>From the log: ./configure --enable-system-site-packagesls (SIC!)
## Checking whether SageMath should install SPKG scipy... ## ## ------------------------------------------------------ ## configure:90867: checking whether any of openblas is installed as or will be installed as SPKG configure:90877: result: no configure:90881: checking if --enable-system-site-packages was used configure:90939: result: no; skipping check configure:90976: no suitable system package found for SPKG scipy So please run ./configure --enable-system-site-packages without a typo. On Tue, Sep 24, 2024 at 10:41 PM Anne Schilling <anne1.schill...@gmail.com> wrote: > > Thank you, Dima! > I am posting the config.log after running > > source .homebrew-build-env > ./bootstrap > ./configure --enable-system-site-packages > > This is what I get when running python3 > > MacBook-Pro-3:sage anne$ python3 > Python 3.12.6 (main, Sep 6 2024, 19:03:47) [Clang 16.0.0 > (clang-1600.0.26.3)] on darwin > Type "help", "copyright", "credits" or "license" for more information. > >>> import scipy > >>> > > Best wishes, > > Anne > > On Tuesday, September 24, 2024 at 2:20:25 PM UTC-7 dim...@gmail.com wrote: >> >> On Tue, Sep 24, 2024 at 9:41 PM Anne Schilling >> <anne1.s...@gmail.com> wrote: >> > >> > Thank you for your suggestions, Dima! >> > >> > I am still having trouble though: >> > >> [...] >> >> > ==> Reinstalling scipy >> > ==> Pouring scipy--1.14.1.arm64_sequoia.bottle.tar.gz >> > 🍺 /opt/homebrew/Cellar/scipy/1.14.1: 1,389 files, 63.8MB >> > ==> Running `brew cleanup scipy`... >> > Disable this behaviour by setting HOMEBREW_NO_INSTALL_CLEANUP. >> > Hide these hints with HOMEBREW_NO_ENV_HINTS (see `man brew`). >> > MacBook-Pro-3:sage anne$ source $SAGE_ROOT/.homebrew-build-env >> > >> > ./bootstrap >> > ... >> > ./configure >> >> You must run >> >> source .homebrew-build-env >> ./bootstrap >> ./configure --enable-system-site-packages >> >> and then you can check its output (or the top-level config.log) for >> >> scipy: using system package; SPKG will not >> be installed >> >> If you have that in, run make. >> >> Else, post said config.log. Also check that you actually got scipy for >> the python you're using, >> by starting it and running "import scipy" >> >> >> Dima >> >> >> > ... >> > >> > make >> > ... >> > [sage_conf-10.4] [spkg-install] Removing file or directory >> > /Users/anne/sage/sage/local/var/lib/sage/venv-python3.9/bin/sage-config >> > [sage_conf-10.4] [spkg-install] Removing file or directory >> > /Users/anne/sage/sage/local/var/lib/sage/venv-python3.9/bin/sage-env-config >> > [sage_conf-10.4] [spkg-install] Removing file or directory >> > /Users/anne/sage/sage/local/var/lib/sage/venv-python3.9/lib/python3.9/site-packages/__editable__.sage_conf-10.4.pth >> > [sage_conf-10.4] [spkg-install] Removing file or directory >> > /Users/anne/sage/sage/local/var/lib/sage/venv-python3.9/lib/python3.9/site-packages/__editable___sage_conf_10_4_finder.py >> > [sage_conf-10.4] [spkg-install] Removing file or directory >> > /Users/anne/sage/sage/local/var/lib/sage/venv-python3.9/lib/python3.9/site-packages/sage_conf-10.4.dist-info/ >> > [sage_conf-10.4] [spkg-install] Successfully uninstalled sage-conf-10.4 >> > [sage_conf-10.4] [spkg-install] changing mode of >> > /Users/anne/sage/sage/local/var/lib/sage/venv-python3.9/bin/sage-config to >> > 755 >> > [sage_conf-10.4] [spkg-install] Successfully installed sage-conf-10.4 >> > [sage_conf-10.4] Moving package files from temporary location >> > /Users/anne/sage/sage/local/var/lib/sage/venv-python3.9/var/tmp/sage/build/sage_conf-10.4/inst >> > to /Users/anne/sage/sage/local/var/lib/sage/venv-python3.9 >> > [scipy-1.12.0] Applying patches from ../patches... >> > [scipy-1.12.0] Applying ../patches/tests_no_internet_dependency.patch >> > [scipy-1.12.0] patching file 'scipy/datasets/meson.build' >> > [sage_conf-10.4] Deleting build directory >> > /Users/anne/sage/sage/local/var/lib/sage/venv-python3.9/var/tmp/sage/build/sage_conf-10.4 >> > [sage_conf-10.4] Finished installing sage_conf-10.4 >> > [scipy-1.12.0] Host system: Darwin MacBook-Pro-3.local 24.0.0 Darwin >> > Kernel Version 24.0.0: Mon Aug 12 20:51:54 PDT 2024; >> > root:xnu-11215.1.10~2/RELEASE_ARM64_T6000 arm64 >> > [scipy-1.12.0] C compiler: gcc, Apple clang version 16.0.0 >> > (clang-1600.0.26.3), Target: arm64-apple-darwin24.0.0, Thread model: >> > posix, InstalledDir: >> > /Applications/Xcode.app/Contents/Developer/Toolchains/XcodeDefault.xctoolchain/usr/bin >> > [scipy-1.12.0] No stamp file for package 'scipy' in >> > /Users/anne/sage/sage/local/var/lib/sage/venv-python3.9/var/lib/sage/installed >> > [scipy-1.12.0] No spkg-legacy-uninstall script; nothing to do >> > [scipy-1.12.0] [spkg-install] Installing scipy-1.12.0 >> > [scipy-1.12.0] [spkg-install] * Building wheel... >> > [scipy-1.12.0] [spkg-install] Project name: scipy >> > [scipy-1.12.0] [spkg-install] Project version: 1.12.0 >> > [scipy-1.12.0] [spkg-install] C compiler for the host machine: gcc (clang >> > 16.0.0 "Apple clang version 16.0.0 (clang-1600.0.26.3)") >> > [scipy-1.12.0] [spkg-install] C linker for the host machine: gcc ld64 >> > classic PROJECT:ld64 >> > [scipy-1.12.0] [spkg-install] C++ compiler for the host machine: g++ >> > (clang 16.0.0 "Apple clang version 16.0.0 (clang-1600.0.26.3)") >> > [scipy-1.12.0] [spkg-install] C++ linker for the host machine: g++ ld64 >> > classic PROJECT:ld64 >> > [scipy-1.12.0] [spkg-install] Cython compiler for the host machine: cython >> > (cython 3.0.10) >> > [scipy-1.12.0] [spkg-install] Host machine cpu family: aarch64 >> > [scipy-1.12.0] [spkg-install] Host machine cpu: aarch64 >> > [scipy-1.12.0] [spkg-install] Program python found: YES >> > (/Users/anne/sage/sage/local/var/lib/sage/venv-python3.9/bin/python3) >> > [scipy-1.12.0] [spkg-install] Found pkg-config: YES >> > (/opt/homebrew/bin/pkg-config) 0.29.2 >> > [scipy-1.12.0] [spkg-install] Run-time dependency python found: YES 3.9 >> > [scipy-1.12.0] [spkg-install] Program cython found: YES >> > (/Users/anne/sage/sage/local/var/lib/sage/venv-python3.9/bin/cython) >> > [scipy-1.12.0] [spkg-install] Compiler for C supports arguments >> > -Wno-unused-but-set-variable: YES >> > [scipy-1.12.0] [spkg-install] Compiler for C supports arguments >> > -Wno-unused-function: YES >> > [scipy-1.12.0] [spkg-install] Compiler for C supports arguments >> > -Wno-conversion: YES >> > [scipy-1.12.0] [spkg-install] Compiler for C supports arguments >> > -Wno-misleading-indentation: YES >> > [scipy-1.12.0] [spkg-install] Library m found: YES >> > [scipy-1.12.0] [spkg-install] >> > [scipy-1.12.0] [spkg-install] ../meson.build:80:0: ERROR: Compiler >> > gfortran cannot compile programs. >> > [scipy-1.12.0] [spkg-install] >> > [scipy-1.12.0] [spkg-install] A full log can be found at >> > /Users/anne/sage/sage/local/var/lib/sage/venv-python3.9/var/tmp/sage/build/scipy-1.12.0/src/.mesonpy-igf88b0d/meson-logs/meson-log.txt >> > [scipy-1.12.0] [spkg-install] >> > [scipy-1.12.0] [spkg-install] ERROR Backend subprocess exited when trying >> > to invoke build_wheel >> > [scipy-1.12.0] [spkg-install] >> > ******************************************************************************** >> > [scipy-1.12.0] [spkg-install] Error