I uninstalled and reinstalled homebrew and that got rid of the brew doctor warnings. I then brewed the suggested packages from the Sage link Zachary provided and the packages listed at the end of the output of configure.
Then from SAGE_ROOT I ran make distclean source .homebrew-build-env ./bootstrap -d ./configure make -j4 build In the end this seems to be working. Thank you so much Dima and Zachary for your help. The reason for running ./bootstrap with the -d flag was because that is what an error message told me to do. Without -d flag: trevorkarn@Trevors-MacBook-Air sage % source .homebrew-build-env trevorkarn@Trevors-MacBook-Air sage % ./bootstrap rm -rf config configure build/make/Makefile-auto.in rm -f src/doc/en/installation/*.txt rm -rf src/doc/en/reference/spkg/*.rst rm -f src/doc/en/reference/repl/*.txt rm -f environment.yml rm -f src/environment.yml rm -f environment-optional.yml rm -f src/environment-optional.yml src/doc/bootstrap:92: installing src/doc/en/installation/arch.txt and src/doc/en/installation/arch-optional.txt src/doc/bootstrap:92: installing src/doc/en/installation/debian.txt and src/doc/en/installation/debian-optional.txt src/doc/bootstrap:92: installing src/doc/en/installation/fedora.txt and src/doc/en/installation/fedora-optional.txt src/doc/bootstrap:92: installing src/doc/en/installation/cygwin.txt and src/doc/en/installation/cygwin-optional.txt src/doc/bootstrap:92: installing src/doc/en/installation/homebrew.txt and src/doc/en/installation/homebrew-optional.txt src/doc/bootstrap:66: installing environment.yml, environment-optional.yml, src/environment.yml and src/environment-optional.yml src/doc/bootstrap:103: installing src/doc/en/reference/spkg/*.rst src/doc/bootstrap:182: installing src/doc/en/reference/repl/options.txt bootstrap:73: installing 'config/config.rpath' ./bootstrap: line 118: aclocal: command not found Bootstrap failed. Either install autotools or run bootstrap with the -d option to download the auto-generated files instead. Best Regards, Trevor Karn On Tue, Feb 9, 2021 at 4:06 AM Dima Pasechnik <[email protected]> wrote: > On Tue, Feb 9, 2021 at 4:07 AM Zachary Scherr <[email protected]> wrote: > > > > I need to sign off for the night, but the numpy error is definitely > related to gfortran. If you have gcc installed via homebrew then it should > come with the latest version of gfortran. You can see from your config.log > file that gfortran is not found: > > > > configure:7281: checking for gfortran > > configure:7311: result: no > > > > and other standard homebrew packages are not found, like openblas: > > > > configure:12171: checking BLAS library > > configure:12190: result: openblas > > configure:12239: checking whether any of gfortran is installed as or > will be installed as SPKG > > configure:12243: result: yes; install openblas as well > > configure:13540: no suitable system package found for SPKG openblas > > > > are you aware if you have gcc and openblas installed via homebrew? I > also see that you didn't run "source .homebrew-build-env" before running > ./configure since I don't see certain items on your path. If you go to the > sage installation guide at > https://doc.sagemath.org/html/en/installation/source.html#macos-recommended-installation > you can see a list of homebrew packages you might want to have before > installing sage. I think if you get everything in working order with > homebrew then you shouldn't have any issues installing sage. Here is my > best suggestion as to what to try: > > > > - fix all "brew doctor" warnings. This might not be necessary, but I > get worried when I see so many warnings. You can probably just delete all > the suggested files and you should be fine. > > > > - install all the recommended homebrew packages. If any are already > installed then maybe try "brew reinstall" to make sure it is installed > properly. If you think you have homebrew gcc installed then you should be > able to do "which gfortran" and "gfortran --version". That should > hopefully show you that you have gfortran 10.2.0_3. > > > > - in your sage folder under the develop branch you should run the > commands