvcvideo
bus-ID: 1-7.4.1:10
Display: x11 server: X.Org v: 1.21.1.6 driver: X: loaded: modesetting
unloaded: fbdev,vesa dri: iris gpu: i915 resolution: 1: 1920x1200~60Hz
2: 1080x1920~60Hz
API: OpenGL v: 4.6 Mesa 22.3.2 renderer: Mesa Intel UHD Graphics 630 (CFL
GT2) direct render: Yes
Network:
Device-1: Intel Ethernet I219-V vendor: Dell driver: e1000e v: kernel
port: N/A bus-ID: 00:1f.6
IF: eno1 state: up speed: 100 Mbps duplex: full mac: 8c:ec:4b:b1:7e:34
Drives:
Local Storage: total: 953.88 GiB used: 721.37 GiB (75.6%)
Info:
Processes: 417 Uptime: 3h 7m Memory: 46.75 GiB used: 8.53 GiB (18.3%)
Init: systemd target: graphical (5) Compilers: gcc: 12.2.0 Packages: 6177
Shell: Bash v: 5.2.15 inxi: 3.3.24
Luis Finotti
Jan 10, 2023, 8:23:39 AM1/10/23
to sage-support
Cannot build sage-9.8.beta6 either...
Luis Finotti
Jan 13, 2023, 9:54:37 AM1/13/23
to sage-support
After some more updated came to Sid, I tried again. Still does not compile, but breaks much sooner. Here is the new log: https://web.math.utk.edu/~finotti/tmp/install-2.log
Sid's own packaged version of Sage also cannot be installed at the moment:
# apt install sagemath
Reading package lists... Done
Building dependency tree... Done
Reading state information... Done
Some packages could not be installed. This may mean that you have
requested an impossible situation or if you are using the unstable
distribution that some required packages have not yet been created
or been moved out of Incoming.
The following information may help to resolve the situation:
The following packages have unmet dependencies:
python3-sage : Depends: python3 (< 3.11) but 3.11.1-1 is to be installed
Depends: libgap7 (>= 4.11.0-1) but it is not installable
E: Unable to correct problems, you have held broken packages.
Reading package lists... Done
Building dependency tree... Done
Reading state information... Done
Some packages could not be installed. This may mean that you have
requested an impossible situation or if you are using the unstable
distribution that some required packages have not yet been created
or been moved out of Incoming.
The following information may help to resolve the situation:
The following packages have unmet dependencies:
python3-sage : Depends: python3 (< 3.11) but 3.11.1-1 is to be installed
Depends: libgap7 (>= 4.11.0-1) but it is not installable
E: Unable to correct problems, you have held broken packages.
John H Palmieri
Jan 13, 2023, 12:33:16 PM1/13/23
to sage-support
It may be (as pointed out on a similar thread in the group sage-devel) that some of the Debian packages have versions that are too new to be used with Sage. You could tell Sage to build its own Python, its own Gap, perhaps its own Singular (if the system one is causing problems):
./configure --with-system-python3=no --with-system-gap=no --with-system-singular=no
Luis Finotti
Jan 13, 2023, 2:14:35 PM1/13/23
to sage-support
On Friday, January 13, 2023 at 12:33:16 PM UTC-5 John H Palmieri wrote:
It may be (as pointed out on a similar thread in the group sage-devel) that some of the Debian packages have versions that are too new to be used with Sage. You could tell Sage to build its own Python, its own Gap, perhaps its own Singular (if the system one is causing problems):
./configure --with-system-python3=no --with-system-gap=no --with-system-singular=no
Yes, that worked! Thanks!
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