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

On 7 April 2013 13:20, Gábor Csárdi <address@hidden> wrote:

Hi Bob,

the XML package compiles and installs fine for me, just like igraph. So I think the problem might be what it described in XML's error message below:

"You are trying to use a version 2.* edition of libxml
but an incompatible library. The header files and library seem to be
mismatched. If you have specified LIBXML_INCDIR, make certain to also

specify an appropriate LIBXML_LIBDIR if the libxml2 library is not in the default
directories."

Maybe you installed another libxml2 version "by hand", in addition to the system provided one, and igraph and XML both find the new version's header and the old library or vice-versa.

G.

On Sun, Apr 7, 2013 at 4:38 AM, Bob Pap <address@hidden> wrote:

Hi Gabor,

Same error with R CMD INSTALL ~/Downloads/igraph_nightly_0.6.5-3106-20130304.tar.gz, and with R CMD INSTALL ~/Downloads/igraph_0.6.5-1.tar.gz.

For XML I noticed that the Mac Binary lags the package:

Package source: XML_3.96-1.1.tar.gz
MacOS X binary: XML_3.95-0.2.tgz

Windows binary: XML_3.96-1.1.zip

And compiling the latest one there is an error (below). I shall contact the author about this. Many thanks.

R CMD INSTALL ~/Downloads/XML_3.96-1.1.tar.gz
* installing to library ‘/Library/Frameworks/R.framework/Versions/3.0/Resources/library’
* installing *source* package ‘XML’ ...

** package ‘XML’ successfully unpacked and MD5 sums checked
checking for gcc... gcc
checking for C compiler default output file name... a.out
checking whether the C compiler works... yes

checking whether we are cross compiling... no
checking for suffix of executables...
checking for suffix of object files... o
checking whether we are using the GNU C compiler... yes

checking whether gcc accepts -g... yes
checking for gcc option to accept ISO C89... none needed
checking how to run the C preprocessor... gcc -E
checking for sed... /usr/bin/sed
checking for pkg-config... no
checking for xml2-config... /Library/Frameworks/EPD64.framework/Versions/Current/bin/xml2-config
USE_XML2 = yes
SED_EXTENDED_ARG: -E
Minor 7, Patch 8 for 2.7.8

Located parser file -I/Library/Frameworks/EPD64.framework/Versions/7.3/include/libxml2/parser.h
Checking for 1.8: -I/Library/Frameworks/EPD64.framework/Versions/7.3/include/libxml2
Using libxml2.*

checking for gzopen in -lz... yes
checking for xmlParseFile in -lxml2... yes
You are trying to use a version 2.* edition of libxml
but an incompatible library. The header files and library seem to be

mismatched. If you have specified LIBXML_INCDIR, make certain to also
specify an appropriate LIBXML_LIBDIR if the libxml2 library is not in the default
directories.
ERROR: configuration failed for package ‘XML’

* removing ‘/Library/Frameworks/R.framework/Versions/3.0/Resources/library/XML’
* restoring previous ‘/Library/Frameworks/R.framework/Versions/3.0/Resources/library/XML’

On 7 April 2013 04:33, Gábor Csárdi <address@hidden> wrote:

Honestly, I have no idea what this is and just vague idea about rpath, but two things you could try quickly are 1) installing the released version of igraph, the same way, to see what happens, and 2) installing the XML package the same way, because that uses libxml2 as well. Just to try to see where exactly the problem is.

Gabor

On Sat, Apr 6, 2013 at 5:07 PM, Bob Pap <address@hidden> wrote:

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,
Bob

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.

G.

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?

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
address@hidden
https://lists.nongnu.org/mailman/listinfo/igraph-help

--
Gabor Csardi <address@hidden>    MTA KFKI RMKI

_______________________________________________
igraph-help mailing list
address@hidden
https://lists.nongnu.org/mailman/listinfo/igraph-help

--
Kindly,
Bob Pap

_______________________________________________
igraph-help mailing list
address@hidden
https://lists.nongnu.org/mailman/listinfo/igraph-help

--
Gabor Csardi <address@hidden>    MTA KFKI RMKI

_______________________________________________
igraph-help mailing list
address@hidden
https://lists.nongnu.org/mailman/listinfo/igraph-help

--
Kindly,
Bob Pap

_______________________________________________
igraph-help mailing list
address@hidden
https://lists.nongnu.org/mailman/listinfo/igraph-help

--
Gabor Csardi <address@hidden>    MTA KFKI RMKI

_______________________________________________
igraph-help mailing list
address@hidden
https://lists.nongnu.org/mailman/listinfo/igraph-help

Kindly,

Bob Pap

From:	Bob Pap
Subject:	Re: [igraph] build or R version fails in R 3.0.0
Date:	Sun, 7 Apr 2013 20:49:20 +0200