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 <juanpool@gmail.com> wrote:
Hi all,
The following seems to fix that problem
http://thinkingcan.blogspot.fi/2013/09/fixed-importerror-cannot-import-name....
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 <juanpool@gmail.com> 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] <ml-node+s982480n4025300h98@n3.nabble.com> 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]>
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-- 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 -- View this message in context: http://main-discussion-list-for-the-graph-tool-project.982480.n3.nabble.com/... Sent from the Main discussion list for the graph-tool project mailing list archive at Nabble.com.