Re: [sage-devel] Re: System upgrades breaking sage frequently
On Tuesday, July 26, 2022 at 5:34:07 PM UTC-7 Nils Bruin wrote: > Things like not having to issue "sage -b" after making a little edit will > be nice to have eventually, > This feature (editable installs) is actually orthogonal to the decision on the conda install method. You can activate it using "configure --enable-editable", and it is slated to become default in one of next betas (see https://trac.sagemath.org/ticket/32406). -- You received this message because you are subscribed to the Google Groups "sage-devel" group. To unsubscribe from this group and stop receiving emails from it, send an email to sage-devel+unsubscr...@googlegroups.com. To view this discussion on the web visit https://groups.google.com/d/msgid/sage-devel/ba5d8fd2-67a7-4820-aa00-4ca30d6c905en%40googlegroups.com.
Re: [sage-devel] Re: System upgrades breaking sage frequently
On Tuesday, 26 July 2022 at 17:27:11 UTC-7 Matthias Koeppe wrote: > Sort of. This is another way to build Sage with conda. It is described in > the 2nd of the 3 sections on the same page, > https://doc.sagemath.org/html/en/installation/conda.html#using-conda-to-provide-system-packages-for-the-sage-distribution, > > "Using conda to provide system packages for the Sage distribution". This > works in the same way that it does on top of Fedora, or on top of any other > package distribution. You can control what packages are taken from the > system and what packages are built by the Sage distribution. And it has the > same restrictions as what the Sage distribution does on top of Fedora etc.: > Only packages for which we have "spkg-configure.m4" scripts can be taken > from the system -- and no Python packages can be taken from the system. Ah, so that sounds like it's a lot closer to how most people have the build-environment organized. Things like not having to issue "sage -b" after making a little edit will be nice to have eventually, but it looks like that stuff is still too much in flux to be reliable at the moment. -- You received this message because you are subscribed to the Google Groups "sage-devel" group. To unsubscribe from this group and stop receiving emails from it, send an email to sage-devel+unsubscr...@googlegroups.com. To view this discussion on the web visit https://groups.google.com/d/msgid/sage-devel/5a8f1de9-a08b-437c-94ba-e4c60d3ad7f3n%40googlegroups.com.
Re: [sage-devel] Re: System upgrades breaking sage frequently
On Tuesday, July 26, 2022 at 5:12:47 PM UTC-7 Nils Bruin wrote: > On Tuesday, 26 July 2022 at 15:58:18 UTC-7 Matthias Koeppe wrote: > >> >> Whether the method described in section >> https://doc.sagemath.org/html/en/installation/conda.html#using-conda-to-provide-all-dependencies-for-the-sage-library-experimental >> >> works always depends on the conda package maintainers providing packages >> that are up to date with respect to our requirements. It's not directly >> under control of our project. >> >> Hm ... so I guess "configure" with these > "--with-system-*=true/false/force" can then determine per-prerequisite > whether to try to get it from the system or build it by itself? > > And that the advantage of conda is that it can distribute binaries, that > are then hopefully built with approrpriate flags for your particular system? > The binaries are not any more tailored to your system than the binaries from the Fedora distribution are. > And that the hope is that conda-provided prereqs are a better match than > what the OS may provide and/or are more stable (mainly because one can > afford to not update a conda env regularly). > ... and you can use conda on machines where you are not root. > Is it possible for prerequisites that conda fails at, such as primesieve > and primecount, to flick the "with-system" switches the other way, so that > sage builds that by itself? Is there a way to tell the system to get from > conda what it can and otherwise build it by itself? It seems like that's > what configure does normally (and with a WAY shorter configure command!), > so would it be able to do that within conda? > Sort of. This is another way to build Sage with conda. It is described in the 2nd of the 3 sections on the same page, https://doc.sagemath.org/html/en/installation/conda.html#using-conda-to-provide-system-packages-for-the-sage-distribution, "Using conda to provide system packages for the Sage distribution". This works in the same way that it does on top of Fedora, or on top of any other package distribution. You can control what packages are taken from the system and what packages are built by the Sage distribution. And it has the same restrictions as what the Sage distribution does on top of Fedora etc.: Only packages for which we have "spkg-configure.m4" scripts can be taken from the system -- and no Python packages can be taken from the system. -- You received this message because you are subscribed to the Google Groups "sage-devel" group. To unsubscribe from this group and stop receiving emails from it, send an email to sage-devel+unsubscr...@googlegroups.com. To view this discussion on the web visit https://groups.google.com/d/msgid/sage-devel/567524a6-74a5-41d6-8383-5f45f300d7dbn%40googlegroups.com.
