Re: [igraph] GraphML in R

[Matthew Walker]

Some extra information: maybe this is useful?  This is the output of 
running ./bootstrap.sh; there appear to be some warnings that might not 
be acceptable:

$ ./bootstrap.sh + aclocal
+ /gel/usr/mawal32/system/bin//libtoolize --force --copy
libtoolize: putting auxiliary files in `.'.
libtoolize: copying file `./ltmain.sh'
libtoolize: Consider adding `AC_CONFIG_MACRO_DIR([m4])' to configure.in and
libtoolize: rerunning libtoolize, to keep the correct libtool macros 
in-tree.
libtoolize: Consider adding `-I m4' to ACLOCAL_AMFLAGS in Makefile.am.
+ autoheader
+ automake --add-missing --copy
doc/Makefile.am:17: patsubst %,$(top_srcdir: non-POSIX variable name
doc/Makefile.am:17: (probably a GNU make extension)
doc/book/Makefile.am:9: patsubst %,$(top_srcdir: non-POSIX variable name
doc/book/Makefile.am:9: (probably a GNU make extension)
interfaces/R/Makefile.am:4: wildcard igraph/R/*.R: non-POSIX variable name
interfaces/R/Makefile.am:4: (probably a GNU make extension)
interfaces/R/Makefile.am:4: wildcard igraph/man/*.Rd: non-POSIX variable 
name
interfaces/R/Makefile.am:4: (probably a GNU make extension)
interfaces/R/Makefile.am:51: wildcard $(top_srcdir: non-POSIX variable name
interfaces/R/Makefile.am:51: (probably a GNU make extension)
interfaces/R/Makefile.am:52: wildcard $(top_srcdir: non-POSIX variable name
interfaces/R/Makefile.am:52: (probably a GNU make extension)
interfaces/R/Makefile.am:53: wildcard $(top_srcdir: non-POSIX variable name
interfaces/R/Makefile.am:53: (probably a GNU make extension)
interfaces/R/Makefile.am:61: wildcard $(top_srcdir: non-POSIX variable name
interfaces/R/Makefile.am:61: (probably a GNU make extension)
interfaces/R/Makefile.am:63: wildcard $(top_srcdir: non-POSIX variable name
interfaces/R/Makefile.am:63: (probably a GNU make extension)
interfaces/R/Makefile.am:65: wildcard $(top_srcdir: non-POSIX variable name
interfaces/R/Makefile.am:65: (probably a GNU make extension)
interfaces/R/Makefile.am:67: wildcard $(top_srcdir: non-POSIX variable name
interfaces/R/Makefile.am:67: (probably a GNU make extension)
interfaces/R/Makefile.am:69: patsubst $(top_srcdir: non-POSIX variable name
interfaces/R/Makefile.am:69: (probably a GNU make extension)
interfaces/R/Makefile.am:75: `%'-style pattern rules are a GNU make 
extension
interfaces/R/Makefile.am:77: `%'-style pattern rules are a GNU make 
extension
interfaces/R/Makefile.am:79: `%'-style pattern rules are a GNU make 
extension
interfaces/R/Makefile.am:81: `%'-style pattern rules are a GNU make 
extension
interfaces/R/Makefile.am:83: `%'-style pattern rules are a GNU make 
extension
interfaces/R/Makefile.am:85: `%'-style pattern rules are a GNU make 
extension
interfaces/R/Makefile.am:88: `%'-style pattern rules are a GNU make 
extension
interfaces/R/Makefile.am:90: `%'-style pattern rules are a GNU make 
extension
interfaces/R/Makefile.am:92: `%'-style pattern rules are a GNU make 
extension
interfaces/R/Makefile.am:94: `%'-style pattern rules are a GNU make 
extension
interfaces/shell/Makefile.am:19: compiling `interface.c' with per-target 
flags requires `AM_PROG_CC_C_O' in `configure.in'
+ autoconf
+ cd interfaces/R
+ autoconf
+ autoheader
+ cd -
/a/chicago/gel/chicago/usr/mawal32/SVN/phase2/igraph/0.5-main
+ cd interfaces/java
+ autoconf
configure.in:8: warning: AC_CACHE_VAL(igraph_java_works, ...): 
suspicious cache-id, must contain _cv_ to be cached
../../lib/autoconf/general.m4:1998: AC_CACHE_VAL is expanded from...
../../lib/autoconf/general.m4:2019: AC_CACHE_CHECK is expanded from...
config/java.m4:3: AC_PROG_JAVA is expanded from...
configure.in:8: the top level
configure.in:8: warning: AC_CACHE_VAL(igraph_java_home, ...): suspicious 
cache-id, must contain _cv_ to be cached
configure.in:8: warning: AC_CACHE_VAL(igraph_jni_works, ...): suspicious 
cache-id, must contain _cv_ to be cached
+ cd -
/a/chicago/gel/chicago/usr/mawal32/SVN/phase2/igraph/0.5-main



Matthew Walker 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
>
>