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 <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 >> > [[alternative HTML version deleted]] _______________________________________________ R-SIG-Mac mailing list R-SIG-Mac@r-project.org https://stat.ethz.ch/mailman/listinfo/r-sig-mac
