After changing the env compiler flags to stop pplpy-0.8.4 from confusing itself, and re-starting the build, it fails in scipy-1.5.2:
[scipy-1.5.2] clang -bundle -undefined dynamic_lookup -L/Applications/SageMath/local/lib -Wl,-rpath,/Applications/SageMath/local/lib -L. -L/Applications/SageMath/local/lib -Wl,-rpath,/Applications/SageMath/local/lib -bundle -undefined dynamic_lookup -L/Applications/SageMath/local/lib -Wl,-rpath,/Applications/SageMath/local/lib -D__ACCELERATE__ build/temp.macosx-10.9-x86_64-3.8/scipy/fftpack/convolve.o -L/Applications/SageMath/local/lib -Lbuild/temp.macosx-10.9-x86_64-3.8 -o build/lib.macosx-10.9-x86_64-3.8/scipy/fftpack/convolve.cpython-38-darwin.so [scipy-1.5.2] building 'scipy.integrate._quadpack' extension [scipy-1.5.2] compiling C sources [scipy-1.5.2] C compiler: clang -Wno-unused-result -Wsign-compare -Wunreachable-code -DNDEBUG -g -fwrapv -O3 -Wall -Wno-unused -O3 -march=native -isysroot /Applications/Xcode.app/Contents/Developer/Platforms/MacOSX.platform/Developer/SDKs/MacOSX11.1.sdk -D__ACCELERATE__ [scipy-1.5.2] [scipy-1.5.2] compile options: '-DHAVE_CBLAS -Iscipy/_lib/src -I/Applications/SageMath/local/lib/python3.8/site-packages/numpy/core/include -I/Applications/SageMath/local/include/python3.8 -c' [scipy-1.5.2] clang: scipy/integrate/_quadpackmodule.c [scipy-1.5.2] In file included from scipy/integrate/_quadpackmodule.c:4: [scipy-1.5.2] In file included from scipy/integrate/__quadpack.h:28: [scipy-1.5.2] In file included from /Applications/SageMath/local/lib/python3.8/site-packages/numpy/core/include/numpy/arrayobject.h:4: [scipy-1.5.2] In file included from /Applications/SageMath/local/lib/python3.8/site-packages/numpy/core/include/numpy/ndarrayobject.h:12: [scipy-1.5.2] In file included from /Applications/SageMath/local/lib/python3.8/site-packages/numpy/core/include/numpy/ndarraytypes.h:1822: [scipy-1.5.2] /Applications/SageMath/local/lib/python3.8/site-packages/numpy/core/include/numpy/npy_1_7_deprecated_api.h:17:2: warning: "Using deprecated NumPy API, disable it with " "#define NPY_NO_DEPRECATED_API NPY_1_7_API_VERSION" [-W#warnings] [scipy-1.5.2] #warning "Using deprecated NumPy API, disable it with " \ [scipy-1.5.2] ^ [scipy-1.5.2] 1 warning generated. [scipy-1.5.2] /Applications/SageMath/local/bin/gfortran -Wall -g -Wall -g -undefined dynamic_lookup -bundle -bundle -undefined dynamic_lookup -L/Applications/SageMath/local/lib -Wl,-rpath,/Applications/SageMath/local/lib build/temp.macosx-10.9-x86_64-3.8/scipy/integrate/_quadpackmodule.o -L/Applications/SageMath/local/lib -L/Applications/SageMath/local/lib/gcc/x86_64-apple-darwin19.6.0/9.2.0 -L/Applications/SageMath/local/lib -L/Applications/SageMath/local/lib -L/Applications/SageMath/local/lib -Lbuild/temp.macosx-10.9-x86_64-3.8 -lquadpack -lmach -lopenblas -lopenblas -lgfortran -o build/lib.macosx-10.9-x86_64-3.8/scipy/integrate/_quadpack.cpython-38-darwin.so [scipy-1.5.2] ld: library not found for -lSystem [scipy-1.5.2] collect2: error: ld returned 1 exit status [scipy-1.5.2] Running from SciPy source directory. [scipy-1.5.2] /Applications/SageMath/local/lib/python3.8/site-packages/numpy/distutils/system_info.py:838: UserWarning: Specified path /usr/local/include/python3.8 is invalid. [scipy-1.5.2] return self.get_paths(self.section, key) [scipy-1.5.2] /Applications/SageMath/local/lib/python3.8/site-packages/numpy/distutils/system_info.py:838: UserWarning: Specified path /opt/local/include/python3.8 is invalid. [scipy-1.5.2] return