Hi all,

Below is my summary. It is a bit messy. In fact, it is the "manual
log" that I have followed through the process. I hope that it is
helpful for you.

Best Regards,
Juan

+++++++++++++++++++++++++++++

installing graph-tool in sagemath

This is creating a lot of problems. So I decided to make a log of the process.

1. The extra things that I need to install previously to installing
graph-tool (the other things are installed in standard ubuntu):

The CGAL C++ geometry library, version 3.5 or above.
The sparsehash template library (optional, but recommended).
The cairomm, pycairo and matplotlib libraries, used for graph drawing
(optional).
The Graphviz packaged for graph drawing, with the python bindings
enabled (optional, deprecated).

In principle, cgal can be installed easily using apt-get.

The library cairomm depends on cairo. Both things can be installed
using apt-get.

Pycairo should be installed in sage. One posibility is to use "pip",
ie. install it from the python repositories. However, pip is not
working from scratch in sage. You can install pip in sage by
downloading (here) the corresponding tar.gz and using easy_install:

easy_install pip-1.5.2.tar.gz

Then, proceed to install pycairo using pip via:

pip install cairocffi

But pip is still not working. The problem seems to be that openssl is
not working, and thus pip cannot understand https. Therefore, it is
necessary to install openssl-dev using apt-get, and then to compile
sage's python using in the decompressed tar.gz directory of sage:

make sll

(ie. instead of the standard make). Things went OK. Only a minor
problem when installing cairocffi. It requires to install via apt-get
libffi-dev.

COMMENTS: make will result in ERROR when compiling pycrypto during the
compilation of sage if you put sage's directory in the PATH variable
environment.

Matplotlib is already installed in sage. This can be seen via:

(sage-sh) juan@mostro:sage-6.1.1$ pip install matplotlib
Requirement already satisfied (use --upgrade to upgrade): matplotlib
in ./local/lib/python2.7/site-packages
Cleaning up.

Now it is time to install sparsehash. But it is already installed as
you can see:

sudo apt-get install libsparsehash-dev
Reading package lists... Done
Building dependency tree
Reading state information... Done
libsparsehash-dev is already the newest version.
libsparsehash-dev set to manually installed.
The following packages were automatically installed and are no longer required:
  gir1.2-ubuntuoneui-3.0 libubuntuoneui-3.0-1 thunderbird-globalmenu
Use 'apt-get autoremove' to remove them.
0 upgraded, 0 newly installed, 0 to remove and 2 not upgraded.

Also cgal is there:

juan@mostro:~/Downloads/sage-6.1.1$ sudo apt-get install libcgal-dev
Reading package lists... Done
Building dependency tree
Reading state information... Done
libcgal-dev is already the newest version.
The following packages were automatically installed and are no longer required:
  gir1.2-ubuntuoneui-3.0 libubuntuoneui-3.0-1 thunderbird-globalmenu
Use 'apt-get autoremove' to remove them.
0 upgraded, 0 newly installed, 0 to remove and 2 not upgraded.

Finally, lets see Graphviz. I installed via apt-get, ie.:

sudo apt-get install graphviz
sudo apt-get install graphviz-dev

Now it is time to try graph-tool !!!

I went to sage directory and entered its virtual environment via sage
-sh. Then I went to graph-tool directory and configured and made it...

juan@mostro:~/Downloads/sage-6.1.1$ ./sage -sh

Starting subshell with Sage environment variables set.  Don't forget
to exit when you are done.  Beware:
 * Do not do anything with other copies of Sage on your system.
 * Do not use this for installing Sage packages using "sage -i" or for
   running "make" at Sage's root directory.  These should be done
   outside the Sage shell.

Bypassing shell configuration files...

Note: SAGE_ROOT=/home/juan/Downloads/sage-6.1.1
(sage-sh) juan@mostro:sage-6.1.1$ cd ..
(sage-sh) juan@mostro:Downloads$ ls
boost_1_55_0         graph-tool-2.2.29.1      LoanStats3a.csv.zip
pip-1.5.2.tar.gz        sage-6.1.1
boost_1_55_0.tar.gz  graph-tool-2.2.29.1.tar.bz2  pip-1.5.2
py2cairo-1.10.0.tar.bz2    sage-6.1.1.tar.gz
(sage-sh) juan@mostro:Downloads$ cd graph-tool-2.2.29.1
(sage-sh) juan@mostro:graph-tool-2.2.29.1$ ls
aclocal.m4  ChangeLog      config.h     configure     depcomp
install-sh  Makefile.am  NEWS       README.jip
AUTHORS     compile      config.h.in  configure.ac  doc      ltmain.sh
  Makefile.in  py-compile  src
autogen.sh  config.guess  config.sub   COPYING         INSTALL  m4
 missing      README       TODO
(sage-sh) juan@mostro:graph-tool-2.2.29.1$ ./configure

However, after some bla bla bla:

===========================
Using python version: 2.7.5
===========================
checking for boostlib >= 1.38.0... yes
checking whether the Boost::Python library is available... yes
checking for exit in -lboost_python... no
checking for exit in -lboost_python-py2.7... no
checking for exit in -lboost_python-2.7... no
checking for exit in -lboost_python-py27... no
checking for exit in -lboost_python-27... no
checking for exit in -lboost_python... (cached) no
checking for exit in -lboost_python-py2.7... (cached) no
checking for exit in -lboost_python-2.7... (cached) no
checking for exit in -lboost_python-py27... (cached) no
checking for exit in -lboost_python-27... (cached) no
checking for exit in -lboost_python-mt... no
checking for exit in -lboost_python-mt-py2.7... no
checking for exit in -lboost_python-mt-2.7... no
checking for exit in -lboost_python-mt-py27... no
checking for exit in -lboost_python-mt-27... no
configure: error: No usable boost::python found

It seems that I need to "compile" Python.Boost within sage's
virtualenv, or something like that. Therefore, from the sage's virtual
environment I went to boost directory (I downloaded boost.tar.gz and
uncompressed it), and then I run:

(sage -sh) $ ./bootstrap.sh
bla bla bla
(sage -sh) $ ./b2
bla bla bla
bla bla bla

But, this did not work :P

According to this:

https://groups.google.com/forum/#!topic/graph-tool/W9J7qV-GqIA

it might be that graph-tool do not find the appropriate python path.
Therefore, I should specify the python path to the configure of
graph-tool via:

./configure PYTHON=/home/juan/Downloads/sage-6.1.1/local/lib/python    (1)

How I found where sage's python path is? According to this:

http://stackoverflow.com/questions/1489599/how-do-i-find-out-my-python-path-using-python

you can find the python path from python itself via:

juan@mostro:~/Downloads/sage-6.1.1$ ./sage -python
Python 2.7.5 (default, Feb 11 2014, 07:30:05)
[GCC 4.6.3] on linux2
Type "help", "copyright", "credits" or "license" for more information.
>>> import os
>>> os.environ['PYTHONPATH'].split(os.pathsep)
['/home/juan/Downloads/sage-6.1.1/local/lib/python']
>>>    (2)

So, lets see what happens when using (1)...

Wow, this was unexpected!

bla bla bla
================
Detecting python
================
checking whether /home/juan/Downloads/sage-6.1.1/local/lib/python
version is >= 2.6... no1
configure: error: Python interpreter is too old

Now I do not known how to proceed :P. This is strange anyway because
in (2) it says that python version is 2.7.5, but graph-tool says that
python version is not >= 2.6.

In fact, there are more than one python in sage's directory. However

./configure PYTHON=/home/juan/Downloads/sage-6.1.1/local/lib/python2.7

does not work either.

Next step:

http://www.boost.org/doc/libs/1_51_0/libs/python/doc/building.html

read "Configuring Boost.Build"

and perhaps also:

https://www.mail-archive.com/graph-tool@.../msg00540.html

What seems to work for python.boost is:

(sage-sh) juan@mostro:graph-tool-2.2.29.1$ ./configure
CPPFLAGS="-I/home/juan/usr/local/include/boost"
LDFLAGS="-L/home/juan/usr/local/lib"

But now ...

bla bla bla
checking for pycairo/pycairo.h... yes
checking whether to enable sparsehash...... yes
checking for SPARSEHASH... no
not found by pkgconfig, trying default...
checking sparsehash/dense_hash_set usability... no
checking sparsehash/dense_hash_set presence... no
checking for sparsehash/dense_hash_set... no
configure: error: sparsehash headers not found

Finally by installing sparsehash from

https://code.google.com/p/sparsehash/

by typing in a normal terminal

xvf sparsehash-2.0.2.tar.gz
cd sparsehash-2.0.2/
./configure
make
sudo make install

and then running in sage's virtualenv

(sage-sh) juan@mostro:graph-tool-2.2.29.1$ ./configure
CPPFLAGS="-I/home/juan/usr/local/include/boost"
LDFLAGS="-L/home/juan/usr/local/lib"
SPARSEHASH_CFLAGS="-I/usr/include/google/sparsehash"
(sage-sh) juan@mostro:graph-tool-2.2.29.1$ make

The make process went well. However the make install did not. There
was a problem with some import in Python and MAXREPEAT. I fixed those
problems following this:

http://thinkingcan.blogspot.fi/2013/09/fixed-importerror-cannot-import-name.html

That I summarize here

++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++

Fixed! ImportError: cannot import name MAXREPEAT

Earlier today, I upgraded my Ubuntu box from 12.04 to 12.10. I noticed
that Pidgin wouldn't launch so I opened up Terminal (ctrl+alt+t) and
tried to run Pidgin through there. I noticed that I got the following
stack trace:

Traceback (most recent call last):
  File "/usr/local/lib/python2.7/site.py", line 548, in <module>
    main()
  File "/usr/local/lib/python2.7/site.py", line 530, in main
    known_paths = addusersitepackages(known_paths)
  File "/usr/local/lib/python2.7/site.py", line 266, in addusersitepackages
    user_site = getusersitepackages()
  File "/usr/local/lib/python2.7/site.py", line 241, in getusersitepackages
    user_base = getuserbase() # this will also set USER_BASE
  File "/usr/local/lib/python2.7/site.py", line 231, in getuserbase
    USER_BASE = get_config_var('userbase')
  File "/usr/local/lib/python2.7/sysconfig.py", line 516, in get_config_var
    return get_config_vars().get(name)
  File "/usr/local/lib/python2.7/sysconfig.py", line 449, in get_config_vars
    import re
  File "/usr/local/lib/python2.7/re.py", line 105, in <module>
    import sre_compile
  File "/usr/local/lib/python2.7/sre_compile.py", line 14, in <module>
    import sre_parse
  File "/usr/local/lib/python2.7/sre_parse.py", line 17, in <module>
    from sre_constants import *
  File "/usr/local/lib/python2.7/sre_constants.py", line 18, in <module>
    from _sre import MAXREPEAT
ImportError: cannot import name MAXREPEAT


After some research, I found that I should run virtualenv. This did
not work. Instead, I found a fix. It doesn't feel right but it's a fix
none the less. If you look closely, you can see that the problem is
that there is a field missing that needs to be accessed in
sre_constants.py. So I changed the

from _sre import MAXREPEAT


To:


try:
        from _sre import MAXREPEAT
except ImportError:
        import _sre
        _sre.MAXREPEAT = 65535 # Oh man. I hate myself so much.


