Installation error in Ubuntu

[Amy Koid]

Hi there,

I get this error message when I try to install pygraphviz.

python setup.py install

library_path=/usr/lib/graphviz

include_path=/usr/include/boost/graph/graphviz

running install

running build

running build_py

creating build

creating build/lib.linux-x86_64-2.7

creating build/lib.linux-x86_64-2.7/pygraphviz

copying pygraphviz/agraph.py -> build/lib.linux-x86_64-2.7/pygraphviz

copying pygraphviz/release.py -> build/lib.linux-x86_64-2.7/pygraphviz

copying pygraphviz/graphviz.py -> build/lib.linux-x86_64-2.7/pygraphviz

copying pygraphviz/__init__.py -> build/lib.linux-x86_64-2.7/pygraphviz

copying pygraphviz/version.py -> build/lib.linux-x86_64-2.7/pygraphviz

creating build/lib.linux-x86_64-2.7/pygraphviz/tests

copying pygraphviz/tests/test.py -> build/lib.linux-x86_64-2.7/pygraphviz/tests

copying pygraphviz/tests/__init__.py -> build/lib.linux-x86_64-2.7/pygraphviz/tests

copying pygraphviz/tests/unicode.txt -> build/lib.linux-x86_64-2.7/pygraphviz/tests

copying pygraphviz/tests/layout_draw.txt -> build/lib.linux-x86_64-2.7/pygraphviz/tests

copying pygraphviz/tests/graph.txt -> build/lib.linux-x86_64-2.7/pygraphviz/tests

copying pygraphviz/tests/attributes.txt -> build/lib.linux-x86_64-2.7/pygraphviz/tests

running build_ext

building 'pygraphviz._graphviz' extension

creating build/temp.linux-x86_64-2.7

creating build/temp.linux-x86_64-2.7/pygraphviz

gcc -pthread -fno-strict-aliasing -DNDEBUG -g -fwrapv -O2 -Wall -Wstrict-prototypes -fPIC -I/usr/include/boost/graph/graphviz -I/usr/include/python2.7 -c pygraphviz/graphviz_wrap.c -o build/temp.linux-x86_64-2.7/pygraphviz/graphviz_wrap.o

pygraphviz/graphviz_wrap.c:2519:20: fatal error: cgraph.h: No such file or directory

compilation terminated.

error: command 'gcc' failed with exit status 1

What is cgraph.h and do I obtain it from somewhere?

Thanks.

Amy

[Aric Hagberg]

You'll need to install Graphviz (graphviz-dev package).
Aric

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Aric Hagberg
Los Alamos National Laboratory
math.lanl.gov/~hagberg

[Amy Koid]

Hi there,

Thanks for your response.

I do have graphviz installed:

locate graphviz

/home/jay/software/boost_1_49_0/boost/graph/graphviz.hpp

/home/jay/software/boost_1_49_0/boost/graph/detail/read_graphviz_new.hpp

/home/jay/software/boost_1_49_0/boost/graph/detail/read_graphviz_spirit.hpp

/home/jay/software/boost_1_49_0/boost/graph/distributed/graphviz.hpp

/home/jay/software/boost_1_49_0/libs/graph/doc/read_graphviz.html

/home/jay/software/boost_1_49_0/libs/graph/doc/read_graphviz.rst

/home/jay/software/boost_1_49_0/libs/graph/doc/write-graphviz.html

/home/jay/software/boost_1_49_0/libs/graph/example/graphviz.cpp

/home/jay/software/boost_1_49_0/libs/graph/example/graphviz_example.dot

/home/jay/software/boost_1_49_0/libs/graph/example/graphviz_test.dot

/home/jay/software/boost_1_49_0/libs/graph/example/read_graphviz.cpp

/home/jay/software/boost_1_49_0/libs/graph/example/write_graphviz.cpp

/home/jay/software/boost_1_49_0/libs/graph/src/read_graphviz_new.cpp

/home/jay/software/boost_1_49_0/libs/graph/test/graphviz_test.cpp

/usr/include/boost/graph/graphviz.hpp

/usr/include/boost/graph/detail/read_graphviz_new.hpp

/usr/include/boost/graph/detail/read_graphviz_spirit.hpp

/usr/include/boost/graph/distributed/graphviz.hpp

/usr/lib/graphviz

/usr/lib/graphviz/config6

/usr/lib/graphviz/libgvplugin_core.so.6

/usr/lib/graphviz/libgvplugin_core.so.6.0.0

/usr/lib/graphviz/libgvplugin_dot_layout.so.6

/usr/lib/graphviz/libgvplugin_dot_layout.so.6.0.0

/usr/lib/graphviz/libgvplugin_gd.so.6

/usr/lib/graphviz/libgvplugin_gd.so.6.0.0

/usr/lib/graphviz/libgvplugin_neato_layout.so.6

/usr/lib/graphviz/libgvplugin_neato_layout.so.6.0.0

/usr/lib/graphviz/libgvplugin_pango.so.6

/usr/lib/graphviz/libgvplugin_pango.so.6.0.0

/usr/lib/graphviz/libgvplugin_xlib.so.6

/usr/lib/graphviz/libgvplugin_xlib.so.6.0.0

/usr/share/graphviz

/usr/share/doc/graphviz

/usr/share/doc/libgraphviz-perl

/usr/share/doc/graphviz/README.Debian

/usr/share/doc/graphviz/TODO.Debian

/usr/share/doc/graphviz/changelog.Debian.gz

/usr/share/doc/graphviz/copyright

/usr/share/doc/libgraphviz-perl/README.gz

/usr/share/doc/libgraphviz-perl/changelog.Debian.gz

/usr/share/doc/libgraphviz-perl/changelog.gz

/usr/share/doc/libgraphviz-perl/copyright

/usr/share/doc/libgraphviz-perl/examples

/usr/share/doc/libgraphviz-perl/examples/README

/usr/share/doc/libgraphviz-perl/examples/Yapp.output.gz

/usr/share/doc/libgraphviz-perl/examples/clusters.pl

/usr/share/doc/libgraphviz-perl/examples/clusters2.pl

/usr/share/doc/libgraphviz-perl/examples/directories.pl

/usr/share/doc/libgraphviz-perl/examples/dprofpp.graphviz

/usr/share/doc/libgraphviz-perl/examples/dumper.pl

/usr/share/doc/libgraphviz-perl/examples/make_all.pl

/usr/share/doc/libgraphviz-perl/examples/perly.output.gz

/usr/share/doc/libgraphviz-perl/examples/port.pl

/usr/share/doc/libgraphviz-perl/examples/ppmgraph.pl

/usr/share/doc/libgraphviz-perl/examples/primes.pl

/usr/share/doc/libgraphviz-perl/examples/primes_aux.pl

/usr/share/doc/libgraphviz-perl/examples/rank.pl

/usr/share/doc/libgraphviz-perl/examples/recdescent.pl

/usr/share/doc/libgraphviz-perl/examples/redcarpet.pl

/usr/share/doc/libgraphviz-perl/examples/regex.pl

/usr/share/doc/libgraphviz-perl/examples/remote.pl

/usr/share/doc/libgraphviz-perl/examples/simple.pl

/usr/share/doc/libgraphviz-perl/examples/text.pl

/usr/share/doc/libgraphviz-perl/examples/tmon.out.gz

/usr/share/doc/libgraphviz-perl/examples/undirected.pl

/usr/share/doc/libgraphviz-perl/examples/xml.pl

/usr/share/doc/libgraphviz-perl/examples/xref.pl

/usr/share/doc/libgraphviz-perl/examples/xref_aux.pl

/usr/share/doc/libgraphviz-perl/examples/yacc.pl

