[R-SIG-Mac] XML packages source compilation on macOS 10.15.7

[Simon Urbanek]

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 using 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 <kma460414 using 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 using 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
> 
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