Simon and Duncan, I had not had time to dig deeper into this issue but recently made the transition to “Big Sur”. With that and "$ sudo rm -rf /Library/Developer/CommandLineTools” followed by "$ xcode-select --install” the compilation is successful now. I have no idea why libxml2 should not where it was supposed to be? Thanks for your help!
Kemal > On Feb 15, 2021, at 11:11 PM, Simon Urbanek <simon.urba...@r-project.org> > wrote: > > Kemal, > > it looks like you're completely missing the libxml2 includes on that system. > XML prefers xml2-config over pkg-config so it will by default pick the system > version of xml2, but you don't have the includes for that. > > According to your setup, they are supposed to be in > /Library/Developer/CommandLineTools/SDKs/MacOSX.sdk/usr/include/libxml > but my guess is they are not. > > Check the usual culprits > sudo xcode-select --install > and if in doubt reset > sudo xcode-select --reset > > If that doesn't help, you can set LIBXML_INCDIR (without the libxml part) and > LIBXML_LIBDIR yourself if you know where they are. > You also have miniconda and /usr/local so if you want to use any of that, > you'd the teh two variables above. Alternatively, you can set > --with-xml-config to point to your non-system xml2-config if it points to > the right includes/libraries. > > Good luck, > Simon > > > >> On Feb 16, 2021, at 4:20 PM, Kemal Akat <kma460...@gmail.com> wrote: >> >> Hi Duncan and Simon, >> >> Thanks for getting back to me. >> >> The R version I use(d) is >> >> R Under development (unstable) (2021-01-15 r79833) >> >> This was installed via the installer package downloaded from >> https://mac.r-project.org. It was not compiled from source. That was the >> case on all Macs. >> >> Please note that the partially log at the bottom of my original message is >> from a successful compilation on a Mac where ‘install.packages(“XML”) works. >> It includes references to the CommandLineTools/SDK but that was completely >> without my doing. I tried it explicitly in various forms, though, when I >> thought this is the right way. Thanks for clarifying it is not. >> >> Now, on the Mac where I still have trouble, the output from >> ‘install.packages(“XML”) is (rather brief): >> >>> install.packages("XML") >> Warning: unable to access index for repository >> https://mac.R-project.org/bin/macosx/contrib/4.1: >> cannot open URL 'https://mac.R-project.org/bin/macosx/contrib/4.1/PACKAGES' >> Package which is only available in source form, and may need compilation of >> C/C++/Fortran: ‘XML’ >> Do you want to attempt to install these from sources? (Yes/no/cancel) Yes >> installing the source package ‘XML’ >> >> trying URL 'https://mac.R-project.org/src/contrib/XML_3.99-0.5.tar.gz' >> Content type 'application/x-gzip' length 968563 bytes (945 KB) >> ================================================== >> downloaded 945 KB >> >> * installing *source* package ‘XML’ ... >> ** package ‘XML’ successfully unpacked and MD5 sums checked >> ** using staged installation >> checking for gcc... gcc >> checking whether the C compiler works... yes >> checking for C compiler default output file name... a.out >> checking for suffix of executables... >> checking whether we are cross compiling... no >> 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... /usr/local/bin/pkg-config >> checking for xml2-config... /usr/bin/xml2-config >> USE_XML2 = yes >> SED_EXTENDED_ARG: -E >> Minor 9, Patch 4 for 2.9.4 >> Located parser file >> -I/Library/Developer/CommandLineTools/SDKs/MacOSX.sdk/usr/include/parser.h >> Checking for 1.8: >> -I/Library/Developer/CommandLineTools/SDKs/MacOSX.sdk/usr/include >> 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/4.1/Resources/library/XML’ >> * restoring previous >> ‘/Library/Frameworks/R.framework/Versions/4.1/Resources/library/XML’ >> >> The downloaded source packages are in >> >> ‘/private/var/folders/j8/1gn6jwcx4bv8td2h83ghk1hh0000gp/T/RtmpXuYoas/downloaded_packages’ >> Warning message: >> In install.packages("XML") : >> installation of package ‘XML’ had non-zero exit status >>> >> >> Best, >> Kemal >> >> >>> On Feb 15, 2021, at 5:42 PM, Simon Urbanek <simon.urba...