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

Mon, 15 Feb 2021 19:46:06 -0800

Sorry, forgot the config.log. Also, I use Apple compilers (Xcode 12.3 at that time) and the GNU Fortran compiler 8.2 as recommended under “Mandatory tools” on https://cran.r-project.org. Now…I have a hunch here may be the root cause for my troubles as I used other compilers in the past (llvm via Homebrew) on that Mac, for instance to compile data.table with openMP support. While I deinstalled those compilers, I may have missed something else?

Attachment: config.log
Description: Binary data


On Feb 15, 2021, at 9:20 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:
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’

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
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--
===============================
Duncan Temple Lang
Associate Dean for Graduate Programs
Professor, Department of Statistics
UC Davis

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