Re: [sage-devel] Re: System upgrades breaking sage frequently
On Tuesday, 26 July 2022 at 15:58:18 UTC-7 Matthias Koeppe wrote: > > Whether the method described in section > https://doc.sagemath.org/html/en/installation/conda.html#using-conda-to-provide-all-dependencies-for-the-sage-library-experimental > > works always depends on the conda package maintainers providing packages > that are up to date with respect to our requirements. It's not directly > under control of our project. > > Hm ... so I guess "configure" with these "--with-system-*=true/false/force" can then determine per-prerequisite whether to try to get it from the system or build it by itself? And that the advantage of conda is that it can distribute binaries, that are then hopefully built with approrpriate flags for your particular system? And that the hope is that conda-provided prereqs are a better match than what the OS may provide and/or are more stable (mainly because one can afford to not update a conda env regularly). Is it possible for prerequisites that conda fails at, such as primesieve and primecount, to flick the "with-system" switches the other way, so that sage builds that by itself? Is there a way to tell the system to get from conda what it can and otherwise build it by itself? It seems like that's what configure does normally (and with a WAY shorter configure command!), so would it be able to do that within conda? It would seem that after: $ conda env update --file environment.yml -n sage-build (which is I think one of the commands where using mamba instead saves gobs of time!!!) conda has already exerted its best efforts to satisfy the prereqs, so anything that now fails should be built by sage itself ... -- You received this message because you are subscribed to the Google Groups "sage-devel" group. To unsubscribe from this group and stop receiving emails from it, send an email to sage-devel+unsubscr...@googlegroups.com. To view this discussion on the web visit https://groups.google.com/d/msgid/sage-devel/106b3d56-51e7-44ff-9761-8e1c40a1f88an%40googlegroups.com.
Re: [sage-devel] Re: System upgrades breaking sage frequently
On Tuesday, July 26, 2022 at 2:08:32 PM UTC-7 Nils Bruin wrote: > > configure: error: > > Given --with-system-primesieve=force, but no system package could be > used. > That's an error. Please install the indicated package to continue. > (To override this error, use ./configure --without-system-primesieve) > Given --with-system-primecount=force, but no system package could be > used. > That's an error. Please install the indicated package to continue. > (To override this error, use ./configure --without-system-primecount) > > The documentation section about this is marked "experimental", and I > think this shows it's indeed not ready for prime time yet. > Whether the method described in section https://doc.sagemath.org/html/en/installation/conda.html#using-conda-to-provide-all-dependencies-for-the-sage-library-experimental works always depends on the conda package maintainers providing packages that are up to date with respect to our requirements. It's not directly under control of our project. -- You received this message because you are subscribed to the Google Groups "sage-devel" group. To unsubscribe from this group and stop receiving emails from it, send an email to sage-devel+unsubscr...@googlegroups.com. To view this discussion on the web visit https://groups.google.com/d/msgid/sage-devel/f3d747b2-e794-487e-b7e9-4524c917ccaan%40googlegroups.com.
[sage-devel] Re: sage error 9.6 I got this errors and I don't know how to fix them
[image: Screenshot from 2022-07-26 15-54-39.png] El lunes, 25 de julio de 2022 a las 3:17:35 UTC-5, Rey David Gutiérrez Torres escribió: > [image: Screenshot from 2022-07-24 23-23-15.png] > -- You received this message because you are subscribed to the Google Groups "sage-devel" group. To unsubscribe from this group and stop receiving emails from it, send an email to sage-devel+unsubscr...@googlegroups.com. To view this discussion on the web visit https://groups.google.com/d/msgid/sage-devel/f0d62754-fafa-4916-a91f-27d433b01faen%40googlegroups.com.
Re: [sage-devel] Re: System upgrades breaking sage frequently
Yup, rerunning "mamba env update -n sage-build -f src/environment.yml" installed eclib and now "./configure ..." produces one less error: configure: error: Given --with-system-primesieve=force, but no system package could be used. That's an error. Please install the indicated package to continue. (To override this error, use ./configure --without-system-primesieve) Given --with-system-primecount=force, but no system package could be used. That's an error. Please install the indicated package to continue. (To override this error, use ./configure --without-system-primecount) The documentation section about this is marked "experimental", and I think this shows it's indeed not ready for prime time yet. It sounds like https://trac.sagemath.org/ticket/33345 would also solve the problem of depending on prone-to-change system libraries. Is that perhaps the route to go for development nowadays? Then there's no conda/mamba to worry about at all. On Tuesday, 26 July 2022 at 06:12:52 UTC-7 Samuel Lelievre wrote: > 2022-07-26 07:13:30 UTC, Dima Pasechnik: > > this says that conda is behind Sage in regard of versions of eclib > and primesieve/count > > - eclib upgrade in Conda now done: > https://github.com/conda-forge/eclib-feedstock/pull/36 > - primesieve and primecount seem up to date > -- You received this message because you are subscribed to the Google Groups "sage-devel" group. To unsubscribe from this group and stop receiving emails from it, send an email to sage-devel+unsubscr...@googlegroups.com. To view this discussion on the web visit https://groups.google.com/d/msgid/sage-devel/7e754a78-42ff-4f88-bea4-31e851bfcbebn%40googlegroups.com.
