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
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