Your message dated Sat, 21 May 2016 17:08:06 +0000
with message-id <e1b4ani-0006ap...@franck.debian.org>
and subject line Bug#824789: Removed package(s) from unstable
has caused the Debian Bug report #782029,
regarding build multiarch installation of suitesparse-metis
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.
(NB: If you are a system administrator and have no idea what this
message is talking about, this may indicate a serious mail system
misconfiguration somewhere. Please contact ow...@bugs.debian.org
immediately.)
--
782029: http://bugs.debian.org/cgi-bin/bugreport.cgi?bug=782029
Debian Bug Tracking System
Contact ow...@bugs.debian.org with problems
--- Begin Message ---
Package: dolfin-bin
Version: 1.5.0-1
Severity: important
Dear Maintainer,
I'm trying to work through the first example at
http://fenicsproject.org/documentation/tutorial/fundamentals.html#implementation-1
(A minimal script of the first 4 lines of that example is attached.)
The compilation of the python.Expression() fails:
$ python fenics_test.py
Calling DOLFIN just-in-time (JIT) compiler, this may take some time.
In instant.recompile: The module did not compile with command 'make VERBOSE=1',
see
'/home/medlock/.instant/error/dolfin_compile_code_b75a7140f4b7f593c8d2e8c722e633c4711e3c15/compile.log'
Traceback (most recent call last):
File "fenics_test.py", line 5, in <module>
u0 = Expression('1 + x[0]*x[0] + 2*x[1]*x[1]')
File "/usr/lib/python2.7/dist-packages/dolfin/functions/expression.py", line
602, in __new__
mpi_comm=mpi_comm)
File "/usr/lib/python2.7/dist-packages/dolfin/compilemodules/expressions.py",
line 217, in compile_expressions
mpi_comm=mpi_comm)
File "/usr/lib/python2.7/dist-packages/dolfin/compilemodules/expressions.py",
line 145, in compile_expression_code
mpi_comm=mpi_comm)
File "/usr/lib/python2.7/dist-packages/dolfin/compilemodules/jit.py", line
64, in mpi_jit
return local_jit(*args, **kwargs)
File
"/usr/lib/python2.7/dist-packages/dolfin/compilemodules/compilemodule.py", line
458, in compile_extension_module
**instant_kwargs)
File "/usr/lib/python2.7/dist-packages/instant/build.py", line 563, in
build_module
recompile(modulename, module_path, new_compilation_checksum, build_system)
File "/usr/lib/python2.7/dist-packages/instant/build.py", line 165, in
recompile
instant_error(msg % (cmd, compile_log_filename_dest))
File "/usr/lib/python2.7/dist-packages/instant/output.py", line 85, in
instant_error
raise RuntimeError(text)
RuntimeError: In instant.recompile: The module did not compile with command
'make VERBOSE=1', see
'/home/medlock/.instant/error/dolfin_compile_code_b75a7140f4b7f593c8d2e8c722e633c4711e3c15/compile.log'
This seems to be the crucial line of the ../compile.log (full log attached):
make[2]: *** No rule to make target '/usr/lib/x86_64-linux-gnu/libumfpack.so',
needed by '_dolfin_compile_code_b75a7140f4b7f593c8d2e8c722e633c4711e3c15.so'.
Stop.
Looking at
~/.instant/error/dolfin_compile_code_*/CMakeFiles/_dolfin_compile_code_*.dir/build.make
(attached) there is indeed a line for
/usr/lib/x86_64-linux-gnu/libumfpack.so, and other .so files
(libamd.so, libcholmod.so, ...) from libsuitesparse.
I see that I have libsuitesparse-metis-dev installed instead of
libsuitesparse-dev. The former puts these files in /usr/lib, while
the latter uses /usr/lib/$ARCH.
Any good ideas for fixing this? Should dolfin work with both
libsuitesparse-dev and libsuitesparse-metis-dev? Perhaps this bug
belongs to libsuitesparse-metis-dev.
Thanks,
JM
*** Reporter, please consider answering these questions, where appropriate ***
* What led up to the situation?
* What exactly did you do (or not do) that was effective (or
ineffective)?
* What was the outcome of this action?
* What outcome did you expect instead?
