Re: [sage-devel] Re: OSX Catalina works
Patch gcc, see: see https://trac.sagemath.org/ticket/28691 On Monday, November 4, 2019 at 11:34:48 AM UTC+1, Dima Pasechnik wrote: > > in view of problems with building gcc/gfortran on osx 10.15 and latest > Xcode, one must wonder what Homebrew does to make it work. > Do they patch system headers, or something like 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/59a143d4-8282-480e-a165-b0aca1e69bdc%40googlegroups.com.
[sage-devel] Sporadic build failure of zope_interface-4.6.0 and entrypoints-0.3
When building 9.0beta3 (or 9.0beta2) in parallel on two CentOS machines, I once got the following two build failures that I do not know how to resolve. Starting the build process again made the build complete successfully, so it looks like these packages do not list all their dependencies. Installing zope_interface-4.6.0 Traceback (most recent call last): File "setup.py", line 26, in from setuptools import setup, Extension, Feature File "/amd/compute/mwagerin/git/sage_compute/python3/local/lib/python3.7/site-packages/setuptools/__init__.py" , line 16, in import setuptools.version File "/amd/compute/mwagerin/git/sage_compute/python3/local/lib/python3.7/site-packages/setuptools/version.py" , line 1, in import pkg_resources File "/amd/compute/mwagerin/git/sage_compute/python3/local/lib/python3.7/site-packages/pkg_resources/__init__.py" , line 3126, in @_call_aside File "/amd/compute/mwagerin/git/sage_compute/python3/local/lib/python3.7/site-packages/pkg_resources/__init__.py" , line 3110, in _call_aside f(*args, **kwargs) File "/amd/compute/mwagerin/git/sage_compute/python3/local/lib/python3.7/site-packages/pkg_resources/__init__.py" , line 3162, in _initialize_master_working_set list(map(working_set.add_entry, sys.path)) File "/amd/compute/mwagerin/git/sage_compute/python3/local/lib/python3.7/site-packages/pkg_resources/__init__.py" , line 621, in add_entry for dist in find_distributions(entry, True): File "/amd/compute/mwagerin/git/sage_compute/python3/local/lib/python3.7/site-packages/pkg_resources/__init__.py" , line 1968, in find_on_path for dist in factory(fullpath): File "/amd/compute/mwagerin/git/sage_compute/python3/local/lib/python3.7/site-packages/pkg_resources/__init__.py" , line 2030, in distributions_from_metadata if len(os.listdir(path)) == 0: FileNotFoundError: [Errno 2] No such file or directory: '/amd/compute/mwagerin/git/sage_compute/python3/local/lib/python3.7/site-packages/mpmath-1.1.0-py3.7.egg-info' Error: could not determine package name Error installing zope_interface-4.6.0 Installing entrypoints-0.3 Traceback (most recent call last): File "setup.py", line 6, in from entrypoints import __version__ as v File "/export/compute/mwagerin/git/sage/python2/local/var/tmp/sage/build/entrypoints-0.3/src/entrypoints.py" , line 19, in from backports import configparser ImportError: No module named backports Error: could not determine package name Error installing entrypoints-0.3 The first occured with a Python 3 build, the other with a Python 2 build in case it matters. -- 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/6bb6547d-9041-46c2-b586-8b57fb33666c%40googlegroups.com.
