Error during make

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Error during make

P-M
Hello,

I am trying to compile the git version of graph-tool. I have configured it
as follows:

./configure --with-boost=/opt/anaconda/anaconda3 --enable-openmp

This returns a configuration summary as follows:
================================================================================
                             CONFIGURATION SUMMARY
================================================================================
Using python version:   2.7.14
Python interpreter:     /opt/anaconda/anaconda3/bin/python
Installation path:    
/opt/anaconda/anaconda3/lib/python2.7/site-packages/graph_tool

C++ compiler (CXX):     g++ -std=gnu++14
C++ compiler version:   5.4.0

Prefix:                 /usr/local
Pkgconfigdir:           ${libdir}/pkgconfig

Python CPP flags:       -I/opt/anaconda/anaconda3/include/python2.7
Python LD flags:        -L/opt/anaconda/anaconda3/lib -lpython2.7
Boost CPP flags:        -pthread -I/opt/anaconda/anaconda3/include
Boost LD flags:         -lboost_iostreams -lboost_python -lboost_regex
-lboost_context -lboost_coroutine
Numpy CPP flags:      
-I/opt/anaconda/anaconda3/lib/python2.7/site-packages/numpy/core/include
Sparsehash CPP flags:
CGAL CPP flags:         -I/usr/include
CGAL LD flags:          -L/usr/lib -lCGAL -lCGAL_Core -lgmp -lboost_thread
-lpthread
Expat CPP flags:        -I/usr/include
Expat LD flags:         -L/usr/lib -lexpat
Cairomm CPP flags:       -I/usr/include/cairomm-1.0
-I/usr/lib/x86_64-linux-gnu/cairomm-1.0/include -I/usr/include/cairo
-I/usr/include/glib-2.0 -I/usr/lib/x86_64-linux-gnu/glib-2.0/include
-I/usr/include/pixman-1 -I/usr/include/freetype2 -I/usr/include/libpng12
-I/usr/include/sigc++-2.0 -I/usr/lib/x86_64-linux-gnu/sigc++-2.0/include
Cairomm LD flags:       -lcairomm-1.0 -lcairo -lsigc-2.0
OpenMP compiler flags:  -fopenmp
OpenMP LD flags:
Extra CPPFLAGS:         -DNDEBUG
Extra CXXFLAGS:         -fopenmp -O3 -fvisibility=default
-fvisibility-inlines-hidden -Wno-deprecated -Wall -Wextra
-ftemplate-backtrace-limit=0
Extra LDFLAGS:

Using OpenMP:           yes
Using sparsehash:       yes
Using cairo:            yes
================================================================================

and the following config.log  config.log
<http://main-discussion-list-for-the-graph-tool-project.982480.n3.nabble.com/file/t495975/config.log>
. I then have run