building a wheel for scipy-1.12.0 >> > [scipy-1.12.0] [spkg-install] >> > ******************************************************************************** >> > [scipy-1.12.0] >> > ************************************************************************ >> > [scipy-1.12.0] Error installing package scipy-1.12.0 >> > [scipy-1.12.0] >> > ************************************************************************ >> > [scipy-1.12.0] Please email sage-devel >> > (http://groups.google.com/group/sage-devel) >> > [scipy-1.12.0] explaining the problem and including the log files >> > [scipy-1.12.0] /Users/anne/sage/sage/logs/pkgs/scipy-1.12.0.log >> > [scipy-1.12.0] and >> > [scipy-1.12.0] /Users/anne/sage/sage/config.log >> > [scipy-1.12.0] Describe your computer, operating system, etc. >> > [scipy-1.12.0] If you want to try to fix the problem yourself, *don't* >> > just cd to >> > [scipy-1.12.0] >> > /Users/anne/sage/sage/local/var/lib/sage/venv-python3.9/var/tmp/sage/build/scipy-1.12.0 >> > and type 'make' or whatever is appropriate. >> > [scipy-1.12.0] Instead, the following commands setup all environment >> > variables >> > [scipy-1.12.0] correctly and load a subshell for you to debug the error: >> > [scipy-1.12.0] (cd >> > '/Users/anne/sage/sage/local/var/lib/sage/venv-python3.9/var/tmp/sage/build/scipy-1.12.0' >> > && '/Users/anne/sage/sage/sage' --buildsh) >> > [scipy-1.12.0] When you are done debugging, you can type "exit" to leave >> > the subshell. >> > [scipy-1.12.0] >> > ************************************************************************ >> > make[4]: *** [scipy-SAGE_VENV-no-deps] Error 1 >> > make[3]: *** >> > [/Users/anne/sage/sage/local/var/lib/sage/venv-python3.9/var/lib/sage/installed/scipy-1.12.0] >> > Error 2 >> > make[2]: *** [all-start] Error 2 >> > *************************************************************** >> > Error building Sage. >> > >> > The following package(s) may have failed to build (not necessarily >> > during this run of 'make all-start'): >> > >> > * package: ipykernel-6.27.1 >> > last build time: Sep 24 13:38 >> > log file: /Users/anne/sage/sage/logs/pkgs/ipykernel-6.27.1.log >> > >> > * package: scipy-1.12.0 >> > last build time: Sep 24 13:38 >> > log file: /Users/anne/sage/sage/logs/pkgs/scipy-1.12.0.log >> > >> > 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-start] Error 1 >> > make: *** [all] Error 2 >> > >> > Even though brew installed scipy-1.14.1, the error is about scipy-1.12.0. >> > >> > Best wishes, >> > >> > Anne >> > >> > On Tuesday, September 24, 2024 at 9:28:14 AM UTC-7 dim...@gmail.com wrote: >> >> >> >> from your scipy log: >> >> >> >> [spkg-install] Library m found: YES >> >> [spkg-install] >> >> [spkg-install] ../meson.build:80:0: ERROR: Compiler gfortran cannot >> >> compile programs. >> >> [spkg-install] >> >> [spkg-install] A full log can be found at >> >> /Users/anne/sage/sage/local/var/lib/sage/venv-python3.9/var/tmp/sage/build/scipy-1.12.0/src/.mesonpy-f8mmdnb8/meson-logs/meson-log.txt >> >> >> >> The scipy version (1.12) pre-dates macOS 15.0 by almost a year. >> >> That's totally unsurprising that it doesn't work. >> >> Note that even the latest scipy version, 1.14.1, was released before >> >> macOS 15.0. >> >> >> >> I'd suggest to install (update) Homebrew, (to) the latest version. >> >> Install as many Homebrew packages usable by Sage as possible, in >> >> particular scipy, pari-gp, singular, etc, and >> >> run (after the all-important step of sourcing .homebrew-build-env) >> >> >> >> ./configure --enable-system-site-packages --disable-notebook >> >> >> >> to get a semi-minimal configuration before running make. Although I >> >> expect more issues with giac, gap, etc. >> >> Another advantage is that building time will be cut to almost the >> >> minimal (basically, the only big thing to build >> >> will be sagelib itself) >> >> >> >> Dima >> >> >> >> >> >> On Tue, Sep 24, 2024 at 4:39 PM Anne Schilling >> >> <anne1.s...