Dear all, In case this is relevant for others, please note that this is an incompatibility between the libxml library installed by Python EPD (which many of you may be using) and the one supplied by Apple. It is simply solved by removing form the PATH the EPD folder before compiling. Curiously, the problem only surfaced with the compilation of R 3.0.0, and may be related to the dependence on 64bit (previously it was both 32 and 64 bit). Many thanks to Gábor for his useful suggestions.
Kind regards, Bob On 7 April 2013 20:49, Bob Pap <[email protected]> wrote: > Many thanks, dear Gábor. I will follow your advice (I certainly did not > instal it manually, but maybe another application did) and investigate > versions. > > Kind regards, > Bob > > > On 7 April 2013 13:20, Gábor Csárdi <[email protected]> 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 <[email protected]> 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 <[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 >>> >>> _______________________________________________ >>> 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 > -- Kindly, Bob Pap
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