Re: [sage-devel] Re: System upgrades breaking sage frequently
On Tuesday, July 26, 2022 at 6:47:47 AM UTC-7 wst...@gmail.com wrote: > For CoCalc, [...] we run a 1-2 > pages long "./configure ..." command before I even do "make". At the > top it starts with > > --with-system-python3=no \ > --with-system-r=no \ > --with-system-primecount=no \ > --with-system-primesieve=no \ > --with-system-qhull=no \ > --with-system-cmake=no \ > [...] > > Could there be a single option to the Sage build system such as: > "--without-system" that disables all system libraries That's https://trac.sagemath.org/ticket/33345 -- You received this message because you are subscribed to the Google Groups "sage-devel" group. To unsubscribe from this group and stop receiving emails from it, send an email to sage-devel+unsubscr...@googlegroups.com. To view this discussion on the web visit https://groups.google.com/d/msgid/sage-devel/96d13526-3cce-426b-9103-1e44d312ed21n%40googlegroups.com.
Re: [sage-devel] Re: Error building Sage 9.6 due to openssl
Ah okay, that's good to know. I probably won't need that feature in the near future anyway. But thank you; I ran `make build` and finally the process terminated without a fatal error. I also ran it and it works fine now. dim...@gmail.com schrieb am Dienstag, 26. Juli 2022 um 18:10:20 UTC+9: > documentation building is currently broken on Cygwin. > > instead of running 'make', run 'make build'. > > Anyhow, you probably have mostly functional Sage installation now. > > > > On Tue, 26 Jul 2022, 10:18 Max Kölbl, wrote: > >> Thank you very much for your help! >> >> >Install the relevant cygwin packages: >> >``` >> >$ apt-cyg install bzip2 libbz2-devel liblzma-devel libffi-devel xz >> >``` >> >Clean up the corresponding Sage packages: >> >``` >> >$ make bzip2-clean liblzma-clean libffi-clean xz-clean >> > >> >Then configure again: >> >``` >> >$ make configure >> >$ ./configure >> >``` >> > >> >Follow any recommendations at end of configure output. >> > >> >Finally decide number of parallel jobs >> >``` >> >$ export MAKE='make -j8' >> >``` >> >and run make again: >> >``` >> >$ make -s V=0 >> >> That helped. Sage is now *almost* completely installed. >> However, now a different problem appeared. >> While installing the docs, the following error occured: >> >> >[reference] /home/Ray/sage/sage/src/doc/en/reference/index.rst:34: >> WARNING: unknown document: categories/index >> >[reference] /home/Ray/sage/sage/src/doc/en/reference/index.rst:76: >> WARNING: unknown document: groups/index >> >[reference] /home/Ray/sage/sage/src/doc/en/reference/index.rst:79: >> WARNING: unknown document: algebras/index >> >[reference] /home/Ray/sage/sage/src/doc/en/reference/index.rst:84: >> WARNING: unknown document: combinat/index >> >[reference] /home/Ray/sage/sage/src/doc/en/reference/index.rst:85: >> WARNING: unknown document: graphs/index >> >[reference] /home/Ray/sage/sage/src/doc/en/reference/index.rst:89: >> WARNING: unknown document: coding/index >> >[reference] /home/Ray/sage/sage/src/doc/en/reference/index.rst:105: >> WARNING: unknown document: knots/index >> >[reference] /home/Ray/sage/sage/src/doc/en/reference/index.rst:157: >> WARNING: unknown document: libs/index >> >[reference] The inventory files are in >> ../../local/share/doc/sage/inventory/en/reference. >> >Error building the documentation. >> >Traceback (most recent call last): >> > File "/usr/lib/python3.9/runpy.py", line 197, in _run_module_as_main >> >return _run_code(code, main_globals, None, >> > File "/usr/lib/python3.9/runpy.py", line 87, in _run_code >> >exec(code, run_globals) >> > File >> "/home/Ray/sage/sage/local/var/lib/sage/venv-python3.9/lib/python3.9/site-packages/sage_docbuild/__main__.py", >> >> line 500, in >> >sys.exit(main()) >> > File >> "/home/Ray/sage/sage/local/var/lib/sage/venv-python3.9/lib/python3.9/site-packages/sage_docbuild/__main__.py", >> >> line 497, in main >> >builder() >> > File >> "/home/Ray/sage/sage/local/var/lib/sage/venv-python3.9/lib/python3.9/site-packages/sage_docbuild/builders.py", >> >> line 167, in f >> >runsphinx() >> > File >> "/home/Ray/sage/sage/local/var/lib/sage/venv-python3.9/lib/python3.9/site-packages/sage_docbuild/sphinxbuild.py", >> >> line 327, in runsphinx >> >sys.stderr.raise_errors() >> > File >> "/home/Ray/sage/sage/local/var/lib/sage/venv-python3.9/lib/python3.9/site-packages/sage_docbuild/sphinxbuild.py", >> >> line 263, in raise_errors >> >raise OSError(self._error) >> >OSError: /home/Ray/sage/sage/src/doc/en/reference/index.rst:34: WARNING: >> unknown document: categories/index >> > >> >Note: incremental documentation builds sometimes cause spurious >> >error messages. To be certain that these are real errors, run >> >"make doc-clean doc-uninstall" first and try again. >> >make[6]: *** [Makefile:27: doc-inventory--reference_top] Error 1 >> >make[5]: *** [Makefile:45: doc-inventory-reference] Error 2 >> >> I tried >> ``` >> $make doc-clean doc-uninstall >> $make configure >> $./configure >> $make -s V=0 >> ``` >> and it raised the same error (log file is attached). >> It appears that some of the docs are not building completely; this is a >> part of the log: >> >[knots] building [inventory]: targets for 4 source files that are >> out of date >> >[knots] updating environment: [new config] 4 added, 0 changed, 0 >> removed >> >[lfunction] building [inventory]: targets for 5 source files that are >> out of date >> >[lfunction] updating environment: [new config] 5 added, 0 changed, 0 >> removed >> >[lfunction] The inventory files are in >> ../../local/share/doc/sage/inventory/en/reference/lfunctions. >> >Build finished. The built documents can be found in >> /home/Ray/sage/sage/local/share/doc/sage/inventory/en/reference/lfunctions >> And later I get this: >> >[reference] /home/Ray/sage/sage/src/doc/en/reference/index.rst:105: >> WARNING: unknown document: knots/index >> >> What is the best thing to do
