Problem installing libxml2 under Homebrew

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Problem installing libxml2 under Homebrew

Peter Meilstrup
i am trying to install xml2 from CRAN, and it is throwing an error
that it cannot find the libxml2 library configuration.

The thing is that pkg-config seems to be set up correctly:

$ echo $PKG_CONFIG_PATH
:/usr/local/opt/libxml2/lib/pkgconfig:/usr/local/opt/libxml2/lib/pkgconfig

$ pkg-config --cflags --libs libxml-2.0
-I/usr/local/Cellar/libxml2/2.9.7/include/libxml2
-L/usr/local/Cellar/libxml2/2.9.7/lib -lx

Output of install.packages:

> install.packages("xml2")
--- Please select a CRAN mirror for use in this session ---
trying URL 'https://cloud.r-project.org/src/contrib/xml2_1.2.0.tar.gz'
Content type 'application/x-gzip' length 251614 bytes (245 KB)
==================================================
downloaded 245 KB

* installing *source* package ‘xml2’ ...
** package ‘xml2’ successfully unpacked and MD5 sums checked
Found pkg-config cflags and libs!
Using PKG_CFLAGS=-I/usr/include/libxml2
Using PKG_LIBS=-L/usr/lib -lxml2 -lz -lpthread -licucore -lm
------------------------- ANTICONF ERROR ---------------------------
Configuration failed because libxml-2.0 was not found. Try installing:
 * deb: libxml2-dev (Debian, Ubuntu, etc)
 * rpm: libxml2-devel (Fedora, CentOS, RHEL)
 * csw: libxml2_dev (Solaris)
If libxml-2.0 is already installed, check that 'pkg-config' is in your
PATH and PKG_CONFIG_PATH contains a libxml-2.0.pc file. If pkg-config
is unavailable you can set INCLUDE_DIR and LIB_DIR manually via:
R CMD INSTALL --configure-vars='INCLUDE_DIR=... LIB_DIR=...'
--------------------------------------------------------------------
ERROR: configuration failed for package ‘xml2’

Homebrew package info:

dekkera:pkgconfig peter$ brew info libxml2 R
libxml2: stable 2.9.7 (bottled), HEAD [keg-only]
GNOME XML library
http://xmlsoft.org
/usr/local/Cellar/libxml2/2.9.7 (281 files, 10.4MB)
  Poured from bottle on 2018-02-16 at 22:42:54
From: https://github.com/Homebrew/homebrew-core/blob/master/Formula/libxml2.rb
==> Options
--HEAD
    Install HEAD version
==> Caveats
This formula is keg-only, which means it was not symlinked into /usr/local,
because macOS already provides this software and installing another version in
parallel can cause all kinds of trouble.

If you need to have this software first in your PATH run:
  echo 'export PATH="/usr/local/opt/libxml2/bin:$PATH"' >> ~/.bash_profile

For compilers to find this software you may need to set:
    LDFLAGS:  -L/usr/local/opt/libxml2/lib
    CPPFLAGS: -I/usr/local/opt/libxml2/include
For pkg-config to find this software you may need to set:
    PKG_CONFIG_PATH: /usr/local/opt/libxml2/lib/pkgconfig

If you need Python to find bindings for this keg-only formula, run:
  echo /usr/local/opt/libxml2/lib/python2.7/site-packages >>
/usr/local/lib/python2.7/site-packages/libxml2.pth
  mkdir -p /Users/peter/Library/Python/2.7/lib/python/site-packages
  echo 'import site;
site.addsitedir("/usr/local/lib/python2.7/site-packages")' >>
/Users/peter/Library/Python/2.7/lib/python/site-packages/homebrew.pth

R: stable 3.4.3 (bottled)
Software environment for statistical computing
https://www.r-project.org/
/usr/local/Cellar/R/3.4.0_1 (2,246 files, 59.1MB)
  Poured from bottle on 2017-05-20 at 17:10:29
/usr/local/Cellar/R/3.4.1_2 (2,114 files, 55.3MB)
  Poured from bottle on 2017-09-19 at 03:23:33
/usr/local/Cellar/R/3.4.2 (2,111 files, 55.1MB)
  Poured from bottle on 2017-11-13 at 22:23:36
/usr/local/Cellar/R/3.4.3 (2,110 files, 55.1MB)
  Poured from bottle on 2017-12-02 at 23:20:16
/usr/local/Cellar/R/3.4.3_1 (3,773 files, 115.4MB)
  Built from source on 2018-02-08 at 22:01:49 with: --with-x11
--with-cairo --with-java
From: https://github.com/Homebrew/homebrew-core/blob/master/Formula/r.rb
==> Dependencies
Build: pkg-config ✔
Required: gcc ✔, gettext ✔, jpeg ✔, libpng ✔, pcre ✔, readline ✔, xz ✔
Optional: openblas ✔
==> Requirements
Optional: java ✔
==> Options
--with-java
    Build with java support
--with-openblas
    Build with openblas support