@gmail.com> wrote: >> >> > >> >> > Hi Dima, >> >> > >> >> > Here is the log for MacOS 10.15.7. >> >> > >> >> > Thank you for your help! >> >> > >> >> > Anne >> >> > >> >> > On Tuesday, September 24, 2024 at 8:38:02 AM UTC-7 dim...@gmail.com >> >> > wrote: >> >> >> >> >> >> Hi Anne, >> >> >> >> >> >> Please post the log file for this: >> >> >> >> >> >> package: ipykernel-6.27.1 >> >> >> last build time: Sep 23 23:48 >> >> >> log file: /Users/anne/sage/sage/logs/pkgs/ipykernel-6.27.1.log >> >> >> >> >> >> On Tue, Sep 24, 2024 at 8:10 AM Anne Schilling >> >> >> <anne1.s...@gmail.com> wrote: >> >> >> > >> >> >> > >> >> >> > Dear All, >> >> >> > >> >> >> > To add further confusion to this issue, I now tried to install sage >> >> >> > from source on an older MacOS 10.15.7 and got this error message. I >> >> >> > followed all the instructions in README.md: >> >> >> > >> >> >> > ... >> >> >> > [cypari-2.1.5] [spkg-pipinst] Looking in links: >> >> >> > /Users/anne/sage/sage/local/var/lib/sage/venv-python3.10/var/lib/sage/wheels >> >> >> > [cypari-2.1.5] [spkg-pipinst] Processing >> >> >> > /Users/anne/sage/sage/local/var/lib/sage/venv-python3.10/var/lib/sage/wheels/cypari2-2.1.5-cp310-cp310-macosx_10_15_x86_64.whl >> >> >> > (from -r >> >> >> > /Users/anne/sage/sage/local/var/lib/sage/venv-python3.10/var/lib/sage/scripts/cypari/spkg-requirements.txt >> >> >> > (line 1)) >> >> >> > [cypari-2.1.5] [spkg-pipinst] Requirement already satisfied: >> >> >> > cysignals>=1.7 in >> >> >> > /Users/anne/sage/sage/local/var/lib/sage/venv-python3.10/lib/python3.10/site-packages >> >> >> > (from cypari2@ >> >> >> > file:///Users/anne/sage/sage/local/var/lib/sage/venv-python3.10/var/lib/sage/wheels/cypari2-2.1.5-cp310-cp310-macosx_10_15_x86_64.whl->-r >> >> >> > >> >> >> > /Users/anne/sage/sage/local/var/lib/sage/venv-python3.10/var/lib/sage/scripts/cypari/spkg-requirements.txt >> >> >> > (line 1)) (1.11.4) >> >> >> > [cypari-2.1.5] [spkg-pipinst] Installing collected packages: cypari2 >> >> >> > [cypari-2.1.5] [spkg-pipinst] Successfully installed cypari2-2.1.5 >> >> >> > [cypari-2.1.5] Deleting build directory >> >> >> > /Users/anne/sage/sage/local/var/lib/sage/venv-python3.10/var/tmp/sage/build/cypari-2.1.5 >> >> >> > [cypari-2.1.5] Finished installing cypari-2.1.5 >> >> >> > [cypari-2.1.5] real 12m29.794s user 10m52.117s sys 0m16.185s >> >> >> > make[2]: *** [all-start] Error 2 >> >> >> > *************************************************************** >> >> >> > Error building Sage. >> >> >> > >> >> >> > The following package(s) may have failed to build (not necessarily >> >> >> > during this run of 'make all-start'): >> >> >> > >> >> >> > * package: ipykernel-6.27.1 >> >> >> > last build time: Sep 23 23:48 >> >> >> > log file: /Users/anne/sage/sage/logs/pkgs/ipykernel-6.27.1.log >> >> >> > >> >> >> > 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. >> >> >> > >> >> >> > real 44m57.426s user 209m54.674s sys 32m35.642s >> >> >> > make[1]: *** [all-start] Error 1 >> >> >> > make: *** [all] Error 2 >> >> >> > >> >> >> > Best wishes, >> >> >> > >> >> >> > Anne >> >> >> > On Monday, September 23, 2024 at 9:10:12 PM UTC-7 Anne Schilling >> >> >> > wrote: >> >> >> >> >> >> >> >> Hi