I mentioned, and don't skip out on "source .homebrew-build-env": > > > > >> make distclean > > >> ./bootstrap > > >> source .homebrew-build-env > > >> ./configure > > > > Before running "make -j4 build" you can look at config.log and make sure > that it picked up all of the relevant homebrew packages. > > > > > source .homebrew-build-env > > should be run before ./bootstrap > > > as well, ./confugure at the end of its run outputs an advice on > packages that can still be installed. > > > > > > > > > On Monday, February 8, 2021 at 10:52:43 PM UTC-5 Trevor Karn wrote: > >> > >> Here is the new one. Thanks so much for all of your help on this, > Zachary. > >> > >> > >> Best Regards, > >> > >> Trevor Karn > >> > >> > >> On Mon, Feb 8, 2021 at 9:40 PM Zachary Scherr <[email protected]> wrote: > >>> > >>> At some point you should deal with those warnings, but I don't think > that is what is causing your problems (although they are probably > symptomatic of other possible issues). > >>> > >>> The config.log file you posted earlier is picking up a lot of packages > that were built by sage and not from homebrew. Do you have the config.log > file that you got after running make distclean? > >>> > >>> On Monday, February 8, 2021 at 10:10:01 PM UTC-5 Trevor Karn wrote: > >>>> > >>>> brew doctor is giving lots of errors about unbrewed files: > >>>> > >>>> trevorkarn@Trevors-MacBook-Air sage % brew doctor > >>>> > >>>> Please note that these warnings are just used to help the Homebrew > maintainers > >>>> > >>>> with debugging if you file an issue. If everything you use Homebrew > for is > >>>> > >>>> working fine: please don't worry or file an issue; just ignore this. > Thanks! > >>>> > >>>> > >>>> Warning: Unbrewed dylibs were found in /usr/local/lib. > >>>> > >>>> If you didn't put them there on purpose they could cause problems when > >>>> > >>>> building Homebrew formulae, and may need to be deleted. > >>>> > >>>> > >>>> Unexpected dylibs: > >>>> > >>>> /usr/local/lib/libtcl8.6.dylib > >>>> > >>>> /usr/local/lib/libtk8.6.dylib > >>>> > >>>> > >>>> Warning: Unbrewed header files were found in /usr/local/include. > >>>> > >>>> If you didn't put them there on purpose they could cause problems when > >>>> > >>>> building Homebrew formulae, and may need to be deleted. > >>>> > >>>> > >>>> Unexpected header files: > >>>> > >>>> /usr/local/include/fakemysql.h > >>>> > >>>> /usr/local/include/fakepq.h > >>>> > >>>> /usr/local/include/fakesql.h > >>>> > >>>> /usr/local/include/itcl.h > >>>> > >>>> /usr/local/include/itcl2TclOO.h > >>>> > >>>> /usr/local/include/itclDecls.h > >>>> > >>>> /usr/local/include/itclInt.h > >>>> > >>>> /usr/local/include/itclIntDecls.h > >>>> > >>>> /usr/local/include/itclMigrate2TclCore.h > >>>> > >>>> /usr/local/include/itclTclIntStubsFcn.h > >>>> > >>>> /usr/local/include/mysqlStubs.h > >>>> > >>>> /usr/local/include/odbcStubs.h > >>>> > >>>> /usr/local/include/pqStubs.h > >>>> > >>>> /usr/local/include/tcl.h > >>>> > >>>> /usr/local/include/tclDecls.h > >>>> > >>>> /usr/local/include/tclOO.h > >>>> > >>>> /usr/local/include/tclOODecls.h > >>>> > >>>> /usr/local/include/tclPlatDecls.h > >>>> > >>>> /usr/local/include/tclThread.h > >>>> > >>>> /usr/local/include/tclTomMath.h > >>>> > >>>> /usr/local/include/tclTomMathDecls.h > >>>> > >>>> /usr/local/include/tdbc.h > >>>> > >>>> /usr/local/include/tdbcDecls.h > >>>> > >>>> /usr/local/include/tdbcInt.h > >>>> > >>>> /usr/local/include/tk.h > >>>> > >>>> /usr/local/include/tkDecls.h > >>>> > >>>> /usr/local/include/tkPlatDecls.h > >>>> > >>>> > >>>> Warning: Unbrewed '.pc' files were found in /usr/local/lib/pkgconfig. > >>>> > >>>> If you didn't put them there on purpose they could cause problems when > >>>> > >>>> building Homebrew formulae, and may need to be deleted. > >>>> > >>>> > >>>> Unexpected '.pc' files: > >>>> > >>>> /usr/local/lib/pkgconfig/tcl.pc > >>>> > >>>> /usr/local/lib/pkgconfig/tk.pc > >>>> > >>>> > >>>> Warning: Unbrewed static libraries were found in /usr/local/lib. > >>>> > >>>> If you didn't put them there on purpose they could cause problems when > >>>> > >>>> building Homebrew formulae, and