Re: [igraph] build or R version fails in R 3.0.0

[Gábor Csárdi]

There is no GPLK in R, but GPLK is included in the igraph R package.
On the other hand as I see colamd_printf is a macro in GPLK, so
something goes wrong during the compilation, a GPLK header is not
included or I don't know what. That's why we would need to see the
whole output.

G.

On Wed, Nov 6, 2013 at 2:47 PM, Tamás Nepusz <address@hidden> wrote:
> Gabor: if that helps, colamd_printf comes from GLPK, so it could be the case
> that igraph is configured to use an external GLPK library (under the
> assumption that R will provide it) and in the end it turns out that the
> custom R version that igraph is loaded into was somehow compiled without
> GLPK support. Or something like that. I know this is totally vague, but
> that’s my best guess so far.
>
> --
> T.
>
> On Wednesday, 6 November 2013 at 18:54, Gábor Csárdi wrote:
>
> The full output would be helpful, I have no idea where the package is
> downloading form, what are the results of the configure checks, etc.
>
> G.
>
> On Wed, Nov 6, 2013 at 12:40 PM, George Dietz <address@hidden>
> wrote:
>
> 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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