Installation failure on macOS 10.14 #232
Description
I apologise if this is something stupid, but I really can't see what I'm doing wrong here. I have updated this machine to macOS Mojave, using Homebrew-installed R. I can't get xml2 to install, either with the system libxml2 or the one from Homebrew:
$ R CMD INSTALL xml2_1.2.0.tar.gz
* installing to library ‘/usr/local/lib/R/3.5/site-library’
* 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’
* removing ‘/usr/local/lib/R/3.5/site-library/xml2’
$ R CMD INSTALL --configure-vars='INCLUDE_DIR=/usr/local/opt/libxml2/include LIB_DIR=/usr/local/opt/libxml2/lib' xml2_1.2.0.tar.gz
* installing to library ‘/usr/local/lib/R/3.5/site-library’
* installing *source* package ‘xml2’ ...
** package ‘xml2’ successfully unpacked and MD5 sums checked
Found INCLUDE_DIR and/or LIB_DIR!
Using PKG_CFLAGS=-I/usr/local/opt/libxml2/include
Using PKG_LIBS=-L/usr/local/opt/libxml2/lib -lxml2
------------------------- 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’
* removing ‘/usr/local/lib/R/3.5/site-library/xml2’
Note that in both cases, pkg-config provides suitable flags, but the configuration rejects them. Any pointers would be appreciated. Session info is below (FWIW):
$ Rscript -e "devtools::session_info()"
Session info ------------------------------------------------------------------
setting value
version R version 3.5.1 (2018-07-02)
system x86_64, darwin18.0.0
ui unknown
language (EN)
collate en_GB.UTF-8
tz Europe/London
date 2018-09-28
Packages ----------------------------------------------------------------------
package * version date source
base * 3.5.1 2018-08-21 local
compiler 3.5.1 2018-08-21 local
datasets * 3.5.1 2018-08-21 local
devtools 1.13.6 2018-06-27 CRAN (R 3.5.1)
digest 0.6.17 2018-09-12 CRAN (R 3.5.1)
graphics * 3.5.1 2018-08-21 local
grDevices * 3.5.1 2018-08-21 local
memoise 1.1.0 2017-04-21 CRAN (R 3.5.1)
methods * 3.5.1 2018-08-21 local
stats * 3.5.1 2018-08-21 local
utils * 3.5.1 2018-08-21 local
withr 2.1.2 2018-03-15 CRAN (R 3.5.1)