______________________________________________
[hidden email] mailing list -- To UNSUBSCRIBE and more, see
https://stat.ethz.ch/mailman/listinfo/r-help
PLEASE do read the posting guide http://www.R-project.org/posting-guide.html
and provide commented, minimal, self-contained, reproducible code.
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Re: Problem installing libxml2 under Homebrew

hadley wickham
Is there a reason that you can't use the binary provided by CRAN?
That's the easiest way to get xml2.
Hadley

On Sat, Feb 17, 2018 at 1:53 AM, Peter Meilstrup
<[hidden email]> wrote:

> i am trying to install xml2 from CRAN, and it is throwing an error
> that it cannot find the libxml2 library configuration.
>
> The thing is that pkg-config seems to be set up correctly:
>
> $ echo $PKG_CONFIG_PATH
> :/usr/local/opt/libxml2/lib/pkgconfig:/usr/local/opt/libxml2/lib/pkgconfig
>
> $ pkg-config --cflags --libs libxml-2.0
> -I/usr/local/Cellar/libxml2/2.9.7/include/libxml2
> -L/usr/local/Cellar/libxml2/2.9.7/lib -lx
>
> Output of install.packages:
>
>> install.packages("xml2")
> --- Please select a CRAN mirror for use in this session ---
> trying URL 'https://cloud.r-project.org/src/contrib/xml2_1.2.0.tar.gz'
> Content type 'application/x-gzip' length 251614 bytes (245 KB)
> ==================================================
> downloaded 245 KB
>
> * installing *source* package ‘xml2’ ...
> ** package ‘xml2’ successfully unpacked and MD5 sums checked
> Found pkg-config cflags and libs!
> Using PKG_CFLAGS=-I/usr/include/libxml2
> Using PKG_LIBS=-L/usr/lib -lxml2 -lz -lpthread -licucore -lm
> ------------------------- ANTICONF ERROR ---------------------------
> Configuration failed because libxml-2.0 was not found. Try installing:
>  * deb: libxml2-dev (Debian, Ubuntu, etc)
>  * rpm: libxml2-devel (Fedora, CentOS, RHEL)
>  * csw: libxml2_dev (Solaris)
> If libxml-2.0 is already installed, check that 'pkg-config' is in your
> PATH and PKG_CONFIG_PATH contains a libxml-2.0.pc file. If pkg-config
> is unavailable you can set INCLUDE_DIR and LIB_DIR manually via:
> R CMD INSTALL --configure-vars='INCLUDE_DIR=... LIB_DIR=...'
> --------------------------------------------------------------------
> ERROR: configuration failed for package ‘xml2’
>
> Homebrew package info:
>
> dekkera:pkgconfig peter$ brew info libxml2 R
> libxml2: stable 2.9.7 (bottled), HEAD [keg-only]
> GNOME XML library
> http://xmlsoft.org
> /usr/local/Cellar/libxml2/2.9.7 (281 files, 10.4MB)
>   Poured from bottle on 2018-02-16 at 22:42:54
> From: https://github.com/Homebrew/homebrew-core/blob/master/Formula/libxml2.rb
> ==> Options
> --HEAD
>     Install HEAD version
> ==> Caveats
> This formula is keg-only, which means it was not symlinked into /usr/local,
> because macOS already provides this software and installing another version in
> parallel can cause all kinds of trouble.
>
> If you need to have this software first in your PATH run:
>   echo 'export PATH="/usr/local/opt/libxml2/bin:$PATH"' >> ~/.bash_profile
>
> For compilers to find this software you may need to set:
>     LDFLAGS:  -L/usr/local/opt/libxml2/lib
>     CPPFLAGS: -I/usr/local/opt/libxml2/include
> For pkg-config to find this software you may need to set:
>     PKG_CONFIG_PATH: /usr/local/opt/libxml2/lib/pkgconfig
>
> If you need Python to find bindings for this keg-only formula, run:
>   echo /usr/local/opt/libxml2/lib/python2.7/site-packages >>
> /usr/local/lib/python2.7/site-packages/libxml2.pth
>   mkdir -p /Users/peter/Library/Python/2.7/lib/python/site-packages
>   echo 'import site;
> site.addsitedir("/usr/local/lib/python2.7/site-packages")' >>
> /Users/peter/Library/Python/2.7/lib/python/site-packages/homebrew.pth
>
> R: stable 3.4.3 (bottled)
> Software environment for statistical computing
> https://www.r-project.org/
> /usr/local/Cellar/R/3.4.0_1 (2,246 files, 59.1MB)
>   Poured from bottle on 2017-05-20 at 17:10:29
> /usr/local/Cellar/R/3.4.1_2 (2,114 files, 55.3MB)
>   Poured from bottle on 2017-09-19 at 03:23:33
> /usr/local/Cellar/R/3.4.2 (2,111 files, 55.1MB)
>   Poured from bottle on 2017-11-13 at 22:23:36
> /usr/local/Cellar/R/3.4.3 (2,110 files, 55.1MB)
>   Poured from bottle on 2017-12-02 at 23:20:16
> /usr/local/Cellar/R/3.4.3_1 (3,773 files, 115.4MB)
>   Built from source on 2018-02-08 at 22:01:49 with: --with-x11
> --with-cairo --with-java
> From: https://github.com/Homebrew/homebrew-core/blob/master/Formula/r.rb
> ==> Dependencies
> Build: pkg-config ✔
> Required: gcc ✔, gettext ✔, jpeg ✔, libpng ✔, pcre ✔, readline ✔, xz ✔
> Optional: openblas ✔
> ==> Requirements
> Optional: java ✔
> ==> Options
> --with-java
>     Build with java support
> --with-openblas
>     Build with openblas support
>
> ______________________________________________
> [hidden email] mailing list -- To UNSUBSCRIBE and more, see
> https://stat.ethz.ch/mailman/listinfo/r-help
> PLEASE do read the posting guide http://www.R-project.org/posting-guide.html
> and provide commented, minimal, self-contained, reproducible code.



