Did you by any chance install fortran via: brew cask install gfortran?
from your config.log file it finds gfortran version 8, but the most recent homebrew fortran is 10.2. Maybe try uninstalling gfortran and then either brew install gcc or brew reinstall gcc to get a more up to date fortran. For example on my Mac when I run gfortran --version I get: GNU Fortran (Homebrew GCC 10.2.0) 10.2.0 On Thursday, October 29, 2020 at 12:34:30 PM UTC-4 modp...@gmail.com wrote: > Okay rebuilding PARI without -mt=pthread option worked. > But now building the documentation fails. Please find the log file > attached. > Anyway, I currently build it without documentation by running 'make build' > only. > But was curious why documentation fails. > > On Wednesday, October 28, 2020 at 8:01:43 PM UTC+1 dim...@gmail.com wrote: > >> >> >> On Wed, 28 Oct 2020, 14:33 Zachary Scherr, <zsc...@gmail.com> wrote: >> >>> Hopefully somebody with more experience can weigh in, but for the record >>> I have pari installed via homebrew and there the configure is only with >>> --with-gmp and --with-readline and that works with building sage. It's >>> plausible that the -mt=pthread is what's causing the issues. >>> >> >> Hombrew does not provide Pari packages. Unless you install them manually >> (these are just data files) >> it will not be used by Sage. >> >> If you install Pari with -mt=pthread >> into /usr/local, with its packages, it will be accepted by Sage, causing >> this problem. >> >> Patches to fix this are welcome. >> Ideally it can be a short C program to link against libpari, which would >> fail with the error message reported on this thread. >> >> >> >> >>> On Wednesday, October 28, 2020 at 10:12:35 AM UTC-4 modp...@gmail.com >>> wrote: >>> >>>> Yes, I have manually installed Pari 2.11.4 after configuring it with: >>>> Confgure --mt=pthread --tune >>>> >>>> On Wednesday, October 28, 2020 at 3:04:01 PM UTC+1 zsc...@gmail.com >>>> wrote: >>>> >>>>> Just wanted to make a couple of comments. First off, brew installs >>>>> llvm as keg-only meaning that sage shouldn't even be able to find it >>>>> unless >>>>> you manually added something like: >>>>> >>>>> export PATH="/usr/local/opt/llvm/bin:$PATH" >>>>> export LDFLAGS="-L/usr/local/opt/llvm/lib" >>>>> export CPPFLAGS="-I/usr/local/opt/llvm/include" >>>>> >>>>> to your profile. But even after I tried that myself, I failed to >>>>> reproduce your error on my own Mac machine. This makes me think that you >>>>> might want to have a look at the version of Pari you installed on your >>>>> computer. I noticed that ./configure finds a copy of Pari in /usr/local >>>>> on >>>>> your computer. You can see that the specific error it references >>>>> mentions: >>>>> >>>>> ld: illegal thread local variable reference to regular symbol >>>>> _PARI_SIGINT_block for architecture x86_64 >>>>> >>>>> If removing llvm and make distclean doesn't solve your problem then >>>>> you may want to look into where you got your Pari. It seems plausible >>>>> that >>>>> Pari might have been built in some funky way and that is what's causing >>>>> your issue. >>>>> On Wednesday, October 28, 2020 at 7:27:27 AM UTC-4 dim...@gmail.com >>>>> wrote: >>>>> >>>>>> try >>>>>> make distclean >>>>>> >>>>>> and the build >>>>>> >>>>>> On Wed, 28 Oct 2020, 09:57 modp...@gmail.com, <modp...