may need to be deleted. > >>>> > >>>> > >>>> Unexpected static libraries: > >>>> > >>>> /usr/local/lib/libtclstub8.6.a > >>>> > >>>> /usr/local/lib/libtkstub8.6.a > >>>> > >>>> > >>>> Warning: You have unlinked kegs in your Cellar. > >>>> > >>>> Leaving kegs unlinked can lead to build-trouble and cause formulae > that depend on > >>>> > >>>> those kegs to fail to run properly once built. Run `brew link` on > these: > >>>> > >>>> ffmpeg > >>>> > >>>> ghostscript > >>>> > >>>> > >>>> Warning: Homebrew's "sbin" was not found in your PATH but you have > installed > >>>> > >>>> formulae that put executables in /usr/local/sbin. > >>>> > >>>> Consider setting your PATH for example like so: > >>>> > >>>> echo 'export PATH="/usr/local/sbin:$PATH"' >> ~/.zshrc > >>>> > >>>> > >>>> Warning: Broken symlinks were found. Remove them with `brew cleanup`: > >>>> > >>>> /usr/local/bin/git-trac > >>>> > >>>> /usr/local/share/ghostscript/9.27/Resource/Font/wasy10.pfb > >>>> > >>>> /usr/local/share/ghostscript/9.27/Resource/Font/wasy5.pfb > >>>> > >>>> /usr/local/share/ghostscript/9.27/Resource/Font/wasy6.pfb > >>>> > >>>> /usr/local/share/ghostscript/9.27/Resource/Font/wasy7.pfb > >>>> > >>>> /usr/local/share/ghostscript/9.27/Resource/Font/wasy8.pfb > >>>> > >>>> /usr/local/share/ghostscript/9.27/Resource/Font/wasy9.pfb > >>>> > >>>> /usr/local/share/ghostscript/9.27/Resource/Font/wasyb10.pfb > >>>> > >>>> /usr/local/share/man/man1/brew-cask.1 > >>>> > >>>> /usr/local/share/zsh/site-functions/_brew_cask > >>>> > >>>> trevorkarn@Trevors-MacBook-Air sage % brew cleanup > >>>> > >>>> Removing: /usr/local/Cellar/gettext/0.20.1... (1,899 files, 18.5MB) > >>>> > >>>> Removing: /usr/local/Cellar/gmp/6.1.2_2... (18 files, 3.1MB) > >>>> > >>>> Removing: /usr/local/Cellar/gnutls/3.6.9... (1,227 files, 9.9MB) > >>>> > >>>> Removing: /usr/local/Cellar/icu4c/64.2... (257 files, 69.2MB) > >>>> > >>>> Removing: /usr/local/Cellar/libevent/2.1.11... (1,063 files, 5MB) > >>>> > >>>> Removing: /usr/local/Cellar/libffi/3.2.1... (16 files, 296.8KB) > >>>> > >>>> Removing: /usr/local/Cellar/libidn2/2.2.0_1... (70 files, 700.9KB) > >>>> > >>>> Removing: /usr/local/Cellar/libtasn1/4.14... (59 files, 384KB) > >>>> > >>>> Removing: /usr/local/Cellar/nettle/3.4.1... (85 files, 2MB) > >>>> > >>>> Error: Interrupted system call @ dir_initialize - > /usr/local/Cellar/opus > >>>> > >>>> trevorkarn@Trevors-MacBook-Air sage % ;2D > >>>> > >>>> > >>>> Best Regards, > >>>> > >>>> Trevor Karn > >>>> > >>>> > >>>> On Mon, Feb 8, 2021 at 8:38 PM Zachary Scherr <[email protected]> > wrote: > >>>>> > >>>>> In your original config.log, it looked like sage was picking up its > own fortran: > >>>>> > >>>>> configure:11991: gfortran has already been installed by SageMath > >>>>> configure:39396: result: gfortran-9.2.0: > already installed as an SPKG > >>>>> > >>>>> The current version of gfortran from homebrew is 10.2.0 version 3 > >>>>> > >>>>> GNU Fortran (Homebrew GCC 10.2.0_3) 10.2.0 > >>>>> Copyright (C) 2020 Free Software Foundation, Inc. > >>>>> This is free software; see the source for copying conditions. There > is NO > >>>>> warranty; not even for MERCHANTABILITY or FITNESS FOR A PARTICULAR > PURPOSE. > >>>>> > >>>>> ./configure should be picking up homebrew's gfortran (installed with > gcc), and it seems from your config.log file that you do have homebrew and > therefore you should have the most recent gfortran. > >>>>> Do you have the newest config.log file from after running make > distclean? You may also want to try running > >>>>> > >>>>> brew doctor > >>>>> > >>>>> to see if there is something wrong with your homebrew. > >>>>> On Monday, February 8, 2021 at 9:27:11 PM UTC-5 Trevor Karn wrote: > >>>>>> > >>>>>> Unfortunately, that did not seem to work. > >>>>>> > >>>>>> Here are the last few lines of the terminal output and I've > attached the numpy log. > >>>>>> > >>>>>> [singular-4.1.1p2.p0] real 28m38.843s > >>>>>> > >>>>>> [singular-4.1.1p2.p0] user 24m18.545s > >>>>>> > >>>>>> [singular-4.1.1p2.p0] sys 3m53.423s > >>>>>> > >>>>>> [singular-4.1.1p2.p0] Copying package files from temporary location > /Users/trevorkarn/Applications/sage/local/var/tmp/sage/build/singular-4.1.1p2.p0/inst > to /Users/trevorkarn/Applications/sage/local > >>>>>> > >>>>>> [singular-4.1.1p2.p0] Successfully installed singular-4.1.1p2.p0 > >>>>>> > >>>>>> [singular-4.1.1p2.p0] Deleting temporary build directory > >>>>>> > >>>>>> [singular-4.1.1p2.p0] > /Users/trevorkarn/Applications/sage/local/var/tmp/sage/build/singular-4.1.1p2.p0 > >>>>>> > >>>>>> [singular-4.1.1p2.p0] Finished installing singular-4.1.1p2.p0 > >>>>>> > >>>>>> make[2]: *** [all-build] Error 2 > >>>>>> > >>>>>> > >>>>>> real 182m14.796s > >>>>>> > >>>>>> user 355m33.883s > >>>>>> > >>>>>> sys 72m32.388s > >>>>>> > >>>>>> *************************************************************** > >>>>>> > >>>>>> Error building Sage. > >>>>>> > >>>>>> > >>>>>> The following package(s) may have failed to build (not necessarily > >>>>>> > >>>>>> during this run of 'make all-build'): > >>>>>> > >>>>>> > >>>>>> * package: numpy-1.19.4 > >>>>>> > >>>>>> last build time: Feb 8 19:48 > >>>>>> > >>>>>> log file: > /Users/trevorkarn/Applications/sage/logs/pkgs/numpy-1.19.4.log > >>>>>> > >>>>>> build directory: > /Users/trevorkarn/Applications/sage/local/var/tmp/sage/build/numpy-1.19.4 > >>>>>> > >>>>>> > >>>>>> 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]: *** [all-build] Error 1 > >>>>>> > >>>>>> make: *** [build] Error 2 > >>>>>> > >>>>>> trevorkarn@Trevors-MacBook-Air sage % > >>>>>> > >>>>>> > >>>>>> > >>>>>> Best Regards, > >>>>>> > >>>>>> Trevor Karn > >>>>>> > >>>>>> > >>>>>> On Mon, Feb 8, 2021 at 1:56 PM Zachary Scherr <[email protected]> > wrote: > >>>>>>> > >>>>>>> yea, something seems messed up. For example, the numpy problem > was fixed on beta 6 and should still be fixed in beta 7. It looks like > somehow you have old files hanging around which are causing problems. > Hopefully make distclean will clean everything and let you start fresh. > >>>>>>> > >>>>>>> On Monday, February 8, 2021 at 2:25:16 PM UTC-5 Trevor Karn wrote: > >>>>>>>> > >>>>>>>> I must have typed it wrong. The second option you gave failed on > numpy, but I tried the first option again, and it is compiling. > >>>>>>>> > >>>>>>>> Best Regards, > >>>>>>>> > >>>>>>>> Trevor Karn > >>>>>>>> > >>>>>>>> > >>>>>>>> On Mon, Feb 8, 2021 at 11:31 AM Zachary Scherr <[email protected]> > wrote: > >>>>>>>>> > >>>>>>>>> Are you sure you typed it correctly? Maybe try running > >>>>>>>>> > >>>>>>>>> ./bootstrap > >>>>>>>>> > >>>>>>>>> to make sure that the make targets are in order. > >>>>>>>>> > >>>>>>>>> On Monday, February 8, 2021 at 12:27:01 PM UTC-5 Trevor Karn > wrote: > >>>>>>>>>> > >>>>>>>>>> I tried make distclean and got an error “make: *** No rule to > make target ‘distclean’. Stop.” > >>>>>>>>>> > >>>>>>>>>> So I tried your second suggestion and it seems to be working so > far, but it is still compiling. > >>>>>>>>>> > >>>>>>>>>> On Mon, Feb 8, 2021 at 10:29 AM Zachary Scherr < > [email protected]> wrote: > >>>>>>>>>>> > >>>>>>>>>>> Probably the thing to try would be: > >>>>>>>>>>> > >>>>>>>>>>> make distclean > >>>>>>>>>>> > >>>>>>>>>>> and then you can build from scratch via: > >>>>>>>>>>> > >>>>>>>>>>> ./bootstrap > >>>>>>>>>>> source .homebrew-build-env > >>>>>>>>>>> ./configure > >>>>>>>>>>> make -j4 build > >>>>>>>>>>> > >>>>>>>>>>> But if you want to try cleaning wheel first before starting > from scratch, you could just try > >>>>>>>>>>> > >>>>>>>>>>> make wheel-clean > >>>>>>>>>>> make -j4 build > >>>>>>>>>>> > >>>>>>>>>>> but it might be better to clean everything and start from > scratch. > >>>>>>>>>>> > >>>>>>>>>>> On Monday, February 8, 2021 at 10:59:05 AM UTC-5 Trevor Karn > wrote: > >>>>>>>>>>>> > >>>>>>>>>>>> I do not see pep425tags.py in that directory. > >>>>>>>>>>>> > >>>>>>>>>>>> trevorkarn@Trevors-MacBook-Air sage % cd > /Users/trevorkarn/Applications/sage/local/lib/python3.9/site-packages/wheel/ > >>>>>>>>>>>> > >>>>>>>>>>>> trevorkarn@Trevors-MacBook-Air wheel % ls > >>>>>>>>>>>> > >>>>>>>>>>>> __init__.py __pycache__ cli metadata.py util.py wheelfile.py > >>>>>>>>>>>> > >>>>>>>>>>>> __main__.py bdist_wheel.py macosx_libfile.py pkginfo.py > vendored > >>>>>>>>>>>> > >>>>>>>>>>>> > >>>>>>>>>>>> Is there a way to clean the build environment? > >>>>>>>>>>>> > >>>>>>>>>>>> Best Regards, > >>>>>>>>>>>> > >>>>>>>>>>>> Trevor Karn > >>>>>>>>>>>> > >>>>>>>>>>>> > >>>>>>>>>>>> On Mon, Feb 8, 2021 at 9:54 AM Dima Pasechnik < > [email protected]> wrote: > >>>>>>>>>>>>> > >>>>>>>>>>>>> the only explanation for pep425tags.py would be an unclean > build > >>>>>>>>>>>>> environment - e.g. weird env vars set, or strange stuff in > PATH. > >>>>>>>>>>>>> > >>>>>>>>>>>>> On Mon, Feb 8, 2021 at 3:51 PM Zachary Scherr < > [email protected]> wrote: > >>>>>>>>>>>>> > > >>>>>>>>>>>>> > and do you see that pep425tags.py file in that directory? > >>>>>>>>>>>>> > > >>>>>>>>>>>>> > On Monday, February 8, 2021 at 10:21:09 AM UTC-5 Trevor > Karn wrote: > >>>>>>>>>>>>> >> > >>>>>>>>>>>>> >> The only contents of the file you pointed me towards are > >>>>>>>>>>>>> >> > >>>>>>>>>>>>> >> __version__ = '0.36.2' > >>>>>>>>>>>>> >> > >>>>>>>>>>>>> >> Best Regards, > >>>>>>>>>>>>> >> > >>>>>>>>>>>>> >> Trevor Karn > >>>>>>>>>>>>> >> > >>>>>>>>>>>>> >> > >>>>>>>>>>>>> >> On Mon, Feb 8, 2021 at 9:09 AM Zachary Scherr < > [email protected]> wrote: > >>>>>>>>>>>>> >>> > >>>>>>>>>>>>> >>> I really don't understand. The Cython log file shows > that the problem is in > >>>>>>>>>>>>> >>> > >>>>>>>>>>>>> >>> > /Users/trevorkarn/Applications/sage/local/lib/python3.9/site-packages/wheel/pep425tags.py > >>>>>>>>>>>>> >>> > >>>>>>>>>>>>> >>> I could be mistaken, but I don't think pep425tags.py has > been a part of the wheel package for a while now. Certainly when I looked > at wheel on my sage there was no such file. > >>>>>>>>>>>>> >>> > >>>>>>>>>>>>> >>> Can you go to your > "/Users/trevorkarn/Applications/sage/local/lib/python3.9/site-packages/wheel/" > directory and take a look at __init__.py. Does the version say 0.36.2? > >>>>>>>>>>>>> >>> > >>>>>>>>>>>>> >>> On Monday, February 8, 2021 at 9:32:20 AM UTC-5 Trevor > Karn wrote: > >>>>>>>>>>>>> >>>> > >>>>>>>>>>>>> >>>> > >>>>>>>>>>>>> >>>> Here is what I get. It seems like it is the same as > yours? > >>>>>>>>>>>>> >>>> > >>>>>>>>>>>>> >>>> > >>>>>>>>>>>>> >>>> trevorkarn@Trevors-MacBook-Air sage % brew info python3 > >>>>>>>>>>>>> >>>> > >>>>>>>>>>>>> >>>> [email protected]: stable 3.9.1 > >>>>>>>>>>>>> >>>> > >>>>>>>>>>>>> >>>> Interpreted, interactive, object-oriented programming > language > >>>>>>>>>>>>> >>>> > >>>>>>>>>>>>> >>>> https://www.python.org/ > >>>>>>>>>>>>> >>>> > >>>>>>>>>>>>> >>>> /usr/local/Cellar/[email protected]/3.9.1_8 (8,665 files, > 129.4MB) * > >>>>>>>>>>>>> >>>> > >>>>>>>>>>>>> >>>> Built from source on 2021-02-05 at 16:39:31 > >>>>>>>>>>>>> >>>> > >>>>>>>>>>>>> >>>> From: > https://github.com/Homebrew/homebrew-core/blob/HEAD/Formula/[email protected] > >>>>>>>>>>>>> >>>> > >>>>>>>>>>>>> >>>> License: Python-2.0 > >>>>>>>>>>>>> >>>> > >>>>>>>>>>>>> >>>> ==> Dependencies > >>>>>>>>>>>>> >>>> > >>>>>>>>>>>>> >>>> Build: pkg-config ✔ > >>>>>>>>>>>>> >>>> > >>>>>>>>>>>>> >>>> Required: gdbm ✔, [email protected] ✔, readline ✔, sqlite ✔, > tcl-tk ✔, xz ✔ > >>>>>>>>>>>>> >>>> > >>>>>>>>>>>>> >>>> ==> Caveats > >>>>>>>>>>>>> >>>> > >>>>>>>>>>>>> >>>> Python has been installed as > >>>>>>>>>>>>> >>>> > >>>>>>>>>>>>> >>>> /usr/local/bin/python3 > >>>>>>>>>>>>> >>>> > >>>>>>>>>>>>> >>>> > >>>>>>>>>>>>> >>>> Unversioned symlinks `python`, `python-config`, `pip` > etc. pointing to > >>>>>>>>>>>>> >>>> > >>>>>>>>>>>>> >>>> `python3`, `python3-config`, `pip3` etc., respectively, > have been installed into > >>>>>>>>>>>>> >>>> > >>>>>>>>>>>>> >>>> /usr/local/opt/[email protected]/libexec/bin > >>>>>>>>>>>>> >>>> > >>>>>>>>>>>>> >>>> > >>>>>>>>>>>>> >>>> You can install Python packages with > >>>>>>>>>>>>> >>>> > >>>>>>>>>>>>> >>>> pip3 install <package> > >>>>>>>>>>>>> >>>> > >>>>>>>>>>>>> >>>> They will install into the site-package directory > >>>>>>>>>>>>> >>>> > >>>>>>>>>>>>> >>>> /usr/local/lib/python3.9/site-packages > >>>>>>>>>>>>> >>>> > >>>>>>>>>>>>> >>>> > >>>>>>>>>>>>> >>>> See: https://docs.brew.sh/Homebrew-and-Python > >>>>>>>>>>>>> >>>> > >>>>>>>>>>>>> >>>> ==> Analytics > >>>>>>>>>>>>> >>>> > >>>>>>>>>>>>> >>>> install: 755,419 (30 days), 2,396,024 (90 days), > 2,995,387 (365 days) > >>>>>>>>>>>>> >>>> > >>>>>>>>>>>>> >>>> install-on-request: 244,063 (30 days), 714,665 (90 > days), 799,812 (365 days) > >>>>>>>>>>>>> >>>> > >>>>>>>>>>>>> >>>> build-error: 0 (30 days) > >>>>>>>>>>>>> >>>> > >>>>>>>>>>>>> >>>> > >>>>>>>>>>>>> >>>> Best Regards, > >>>>>>>>>>>>> >>>> > >>>>>>>>>>>>> >>>> Trevor Karn > >>>>>>>>>>>>> >>>> > >>>>>>>>>>>>> >>>> > >>>>>>>>>>>>> >>>> On Mon, Feb 8, 2021 at 8:17 AM Dima Pasechnik < > [email protected]> wrote: > >>>>>>>>>>>>> >>>>> > >>>>>>>>>>>>> >>>>> Could it be that you need to update your Homebrew (?) > python3 package? > >>>>>>>>>>>>> >>>>> What version do you have now? > >>>>>>>>>>>>> >>>>> E.g. on a box where the latest Sage builds I have > >>>>>>>>>>>>> >>>>> > >>>>>>>>>>>>> >>>>> % brew info python3 > >>>>>>>>>>>>> >>>>> > >>>>>>>>>>>>> >>>>> [email protected]: stable 3.9.1 (bottled) > >>>>>>>>>>>>> >>>>> Interpreted, interactive, object-oriented programming > language > >>>>>>>>>>>>> >>>>> https://www.python.org/ > >>>>>>>>>>>>> >>>>> /usr/local/Cellar/[email protected]/3.9.1_8 (4,057 files, > 67.8MB) * > >>>>>>>>>>>>> >>>>> Poured from bottle on 2021-02-06 at 10:13:24 > >>>>>>>>>>>>> >>>>> From: > https://github.com/Homebrew/homebrew-core/blob/HEAD/Formula/[email protected] > >>>>>>>>>>>>> >>>>> > >>>>>>>>>>>>> >>>>> > >>>>>>>>>>>>> >>>>> On Mon, Feb 8, 2021 at 1:53 PM Trevor Karn < > [email protected]> wrote: > >>>>>>>>>>>>> >>>>> > > >>>>>>>>>>>>> >>>>> > Ah I see, thanks for explaining. > >>>>>>>>>>>>> >>>>> > > >>>>>>>>>>>>> >>>>> > Here is my top-level config.log. > >>>>>>>>>>>>> >>>>> > > >>>>>>>>>>>>> >>>>> > Best Regards, > >>>>>>>>>>>>> >>>>> > > >>>>>>>>>>>>> >>>>> > Trevor Karn > >>>>>>>>>>>>> >>>>> > > >>>>>>>>>>>>> >>>>> > > >>>>>>>>>>>>> >>>>> > On Mon, Feb 8, 2021 at 7:09 AM Dima Pasechnik < > [email protected]> wrote: > >>>>>>>>>>>>> >>>>> >> > >>>>>>>>>>>>> >>>>> >> > >>>>>>>>>>>>> >>>>> >> > >>>>>>>>>>>>> >>>>> >> On Mon, 8 Feb 2021, 13:02 Trevor Karn, < > [email protected]> wrote: > >>>>>>>>>>>>> >>>>> >>> > >>>>>>>>>>>>> >>>>> >>> Thanks for sending that link. I am confused > though, because it says a fix was issued. Does that mean it should work now? > >>>>>>>>>>>>> >>>>> >> > >>>>>>>>>>>>> >>>>> >> > >>>>>>>>>>>>> >>>>> >> sorry, I was not clear. What I meant to say that it > appears to be a well-known issue in the Python@macOS universe, > >>>>>>>>>>>>> >>>>> >> and lately all seems to be OK with Sage. > >>>>>>>>>>>>> >>>>> >> > >>>>>>>>>>>>> >>>>> >> To figure out exactly goes wrong in your case, we > need to know where Python3 used in Sage is coming from. > >>>>>>>>>>>>> >>>>> >> Please post the top-level config.log > >>>>>>>>>>>>> >>>>> >> > >>>>>>>>>>>>> >>>>> >> > >>>>>>>>>>>>> >>>>> >>> > >>>>>>>>>>>>> >>>>> >>> And yes, I am on the most recent develop branch > >>>>>>>>>>>>> >>>>> >>> > >>>>>>>>>>>>> >>>>> >>> On Mon, Feb 8, 2021 at 5:42 AM Dima Pasechnik < > [email protected]> wrote: > >>>>>>>>>>>>> >>>>> >>>> > >>>>>>>>>>>>> >>>>> >>>> This seems to be well-known issue, see e.g > >>>>>>>>>>>>> >>>>> >>>> https://github.com/pypa/virtualenv/issues/2027 > >>>>>>>>>>>>> >>>>> >>>> > >>>>>>>>>>>>> >>>>> >>>> Are you on the most recent develop branch > (9.3.beta7)? > >>>>>>>>>>>>> >>>>> >>>> > >>>>>>>>>>>>> >>>>> >>>> On Mon, Feb 8, 2021 at 9:20 AM Trevor Karn < > [email protected]> wrote: > >>>>>>>>>>>>> >>>>> >>>> > > >>>>>>>>>>>>> >>>>> >>>> > Hi, > >>>>>>>>>>>>> >>>>> >>>> > > >>>>>>>>>>>>> >>>>> >>>> > I'm trying to build Sage from the source code. > I cloned it from git, and tried to build from the develop branch using make > from the sage directory. I ran into trouble building cython. The error > message suggested that I email this group. Does anyone have any advice on > how to proceed? > >>>>>>>>>>>>> >>>>> >>>> > > >>>>>>>>>>>>> >>>>> >>>> > I am using macOS Big Sur 11.2 on a MacBook Air. > >>>>>>>>>>>>> >>>>> >>>> > > >>>>>>>>>>>>> >>>>> >>>> > The log file is attached, this is from a second > run - it failed once, and I tried running make a second time without any > changes and this