Re: [sage-devel] Re: OSX Catalina works
configure:12690: g++ -E -std=gnu++11 -I/Volumes/Transcend/wooster/computer-algebra/anaconda3/include conftest.cpp anaconda conflict? On Mon, Nov 4, 2019 at 5:37 PM David Joyner wrote: > > > > On Sun, Nov 3, 2019 at 11:07 AM Dima Pasechnik wrote: >> >> could you post config.log ? > > > It is attached. > >> >> >> On Sun, 3 Nov 2019, 15:03 David Joyner, wrote: >>> >>> >>> >>> On Sun, Nov 3, 2019 at 6:49 AM David Joyner wrote: On Sun, Nov 3, 2019 at 3:00 AM Dima Pasechnik wrote: > > looks like gd package didn't install right. > > you can install gd via Homebrew: > > https://formulae.brew.sh/formula/gd > > also, by the way, install pkg-config > > https://formulae.brew.sh/formula/pkg-config > > (it would be great if someone with well-working osx system updated > Installation guide to list names of Homebrew packages to match Sage ones, > listed on > https://trac.sagemath.org/ticket/27330) > I'll do that and try again. >>> >>> >>> This time it failed while compiling m4ri. >>> >>> >>> m4ri-20140914.p0] ld: library not found for -lpng12 >>> [m4ri-20140914.p0] clang: error: linker command failed with exit code 1 >>> (use -v to see invocation) >>> [m4ri-20140914.p0] make[5]: *** [libm4ri.la] Error 1 >>> [m4ri-20140914.p0] make[4]: *** [all] Error 2 >>> [m4ri-20140914.p0] >>> BTW, I added gdlib.pc to PKG_CONFIG_PATH and reran make. This time it got all the way to sagelib before stalling: [sagelib-9.0.beta3] /Volumes/Transcend/wooster/computer-algebra/sage-9.0.beta3/local/include/omalloc/omalloc.h:20:20: note: expanded from macro 'REGISTER' [sagelib-9.0.beta3] #define REGISTER register [sagelib-9.0.beta3]^ [sagelib-9.0.beta3] 96 warnings generated. make[3]: *** [sagelib] Error 2 make[2]: *** [all-start] Error 2 > > > I also have formulas for flint and arb, they would be built from source > and installed in Homebrew structure. > > > > > > > > > On Sat, 2 Nov 2019, 23:46 David Joyner, wrote: >> >> >> >> On Fri, Nov 1, 2019 at 1:15 PM John H Palmieri >> wrote: >>> >>> If you have the time, could you try uninstalling Xcode and then >>> reinstalling it? You might also try uninstalling and reinstalling >>> homebrew's gcc and any other homebrew components that are relevant to >>> Sage. There may be some remnants of previously installed software that >>> is somehow interfering. >>> >>> John >>> >> >> I uninstalled xcode (including the CL tools) then reinstalled the latest >> version >> (including the CL tools, which now go in a new directory). I also >> uninstalled and reinstalled >> homebrew. >> >> This time homebrew installed gcc fine. The compilation of sage-9.0b3 >> went fine until >> it hit brial-1.2.5. Then I got: >> >> [brial-1.2.5] Package gdlib was not found in the pkg-config search path. >> [brial-1.2.5] Perhaps you should add the directory containing `gdlib.pc' >> [brial-1.2.5] to the PKG_CONFIG_PATH environment variable >> [brial-1.2.5] Package 'gdlib', required by 'world', not found >> >> FWIW, I did find gdlib.pc in a directory of a non-working older sage: >> >> /Users/wdj/sagefiles/SageMath/local/lib/pkgconfig/gdlib.pc >> >> >> Any suggestions? >> >>> >>> On Wednesday, October 30, 2019 at 8:58:38 PM UTC-7, Andrew wrote: On Wednesday, 30 October 2019 23:27:45 UTC+11, Dima Pasechnik wrote: > > I meant cmath files without extensions. These are C++ header files. > It appears there are two such files on the list. Are they different? > In the interim have have installed homebrew's gcc to see if this helps, but it doesn't. The cmath files that I now have on my system are: -rw-r--r-- 1 rootwheel 14515 23 Jul 03:08 /Applications/Xcode.app/Contents/Developer/Toolchains/XcodeDefault.xctoolchain/usr/include/c++/v1/cmath -rw-r--r-- 1 rootwheel 14515 23 Jul 03:08 /Library/Developer/CommandLineTools/usr/include/c++/v1/cmath As you suspected, these two files are identical. from homebrew's gcc: -rw-r--r-- 1 andrew staff619 14 Aug 22:29 /usr/local/Cellar/boost/1.71.0/include/boost/compatibility/cpp_c_headers/cmath -rw-r--r-- 1 andrew staff 49094 12 Aug 17:58 /usr/local/Cellar/gcc/9.2.0_1/include/c++/9.2.0/cmath -rw-r--r-- 1 andrew staff 6570 12 Aug 17:58 /usr/local/Cellar/gcc/9.2.0_1/include/c++/9.2.0/ext/cmath -rw-r--r-- 1 andrew staff 43806 12 Aug 17:58
Re: [sage-devel] Re: Switch to Python 3 by default
On 11/3/19 4:55 PM, VulK wrote: On the same note: the current implementation of `is_jvm_available` is not really robust and I should open a ticket about this; any suggestion for a better implementation? S. const false Does it do anything except jmol? The right way to do it would be to add --with-jvm=/path/to/jvm or something like that to the ./configure script. The is_jvm_available() implementation would then be hard-coded at build time, and not enabled automagically. But that's a lot of work a a feature that no one's going to use after jmol is replaced. -- 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/e01aeb45-7170-ef2e-9f0b-77f5c8301a5b%40orlitzky.com.
