Not sure if this is relevant, but I get the following messages when I try running 'conda update givaro' in my sage conda environment (attached). I apologize for multiple messages!
On Wed, Mar 24, 2021 at 8:42 AM Mike Lee <symle...@gmail.com> wrote: > I believe the following line in the output of the nm command you > suggested is the corresponding symbol? > > 0000000000017da0 T Givaro::Integer::operator > std::__cxx11::basic_string<char, std::char_traits<char>, > std::allocator<char> >() const > > I've also attached the full output of the nm command as a txt file below > in case it's helpful! > > On Wed, Mar 24, 2021 at 5:41 AM Dima Pasechnik <dimp...@gmail.com> wrote: > >> On Tue, Mar 23, 2021 at 10:27 PM Mike Lee <symle...@gmail.com> wrote: >> > >> > Hi, >> > >> > I'm facing a similar issue when I tried to install Sage through conda >> (I followed the 'Setting Up' directions in >> https://wiki.sagemath.org/Conda). I get the following error in my >> Sage_crash_report.txt (attached) >> > >> > 'ImportError: >> /home/msl/software/miniconda3/envs/sage/lib/python3.9/site-packages/sage/matrix/ >> matrix_modn_sparse.cpython-39-x86_64-linux-gnu.so: undefined symbol: >> _ZNK6Givaro7IntegercvNSt7__cxx1112basic_stringIcSt11char_traitsIcESaIcEEEB5cxx11Ev' >> >> this is, demangled: >> >> $ c++filt >> _ZNK6Givaro7IntegercvNSt7__cxx1112basic_stringIcSt11char_traitsIcESaIcEEEB5cxx11Ev >> Givaro::Integer::operator std::__cxx11::basic_string<char, >> std::char_traits<char>, std::allocator<char> >[abi:cxx11]() const >> >> Can you find this in the output of >> >> $ nm -D --demangle >> /home/msl/software/miniconda3/envs/sage/lib/libgivaro.so.9 >> >> Perhaps, wrong C++ standard version chosen somewhere? >> >> Maybe Isuru knows what's wrong there. >> >> > >> > What could I do to fix this issue? Thank you in advance for the help! >> > >> > By the way, when I run 'ldd >> /home/msl/software/miniconda3/envs/sage/lib/python3.9/site-packages/sage/matrix/ >> matrix_modn_sparse.cpython-39-x86_64-linux-gnu.so ' I get the following >> output: >> > >> > linux-vdso.so.1 (0x00007ffde17a7000) >> > liblinbox.so.0 => >> /home/msl/software/miniconda3/envs/sage/lib/python3.9/site-packages/sage/matrix/../../../../liblinbox.so.0 >> (0x00007fa325ba0000) >> > libfflas.so.1 => >> /home/msl/software/miniconda3/envs/sage/lib/python3.9/site-packages/sage/matrix/../../../../libfflas.so.1 >> (0x00007fa325ad4000) >> > libblas.so.3 => >> /home/msl/software/miniconda3/envs/sage/lib/python3.9/site-packages/sage/matrix/../../../../libblas.so.3 >> (0x00007fa323ae3000) >> > libgivaro.so.9 => >> /home/msl/software/miniconda3/envs/sage/lib/python3.9/site-packages/sage/matrix/../../../../libgivaro.so.9 >> (0x00007fa323a88000) >> > libflint.so.14 => >> /home/msl/software/miniconda3/envs/sage/lib/python3.9/site-packages/sage/matrix/../../../../libflint.so.14 >> (0x00007fa32320d000) >> > libntl.so.43 => >> /home/msl/software/miniconda3/envs/sage/lib/python3.9/site-packages/sage/matrix/../../../../libntl.so.43 >> (0x00007fa322fca000) >> > libgmp.so.10 => >> /home/msl/software/miniconda3/envs/sage/lib/python3.9/site-packages/sage/matrix/../../../../libgmp.so.10 >> (0x00007fa322f24000) >> > libstdc++.so.6 => >> /home/msl/software/miniconda3/envs/sage/lib/python3.9/site-packages/sage/matrix/../../../../libstdc++.so.6 >> (0x00007fa322daf000) >> > libm.so.6 => /lib/x86_64-linux-gnu/libm.so.6 (0x00007fa3229fb000) >> > libgcc_s.so.1 => >> /home/msl/software/miniconda3/envs/sage/lib/python3.9/site-packages/sage/matrix/../../../../libgcc_s.so.1 >> (0x00007fa3229e7000) >> > libc.so.6 => /lib/x86_64-linux-gnu/libc.so.6 (0x00007fa3225f6000) >> > libffpack.so.1 => >> /home/msl/software/miniconda3/envs/sage/lib/python3.9/site-packages/sage/matrix/../../../.././libffpack.so.1 >> (0x00007fa3224e3000) >> > libgmpxx.so.4 => >> /home/msl/software/miniconda3/envs/sage/lib/python3.9/site-packages/sage/matrix/../../../.././libgmpxx.so.4 >> (0x00007fa3224da000) >> > libmpfr.so.6 => >> /home/msl/software/miniconda3/envs/sage/lib/python3.9/site-packages/sage/matrix/../../../.././libmpfr.so.6 >> (0x00007fa32245b000) >> > libiml.so.0 => >> /home/msl/software/miniconda3/envs/sage/lib/python3.9/site-packages/sage/matrix/../../../.././libiml.so.0 >> (0x00007fa322436000) >> > libpthread.so.0 => /lib/x86_64-linux-gnu/libpthread.so.0 >> (0x00007fa322217000) >> > libgfortran.so.5 => >> /home/msl/software/miniconda3/envs/sage/lib/python3.9/site-packages/sage/matrix/../../../.././libgfortran.so.5 >> (0x00007fa322075000) >> > /lib64/ld-linux-x86-64.so.2 (0x00007fa325aa8000) >> > libgf2x.so.3 => >> /home/msl/software/miniconda3/envs/sage/lib/python3.9/site-packages/sage/matrix/../../../.././libgf2x.so.3 >> (0x00007fa322062000) >> > libquadmath.so.0 => >> /home/msl/software/miniconda3/envs/sage/lib/python3.9/site-packages/sage/matrix/../../../.././libquadmath.so.0 >> (0x00007fa322028000) >> > >> > Mike >> > >> > On Sunday, January 24, 2021 at 1:16:24 PM UTC-5 dim...@gmail.com wrote: >> >> >> >> at the bottom of the log you see >> >> >> >> ImportError: >> /home/mathieu/opt/SageMath/local/lib/python3.8/site-packages/sage/matrix/ >> matrix_modn_sparse.cpython-38-x86_64-linux-gnu.so: >> >> undefined symbol: >> >> >> _ZNK6Givaro7IntegercvNSt7__cxx1112basic_stringIcSt11char_traitsIcESaIcEEEB5cxx11Ev >> >> >> >> >> >> which is an indication that something went wrong with linking givaro. >> >> E.g. you might be linking to a system-wide >> >> installed givaro, but it's expected to be the one built by Sage - >> >> whether the latter is the case can be found out in the top-level >> >> config.log. >> >> >> >> What is the output of >> >> >> >> ldd >> /home/mathieu/opt/SageMath/local/lib/python3.8/site-packages/sage/matrix/ >> matrix_modn_sparse.cpython-38-x86_64-linux-gnu.so >> >> >> >> ? >> >> >> >> >> >> On Sun, Jan 24, 2021 at 4:22 PM Mathieu Dutour <mathieu...@gmail.com> >> wrote: >> >> > >> >> > >> >> > -- >> >> > 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/CADm_teOrk03gf8bzyUxtvt9m16wEAP3%2BOsfkzxbjSjz4VN9bKw%40mail.gmail.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/3af54436-2cb1-4a8f-ac5e-ef109602fa0en%40googlegroups.com >> . >> >> -- >> You received this message because you are subscribed to a topic in the >> Google Groups "sage-support" group. >> To unsubscribe from this topic, visit >> https://groups.google.com/d/topic/sage-support/uLLCi94RQAU/unsubscribe. >> To unsubscribe from this group and all its topics, 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/CAAWYfq1nH_hnH3kv7iAGoUtuv_Tm1keTSh-KLhVagz64AzDgFQ%40mail.gmail.com >> . >> > -- You received this message because you are subscribed to the Google Groups "sage-support" group. 