@r-project.org> >>> wrote: >>> >>> Kemal, >>> >>> what Duncan said, since what you provided does not include any of the >>> information needed. >>> >>> In addition, you should not include SDK paths directly - SDK is used by the >>> dev tools and does *not* include the actual libraries. So when you say >>> /foo/bar it is actually searched inside the SDK the compiler is using. If >>> you happen to use compilers that don't use SDKs (non-Apple) then you can >>> use -isysroot to specify the SDK root (hopefully not your case as that is a >>> whole can of worms). In addition, the issue may come from your version of R >>> as well so the exact information about that is also need (how you compiled >>> it, which flags etc.). >>> >>> Cheers, >>> Simon >>> >>> >>>> On Feb 16, 2021, at 4:26 AM, Duncan Temple Lang via R-SIG-Mac >>>> <r-sig-mac@r-project.org> wrote: >>>> >>>> Hi Kemal >>>> Can you please send the output from the entire installation attempt, and >>>> also the config.log file. >>>> >>>> Thanks >>>> Duncan >>>> >>>> >>>> On Mon, Feb 15, 2021 at 5:14 AM Kemal Akat <kma460...@gmail.com> wrote: >>>> >>>>> Hello all, >>>>> >>>>> I have to compile the XML package from source for R 4.1 (development >>>>> version) on a Mac with OS version 10.15.7. It works well on all machines >>>>> that do not come with any significant ballast on developer tools. One >>>>> machine, however, that I have used for some time returns a mismatch of >>>>> header files and library. I looked into possible offenders and purged what >>>>> I could (e.g. deleted Homebrew although the other machines have Homebrew >>>>> and Miniconda installed as well) but to no avail. >>>>> >>>>> install.packages(“XML”) fails and install.packages("XML", >>>>> configure.args=c("LIBXML_INCDIR=/Library/Developer/CommandLineTools/SDKs/MacOSX.sdk/usr/include/libxml2", >>>>> "LIBXML_LIBDIR=/Library/Developer/CommandLineTools/SDKs/MacOSX.sdk/usr/lib”)) >>>>> also fails. >>>>> >>>>> There are obviously differences I cannot track down so far but I am >>>>> running out of ideas. Both machines have MacOSX10.14.sdk and >>>>> MacOSX10.15.sdk installed with MacOSX.sdk linking to MacOSX10.15.sdk. >>>>> >>>>> Here is part of the log of a successful compilation, and I was hoping >>>>> someone could point me towards a solution. >>>>> >>>>> libxml include directory: >>>>> -I/Library/Developer/CommandLineTools/SDKs/MacOSX.sdk/usr/include >>>>> libxml library directory: >>>>> -L/Library/Developer/CommandLineTools/SDKs/MacOSX.sdk/usr/lib -lxml2 -lz >>>>> -lpthread -licucore -lm -lz -lxml2 >>>>> libxml 2: -DLIBXML2=1 >>>>> >>>>> Compilation flags: -DLIBXML >>>>> -I/Library/Developer/CommandLineTools/SDKs/MacOSX.sdk/usr/include >>>>> -DUSE_EXTERNAL_SUBSET=1 -DROOT_HAS_DTD_NODE=1 -DDUMP_WITH_ENCODING=1 >>>>> -DUSE_XML_VERSION_H=1 -DXML_ELEMENT_ETYPE=1 -DXML_ATTRIBUTE_ATYPE=1 >>>>> -DNO_XML_HASH_SCANNER_RETURN=1 -DLIBXML_NAMESPACE_HAS_CONTEXT=1 >>>>> -DHAVE_R_CETYPE_T=1 -DHAVE_XML_WITH_ZLIB=1 -DHAVE_XML_HAS_FEATURE=1 >>>>> -DUSE_R=1 -D_R_=1 -DHAVE_VALIDITY=1 -DXML_REF_COUNT_NODES=1 >>>>> Link flags: >>>>> -L/Library/Developer/CommandLineTools/SDKs/MacOSX.sdk/usr/lib -lxml2 -lz >>>>> -lpthread -licucore -lm -lz -lxml2 >>>>> >>>>> >>>>> Thanks, >>>>> Kemal >>>>> _______________________________________________ >>>>> R-SIG-Mac mailing list >>>>> R-SIG-Mac@r-project.org >>>>> https://stat.ethz.ch/mailman/listinfo/r-sig-mac >>>>> >>>> >>>> >>>> -- >>>> =============================== >>>> Duncan Temple Lang >>>> Associate Dean for Graduate Programs >>>> Professor, Department of Statistics >>>> UC Davis >>>> >>>> [[alternative HTML version deleted]] >>>> >>>> _______________________________________________ >>>> R-SIG-Mac mailing list >>>> R-SIG-Mac@r-project.org >>>> https://stat.ethz.ch/mailman/listinfo/r-sig-mac >>>> >>> >> > _______________________________________________ R-SIG-Mac mailing list R-SIG-Mac@r-project.org https://stat.ethz.ch/mailman/listinfo/r-sig-mac