[sage-devel] building Sage docs on small VMs
How does one switch off multiprocessing in docbuild? (it's ludicrous not being able to build docs on a VM with 2GB of memory) [dochtml] [reference] valuations: 1 todos, 14 index, 1495 citations, 13 modules [dochtml] [reference] ... done (483 todos, 2097 index, 1506 citations, 2047 modules) [dochtml] [reference] preparing documents... skipping loading of indexes... done [dochtml] [reference] The inventory files are in local/share/doc/sage/inventory/en/reference. [dochtml] Build finished. The built documents can be found in /home/dimpase/sage/local/share/doc/sage/inventory/en/reference [dochtml] Building reference manual, second pass. [dochtml] [dochtml] Error building the documentation. [dochtml] Traceback (most recent call last): [dochtml] File "/home/dimpase/sage/local/lib/python2.7/runpy.py", line 174, in _run_module_as_main [dochtml] "__main__", fname, loader, pkg_name) [dochtml] File "/home/dimpase/sage/local/lib/python2.7/runpy.py", line 72, in _run_code [dochtml] exec code in run_globals [dochtml] File "/home/dimpase/sage/local/lib/python2.7/site-packages/sage_setup/docbuild/__main__.py", line 2, in [dochtml] main() [dochtml] File "/home/dimpase/sage/local/lib/python2.7/site-packages/sage_setup/docbuild/__init__.py", line 1693, in main [dochtml] builder() [dochtml] File "/home/dimpase/sage/local/lib/python2.7/site-packages/sage_setup/docbuild/__init__.py", line 332, in _wrapper [dochtml] getattr(get_builder(document), name)(*args, **kwds) [dochtml] File "/home/dimpase/sage/local/lib/python2.7/site-packages/sage_setup/docbuild/__init__.py", line 526, in _wrapper [dochtml] build_many(build_ref_doc, L) [dochtml] File "/home/dimpase/sage/local/lib/python2.7/site-packages/sage_setup/docbuild/__init__.py", line 280, in build_many [dochtml] _build_many(target, args, processes=NUM_THREADS) [dochtml] File "/home/dimpase/sage/local/lib/python2.7/site-packages/sage_setup/docbuild/utils.py", line 257, in build_many [dochtml] if reap_workers(waited_pid, waited_exitcode): [dochtml] File "/home/dimpase/sage/local/lib/python2.7/site-packages/sage_setup/docbuild/utils.py", line 227, in reap_workers [dochtml] w.start() [dochtml] File "/home/dimpase/sage/local/lib/python2.7/multiprocessing/process.py", line 130, in start [dochtml] self._popen = Popen(self) [dochtml] File "/home/dimpase/sage/local/lib/python2.7/multiprocessing/forking.py", line 121, in __init__ [dochtml] self.pid = os.fork() [dochtml] OSError: [Errno 12] Cannot allocate memory [dochtml] [dochtml] Note: incremental documentation builds sometimes cause spurious [dochtml] error messages. To be certain that these are real errors, run [dochtml] "make doc-clean" first and try again. make[3]: *** [Makefile:2041: doc-html] Error 1 make[3]: Leaving directory '/home/dimpase/sage/build/make' make[2]: *** [Makefile:1852: all-start] Error 2 make[2]: Leaving directory '/home/dimpase/sage/build/make' real 14m21.762s user 13m16.489s sys 0m30.801s *** Error building Sage. -- 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/CAAWYfq3-nciiFX_WQ8D%3DrUc5%2BMifgVYZKNj7ben7a3h2SYd%3Dcg%40mail.gmail.com.
