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