--
http://hadley.nz

______________________________________________
[hidden email] mailing list -- To UNSUBSCRIBE and more, see
https://stat.ethz.ch/mailman/listinfo/r-help
PLEASE do read the posting guide http://www.R-project.org/posting-guide.html
and provide commented, minimal, self-contained, reproducible code.
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Re: Problem installing libxml2 under Homebrew

Jeroen Ooms
In reply to this post by Peter Meilstrup
You probably have a malconfigured homebrew installation of R. On MacOS
it is recommended to use the CRAN version of R
https://cran.r-project.org/bin/macosx/. The homebrew version depends
on gcc compilers and does not support cran binary packages.

If you really want to use the homebrew R try ruling out the following problems:

 - Check for conflicting compilers in your path (gcc, ccache, clang4).
Unless you have good reasons not to, you should use the native xcode
compilers to build R packages.
 - Comment out custom compilers/flags that you may have in your
~/.R/Makevars file.

Use the following script to check why the configuration is failing:

  CPP=$(R CMD config CPP)
  CFLAGS=$(xml2-config --cflags)
  echo '#include <libxml/tree.h>' | $CPP $CFLAGS -E -xc - > /dev/null




On Sat, Feb 17, 2018 at 8:53 AM, Peter Meilstrup
<[hidden email]> wrote:

