On Thu, Sep 30, 2010 at 2:35 AM, Johan <charls...@gmail.com> wrote:
> Hi,

> Not sure if this is the correct forum but I'm having some problems
> installing pygraphviz that I hope you can help me with.

> When I run python setup.py install I get the result:

> error: command 'gcc' failed with exit status 1

> together with a lot of compile errors in pygraphviz/graphviz_wrap.c
> such as:

> pygraphviz/graphviz_wrap.c:5266: error: ‘Swig_var_Agdirected_get’
> undeclared (first use in this function)
> pygraphviz/graphviz_wrap.c:5266: error: ‘Swig_var_Agdirected_set’
> undeclared (first use in this function)

> My system is a Red Hat Enterprise Linux Server release 5.4 (Tikanga)
> with Python 2.4.
> Graphviz is installed with the following packages (without problems):
> graphviz-2.26.3-1.el5.x86_64.rpm
> graphviz-devel-2.26.3-1.el5.x86_64.rpm
> graphviz-python-2.26.3-1.el5.x86_64.rpm

> What simple mistake am I making?

> On Thu, Sep 30, 2010 at 2:35 AM, Johan <charls...@gmail.com> wrote:
> > Hi,

> > Not sure if this is the correct forum but I'm having some problems
> > installing pygraphviz that I hope you can help me with.

> > When I run python setup.py install I get the result:

> > error: command 'gcc' failed with exit status 1

> > together with a lot of compile errors in pygraphviz/graphviz_wrap.c
> > such as:

> > pygraphviz/graphviz_wrap.c:5266: error: ‘Swig_var_Agdirected_get’
> > undeclared (first use in this function)
> > pygraphviz/graphviz_wrap.c:5266: error: ‘Swig_var_Agdirected_set’
> > undeclared (first use in this function)

> > My system is a Red Hat Enterprise Linux Server release 5.4 (Tikanga)
> > with Python 2.4.
> > Graphviz is installed with the following packages (without problems):
> > graphviz-2.26.3-1.el5.x86_64.rpm
> > graphviz-devel-2.26.3-1.el5.x86_64.rpm
> > graphviz-python-2.26.3-1.el5.x86_64.rpm

> > What simple mistake am I making?

> It's hard to tell without the entire error message.  But maybe you are
> missing
> python-devel?

> Aric

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> On Thu, Sep 30, 2010 at 2:35 AM, Johan <charls...@gmail.com> wrote:
> > Hi,

> > Not sure if this is the correct forum but I'm having some problems
> > installing pygraphviz that I hope you can help me with.

> > When I run python setup.py install I get the result:

> > error: command 'gcc' failed with exit status 1

> > together with a lot of compile errors in pygraphviz/graphviz_wrap.c
> > such as:

> > pygraphviz/graphviz_wrap.c:5266: error: ‘Swig_var_Agdirected_get’
> > undeclared (first use in this function)
> > pygraphviz/graphviz_wrap.c:5266: error: ‘Swig_var_Agdirected_set’
> > undeclared (first use in this function)

> > My system is a Red Hat Enterprise Linux Server release 5.4 (Tikanga)
> > with Python 2.4.
> > Graphviz is installed with the following packages (without problems):
> > graphviz-2.26.3-1.el5.x86_64.rpm
> > graphviz-devel-2.26.3-1.el5.x86_64.rpm
> > graphviz-python-2.26.3-1.el5.x86_64.rpm

> > What simple mistake am I making?

> It's hard to tell without the entire error message.  But maybe you are missing
> python-devel?

> Aric

On Wed, Nov 24, 2010 at 12:39 AM, martin <martin.hobelsber...@las3.de> wrote:
> pygraphviz/graphviz_wrap.c:2519: fatal error: cgraph.h: No such file
> or directory
> compilation terminated.
> error: command 'gcc' failed with exit status 1

> any idea how i can get this working? I recently switched from python> 2.x to 3.x because the graph generation (post in networkx about huge
> graph) is much faster (from 14 hours with 2.x to 1,6 hours with python
> 3.1!)