*** End of the template - remove these template lines ***
-- System Information:
Debian Release: 8.0
APT prefers unstable
APT policy: (500, 'unstable'), (500, 'testing'), (1, 'experimental')
Architecture: amd64 (x86_64)
Kernel: Linux 3.16.0-4-amd64 (SMP w/8 CPU cores)
Locale: LANG=en_US.utf8, LC_CTYPE=en_US.utf8 (charmap=UTF-8)
Shell: /bin/sh linked to /bin/dash
Init: systemd (via /run/systemd/system)
Versions of packages dolfin-bin depends on:
ii python 2.7.9-1
ii python-dolfin 1.5.0-1
ii python-numpy 1:1.8.2-2
pn python:any <none>
dolfin-bin recommends no packages.
dolfin-bin suggests no packages.
-- no debconf information
from dolfin import *
mesh = UnitIntervalMesh(4)
V = FunctionSpace(mesh, 'Lagrange', 1)
u0 = Expression('1 + x[0]*x[0] + 2*x[1]*x[1]')
-- The C compiler identification is GNU 4.9.2
-- The CXX compiler identification is GNU 4.9.2
-- Check for working C compiler: /usr/bin/cc
-- Check for working C compiler: /usr/bin/cc -- works
-- Detecting C compiler ABI info
-- Detecting C compiler ABI info - done
-- Check for working CXX compiler: /usr/bin/c++
-- Check for working CXX compiler: /usr/bin/c++ -- works
-- Detecting CXX compiler ABI info
-- Detecting CXX compiler ABI info - done
-- Found SWIG: /usr/bin/swig (found version "2.0.12")
-- Configuring done
-- Generating done
CMake Warning:
Manually-specified variables were not used by the project:
DEBUG
-- Build files have been written to:
/tmp/user/1000/tmp4mcOz32015-4-6-10-09_instant_cf7560cc442257e4cd3a87a4673da8832b79fa28/dolfin_compile_code_b75a7140f4b7f593c8d2e8c722e633c4711e3c15
/usr/bin/cmake
-H/tmp/user/1000/tmp4mcOz32015-4-6-10-09_instant_cf7560cc442257e4cd3a87a4673da8832b79fa28/dolfin_compile_code_b75a7140f4b7f593c8d2e8c722e633c4711e3c15
-B/tmp/user/1000/tmp4mcOz32015-4-6-10-09_instant_cf7560cc442257e4cd3a87a4673da8832b79fa28/dolfin_compile_code_b75a7140f4b7f593c8d2e8c722e633c4711e3c15
--check-build-system CMakeFiles/Makefile.cmake 0
/usr/bin/cmake -E cmake_progress_start
/tmp/user/1000/tmp4mcOz32015-4-6-10-09_instant_cf7560cc442257e4cd3a87a4673da8832b79fa28/dolfin_compile_code_b75a7140f4b7f593c8d2e8c722e633c4711e3c15/CMakeFiles
/tmp/user/1000/tmp4mcOz32015-4-6-10-09_instant_cf7560cc442257e4cd3a87a4673da8832b79fa28/dolfin_compile_code_b75a7140f4b7f593c8d2e8c722e633c4711e3c15/CMakeFiles/progress.marks
make -f CMakeFiles/Makefile2 all
make[1]: Entering directory
'/tmp/user/1000/tmp4mcOz32015-4-6-10-09_instant_cf7560cc442257e4cd3a87a4673da8832b79fa28/dolfin_compile_code_b75a7140f4b7f593c8d2e8c722e633c4711e3c15'
make -f
CMakeFiles/_dolfin_compile_code_b75a7140f4b7f593c8d2e8c722e633c4711e3c15.dir/build.make
CMakeFiles/_dolfin_compile_code_b75a7140f4b7f593c8d2e8c722e633c4711e3c15.dir/depend
make[2]: Entering directory
'/tmp/user/1000/tmp4mcOz32015-4-6-10-09_instant_cf7560cc442257e4cd3a87a4673da8832b79fa28/dolfin_compile_code_b75a7140f4b7f593c8d2e8c722e633c4711e3c15'
