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+unsubscr...@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.
Found local metadata for cysignals-1.10.2 Using cached file /Users/etairi/app/sage-9.2/upstream/cysignals-1.10.2.tar.gz cysignals-1.10.2 ==================================================== Setting up build directory for cysignals-1.10.2 Finished extraction No patch files found in ../patches **************************************************** Host system: Darwin tuwien 19.6.0 Darwin Kernel Version 19.6.0: Mon Aug 31 22:12:52 PDT 2020; root:xnu-6153.141.2~1/RELEASE_X86_64 x86_64 **************************************************** C compiler: gcc C 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 **************************************************** Package 'cysignals' is currently not installed No legacy uninstaller found for 'cysignals'; nothing to do Configuring cysignals-1.10.2 configure: WARNING: unrecognized options: --disable-maintainer-mode, --disable-dependency-tracking checking for gcc... gcc checking whether the C compiler works... yes checking for C compiler default output file name... a.out checking for suffix of executables... checking whether we are cross compiling... no checking for suffix of object files... o checking whether we are using the GNU C compiler... yes checking whether gcc accepts -g... yes checking for gcc option to accept ISO C89... none needed checking whether we are using the GNU C++ compiler... yes checking whether gcc accepts -g... yes checking how to run the C preprocessor... gcc -E checking for grep that handles long lines and -e... /usr/bin/grep checking for egrep... /usr/bin/grep -E checking for ANSI C header files... yes checking for sys/types.h... yes checking for sys/stat.h... yes checking for stdlib.h... yes checking for string.h... yes checking for memory.h... yes checking for strings.h... yes checking for inttypes.h... yes checking for stdint.h... yes checking for unistd.h... yes checking execinfo.h usability... yes checking execinfo.h presence... yes checking for execinfo.h... yes checking sys/mman.h usability... yes checking sys/mman.h presence... yes checking for sys/mman.h... yes checking sys/prctl.h usability... no checking sys/prctl.h presence... no checking for sys/prctl.h... no checking sys/time.h usability... yes checking sys/time.h presence... yes checking for sys/time.h... yes checking sys/wait.h usability... yes checking sys/wait.h presence... yes checking for sys/wait.h... yes checking windows.h usability... no checking windows.h presence... no checking for windows.h... no checking for fork... yes checking for kill... yes checking for sigprocmask... yes checking for sigaltstack... yes checking for backtrace... yes checking for library containing pari_init... -lpari checking whether PARI_SIGINT_block is declared... yes checking for emms instruction... yes checking whether setjmp() saves the signal mask... yes checking for GNU libc... no checking for _Atomic in C code... yes checking for _Atomic in C++ code... yes checking for std::atomic... yes configure: creating ./config.status config.status: creating src/cysignals/signals.pxd config.status: creating src/config.h config.status: creating src/cysignals/cysignals_config.h configure: WARNING: unrecognized options: --disable-maintainer-mode, --disable-dependency-tracking Installing cysignals-1.10.2 Ignoring indexes: https://pypi.org/simple Created temporary directory: /private/var/folders/ln/t_25pvmj4m7060k_wc76hnrr0000gn/T/pip-ephem-wheel-cache-4_vvwh0m Created temporary directory: /private/var/folders/ln/t_25pvmj4m7060k_wc76hnrr0000gn/T/pip-req-tracker-q6hsrr5t Initialized build tracking at /private/var/folders/ln/t_25pvmj4m7060k_wc76hnrr0000gn/T/pip-req-tracker-q6hsrr5t Created build tracker: /private/var/folders/ln/t_25pvmj4m7060k_wc76hnrr0000gn/T/pip-req-tracker-q6hsrr5t Entered build tracker: /private/var/folders/ln/t_25pvmj4m7060k_wc76hnrr0000gn/T/pip-req-tracker-q6hsrr5t Created temporary directory: /private/var/folders/ln/t_25pvmj4m7060k_wc76hnrr0000gn/T/pip-wheel-si1ny2eo Processing /Users/etairi/app/sage-9.2/local/var/tmp/sage/build/cysignals-1.10.2/src Created temporary directory: /private/var/folders/ln/t_25pvmj4m7060k_wc76hnrr0000gn/T/pip-req-build-5yc6io_b Added file:///Users/etairi/app/sage-9.2/local/var/tmp/sage/build/cysignals-1.10.2/src to build tracker '/private/var/folders/ln/t_25pvmj4m7060k_wc76hnrr0000gn/T/pip-req-tracker-q6hsrr5t' Running setup.py (path:/private/var/folders/ln/t_25pvmj4m7060k_wc76hnrr0000gn/T/pip-req-build-5yc6io_b/setup.py) egg_info for package from file:///Users/etairi/app/sage-9.2/local/var/tmp/sage/build/cysignals-1.10.2/src Created temporary directory: /private/var/folders/ln/t_25pvmj4m7060k_wc76hnrr0000gn/T/pip-pip-egg-info-vjhsd4tf Running command python setup.py egg_info running egg_info creating /private/var/folders/ln/t_25pvmj4m7060k_wc76hnrr0000gn/T/pip-pip-egg-info-vjhsd4tf/cysignals.egg-info writing /private/var/folders/ln/t_25pvmj4m7060k_wc76hnrr0000gn/T/pip-pip-egg-info-vjhsd4tf/cysignals.egg-info/PKG-INFO writing dependency_links to /private/var/folders/ln/t_25pvmj4m7060k_wc76hnrr0000gn/T/pip-pip-egg-info-vjhsd4tf/cysignals.egg-info/dependency_links.txt writing requirements to /private/var/folders/ln/t_25pvmj4m7060k_wc76hnrr0000gn/T/pip-pip-egg-info-vjhsd4tf/cysignals.egg-info/requires.txt writing top-level names to /private/var/folders/ln/t_25pvmj4m7060k_wc76hnrr0000gn/T/pip-pip-egg-info-vjhsd4tf/cysignals.egg-info/top_level.txt writing manifest file '/private/var/folders/ln/t_25pvmj4m7060k_wc76hnrr0000gn/T/pip-pip-egg-info-vjhsd4tf/cysignals.egg-info/SOURCES.txt' reading manifest file '/private/var/folders/ln/t_25pvmj4m7060k_wc76hnrr0000gn/T/pip-pip-egg-info-vjhsd4tf/cysignals.egg-info/SOURCES.txt' reading manifest template 'MANIFEST.in' no previously-included directories found matching 'build' no previously-included directories found matching 'dist' no previously-included directories found matching 'tmp' no previously-included directories found matching '.*' no previously-included directories found matching 'example/.*' writing manifest file '/private/var/folders/ln/t_25pvmj4m7060k_wc76hnrr0000gn/T/pip-pip-egg-info-vjhsd4tf/cysignals.egg-info/SOURCES.txt' Source in /private/var/folders/ln/t_25pvmj4m7060k_wc76hnrr0000gn/T/pip-req-build-5yc6io_b has version 1.10.2, which satisfies requirement cysignals==1.10.2 from file:///Users/etairi/app/sage-9.2/local/var/tmp/sage/build/cysignals-1.10.2/src Removed cysignals==1.10.2 from file:///Users/etairi/app/sage-9.2/local/var/tmp/sage/build/cysignals-1.10.2/src from build tracker '/private/var/folders/ln/t_25pvmj4m7060k_wc76hnrr0000gn/T/pip-req-tracker-q6hsrr5t' Building wheels for collected packages: cysignals Created temporary directory: /private/var/folders/ln/t_25pvmj4m7060k_wc76hnrr0000gn/T/pip-wheel-7njmeohe Building wheel for cysignals (setup.py): started Destination directory: /private/var/folders/ln/t_25pvmj4m7060k_wc76hnrr0000gn/T/pip-wheel-7njmeohe Running command /Users/etairi/app/sage-9.2/local/bin/python3 -u -c 'import