Re: [sage-devel] Re: System upgrades breaking sage frequently
For CoCalc, where we have a bunch of different specific versions of Sage pre-installed that all stay stable over *years*, we run a 1-2 pages long "./configure ..." command before I even do "make". At the top it starts with --with-system-python3=no \ --with-system-r=no \ --with-system-primecount=no \ --with-system-primesieve=no \ --with-system-qhull=no \ --with-system-cmake=no \ ... … so,that's why R, Python interpreter, and other stuff is independent. … We should definitely check if there is more I could make independent. I mean, technically it's not independent, because some underlying libs are shared, but there are certainly less surprises and the dependency graph is not a wide blinking christmas tree. What we are not doing is sharing Sage across linux editions. i.e. 20.04 will have a couple of Sage installs and with 22.04 there will be a new 9.6 one. But that's not the issue in the thread. Could there be a single option to the Sage build system such as: "--without-system" that disables all system libraries, and hence behaves exactly like Sage used to? Is there already such an option that I don't know about? William On Mon, Jul 25, 2022 at 12:44 PM Nils Bruin wrote: > > On Thursday, 21 July 2022 at 11:52:42 UTC-7 Nils Bruin wrote: >> >> On Thursday, 21 July 2022 at 11:31:35 UTC-7 Matthias Koeppe wrote: >>> >>> >>> You really just need to stop your distribution from automatically >>> uninstalling the old shared library packages when you do upgrades. Both the >>> old version (needed for your from-source installation of Sage) and the new >>> version (needed as dependencies of upgraded system packages) can coexist in >>> your system. >>> >> >> Right .. but that would require telling the system which libraries need to >> be preserved ... I guess one could collect the dependencies by a liberal ldd >> application, but then one would need to query the package manager which >> packages provide the requisite library files and then somehow register those >> packages *are* dependencies ... I guess that could be done by building a >> placeholder package (rpm or deb) that declares all the specific >> dependencies. And to "declare" these, one could install that package. Upon a >> reconfigure+rebuild, one could uninstall the old placeholder, recompute the >> new dependencies, and install a new placeholder ... > > > Ouch ... and it looks like this wouldn't even work: if I try > > dnf whatprovides /usr/lib64/libflint.so.17 > > I get: > > flint-2.9.0-1.fc36.x86_64 > > and similarly > > dnf whatprovides /usr.lib64/libflint.so.16 > flint-2.8.4-2.fc36.x86_64 > > Hence, if a compiled-from-source sagemath were to declare its dependencies to > the package manager it would have to do so by depending on a *specific > version* of flint, and hence "updating" flint should lead to a dependency > conflict. As long as fedora doesn't allow two different version of flint to > be installed at the same time (and the fact that flint-2.9 "upgrades" > flint-2.8 suggests that it won't), we'd need a version lock: just keeping an > unmanaged so-file hang around in space that's supposed to be managed by a > package manager would lead to a rather messy system state. > > So, based on that, I think build-from-source using these kinds of system > resources should actually *not* be a recommended install method: > build-from-source should have its less stable prerequisites satisfied by some > separate environment -- possibly/likely conda. Resources/libraries such as > libflint are clearly *only* managed and provided by the OS in a way that is > appropriate for other OS-managed/packaged software. Turns out there's still a > niche for sage-the-distribution; possibly replaced by > sage-in-conda-the-distribution. Can we get sage-on-conda modified so that it > works nicely with git-trac, so that a sage-conda container can be used for > development? I would be very interested in a guide to that. > > > -- > You received this message because you are subscribed to the Google Groups > "sage-devel" group. > To unsubscribe from this group and stop receiving emails from it, send an > email to sage-devel+unsubscr...@googlegroups.com. > To view this discussion on the web visit > https://groups.google.com/d/msgid/sage-devel/6aea8da4-bd04-4eda-914a-c04a6fcbb4e6n%40googlegroups.com. -- William (http://wstein.org) -- You received this message because you are subscribed to the Google Groups "sage-devel" group. To unsubscribe from this group and stop receiving emails from it, send an email to sage-devel+unsubscr...@googlegroups.com. To view this discussion on the web visit https://groups.google.com/d/msgid/sage-devel/CACLE5GDv4ntTNay8j9UgOPrAyn_PpExNy4FPRyHt_bKc1RFFcA%40mail.gmail.com.