self.get_paths(self.section, key) [scipy-1.5.2] error: Command "/Applications/SageMath/local/bin/gfortran -Wall -g -Wall -g -undefined dynamic_lookup -bundle -bundle -undefined dynamic_lookup -L/Applications/SageMath/local/lib -Wl,-rpath,/Applications/SageMath/local/lib build/temp.macosx-10.9-x86_64-3.8/scipy/integrate/_quadpackmodule.o -L/Applications/SageMath/local/lib -L/Applications/SageMath/local/lib/gcc/x86_64-apple-darwin19.6.0/9.2.0 -L/Applications/SageMath/local/lib -L/Applications/SageMath/local/lib -L/Applications/SageMath/local/lib -Lbuild/temp.macosx-10.9-x86_64-3.8 -lquadpack -lmach -lopenblas -lopenblas -lgfortran -o build/lib.macosx-10.9-x86_64-3.8/scipy/integrate/_quadpack.cpython-38-darwin.so" failed with exit status 1 [scipy-1.5.2] Building wheel for scipy (PEP 517): finished with status 'error' [scipy-1.5.2] ERROR: Failed building wheel for scipy [scipy-1.5.2] Failed to build scipy [scipy-1.5.2] ERROR: Failed to build one or more wheels [scipy-1.5.2] Exception information: [scipy-1.5.2] Traceback (most recent call last): [scipy-1.5.2] File "/Applications/SageMath/local/lib/python3.8/site-packages/pip/_internal/cli/base_command.py", line 228, in _main [scipy-1.5.2] status = self.run(options, args) [scipy-1.5.2] File "/Applications/SageMath/local/lib/python3.8/site-packages/pip/_internal/cli/req_command.py", line 182, in wrapper [scipy-1.5.2] return func(self, options, args) [scipy-1.5.2] File "/Applications/SageMath/local/lib/python3.8/site-packages/pip/_internal/commands/wheel.py", line 184, in run [scipy-1.5.2] raise CommandError( [scipy-1.5.2] pip._internal.exceptions.CommandError: Failed to build one or more wheels [scipy-1.5.2] Removed build tracker: '/private/var/folders/_l/4q83bg9j5ysb7qd1n9xpnb4h0000gn/T/pip-req-tracker-ybfte_50' [scipy-1.5.2] ******************************************************************************** [scipy-1.5.2] Error building a wheel for scipy-1.5.2 On Tuesday, December 22, 2020 at 9:40:17 PM UTC-5 Mouse Mousevich wrote: > A lot of people have a lot of problems with Sage-9.2 on MacOS, installing > pre-compiled or building from the source. > > Sage-9.2 has several idiosyncrasies that for me are hard to explain. One - > it deliberately refuses to work with Macports-installed packages, even > though their main difference from similar ones installed via Brew is their > location. How crazy is that? > > Second, pplpy-0.8.4 is "obtuse" enough to try compiling C++ file > linear_algebra.cpp with clang instead of clang++, and then complain that > CFLAGS that are (surprise!) C-specific, do not make sense for C++. Need I > mention that it is impossible to locate clang but not clang++? > > Now, from generic criticisms to specific errors and logs. > > *Platform* > *-* iMac 2020, Intel Core i9 CPU, 32GM RAM > - macOS Catalina 10.15.7 > - Xcode-12.3 (with command-line tools installed) in > /Applications/Xcode.app, and separately installed CLT 12.3 in > /Library/Developer/CommandLineTools. > - Macports 2.6.4, with a ton of packages installed in /opt/local, which > include clang-11, gcc-10, python38 and python39, and OpenSSL-1.1.1i. > > *Problems* > > 1. Sage-9.2 config refuses to use already-installed packages in > /opt/local, spends sh*tload of time and bandwidth downloading what's > already there (except that it downloads Python-3.8.5, and my machine has > Python-3.8.6), and finally fails to compile that pile: > 2. pplpy-0.8.4 uses clang (*not* clang++? Why?) to compile ppl/ > linear_algebra.cpp files, and