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

From: Bob Pap
Subject: Re: [igraph] build or R version fails in R 3.0.0
Date: Sat, 6 Apr 2013 23:07:19 +0200

Hi Gábor,

I do not seem to have a problem with libxml (the compilation before worked fine with only 64 bit, and the error is the same not using the --no-multiarch flag).  I rather think form the message that igraph cannot find the location of libxml

ls -l /usr/lib/libxml*
-rwxr-xr-x  1 root  wheel  2390032  3 Oct  2012 /usr/lib/libxml2.2.dylib
lrwxr-xr-x  1 root  wheel       15  3 Oct  2012 /usr/lib/libxml2.dylib -> libxml2.2.dylib

I recall that there were some issues reported in R help with some libraries getting installed (referenced?) in the wrong places in version 3.0.0.  I think this is the case:@rpath/libxml2.2.dylib does not seem to be found (what is @rpath?)

Sorry to bother you, but my knowledge of compilation is VERY limited and use version 0.7 since some of the functionality is not available in the official release.

KInd regards,

On 6 April 2013 16:12, Gábor Csárdi <address@hidden> wrote:
Hi Bob,

R CMD INSTALL igraph_nightly_0.6.5-3106-20130304.tar.gz

works fine for me on OS X 10.6.8. From R 3.0 R itself and all packages are 64 bit only, so you don't need the --no-multiarch flag. But you do need some 64 bit system libraries, like libxml2.2. 

So I guess that the problem is that libxml2.2 is 32-bit only on your system.


On Sat, Apr 6, 2013 at 8:32 AM, Bob Pap <address@hidden> wrote:
Dear Tamás,

Build fails in the new R (3.0.0).  Any suggestions?


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’

Bob Pap

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