sys, setuptools, tokenize; sys.argv[0] = '"'"'/private/var/folders/ln/t_25pvmj4m7060k_wc76hnrr0000gn/T/pip-req-build-5yc6io_b/setup.py'"'"'; __file__='"'"'/private/var/folders/ln/t_25pvmj4m7060k_wc76hnrr0000gn/T/pip-req-build-5yc6io_b/setup.py'"'"';f=getattr(tokenize, '"'"'open'"'"', open)(__file__);code=f.read().replace('"'"'\r\n'"'"', '"'"'\n'"'"');f.close();exec(compile(code, __file__, '"'"'exec'"'"'))' bdist_wheel -d /private/var/folders/ln/t_25pvmj4m7060k_wc76hnrr0000gn/T/pip-wheel-7njmeohe running bdist_wheel running build Compiling src/cysignals/signals.pyx because it changed. Compiling src/cysignals/pysignals.pyx because it changed. Compiling src/cysignals/alarm.pyx because it changed. Compiling src/cysignals/pselect.pyx because it changed. Compiling src/cysignals/tests.pyx because it changed. [1/5] Cythonizing src/cysignals/alarm.pyx [2/5] Cythonizing src/cysignals/pselect.pyx [3/5] Cythonizing src/cysignals/pysignals.pyx [4/5] Cythonizing src/cysignals/signals.pyx [5/5] Cythonizing src/cysignals/tests.pyx running build_py creating build/lib.macosx-10.15-x86_64-3.8 creating build/lib.macosx-10.15-x86_64-3.8/cysignals copying src/cysignals/__init__.py -> build/lib.macosx-10.15-x86_64-3.8/cysignals copying src/cysignals/signals.pxi -> build/lib.macosx-10.15-x86_64-3.8/cysignals copying src/cysignals/memory.pxi -> build/lib.macosx-10.15-x86_64-3.8/cysignals copying src/cysignals/memory.pxd -> build/lib.macosx-10.15-x86_64-3.8/cysignals copying src/cysignals/pysignals.pxd -> build/lib.macosx-10.15-x86_64-3.8/cysignals copying src/cysignals/signals.pxd -> build/lib.macosx-10.15-x86_64-3.8/cysignals copying src/cysignals/cysignals_config.h -> build/lib.macosx-10.15-x86_64-3.8/cysignals copying src/cysignals/macros.h -> build/lib.macosx-10.15-x86_64-3.8/cysignals copying src/cysignals/struct_signals.h -> build/lib.macosx-10.15-x86_64-3.8/cysignals copying src/cysignals/pxi_warning.h -> build/lib.macosx-10.15-x86_64-3.8/cysignals running build_ext building 'cysignals.signals' extension creating build/temp.macosx-10.15-x86_64-3.8 creating build/temp.macosx-10.15-x86_64-3.8/build creating build/temp.macosx-10.15-x86_64-3.8/build/src creating build/temp.macosx-10.15-x86_64-3.8/build/src/cysignals gcc -Wno-unused-result -Wsign-compare -Wunreachable-code -fno-common -dynamic -DNDEBUG -g -fwrapv -O3 -Wall -isysroot /Applications/Xcode.app/Contents/Developer/Platforms/MacOSX.platform/Developer/SDKs/MacOSX10.15.sdk -I/Applications/Xcode.app/Contents/Developer/Platforms/MacOSX.platform/Developer/SDKs/MacOSX10.15.sdk/usr/include -I/Applications/Xcode.app/Contents/Developer/Platforms/MacOSX.platform/Developer/SDKs/MacOSX10.15.sdk/System/Library/Frameworks/Tk.framework/Versions/8.5/Headers -I/usr/local/opt/llvm/include -Wp,-U_FORTIFY_SOURCE -DCYTHON_CLINE_IN_TRACEBACK=0 -U_FORTIFY_SOURCE -Isrc/cysignals -Isrc -I/usr/local/include -I/usr/local/opt/openssl@1.1/include -I/usr/local/opt/sqlite/include -I/Users/etairi/app/sage-9.2/local/include -I/usr/local/Cellar/python@3.8/3.8.6/Frameworks/Python.framework/Versions/3.8/include/python3.8 -c build/src/cysignals/signals.c -o build/temp.macosx-10.15-x86_64-3.8/build/src/cysignals/signals.o -pthread build/src/cysignals/signals.c:6449:5: warning: 'tp_print' is deprecated [-Wdeprecated-declarations] 0, ^ /usr/local/Cellar/python@3.8/3.8.6/Frameworks/Python.framework/Versions/3.8/include/python3.8/cpython/object.h:260:5: note: 'tp_print' has been explicitly marked deprecated here Py_DEPRECATED(3.8) int (*tp_print)(PyObject *, FILE *, int); ^ /usr/local/Cellar/python@3.8/3.8.6/Frameworks/Python.framework/Versions/3.8/include/python3.8/pyport.h:515:54: note: expanded from macro 'Py_DEPRECATED' #define Py_DEPRECATED(VERSION_UNUSED) __attribute__((__deprecated__)) ^ In file included from build/src/cysignals/signals.c:1570: build/src/cysignals/implementation.c:516:13: warning: unused function 'print_enhanced_backtrace' [-Wunused-function] static void print_enhanced_backtrace(void) ^ 2 warnings generated. gcc -bundle -undefined dynamic_lookup -isysroot /Applications/Xcode.app/Contents/Developer/Platforms/MacOSX.platform/Developer/SDKs/MacOSX10.15.sdk -L/Users/etairi/app/sage-9.2/local/lib -Wl,-rpath,/Users/etairi/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: warning: directory not found for option '-L/usr/local/opt/llvm/lib' 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 Running setup.py clean for cysignals Running command /Users/etairi/app/sage-9.2/local/bin/python3 -u -c 'import sys, setuptools, tokenize; sys.argv[0] = '"'"'/private/var/folders/ln/t_25pvmj4m7060k_wc76hnrr0000gn/T/pip-req-build-5yc6io_b/setup.py'"'"'; __file__='"'"'/private/var/folders/ln/t_25pvmj4m7060k_wc76hnrr0000gn/T/pip-req-build-5yc6io_b/setup.py'"'"';f=getattr(tokenize, '"'"'open'"'"', open)(__file__);code=f.read().replace('"'"'\r\n'"'"', '"'"'\n'"'"');f.close();exec(compile(code, __file__, '"'"'exec'"'"'))' clean --all running clean removing 'build/temp.macosx-10.15-x86_64-3.8' (and everything under it) removing 'build/lib.macosx-10.15-x86_64-3.8' (and everything under it) 'build/bdist.macosx-10.15-x86_64' does not exist -- can't clean it 'build/scripts-3.8' does not exist -- can't clean it Failed to build cysignals ERROR: Failed to build one or more wheels Exception information: Traceback (most recent call last): File "/Users/etairi/app/sage-9.2/local/lib/python3.8/site-packages/pip/_internal/cli/base_command.py", line 228, in _main status = self.run(options, args) File "/Users/etairi/app/sage-9.2/local/lib/python3.8/site-packages/pip/_internal/cli/req_command.py", line 182, in wrapper return func(self, options, args) File "/Users/etairi/app/sage-9.2/local/lib/python3.8/site-packages/pip/_internal/commands/wheel.py", line 184, in run raise CommandError( pip._internal.exceptions.CommandError: Failed to build one or more wheels Removed build tracker: '/private/var/folders/ln/t_25pvmj4m7060k_wc76hnrr0000gn/T/pip-req-tracker-q6hsrr5t' ******************************************************************************** Error building a wheel for cysignals-1.10.2 ******************************************************************************** real 0m17.623s user 0m8.305s sys 0m3.604s ************************************************************************ Error installing package cysignals-1.10.2 ************************************************************************ Please email sage-devel (http://groups.google.com/group/sage-devel) explaining the problem and including the log file /Users/etairi/app/sage-9.2/logs/pkgs/cysignals-1.10.2.log Describe your computer, operating system, etc. If you want to try to fix the problem yourself, *don't* just cd to /Users/etairi/app/sage-9.2/local/var/tmp/sage/build/cysignals-1.10.2 and type 'make' or whatever is appropriate. Instead, the following commands setup all environment variables correctly and load a subshell for you to debug the error: (cd '/Users/etairi/app/sage-9.2/local/var/tmp/sage/build/cysignals-1.10.2' && '/Users/etairi/app/sage-9.2/sage' --buildsh) When you are done debugging, you can type "exit" to leave the subshell. ************************************************************************