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Collecting package metadata (current_repodata.json): done Solving environment: failed with repodata from current_repodata.json, will retry with next repodata source. Collecting package metadata (repodata.json): done Solving environment: failed Solving environment: - Found conflicts! Looking for incompatible packages. This can take several minutes. Press CTRL-C to abort. failed UnsatisfiableError: The following specifications were found to be incompatible with a past explicit spec that is not an explicit spec in this operation (givaro): - givaro The following specifications were found to be incompatible with each other: Output in format: Requested package -> Available versions Package _libgcc_mutex conflicts for: givaro -> libgcc-ng[version='>=9.3.0'] -> _libgcc_mutex[version='*|0.1',build='conda_forge|main'] python==3.7 -> libgcc-ng[version='>=7.3.0'] -> _libgcc_mutex[version='*|0.1',build='conda_forge|main'] openssl -> libgcc-ng[version='>=9.3.0'] -> _libgcc_mutex[version='*|0.1',build='conda_forge|main'] Package openssl conflicts for: sage==9.2 -> pari[version='>=2.11.4,<3'] -> openssl[version='1.0.*|>=1.0.2o,<1.0.3a|>=1.0.2p,<1.0.3a|>=1.1.1a,<1.1.2a|>=1.1.1e,<1.1.2a|>=1.1.1g,<1.1.2a|>=1.1.1h,<1.1.2a|>=1.1.1j,<1.1.2a|>=1.1.1i,<1.1.2a|>=1.1.1d,<1.1.2a|>=1.1.1c,<1.1.2a|>=1.1.1b,<1.1.2a|>=1.1.1f,<1.1.2a|>=1.0.2n,<1.0.3a|>=1.0.2m,<1.0.3a|>=1.0.2l,<1.0.3a'] certifi -> pypy3.7[version='>=7.3.3'] -> openssl[version='1.0.*|>=1.0.2o,<1.0.3a|>=1.0.2p,<1.0.3a|>=1.1.1a,<1.1.2a|>=1.1.1e,<1.1.2a|>=1.1.1g,<1.1.2a|>=1.1.1h,<1.1.2a|>=1.1.1i,<1.1.2a|>=1.1.1j,<1.1.2a|>=1.1.1d,<1.1.2a|>=1.1.1c,<1.1.2a|>=1.1.1b,<1.1.2a|>=1.1.1f,<1.1.2a|>=1.0.2n,<1.0.3a|>=1.0.2m,<1.0.3a|>=1.0.2l,<1.0.3a'] openssl Package libgcc-ng conflicts for: givaro -> gmp[version='>=6.1.2,<7.0a0'] -> libgcc-ng[version='>=4.9|>=7.2.0'] openssl -> libgcc-ng[version='>=4.9|>=7.3.0|>=7.5.0|>=9.3.0|>=7.2.0'] python==3.7 -> bzip2[version='>=1.0.6,<2.0a0'] -> libgcc-ng[version='>=7.5.0|>=9.3.0'] python==3.7 -> libgcc-ng[version='>=4.9|>=7.3.0|>=7.2.0'] sage==9.2 -> arb -> libgcc-ng[version='>=4.9|>=7.3.0|>=7.5.0|>=9.3.0|>=7.2.0'] givaro -> libgcc-ng[version='>=7.3.0|>=7.5.0|>=9.3.0'] certifi -> pypy3.7[version='>=7.3.3'] -> libgcc-ng[version='>=4.9|>=7.3.0|>=7.5.0|>=9.3.0|>=7.2.0'] Package libstdcxx-ng conflicts for: sage==9.2 -> bdw-gc[version='>=8.0.4,<9'] -> libstdcxx-ng[version='>=4.9|>=7.3.0|>=7.5.0|>=9.3.0|>=7.2.0'] python==3.7 -> libstdcxx-ng[version='>=4.9|>=7.3.0|>=7.2.0'] python==3.7 -> ncurses[version='>=6.1,<6.3.0a0'] -> libstdcxx-ng[version='>=7.5.0'] givaro -> libstdcxx-ng[version='>=4.9|>=7.3.0|>=7.5.0|>=9.3.0'] givaro -> gmp[version='>=6.1.2,<7.0a0'] -> libstdcxx-ng[version='>=7.2.0'] certifi -> python[version='>=3.7,<3.8.0a0'] -> libstdcxx-ng[version='>=4.9|>=7.3.0|>=7.5.0|>=9.3.0|>=7.2.0'] Package certifi conflicts for: certifi sage==9.2 -> certifi sage==9.2 -> matplotlib-base[version='>=3.3.1,<4'] -> certifi[version='>=2020.06.20'] Package givaro conflicts for: sage==9.2 -> fflas-ffpack[version='>=2.4.3'] -> givaro[version='>=4.1.1,<4.1.2.0a0|>=4.1.1,<5.0a0'] sage==9.2 -> givaro[version='>=4.1.1,<5'] Package ca-certificates conflicts for: openssl -> ca-certificates ca-certificates certifi -> python[version='>=2.7,<2.8.0a0'] -> ca-certificates Package setuptools conflicts for: sage==9.2 -> bleach[version='>=3.1.5,<4'] -> setuptools[version='>=18.5'] python==3.7 -> pip -> setuptools