fails because on my machine CFLAGS > differ from CXXFLAGS (surprise! one sets -std=gnu18, and other one > sets -std=gnu++17). This bug should manifest on all the .cpp files. > > *Logs* > The main log is 5.7 MB, so I don't want to post it unless asked to. > Excerpts: > > Error building Sage. > > The following package(s) may have failed to build (not necessarily > > during this run of 'make all-build'): > > * package: pplpy-0.8.4 > > last build time: Dec 20 22:51 > > log file: /Applications/SageMath/logs/pkgs/pplpy-0.8.4.log > build directory: > /Applications/SageMath/local/var/tmp/sage/build/pplpy-0.8.4 > > and more specifically: > > [pplpy-0.8.4] creating build/temp.macosx-10.9-x86_64-3.8/ppl > > [pplpy-0.8.4] *clang* -Wno-unused-result -Wsign-compare > -Wunreachable-code -DNDEBUG -g -fwrapv -O3 -Wall -Wno-unused -O3 -std=gnu18 > -march=native -isysroot > /Applications/Xcode.app/Contents/Developer/Platforms/MacOSX.platform/Developer/SDKs/MacOSX11.1.sdk > > -O3 *-std=gnu18* -march=native -isysroot > /Applications/Xcode.app/Contents/Developer/Platforms/MacOSX.platform/Developer/SDKs/MacOSX11.1.sdk > > -Ippl -I/Applications/SageMath/local/lib/python3.8/site-packages/gmpy2 > -Ippl -I -I/Applications/SageMath/local > -I/Applications/SageMath/local/lib/python38.zip > -I/Applications/SageMath/local/lib/python3.8 > -I/Applications/SageMath/local/lib/python3.8/lib-dynload > -I/Applications/SageMath/local/lib/python3.8/site-packages > -I/private/var/folders/_l/4q83bg9j5ysb7qd1n9xpnb4h0000gn/T/pip-req-build-_4gwq_tw > > -I/Applications/SageMath/local/include/python3.8 -c ppl/linear_algebra.cpp > -o build/temp.macosx-10.9-x86_64-3.8/ppl/linear_algebra.o > > [pplpy-0.8.4] error: *invalid argument '-std=gnu18' not allowed with > 'C++'* > > [pplpy-0.8.4] error: *command 'clang' failed* with exit status 1 > > [pplpy-0.8.4] Building wheel for pplpy (setup.py): finished with status > 'error' > > [pplpy-0.8.4] ERROR: Failed building wheel for pplpy > > BTW, why is it creating build for macosx-10.9 when the current version of > the OS is 10.15, and SDK is for 11.1? > > On Friday, December 4, 2020 at 11:30:57 AM UTC-5 dim...@gmail.com wrote: > >> On Fri, Dec 4, 2020 at 3:26 PM Mathieu Dutour <mathieu...@gmail.com> >> wrote: >> > >> > On Thursday, 3 December 2020 at 19:13:28 UTC+1 dim...@gmail.com wrote: >> >> >> >> On Thu, Dec 3, 2020 at 5:39 PM Mathieu Dutour <mathieu...@gmail.com> >> wrote: >> >>> >> >>> Thank you for providing this. Keep that in mind for future. >> >>> >> >>> As it turns out, the solution to installing was incredibly simple: >> >>> "brew install sage" >> >> >> >> >> >> on macOS 10.15.7 this appears to install the version 9.2 of >> x86_64.app.dmg by >> >> pulling it from a Sage mirror. >> >> >> >> Does Sage installed this way work? >> >> (I'd be surprised it was the case) >> > >> > That is correct. >> > However, I had to give authorization only one time which represent >> > a progress and allowed me to run sage on macintosh. >> > >> > I still think it should be mentioned in the Sage Installation Guide. >> >> as I already mentioned, for some reason this does not work on a macOS >> 10.15.7 machine I have access to. >> >> Strangely enough, I needed to run first a command >> >> brew cask >> >> (don't know what it actually does, it did >> download (probably git-cloned) something >> >> ==> Tapping homebrew/cask >> Cloning into '/usr/local/Homebrew/Library/Taps/homebrew/homebrew-cask'... >> remote: Enumerating objects: 55, done. >> remote: Counting objects: 100% (55/55), done. >> remote: Compressing objects: 100% (41/41), done. >> remote: Total 574981 (delta 26), reused 19 (delta 14), pack-reused 574926 >> Receiving objects: 100% (574981/574981), 240.80 MiB | 7.59 MiB/s, done. >> Resolving deltas: 100% (409134/409134), done. >> Tapped 1 command and 3739 casks (3,857 files, 259MB). >> >> >> >> brew cask >> >> after which >> >> brew install --cask sage >> >> did seem to work. >> >> Starting sage brought up the popup: >> >> ---------------------------------- >> “SageMath-9.2” cannot be opened because the developer cannot be verified. >> macOS cannot verify that this app is free from malware. >> --------------- >> [move to bin] [cancel] >> ------------------------------------- >> >> So I did >> >> % sudo xattr -r -d com.apple.quarantine /Applications/SageMath-9.2.app >> xattr: No such file: >> /Applications/SageMath-9.2.app/Contents/Resources/sage/local/share/jupyter/kernels/sagemath/doc >> >> >> >> Apparently there is a dangling link pointing there, but OK. It has done >> the job, >> and have an apparently working sage in terminal. Jupyter is broken: >> >> % sage -n >> >> ┌────────────────────────────────────────────────────────────────────┐ >> │ SageMath version 9.2, Release Date: 2020-10-24 │ >> │ Using Python 3.8.5. Type "help()" for help. │ >> └────────────────────────────────────────────────────────────────────┘ >> Please wait while the Sage Jupyter Notebook server starts... >> Traceback (most recent call last): >> File >> "/Applications/SageMath-9.2.app/Contents/Resources/sage/local/lib/python3.8/site-packages/sage/repl/ipython_kernel/install.py", >> >> >> line 307, in have_prerequisites >> from notebook.notebookapp import NotebookApp >> File >> "/Applications/SageMath-9.2.app/Contents/Resources/sage/local/lib/python3.8/site-packages/notebook/notebookapp.py", >> >> >> line 66, in <module> >> from tornado import httpserver >> File >> "/Applications/SageMath-9.2.app/Contents/Resources/sage/local/lib/python3.8/site-packages/tornado/httpserver.py", >> >> >> line 29, in <module> >> import ssl >> File >> "/Applications/SageMath-9.2.app/Contents/Resources/sage/local/lib/python3.8/ssl.py", >> >> >> line 98, in <module> >> import _ssl # if we can't import it, let the error propagate >> ModuleNotFoundError: No module named '_ssl' >> The Jupyter notebook requires ssl, even if you do not use >> https. Install the openssl development packages in your system and >> then rebuild Python (sage -f python3). >> >> >> Also, the app in /Applications/SageMath-9.2 >> >> does not quite work, most stuff from the menu's does not launch, etc. >> >> So this is not really working well, still. :-( >> >> >> >> >> >> >> >> > >> > Mathieu >> > >> > -- >> > You received this message because you are subscribed to the Google >> Groups "sage-support" group. >> > To unsubscribe from this group and stop receiving emails from it, send >> an email to sage-support...@googlegroups.com. >> > To view this discussion on the web visit >> https://groups.google.com/d/msgid/sage-support/4cafb667-ca96-4417-b57e-c3341bafb041n%40googlegroups.com. >> >> >> > -- You received this message because you are subscribed to the Google Groups "sage-support" group. To unsubscribe from this group and stop receiving emails from it, send an email to sage-support+unsubscr...@googlegroups.com. To view this discussion on the web visit https://groups.google.com/d/msgid/sage-support/322f7e81-a0a3-4f07-bd8b-07d54a39a32cn%40googlegroups.com.
