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
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