Bug 676640 – sci-libs/scipy-1.1.0 python-3.7 "object of type 'type' has no len()" in evaluating 'len(list)' (available names: [])

• Product: Gentoo Linux
• Status: RESOLVED DUPLICATE

[Description Nowa Ammerlaan 2019-01-28 15:55:08 UTC]

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

[Comment 1 Nowa Ammerlaan 2019-01-28 15:56:59 UTC]

Created attachment 563068 [details]
build.log.bz2

[Comment 2 Nowa Ammerlaan 2019-01-28 15:57:53 UTC]

Created attachment 563070 [details]
emergeinfo

[Comment 3 Nowa Ammerlaan 2019-01-28 15:59:01 UTC]

Created attachment 563072 [details]
emergepqv

[Comment 4 Aweal 2019-01-29 20:16:14 UTC]

(In reply to Andrew Ammerlaan from comment #3)
> Created attachment 563072 [details]
> emergepqv

MAKEOPTS="-j1" emerge --ignore-default-opts --jobs=1 sci-libs/scipy

?

[Comment 5 Nowa Ammerlaan 2019-01-30 18:31:12 UTC]

(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?

[Comment 6 François Bissey 2019-01-30 18:55:23 UTC]

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.

[Comment 7 Tom Gillespie 2019-02-14 07:18:49 UTC]

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.

[Comment 8 email200202 2019-03-22 12:15:41 UTC]

I can confirm the problem and it is solved by the above workaround.

[Comment 9 Pacho Ramos 2019-06-03 12:41:19 UTC]

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 :/

[Comment 10 Michał Górny 2019-07-07 08:20:17 UTC]

If the code that's apparently supposed to prevent parallel build is commented out, it obviously can't help preventing the issue.

[Comment 11 mercuriete 2020-05-08 01:11:14 UTC]

I can confirm the problem and it is solved by the above workaround.

[Comment 12 Nowa Ammerlaan 2020-08-18 11:39:37 UTC]

*** This bug has been marked as a duplicate of bug 614464 ***