Hope that works for you!

+++++++++++++++++++++++++++++++++++++

Then, make install went well. However, after running sage, it failed
to import graph_tool. It fails to find the boost libraries. I fixed
that problem by doing:

juan@mostro:~/Downloads/sage-6.1.1$ export
LD_LIBRARY_PATH=/home/juan/usr/local/lib/
juan@mostro:~/Downloads/sage-6.1.1$ ./sage -python
Python 2.7.5 (default, Feb 11 2014, 07:30:05)
[GCC 4.6.3] on linux2
Type "help", "copyright", "credits" or "license" for more information.
>>> import graph_tool
>>> g = graph_tool.Graph()
>>>

On Wed, Feb 12, 2014 at 8:36 AM, Juan Ignacio Perotti
<[hidden email]> wrote:

> Hi all,
>
> This seems to solve the problem:
>
> juan@mostro:~/Downloads/sage-6.1.1$ export
> LD_LIBRARY_PATH=/home/juan/usr/local/lib/
> juan@mostro:~/Downloads/sage-6.1.1$ ./sage -python
> Python 2.7.5 (default, Feb 11 2014, 07:30:05)
> [GCC 4.6.3] on linux2
> Type "help", "copyright", "credits" or "license" for more information.
>>>> import graph_tool
>>>> g = graph_tool.Graph()
>
> Wow! That was a though one. I still need to check that it works
> properly. After this I will try to summarize the installation process
> of graph_tool into sage so others can follow similar steps.
>
> Best Regards,
> Juan
>
> On Wed, Feb 12, 2014 at 8:30 AM, Juan Ignacio Perotti
> <[hidden email]> wrote:
>> Hi all,
>>
>> The following seems to fix that problem
>>
>> http://thinkingcan.blogspot.fi/2013/09/fixed-importerror-cannot-import-name.html
>>
>> I will summarize here:
>>
>> +++++++++++++++++++++++++++++++++++++++++++++++++++++++++++
>>
>> Fixed! ImportError: cannot import name MAXREPEAT
>>
>> Earlier today, I upgraded my Ubuntu box from 12.04 to 12.10. I noticed
>> that Pidgin wouldn't launch so I opened up Terminal (ctrl+alt+t) and
>> tried to run Pidgin through there. I noticed that I got the following
>> stack trace:
>>
>> Traceback (most recent call last):
>>   File "/usr/local/lib/python2.7/site.py", line 548, in <module>
>>     main()
>>   File "/usr/local/lib/python2.7/site.py", line 530, in main
>>     known_paths = addusersitepackages(known_paths)
>>   File "/usr/local/lib/python2.7/site.py", line 266, in addusersitepackages
>>     user_site = getusersitepackages()
>>   File "/usr/local/lib/python2.7/site.py", line 241, in getusersitepackages
>>     user_base = getuserbase() # this will also set USER_BASE
>>   File "/usr/local/lib/python2.7/site.py", line 231, in getuserbase
>>     USER_BASE = get_config_var('userbase')
>>   File "/usr/local/lib/python2.7/sysconfig.py", line 516, in get_config_var
>>     return get_config_vars().get(name)
>>   File "/usr/local/lib/python2.7/sysconfig.py", line 449, in get_config_vars
>>     import re
>>   File "/usr/local/lib/python2.7/re.py", line 105, in <module>
>>     import sre_compile
>>   File "/usr/local/lib/python2.7/sre_compile.py", line 14, in <module>
>>     import sre_parse
>>   File "/usr/local/lib/python2.7/sre_parse.py", line 17, in <module>
>>     from sre_constants import *
>>   File "/usr/local/lib/python2.7/sre_constants.py", line 18, in <module>
>>     from _sre import MAXREPEAT
>> ImportError: cannot import name MAXREPEAT
>>
>>
>> After some research, I found that I should run virtualenv. This did
>> not work. Instead, I found a fix. It doesn't feel right but it's a fix
>> none the less. If you look closely, you can see that the problem is
>> that there is a field missing that needs to be accessed in
>> sre_constants.py. So I changed the
>>
>> from _sre import MAXREPEAT
>>
>>
>> To:
>>
>> try:
>>         from _sre import MAXREPEAT
>> except ImportError:
>>         import _sre
>>         _sre.MAXREPEAT = 65535 # Oh man. I hate myself so much.
>>
>> Hope that works for you!
>>
>> +++++++++++++++++++++++++++++++++++++++++++++++++
>>
>> Now make install seems to runs properly. However, when I try to import
>> graph_tool from sage it do not succeed:
>>
>> juan@mostro:~/Downloads/sage-6.1.1$ ./sage -python
>> Python 2.7.5 (default, Feb 11 2014, 07:30:05)
>> [GCC 4.6.3] on linux2
>> Type "help", "copyright", "credits" or "license" for more information.
>>>>> import graph_tool
>> Traceback (most recent call last):
>>   File "<stdin>", line 1, in <module>
>>   File "/home/juan/Downloads/sage-6.1.1/local/lib/python2.7/site-packages/graph_tool/__init__.py",
>> line 100, in <module>
>>     dl_import("from . import libgraph_tool_core as libcore")
>>   File "/home/juan/Downloads/sage-6.1.1/local/lib/python2.7/site-packages/graph_tool/dl_import.py",
>> line 57, in dl_import
>>     exec(import_expr, local_dict, global_dict)
>>   File "<string>", line 1, in <module>
>> ImportError: libboost_iostreams.so.1.55.0: cannot open shared object
>> file: No such file or directory
>>
>> So, it seems that graph-tool is not finding the "python.boost" lib
>> required. However, this is strange as I provided to configure the path
>> to a local (at my home directory) installation of boost. More
>> specifically, I had run
>>
>> (sage-sh) juan@mostro:graph-tool-2.2.29.1$ ./configure
>> CPPFLAGS="-I/home/juan/usr/local/include/boost"
>> LDFLAGS="-L/home/juan/usr/local/lib"
>> SPARSEHASH_CFLAGS="-I/usr/include/google/sparsehash"
>>
>> The local installation of boost is at /home/juan/usr/local/, and the
>> corresponding paths seems to be provided at the configuration stage of
>> graph-tool. I do not understand what went wrong. Any ideas?
>>
>> Best Regards,
>> Juan
>>
>> On Wed, Feb 12, 2014 at 8:12 AM, Juan Ignacio Perotti
>> <[hidden email]> wrote:
>>> Hi,
>>>
>>> Thanks for the recommendation Tiago. I went further this time and
>>> successfully went though the ./configure and make stage. However, when I run
>>> make install something goes wrong. Below I post the relevant part of the
>>> procedure according to my judgement. First I go into sage's virtual
>>> environment by typing
>>>
>>> $ sage -sh
>>>
>>> Then I run:
>>>
>>> (sage-sh) juan@mostro:graph-tool-2.2.29.1$ ./configure
>>> CPPFLAGS="-I/home/juan/usr/local/include/boost"
>>> LDFLAGS="-L/home/juan/usr/local/lib"
>>> SPARSEHASH_CFLAGS="-I/usr/include/google/sparsehash"
>>>
>>> some bla bla bla
>>>
>>> (sage-sh) juan@mostro:graph-tool-2.2.29.1$ make
>>>
>>> after many hours...it seems to success. Finally I try to install
>>>
>>> (sage-sh) juan@mostro:graph-tool-2.2.29.1$ sudo make install
>>>
>>> Making install in src
>>> make[1]: Entering directory `/home/juan/Downloads/graph-tool-2.2.29.1/src'
>>> Making install in graph
>>> make[2]: Entering directory
>>> `/home/juan/Downloads/graph-tool-2.2.29.1/src/graph'
>>> Making install in centrality
>>> make[3]: Entering directory
>>> `/home/juan/Downloads/graph-tool-2.2.29.1/src/graph/centrality'
>>> make[4]: Entering directory
>>> `/home/juan/Downloads/graph-tool-2.2.29.1/src/graph/centrality'
>>> make[4]: Nothing to be done for `install-exec-am'.
>>>  /bin/mkdir -p
>>> '/home/juan/Downloads/sage-6.1.1/local/lib/python2.7/site-packages/graph_tool/centrality'
>>>  /bin/bash ../../../libtool   --mode=install /usr/bin/install -c
>>> libgraph_tool_centrality.la
>>> '/home/juan/Downloads/sage-6.1.1/local/lib/python2.7/site-packages/graph_tool/centrality'
>>> libtool: install: /usr/bin/install -c .libs/libgraph_tool_centrality.so
>>> /home/juan/Downloads/sage-6.1.1/local/lib/python2.7/site-packages/graph_tool/centrality/libgraph_tool_centrality.so
>>> libtool: install: /usr/bin/install -c .libs/libgraph_tool_centrality.lai
>>> /home/juan/Downloads/sage-6.1.1/local/lib/python2.7/site-packages/graph_tool/centrality/libgraph_tool_centrality.la
>>> libtool: finish:
>>> PATH="/usr/local/sbin:/usr/local/bin:/usr/sbin:/usr/bin:/sbin:/bin:/sbin"
>>> ldconfig -n
>>> /home/juan/Downloads/sage-6.1.1/local/lib/python2.7/site-packages/graph_tool/centrality
>>> ----------------------------------------------------------------------
>>> Libraries have been installed in:
>>>
>>> /home/juan/Downloads/sage-6.1.1/local/lib/python2.7/site-packages/graph_tool/centrality
>>>
>>> If you ever happen to want to link against installed libraries
>>> in a given directory, LIBDIR, you must either use libtool, and
>>> specify the full pathname of the library, or use the `-LLIBDIR'
>>> flag during linking and do at least one of the following:
>>>    - add LIBDIR to the `LD_LIBRARY_PATH' environment variable
>>>      during execution
>>>    - add LIBDIR to the `LD_RUN_PATH' environment variable
>>>      during linking
>>>    - use the `-Wl,-rpath -Wl,LIBDIR' linker flag
>>>    - have your system administrator add LIBDIR to `/etc/ld.so.conf'
>>>
>>> See any operating system documentation about shared libraries for
>>> more information, such as the ld(1) and ld.so(8) manual pages.
>>> ----------------------------------------------------------------------
>>>  /bin/mkdir -p
>>> '/home/juan/Downloads/sage-6.1.1/local/lib/python2.7/site-packages/graph_tool/include'