@gmail.com> >>>>>> wrote: >>>>>> >>>>>>> >>>>>>> I tried uninstalling LLVM and building it again, but it fails again >>>>>>> for cysignals. >>>>>>> But the problem now seems that it still sets -I and -L flags with >>>>>>> non-existent LLVM directories. >>>>>>> On Tuesday, October 27, 2020 at 5:10:58 PM UTC+1 Matthias Koeppe >>>>>>> wrote: >>>>>>> >>>>>>>> From config.log: >>>>>>>> >>>>>>>> configure:5906: gcc -v >&5 >>>>>>>> Configured with: >>>>>>>> --prefix=/Applications/Xcode.app/Contents/Developer/usr >>>>>>>> --with-gxx-include-dir=/Applications/Xcode.app/Contents/Developer/Platforms/MacOSX.platform/Developer/SDKs/MacOSX.sdk/usr/include/c++/4.2.1 >>>>>>>> Apple clang version 12.0.0 (clang-1200.0.32.21) >>>>>>>> Target: x86_64-apple-darwin19.6.0 >>>>>>>> Thread model: posix >>>>>>>> InstalledDir: >>>>>>>> /Applications/Xcode.app/Contents/Developer/Toolchains/XcodeDefault.xctoolchain/usr/bin >>>>>>>> configure:5917: $? = 0 >>>>>>>> ... >>>>>>>> >>>>>>>> configure:6029: gcc -o conftest -I/usr/local/opt/llvm/include >>>>>>>> -L/usr/local/opt/llvm/lib conftest.c >&5 >>>>>>>> >>>>>>>> >>>>>>>> This looks like an unsupported configuration - injecting these -L >>>>>>>> and -I flags via environment variables, but continuing to use Apple's >>>>>>>> gcc. >>>>>>>> If you are trying to compile with homebrew's llvm, you should >>>>>>>> probably configure by setting CC and CXX as well. But this is also >>>>>>>> untested >>>>>>>> - I have created https://trac.sagemath.org/ticket/30835#ticket for >>>>>>>> testing such a configuration. >>>>>>>> >>>>>>>> >>>>>>>> On Tuesday, October 27, 2020 at 3:46:10 AM UTC-7, Dima Pasechnik >>>>>>>> wrote: >>>>>>>> >>>>>>>>> I'd have tried removing llvm and trying again. Perhaps this is a >>>>>>>>> conflict between Homebrew packages. >>>>>>>>> >>>>>>>>> On Tue, Oct 27, 2020 at 8:42 AM modp...@gmail.com < >>>>>>>>> modp...@gmail.com> wrote: >>>>>>>>> >>>>>>>> Please find config.log and cysignals-1.10.2.log attached. I already >>>>>>>>>> run "source .homebrew-build-env" before configuring. >>>>>>>>>> And yes I also have llvm installed through Homebrew. >>>>>>>>>> >>>>>>>>>> On Monday, October 26, 2020 at 3:23:38 PM UTC+1 dim...@gmail.com >>>>>>>>>> wrote: >>>>>>>>>> >>>>>>>>>>> also note that you apparently have something in >>>>>>>>>>> -L/usr/local/opt/llvm/lib (installed from Homebrew ?) which >>>>>>>>>>> might lead >>>>>>>>>>> to surprises. >>>>>>>>>>> Do you have some LDFLAGS set? >>>>>>>>>>> It would help if you also post logs/pkgs/cysignals-1.10.2.log >>>>>>>>>>> >>>>>>>>>>> On Mon, Oct 26, 2020 at 2:15 PM Dima Pasechnik <dim...@gmail.com> >>>>>>>>>>> wrote: >>>>>>>>>>> > >>>>>>>>>>> > also, if you have Homebrew, you should run >>>>>>>>>>> > >>>>>>>>>>> > source .homebrew-build-env >>>>>>>>>>> > >>>>>>>>>>> > before >>>>>>>>>>> > >>>>>>>>>>> > ./configure >>>>>>>>>>> > >>>>>>>>>>> > On Mon, Oct 26, 2020 at 1:50 PM Dima Pasechnik < >>>>>>>>>>> dim...@gmail.com> wrote: >>>>>>>>>>> >> >>>>>>>>>>> >> please post the top-level config.log here >>>>>>>>>>> >> >>>>>>>>>>> >> On Mon, 26 Oct 2020, 13:45 modp...@gmail.com, < >>>>>>>>>>> modp...