Your message dated Mon, 25 Jun 2018 18:04:20 +0000
with message-id <[email protected]>
and subject line Bug#895419: fixed in dolfin 2018.1.0.post0-1exp1
has caused the Debian Bug report #895419,
regarding python3-dolfin: JIT compilation fails as python3-instant tries to
includes petsc4py from python2
to be marked as done.
This means that you claim that the problem has been dealt with.
If this is not the case it is now your responsibility to reopen the
Bug report if necessary, and/or fix the problem forthwith.
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--
895419: https://bugs.debian.org/cgi-bin/bugreport.cgi?bug=895419
Debian Bug Tracking System
Contact [email protected] with problems
--- Begin Message ---
Package: python3-dolfin
Version: 2017.2.0.post0-3
Severity: important
Dear Maintainer,
trying to run the simple following script:
-- test_fenics.py --
import fenics as fe
tmp = fe.Expression("1/x[0]")
-- end test_fenics.py --
the DOLFIN just-in-time compiler is called but fails.
stdout and stderr were captured (see attached files)
$ python3 test_fenics.py >> stdout.log 2>> stderr.log
Is also attached an archive with the .cache/instant folder containing in
particular the compile.log generated by fenics/dolfin.
The following lines are relevant
CMake Error in CMakeLists.txt:
Imported target "dolfin" includes non-existent path
"/usr/lib/python2.7/dist-packages/petsc4py/include"
python3-petsc4py is installed (3.8.1-3), while python-petsc4py is not (and
needs not to be installed)
It makes the package unusable, as no expression can be compiled and used in
finite elements computation
-- System Information:
Debian Release: buster/sid
APT prefers oldstable-updates
APT policy: (500, 'oldstable-updates'), (500, 'unstable'), (500, 'oldstable')
Architecture: amd64 (x86_64)
Kernel: Linux 4.15.0-2-amd64 (SMP w/8 CPU cores)
Locale: LANG=fr_FR.utf8, LC_CTYPE=fr_FR.utf8 (charmap=UTF-8),
LANGUAGE=fr_FR.utf8 (charmap=UTF-8)
Shell: /bin/sh linked to /bin/dash
Init: systemd (via /run/systemd/system)
Versions of packages python3-dolfin depends on:
ii libboost-timer1.62.0 1.62.0+dfsg-5
ii libc6 2.27-3
ii libdolfin-dev 2017.2.0.post0-3
ii libdolfin2017.2 2017.2.0.post0-3
ii libgcc1 1:8-20180402-1
ii libhdf5-openmpi-100 1.10.0-patch1+docs-4
ii libopenmpi2 2.1.1-8
ii libpetsc-real3.8 3.8.4+dfsg1-1
ii libpython3.6 3.6.5-3
ii libslepc-real3.8 3.8.2+dfsg1-4
ii libstdc++6 8-20180402-1
ii libsz2 1.0.2-1
ii python3 3.6.5-2
ii python3-dijitso 2017.2.0.0-2
ii python3-ffc 2017.2.0.post0-2
ii python3-instant 2017.2.0.0-2
ii python3-numpy [python3-numpy-abi9] 1:1.13.3-2
ii python3-petsc4py 3.8.1-3
ii python3-ply 3.11-1
ii python3-six 1.11.0-2
ii python3-slepc4py 3.8.0-3
ii python3-sympy 1.1.1-5
ii python3-ufl 2017.2.0.0-2
ii zlib1g 1:1.2.8.dfsg-5
python3-dolfin recommends no packages.
Versions of packages python3-dolfin suggests:
pn dolfin-doc <none>
-- no debconf information
instant.tar.xz
Description: application/xz
Calling DOLFIN just-in-time (JIT) compiler, this may take some time.
Calling DOLFIN just-in-time (JIT) compiler, this may take some time.
Calling DOLFIN just-in-time (JIT) compiler, this may take some time.