/usr/bin/cmake -E cmake_progress_report
/tmp/user/1000/tmp4mcOz32015-4-6-10-09_instant_cf7560cc442257e4cd3a87a4673da8832b79fa28/dolfin_compile_code_b75a7140f4b7f593c8d2e8c722e633c4711e3c15/CMakeFiles
1
[ 50%] Swig source
/usr/bin/cmake -E make_directory
/tmp/user/1000/tmp4mcOz32015-4-6-10-09_instant_cf7560cc442257e4cd3a87a4673da8832b79fa28/dolfin_compile_code_b75a7140f4b7f593c8d2e8c722e633c4711e3c15
/usr/bin/swig -python -module
dolfin_compile_code_b75a7140f4b7f593c8d2e8c722e633c4711e3c15 -shadow -modern
-modernargs -fastdispatch -fvirtual -nosafecstrings -noproxydel -fastproxy
-fastinit -fastunpack -fastquery -nobuildnone -DDOLFIN_VERSION="1.5.0"
-DBOOST_UBLAS_NDEBUG -DDOLFIN_SIZE_T=8 -DDOLFIN_LA_INDEX_SIZE=4 -DHAS_HDF5
-D_LARGEFILE_SOURCE -D_LARGEFILE64_SOURCE -D_BSD_SOURCE -D_FORTIFY_SOURCE=2
-DHAS_SLEPC -DHAS_PETSC -DENABLE_PETSC_SNES -DHAS_UMFPACK -DHAS_CHOLMOD
-DHAS_ZLIB -DHAS_MPI -DHAS_OPENMP -DHAS_QT4 -DHAS_VTK -DHAS_QVTK
-DNUMPY_VERSION_MAJOR=1 -DNUMPY_VERSION_MINOR=8 -DNUMPY_VERSION_MICRO=2
-DNPY_NO_DEPRECATED_API=NPY_1_8_API_VERSION -c++ -fcompact -O -I. -small
-outdir
/tmp/user/1000/tmp4mcOz32015-4-6-10-09_instant_cf7560cc442257e4cd3a87a4673da8832b79fa28/dolfin_compile_code_b75a7140f4b7f593c8d2e8c722e633c4711e3c15
-c++ -I/usr/include -I/usr/include/libxml2 -I/usr/local/include
-I/usr/lib/slepcdir/3.4.2 -I/usr/lib/slepcdir/3.4.2/linux-gnu-c-opt/include
-I/usr/
lib/slepcdir/3.4.2/include -I/usr/include/suitesparse
-I/usr/lib/openmpi/include -I/usr/lib/openmpi/include/openmpi
-I/usr/include/eigen3 -I/usr/include/hdf5/openmpi
-I/usr/lib/petscdir/3.4.2/include
-I/usr/lib/petscdir/3.4.2/linux-gnu-c-opt/include -I/usr/include/scotch
-I/usr/lib/x86_64-linux-gnu/hdf5/openmpi/include -I/usr/include/qt4
-I/usr/include/vtk-5.8
-I/tmp/user/1000/tmp4mcOz32015-4-6-10-09_instant_cf7560cc442257e4cd3a87a4673da8832b79fa28/dolfin_compile_code_b75a7140f4b7f593c8d2e8c722e633c4711e3c15/.
-I/usr/lib/python2.7/dist-packages/numpy/core/include -I/usr/include/python2.7
-I/tmp/user/1000/tmp4mcOz32015-4-6-10-09_instant_cf7560cc442257e4cd3a87a4673da8832b79fa28/dolfin_compile_code_b75a7140f4b7f593c8d2e8c722e633c4711e3c15
-o
/tmp/user/1000/tmp4mcOz32015-4-6-10-09_instant_cf7560cc442257e4cd3a87a4673da8832b79fa28/dolfin_compile_code_b75a7140f4b7f593c8d2e8c722e633c4711e3c15/dolfin_compile_code_b75a7140f4b7f593c8d2e8c722e633c4711e3c15PYTHON_wrap.cxx
/tmp/user/1000/
tmp4mcOz32015-4-6-10-09_instant_cf7560cc442257e4cd3a87a4673da8832b79fa28/dolfin_compile_code_b75a7140f4b7f593c8d2e8c722e633c4711e3c15/dolfin_compile_code_b75a7140f4b7f593c8d2e8c722e633c4711e3c15.i
/usr/include/dolfin/la/LinearAlgebraObject.h:36: Warning 520: Derived class
'LinearAlgebraObject' of 'dolfin::Variable' is not similarly marked as a smart
pointer.
