Hi Tiago, I'm very interested in using graph-tools to do network analysis since my network is pretty large. After I installed those required dependency packages, I still got errors when I run make. The error message is as following which I could not figure out. ./configure CPPFLAGS="-I/home/gaol3/Software/Tools/boost/include -I/home/gaol3/Software/Tools/CGAL/include" LDFLAGS="-L/home/gaol3/Software/Tools/boost/lib -L/home/gaol3/Software/Tools/CGAL/lib" --disable-sparsehash make make[4]: *** [graph_hits.lo] Error 1 make[4]: Leaving directory `/mnt/isilon/cbmi/tan_lab/gaol3/Software/Downloads/graph-tool-2.12/src/graph/centrality' make[3]: *** [all-recursive] Error 1 make[3]: Leaving directory `/mnt/isilon/cbmi/tan_lab/gaol3/Software/Downloads/graph-tool-2.12/src/graph' make[2]: *** [all-recursive] Error 1 make[2]: Leaving directory `/mnt/isilon/cbmi/tan_lab/gaol3/Software/Downloads/graph-tool-2.12/src' make[1]: *** [all-recursive] Error 1 make[1]: Leaving directory `/mnt/isilon/cbmi/tan_lab/gaol3/Software/Downloads/graph-tool-2.12' make: *** [all] Error 2 Thanks, Long -- 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.
On 25.02.2016 23:34, gaolongnuaa wrote:
I'm very interested in using graph-tools to do network analysis since my network is pretty large. After I installed those required dependency packages, I still got errors when I run make. The error message is as following which I could not figure out.
./configure CPPFLAGS="-I/home/gaol3/Software/Tools/boost/include -I/home/gaol3/Software/Tools/CGAL/include" LDFLAGS="-L/home/gaol3/Software/Tools/boost/lib -L/home/gaol3/Software/Tools/CGAL/lib" --disable-sparsehash make
make[4]: *** [graph_hits.lo] Error 1 make[4]: Leaving directory `/mnt/isilon/cbmi/tan_lab/gaol3/Software/Downloads/graph-tool-2.12/src/graph/centrality' make[3]: *** [all-recursive] Error 1 make[3]: Leaving directory `/mnt/isilon/cbmi/tan_lab/gaol3/Software/Downloads/graph-tool-2.12/src/graph' make[2]: *** [all-recursive] Error 1 make[2]: Leaving directory `/mnt/isilon/cbmi/tan_lab/gaol3/Software/Downloads/graph-tool-2.12/src' make[1]: *** [all-recursive] Error 1 make[1]: Leaving directory `/mnt/isilon/cbmi/tan_lab/gaol3/Software/Downloads/graph-tool-2.12' make: *** [all] Error 2
Please post the *entire* output of ./configure and make, as well as the contents of the config.log file, otherwise it is not possible to say what is going on. Best, Tiago -- Tiago de Paula Peixoto <tiago@skewed.de>
Hi, Sorry for the confusion! Attached are those files you may need, and please take a look. Thanks, Long config.log <http://main-discussion-list-for-the-graph-tool-project.982480.n3.nabble.com/file/n4026429/config.log> configure_output.txt <http://main-discussion-list-for-the-graph-tool-project.982480.n3.nabble.com/file/n4026429/configure_output.txt> make_output.txt <http://main-discussion-list-for-the-graph-tool-project.982480.n3.nabble.com/file/n4026429/make_output.txt> -- 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.
On 26.02.2016 03:34, gaolongnuaa wrote:
Hi,
Sorry for the confusion! Attached are those files you may need, and please take a look.
Thanks, Long config.log <http://main-discussion-list-for-the-graph-tool-project.982480.n3.nabble.com/file/n4026429/config.log> configure_output.txt <http://main-discussion-list-for-the-graph-tool-project.982480.n3.nabble.com/file/n4026429/configure_output.txt> make_output.txt <http://main-discussion-list-for-the-graph-tool-project.982480.n3.nabble.com/file/n4026429/make_output.txt>
Thanks for the detailed information. This is an incompatibility bug with boost 1.60. This has been fixed in git already, and the fix will be available also in the next release. In the meantime, you should use the git version instead. Best, Tiago -- Tiago de Paula Peixoto <tiago@skewed.de>
Hi Tiago, Thank you for the advice! I think I successfully installed the graph-tool, but it turned out a segmentation error when I entered "import graph_tool". I saw someone also had the same error in another post, and I did something you suggested in that post. Following is the output, bash-4.2$ gdb python GNU gdb (GDB) Red Hat Enterprise Linux 7.6.1-80.el7 Copyright (C) 2013 Free Software Foundation, Inc. License GPLv3+: GNU GPL version 3 or later <http://gnu.org/licenses/gpl.html> This is free software: you are free to change and redistribute it. There is NO WARRANTY, to the extent permitted by law. Type "show copying" and "show warranty" for details. This GDB was configured as "x86_64-redhat-linux-gnu". For bug reporting instructions, please see: <http://www.gnu.org/software/gdb/bugs/>... Reading symbols from /mnt/isilon/cbmi/tan_lab/gaol3/Software/Tools/Python/bin/python2.7...done. (gdb) run test.py Starting program: /home/gaol3/Software/Tools/Python/bin/python test.py [Thread debugging using libthread_db enabled] Using host libthread_db library "/lib64/libthread_db.so.1". Detaching after fork from child process 11698. Detaching after fork from child process 11700. Program received signal SIGSEGV, Segmentation fault. 0x00007ffff7de6976 in _dl_relocate_object () from /lib64/ld-linux-x86-64.so.2 Missing separate debuginfos, use: debuginfo-install blas-3.4.2-5.el7.x86_64 glibc-2.17-106.el7_2.4.x86_64 jbigkit-libs-2.0-11.el7.x86_64 keyutils-libs-1.5.8-3.el7.x86_64 krb5-libs-1.13.2-10.el7.x86_64 lapack-3.4.2-5.el7.x86_64 libcom_err-1.42.9-7.el7.x86_64 libffi-3.0.13-16.el7.x86_64 libgcc-4.8.5-4.el7.x86_64 libgfortran-4.8.5-4.el7.x86_64 libjpeg-turbo-1.2.90-5.el7.x86_64 libquadmath-4.8.5-4.el7.x86_64 libselinux-2.2.2-6.el7.x86_64 libstdc++-4.8.5-4.el7.x86_64 libtiff-4.0.3-14.el7.x86_64 libuuid-2.23.2-26.el7.x86_64 openssl-libs-1.0.1e-51.el7_2.2.x86_64 pcre-8.32-15.el7.x86_64 python-libs-2.7.5-34.el7.x86_64 python-pillow-2.0.0-19.gitd1c6db8.el7.x86_64 xz-libs-5.1.2-12alpha.el7.x86_64 zlib-1.2.7-15.el7.x86_64 (gdb) Do you have any ideas about this segmentation error? Thanks, Long -- 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.
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Tiago de Paula Peixoto