Hi list,
I have encountered the "Cannot find xml2-config" problem too during XML package
installation on my 64-bit Redhat (v. 6.4) linux machine. After looking through
the old posts I checked all the necessary libraries and they all seem to be
properly installed (see below). I don't understand why R can't see the
xml2-confg during the installation process. Help, please!
Many thanks!
Tao
==================================================
[root ~]# yum install libxml2
Setting up Install Process
Package matching libxml2-2.7.6-8.el6_3.3.x86_64 already installed. Checking for
update.
Nothing to do
[root ~]# yum install libxml2-devel
Setting up Install Process
Package matching libxml2-devel-2.7.6-8.el6_3.3.x86_64 already installed.
Checking for update.
Nothing to do
[root ~]# xml2-config --version
2.7.6
[root ~]# curl-config --version
libcurl 7.19.7
============ R session ======================
> install.packages("XML")
Installing package into \u2018/usr/lib64/R/library\u2019
(as \u2018lib\u2019 is unspecified)
trying URL 'http://cran.stat.ucla.edu/src/contrib/XML_3.98-1.1.tar.gz'
Content type 'application/x-tar' length 1582216 bytes (1.5 Mb)
opened URL
==================================================
downloaded 1.5 Mb
* installing *source* package \u2018XML\u2019 ...
** package \u2018XML\u2019 successfully unpacked and MD5 sums checked
checking for gcc... gcc
checking for C compiler default output file name... rm: cannot remove
`a.out.dSYM': Is a directory
a.out
checking whether the C compiler works... yes
checking whether we are cross compiling... no
checking for suffix of executables...
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... /bin/sed
checking for pkg-config... /usr/bin/pkg-config
checking for xml2-config... no
Cannot find xml2-config
ERROR: configuration failed for package \u2018XML\u2019
* removing \u2018/usr/lib64/R/library/XML\u2019
The downloaded source packages are in
\u2018/tmp/RtmpwnAIFH/downloaded_packages\u2019
Updating HTML index of packages in '.Library'
Making 'packages.html' ... done
Warning message:
In install.packages("XML") :
installation of package \u2018XML\u2019 had non-zero exit status
> sessionInfo()
R version 3.0.1 (2013-05-16)
Platform: x86_64-redhat-linux-gnu (64-bit)
locale:
[1] LC_CTYPE=en_US.UTF-8 LC_NUMERIC=C
[3] LC_TIME=en_US.UTF-8 LC_COLLATE=en_US.UTF-8
[5] LC_MONETARY=en_US.UTF-8 LC_MESSAGES=en_US.UTF-8
[7] LC_PAPER=C LC_NAME=C
[9] LC_ADDRESS=C LC_TELEPHONE=C
[11] LC_MEASUREMENT=en_US.UTF-8 LC_IDENTIFICATION=C
attached base packages:
[1] stats graphics grDevices utils datasets methods base
other attached packages:
[1] BiocInstaller_1.10.3
loaded via a namespace (and not attached):
[1] tcltk_3.0.1 tools_3.0.1
>
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