/usr/include/dolfin/function/Function.h:63: Warning 402: Base class
'Hierarchical< Function >' is incomplete.
/usr/include/dolfin/swig/function/pre.i:219: Warning 402: Only forward
declaration 'Hierarchical< Function >' was found.
/usr/include/dolfin/function/Function.h:64: Warning 520: Derived class
'Function' of 'dolfin::GenericFunction' is not similarly marked as a smart
pointer.
/usr/include/dolfin/function/Function.h:64: Warning 520: Derived class
'Function' of 'ufc::function' is not similarly marked as a smart pointer.
/usr/include/dolfin/function/Function.h:64: Warning 520: Derived class
'Function' of 'dolfin::Variable' is not similarly marked as a smart pointer.
/usr/include/dolfin/function/FunctionSpace.h:53: Warning 402: Base class
'Hierarchical< FunctionSpace >' is incomplete.
/usr/include/dolfin/swig/function/pre.i:218: Warning 402: Only forward
declaration 'Hierarchical< FunctionSpace >' was found.
/usr/include/dolfin/function/FunctionSpace.h:54: Warning 520: Derived class
'FunctionSpace' of 'dolfin::Variable' is not similarly marked as a smart
pointer.
/tmp/user/1000/tmp4mcOz32015-4-6-10-09_instant_cf7560cc442257e4cd3a87a4673da8832b79fa28/dolfin_compile_code_b75a7140f4b7f593c8d2e8c722e633c4711e3c15/dolfin_compile_code_b75a7140f4b7f593c8d2e8c722e633c4711e3c15.i:170:
Warning 315: Nothing known about 'std::cos'.
/tmp/user/1000/tmp4mcOz32015-4-6-10-09_instant_cf7560cc442257e4cd3a87a4673da8832b79fa28/dolfin_compile_code_b75a7140f4b7f593c8d2e8c722e633c4711e3c15/dolfin_compile_code_b75a7140f4b7f593c8d2e8c722e633c4711e3c15.i:171:
Warning 315: Nothing known about 'std::sin'.
/tmp/user/1000/tmp4mcOz32015-4-6-10-09_instant_cf7560cc442257e4cd3a87a4673da8832b79fa28/dolfin_compile_code_b75a7140f4b7f593c8d2e8c722e633c4711e3c15/dolfin_compile_code_b75a7140f4b7f593c8d2e8c722e633c4711e3c15.i:172:
Warning 315: Nothing known about 'std::tan'.
/tmp/user/1000/tmp4mcOz32015-4-6-10-09_instant_cf7560cc442257e4cd3a87a4673da8832b79fa28/dolfin_compile_code_b75a7140f4b7f593c8d2e8c722e633c4711e3c15/dolfin_compile_code_b75a7140f4b7f593c8d2e8c722e633c4711e3c15.i:173:
Warning 315: Nothing known about 'std::acos'.
/tmp/user/1000/tmp4mcOz32015-4-6-10-09_instant_cf7560cc442257e4cd3a87a4673da8832b79fa28/dolfin_compile_code_b75a7140f4b7f593c8d2e8c722e633c4711e3c15/dolfin_compile_code_b75a7140f4b7f593c8d2e8c722e633c4711e3c15.i:174:
Warning 315: Nothing known about 'std::asin'.
/tmp/user/1000/tmp4mcOz32015-4-6-10-09_instant_cf7560cc442257e4cd3a87a4673da8832b79fa28/dolfin_compile_code_b75a7140f4b7f593c8d2e8c722e633c4711e3c15/dolfin_compile_code_b75a7140f4b7f593c8d2e8c722e633c4711e3c15.i:175:
Warning 315: Nothing known about 'std::atan'.
/tmp/user/1000/tmp4mcOz32015-4-6-10-09_instant_cf7560cc442257e4cd3a87a4673da8832b79fa28/dolfin_compile_code_b75a7140f4b7f593c8d2e8c722e633c4711e3c15/dolfin_compile_code_b75a7140f4b7f593c8d2e8c722e633c4711e3c15.i:176:
Warning 315: Nothing known about 'std::atan2'.
