You suffer from a classic case of gcc/gfortran upgrade. I have been fielding bugs for the same kind of errors in Gentoo for a number of months now. up to gcc-6, gfortran provided its runtime with libgfortran.so.3. But gcc-7 broke the compatibility and provided libgfortran.so.4. And gcc-8 broke the compatibility again providing libgfortran.so.5. After upgrading gcc/gfortran from one of the version above to another you need to rebuild all packages linking to libgfortran. That means anything that uses lapack and in particular numpy when compiled with lapack bindings like in sage.
> On 3/03/2019, at 19:16, Ike Stoddard <isaac.a.stodd...@gmail.com> wrote: > > Linux xxxxxxx 4.20.12-arch1-1-ARCH #1 SMP PREEMPT Sat Feb 23 15:11:34 UTC > 2019 x86_64 GNU/Linux > > Building from source; make fails at sagelib, but implies "numpy" is at fault: > [sagelib-8.6] ImportError: > [sagelib-8.6] Importing the multiarray numpy extension module failed. Most > [sagelib-8.6] likely you are trying to import a failed build of numpy. > [sagelib-8.6] If you're working with a numpy git repo, try `git clean -xdf` > (removes all > [sagelib-8.6] files not under version control). Otherwise reinstall numpy. > [sagelib-8.6] > [sagelib-8.6] Original error was: libgfortran.so.3: cannot open shared object > file: No such file or directory > .....................................................^^^^^^^^^^^^^^^^I cannot > see where this originates? > [sagelib-8.6] > [sagelib-8.6] > ************************************************************************ > [sagelib-8.6] Error building the Sage library > [sagelib-8.6] > ************************************************************************ > [sagelib-8.6] Please email sage-devel > (http://groups.google.com/group/sage-devel) > [sagelib-8.6] explaining the problem and including the relevant part of the > log file > [sagelib-8.6] /usr/local/src/Misc/sage-8.6/logs/pkgs/sagelib-8.6.log > > Now I have already got python2-numpy and python-numpy installed (Arch Linux, > via pacman [canonical installer]) > warning: python2-numpy-1.16.1-1 is up to date -- reinstalling > warning: python-numpy-1.16.1-1 is up to date -- reinstalling > > yet it builds its own "upstream" numpy that is not the latest: > ./logs/pkgs/numpy-1.15.4.p0.log > > I cannot at this point find where to substitute installed numpy. I have > already redirected ATLAS and gcc: > declare -x SAGE_ATLAS_LIB="/usr/local/atlas/lib" > declare -x SAGE_INSTALL_GCC="no" > > 1) Why does this not find my numpy? > 2) Is there another environment variable to set for that? I cannot find it. > > Logs for numpy and sagelib are attached. Pointing me to the correct > diagnostic lines in my logs will help. > > -- > 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 post to this group, send email to sage-devel@googlegroups.com. > Visit this group at https://groups.google.com/group/sage-devel. > For more options, visit https://groups.google.com/d/optout. > <sagelib-8.6.log><numpy-1.15.4.p0.log> -- 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 post to this group, send email to sage-devel@googlegroups.com. Visit this group at https://groups.google.com/group/sage-devel. For more options, visit https://groups.google.com/d/optout.