--- Instant: compiling ---
In instant.recompile: The module did not compile with command 'cmake
-DDEBUG=TRUE .', see
'/home/fab/.cache/instant/python3.6/error/dolfin_4bedd8911ad2fa3696d85d184d02a288d3294659/compile.log'
Traceback (most recent call last):
File "test_fenics.py", line 57, in <module>
aux_invr = fe.Expression("1/x[0]")
File "/usr/lib/python3/dist-packages/dolfin/functions/expression.py", line
679, in __new__
mpi_comm=kwargs.get("mpi_comm"))
File "/usr/lib/python3/dist-packages/dolfin/compilemodules/expressions.py",
line 266, in compile_expressions
mpi_comm=mpi_comm)
File "/usr/lib/python3/dist-packages/dolfin/compilemodules/expressions.py",
line 183, in compile_expression_code
mpi_comm=mpi_comm)
File "/usr/lib/python3/dist-packages/dolfin/compilemodules/jit.py", line 70,
in mpi_jit
return local_jit(*args, **kwargs)
File "/usr/lib/python3/dist-packages/dolfin/compilemodules/compilemodule.py",
line 603, in compile_extension_module
**instant_kwargs)
File "/usr/lib/python3/dist-packages/instant/build.py", line 577, in
build_module
build_system)
File "/usr/lib/python3/dist-packages/instant/build.py", line 158, in recompile
instant_error(msg % (cmd, compile_log_filename_dest))
File "/usr/lib/python3/dist-packages/instant/output.py", line 96, in
instant_error
raise RuntimeError(text)
RuntimeError: In instant.recompile: The module did not compile with command
'cmake -DDEBUG=TRUE .', see
'/home/fab/.cache/instant/python3.6/error/dolfin_4bedd8911ad2fa3696d85d184d02a288d3294659/compile.log'
--- Instant: compiling ---
In instant.recompile: The module did not compile with command 'cmake
-DDEBUG=TRUE .', see
'/home/fab/.cache/instant/python3.6/error/dolfin_4bedd8911ad2fa3696d85d184d02a288d3294659/compile.log'
Traceback (most recent call last):
File "bug_instant.py", line 9, in <module>
aux_invr = fe.Expression("1/x[0]")
File "/usr/lib/python3/dist-packages/dolfin/functions/expression.py", line
679, in __new__
mpi_comm=kwargs.get("mpi_comm"))
File "/usr/lib/python3/dist-packages/dolfin/compilemodules/expressions.py",
line 266, in compile_expressions
mpi_comm=mpi_comm)
File "/usr/lib/python3/dist-packages/dolfin/compilemodules/expressions.py",
line 183, in compile_expression_code
mpi_comm=mpi_comm)
File "/usr/lib/python3/dist-packages/dolfin/compilemodules/jit.py", line 70,
in mpi_jit
return local_jit(*args, **kwargs)
File "/usr/lib/python3/dist-packages/dolfin/compilemodules/compilemodule.py",
line 603, in compile_extension_module
**instant_kwargs)
File "/usr/lib/python3/dist-packages/instant/build.py", line 577, in
build_module
build_system)
File "/usr/lib/python3/dist-packages/instant/build.py", line 158, in recompile
instant_error(msg % (cmd, compile_log_filename_dest))
File "/usr/lib/python3/dist-packages/instant/output.py", line 96, in
instant_error
raise RuntimeError(text)
RuntimeError: In instant.recompile: The module did not compile with command
'cmake -DDEBUG=TRUE .', see
'/home/fab/.cache/instant/python3.6/error/dolfin_4bedd8911ad2fa3696d85d184d02a288d3294659/compile.log'
--- End Message ---
--- Begin Message ---
Source: dolfin
Source-Version: 2018.1.0.post0-1exp1
We believe that the bug you reported is fixed in the latest version of
dolfin, which is due to be installed in the Debian FTP archive.
A summary of the changes between this version and the previous one is
attached.
Thank you for reporting the bug, which will now be closed. If you
have further comments please address them to [email protected],
and the maintainer will reopen the bug report if appropriate.
Debian distribution maintenance software
pp.
Drew Parsons <[email protected]> (supplier of updated dolfin package)
(This message was generated automatically at their request; if you
believe that there is a problem with it please contact the archive
administrators by mailing [email protected])
-----BEGIN PGP SIGNED MESSAGE-----
Hash: SHA512
Format: 1.8
Date: Tue, 26 Jun 2018 01:38:04 +0800
Source: dolfin
Binary: libdolfin-dev libdolfin2018.1 python3-dolfin python-dolfin dolfin-doc
dolfin-bin
Architecture: source
Version: 2018.1.0.post0-1exp1
Distribution: experimental
Urgency: medium
Maintainer: Debian Science Team
<[email protected]>
Changed-By: Drew Parsons <[email protected]>
Description:
dolfin-bin - Executable scripts for DOLFIN
dolfin-doc - Documentation and demo programs for DOLFIN
libdolfin-dev - Shared links and header files for DOLFIN
libdolfin2018.1 - Shared libraries for DOLFIN
python-dolfin - Python interface for DOLFIN
python3-dolfin - Python interface for DOLFIN (Python 3)
Closes: 895419
Changes:
dolfin (2018.1.0.post0-1exp1) experimental; urgency=medium
.
* Corrected upstream release.
- includes the fenics python module.
- petsc4py and other include dirs are no longer added to
DOLFIN_3RD_PARTY_INCLUDE_DIRS in DOLFINConfig.cmake.
Closes: #895419.
* Use override_dh_auto_test instead of DEB_BUILD_OPTIONS=nocheck
to skip build time tests without triggering a lintian warning.
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