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 <[email protected]> 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 <[email protected]> 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 <[email protected]> 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 <[email protected]> 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 >>>> >>>> >>> >>> >>> -- >>> Gabor Csardi <[email protected]> MTA KFKI RMKI >>> >>> _______________________________________________ >>> igraph-help mailing list >>> [email protected] >>> https://lists.nongnu.org/mailman/listinfo/igraph-help >>> >>> >> >> >> -- >> Kindly, >> Bob Pap >> >> _______________________________________________ >> igraph-help mailing list >> [email protected] >> https://lists.nongnu.org/mailman/listinfo/igraph-help >> >> > > > -- > Gabor Csardi <[email protected]> MTA KFKI RMKI > > _______________________________________________ > igraph-help mailing list > [email protected] > https://lists.nongnu.org/mailman/listinfo/igraph-help > > -- Kindly, Bob Pap
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