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

[George Dietz]

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