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From: | Matthew Walker |
Subject: | Re: [igraph] GraphML in R |
Date: | Mon, 11 Jan 2010 15:51:00 -0500 |
User-agent: | Thunderbird 2.0.0.23 (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: $? = 1 And GraphML was not supported. (Note the lack of paths specified in the above call to gcc.) Now, with the newer tools, I do not have this issue and, as well, support for GMP now appears. Thanks for your help, Matthew Gábor Csárdi wrote: Hmmm, strange, though. The R package builder should find xml2-config as well.... Anyway, thanks for updating the wiki page! Best, Gabor On Mon, Jan 11, 2010 at 5:42 PM, Matthew Walker <address@hidden> wrote:Hi Gábor, xml2-config has always been in my path, so it was not that. However, I was finally able to solve this problem by exporting the variables rather than specifying them on the command line. Thus, this did not work: ./configure --prefix=$HOME/system LDFLAGS=-L$HOME/system/lib/ CPPFLAGS=-I$HOME/system/include 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. Cheers, Matthew Gábor Csárdi wrote: Matthew, 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. Best, Gabor On Sat, Jan 9, 2010 at 12:47 AM, Matthew Walker <address@hidden> wrote: Hi, 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: library(igraph) 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! Thanks, Matthew [1] http://lists.gnu.org/archive/html/igraph-help/2007-04/msg00025.html _______________________________________________ igraph-help mailing list address@hidden http://lists.nongnu.org/mailman/listinfo/igraph-help _______________________________________________ igraph-help mailing list address@hidden http://lists.nongnu.org/mailman/listinfo/igraph-help |
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