Skip to end of metadata
Go to start of metadata

You are viewing an old version of this page. View the current version.

Compare with Current View Page History

« Previous Version 2 Next »

Issue

When installing the R XML package either explicitly, or as part of a dependency to a parent package, XML package fails to install:

 Error Message
* installing *source* package ‘XML’ ...
** package ‘XML’ successfully unpacked and MD5 sums checked
** using staged installation
checking for gcc... /apps/u/spack/gcc/8.5.0/gcc/12.2.0-orvuxnl/bin/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 the compiler supports GNU C... yes
checking whether /apps/u/spack/gcc/8.5.0/gcc/12.2.0-orvuxnl/bin/gcc accepts -g... yes
checking for /apps/u/spack/gcc/8.5.0/gcc/12.2.0-orvuxnl/bin/gcc option to enable C11 features... none needed
checking how to run the C preprocessor... /apps/u/spack/gcc/8.5.0/gcc/12.2.0-orvuxnl/bin/gcc -E
checking for sed... /usr/bin/sed
checking for pkg-config... /usr/bin/pkg-config
User defined xml-config: /apps/u/spack/gcc/12.2.0/libxml2/2.10.1-yr4vwha/bin/xml2-config, XML Version: 2, XML2: yes
checking for stdio.h... yes
checking for stdlib.h... yes
checking for string.h... yes
checking for inttypes.h... yes
checking for stdint.h... yes
checking for strings.h... yes
checking for sys/stat.h... yes
checking for sys/types.h... yes
checking for unistd.h... yes
checking for libxml/parser.h... yes
Found the libxml parser.h in /apps/u/spack/gcc/12.2.0/libxml2/2.10.1-yr4vwha/include/libxml2//libxml/
Located parser file -I/apps/u/spack/gcc/12.2.0/libxml2/2.10.1-yr4vwha/include/libxml2//parser.h
checking for gzopen in -lz... yes
checking for xmlParseFile in -lxml2... no
checking for xmlParseFile in -lxml... no
configure: error: "libxml not found"
ERROR: configuration failed for package ‘XML’
* removing ‘/pfs/tc1/home/sthiongo/R/x86_64-pc-linux-gnu-library/4.2/XML’

Resolve:

# Load and start R:
> Sys.setenv(XML_CONFIG="/apps/u/spack/gcc/12.2.0/libxml2/2.10.1-yr4vwha/bin/xml2-config")
> install.packages('XML', configure.args=c('--with-libxml2=/apps/u/spack/gcc/12.2.0/libxml2/2.10.1-yr4vwha/bin/xml2-config LIBXML_LIBDIR=-L/apps/u/spack/gcc/12.2.0/libxml2/2.10.1-yr4vwha/lib/ LIBXML_INCDIR=/apps/u/spack/gcc/12.2.0/libxml2/2.10.1-yr4vwha/include/libxml2/'))

  • No labels