/usr/share/doc/libgraphviz-perl/examples/yapp.pl

/usr/share/graphviz/lefty

/usr/share/graphviz/lefty/box.lefty

/usr/share/graphviz/lefty/def.lefty

/usr/share/graphviz/lefty/dotty.lefty

/usr/share/graphviz/lefty/dotty_draw.lefty

/usr/share/graphviz/lefty/dotty_edit.lefty

/usr/share/graphviz/lefty/dotty_layout.lefty

/usr/share/graphviz/lefty/dotty_ui.lefty

/usr/share/graphviz/lefty/fractal.lefty

/usr/share/graphviz/lefty/fractal2.lefty

/usr/share/graphviz/lefty/lefty.psp

/usr/share/graphviz/lefty/slides.lefty

/usr/share/graphviz/lefty/tree.lefty

/usr/share/man/man7/graphviz.7.gz

/usr/share/menu/graphviz

/usr/share/mime/text/vnd.graphviz.xml

/var/lib/dpkg/info/graphviz.list

/var/lib/dpkg/info/graphviz.md5sums

/var/lib/dpkg/info/graphviz.postinst

/var/lib/dpkg/info/graphviz.postrm

/var/lib/dpkg/info/libgraphviz-perl.list

/var/lib/dpkg/info/libgraphviz-perl.md5sums

> email to pygraphviz-discuss+unsub...@googlegroups.com.

[Aric Hagberg]

Right, you need graphviz-dev too.
Aric

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>> >
>>
>>
>>
>> --
>> Aric Hagberg
>> Los Alamos National Laboratory
>> math.lanl.gov/~hagberg
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[Amy Koid]

Hi there,

Thank you for your help. It worked after I installed graphviz-dev.

>> > email to pygraphviz-discuss+unsub...@googlegroups.com.

>> > To post to this group, send email to pygraphvi...@googlegroups.com.
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>> > For more options, visit https://groups.google.com/groups/opt_out.
>> >
>> >
>>
>>
>>
>> --
>> Aric Hagberg
>> Los Alamos National Laboratory
>> math.lanl.gov/~hagberg
>
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[Colin Wilder]

I know this is an old thread but I'm hoping for some help. I'm an unsophisticated user compared to earlier folks here. I am running Windows 64 bit, with Python 2.7 in the Anaconda distribution. I'm using networkX (a package for manipulating network data). NetworkX interfaces with Pygraphviz and Graphviz and I'm at a roadblock installing Pygraphviz. Here's the error I'm getting:

C:\Anaconda\Lib\site-packages\pygraphviz-1.3rc1>python setup.py install

library_dirs=None

include_dirs=None

running install

running build

running build_py

running build_ext

building 'pygraphviz._graphviz' extension

C:\Anaconda\Scripts\gcc.bat -mdll -O -Wall -DGVDLL -IC:\Anaconda\include -IC:\An

aconda\PC -c pygraphviz/graphviz_wrap.c -o build\temp.win32-2.7\Release\pygraphv

iz\graphviz_wrap.o

pygraphviz/graphviz_wrap.c:2954:29: fatal error: graphviz/cgraph.h: No such file or directory

compilation terminated.

error: command 'gcc' failed with exit status 1

I can't decipher the error message - what do I need to do? From web searching, I think I need to have graphviz, graphviz-dev and/or libgraphviz-dev. I've tracked down versions of graphviz and graphviz-dev I think, but neither one has a setup.py file in it. I usually use pip install in my windows command line but that doesn't work with these. Anyone know what exactly I should do with these files? 

One lead I had is that the libgraphviz-dev (downloaded from http://packages.ubuntu.com/da/lucid/libgraphviz-dev) arrived as a zip file called data, and in its hierarchy included a file called cgraph.h (see error message above), specifically in C:\Anaconda\Lib\site-packages\pygraphviz-1.3rc1\data\usr\include\graphviz. So I kinda think that there are files that pygraphviz needs during installation that are not in the downloaded pygraphviz package, but are in libgraphviz. But do I put the libgraphviz folders somewhere manually? Should I use pip or something? Help! Thanks!