/tmp/user/1000/tmp4mcOz32015-4-6-10-09_instant_cf7560cc442257e4cd3a87a4673da8832b79fa28/dolfin_compile_code_b75a7140f4b7f593c8d2e8c722e633c4711e3c15/dolfin_compile_code_b75a7140f4b7f593c8d2e8c722e633c4711e3c15.i:177:
Warning 315: Nothing known about 'std::cosh'.
/tmp/user/1000/tmp4mcOz32015-4-6-10-09_instant_cf7560cc442257e4cd3a87a4673da8832b79fa28/dolfin_compile_code_b75a7140f4b7f593c8d2e8c722e633c4711e3c15/dolfin_compile_code_b75a7140f4b7f593c8d2e8c722e633c4711e3c15.i:178:
Warning 315: Nothing known about 'std::sinh'.
/tmp/user/1000/tmp4mcOz32015-4-6-10-09_instant_cf7560cc442257e4cd3a87a4673da8832b79fa28/dolfin_compile_code_b75a7140f4b7f593c8d2e8c722e633c4711e3c15/dolfin_compile_code_b75a7140f4b7f593c8d2e8c722e633c4711e3c15.i:179:
Warning 315: Nothing known about 'std::tanh'.
/tmp/user/1000/tmp4mcOz32015-4-6-10-09_instant_cf7560cc442257e4cd3a87a4673da8832b79fa28/dolfin_compile_code_b75a7140f4b7f593c8d2e8c722e633c4711e3c15/dolfin_compile_code_b75a7140f4b7f593c8d2e8c722e633c4711e3c15.i:180:
Warning 315: Nothing known about 'std::exp'.
/tmp/user/1000/tmp4mcOz32015-4-6-10-09_instant_cf7560cc442257e4cd3a87a4673da8832b79fa28/dolfin_compile_code_b75a7140f4b7f593c8d2e8c722e633c4711e3c15/dolfin_compile_code_b75a7140f4b7f593c8d2e8c722e633c4711e3c15.i:181:
Warning 315: Nothing known about 'std::frexp'.
/tmp/user/1000/tmp4mcOz32015-4-6-10-09_instant_cf7560cc442257e4cd3a87a4673da8832b79fa28/dolfin_compile_code_b75a7140f4b7f593c8d2e8c722e633c4711e3c15/dolfin_compile_code_b75a7140f4b7f593c8d2e8c722e633c4711e3c15.i:182:
Warning 315: Nothing known about 'std::ldexp'.
/tmp/user/1000/tmp4mcOz32015-4-6-10-09_instant_cf7560cc442257e4cd3a87a4673da8832b79fa28/dolfin_compile_code_b75a7140f4b7f593c8d2e8c722e633c4711e3c15/dolfin_compile_code_b75a7140f4b7f593c8d2e8c722e633c4711e3c15.i:183:
Warning 315: Nothing known about 'std::log'.
/tmp/user/1000/tmp4mcOz32015-4-6-10-09_instant_cf7560cc442257e4cd3a87a4673da8832b79fa28/dolfin_compile_code_b75a7140f4b7f593c8d2e8c722e633c4711e3c15/dolfin_compile_code_b75a7140f4b7f593c8d2e8c722e633c4711e3c15.i:184:
Warning 315: Nothing known about 'std::log10'.
/tmp/user/1000/tmp4mcOz32015-4-6-10-09_instant_cf7560cc442257e4cd3a87a4673da8832b79fa28/dolfin_compile_code_b75a7140f4b7f593c8d2e8c722e633c4711e3c15/dolfin_compile_code_b75a7140f4b7f593c8d2e8c722e633c4711e3c15.i:185:
Warning 315: Nothing known about 'std::modf'.
/tmp/user/1000/tmp4mcOz32015-4-6-10-09_instant_cf7560cc442257e4cd3a87a4673da8832b79fa28/dolfin_compile_code_b75a7140f4b7f593c8d2e8c722e633c4711e3c15/dolfin_compile_code_b75a7140f4b7f593c8d2e8c722e633c4711e3c15.i:186:
Warning 315: Nothing known about 'std::pow'.
