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Re: [igraph] GraphML in R

From: Matthew Walker
Subject: Re: [igraph] GraphML in R
Date: Mon, 11 Jan 2010 15:51:00 -0500
User-agent: Thunderbird (X11/20090812)

Oh, maybe it was a compiler (or other tool) issue.  I just upgraded the version of gcc and some other tools, and now things seem to be more normal.

Previously if I specified neither LDFLAGS nor CPPFLAGS (using neither the command line options nor the export command) then config.log had this regarding xml2-config:

configure:15612: checking for xml2-config
configure:15630: found /gel/usr/mawal32/system/bin//xml2-config
configure:15643: result: /gel/usr/mawal32/system/bin//xml2-config
configure:15660: checking for xmlSAXUserParseFile in -lxml2
configure:15685: gcc -o conftest -g -O2   conftest.c -lxml2   >&5
/usr/bin/ld: cannot find -lxml2
collect2: ld returned 1 exit status
configure:15685: $? = 1

And GraphML was not supported.  (Note the lack of paths specified in the above call to gcc.)

Now, with the newer tools, I do not have this issue and, as well, support for GMP now appears.

Thanks for your help,


Gábor Csárdi wrote:
Hmmm, strange, though. The R package builder should find xml2-config as well....

Anyway, thanks for updating the wiki page!

On Mon, Jan 11, 2010 at 5:42 PM, Matthew Walker
<address@hidden> wrote:
Hi Gábor,

xml2-config has always been in my path, so it was not that.  However, I was
finally able to solve this problem by exporting the variables rather than
specifying them on the command line.  Thus, this did not work:

./configure --prefix=$HOME/system LDFLAGS=-L$HOME/system/lib/

But this does work:

export CPPFLAGS=-I$HOME/system/include
export LDFLAGS=-L$HOME/system/lib/
./configure --prefix=$HOME/system

I think this works because the exported parameters are then also used for
the compilation of the R library.



Gábor Csárdi wrote:


thanks for the wiki page. igraph searches for the program called
xml2-config to find the libxml2 installation. Maybe all you need to do
is to make sure that it is in your PATH. (This is true for Linux and
maybe other Unix-like systems.) Could you please check this?

Otherwise the wiki page is fine, setting the compilation flags always
works. But it is easier to just use xml2-config if your system has it.


On Sat, Jan 9, 2010 at 12:47 AM, Matthew Walker
<address@hidden> wrote:


I was trying to get GraphML support for the R interface to iGraph.  I
finally learnt that I must pass to configure the path I used to install
libxml2.  This took me a wee while to figure out so I have written up a few
lines on the wiki (http://igraph.wikidot.com/installation-issues) in case
anyone else has the same desire.  I would love to know if this is the
"correct" way to get iGraph to work with libxml2 as I was surprised that
iGraph didn't just take the information offered by pkg-config.

While doing that however, I noticed that support for GMP was turned off.
 Out of curiosity I installed GMP but it was still "off" no matter what
options I passed to ./configure.  I looked at the configure.ac and it
appears that the line "gmp_support=no" might be the cause.  Setting
"gmp_support=yes" seems to work.  Is this "no" intentional?  What does GMP
support offer anyway?

I then uninstalled igraph from R (using remove.package()) and then followed
Gabor's instructions on how create an R package [1] however, despite all
this, I still do not have GraphML support in R:

read.graph("~/Desktop/example.graphml.xml", format="graphml")

Error in read.graph.graphml(file, ...) :
 At foreign-graphml.c:1033 : GraphML support is disabled, Unimplemented
function call

Do you have any suggestions for what I am doing wrong?  I would greatly
appreciate your help!



[1] http://lists.gnu.org/archive/html/igraph-help/2007-04/msg00025.html

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