>>>  /usr/bin/install -c -m 644 graph_closeness.hh graph_eigentrust.hh
>>> graph_eigenvector.hh graph_pagerank.hh graph_hits.hh graph_katz.hh
>>> graph_trust_transitivity.hh minmax.hh
>>> '/home/juan/Downloads/sage-6.1.1/local/lib/python2.7/site-packages/graph_tool/include'
>>> make[4]: Leaving directory
>>> `/home/juan/Downloads/graph-tool-2.2.29.1/src/graph/centrality'
>>> make[3]: Leaving directory
>>> `/home/juan/Downloads/graph-tool-2.2.29.1/src/graph/centrality'
>>> Making install in clustering
>>> make[3]: Entering directory
>>> `/home/juan/Downloads/graph-tool-2.2.29.1/src/graph/clustering'
>>> make[4]: Entering directory
>>> `/home/juan/Downloads/graph-tool-2.2.29.1/src/graph/clustering'
>>> make[4]: Nothing to be done for `install-exec-am'.
>>>  /bin/mkdir -p
>>> '/home/juan/Downloads/sage-6.1.1/local/lib/python2.7/site-packages/graph_tool/clustering'
>>>  /bin/bash ../../../libtool   --mode=install /usr/bin/install -c
>>> libgraph_tool_clustering.la
>>> '/home/juan/Downloads/sage-6.1.1/local/lib/python2.7/site-packages/graph_tool/clustering'
>>> libtool: install: /usr/bin/install -c .libs/libgraph_tool_clustering.so
>>> /home/juan/Downloads/sage-6.1.1/local/lib/python2.7/site-packages/graph_tool/clustering/libgraph_tool_clustering.so
>>> libtool: install: /usr/bin/install -c .libs/libgraph_tool_clustering.lai
>>> /home/juan/Downloads/sage-6.1.1/local/lib/python2.7/site-packages/graph_tool/clustering/libgraph_tool_clustering.la
>>> libtool: finish:
>>> PATH="/usr/local/sbin:/usr/local/bin:/usr/sbin:/usr/bin:/sbin:/bin:/sbin"
>>> ldconfig -n
>>> /home/juan/Downloads/sage-6.1.1/local/lib/python2.7/site-packages/graph_tool/clustering
>>> ----------------------------------------------------------------------
>>> Libraries have been installed in:
>>>
>>> /home/juan/Downloads/sage-6.1.1/local/lib/python2.7/site-packages/graph_tool/clustering
>>>
>>> If you ever happen to want to link against installed libraries
>>> in a given directory, LIBDIR, you must either use libtool, and
>>> specify the full pathname of the library, or use the `-LLIBDIR'
>>> flag during linking and do at least one of the following:
>>>    - add LIBDIR to the `LD_LIBRARY_PATH' environment variable
>>>      during execution
>>>    - add LIBDIR to the `LD_RUN_PATH' environment variable
>>>      during linking
>>>    - use the `-Wl,-rpath -Wl,LIBDIR' linker flag
>>>    - have your system administrator add LIBDIR to `/etc/ld.so.conf'
>>>
>>> See any operating system documentation about shared libraries for
>>> more information, such as the ld(1) and ld.so(8) manual pages.
>>> ----------------------------------------------------------------------
>>>  /bin/mkdir -p
>>> '/home/juan/Downloads/sage-6.1.1/local/lib/python2.7/site-packages/graph_tool/include'
>>>  /usr/bin/install -c -m 644 graph_clustering.hh graph_extended_clustering.hh
>>> graph_motifs.hh
>>> '/home/juan/Downloads/sage-6.1.1/local/lib/python2.7/site-packages/graph_tool/include'
>>> make[4]: Leaving directory
>>> `/home/juan/Downloads/graph-tool-2.2.29.1/src/graph/clustering'
>>> make[3]: Leaving directory
>>> `/home/juan/Downloads/graph-tool-2.2.29.1/src/graph/clustering'
>>> Making install in community
>>> make[3]: Entering directory
>>> `/home/juan/Downloads/graph-tool-2.2.29.1/src/graph/community'
>>> make[4]: Entering directory
>>> `/home/juan/Downloads/graph-tool-2.2.29.1/src/graph/community'
>>> make[4]: Nothing to be done for `install-exec-am'.
>>>  /bin/mkdir -p
>>> '/home/juan/Downloads/sage-6.1.1/local/lib/python2.7/site-packages/graph_tool/community'
>>>  /bin/bash ../../../libtool   --mode=install /usr/bin/install -c
>>> libgraph_tool_community.la
>>> '/home/juan/Downloads/sage-6.1.1/local/lib/python2.7/site-packages/graph_tool/community'
>>> libtool: install: /usr/bin/install -c .libs/libgraph_tool_community.so
>>> /home/juan/Downloads/sage-6.1.1/local/lib/python2.7/site-packages/graph_tool/community/libgraph_tool_community.so
>>> libtool: install: /usr/bin/install -c .libs/libgraph_tool_community.lai
>>> /home/juan/Downloads/sage-6.1.1/local/lib/python2.7/site-packages/graph_tool/community/libgraph_tool_community.la
>>> libtool: finish:
>>> PATH="/usr/local/sbin:/usr/local/bin:/usr/sbin:/usr/bin:/sbin:/bin:/sbin"
>>> ldconfig -n
>>> /home/juan/Downloads/sage-6.1.1/local/lib/python2.7/site-packages/graph_tool/community
>>> ----------------------------------------------------------------------
>>> Libraries have been installed in:
>>>
>>> /home/juan/Downloads/sage-6.1.1/local/lib/python2.7/site-packages/graph_tool/community
>>>
>>> If you ever happen to want to link against installed libraries
>>> in a given directory, LIBDIR, you must either use libtool, and
>>> specify the full pathname of the library, or use the `-LLIBDIR'
>>> flag during linking and do at least one of the following:
>>>    - add LIBDIR to the `LD_LIBRARY_PATH' environment variable
>>>      during execution
>>>    - add LIBDIR to the `LD_RUN_PATH' environment variable
>>>      during linking
>>>    - use the `-Wl,-rpath -Wl,LIBDIR' linker flag
>>>    - have your system administrator add LIBDIR to `/etc/ld.so.conf'
>>>
>>> See any operating system documentation about shared libraries for
>>> more information, such as the ld(1) and ld.so(8) manual pages.
>>> ----------------------------------------------------------------------
>>>  /bin/mkdir -p
>>> '/home/juan/Downloads/sage-6.1.1/local/lib/python2.7/site-packages/graph_tool/include'
>>>  /usr/bin/install -c -m 644 graph_blockmodel.hh graph_community.hh
>>> graph_community_network.hh
>>> '/home/juan/Downloads/sage-6.1.1/local/lib/python2.7/site-packages/graph_tool/include'
>>> make[4]: Leaving directory
>>> `/home/juan/Downloads/graph-tool-2.2.29.1/src/graph/community'
>>> make[3]: Leaving directory
>>> `/home/juan/Downloads/graph-tool-2.2.29.1/src/graph/community'
>>> Making install in correlations
>>> make[3]: Entering directory
>>> `/home/juan/Downloads/graph-tool-2.2.29.1/src/graph/correlations'
>>> make[4]: Entering directory
>>> `/home/juan/Downloads/graph-tool-2.2.29.1/src/graph/correlations'
>>> make[4]: Nothing to be done for `install-exec-am'.
>>>  /bin/mkdir -p
>>> '/home/juan/Downloads/sage-6.1.1/local/lib/python2.7/site-packages/graph_tool/correlations'
>>>  /bin/bash ../../../libtool   --mode=install /usr/bin/install -c
>>> libgraph_tool_correlations.la
>>> '/home/juan/Downloads/sage-6.1.1/local/lib/python2.7/site-packages/graph_tool/correlations'
>>> libtool: install: /usr/bin/install -c .libs/libgraph_tool_correlations.so
>>> /home/juan/Downloads/sage-6.1.1/local/lib/python2.7/site-packages/graph_tool/correlations/libgraph_tool_correlations.so
>>> libtool: install: /usr/bin/install -c .libs/libgraph_tool_correlations.lai
>>> /home/juan/Downloads/sage-6.1.1/local/lib/python2.7/site-packages/graph_tool/correlations/libgraph_tool_correlations.la
>>> libtool: finish:
>>> PATH="/usr/local/sbin:/usr/local/bin:/usr/sbin:/usr/bin:/sbin:/bin:/sbin"
>>> ldconfig -n
>>> /home/juan/Downloads/sage-6.1.1/local/lib/python2.7/site-packages/graph_tool/correlations
>>> ----------------------------------------------------------------------
>>> Libraries have been installed in:
>>>
>>> /home/juan/Downloads/sage-6.1.1/local/lib/python2.7/site-packages/graph_tool/correlations
>>>
>>> If you ever happen to want to link against installed libraries
>>> in a given directory, LIBDIR, you must either use libtool, and
>>> specify the full pathname of the library, or use the `-LLIBDIR'
>>> flag during linking and do at least one of the following:
>>>    - add LIBDIR to the `LD_LIBRARY_PATH' environment variable
>>>      during execution
>>>    - add LIBDIR to the `LD_RUN_PATH' environment variable
>>>      during linking
>>>    - use the `-Wl,-rpath -Wl,LIBDIR' linker flag
>>>    - have your system administrator add LIBDIR to `/etc/ld.so.conf'
>>>
>>> See any operating system documentation about shared libraries for
>>> more information, such as the ld(1) and ld.so(8) manual pages.
>>> ----------------------------------------------------------------------
>>>  /bin/mkdir -p
>>> '/home/juan/Downloads/sage-6.1.1/local/lib/python2.7/site-packages/graph_tool/include'
>>>  /usr/bin/install -c -m 644 graph_assortativity.hh graph_correlations.hh
>>> graph_corr_hist.hh graph_avg_correlations.hh
>>> '/home/juan/Downloads/sage-6.1.1/local/lib/python2.7/site-packages/graph_tool/include'
>>> make[4]: Leaving directory
>>> `/home/juan/Downloads/graph-tool-2.2.29.1/src/graph/correlations'
>>> make[3]: Leaving directory
>>> `/home/juan/Downloads/graph-tool-2.2.29.1/src/graph/correlations'
>>> Making install in draw
>>> make[3]: Entering directory
>>> `/home/juan/Downloads/graph-tool-2.2.29.1/src/graph/draw'
>>> make[4]: Entering directory
>>> `/home/juan/Downloads/graph-tool-2.2.29.1/src/graph/draw'