Re: [sage-devel] Can we adopt "orphan" Sage-related packages ?
On Sun, Nov 3, 2019 at 2:59 PM Emmanuel Charpentier wrote: > > Case in point: > > During a few years, someone called Sho Katemori created and maintained a > couple of (very) useful Sage-related packages fpr emacs users: > > sage-shell-mode: an emacs interface to Sage, allowing the integration of > typeset maths and 2D graphics in an emacs buffer managing a Sage interactive > session ; > ob-sagemath, an org-mode interface to Sage, alowing integration of "live" > Sage code snippets in a document ; > anything-sage, auto-complete-sage and helm sage, Sage extensions of various > emacs utilities. > > > Note: sage-shell-mode was a very welcome and timely replacement for the old > sage-mode package, deemed unmaintainable by its maintainer (Ivan Andrus). It > seems to have become popular (for Sage-reasonable values of "popular", of > course...). > > However, Sho Katemori seems to have dropped off the Net: his (her ?) last > contribution to his/hers Github repositories dates back to march 2018 ; an > attempt to mail him/her is still unanswered. As a consequence, those package > have some unanswered issues. > > It seems that sage-shell mode has been somehow "adopted" by Sage : its > current repository is now part of the Sage hierarchy on Github, which allowed > Frédéric Chapoton, then myself, to integrate some change needed for Python 3 > compatibility. > > I'd like to propose similar change to ob-sagemath ; it is also possible that > some other users may propose changes to the other packages (which are not > (yet) my cup of tea...). > > Hence the questions: > > Can we "adopt" these packages as we did for sage-shell-mode ? > If so, how ? The easiest would be if the author transferred the github repos to Sagemath github organization. I'm cc-ing this to all the email addresses I found on the web... If we don't get such a transfer done (which obviously needs the author's involvement) then we can just have copies of anything-sage, auto-complete-sage and helm sage hosted. ob-sage is harder, as it does not have a license... Best Dima > > > And, more generally: > > Do we have a policy about external but sage-related software suffering > "abandon" by their original authors/maintainers ? > > Advice requested... > > -- > 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/04893dfc-54d7-4edb-99c1-4ac9f50a9aef%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/CAAWYfq1WQ27SOjf_2jtWG9M37ZSgHswCaFqS8A8pQYjyp%3DZv1Q%40mail.gmail.com.
[sage-devel] Symbolic equations and factor
I found some old code that seems to have broken due to a change of behavior
when calling `factor()` on symbolic equations.
In the old version (can't really tie it to a specific SageMath version;
maybe 2 years old or so), it would simply factor both sides of an equation,
i.e., something along the lines of
sage: var('x y')
(x, y)
sage: (x^2 + 2*x + 1 == y^2 + y).factor()
(x + 1)^2 == (y + 1)*y
Currently, however,
sage: (x^2 + 2*x + 1 == y^2 + y).factor()
Traceback (most recent call last):
...
RuntimeError: can't happen in factor
Was this an intentional change at some point? (I did not find a specific
ticket for it, so I am guessing that the answer is no.)
I liked that there was a convenience method for factoring both sides of an
equation, and I used this quite a bit at some point; especially for
improving output from `solve`.
Do you feel that the error is appropriate? (If so, the message needs to be
improved, though.) Or would you be ok with changing back to factoring both
sides when calling factor on a symbolic equation?