> On Wed, Nov 24, 2010 at 12:39 AM, martin <martin.hobelsber...@las3.de> wrote:
> > pygraphviz/graphviz_wrap.c:2519: fatal error: cgraph.h: No such file
> > or directory
> > compilation terminated.
> > error: command 'gcc' failed with exit status 1

> For some reason the setup isn't finding cgraph.h (in libgraphviz-dev).
> But PyGraphviz doesn't work with Python3 so you wouldn't get much
> farther anyway I suspect.

> I personally don't have any plans to port PyGraphviz to Python3.

> > any idea how i can get this working? I recently switched from python> 2.x to 3.x because the graph generation (post in networkx about huge
> > graph) is much faster (from 14 hours with 2.x to 1,6 hours with python
> > 3.1!)

> What is the issue here?  Maybe we can fix that.

> Aric

On Wed, Nov 24, 2010 at 12:48 PM, martin <martin.hobelsber...@las3.de> wrote:
> As i wrote in the networkx group i construct a pretty huge graph (50k
> nodes and 19mio edges, with node labels (pagerank,class attribute) and
> edge labels (weight and a list to which i append strings iteratively
> (for certain nodes that are used together in the same context) while
> the graph is constructed...)).

> fine with dummy data. To iteratively fill the graph with data it took
> about 14 hours with python 2.7. I tried python 3.1 and now the graph
> is finished in around one and a half hours (by finished i mean it is
> in the memory. 11gig of ram is used). I tried to dump it to the
> harddisk (with pickle, as text file with dot) but it didn´t work out.
> It  seems pickle can´t handle so much data.

> i also tried the persistent shelve (thanks so much for providing it)
> but after around one third of the graph (which took 11 hours) the
> graph.db file was already 31 gig big on my harddisk. I am not sure
> why. Maybe the shelve has so much overhead? Or i just implemented it
> wrong. Anyway this did´t work out as well. :)

> So i was quite happy after the 1.5 hours with python 3.1 (because i
> think even if i could have dumped the graph to the disk to load it
> would have taken almost the same amount of time). With pygraphviz i
> just wanted to give the write_dot another try with python 3.1.

On Wednesday, 24 November 2010 13:09:43 UTC+5:30, martin wrote:

> Hi,

> i have a similar problem (trying to install pygraphviz on ubuntu).

> Here is the error message:

> las3@las3-Ubuntu:~/Downloads/pygraphviz-1.0$ python3 setup.py install
> Trying pkg-config
> library_path=b''
> include_path=b'/usr/include/graphviz'
> running install
> running build
> running build_py
> running build_ext
> building 'pygraphviz._graphviz' extension
> gcc -pthread -DNDEBUG -g -fwrapv -O2 -Wall -Wstrict-prototypes -fPIC -
> Ib'/usr/include/graphviz' -I/usr/include/python3.1 -c pygraphviz/
> graphviz_wrap.c -o build/temp.linux-x86_64-3.1/pygraphviz/
> graphviz_wrap.o
> pygraphviz/graphviz_wrap.c: In function ‘SWIG_Python_AddErrorMsg’:
> pygraphviz/graphviz_wrap.c:862: warning: implicit declaration of
> function ‘PyString_AsString’
> pygraphviz/graphviz_wrap.c: In function ‘PySwigClientData_New’:
> pygraphviz/graphviz_wrap.c:1253: warning: implicit declaration of
> function ‘PyClass_Check’
> pygraphviz/graphviz_wrap.c: In function ‘PySwigObject_format’:
> pygraphviz/graphviz_wrap.c:1326: warning: implicit declaration of
> function ‘PyString_FromString’
> pygraphviz/graphviz_wrap.c:1326: warning: initialization makes pointer
> from integer without a cast
> pygraphviz/graphviz_wrap.c:1328: warning: implicit declaration of
> function ‘PyString_Format’
> pygraphviz/graphviz_wrap.c:1328: warning: assignment makes pointer
> from integer without a cast
> pygraphviz/graphviz_wrap.c: In function ‘PySwigObject_repr’:
> pygraphviz/graphviz_wrap.c:1358: warning: implicit declaration of
> function ‘PyString_FromFormat’
> pygraphviz/graphviz_wrap.c:1358: warning: initialization makes pointer
> from integer without a cast
> pygraphviz/graphviz_wrap.c:1366: warning: implicit declaration of
> function ‘PyString_ConcatAndDel’
> pygraphviz/graphviz_wrap.c: In function ‘PySwigObject_print’:
> pygraphviz/graphviz_wrap.c:1380: warning: passing argument 1 of
> ‘fputs’ makes pointer from integer without a cast
> /usr/include/stdio.h:682: note: expected ‘const char * __restrict__’
> but argument is of type ‘int’
> pygraphviz/graphviz_wrap.c: In function ‘PySwigObject_str’:
> pygraphviz/graphviz_wrap.c:1393: warning: return makes pointer from
> integer without a cast
> pygraphviz/graphviz_wrap.c: In function ‘_PySwigObject_type’:
> pygraphviz/graphviz_wrap.c:1590: warning: initialization from
> incompatible pointer type
> pygraphviz/graphviz_wrap.c:1591: warning: initialization from
> incompatible pointer type
> pygraphviz/graphviz_wrap.c:1594: warning: initialization from
> incompatible pointer type
> pygraphviz/graphviz_wrap.c:1595: warning: initialization from
> incompatible pointer type
> pygraphviz/graphviz_wrap.c:1602: error: ‘coercion’ undeclared (first
> use in this function)
> pygraphviz/graphviz_wrap.c:1602: error: (Each undeclared identifier is
> reported only once
> pygraphviz/graphviz_wrap.c:1602: error: for each function it appears
> in.)
> pygraphviz/graphviz_wrap.c:1602: error: expected ‘}’ before numeric
> constant
> pygraphviz/graphviz_wrap.c:1622: warning: missing braces around
> initializer
> pygraphviz/graphviz_wrap.c:1622: warning: (near initialization for
> ‘tmp.ob_base.ob_base’)
> pygraphviz/graphviz_wrap.c:1624: warning: initialization makes integer
> from pointer without a cast
> pygraphviz/graphviz_wrap.c:1627: warning: initialization from
> incompatible pointer type
> pygraphviz/graphviz_wrap.c:1628: warning: initialization from
> incompatible pointer type
> pygraphviz/graphviz_wrap.c:1632: warning: initialization from
> incompatible pointer type
> pygraphviz/graphviz_wrap.c:1635: error: ‘cmpfunc’ undeclared (first
> use in this function)
> pygraphviz/graphviz_wrap.c:1635: error: expected ‘}’ before
> ‘PySwigObject_compare’
> pygraphviz/graphviz_wrap.c:1682: error: ‘PyTypeObject’ has no member
> named ‘ob_type’
> pygraphviz/graphviz_wrap.c:1584: warning: unused variable
> ‘PySwigObject_as_number’
> pygraphviz/graphviz_wrap.c:1582: warning: unused variable
> ‘swigobject_doc’
> pygraphviz/graphviz_wrap.c: In function ‘PySwigPacked_repr’:
> pygraphviz/graphviz_wrap.c:1731: warning: return makes pointer from
> integer without a cast
> pygraphviz/graphviz_wrap.c:1733: warning: return makes pointer from
> integer without a cast
> pygraphviz/graphviz_wrap.c: In function ‘PySwigPacked_str’:
> pygraphviz/graphviz_wrap.c:1742: warning: return makes pointer from
> integer without a cast
> pygraphviz/graphviz_wrap.c:1744: warning: return makes pointer from
> integer without a cast
> pygraphviz/graphviz_wrap.c: In function ‘_PySwigPacked_type’:
> pygraphviz/graphviz_wrap.c:1789: warning: missing braces around
> initializer
> pygraphviz/graphviz_wrap.c:1789: warning: (near initialization for
> ‘tmp.ob_base.ob_base’)
> pygraphviz/graphviz_wrap.c:1791: warning: initialization makes integer
> from pointer without a cast
> pygraphviz/graphviz_wrap.c:1794: warning: initialization from
> incompatible pointer type
> pygraphviz/graphviz_wrap.c:1795: warning: initialization from
> incompatible pointer type
> pygraphviz/graphviz_wrap.c:1796: warning: initialization from
> incompatible pointer type
> pygraphviz/graphviz_wrap.c:1798: error: ‘cmpfunc’ undeclared (first
> use in this function)
> pygraphviz/graphviz_wrap.c:1798: error: expected ‘}’ before
> ‘PySwigPacked_compare’
> pygraphviz/graphviz_wrap.c:1845: error: ‘PyTypeObject’ has no member
> named ‘ob_type’
> pygraphviz/graphviz_wrap.c:1783: warning: unused variable
> ‘swigpacked_doc’
> pygraphviz/graphviz_wrap.c: In function ‘_SWIG_This’:
> pygraphviz/graphviz_wrap.c:1890: warning: return makes pointer from
> integer without a cast
> pygraphviz/graphviz_wrap.c: In function ‘SWIG_Python_GetSwigThis’:
> pygraphviz/graphviz_wrap.c:1910: warning: implicit declaration of
> function ‘PyInstance_Check’
> pygraphviz/graphviz_wrap.c:1911: warning: implicit declaration of
> function ‘_PyInstance_Lookup’
> pygraphviz/graphviz_wrap.c:1911: warning: assignment makes pointer
> from integer without a cast
> pygraphviz/graphviz_wrap.c: In function
> ‘SWIG_Python_NewShadowInstance’:
> pygraphviz/graphviz_wrap.c:2141: warning: implicit declaration of
> function ‘PyInstance_NewRaw’
> pygraphviz/graphviz_wrap.c:2141: warning: assignment makes pointer
> from integer without a cast
> pygraphviz/graphviz_wrap.c: In function ‘SWIG_Python_SetModule’:
> pygraphviz/graphviz_wrap.c:2322: warning: implicit declaration of
> function ‘Py_InitModule’
> pygraphviz/graphviz_wrap.c:2323: warning: initialization makes pointer
> from integer without a cast
> pygraphviz/graphviz_wrap.c: In function ‘SWIG_Python_TypeQuery’:
> pygraphviz/graphviz_wrap.c:2343: warning: initialization makes pointer
> from integer without a cast
> pygraphviz/graphviz_wrap.c: In function ‘SWIG_Python_TypeError’:
> pygraphviz/graphviz_wrap.c:2432: warning: initialization makes pointer
> from integer without a cast
> pygraphviz/graphviz_wrap.c: At top level:
> pygraphviz/graphviz_wrap.c:2519: fatal error: cgraph.h: No such file
> or directory
> compilation terminated.
> error: command 'gcc' failed with exit status 1