>>> make[4]: Nothing to be done for `install-exec-am'.
>>>  /bin/mkdir -p
>>> '/home/juan/Downloads/sage-6.1.1/local/lib/python2.7/site-packages/graph_tool/draw'
>>>  /bin/bash ../../../libtool   --mode=install /usr/bin/install -c
>>> libgraph_tool_draw.la
>>> '/home/juan/Downloads/sage-6.1.1/local/lib/python2.7/site-packages/graph_tool/draw'
>>> libtool: install: /usr/bin/install -c .libs/libgraph_tool_draw.so
>>> /home/juan/Downloads/sage-6.1.1/local/lib/python2.7/site-packages/graph_tool/draw/libgraph_tool_draw.so
>>> libtool: install: /usr/bin/install -c .libs/libgraph_tool_draw.lai
>>> /home/juan/Downloads/sage-6.1.1/local/lib/python2.7/site-packages/graph_tool/draw/libgraph_tool_draw.la
>>> libtool: finish:
>>> PATH="/usr/local/sbin:/usr/local/bin:/usr/sbin:/usr/bin:/sbin:/bin:/sbin"
>>> ldconfig -n
>>> /home/juan/Downloads/sage-6.1.1/local/lib/python2.7/site-packages/graph_tool/draw
>>> ----------------------------------------------------------------------
>>> Libraries have been installed in:
>>>
>>> /home/juan/Downloads/sage-6.1.1/local/lib/python2.7/site-packages/graph_tool/draw
>>>
>>> If you ever happen to want to link against installed libraries
>>> in a given directory, LIBDIR, you must either use libtool, and
>>> specify the full pathname of the library, or use the `-LLIBDIR'
>>> flag during linking and do at least one of the following:
>>>    - add LIBDIR to the `LD_LIBRARY_PATH' environment variable
>>>      during execution
>>>    - add LIBDIR to the `LD_RUN_PATH' environment variable
>>>      during linking
>>>    - use the `-Wl,-rpath -Wl,LIBDIR' linker flag
>>>    - have your system administrator add LIBDIR to `/etc/ld.so.conf'
>>>
>>> See any operating system documentation about shared libraries for
>>> more information, such as the ld(1) and ld.so(8) manual pages.
>>> ----------------------------------------------------------------------
>>> make[4]: Leaving directory
>>> `/home/juan/Downloads/graph-tool-2.2.29.1/src/graph/draw'
>>> make[3]: Leaving directory
>>> `/home/juan/Downloads/graph-tool-2.2.29.1/src/graph/draw'
>>> Making install in flow
>>> make[3]: Entering directory
>>> `/home/juan/Downloads/graph-tool-2.2.29.1/src/graph/flow'
>>> make[4]: Entering directory
>>> `/home/juan/Downloads/graph-tool-2.2.29.1/src/graph/flow'
>>> make[4]: Nothing to be done for `install-exec-am'.
>>>  /bin/mkdir -p
>>> '/home/juan/Downloads/sage-6.1.1/local/lib/python2.7/site-packages/graph_tool/flow'
>>>  /bin/bash ../../../libtool   --mode=install /usr/bin/install -c
>>> libgraph_tool_flow.la
>>> '/home/juan/Downloads/sage-6.1.1/local/lib/python2.7/site-packages/graph_tool/flow'
>>> libtool: install: /usr/bin/install -c .libs/libgraph_tool_flow.so
>>> /home/juan/Downloads/sage-6.1.1/local/lib/python2.7/site-packages/graph_tool/flow/libgraph_tool_flow.so
>>> libtool: install: /usr/bin/install -c .libs/libgraph_tool_flow.lai
>>> /home/juan/Downloads/sage-6.1.1/local/lib/python2.7/site-packages/graph_tool/flow/libgraph_tool_flow.la
>>> libtool: finish:
>>> PATH="/usr/local/sbin:/usr/local/bin:/usr/sbin:/usr/bin:/sbin:/bin:/sbin"
>>> ldconfig -n
>>> /home/juan/Downloads/sage-6.1.1/local/lib/python2.7/site-packages/graph_tool/flow
>>> ----------------------------------------------------------------------
>>> Libraries have been installed in:
>>>
>>> /home/juan/Downloads/sage-6.1.1/local/lib/python2.7/site-packages/graph_tool/flow
>>>
>>> If you ever happen to want to link against installed libraries
>>> in a given directory, LIBDIR, you must either use libtool, and
>>> specify the full pathname of the library, or use the `-LLIBDIR'
>>> flag during linking and do at least one of the following:
>>>    - add LIBDIR to the `LD_LIBRARY_PATH' environment variable
>>>      during execution
>>>    - add LIBDIR to the `LD_RUN_PATH' environment variable
>>>      during linking
>>>    - use the `-Wl,-rpath -Wl,LIBDIR' linker flag
>>>    - have your system administrator add LIBDIR to `/etc/ld.so.conf'
>>>
>>> See any operating system documentation about shared libraries for
>>> more information, such as the ld(1) and ld.so(8) manual pages.
>>> ----------------------------------------------------------------------
>>>  /bin/mkdir -p
>>> '/home/juan/Downloads/sage-6.1.1/local/lib/python2.7/site-packages/graph_tool/include'
>>>  /usr/bin/install -c -m 644 graph_augment.hh
>>> '/home/juan/Downloads/sage-6.1.1/local/lib/python2.7/site-packages/graph_tool/include'
>>> make[4]: Leaving directory
>>> `/home/juan/Downloads/graph-tool-2.2.29.1/src/graph/flow'
>>> make[3]: Leaving directory
>>> `/home/juan/Downloads/graph-tool-2.2.29.1/src/graph/flow'
>>> Making install in generation
>>> make[3]: Entering directory
>>> `/home/juan/Downloads/graph-tool-2.2.29.1/src/graph/generation'
>>> make[4]: Entering directory
>>> `/home/juan/Downloads/graph-tool-2.2.29.1/src/graph/generation'
>>> make[4]: Nothing to be done for `install-exec-am'.
>>>  /bin/mkdir -p
>>> '/home/juan/Downloads/sage-6.1.1/local/lib/python2.7/site-packages/graph_tool/generation'
>>>  /bin/bash ../../../libtool   --mode=install /usr/bin/install -c
>>> libgraph_tool_generation.la
>>> '/home/juan/Downloads/sage-6.1.1/local/lib/python2.7/site-packages/graph_tool/generation'
>>> libtool: install: /usr/bin/install -c .libs/libgraph_tool_generation.so
>>> /home/juan/Downloads/sage-6.1.1/local/lib/python2.7/site-packages/graph_tool/generation/libgraph_tool_generation.so
>>> libtool: install: /usr/bin/install -c .libs/libgraph_tool_generation.lai
>>> /home/juan/Downloads/sage-6.1.1/local/lib/python2.7/site-packages/graph_tool/generation/libgraph_tool_generation.la
>>> libtool: finish:
>>> PATH="/usr/local/sbin:/usr/local/bin:/usr/sbin:/usr/bin:/sbin:/bin:/sbin"
>>> ldconfig -n
>>> /home/juan/Downloads/sage-6.1.1/local/lib/python2.7/site-packages/graph_tool/generation
>>> ----------------------------------------------------------------------
>>> Libraries have been installed in:
>>>
>>> /home/juan/Downloads/sage-6.1.1/local/lib/python2.7/site-packages/graph_tool/generation
>>>
>>> If you ever happen to want to link against installed libraries
>>> in a given directory, LIBDIR, you must either use libtool, and
>>> specify the full pathname of the library, or use the `-LLIBDIR'
>>> flag during linking and do at least one of the following:
>>>    - add LIBDIR to the `LD_LIBRARY_PATH' environment variable
>>>      during execution
>>>    - add LIBDIR to the `LD_RUN_PATH' environment variable
>>>      during linking
>>>    - use the `-Wl,-rpath -Wl,LIBDIR' linker flag
>>>    - have your system administrator add LIBDIR to `/etc/ld.so.conf'
>>>
>>> See any operating system documentation about shared libraries for
>>> more information, such as the ld(1) and ld.so(8) manual pages.
>>> ----------------------------------------------------------------------
>>>  /bin/mkdir -p
>>> '/home/juan/Downloads/sage-6.1.1/local/lib/python2.7/site-packages/graph_tool/include'
>>>  /usr/bin/install -c -m 644 graph_generation.hh graph_rewiring.hh
>>> graph_predecessor.hh graph_union.hh graph_triangulation.hh graph_lattice.hh
>>> graph_geometric.hh graph_complete.hh graph_price.hh dynamic_sampler.hh
>>> sampler.hh
>>> '/home/juan/Downloads/sage-6.1.1/local/lib/python2.7/site-packages/graph_tool/include'
>>> make[4]: Leaving directory
>>> `/home/juan/Downloads/graph-tool-2.2.29.1/src/graph/generation'
>>> make[3]: Leaving directory
>>> `/home/juan/Downloads/graph-tool-2.2.29.1/src/graph/generation'
>>> Making install in layout
>>> make[3]: Entering directory
>>> `/home/juan/Downloads/graph-tool-2.2.29.1/src/graph/layout'
>>> make[4]: Entering directory
>>> `/home/juan/Downloads/graph-tool-2.2.29.1/src/graph/layout'
>>> make[4]: Nothing to be done for `install-exec-am'.
>>>  /bin/mkdir -p
>>> '/home/juan/Downloads/sage-6.1.1/local/lib/python2.7/site-packages/graph_tool/draw'
>>>  /bin/bash ../../../libtool   --mode=install /usr/bin/install -c
>>> libgraph_tool_layout.la
>>> '/home/juan/Downloads/sage-6.1.1/local/lib/python2.7/site-packages/graph_tool/draw'
>>> libtool: install: /usr/bin/install -c .libs/libgraph_tool_layout.so
>>> /home/juan/Downloads/sage-6.1.1/local/lib/python2.7/site-packages/graph_tool/draw/libgraph_tool_layout.so
>>> libtool: install: /usr/bin/install -c .libs/libgraph_tool_layout.lai
>>> /home/juan/Downloads/sage-6.1.1/local/lib/python2.7/site-packages/graph_tool/draw/libgraph_tool_layout.la
>>> libtool: finish:
>>> PATH="/usr/local/sbin:/usr/local/bin:/usr/sbin:/usr/bin:/sbin:/bin:/sbin"
>>> ldconfig -n
>>> /home/juan/Downloads/sage-6.1.1/local/lib/python2.7/site-packages/graph_tool/draw
>>> ----------------------------------------------------------------------
>>> Libraries have been installed in:
>>>
>>> /home/juan/Downloads/sage-6.1.1/local/lib/python2.7/site-packages/graph_tool/draw
>>>