/tmp/user/1000/tmp4mcOz32015-4-6-10-09_instant_cf7560cc442257e4cd3a87a4673da8832b79fa28/dolfin_compile_code_b75a7140f4b7f593c8d2e8c722e633c4711e3c15/dolfin_compile_code_b75a7140f4b7f593c8d2e8c722e633c4711e3c15.i:187:
Warning 315: Nothing known about 'std::sqrt'.
/tmp/user/1000/tmp4mcOz32015-4-6-10-09_instant_cf7560cc442257e4cd3a87a4673da8832b79fa28/dolfin_compile_code_b75a7140f4b7f593c8d2e8c722e633c4711e3c15/dolfin_compile_code_b75a7140f4b7f593c8d2e8c722e633c4711e3c15.i:188:
Warning 315: Nothing known about 'std::ceil'.
/tmp/user/1000/tmp4mcOz32015-4-6-10-09_instant_cf7560cc442257e4cd3a87a4673da8832b79fa28/dolfin_compile_code_b75a7140f4b7f593c8d2e8c722e633c4711e3c15/dolfin_compile_code_b75a7140f4b7f593c8d2e8c722e633c4711e3c15.i:189:
Warning 315: Nothing known about 'std::fabs'.
/tmp/user/1000/tmp4mcOz32015-4-6-10-09_instant_cf7560cc442257e4cd3a87a4673da8832b79fa28/dolfin_compile_code_b75a7140f4b7f593c8d2e8c722e633c4711e3c15/dolfin_compile_code_b75a7140f4b7f593c8d2e8c722e633c4711e3c15.i:190:
Warning 315: Nothing known about 'std::floor'.
/tmp/user/1000/tmp4mcOz32015-4-6-10-09_instant_cf7560cc442257e4cd3a87a4673da8832b79fa28/dolfin_compile_code_b75a7140f4b7f593c8d2e8c722e633c4711e3c15/dolfin_compile_code_b75a7140f4b7f593c8d2e8c722e633c4711e3c15.i:191:
Warning 315: Nothing known about 'std::fmod'.
/tmp/user/1000/tmp4mcOz32015-4-6-10-09_instant_cf7560cc442257e4cd3a87a4673da8832b79fa28/dolfin_compile_code_b75a7140f4b7f593c8d2e8c722e633c4711e3c15/dolfin_compile_code_b75a7140f4b7f593c8d2e8c722e633c4711e3c15.i:192:
Warning 315: Nothing known about 'std::max'.
/tmp/user/1000/tmp4mcOz32015-4-6-10-09_instant_cf7560cc442257e4cd3a87a4673da8832b79fa28/dolfin_compile_code_b75a7140f4b7f593c8d2e8c722e633c4711e3c15/dolfin_compile_code_b75a7140f4b7f593c8d2e8c722e633c4711e3c15.i:193:
Warning 315: Nothing known about 'std::min'.
cd
/tmp/user/1000/tmp4mcOz32015-4-6-10-09_instant_cf7560cc442257e4cd3a87a4673da8832b79fa28/dolfin_compile_code_b75a7140f4b7f593c8d2e8c722e633c4711e3c15
&& /usr/bin/cmake -E cmake_depends "Unix Makefiles"
/tmp/user/1000/tmp4mcOz32015-4-6-10-09_instant_cf7560cc442257e4cd3a87a4673da8832b79fa28/dolfin_compile_code_b75a7140f4b7f593c8d2e8c722e633c4711e3c15
/tmp/user/1000/tmp4mcOz32015-4-6-10-09_instant_cf7560cc442257e4cd3a87a4673da8832b79fa28/dolfin_compile_code_b75a7140f4b7f593c8d2e8c722e633c4711e3c15
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--- End Message ---
--- Begin Message ---
Version: 3.1.0-2+rm
Dear submitter,
as the package suitesparse-metis has just been removed from the Debian archive
unstable we hereby close the associated bug reports. We are sorry
that we couldn't deal with your issue properly.
For details on the removal, please see https://bugs.debian.org/824789
The version of this package that was in Debian prior to this removal
can still be found using http://snapshot.debian.org/.
This message was generated automatically; if you believe that there is
a problem with it please contact the archive administrators by mailing
ftpmas...@ftp-master.debian.org.
Debian distribution maintenance software
pp.
Scott Kitterman (the ftpmaster behind the curtain)
--- End Message ---