is the log from the second run, which returns the same > error just without all of the info before it (eg. the flint installation). > >>>>>>>>>>>>> >>>>> >>>> > > >>>>>>>>>>>>> >>>>> >>>> > Thanks so much. > >>>>>>>>>>>>> >>>>> >>>> > > >>>>>>>>>>>>> >>>>> >>>> > Best, > >>>>>>>>>>>>> >>>>> >>>> > Trevor > >>>>>>>>>>>>> >>>>> >>>> > > >>>>>>>>>>>>> >>>>> >>>> > -- > >>>>>>>>>>>>> >>>>> >>>> > 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 [email protected] > . > >>>>>>>>>>>>> >>>>> >>>> > To view this discussion on the web visit > https://groups.google.com/d/msgid/sage-devel/1c93ec2e-86bd-45f0-bba0-cc254a392305n%40googlegroups.com > . > >>>>>>>>>>>>> >>>>> >>>> > >>>>>>>>>>>>> >>>>> >>>> -- > >>>>>>>>>>>>> >>>>> >>>> You received this message because you are > subscribed to a topic in the Google Groups "sage-devel" group. > >>>>>>>>>>>>> >>>>> >>>> To unsubscribe from this topic, visit > https://groups.google.com/d/topic/sage-devel/TmbLnmwz2mg/unsubscribe. > >>>>>>>>>>>>> >>>>> >>>> To unsubscribe from this group and all its > topics, send an email to [email protected]. > >>>>>>>>>>>>> >>>>> >>>> To view this discussion on the web visit > https://groups.google.com/d/msgid/sage-devel/CAAWYfq3CFFAYzUtNnSrt_RPKW7X_p8j_VXGtZbKLWG%2BST%3DCO%2BQ%40mail.gmail.com > . > >>>>>>>>>>>>> >>>>> >>> > >>>>>>>>>>>>> >>>>> >>> -- > >>>>>>>>>>>>> >>>>> >>> Best, > >>>>>>>>>>>>> >>>>> >>> > >>>>>>>>>>>>> >>>>> >>> Trevor > >>>>>>>>>>>>> >>>>> >>> > >>>>>>>>>>>>> >>>>> >>> -- > >>>>>>>>>>>>> >>>>> >>> 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 [email protected]. > >>>>>>>>>>>>> >>>>> >>> To view this discussion on the web visit > https://groups.google.com/d/msgid/sage-devel/CAJ6VCMAVGG57CHovd7zoXa0C3Nxsr3WfXi0FWwapKrDfup7_sA%40mail.gmail.com > . > >>>>>>>>>>>>> >>>>> >> > >>>>>>>>>>>>> >>>>> >> -- > >>>>>>>>>>>>> >>>>> >> You received this message because you are > subscribed to a topic in the Google Groups "sage-devel" group. > >>>>>>>>>>>>> >>>>> >> To unsubscribe from this topic, visit > https://groups.google.com/d/topic/sage-devel/TmbLnmwz2mg/unsubscribe. > >>>>>>>>>>>>> >>>>> >> To unsubscribe from this group and all its topics, > send an email to [email protected]. > >>>>>>>>>>>>> >>>>> >> To view this discussion on the web visit > https://groups.google.com/d/msgid/sage-devel/CAAWYfq026cNP9FTmBySPskZZoc%2BH4ykTQO7je6TW4YTkirg_qw%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 [email protected]. > >>>>>>>>>>>>> >>>>> > To view this discussion on the web visit > https://groups.google.com/d/msgid/sage-devel/CAJ6VCMDJEN7KzDmvB0x0GDrXiQrK3F_e_eBZvSJf-JxVre0n-Q%40mail.gmail.com > . > >>>>>>>>>>>>> >>>>> > >>>>>>>>>>>>> >>>>> -- > >>>>>>>>>>>>> >>>>> You received this message because you are subscribed > to a topic in the Google Groups "sage-devel" group. > >>>>>>>>>>>>> >>>>> To unsubscribe from this topic, visit > https://groups.google.com/d/topic/sage-devel/TmbLnmwz2mg/unsubscribe. > >>>>>>>>>>>>> >>>>> To unsubscribe from this group and all its topics, > send an email to [email protected]. > >>>>>>>>>>>>> >>>>> > >>>>>>>>>>>>> >>>>> To view this discussion on the web visit > https://groups.google.com/d/msgid/sage-devel/CAAWYfq3meWN5AWip9BG5GzJ%3DFfLvoHKFrpS6Ezmq4X2GWH8mQw%40mail.gmail.com > . > >>>>>>>>>>>>> >>> > >>>>>>>>>>>>> >>> -- > >>>>>>>>>>>>> >>> You received this message because you are subscribed to > a topic in the Google Groups "sage-devel" group. > >>>>>>>>>>>>> >>> To unsubscribe from this topic, visit > https://groups.google.com/d/topic/sage-devel/TmbLnmwz2mg/unsubscribe. > >>>>>>>>>>>>> >>> To unsubscribe from this group and all its topics, send > an email to [email protected]. > >>>>>>>>>>>>> >>> > >>>>>>>>>>>>> >>> To view this discussion on the web visit > https://groups.google.com/d/msgid/sage-devel/c02796d9-9057-41e2-829f-eeb933132d42n%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 [email protected]. > >>>>>>>>>>>>> > >>>>>>>>>>>>> > To view this discussion on the web visit > https://groups.google.com/d/msgid/sage-devel/bd636baa-f6b1-42f7-866b-77ba0af40b6en%40googlegroups.com > . > >>>>>>>>>>>>> > >>>>>>>>>>>>> -- > >>>>>>>>>>>>> You