>>> If you ever happen to want to link against installed libraries
>>> in a given directory, LIBDIR, you must either use libtool, and
>>> specify the full pathname of the library, or use the `-LLIBDIR'
>>> flag during linking and do at least one of the following:
>>>    - add LIBDIR to the `LD_LIBRARY_PATH' environment variable
>>>      during execution
>>>    - add LIBDIR to the `LD_RUN_PATH' environment variable
>>>      during linking
>>>    - use the `-Wl,-rpath -Wl,LIBDIR' linker flag
>>>    - have your system administrator add LIBDIR to `/etc/ld.so.conf'
>>>
>>> See any operating system documentation about shared libraries for
>>> more information, such as the ld(1) and ld.so(8) manual pages.
>>> ----------------------------------------------------------------------
>>>  /bin/mkdir -p
>>> '/home/juan/Downloads/sage-6.1.1/local/lib/python2.7/site-packages/graph_tool/include'
>>>  /usr/bin/install -c -m 644 graph_arf.hh graph_sfdp.hh
>>> '/home/juan/Downloads/sage-6.1.1/local/lib/python2.7/site-packages/graph_tool/include'
>>> make[4]: Leaving directory
>>> `/home/juan/Downloads/graph-tool-2.2.29.1/src/graph/layout'
>>> make[3]: Leaving directory
>>> `/home/juan/Downloads/graph-tool-2.2.29.1/src/graph/layout'
>>> Making install in search
>>> make[3]: Entering directory
>>> `/home/juan/Downloads/graph-tool-2.2.29.1/src/graph/search'
>>> make[4]: Entering directory
>>> `/home/juan/Downloads/graph-tool-2.2.29.1/src/graph/search'
>>> make[4]: Nothing to be done for `install-exec-am'.
>>>  /bin/mkdir -p
>>> '/home/juan/Downloads/sage-6.1.1/local/lib/python2.7/site-packages/graph_tool/search'
>>>  /bin/bash ../../../libtool   --mode=install /usr/bin/install -c
>>> libgraph_tool_search.la
>>> '/home/juan/Downloads/sage-6.1.1/local/lib/python2.7/site-packages/graph_tool/search'
>>> libtool: install: /usr/bin/install -c .libs/libgraph_tool_search.so
>>> /home/juan/Downloads/sage-6.1.1/local/lib/python2.7/site-packages/graph_tool/search/libgraph_tool_search.so
>>> libtool: install: /usr/bin/install -c .libs/libgraph_tool_search.lai
>>> /home/juan/Downloads/sage-6.1.1/local/lib/python2.7/site-packages/graph_tool/search/libgraph_tool_search.la
>>> libtool: finish:
>>> PATH="/usr/local/sbin:/usr/local/bin:/usr/sbin:/usr/bin:/sbin:/bin:/sbin"
>>> ldconfig -n
>>> /home/juan/Downloads/sage-6.1.1/local/lib/python2.7/site-packages/graph_tool/search
>>> ----------------------------------------------------------------------
>>> Libraries have been installed in:
>>>
>>> /home/juan/Downloads/sage-6.1.1/local/lib/python2.7/site-packages/graph_tool/search
>>>
>>> If you ever happen to want to link against installed libraries
>>> in a given directory, LIBDIR, you must either use libtool, and
>>> specify the full pathname of the library, or use the `-LLIBDIR'
>>> flag during linking and do at least one of the following:
>>>    - add LIBDIR to the `LD_LIBRARY_PATH' environment variable
>>>      during execution
>>>    - add LIBDIR to the `LD_RUN_PATH' environment variable
>>>      during linking
>>>    - use the `-Wl,-rpath -Wl,LIBDIR' linker flag
>>>    - have your system administrator add LIBDIR to `/etc/ld.so.conf'
>>>
>>> See any operating system documentation about shared libraries for
>>> more information, such as the ld(1) and ld.so(8) manual pages.
>>> ----------------------------------------------------------------------
>>> make[4]: Leaving directory
>>> `/home/juan/Downloads/graph-tool-2.2.29.1/src/graph/search'
>>> make[3]: Leaving directory
>>> `/home/juan/Downloads/graph-tool-2.2.29.1/src/graph/search'
>>> Making install in spectral
>>> make[3]: Entering directory
>>> `/home/juan/Downloads/graph-tool-2.2.29.1/src/graph/spectral'
>>> make[4]: Entering directory
>>> `/home/juan/Downloads/graph-tool-2.2.29.1/src/graph/spectral'
>>> make[4]: Nothing to be done for `install-exec-am'.
>>>  /bin/mkdir -p
>>> '/home/juan/Downloads/sage-6.1.1/local/lib/python2.7/site-packages/graph_tool/spectral'
>>>  /bin/bash ../../../libtool   --mode=install /usr/bin/install -c
>>> libgraph_tool_spectral.la
>>> '/home/juan/Downloads/sage-6.1.1/local/lib/python2.7/site-packages/graph_tool/spectral'
>>> libtool: install: /usr/bin/install -c .libs/libgraph_tool_spectral.so
>>> /home/juan/Downloads/sage-6.1.1/local/lib/python2.7/site-packages/graph_tool/spectral/libgraph_tool_spectral.so
>>> libtool: install: /usr/bin/install -c .libs/libgraph_tool_spectral.lai
>>> /home/juan/Downloads/sage-6.1.1/local/lib/python2.7/site-packages/graph_tool/spectral/libgraph_tool_spectral.la
>>> libtool: finish:
>>> PATH="/usr/local/sbin:/usr/local/bin:/usr/sbin:/usr/bin:/sbin:/bin:/sbin"
>>> ldconfig -n
>>> /home/juan/Downloads/sage-6.1.1/local/lib/python2.7/site-packages/graph_tool/spectral
>>> ----------------------------------------------------------------------
>>> Libraries have been installed in:
>>>
>>> /home/juan/Downloads/sage-6.1.1/local/lib/python2.7/site-packages/graph_tool/spectral
>>>
>>> If you ever happen to want to link against installed libraries
>>> in a given directory, LIBDIR, you must either use libtool, and
>>> specify the full pathname of the library, or use the `-LLIBDIR'
>>> flag during linking and do at least one of the following:
>>>    - add LIBDIR to the `LD_LIBRARY_PATH' environment variable
>>>      during execution
>>>    - add LIBDIR to the `LD_RUN_PATH' environment variable
>>>      during linking
>>>    - use the `-Wl,-rpath -Wl,LIBDIR' linker flag
>>>    - have your system administrator add LIBDIR to `/etc/ld.so.conf'
>>>
>>> See any operating system documentation about shared libraries for
>>> more information, such as the ld(1) and ld.so(8) manual pages.
>>> ----------------------------------------------------------------------
>>>  /bin/mkdir -p
>>> '/home/juan/Downloads/sage-6.1.1/local/lib/python2.7/site-packages/graph_tool/include'
>>>  /usr/bin/install -c -m 644 graph_adjacency.hh graph_incidence.hh
>>> graph_laplacian.hh graph_transition.hh
>>> '/home/juan/Downloads/sage-6.1.1/local/lib/python2.7/site-packages/graph_tool/include'
>>> make[4]: Leaving directory
>>> `/home/juan/Downloads/graph-tool-2.2.29.1/src/graph/spectral'
>>> make[3]: Leaving directory
>>> `/home/juan/Downloads/graph-tool-2.2.29.1/src/graph/spectral'
>>> Making install in stats
>>> make[3]: Entering directory
>>> `/home/juan/Downloads/graph-tool-2.2.29.1/src/graph/stats'
>>> make[4]: Entering directory
>>> `/home/juan/Downloads/graph-tool-2.2.29.1/src/graph/stats'
>>> make[4]: Nothing to be done for `install-exec-am'.
>>>  /bin/mkdir -p
>>> '/home/juan/Downloads/sage-6.1.1/local/lib/python2.7/site-packages/graph_tool/stats'
>>>  /bin/bash ../../../libtool   --mode=install /usr/bin/install -c
>>> libgraph_tool_stats.la
>>> '/home/juan/Downloads/sage-6.1.1/local/lib/python2.7/site-packages/graph_tool/stats'
>>> libtool: install: /usr/bin/install -c .libs/libgraph_tool_stats.so
>>> /home/juan/Downloads/sage-6.1.1/local/lib/python2.7/site-packages/graph_tool/stats/libgraph_tool_stats.so
>>> libtool: install: /usr/bin/install -c .libs/libgraph_tool_stats.lai
>>> /home/juan/Downloads/sage-6.1.1/local/lib/python2.7/site-packages/graph_tool/stats/libgraph_tool_stats.la
>>> libtool: finish:
>>> PATH="/usr/local/sbin:/usr/local/bin:/usr/sbin:/usr/bin:/sbin:/bin:/sbin"
>>> ldconfig -n
>>> /home/juan/Downloads/sage-6.1.1/local/lib/python2.7/site-packages/graph_tool/stats
>>> ----------------------------------------------------------------------
>>> Libraries have been installed in:
>>>
>>> /home/juan/Downloads/sage-6.1.1/local/lib/python2.7/site-packages/graph_tool/stats
>>>
>>> If you ever happen to want to link against installed libraries
>>> in a given directory, LIBDIR, you must either use libtool, and
>>> specify the full pathname of the library, or use the `-LLIBDIR'
>>> flag during linking and do at least one of the following:
>>>    - add LIBDIR to the `LD_LIBRARY_PATH' environment variable
>>>      during execution
>>>    - add LIBDIR to the `LD_RUN_PATH' environment variable
>>>      during linking
>>>    - use the `-Wl,-rpath -Wl,LIBDIR' linker flag
>>>    - have your system administrator add LIBDIR to `/etc/ld.so.conf'
>>>
>>> See any operating system documentation about shared libraries for
>>> more information, such as the ld(1) and ld.so(8) manual pages.
>>> ----------------------------------------------------------------------
>>>  /bin/mkdir -p
>>> '/home/juan/Downloads/sage-6.1.1/local/lib/python2.7/site-packages/graph_tool/include'
>>>  /usr/bin/install -c -m 644 graph_parallel.hh graph_histograms.hh
>>> graph_average.hh graph_distance_sampled.hh graph_distance.hh
>>> '/home/juan/Downloads/sage-6.1.1/local/lib/python2.7/site-packages/graph_tool/include'
>>> make[4]: Leaving directory
>>> `/home/juan/Downloads/graph-tool-2.2.29.1/src/graph/stats'
>>> make[3]: Leaving directory