Re: [sage-devel] Re: System upgrades breaking sage frequently
2022-07-26 07:13:30 UTC, Dima Pasechnik: this says that conda is behind Sage in regard of versions of eclib and primesieve/count - eclib upgrade in Conda now done: https://github.com/conda-forge/eclib-feedstock/pull/36 - primesieve and primecount seem up to date -- You received this message because you are subscribed to the Google Groups "sage-devel" group. To unsubscribe from this group and stop receiving emails from it, send an email to sage-devel+unsubscr...@googlegroups.com. To view this discussion on the web visit https://groups.google.com/d/msgid/sage-devel/d6691e06-ba46-4c29-9cd1-870a01ab56ccn%40googlegroups.com.
[sage-devel] Display of scale multiplier in scientific notation (the e notation for powers of ten) is missing for plots starting with 0
Dear all, "2D plotting" doc says, "Another thing to be aware of with axis labeling is that when the labels have quite different orders of magnitude or are very large, scientific notation (the e notation for powers of ten) is used." But display of this multiplier power for the scaled y-axis is missing if the plot starts with x=0 or at most will be missing till the x-axis detaches from the origin. Following examples illustrates it, *sage:* plot(x^2,(x,0,5000)) # missing display of 1e7 above y-axis *sage:* plot(x^2,(x,50,5000)) # missing display of 1e7 above y-axis *sage:* plot(x^2,(x,100,5000)) # display of 1e7 above y-axis is visible On the other side matplotlib natively always displays the scale multiplier (if any) whenever numbers are large. For example: *sage:* import matplotlib.pyplot as plt *sage:* import numpy as np *sage:* z = np.linspace(0, 5000, 100) *sage:* plt.plot(z, z**2) *sage:* plt.show() My other plots involved electric field calculations which had magnitudes around 1/epsilon_0 which is 1/(8.85E-12) =~ 10^11. For those plots starting with x=0 the display of multiplier used for y-axis were missing. With regards Niranjana -- You received this message because you are subscribed to the Google Groups "sage-devel" group. To unsubscribe from this group and stop receiving emails from it, send an email to sage-devel+unsubscr...@googlegroups.com. To view this discussion on the web visit https://groups.google.com/d/msgid/sage-devel/81e1349d-73f1-493b-9109-54ccf669fb9an%40googlegroups.com.
Re: [sage-devel] Re: Error building Sage 9.6 due to openssl
documentation building is currently broken on Cygwin. instead of running 'make', run 'make build'. Anyhow, you probably have mostly functional Sage installation now. On Tue, 26 Jul 2022, 10:18 Max Kölbl, wrote: > Thank you very much for your help! > > >Install the relevant cygwin packages: > >``` > >$ apt-cyg install bzip2 libbz2-devel liblzma-devel libffi-devel xz > >``` > >Clean up the corresponding Sage packages: > >``` > >$ make bzip2-clean liblzma-clean libffi-clean xz-clean > > > >Then configure again: > >``` > >$ make configure > >$ ./configure > >``` > > > >Follow any recommendations at end of configure output. > > > >Finally decide number of parallel jobs > >``` > >$ export MAKE='make -j8' > >``` > >and run make again: > >``` > >$ make -s V=0 > > That helped. Sage is now *almost* completely installed. > However, now a different problem appeared. > While installing the docs, the following error occured: > > >[reference] /home/Ray/sage/sage/src/doc/en/reference/index.rst:34: > WARNING: unknown document: categories/index > >[reference] /home/Ray/sage/sage/src/doc/en/reference/index.rst:76: > WARNING: unknown document: groups/index > >[reference] /home/Ray/sage/sage/src/doc/en/reference/index.rst:79: > WARNING: unknown document: algebras/index > >[reference] /home/Ray/sage/sage/src/doc/en/reference/index.rst:84: > WARNING: unknown document: combinat/index > >[reference] /home/Ray/sage/sage/src/doc/en/reference/index.rst:85: > WARNING: unknown document: graphs/index > >[reference] /home/Ray/sage/sage/src/doc/en/reference/index.rst:89: > WARNING: unknown document: coding/index > >[reference] /home/Ray/sage/sage/src/doc/en/reference/index.rst:105: > WARNING: unknown document: knots/index > >[reference] /home/Ray/sage/sage/src/doc/en/reference/index.rst:157: > WARNING: unknown document: libs/index > >[reference] The inventory files are in > ../../local/share/doc/sage/inventory/en/reference. > >Error building the documentation. > >Traceback (most recent call last): > > File "/usr/lib/python3.9/runpy.py", line 197, in _run_module_as_main > >return _run_code(code, main_globals, None, > > File "/usr/lib/python3.9/runpy.py", line 87, in _run_code > >exec(code, run_globals) > > File > "/home/Ray/sage/sage/local/var/lib/sage/venv-python3.9/lib/python3.9/site-packages/sage_docbuild/__main__.py", > line 500, in > >sys.exit(main()) > > File > "/home/Ray/sage/sage/local/var/lib/sage/venv-python3.9/lib/python3.9/site-packages/sage_docbuild/__main__.py", > line 497, in main > >builder() > > File > "/home/Ray/sage/sage/local/var/lib/sage/venv-python3.9/lib/python3.9/site-packages/sage_docbuild/builders.py", > line 167, in f > >runsphinx() > > File > "/home/Ray/sage/sage/local/var/lib/sage/venv-python3.9/lib/python3.9/site-packages/sage_docbuild/sphinxbuild.py", > line 327, in runsphinx > >sys.stderr.raise_errors() > > File > "/home/Ray/sage/sage/local/var/lib/sage/venv-python3.9/lib/python3.9/site-packages/sage_docbuild/sphinxbuild.py", > line 263, in raise_errors > >raise OSError(self._error) > >OSError: /home/Ray/sage/sage/src/doc/en/reference/index.rst:34: WARNING: > unknown document: categories/index > > > >Note: incremental documentation builds sometimes cause spurious > >error messages. To be certain that these are real errors, run > >"make doc-clean doc-uninstall" first and try again. > >make[6]: *** [Makefile:27: doc-inventory--reference_top] Error 1 > >make[5]: *** [Makefile:45: doc-inventory-reference] Error 2 > > I tried > ``` > $make doc-clean doc-uninstall > $make configure > $./configure > $make -s V=0 > ``` > and it raised the same error (log file is attached). > It appears that some of the docs are not building completely; this is a > part of the log: > >[knots] building [inventory]: targets for 4 source files that are out > of date > >[knots] updating environment: [new config] 4 added, 0 changed, 0 > removed > >[lfunction] building [inventory]: targets for 5 source files that are out > of date > >[lfunction] updating environment: [new config] 5 added, 0 changed, 0 > removed > >[lfunction] The inventory files are in > ../../local/share/doc/sage/inventory/en/reference/lfunctions. > >Build finished. The built documents can be found in > /home/Ray/sage/sage/local/share/doc/sage/inventory/en/reference/lfunctions > And later I get this: > >[reference] /home/Ray/sage/sage/src/doc/en/reference/index.rst:105: > WARNING: unknown document: knots/index > > What is the best thing to do there? > It's the same packages that cause the trouble in both runs. > > Thank you very much in advance! > > Max > > Samuel Lelievre schrieb am Montag, 25. Juli 2022 um 09:17:47 UTC+9: > >> Install the relevant cygwin packages: >> ``` >> $ apt-cyg install bzip2 libbz2-devel liblzma-devel libffi-devel xz >> ``` >> Clean up the corresponding Sage packages: >> ``` >> $ make bzip2-clean liblzma-clean libffi-clean xz-clean >> >> Then configure again: >> ``` >> $ make
Re: [sage-devel] Re: Error building Sage 9.6 due to openssl
Thank you very much for your help! >Install the relevant cygwin packages: >``` >$ apt-cyg install bzip2 libbz2-devel liblzma-devel libffi-devel xz >``` >Clean up the corresponding Sage packages: >``` >$ make bzip2-clean liblzma-clean libffi-clean xz-clean > >Then configure again: >``` >$ make configure >$ ./configure >``` > >Follow any recommendations at end of configure output. > >Finally decide number of parallel jobs >``` >$ export MAKE='make -j8' >``` >and run make again: >``` >$ make -s V=0 That helped. Sage is now *almost* completely installed. However, now a different problem appeared. While installing the docs, the following error occured: >[reference] /home/Ray/sage/sage/src/doc/en/reference/index.rst:34: WARNING: unknown document: categories/index >[reference] /home/Ray/sage/sage/src/doc/en/reference/index.rst:76: WARNING: unknown document: groups/index >[reference] /home/Ray/sage/sage/src/doc/en/reference/index.rst:79: WARNING: unknown document: algebras/index >[reference] /home/Ray/sage/sage/src/doc/en/reference/index.rst:84: WARNING: unknown document: combinat/index >[reference] /home/Ray/sage/sage/src/doc/en/reference/index.rst:85: WARNING: unknown document: graphs/index >[reference] /home/Ray/sage/sage/src/doc/en/reference/index.rst:89: WARNING: unknown document: coding/index >[reference] /home/Ray/sage/sage/src/doc/en/reference/index.rst:105: WARNING: unknown document: knots/index >[reference] /home/Ray/sage/sage/src/doc/en/reference/index.rst:157: WARNING: unknown document: libs/index >[reference] The inventory files are in ../../local/share/doc/sage/inventory/en/reference. >Error building the documentation. >Traceback (most recent call last): > File "/usr/lib/python3.9/runpy.py", line 197, in _run_module_as_main >return _run_code(code, main_globals, None, > File "/usr/lib/python3.9/runpy.py", line 87, in _run_code >exec(code, run_globals) > File "/home/Ray/sage/sage/local/var/lib/sage/venv-python3.9/lib/python3.9/site-packages/sage_docbuild/__main__.py", line 500, in >sys.exit(main()) > File "/home/Ray/sage/sage/local/var/lib/sage/venv-python3.9/lib/python3.9/site-packages/sage_docbuild/__main__.py", line 497, in main >builder() > File "/home/Ray/sage/sage/local/var/lib/sage/venv-python3.9/lib/python3.9/site-packages/sage_docbuild/builders.py", line 167, in f >runsphinx() > File "/home/Ray/sage/sage/local/var/lib/sage/venv-python3.9/lib/python3.9/site-packages/sage_docbuild/sphinxbuild.py", line 327, in runsphinx >sys.stderr.raise_errors() > File "/home/Ray/sage/sage/local/var/lib/sage/venv-python3.9/lib/python3.9/site-packages/sage_docbuild/sphinxbuild.py", line 263, in raise_errors >raise OSError(self._error) >OSError: /home/Ray/sage/sage/src/doc/en/reference/index.rst:34: WARNING: unknown document: