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

Thu Mar 18 03:04:43 CET 2021

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.urbanek using 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 <kma460414 using 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.urbanek using 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 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
>>>> 
>>>> 	[[alternative HTML version deleted]]
>>>> 
>>>> _______________________________________________
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>>>> 
>>> 
>> 
> 