Hello, I am unable to build scipy, it fails with this error: In file included from scipy/integrate/_quadpackmodule.c:4: scipy/integrate/__quadpack.h: In function ‘quad_thunk’: scipy/integrate/__quadpack.h:312:9: warning: ‘PyEval_CallObjectWithKeywords’ is deprecated [-Wdeprecated-declarations] 312 | res = PyEval_CallObject(callback->py_function, arglist); | ^~~ In file included from /usr/include/python3.10/Python.h:146, from scipy/integrate/__quadpack.h:23, from scipy/integrate/_quadpackmodule.c:4: /usr/include/python3.10/ceval.h:17:43: note: declared here 17 | Py_DEPRECATED(3.9) PyAPI_FUNC(PyObject *) PyEval_CallObjectWithKeywords( | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /usr/bin/gfortran -Wall -g -Wall -g -shared build/temp.linux-x86_64-3.10/scipy/integrate/_quadpackmodule.o -L/usr/lib64 -L/usr/lib/gcc/x86_64-redhat-linux/10 -L/usr/lib/gcc/x86_64-redhat-linux/10 -L/usr/lib64 -Lbuild/temp.linux-x86_64-3.10 -Wl,-rpath=/usr/lib64 -lquadpack -lmach -lflexiblas -lflexiblas -lgfortran -o build/lib.linux-x86_64-3.10/scipy/integrate/_quadpack.cpython-310-x86_64-linux-gnu.so -Wl,--version-script=build/temp.linux-x86_64-3.10/link-version-scipy.integrate._quadpack.map collect2: fatal error: ld terminated with signal 11 [Segmentation fault], core dumped compilation terminated. error: Command "/usr/bin/gfortran -Wall -g -Wall -g -shared build/temp.linux-x86_64-3.10/scipy/integrate/_quadpackmodule.o -L/usr/lib64 -L/usr/lib/gcc/x86_64-redhat-linux/10 -L/usr/lib/gcc/x86_64-redhat-linux/10 -L/usr/lib64 -Lbuild/temp.linux-x86_64-3.10 -Wl,-rpath=/usr/lib64 -lquadpack -lmach -lflexiblas -lflexiblas -lgfortran -o build/lib.linux-x86_64-3.10/scipy/integrate/_quadpack.cpython-310-x86_64-linux-gnu.so -Wl,--version-script=build/temp.linux-x86_64-3.10/link-version-scipy.integrate._quadpack.map" failed with exit status 1 error: Bad exit status from /var/tmp/rpm-tmp.J0N25t (%build) Bad exit status from /var/tmp/rpm-tmp.J0N25t (%build) I have tried to build it in Koji, Copr also in Mock, but everywhere same segfault. Here is the link for Koji: https://koji.fedoraproject.org/koji/taskinfo?taskID=54764233
I just got a notification from Koschei. It seems that binutils update broke quite a lot of packages (including scipy): https://koschei.fedoraproject.org/affected-by/binutils?epoch1=0&version1=2.35.1&release1=8.fc34&epoch2=0&version2=2.35.1&release2=11.fc34&collection=f34
I'll start a thread on devel.
https://lists.fedoraproject.org/archives/list/devel@lists.fedoraproject.org/thread/XH22TZWCLRUC5GOOVH4ZB5QPDRYAN4CJ/
*** Bug 1893664 has been marked as a duplicate of this bug. ***
Setting severity to high, this affects dozens of packages including rpm.
A fix is in the works. Build should complete in ~ 1 hour.
Fixed in binutils-2.35.1-12.fc34 Sorry about that guys. My -11.fc34 update was broken and it took me a while to track down the problem. Please try the -12.fc34 binutils - they should work properly.
It appears to be fixed in binutils 2.35.1-12.fc34 At least rpm and scipy* build again. Thanks for the fix. * scipy successfully passed the %build phase on x86_64
Still segfaults, now inside using clang++-11: Program received signal SIGSEGV, Segmentation fault. 0x00007fb81e40aa88 in bfd_elf_link_add_symbols () from /usr/lib64/libbfd-2.35.1-11.fc34.so (gdb) bt #0 0x00007fb81e40aa88 in bfd_elf_link_add_symbols () from /usr/lib64/libbfd-2.35.1-11.fc34.so #1 0x000055745267e16c in load_symbols.part () #2 0x000055745267304c in open_input_bfds.lto_priv () #3 0x0000557452673116 in open_input_bfds.lto_priv () #4 0x000055745267b538 in lang_process () #5 0x000055745266bf97 in main () (from building votca-xtp with clang-11 on rawhide) To reproduce, run: $ docker run -it fedora:rawhide /bin/bash in the container $ dnf install git cmake eigen3-devel libint2-devel hdf5-devel libxc-devel expat-devel boost-devel $ git clone --recursive https://github.com/votca/votca $ cmake -B build -DBUILD_XTP=ON votca $ cmake --build build ....wait and see the segfault.
(In reply to Christoph Junghans from comment #9) > Still segfaults, now inside using clang++-11: > To reproduce, run: > $ docker run -it fedora:rawhide /bin/bash > in the container > $ dnf install git cmake eigen3-devel libint2-devel hdf5-devel > libxc-devel expat-devel boost-devel > $ git clone --recursive https://github.com/votca/votca > $ cmake -B build -DBUILD_XTP=ON votca > $ cmake --build build > ....wait and see the segfault. Err, I just tried that, and there was no seg-fault.... Actually to be strictly accurate I used a mock chroot instead of a container, but it was still based on rawhide. I'll try using docker and see if that makes the problem happen.
The log says: 2.35.1-11.fc34 You need to get the updated 2.35.1-12.fc34. It is not yet on the mirrors.
This is on the mirrors.