categories/index > >Note: incremental documentation builds sometimes cause spurious >error messages. To be certain that these are real errors, run >"make doc-clean doc-uninstall" first and try again. >make[6]: *** [Makefile:27: doc-inventory--reference_top] Error 1 >make[5]: *** [Makefile:45: doc-inventory-reference] Error 2 I tried ``` $make doc-clean doc-uninstall $make configure $./configure $make -s V=0 ``` and it raised the same error (log file is attached). It appears that some of the docs are not building completely; this is a part of the log: >[knots] building [inventory]: targets for 4 source files that are out of date >[knots] updating environment: [new config] 4 added, 0 changed, 0 removed >[lfunction] building [inventory]: targets for 5 source files that are out of date >[lfunction] updating environment: [new config] 5 added, 0 changed, 0 removed >[lfunction] The inventory files are in ../../local/share/doc/sage/inventory/en/reference/lfunctions. >Build finished. The built documents can be found in /home/Ray/sage/sage/local/share/doc/sage/inventory/en/reference/lfunctions And later I get this: >[reference] /home/Ray/sage/sage/src/doc/en/reference/index.rst:105: WARNING: unknown document: knots/index What is the best thing to do there? It's the same packages that cause the trouble in both runs. Thank you very much in advance! Max Samuel Lelievre schrieb am Montag, 25. Juli 2022 um 09:17:47 UTC+9: > Install the relevant cygwin packages: > ``` > $ apt-cyg install bzip2 libbz2-devel liblzma-devel libffi-devel xz > ``` > Clean up the corresponding Sage packages: > ``` > $ make bzip2-clean liblzma-clean libffi-clean xz-clean > > Then configure again: > ``` > $ make configure > $ ./configure > ``` > > Follow any recommendations at end of configure output. > > Finally decide number of parallel jobs > ``` > $ export MAKE='make -j8' > ``` > and run make again: > ``` > $ make -s V=0 > ``` > > -- You received this message because you are subscribed to the Google Groups "sage-devel" group. To unsubscribe from this group and stop receiving emails from it, send an email to
Re: [sage-devel] Re: System upgrades breaking sage frequently
On Tue, 26 Jul 2022 at 08:13, Dima Pasechnik wrote: > > On Tue, Jul 26, 2022 at 8:24 AM Nils Bruin wrote: > > > > On Monday, 25 July 2022 at 12:53:08 UTC-7 Matthias Koeppe wrote: > >> > >> Have you tried the existing instructions that I pointed you to? > > > > > > I have now. I'm stuck on running configure. > > > > * the ./configure command suggested doesn't work in my bash. I'm getting: > > bash: unexpected EOF while looking for matching `)' > > > > Instead I split it up a bit: > > $ for pkg in $(./sage -package list :standard: \ > >--has-file spkg-configure.m4 \ > >--has-file distros/conda.txt); do > > echo --with-system-$pkg=force; done > with > > $ ./configure --with-python=$CONDA_PREFIX/bin/python --prefix=$CONDA_PREFIX > > `cat with` > > That seemed to succeed in running configure, but resulted in an error: > > configure: error: > > > > Given --with-system-eclib=force, but no system package could be used. > > That's an error. Please install the indicated package to continue. > > (To override this error, use ./configure --without-system-eclib) > > Given --with-system-primesieve=force, but no system package could be > > used. > > That's an error. Please install the indicated package to continue. > > (To override this error, use ./configure --without-system-primesieve) > > Given --with-system-primecount=force, but no system package could be > > used. > > That's an error. Please install the indicated package to continue. > > (To override this error, use ./configure --without-system-primecount) > > this says that conda is behind Sage in regard of versions of eclib For what it's worth, Nils, Sage's eclib was recently updated: not major but a bugfix. See https://trac.sagemath.org/ticket/34029. John > and primesieve/count > > > > > -- > > You received this message because you are subscribed to the Google Groups > > "sage-devel" group. > > To unsubscribe from this group and stop receiving emails from it, send an > > email to sage-devel+unsubscr...@googlegroups.com. > > To view this discussion on the web visit > > https://groups.google.com/d/msgid/sage-devel/f432a44d-fa4b-4ae9-855c-91219258f2bcn%40googlegroups.com. > > -- > You received this message because you are subscribed to the Google Groups > "sage-devel" group. > To unsubscribe from this group and stop receiving emails from it, send an > email to sage-devel+unsubscr...@googlegroups.com. > To view this discussion on the web visit > https://groups.google.com/d/msgid/sage-devel/CAAWYfq3bUXCivTEz7tmJSXnVf9auBQtg_bDPfOYmiKUX4EPaHA%40mail.gmail.com. -- You received this message because you are subscribed to the Google Groups "sage-devel" group. To unsubscribe from this group and stop receiving emails from it, send an email to sage-devel+unsubscr...@googlegroups.com. To view this discussion on the web visit https://groups.google.com/d/msgid/sage-devel/CAD0p0K5XPV%2BdJkn69i09cKYDRas9h6ZtFGfe5kLREBUi0ZTibg%40mail.gmail.com.
