I am having a similiar problem but on Mavericks. Igraph fails in the same
place but no mention of libxml. I am using the macports version of R. Here
is the output:
spectral_properties.o spmatrix.o st-cuts.o statusbar.o
structural_properties.o structure_generators.o sugiyama.o topology.o
type_indexededgelist.o types.o unit_limiter.o vector.o vector_ptr.o
version.o visitors.o walktrap.o walktrap_communities.o walktrap_graph.o
walktrap_heap.o zeroin.o zeta.o -L/opt/local/lib -lxml2 -lz -lpthread
-liconv -lm -L/opt/local/lib/gcc48/gcc/x86_64-apple-darwin13/4.8.2
-L/opt/local/lib/gcc48 -lgfortran -lquadmath -lm
-L/opt/local/Library/Frameworks/R.framework/Resources/lib -lRlapack
-L/opt/local/Library/Frameworks/R.framework/Resources/lib -lRblas
-L/opt/local/lib/gcc48/gcc/x86_64-apple-darwin13/4.8.2
-L/opt/local/lib/gcc48 -lgfortran -lquadmath -lm
-F/opt/local/Library/Frameworks/R.framework/.. -framework R -Wl,-framework
-Wl,CoreFoundation
installing to
/opt/local/Library/Frameworks/R.framework/Versions/3.0/Resources/library/igraph/libs
** R
** demo
** inst
** preparing package for lazy loading
** help
*** installing help indices
** building package indices
** testing if installed package can be loaded
Error : .onLoad failed in loadNamespace() for 'igraph', details:
call: dyn.load(file, DLLpath = DLLpath, ...)
error: unable to load shared object
'/opt/local/Library/Frameworks/R.framework/Versions/3.0/Resources/library/igraph/libs/igraph.so':
dlopen(/opt/local/Library/Frameworks/R.framework/Versions/3.0/Resources/library/igraph/libs/igraph.so,
10): Symbol not found: _colamd_printf
Referenced from:
/opt/local/Library/Frameworks/R.framework/Versions/3.0/Resources/library/igraph/libs/igraph.so
Expected in: flat namespace
in
/opt/local/Library/Frameworks/R.framework/Versions/3.0/Resources/library/igraph/libs/igraph.so
Error: loading failed
Execution halted
ERROR: loading failed
* removing
‘/opt/local/Library/Frameworks/R.framework/Versions/3.0/Resources/library/igraph’
* restoring previous
‘/opt/local/Library/Frameworks/R.framework/Versions/3.0/Resources/library/igraph’
The downloaded source packages are in
‘/private/tmp/RtmpVsVUxE/downloaded_packages’
Warning message:
In install.packages("igraph") :
installation of package ‘igraph’ had non-zero exit status
>
> Sys.info()
sysname
"Darwin"
release
"13.0.0"
version
"Darwin Kernel Version 13.0.0: Thu Sep 19 22:22:27 PDT 2013;
root:xnu-2422.1.72~6/RELEASE_X86_64"
nodename
"le-iMac-de-travail.local"
machine
"x86_64"
On Saturday, April 6, 2013 8:32:36 AM UTC-4, Bob Pap wrote:
>
> Dear Tamás,
>
> Build fails in the new R (3.0.0). Any suggestions?
>
> command:
>
> R CMD INSTALL --no-multiarch
> ~/Downloads/igraph_nightly_0.7-3137-20130302.tar.gz
>
> compilation works, but test fails
>
> installing to
> /Library/Frameworks/R.framework/Versions/3.0/Resources/library/igraph/libs
> ** R
> ** demo
> ** inst
> ** preparing package for lazy loading
> ** help
> *** installing help indices
> ** building package indices
> ** testing if installed package can be loaded
> Error : .onLoad failed in loadNamespace() for 'igraph', details:
> call: dyn.load(file, DLLpath = DLLpath, ...)
> error: unable to load shared object
> '/Library/Frameworks/R.framework/Versions/3.0/Resources/library/igraph/libs/igraph.so':
>
> dlopen(/Library/Frameworks/R.framework/Versions/3.0/Resources/library/igraph/libs/igraph.so,
>
> 10): Library not loaded: @rpath/libxml2.2.dylib
> Referenced from:
> /Library/Frameworks/R.framework/Versions/3.0/Resources/library/igraph/libs/igraph.so
> Reason: image not found
> Error: loading failed
> Execution halted
> ERROR: loading failed
> * removing
> ‘/Library/Frameworks/R.framework/Versions/3.0/Resources/library/igraph’
> * restoring previous
> ‘/Library/Frameworks/R.framework/Versions/3.0/Resources/library/igraph’
>
>
> --
> Kindly,
> Bob Pap
>
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