>>> `/home/juan/Downloads/graph-tool-2.2.29.1/src/graph/stats'
>>> Making install in topology
>>> make[3]: Entering directory
>>> `/home/juan/Downloads/graph-tool-2.2.29.1/src/graph/topology'
>>> make[4]: Entering directory
>>> `/home/juan/Downloads/graph-tool-2.2.29.1/src/graph/topology'
>>> make[4]: Nothing to be done for `install-exec-am'.
>>>  /bin/mkdir -p
>>> '/home/juan/Downloads/sage-6.1.1/local/lib/python2.7/site-packages/graph_tool/topology'
>>>  /bin/bash ../../../libtool   --mode=install /usr/bin/install -c
>>> libgraph_tool_topology.la
>>> '/home/juan/Downloads/sage-6.1.1/local/lib/python2.7/site-packages/graph_tool/topology'
>>> libtool: install: /usr/bin/install -c .libs/libgraph_tool_topology.so
>>> /home/juan/Downloads/sage-6.1.1/local/lib/python2.7/site-packages/graph_tool/topology/libgraph_tool_topology.so
>>> libtool: install: /usr/bin/install -c .libs/libgraph_tool_topology.lai
>>> /home/juan/Downloads/sage-6.1.1/local/lib/python2.7/site-packages/graph_tool/topology/libgraph_tool_topology.la
>>> libtool: finish:
>>> PATH="/usr/local/sbin:/usr/local/bin:/usr/sbin:/usr/bin:/sbin:/bin:/sbin"
>>> ldconfig -n
>>> /home/juan/Downloads/sage-6.1.1/local/lib/python2.7/site-packages/graph_tool/topology
>>> ----------------------------------------------------------------------
>>> Libraries have been installed in:
>>>
>>> /home/juan/Downloads/sage-6.1.1/local/lib/python2.7/site-packages/graph_tool/topology
>>>
>>> If you ever happen to want to link against installed libraries
>>> in a given directory, LIBDIR, you must either use libtool, and
>>> specify the full pathname of the library, or use the `-LLIBDIR'
>>> flag during linking and do at least one of the following:
>>>    - add LIBDIR to the `LD_LIBRARY_PATH' environment variable
>>>      during execution
>>>    - add LIBDIR to the `LD_RUN_PATH' environment variable
>>>      during linking
>>>    - use the `-Wl,-rpath -Wl,LIBDIR' linker flag
>>>    - have your system administrator add LIBDIR to `/etc/ld.so.conf'
>>>
>>> See any operating system documentation about shared libraries for
>>> more information, such as the ld(1) and ld.so(8) manual pages.
>>> ----------------------------------------------------------------------
>>>  /bin/mkdir -p
>>> '/home/juan/Downloads/sage-6.1.1/local/lib/python2.7/site-packages/graph_tool/include'
>>>  /usr/bin/install -c -m 644 graph_components.hh graph_kcore.hh
>>> graph_similarity.hh graph_subgraph_isomorphism.hh
>>> '/home/juan/Downloads/sage-6.1.1/local/lib/python2.7/site-packages/graph_tool/include'
>>> make[4]: Leaving directory
>>> `/home/juan/Downloads/graph-tool-2.2.29.1/src/graph/topology'
>>> make[3]: Leaving directory
>>> `/home/juan/Downloads/graph-tool-2.2.29.1/src/graph/topology'
>>> Making install in util
>>> make[3]: Entering directory
>>> `/home/juan/Downloads/graph-tool-2.2.29.1/src/graph/util'
>>> make[4]: Entering directory
>>> `/home/juan/Downloads/graph-tool-2.2.29.1/src/graph/util'
>>> make[4]: Nothing to be done for `install-exec-am'.
>>>  /bin/mkdir -p
>>> '/home/juan/Downloads/sage-6.1.1/local/lib/python2.7/site-packages/graph_tool/util'
>>>  /bin/bash ../../../libtool   --mode=install /usr/bin/install -c
>>> libgraph_tool_util.la
>>> '/home/juan/Downloads/sage-6.1.1/local/lib/python2.7/site-packages/graph_tool/util'
>>> libtool: install: /usr/bin/install -c .libs/libgraph_tool_util.so
>>> /home/juan/Downloads/sage-6.1.1/local/lib/python2.7/site-packages/graph_tool/util/libgraph_tool_util.so
>>> libtool: install: /usr/bin/install -c .libs/libgraph_tool_util.lai
>>> /home/juan/Downloads/sage-6.1.1/local/lib/python2.7/site-packages/graph_tool/util/libgraph_tool_util.la
>>> libtool: finish:
>>> PATH="/usr/local/sbin:/usr/local/bin:/usr/sbin:/usr/bin:/sbin:/bin:/sbin"
>>> ldconfig -n
>>> /home/juan/Downloads/sage-6.1.1/local/lib/python2.7/site-packages/graph_tool/util
>>> ----------------------------------------------------------------------
>>> Libraries have been installed in:
>>>
>>> /home/juan/Downloads/sage-6.1.1/local/lib/python2.7/site-packages/graph_tool/util
>>>
>>> If you ever happen to want to link against installed libraries
>>> in a given directory, LIBDIR, you must either use libtool, and
>>> specify the full pathname of the library, or use the `-LLIBDIR'
>>> flag during linking and do at least one of the following:
>>>    - add LIBDIR to the `LD_LIBRARY_PATH' environment variable
>>>      during execution
>>>    - add LIBDIR to the `LD_RUN_PATH' environment variable
>>>      during linking
>>>    - use the `-Wl,-rpath -Wl,LIBDIR' linker flag
>>>    - have your system administrator add LIBDIR to `/etc/ld.so.conf'
>>>
>>> See any operating system documentation about shared libraries for
>>> more information, such as the ld(1) and ld.so(8) manual pages.
>>> ----------------------------------------------------------------------
>>>  /bin/mkdir -p
>>> '/home/juan/Downloads/sage-6.1.1/local/lib/python2.7/site-packages/graph_tool/include'
>>>  /usr/bin/install -c -m 644 graph_search.hh
>>> '/home/juan/Downloads/sage-6.1.1/local/lib/python2.7/site-packages/graph_tool/include'
>>> make[4]: Leaving directory
>>> `/home/juan/Downloads/graph-tool-2.2.29.1/src/graph/util'
>>> make[3]: Leaving directory
>>> `/home/juan/Downloads/graph-tool-2.2.29.1/src/graph/util'
>>> make[3]: Entering directory
>>> `/home/juan/Downloads/graph-tool-2.2.29.1/src/graph'
>>> make[4]: Entering directory
>>> `/home/juan/Downloads/graph-tool-2.2.29.1/src/graph'
>>> make[4]: Nothing to be done for `install-exec-am'.
>>>  /bin/mkdir -p
>>> '/home/juan/Downloads/sage-6.1.1/local/lib/python2.7/site-packages/graph_tool'
>>>  /bin/bash ../../libtool   --mode=install /usr/bin/install -c
>>> libgraph_tool_core.la
>>> '/home/juan/Downloads/sage-6.1.1/local/lib/python2.7/site-packages/graph_tool'
>>> libtool: install: /usr/bin/install -c .libs/libgraph_tool_core.so
>>> /home/juan/Downloads/sage-6.1.1/local/lib/python2.7/site-packages/graph_tool/libgraph_tool_core.so
>>> libtool: install: /usr/bin/install -c .libs/libgraph_tool_core.lai
>>> /home/juan/Downloads/sage-6.1.1/local/lib/python2.7/site-packages/graph_tool/libgraph_tool_core.la
>>> libtool: finish:
>>> PATH="/usr/local/sbin:/usr/local/bin:/usr/sbin:/usr/bin:/sbin:/bin:/sbin"
>>> ldconfig -n
>>> /home/juan/Downloads/sage-6.1.1/local/lib/python2.7/site-packages/graph_tool
>>> ----------------------------------------------------------------------
>>> Libraries have been installed in:
>>>
>>> /home/juan/Downloads/sage-6.1.1/local/lib/python2.7/site-packages/graph_tool
>>>
>>> If you ever happen to want to link against installed libraries
>>> in a given directory, LIBDIR, you must either use libtool, and
>>> specify the full pathname of the library, or use the `-LLIBDIR'
>>> flag during linking and do at least one of the following:
>>>    - add LIBDIR to the `LD_LIBRARY_PATH' environment variable
>>>      during execution
>>>    - add LIBDIR to the `LD_RUN_PATH' environment variable
>>>      during linking
>>>    - use the `-Wl,-rpath -Wl,LIBDIR' linker flag
>>>    - have your system administrator add LIBDIR to `/etc/ld.so.conf'
>>>
>>> See any operating system documentation about shared libraries for
>>> more information, such as the ld(1) and ld.so(8) manual pages.
>>> ----------------------------------------------------------------------
>>>  /bin/mkdir -p
>>> '/home/juan/Downloads/sage-6.1.1/local/lib/python2.7/site-packages/graph_tool/include'
>>>  /usr/bin/install -c -m 644 ../../config.h fast_vector_property_map.hh
>>> gml.hh graph.hh graph_adjacency.hh graph_adaptor.hh graph_exceptions.hh
>>> graph_filtering.hh graph_properties.hh graph_properties_group.hh
>>> graph_python_interface.hh graph_selectors.hh graph_util.hh histogram.hh
>>> mpl_nested_loop.hh numpy_bind.hh numpy_bind_old.hh random.hh str_repr.hh
>>> shared_map.hh transform_iterator.hh
>>> '/home/juan/Downloads/sage-6.1.1/local/lib/python2.7/site-packages/graph_tool/include'
>>>  /bin/mkdir -p
>>> '/home/juan/Downloads/sage-6.1.1/local/lib/python2.7/site-packages/graph_tool/include/boost-workaround/boost/graph/'
>>>  /usr/bin/install -c -m 644
>>> ../boost-workaround/boost/graph/betweenness_centrality.hpp
>>> ../boost-workaround/boost/graph/detail/read_graphviz_new.hpp
>>> ../boost-workaround/boost/graph/graphml.hpp
>>> ../boost-workaround/boost/graph/graphviz.hpp
>>> ../boost-workaround/boost/graph/isomorphism.hpp
>>> ../boost-workaround/boost/graph/kamada_kawai_spring_layout.hpp
>>> ../boost-workaround/boost/graph/metric_tsp_approx.hpp
>>> ../boost-workaround/boost/graph/named_function_params-alt.hpp
>>> ../boost-workaround/boost/graph/overloading.hpp
>>> ../boost-workaround/boost/graph/push_relabel_max_flow.hpp
>>> ../boost-workaround/boost/graph/copy_alt.hpp
>>> ../boost-workaround/boost/graph/reverse_graph_alt.hpp