Benjamin
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Re: [sage-devel] Re: OSX Catalina works
in view of problems with building gcc/gfortran on osx 10.15 and latest Xcode, one must wonder what Homebrew does to make it work. Do they patch system headers, or something like that? On Mon, 4 Nov 2019 at 07:37, Andrew wrote: > Great, thanks John. I have essentially the same version of brew: > Homebrew 2.1.15 > Homebrew/homebrew-core (git revision 89bf3; last commit 2019-11-04) > Homebrew/homebrew-cask (git revision e317e; last commit 2019-11-04) > > but I have many more brew packages installed. I reinstalled all of the > brew packages last week but I have just uninstalled all of the brew > packages. I will now add everything back in one at a time, starting with > things on your list, and see if I can compile sage. I'll report back what I > find. > > Andrew > > > On Monday, 4 November 2019 16:35:55 UTC+11, John H Palmieri wrote: >> >> I am using the same versions of OS and Xcode as you. I am now doing this >> with a third computer. This one had an old Xcode and some homebrew stuff >> already installed, and it gave me some problems. I ended up uninstalling >> and then reinstalling various parts of homebrew, and Sage now builds for >> me. (I had also first installed some things by hand, like gfortran many >> months ago. So I had to delete things like that when doing the homebrew >> installation.) >> >> $ brew list >> autoconflibdvdcss p7zip >> automakelibeventpari >> boost libffi pcre >> cabextract libidn2 pkg-config >> cimglibmpc python >> cmake libomp readline >> emacs-mac libpng shared-mime-info >> gcc libtasn1sqlite >> gdbmlibtool texinfo >> gettext libunistringunbound >> glibmpfiunrar >> gmp mpfrwine >> gnutls nettle winetricks >> gpatch ntl x265 >> icu4c openexr xz >> ilmbase openssl yasm >> isl openssl@1.1 >> libde265p11-kit >> >> >> $ brew --version >> Homebrew 2.1.15 >> Homebrew/homebrew-core (git revision d191f; last commit 2019-11-03) >> Homebrew/homebrew-cask (git revision cbd79; last commit 2019-11-03) >> >> >> >> >> On Sunday, November 3, 2019 at 8:53:57 PM UTC-8, Andrew wrote: >>> >>> I uninstalled xcode and brew's gcc and then reinstall them both but I >>> still the the same failure with givaro. >>> I don't know if this is related, but even though I installed ntl using >>> brew it is not used when I compile sage as the log file reports: >>> >>> checking NTL/ZZ.h usability... no >>> checking NTL/ZZ.h presence... yes >>> configure: WARNING: NTL/ZZ.h: present but cannot be compiled >>> configure: WARNING: NTL/ZZ.h: check for missing prerequisite headers? >>> configure: WARNING: NTL/ZZ.h: see the Autoconf documentation >>> configure: WARNING: NTL/ZZ.h: section "Present But Cannot Be >>> Compiled" >>> configure: WARNING: NTL/ZZ.h: proceeding with the compiler's result >>> configure: WARNING: ## -- ## >>> configure: WARNING: ## Report this to sage-...@googlegroups.com ## >>> configure: WARNING: ## -- ## >>> checking for NTL/ZZ.h... no >>> checking whether we can link a program using NTL... no >>> checking NTL version >= 10.3... 11.4.1 >>> using Sage's ntl SPKG >>> configure: === checking whether to install the flint SPKG === >>> checking installing mpfr or ntl? ... yes; install flint as well >>> using Sage's flint SPKG >>> configure: === checking whether to install the arb SPKG === >>> checking installing flint? ... yes; install arb as well >>> configure: === checking whether to install the bzip2 SPKG === >>> >>> That sage wants compile flint and arb is expected because I try to >>> install them with brew I get errors like: >>> >>> ==> make >>> Last 15 lines from /Users/andrew/Library/Logs/Homebrew/flint/02.make: >>> ~~^ >>> /Applications/Xcode.app/Contents/Developer/Toolchains/XcodeDefault.xctoolchain/usr/bin/../include/c++/v1/cmath:324:9: >>> error: no member named 'islessgreater' in the global namespace >>> using ::islessgreater; >>> ~~^ >>> /Applications/Xcode.app/Contents/Developer/Toolchains/XcodeDefault.xctoolchain/usr/bin/../include/c++/v1/cmath:325:9: >>> error: no member named 'isunordered' in the global namespace >>> using ::isunordered; >>> ~~^ >>> /Applications/Xcode.app/Contents/Developer/Toolchains/XcodeDefault.xctoolchain/usr/bin/../include/c++/v1/cmath:326:9: >>> error: no member named 'isunordered' in the global namespace >>> using ::isunordered; >>> ~~^ >>> 13 errors generated. >>> make[2]: *** [build/interfaces/NTL-interface.lo] Error 1 >>> >>> These are similar to the errors that I get with givaro when compiling >>> sage. >>> >>> John: what version of xcode and the command line tools are using and if >>> you first do >>> >>> make distclean >>>