> i have installed everything successfully with python2.7 but now i
> wanted to install it with python3.1.
> I also have python-dev installed.

> las3@las3-Ubuntu:~/Downloads/pygraphviz-1.0$ sudo apt-get install
> python3.1-dev
> [sudo] password for las3:
> Reading package lists... Done
> Building dependency tree
> Reading state information... Done
> python3.1-dev is already the newest version.

> any idea how i can get this working? I recently switched from python
> 2.x to 3.x because the graph generation (post in networkx about huge
> graph) is much faster (from 14 hours with 2.x to 1,6 hours with python
> 3.1!)

> thanks a lot

> Martin

> On Sep 30, 10:53 am, Aric Hagberg <ahagb...@gmail.com> wrote:
> > On Thu, Sep 30, 2010 at 2:35 AM, Johan <charls...@gmail.com> wrote:
> > > Hi,

> > > Not sure if this is the correct forum but I'm having some problems
> > > installing pygraphviz that I hope you can help me with.

> > > When I run python setup.py install I get the result:

> > > error: command 'gcc' failed with exit status 1

> > > together with a lot of compile errors in pygraphviz/graphviz_wrap.c
> > > such as:

> > > pygraphviz/graphviz_wrap.c:5266: error: ‘Swig_var_Agdirected_get’
> > > undeclared (first use in this function)
> > > pygraphviz/graphviz_wrap.c:5266: error: ‘Swig_var_Agdirected_set’
> > > undeclared (first use in this function)

> > > My system is a Red Hat Enterprise Linux Server release 5.4 (Tikanga)
> > > with Python 2.4.
> > > Graphviz is installed with the following packages (without problems):
> > > graphviz-2.26.3-1.el5.x86_64.rpm
> > > graphviz-devel-2.26.3-1.el5.x86_64.rpm
> > > graphviz-python-2.26.3-1.el5.x86_64.rpm

> > > What simple mistake am I making?

> > It's hard to tell without the entire error message.  But maybe you are
> missing
> > python-devel?

> > Aric