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 <[email protected]> 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 <[email protected]> > 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 > > > > _______________________________________________ > igraph-help mailing list > [email protected] > https://lists.nongnu.org/mailman/listinfo/igraph-help > > > _______________________________________________ > igraph-help mailing list > [email protected] > https://lists.nongnu.org/mailman/listinfo/igraph-help > > > > _______________________________________________ > igraph-help mailing list > [email protected] > https://lists.nongnu.org/mailman/listinfo/igraph-help > _______________________________________________ igraph-help mailing list [email protected] https://lists.nongnu.org/mailman/listinfo/igraph-help