make -j20

This seems to fail with the following output

 make -j20
make  all-recursive
make[1]: Entering directory '/home/pmj27/graph-tool'
Making all in src
make[2]: Entering directory '/home/pmj27/graph-tool/src'
Making all in graph
make[3]: Entering directory '/home/pmj27/graph-tool/src/graph'
Making all in centrality
make[4]: Entering directory '/home/pmj27/graph-tool/src/graph/centrality'
  CXX      graph_betweenness.lo
  CXX      graph_centrality_bind.lo
  CXX      graph_closeness.lo
  CXX      graph_eigenvector.lo
  CXX      graph_hits.lo
  CXX      graph_eigentrust.lo
  CXX      graph_pagerank.lo
  CXX      graph_katz.lo
  CXX      graph_trust_transitivity.lo
  CXXLD    libgraph_tool_centrality.la
make[4]: Leaving directory '/home/pmj27/graph-tool/src/graph/centrality'
Making all in clustering
make[4]: Entering directory '/home/pmj27/graph-tool/src/graph/clustering'
  CXX      graph_clustering.lo
  CXX      graph_extended_clustering.lo
  CXX      graph_motifs.lo
  CXXLD    libgraph_tool_clustering.la
make[4]: Leaving directory '/home/pmj27/graph-tool/src/graph/clustering'
Making all in correlations
make[4]: Entering directory '/home/pmj27/graph-tool/src/graph/correlations'
  CXX      graph_assortativity.lo
  CXX      graph_correlations.lo
  CXX      graph_correlations_imp1.lo
  CXX      graph_correlations_bind.lo
  CXX      graph_correlations_combined.lo
  CXX      graph_avg_correlations.lo
  CXX      graph_avg_correlations_imp1.lo
  CXX      graph_avg_correlations_combined.lo
In file included from
/opt/anaconda/anaconda3/include/boost/multi_array.hpp:26:0,
                 from ../../../src/graph/histogram.hh:26,
                 from graph_correlations.hh:27,
                 from graph_avg_correlations.hh:21,
                 from graph_avg_correlations_combined.cc:26:
/opt/anaconda/anaconda3/include/boost/multi_array/base.hpp: In member
function ‘boost::multi_array<T, NumDims, Allocator>& boost::multi_array<T,
NumDims, Allocator>::resize(const
boost::detail::multi_array::extent_gen<NumDims>&) [with T = double; long
unsigned int NumDims = 1ul; Allocator = std::allocator<double>]’:
/opt/anaconda/anaconda3/include/boost/multi_array/base.hpp:416:31: warning:
‘new_strides.boost::array<long int, 1ul>::elems[0ul]’ may be used
uninitialized in this function [-Wmaybe-uninitialized]
     boost::array<index,NDims> new_strides;
                               ^
/opt/anaconda/anaconda3/include/boost/multi_array/base.hpp: In member
function ‘boost::multi_array<T, NumDims, Allocator>& boost::multi_array<T,
NumDims, Allocator>::resize(const
boost::detail::multi_array::extent_gen<NumDims>&) [with T = int; long
unsigned int NumDims = 1ul; Allocator = std::allocator<int>]’:
/opt/anaconda/anaconda3/include/boost/multi_array/base.hpp:416:31: warning:
‘new_strides.boost::array<long int, 1ul>::elems[0ul]’ may be used
uninitialized in this function [-Wmaybe-uninitialized]
In file included from
/opt/anaconda/anaconda3/include/boost/multi_array.hpp:26:0,
                 from ../../../src/graph/histogram.hh:26,
                 from graph_correlations.hh:27,
                 from graph_avg_correlations.hh:21,
                 from graph_avg_correlations.cc:26:
/opt/anaconda/anaconda3/include/boost/multi_array/base.hpp: In member
function ‘boost::multi_array<T, NumDims, Allocator>& boost::multi_array<T,
NumDims, Allocator>::resize(const
boost::detail::multi_array::extent_gen<NumDims>&) [with T = double; long
unsigned int NumDims = 1ul; Allocator = std::allocator<double>]’:
/opt/anaconda/anaconda3/include/boost/multi_array/base.hpp:416:31: warning:
‘new_strides.boost::array<long int, 1ul>::elems[0ul]’ may be used
uninitialized in this function [-Wmaybe-uninitialized]
     boost::array<index,NDims> new_strides;
                               ^
/opt/anaconda/anaconda3/include/boost/multi_array/base.hpp: In member
function ‘boost::multi_array<T, NumDims, Allocator>& boost::multi_array<T,
NumDims, Allocator>::resize(const
boost::detail::multi_array::extent_gen<NumDims>&) [with T = int; long
unsigned int NumDims = 1ul; Allocator = std::allocator<int>]’:
/opt/anaconda/anaconda3/include/boost/multi_array/base.hpp:416:31: warning:
‘new_strides.boost::array<long int, 1ul>::elems[0ul]’ may be used
uninitialized in this function [-Wmaybe-uninitialized]
In file included from
/opt/anaconda/anaconda3/include/boost/multi_array.hpp:26:0,
                 from ../../../src/graph/histogram.hh:26,
                 from graph_avg_correlations_imp1.cc:21:
/opt/anaconda/anaconda3/include/boost/multi_array/base.hpp: In member
function ‘boost::multi_array<T, NumDims, Allocator>& boost::multi_array<T,
NumDims, Allocator>::resize(const
boost::detail::multi_array::extent_gen<NumDims>&) [with T = double; long
unsigned int NumDims = 1ul; Allocator = std::allocator<double>]’:
/opt/anaconda/anaconda3/include/boost/multi_array/base.hpp:416:31: warning:
‘new_strides.boost::array<long int, 1ul>::elems[0ul]’ may be used
uninitialized in this function [-Wmaybe-uninitialized]
     boost::array<index,NDims> new_strides;
                               ^
/opt/anaconda/anaconda3/include/boost/multi_array/base.hpp: In member
function ‘boost::multi_array<T, NumDims, Allocator>& boost::multi_array<T,
NumDims, Allocator>::resize(const
boost::detail::multi_array::extent_gen<NumDims>&) [with T = long double;
long unsigned int NumDims = 1ul; Allocator = std::allocator<long double>]’:
/opt/anaconda/anaconda3/include/boost/multi_array/base.hpp:416:31: warning:
‘new_strides.boost::array<long int, 1ul>::elems[0ul]’ may be used
uninitialized in this function [-Wmaybe-uninitialized]
/opt/anaconda/anaconda3/include/boost/multi_array/base.hpp: In member
function ‘boost::multi_array<T, NumDims, Allocator>& boost::multi_array<T,
NumDims, Allocator>::resize(const
boost::detail::multi_array::extent_gen<NumDims>&) [with T = long double;
long unsigned int NumDims = 1ul; Allocator = std::allocator<long double>]’:
/opt/anaconda/anaconda3/include/boost/multi_array/base.hpp:416:31: warning:
‘new_strides.boost::array<long int, 1ul>::elems[0ul]’ may be used
uninitialized in this function [-Wmaybe-uninitialized]
/opt/anaconda/anaconda3/include/boost/multi_array/base.hpp: In member
function ‘boost::multi_array<T, NumDims, Allocator>& boost::multi_array<T,
NumDims, Allocator>::resize(const
boost::detail::multi_array::extent_gen<NumDims>&) [with T = long double;
long unsigned int NumDims = 1ul; Allocator = std::allocator<long double>]’:
/opt/anaconda/anaconda3/include/boost/multi_array/base.hpp:416:31: warning:
‘new_strides.boost::array<long int, 1ul>::elems[0ul]’ may be used
uninitialized in this function [-Wmaybe-uninitialized]
  CXXLD    libgraph_tool_correlations.la
make[4]: Leaving directory '/home/pmj27/graph-tool/src/graph/correlations'
Making all in draw
make[4]: Entering directory '/home/pmj27/graph-tool/src/graph/draw'
  CXX      graph_cairo_draw.lo
  CXX      graph_tree_cts.lo
  CXX      pycairo_aux.lo
In file included from pycairo_aux.cc:20:0:
pycairo_aux.cc: In function ‘PyObject*
gt_PycairoContext_FromContext(cairo_t*, PyTypeObject*, PyObject*)’:
/opt/anaconda/anaconda3/include/pycairo/pycairo.h:171:39: error:
‘Pycairo_CAPI’ was not declared in this scope
 #define PycairoContext_FromContext   (Pycairo_CAPI->Context_FromContext)
                                       ^
pycairo_aux.cc:26:12: note: in expansion of macro
‘PycairoContext_FromContext’
     return PycairoContext_FromContext(ctx, type, base);
            ^
Makefile:575: recipe for target 'pycairo_aux.lo' failed
make[4]: *** [pycairo_aux.lo] Error 1
make[4]: *** Waiting for unfinished jobs....
make[4]: Leaving directory '/home/pmj27/graph-tool/src/graph/draw'
Makefile:753: recipe for target 'all-recursive' failed
make[3]: *** [all-recursive] Error 1
make[3]: Leaving directory '/home/pmj27/graph-tool/src/graph'
Makefile:423: recipe for target 'all-recursive' failed
make[2]: *** [all-recursive] Error 1
make[2]: Leaving directory '/home/pmj27/graph-tool/src'
Makefile:595: recipe for target 'all-recursive' failed
make[1]: *** [all-recursive] Error 1
make[1]: Leaving directory '/home/pmj27/graph-tool'
Makefile:482: recipe for target 'all' failed
make: *** [all] Error 2

Could somebody help me identify where I am going wrong? I am running Ubuntu
16.04 and python2.7 (Anaconda).

Best,

Philipp



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Re: Error during make

Tiago Peixoto
Administrator
Am 23.05.2018 um 16:07 schrieb P-M:
> Could somebody help me identify where I am going wrong? I am running Ubuntu
> 16.04 and python2.7 (Anaconda).

There is a known compilation problem with Python 2 with the current git
version. It is a simple problem, and I will fix it soon.

With Python 3 it should work fine.

Best,
Tiago

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Re: Error during make

P-M
OK, I will wait for the new git version then. Thanks for the quick response!

Best,

Philipp



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Re: Error during make

P-M
In reply to this post by Tiago Peixoto
Hi Tiago,

There seems to have been an updated to the code on GIT. Does it address this
issue or is it about something else?

Best,

Philipp



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Re: Error during make

Tiago Peixoto
Administrator
Am 05.06.2018 um 13:20 schrieb P-M:
> Hi Tiago,
>
> There seems to have been an updated to the code on GIT. Does it address this
> issue or is it about something else?

This has been fixed now in git.

Next time you want to keep track of a bug, it is best to open an issue.

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