@gmail.com> wrote: >>>>>>>>>>> >>> >>>>>>>>>>> >>> >>>>>>>>>>> >>> I'm building Sage 9.2 from source on macOS Catalina 10.15.7, >>>>>>>>>>> however, it fails >>>>>>>>>>> >>> when trying to install cysignals. More precisely, it throws >>>>>>>>>>> the following error: >>>>>>>>>>> >>> >>>>>>>>>>> >>> gcc -bundle -undefined dynamic_lookup -isysroot >>>>>>>>>>> /Applications/Xcode.app/Contents/Developer/Platforms/MacOSX.platform/Developer/SDKs/MacOSX10.15.sdk >>>>>>>>>>> >>>>>>>>>>> -L/Users/myUser/app/sage-9.2/local/lib >>>>>>>>>>> -Wl,-rpath,/Users/myUser/app/sage-9.2/local/lib >>>>>>>>>>> -L/usr/local/opt/llvm/lib >>>>>>>>>>> -I/usr/local/opt/llvm/include -Wp,-U_FORTIFY_SOURCE >>>>>>>>>>> build/temp.macosx-10.15-x86_64-3.8/build/src/cysignals/signals.o >>>>>>>>>>> -L/usr/local/lib -L/usr/local/opt/openssl@1.1/lib >>>>>>>>>>> -L/usr/local/opt/sqlite/lib -o >>>>>>>>>>> build/lib.macosx-10.15-x86_64-3.8/cysignals/ >>>>>>>>>>> signals.cpython-38-darwin.so -lpari -pthread >>>>>>>>>>> >>> ld: illegal thread local variable reference to regular >>>>>>>>>>> symbol _PARI_SIGINT_block for architecture x86_64 >>>>>>>>>>> >>> clang: error: linker command failed with exit code 1 (use -v >>>>>>>>>>> to see invocation) >>>>>>>>>>> >>> error: command 'gcc' failed with exit status 1 >>>>>>>>>>> >>> Building wheel for cysignals (setup.py): finished with >>>>>>>>>>> status 'error' >>>>>>>>>>> >>> ERROR: Failed building wheel for cysignals >>>>>>>>>>> >>> >>>>>>>>>>> >>> This is my compiler version: >>>>>>>>>>> >>> >>>>>>>>>>> >>> Configured with: >>>>>>>>>>> --prefix=/Applications/Xcode.app/Contents/Developer/usr >>>>>>>>>>> --with-gxx-include-dir=/Applications/Xcode.app/Contents/Developer/Platforms/MacOSX.platform/Developer/SDKs/MacOSX.sdk/usr/include/c++/4.2.1 >>>>>>>>>>> >>>>>>>>>>> >>>>>>>>>>> >>> Apple clang version 12.0.0 (clang-1200.0.32.21) >>>>>>>>>>> >>> Target: x86_64-apple-darwin19.6.0 >>>>>>>>>>> >>> Thread model: posix >>>>>>>>>>> >>> InstalledDir: >>>>>>>>>>> /Applications/Xcode.app/Contents/Developer/Toolchains/XcodeDefault.xctoolchain/usr/bin >>>>>>>>>>> >>>>>>>>>>> >>>>>>>>>>> >>> >>>>>>>>>>> >>> Any idea what the problem might be, and how to solve it? >>>>>>>>>>> >>> >>>>>>>>>>> >>> -- >>>>>>>>>>> >>> 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/38ff74b7-a4bf-4118-8519-9f57736ba532n%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-...@googlegroups.com. >>>>>>>>> >>>>>>>>> >>>>>>>>>> To view this discussion on the web visit >>>>>>>>>> https://groups.google.com/d/msgid/sage-devel/c76466bf-9141-4761-83ef-e97b7d28d691n%40googlegroups.com >>>>>>>>>> >>>>>>>>>> <https://groups.google.com/d/msgid/sage-devel/c76466bf-9141-4761-83ef-e97b7d28d691n%40googlegroups.com?utm_medium=email&utm_source=footer> >>>>>>>>>> . >>>>>>>>>> >>>>>>>>> -- >>>>>>> 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/e5318380-9c73-4a85-93de-3583b3be4f6cn%40googlegroups.com >>>>>>> >>>>>>> <https://groups.google.com/d/msgid/sage-devel/e5318380-9c73-4a85-93de-3583b3be4f6cn%40googlegroups.com?utm_medium=email&utm_source=footer> >>>>>>> . >>>>>>> >>>>>> -- >>> 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/bce36b24-7c6f-42db-875d-a0b07c86927fn%40googlegroups.com >>> >>> <https://groups.google.com/d/msgid/sage-devel/bce36b24-7c6f-42db-875d-a0b07c86927fn%40googlegroups.com?utm_medium=email&utm_source=footer> >>> . >>> >> -- You received this message because you are subscribed to the Google Groups "sage-devel" group. 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