Re: [sage-devel] Re: System upgrades breaking sage frequently
On Tue, Jul 26, 2022 at 8:24 AM Nils Bruin wrote: > > On Monday, 25 July 2022 at 12:53:08 UTC-7 Matthias Koeppe wrote: >> >> Have you tried the existing instructions that I pointed you to? > > > I have now. I'm stuck on running configure. > > * the ./configure command suggested doesn't work in my bash. I'm getting: > bash: unexpected EOF while looking for matching `)' > > Instead I split it up a bit: > $ for pkg in $(./sage -package list :standard: \ >--has-file spkg-configure.m4 \ >--has-file distros/conda.txt); do >echo --with-system-$pkg=force; done > with > $ ./configure --with-python=$CONDA_PREFIX/bin/python --prefix=$CONDA_PREFIX > `cat with` > That seemed to succeed in running configure, but resulted in an error: > configure: error: > > Given --with-system-eclib=force, but no system package could be used. > That's an error. Please install the indicated package to continue. > (To override this error, use ./configure --without-system-eclib) > Given --with-system-primesieve=force, but no system package could be used. > That's an error. Please install the indicated package to continue. > (To override this error, use ./configure --without-system-primesieve) > Given --with-system-primecount=force, but no system package could be used. > That's an error. Please install the indicated package to continue. > (To override this error, use ./configure --without-system-primecount) this says that conda is behind Sage in regard of versions of eclib and primesieve/count > > -- > You received this message because you are subscribed to the Google Groups > "sage-devel" group. > To unsubscribe from this group and stop receiving emails from it, send an > email to sage-devel+unsubscr...@googlegroups.com. > To view this discussion on the web visit > https://groups.google.com/d/msgid/sage-devel/f432a44d-fa4b-4ae9-855c-91219258f2bcn%40googlegroups.com. -- You received this message because you are subscribed to the Google Groups "sage-devel" group. To unsubscribe from this group and stop receiving emails from it, send an email to sage-devel+unsubscr...@googlegroups.com. To view this discussion on the web visit https://groups.google.com/d/msgid/sage-devel/CAAWYfq3bUXCivTEz7tmJSXnVf9auBQtg_bDPfOYmiKUX4EPaHA%40mail.gmail.com.
[sage-devel] Re: System upgrades breaking sage frequently
On Monday, 25 July 2022 at 12:53:08 UTC-7 Matthias Koeppe wrote: > Have you tried the existing instructions that I pointed you to? > I have now. I'm stuck on running configure. * the ./configure command suggested doesn't work in my bash. I'm getting: bash: unexpected EOF while looking for matching `)' Instead I split it up a bit: $ for pkg in $(./sage -package list :standard: \ --has-file spkg-configure.m4 \ --has-file distros/conda.txt); do echo --with-system-$pkg=force; done > with $ ./configure --with-python=$CONDA_PREFIX/bin/python --prefix=$CONDA_PREFIX `cat with` That seemed to succeed in running configure, but resulted in an error: configure: error: Given --with-system-eclib=force, but no system package could be used. That's an error. Please install the indicated package to continue. (To override this error, use ./configure --without-system-eclib) Given --with-system-primesieve=force, but no system package could be used. That's an error. Please install the indicated package to continue. (To override this error, use ./configure --without-system-primesieve) Given --with-system-primecount=force, but no system package could be used. That's an error. Please install the indicated package to continue. (To override this error, use ./configure --without-system-primecount) -- You received this message because you are subscribed to the Google Groups "sage-devel" group. To unsubscribe from this group and stop receiving emails from it, send an email to sage-devel+unsubscr...@googlegroups.com. To view this discussion on the web visit https://groups.google.com/d/msgid/sage-devel/f432a44d-fa4b-4ae9-855c-91219258f2bcn%40googlegroups.com.