received this message because you are subscribed to a > topic in the Google Groups "sage-devel" group. > >>>>>>>>>>>>> To unsubscribe from this topic, visit > https://groups.google.com/d/topic/sage-devel/TmbLnmwz2mg/unsubscribe. > >>>>>>>>>>>>> To unsubscribe from this group and all its topics, send an > email to [email protected]. > >>>>>>>>>>>>> > >>>>>>>>>>>>> To view this discussion on the web visit > https://groups.google.com/d/msgid/sage-devel/CAAWYfq08zf6vp0LfT%2BGfAy25ML95cxTyxAQho9gB_UdGjqpHFA%40mail.gmail.com > . > >>>>>>>>>>> > >>>>>>>>>>> -- > >>>>>>>>>>> You received this message because you are subscribed to a > topic in the Google Groups "sage-devel" group. > >>>>>>>>>>> To unsubscribe from this topic, visit > https://groups.google.com/d/topic/sage-devel/TmbLnmwz2mg/unsubscribe. > >>>>>>>>>>> To unsubscribe from this group and all its topics, send an > email to [email protected]. > >>>>>>>>>>> > >>>>>>>>>>> To view this discussion on the web visit > https://groups.google.com/d/msgid/sage-devel/c6d5aec3-7f1c-4dc7-a94b-d1e2ab5fdf53n%40googlegroups.com > . > >>>>>>>>>> > >>>>>>>>>> -- > >>>>>>>>>> Best, > >>>>>>>>>> > >>>>>>>>>> Trevor > >>>>>>>>> > >>>>>>>>> -- > >>>>>>>>> You received this message because you are subscribed to a topic > in the Google Groups "sage-devel" group. > >>>>>>>>> To unsubscribe from this topic, visit > https://groups.google.com/d/topic/sage-devel/TmbLnmwz2mg/unsubscribe. > >>>>>>>>> To unsubscribe from this group and all its topics, send an email > to [email protected]. > >>>>>>>>> > >>>>>>>>> To view this discussion on the web visit > https://groups.google.com/d/msgid/sage-devel/47b9954f-e37a-4a81-a7f4-7747b8139e5an%40googlegroups.com > . > >>>>>>> > >>>>>>> -- > >>>>>>> You received this message because you are subscribed to a topic in > the Google Groups "sage-devel" group. > >>>>>>> To unsubscribe from this topic, visit > https://groups.google.com/d/topic/sage-devel/TmbLnmwz2mg/unsubscribe. > >>>>>>> To unsubscribe from this group and all its topics, send an email > to [email protected]. > >>>>>>> > >>>>>>> To view this discussion on the web visit > https://groups.google.com/d/msgid/sage-devel/415b45c0-6ee0-41bf-ab36-0a82153fd66fn%40googlegroups.com > . > >>>>> > >>>>> -- > >>>>> You received this message because you are subscribed to a topic in > the Google Groups "sage-devel" group. > >>>>> To unsubscribe from this topic, visit > https://groups.google.com/d/topic/sage-devel/TmbLnmwz2mg/unsubscribe. > >>>>> To unsubscribe from this group and all its topics, send an email to > [email protected]. > >>>>> > >>>>> To view this discussion on the web visit > https://groups.google.com/d/msgid/sage-devel/aafdb9d9-fdc8-4761-864d-051ee78536b3n%40googlegroups.com > . > >>> > >>> -- > >>> You received this message because you are subscribed to a topic in the > Google Groups "sage-devel" group. > >>> To unsubscribe from this topic, visit > https://groups.google.com/d/topic/sage-devel/TmbLnmwz2mg/unsubscribe. > >>> To unsubscribe from this group and all its topics, send an email to > [email protected]. > >>> > >>> To view this discussion on the web visit > https://groups.google.com/d/msgid/sage-devel/34970320-117f-406c-9e28-9c8fbb7a87d6n%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 [email protected]. > > To view this discussion on the web visit > https://groups.google.com/d/msgid/sage-devel/b66c5f47-43b6-4b27-8d3f-b0962b57dd75n%40googlegroups.com > . > > -- > You received this message because you are subscribed to a topic in the > Google Groups "sage-devel" group. > To unsubscribe from this topic, visit > https://groups.google.com/d/topic/sage-devel/TmbLnmwz2mg/unsubscribe. > To unsubscribe from this group and all its topics, send an email to > [email protected]. > To view this discussion on the web visit > https://groups.google.com/d/msgid/sage-devel/CAAWYfq05FEVaYHmt%2BkCuqWCmrmETZ1GjPm7_KmGLtBnyk0v%3DHw%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 [email protected]. To view this discussion on the web visit https://groups.google.com/d/msgid/sage-devel/CAJ6VCMDbN4HT-rxZZmQTPRGy%3Dja5KeAZfqk_9CzmWCjZVD9zoQ%40mail.gmail.com.