> i am trying to install xml2 from CRAN, and it is throwing an error
> that it cannot find the libxml2 library configuration.
>
> The thing is that pkg-config seems to be set up correctly:
>
> $ echo $PKG_CONFIG_PATH
> :/usr/local/opt/libxml2/lib/pkgconfig:/usr/local/opt/libxml2/lib/pkgconfig
>
> $ pkg-config --cflags --libs libxml-2.0
> -I/usr/local/Cellar/libxml2/2.9.7/include/libxml2
> -L/usr/local/Cellar/libxml2/2.9.7/lib -lx
>
> Output of install.packages:
>
>> install.packages("xml2")
> --- Please select a CRAN mirror for use in this session ---
> trying URL 'https://cloud.r-project.org/src/contrib/xml2_1.2.0.tar.gz'
> Content type 'application/x-gzip' length 251614 bytes (245 KB)
> ==================================================
> downloaded 245 KB
>
> * installing *source* package ‘xml2’ ...
> ** package ‘xml2’ successfully unpacked and MD5 sums checked
> Found pkg-config cflags and libs!
> Using PKG_CFLAGS=-I/usr/include/libxml2
> Using PKG_LIBS=-L/usr/lib -lxml2 -lz -lpthread -licucore -lm
> ------------------------- ANTICONF ERROR ---------------------------
> Configuration failed because libxml-2.0 was not found. Try installing:
>  * deb: libxml2-dev (Debian, Ubuntu, etc)
>  * rpm: libxml2-devel (Fedora, CentOS, RHEL)
>  * csw: libxml2_dev (Solaris)
> If libxml-2.0 is already installed, check that 'pkg-config' is in your
> PATH and PKG_CONFIG_PATH contains a libxml-2.0.pc file. If pkg-config
> is unavailable you can set INCLUDE_DIR and LIB_DIR manually via:
> R CMD INSTALL --configure-vars='INCLUDE_DIR=... LIB_DIR=...'
> --------------------------------------------------------------------
> ERROR: configuration failed for package ‘xml2’
>
> Homebrew package info:
>
> dekkera:pkgconfig peter$ brew info libxml2 R
> libxml2: stable 2.9.7 (bottled), HEAD [keg-only]
> GNOME XML library
> http://xmlsoft.org
> /usr/local/Cellar/libxml2/2.9.7 (281 files, 10.4MB)
>   Poured from bottle on 2018-02-16 at 22:42:54
> From: https://github.com/Homebrew/homebrew-core/blob/master/Formula/libxml2.rb
> ==> Options
> --HEAD
>     Install HEAD version
> ==> Caveats
> This formula is keg-only, which means it was not symlinked into /usr/local,
> because macOS already provides this software and installing another version in
> parallel can cause all kinds of trouble.
>
> If you need to have this software first in your PATH run:
>   echo 'export PATH="/usr/local/opt/libxml2/bin:$PATH"' >> ~/.bash_profile
>
> For compilers to find this software you may need to set:
>     LDFLAGS:  -L/usr/local/opt/libxml2/lib
>     CPPFLAGS: -I/usr/local/opt/libxml2/include
> For pkg-config to find this software you may need to set:
>     PKG_CONFIG_PATH: /usr/local/opt/libxml2/lib/pkgconfig
>
> If you need Python to find bindings for this keg-only formula, run:
>   echo /usr/local/opt/libxml2/lib/python2.7/site-packages >>
> /usr/local/lib/python2.7/site-packages/libxml2.pth
>   mkdir -p /Users/peter/Library/Python/2.7/lib/python/site-packages
>   echo 'import site;
> site.addsitedir("/usr/local/lib/python2.7/site-packages")' >>
> /Users/peter/Library/Python/2.7/lib/python/site-packages/homebrew.pth
>
> R: stable 3.4.3 (bottled)
> Software environment for statistical computing
> https://www.r-project.org/
> /usr/local/Cellar/R/3.4.0_1 (2,246 files, 59.1MB)
>   Poured from bottle on 2017-05-20 at 17:10:29
> /usr/local/Cellar/R/3.4.1_2 (2,114 files, 55.3MB)
>   Poured from bottle on 2017-09-19 at 03:23:33
> /usr/local/Cellar/R/3.4.2 (2,111 files, 55.1MB)
>   Poured from bottle on 2017-11-13 at 22:23:36
> /usr/local/Cellar/R/3.4.3 (2,110 files, 55.1MB)
>   Poured from bottle on 2017-12-02 at 23:20:16
> /usr/local/Cellar/R/3.4.3_1 (3,773 files, 115.4MB)
>   Built from source on 2018-02-08 at 22:01:49 with: --with-x11
> --with-cairo --with-java
> From: https://github.com/Homebrew/homebrew-core/blob/master/Formula/r.rb
> ==> Dependencies
> Build: pkg-config ✔
> Required: gcc ✔, gettext ✔, jpeg ✔, libpng ✔, pcre ✔, readline ✔, xz ✔
> Optional: openblas ✔
> ==> Requirements
> Optional: java ✔
> ==> Options
> --with-java
>     Build with java support
> --with-openblas
>     Build with openblas support
>
> ______________________________________________
> [hidden email] mailing list -- To UNSUBSCRIBE and more, see
> https://stat.ethz.ch/mailman/listinfo/r-help
> PLEASE do read the posting guide http://www.R-project.org/posting-guide.html
> and provide commented, minimal, self-contained, reproducible code.

______________________________________________
[hidden email] mailing list -- To UNSUBSCRIBE and more, see
https://stat.ethz.ch/mailman/listinfo/r-help
PLEASE do read the posting guide http://www.R-project.org/posting-guide.html
and provide commented, minimal, self-contained, reproducible code.