>>> ../boost-workaround/boost/graph/stoer_wagner_min_cut.hpp
>>> '/home/juan/Downloads/sage-6.1.1/local/lib/python2.7/site-packages/graph_tool/include/boost-workaround/boost/graph/'
>>> make[4]: Leaving directory
>>> `/home/juan/Downloads/graph-tool-2.2.29.1/src/graph'
>>> make[3]: Leaving directory
>>> `/home/juan/Downloads/graph-tool-2.2.29.1/src/graph'
>>> make[2]: Leaving directory
>>> `/home/juan/Downloads/graph-tool-2.2.29.1/src/graph'
>>> Making install in graph_tool
>>> make[2]: Entering directory
>>> `/home/juan/Downloads/graph-tool-2.2.29.1/src/graph_tool'
>>> make[3]: Entering directory
>>> `/home/juan/Downloads/graph-tool-2.2.29.1/src/graph_tool'
>>> make[3]: Nothing to be done for `install-exec-am'.
>>>  /bin/mkdir -p
>>> '/home/juan/Downloads/sage-6.1.1/local/lib/python2.7/site-packages/graph_tool'
>>>  /usr/bin/install -c -m 644 __init__.py dl_import.py decorators.py io.py
>>> all.py
>>> '/home/juan/Downloads/sage-6.1.1/local/lib/python2.7/site-packages/graph_tool'
>>> make[3]: Leaving directory
>>> `/home/juan/Downloads/graph-tool-2.2.29.1/src/graph_tool'
>>> make[2]: Leaving directory
>>> `/home/juan/Downloads/graph-tool-2.2.29.1/src/graph_tool'
>>> make[1]: Leaving directory `/home/juan/Downloads/graph-tool-2.2.29.1/src'
>>> Traceback (most recent call last):
>>>   File "/home/juan/Downloads/sage-6.1.1/local/lib/python2.7/site.py", line
>>> 548, in <module>
>>>     main()
>>>   File "/home/juan/Downloads/sage-6.1.1/local/lib/python2.7/site.py", line
>>> 530, in main
>>>     known_paths = addusersitepackages(known_paths)
>>>   File "/home/juan/Downloads/sage-6.1.1/local/lib/python2.7/site.py", line
>>> 266, in addusersitepackages
>>>     user_site = getusersitepackages()
>>>   File "/home/juan/Downloads/sage-6.1.1/local/lib/python2.7/site.py", line
>>> 241, in getusersitepackages
>>>     user_base = getuserbase() # this will also set USER_BASE
>>>   File "/home/juan/Downloads/sage-6.1.1/local/lib/python2.7/site.py", line
>>> 231, in getuserbase
>>>     USER_BASE = get_config_var('userbase')
>>>   File "/home/juan/Downloads/sage-6.1.1/local/lib/python2.7/sysconfig.py",
>>> line 516, in get_config_var
>>>     return get_config_vars().get(name)
>>>   File "/home/juan/Downloads/sage-6.1.1/local/lib/python2.7/sysconfig.py",
>>> line 449, in get_config_vars
>>>     import re
>>>   File "/home/juan/Downloads/sage-6.1.1/local/lib/python2.7/re.py", line
>>> 105, in <module>
>>>     import sre_compile
>>>   File "/home/juan/Downloads/sage-6.1.1/local/lib/python2.7/sre_compile.py",
>>> line 14, in <module>
>>>     import sre_parse
>>>   File "/home/juan/Downloads/sage-6.1.1/local/lib/python2.7/sre_parse.py",
>>> line 17, in <module>
>>>     from sre_constants import *
>>>   File
>>> "/home/juan/Downloads/sage-6.1.1/local/lib/python2.7/sre_constants.py", line
>>> 18, in <module>
>>>     from _sre import MAXREPEAT
>>> ImportError: cannot import name MAXREPEAT
>>> make[3]: *** [install-graph_toolPYTHON] Error 1
>>> make[2]: *** [install-am] Error 2
>>> make[1]: *** [install-recursive] Error 1
>>> make: *** [install-recursive] Error 1
>>>
>>> It seems that sage's Python is trying to import recursively some module. But
>>> I am not sure how to fix this. Any ideas?
>>>
>>> Best Regards,
>>> Juan
>>>
>>>
>>>
>>> On Tue, Feb 11, 2014 at 11:45 AM, Tiago Peixoto [via Main discussion list
>>> for the graph-tool project] <[hidden email]>
>>> wrote:
>>>>
>>>> On 02/09/2014 09:01 AM, Juan I. Perotti wrote:
>>>>
>>>> > Hello,
>>>> >
>>>> > I am trying to install graph-tool in sagemath ( check
>>>> > http://www.sagemath.org/ <http://www.sagemath.org/>   ), under Ubuntu
>>>> > 12.04.
>>>> >
>>>> > Basically, sagemath is python with many good modules helpful for
>>>> > mathematics, and why not physics.
>>>> >
>>>> > sagemath has its own built version of python, which is standard by using
>>>> > a
>>>> > virtual environment. The idea is, I guess, not to mess up with your
>>>> > system
>>>> > python.
>>>> >
>>>> > By typing in a terminal
>>>> >
>>>> > $ sage -sh
>>>> >
>>>> >
>>>> > you enter into sagemath virtual environment, which looks like:
>>>> >
>>>> > (sage -sh) $
>>>> >
>>>> >
>>>> > therefore, if you try to run a python console by typing
>>>> >
>>>> > (sage -sh)$ python
>>>> >
>>>> >
>>>> > then, it will run the python built in sage's virtual environment.
>>>> >
>>>> > From the virtual environment I have installed CGAL, and then, I tried to
>>>> > configure graph-tool typing:
>>>> >
>>>> > (sage -sh) graph-tool-2.2.29$ ./configure
>>>> > checking for a BSD-compatible install... /usr/bin/install -c
>>>> > checking whether build environment is sane... yes
>>>> > checking for a thread-safe mkdir -p... /bin/mkdir -p
>>>> > checking for gawk... no
>>>> > checking for mawk... mawk
>>>> > checking whether make sets $(MAKE)... yes
>>>> > checking whether make supports nested variables... yes
>>>> > checking whether make supports nested variables... (cached) yes
>>>> > checking for style of include used by make... GNU
>>>> > checking for gcc... gcc
>>>> > checking whether the C compiler works... yes
>>>> > checking for C compiler default output file name... a.out
>>>> > checking for suffix of executables...
>>>> > checking whether we are cross compiling... no
>>>> > checking for suffix of object files... o
>>>> > checking whether we are using the GNU C compiler... yes
>>>> > checking whether gcc accepts -g... yes
>>>> > checking for gcc option to accept ISO C89... none needed
>>>> > checking whether gcc understands -c and -o together... yes
>>>> > checking dependency style of gcc... gcc3
>>>> > checking for library containing strerror... none required
>>>> > checking how to run the C preprocessor... cpp
>>>> > checking for grep that handles long lines and -e... /bin/grep
>>>> > checking for egrep... /bin/grep -E
>>>> > checking for ANSI C header files... yes
>>>> > checking for sys/types.h... yes
>>>> > checking for sys/stat.h... yes
>>>> > checking for stdlib.h... yes
>>>> > checking for string.h... yes
>>>> > checking for memory.h... yes
>>>> > checking for strings.h... yes
>>>> > checking for inttypes.h... yes
>>>> > checking for stdint.h... yes
>>>> > checking for unistd.h... yes
>>>> > checking minix/config.h usability... no
>>>> > checking minix/config.h presence... no
>>>> > checking for minix/config.h... no
>>>> > checking whether it is safe to define __EXTENSIONS__... yes
>>>> > checking whether we are using the GNU C++ compiler... yes
>>>> > checking whether g++ accepts -g... yes
>>>> > checking dependency style of g++... gcc3
>>>> > checking for gcc option to accept ISO C99... unsupported
>>>> > checking for gcc option to accept ISO C89... (cached) none needed
>>>> > checking for gcc option to accept ISO Standard C... (cached) none needed
>>>> > checking how to run the C++ preprocessor... g++ -E
>>>> > checking for ANSI C header files... (cached) yes
>>>> > checking build system type... x86_64-unknown-linux-gnu
>>>> > checking host system type... x86_64-unknown-linux-gnu
>>>> > checking how to print strings... printf
>>>> > checking for a sed that does not truncate output... /bin/sed
>>>> > checking for fgrep... /bin/grep -F
>>>> > checking for ld used by gcc... ld
>>>> > checking if the linker (ld) is GNU ld... yes
>>>> > checking for BSD- or MS-compatible name lister (nm)... /usr/bin/nm -B
>>>> > checking the name lister (/usr/bin/nm -B) interface... BSD nm
>>>> > checking whether ln -s works... yes
>>>> > checking the maximum length of command line arguments... 1572864
>>>> > checking whether the shell understands some XSI constructs... yes
>>>> > checking whether the shell understands "+="... yes
>>>> > checking how to convert x86_64-unknown-linux-gnu file names to
>>>> > x86_64-unknown-linux-gnu format... func_convert_file_noop
>>>> > checking how to convert x86_64-unknown-linux-gnu file names to toolchain
>>>> > format... func_convert_file_noop
>>>> > checking for ld option to reload object files... -r
>>>> > checking for objdump... objdump
>>>> > checking how to recognize dependent libraries... pass_all
>>>> > checking for dlltool... no
>>>> > checking how to associate runtime and link libraries... printf %s\n
>>>> > checking for archiver @FILE support... @
>>>> > checking for strip... strip
>>>> > checking for ranlib... ranlib
>>>> > checking command to parse /usr/bin/nm -B output from gcc object... ok
>>>> > checking for sysroot... no
>>>> > checking for mt... mt
>>>> > checking if mt is a manifest tool... no
>>>> > checking for dlfcn.h... yes
>>>> > checking for objdir... .libs
>>>> > checking if gcc supports -fno-rtti -fno-exceptions... no
>>>> > checking for gcc option to produce PIC... -fPIC -DPIC
>>>> > checking if gcc PIC flag -fPIC -DPIC works... yes
>>>> > checking if gcc static flag -static works... yes
>>>> > checking if gcc supports -c -o file.o... yes