Kwankyu, >> >> >> >> >> >> >> >> I tried the simplified installation instructions in 38659. Now I >> >> >> >> get the following error message (after doing make distclean as >> >> >> >> well): >> >> >> >> >> >> >> >> [cypari-2.2.0] [spkg-pipinst] Requirement already satisfied: >> >> >> >> cysignals>=1.11.3 in >> >> >> >> /Applications/sage/local/var/lib/sage/venv-python3.9/lib/python3.9/site-packages >> >> >> >> (from cypari2@ >> >> >> >> file:///Applications/sage/local/var/lib/sage/venv-python3.9/var/lib/sage/wheels/cypari2-2.2.0-cp39-cp39-macosx_11_0_universal2.whl->-r >> >> >> >> >> >> >> >> /Applications/sage/local/var/lib/sage/venv-python3.9/var/lib/sage/scripts/cypari/spkg-requirements.txt >> >> >> >> (line 1)) (1.11.4) >> >> >> >> [cypari-2.2.0] [spkg-pipinst] Installing collected packages: cypari2 >> >> >> >> [cypari-2.2.0] [spkg-pipinst] Successfully installed cypari2-2.2.0 >> >> >> >> [cypari-2.2.0] Deleting build directory >> >> >> >> /Applications/sage/local/var/lib/sage/venv-python3.9/var/tmp/sage/build/cypari-2.2.0 >> >> >> >> [cypari-2.2.0] Finished installing cypari-2.2.0 >> >> >> >> [cypari-2.2.0] real 1m44.371s user 1m31.273s sys 0m7.499s >> >> >> >> >> >> >> >> make[2]: *** [all-start] Error 2 >> >> >> >> *************************************************************** >> >> >> >> Error building Sage. >> >> >> >> >> >> >> >> The following package(s) may have failed to build (not necessarily >> >> >> >> during this run of 'make all-start'): >> >> >> >> >> >> >> >> * package: ipykernel-6.27.1 >> >> >> >> last build time: Sep 23 20:59 >> >> >> >> log file: /Applications/sage/logs/pkgs/ipykernel-6.27.1.log >> >> >> >> >> >> >> >> * package: scipy-1.12.0 >> >> >> >> last build time: Sep 23 20:59 >> >> >> >> log file: /Applications/sage/logs/pkgs/scipy-1.12.0.log >> >> >> >> >> >> >> >> >> >> >> >> 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. >> >> >> >> >> >> >> >> real 33m20.291s user 80m26.058s sys 15m16.308s >> >> >> >> >> >> >> >> make[1]: *** [all-start] Error 1 >> >> >> >> make: *** [all] Error 2 >> >> >> >> >> >> >> >> Best wishes, >> >> >> >> >> >> >> >> Anne >> >> >> >> >> >> >> >> On Monday, September 23, 2024 at 5:59:17 PM UTC-7 Kwankyu Lee wrote: >> >> >> >>> >> >> >> >>> Hi Anne, >> >> >> >>> >> >> >> >>> The PR https://github.com/sagemath/sage/pull/38659 aims to >> >> >> >>> simplify the installation instructions in README. >> >> >> >>> >> >> >> >>> As you seem to have a new macOS, would you try the guide in the >> >> >> >>> new README on your platform? >> >> >> >>> >> >> >> >>> I have no idea about the cause of your troubles though. >> >> >> >>> >> >> >> >>> Kwankyu >> >> >> > >> >> >> > -- >> >> >> > 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+...@googlegroups.com. >> >> >> > To view this discussion on the web visit >> >> >> > https://groups.google.com/d/msgid/sage-devel/a53e3416-59c2-4364-9a2d-b5e031d99916n%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+...@googlegroups.com. >> >> > To view this discussion on the web visit >> >> > https://groups.google.com/d/msgid/sage-devel/a32bf782-ac78-4fec-90d2-a1254653e30bn%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+...@googlegroups.com. >> > To view this discussion on the web visit >> > https://groups.google.com/d/msgid/sage-devel/8b8f08c4-4470-4d53-98b7-ac044398e3c4n%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/fcaa0468-9562-4191-bac0-808e7fd7523fn%40googlegroups.com. -- You received this message because you are subscribed to the Google Groups "sage-devel" group. 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