Scipy-1.1.0 with USE="python_targets3_7" fails to merge: x86_64-pc-linux-gnu-g++ -shared -Wl,-O1 -Wl,--as-needed -shared -O2 -pipe -march=native /var/tmp/portage/sci-libs/scipy-1.1.0/work/scipy-1.1.0-python3_7/build/temp.linux-x86_64-3.7/scipy/sparse/sparsetools/sparsetools.o /var/tmp/portage/sci-libs/scipy-1.1.0/work/scipy-1.1.0-python3_7/build/temp.linux-x86_64-3.7/scipy/sparse/sparsetools/csr.o /var/tmp/portage/sci-libs/scipy-1.1.0/work/scipy-1.1.0-python3_7/build/temp.linux-x86_64-3.7/scipy/sparse/sparsetools/csc.o /var/tmp/portage/sci-libs/scipy-1.1.0/work/scipy-1.1.0-python3_7/build/temp.linux-x86_64-3.7/scipy/sparse/sparsetools/bsr.o /var/tmp/portage/sci-libs/scipy-1.1.0/work/scipy-1.1.0-python3_7/build/temp.linux-x86_64-3.7/scipy/sparse/sparsetools/other.o -L/usr/lib64 -L/var/tmp/portage/sci-libs/scipy-1.1.0/work/scipy-1.1.0-python3_7/build/temp.linux-x86_64-3.7 -lpython3.7m -o /var/tmp/portage/sci-libs/scipy-1.1.0/work/scipy-1.1.0-python3_7/build/lib/scipy/sparse/_sparsetools.cpython-37m-x86_64-linux-gnu.so -Wl,--version-script=/var/tmp/portage/sci-libs/scipy-1.1.0/work/scipy-1.1.0-python3_7/build/temp.linux-x86_64-3.7/link-version-scipy.sparse._sparsetools.map setup.py:114: DeprecationWarning: the imp module is deprecated in favour of importlib; see the module's documentation for alternative uses import imp /usr/lib/python3.7/site-packages/numpy/distutils/system_info.py:603: UserWarning: Atlas (http://math-atlas.sourceforge.net/) libraries not found. Directories to search for the libraries can be specified in the numpy/distutils/site.cfg file (section [atlas]) or by setting the ATLAS environment variable. self.calc_info() Running from scipy source directory. "object of type 'type' has no len()" in evaluating 'len(list)' (available names: []) "object of type 'type' has no len()" in evaluating 'len(list)' (available names: []) "object of type 'type' has no len()" in evaluating 'len(list)' (available names: []) "object of type 'type' has no len()" in evaluating 'len(list)' (available names: []) "object of type 'type' has no len()" in evaluating 'len(list)' (available names: []) "object of type 'type' has no len()" in evaluating 'len(list)' (available names: []) error: Command "/usr/bin/gfortran -Wall -g -Wl,-O1 -Wl,--as-needed -shared /var/tmp/portage/sci-libs/scipy-1.1.0/work/scipy-1.1.0-python3_7/build/temp.linux-x86_64-3.7/var/tmp/portage/sci-libs/scipy-1.1.0/work/scipy-1.1.0-python3_7/build/src.linux-x86_64-3.7/scipy/integrate/_test_odeint_bandedmodule.o /var/tmp/portage/sci-libs/scipy-1.1.0/work/scipy-1.1.0-python3_7/build/temp.linux-x86_64-3.7/var/tmp/portage/sci-libs/scipy-1.1.0/work/scipy-1.1.0-python3_7/build/src.linux-x86_64-3.7/scipy/integrate/fortranobject.o /var/tmp/portage/sci-libs/scipy-1.1.0/work/scipy-1.1.0-python3_7/build/temp.linux-x86_64-3.7/scipy/integrate/tests/banded5x5.o /var/tmp/portage/sci-libs/scipy-1.1.0/work/scipy-1.1.0-python3_7/build/temp.linux-x86_64-3.7/var/tmp/portage/sci-libs/scipy-1.1.0/work/scipy-1.1.0-python3_7/build/src.linux-x86_64-3.7/scipy/integrate/_test_odeint_banded-f2pywrappers.o -L/usr/lib64 -L/usr/lib/gcc/x86_64-pc-linux-gnu/8.2.0 -L/usr/lib/gcc/x86_64-pc-linux-gnu/8.2.0 -L/usr/lib64 -L/var/tmp/portage/sci-libs/scipy-1.1.0/work/scipy-1.1.0-python3_7/build/temp.linux-x86_64-3.7 -llsoda -lmach -lblas -llapack -lblas -lcblas -lpython3.7m -lgfortran -o /var/tmp/portage/sci-libs/scipy-1.1.0/work/scipy-1.1.0-python3_7/build/lib/scipy/integrate/_test_odeint_banded.cpython-37m-x86_64-linux-gnu.so -Wl,--version-script=/var/tmp/portage/sci-libs/scipy-1.1.0/work/scipy-1.1.0-python3_7/build/temp.linux-x86_64-3.7/link-version-scipy.integrate._test_odeint_banded.map" failed with exit status 1
Created attachment 563068 [details] build.log.bz2
Created attachment 563070 [details] emergeinfo
Created attachment 563072 [details] emergepqv
(In reply to Andrew Ammerlaan from comment #3) > Created attachment 563072 [details] > emergepqv MAKEOPTS="-j1" emerge --ignore-default-opts --jobs=1 sci-libs/scipy ?
(In reply to Aweal from comment #4) > (In reply to Andrew Ammerlaan from comment #3) > > Created attachment 563072 [details] > > emergepqv > > MAKEOPTS="-j1" emerge --ignore-default-opts --jobs=1 sci-libs/scipy > > ? That worked :D Thanks, Is this just an issue with parallel jobs then?
i thought the ebuild had stuff to prevent parallel build in it now. python 3.5+ (I think) can do parallel build. But it seems resolution for fortran objects, at least, is spotty and you can end trying to link with an object for which the compilation hasn't finished. We have plagued by this problem for a little while now.
I have also encountered this issue and can confirm that building with MAKEOPTS="-j1" emerge --ignore-default-opts --jobs=1 sci-libs/scipy fixes the problem.
I can confirm the problem and it is solved by the above workaround.
I think I saw in the past another bug related with parallel building working with some python versions but not others... but I am unsure about what was the proper fix there... maybe someone in python team will remember better :/
If the code that's apparently supposed to prevent parallel build is commented out, it obviously can't help preventing the issue.
*** This bug has been marked as a duplicate of bug 614464 ***