>>>> > checking if gcc supports -c -o file.o... (cached) yes
>>>> > checking whether the gcc linker (ld -m elf_x86_64) supports shared
>>>> > libraries... yes
>>>> > checking whether -lc should be explicitly linked in... no
>>>> > checking dynamic linker characteristics... GNU/Linux ld.so
>>>> > checking how to hardcode library paths into programs... immediate
>>>> > checking whether stripping libraries is possible... yes
>>>> > checking if libtool supports shared libraries... yes
>>>> > checking whether to build shared libraries... yes
>>>> > checking whether to build static libraries... no
>>>> > checking how to run the C++ preprocessor... g++ -E
>>>> > checking for ld used by g++... ld -m elf_x86_64
>>>> > checking if the linker (ld -m elf_x86_64) is GNU ld... yes
>>>> > checking whether the g++ linker (ld -m elf_x86_64) supports shared
>>>> > libraries... yes
>>>> > checking for g++ option to produce PIC... -fPIC -DPIC
>>>> > checking if g++ PIC flag -fPIC -DPIC works... yes
>>>> > checking if g++ static flag -static works... yes
>>>> > checking if g++ supports -c -o file.o... yes
>>>> > checking if g++ supports -c -o file.o... (cached) yes
>>>> > checking whether the g++ linker (ld -m elf_x86_64) supports shared
>>>> > libraries... yes
>>>> > checking dynamic linker characteristics... (cached) GNU/Linux ld.so
>>>> > checking how to hardcode library paths into programs... immediate
>>>> > checking target system type... x86_64-unknown-linux-gnu
>>>> > checking whether to enable debug info...... no
>>>> > checking whether C++ compiler supports -std=gnu++11... yes
>>>> > checking whether to enable function inlining...... yes
>>>> > checking whether to enable optimizations...... yes
>>>> > checking whether to enable symbol visibility manipulation...... yes
>>>> > checking whether to enable graph filtering...... yes
>>>> > checking whether to enable parallel algorithms with openmp...... no
>>>> > checking whether to enable cairo drawing...... yes
>>>> > checking whether to enable sparsehash...... yes
>>>> > checking for main in -lm... yes
>>>> > checking for main in -lbz2... yes
>>>> > checking for main in -lexpat... yes
>>>> > ================
>>>> > Detecting python
>>>> > ================
>>>> > checking for a Python interpreter with version >= 2.6... python
>>>> > checking for python...
>>>> >
>>>> > /home/juan/Downloads/software/sage-5.12-linux-64bit-ubuntu_12.04.3_lts-x86_64-Linux/local/bin/python
>>>> > checking for python version... 2.7
>>>> > checking for python platform... linux2
>>>> > checking for python script directory...
>>>> > ${prefix}/lib/python2.7/site-packages
>>>> > checking for python extension module directory...
>>>> > ${exec_prefix}/lib/python2.7/site-packages
>>>> > checking for python2.7... (cached)
>>>> >
>>>> > /home/juan/Downloads/software/sage-5.12-linux-64bit-ubuntu_12.04.3_lts-x86_64-Linux/local/bin/python
>>>> > checking for a version of Python >= '2.1.0'... yes
>>>> > checking for a version of Python == '2.7.5'... yes
>>>> > checking for the distutils Python package... yes
>>>> > checking for Python include path...
>>>> >
>>>> > -I/home/juan/Downloads/software/sage-5.12-linux-64bit-ubuntu_12.04.3_lts-x86_64-Linux/local/include/python2.7
>>>> > checking for Python library path...
>>>> >
>>>> > -L/home/buildbot/build/sage/snapperkob/snapperkob_binary/build/sage-5.12/local/lib
>>>> > -lpython2.7
>>>> > checking for Python site-packages path...
>>>> >
>>>> > /home/juan/Downloads/software/sage-5.12-linux-64bit-ubuntu_12.04.3_lts-x86_64-Linux/local/lib/python2.7/site-packages
>>>> > checking python extra libraries...  -lpthread -ldl  -lutil
>>>> > checking python extra linking flags... -Xlinker -export-dynamic
>>>> > checking consistency of all components of python development
>>>> > environment...
>>>> > yes
>>>> > graph-tool will be installed at:
>>>> >
>>>> > /home/juan/Downloads/software/sage-5.12-linux-64bit-ubuntu_12.04.3_lts-x86_64-Linux/local/lib/python2.7/site-packages
>>>> > ===========================
>>>> > Using python version: 2.7.5
>>>> > ===========================
>>>> > checking for boostlib >= 1.38.0... yes
>>>> > checking whether the Boost::Python library is available... yes
>>>> > checking for exit in -lboost_python... yes
>>>> > checking whether the Boost::Iostreams library is available... yes
>>>> > checking for exit in -lboost_iostreams... yes
>>>> > checking whether the Boost::Regex library is available... yes
>>>> > checking for exit in -lboost_regex... yes
>>>> > checking whether the Boost::Graph library is available... yes
>>>> > checking for exit in -lboost_graph... yes
>>>> > checking for main in -lCGAL... yes
>>>> > checking whether to cgal debbuging with valgrind...... no
>>>> > checking python module: numpy... yes
>>>> > checking for
>>>> >
>>>> > /home/juan/Downloads/software/sage-5.12-linux-64bit-ubuntu_12.04.3_lts-x86_64-Linux/local/lib/python2.7/site-packages/numpy/core/include/numpy/arrayobject.h...
>>>> > yes
>>>> > checking python module: scipy... yes
>>>> > checking
>>>> >
>>>> > /home/juan/Downloads/software/sage-5.12-linux-64bit-ubuntu_12.04.3_lts-x86_64-Linux/local/lib/python2.7/site-packages/scipy/weave/scxx/object.h
>>>> > usability... yes
>>>> > checking
>>>> >
>>>> > /home/juan/Downloads/software/sage-5.12-linux-64bit-ubuntu_12.04.3_lts-x86_64-Linux/local/lib/python2.7/site-packages/scipy/weave/scxx/object.h
>>>> > presence... yes
>>>> > checking for
>>>> >
>>>> > /home/juan/Downloads/software/sage-5.12-linux-64bit-ubuntu_12.04.3_lts-x86_64-Linux/local/lib/python2.7/site-packages/scipy/weave/scxx/object.h...
>>>> > yes
>>>> > checking expat.h usability... yes
>>>> > checking expat.h presence... yes
>>>> > checking for expat.h... yes
>>>> > checking CGAL/version.h usability... no
>>>> > checking CGAL/version.h presence... no
>>>> > checking for CGAL/version.h... no
>>>> > configure: error: CGAL headers not found
>>>> >
>>>> >
>>>> > As you can see, the config is using sage's version of python. However,
>>>> > it
>>>> > does not find CGAL's headers. Do you know why?
>>>> Where did you install CGAL? If you installed it in a non-standard
>>>> directory, this needs to be passed to the configure script via the
>>>> CPPFLAGS and LDFLAGS variables.
>>>>
>>>> Check the output in the config.log file, which includes the reason why
>>>> CGAL was not found. You can post the contents of this file to the list,
>>>> if you are unable to find the problem.
>>>>
>>>> Best,
>>>> Tiago
>>>>
>>>> --
>>>> Tiago de Paula Peixoto <[hidden email]>
>>>>
>>>>
>>>> _______________________________________________
>>>> graph-tool mailing list
>>>> [hidden email]
>>>> http://lists.skewed.de/mailman/listinfo/graph-tool
>>>>
>>>> signature.asc (919 bytes) Download Attachment
>>>> --
>>>> Tiago de Paula Peixoto <[hidden email]>
>>>>
>>>>
>>>> ________________________________
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>>>>
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>>>> NAML
>>>
>>>
>>>
>>>
>>> --
>>> Dr. Juan I. Perotti
>>>
>>> Postal Address:
>>> Aalto University
>>> Department of Biomedical Engineering and Computational Science (BECS)
>>> P.O. Box 12200
>>> FI-00076 AALTO, FINLAND
>>> Visiting Address:
>>> F-building, room F344, Rakentajanaukio 2, Otaniemi campus, Espoo
>>> Tel. + 358 50 5927 858 / + 358 46 6306 650
>>> Email: juanpool (at) gmail (dot) com
>>> Email: juan.perotti (at) aalto (dot) fi
>>> Home page: www.perottijuanignacio.com.ar
>>
>>
>>
>> --
>> Dr. Juan I. Perotti
>>
>> Postal Address:
>> Aalto University
>> Department of Biomedical Engineering and Computational Science (BECS)
>> P.O. Box 12200
>> FI-00076 AALTO, FINLAND
>> Visiting Address:
>> F-building, room F344, Rakentajanaukio 2, Otaniemi campus, Espoo
>> Tel. + 358 50 5927 858 / + 358 46 6306 650
>> Email: juanpool (at) gmail (dot) com
>> Email: juan.perotti (at) aalto (dot) fi
>> Home page: www.perottijuanignacio.com.ar
>
>
>
> --
> Dr. Juan I. Perotti
>
> Postal Address:
> Aalto University
> Department of Biomedical Engineering and Computational Science (BECS)
> P.O. Box 12200
> FI-00076 AALTO, FINLAND
> Visiting Address:
> F-building, room F344, Rakentajanaukio 2, Otaniemi campus, Espoo
> Tel. + 358 50 5927 858 / + 358 46 6306 650
> Email: juanpool (at) gmail (dot) com
> Email: juan.perotti (at) aalto (dot) fi
> Home page: www.perottijuanignacio.com.ar



--
Dr. Juan I. Perotti

Postal Address:
Aalto University
Department of Biomedical Engineering and Computational Science (BECS)
P.O. Box 12200
FI-00076 AALTO, FINLAND
Visiting Address:
F-building, room F344, Rakentajanaukio 2, Otaniemi campus, Espoo
Tel. + 358 50 5927 858 / + 358 46 6306 650
Email: juanpool (at) gmail (dot) com
Email: juan.perotti (at) aalto (dot) fi
Home page: www.perottijuanignacio.com.ar

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