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


From: Tamás Nepusz
Subject: Re: [igraph] build or R version fails in R 3.0.0
Date: Wed, 6 Nov 2013 20:47:18 +0100

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




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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