Hi Duncan,
Thank you very much for your quick response!
It turns out I was typing the shell commands in another xterm which was ssh'ed
to another linux computer and I completely forgot about it. After finding that
out and checking with my own computer, the libxml2 is installed but
libxml2-devel is missing. Installation libxml2-devel solved the problem. My
mistake! Sorry about that.
Tao
----- Original Message -----
From: Duncan Temple Lang <dtemplel...@ucdavis.edu>
To: r-help@r-project.org
Cc:
Sent: Thursday, August 15, 2013 10:38 AM
Subject: Re: [R] XML package installation -- an old question
Hi Tao
In the same R session as you call install.packages(),
what does
system("which xml2-config", intern = TRUE)
return?
Basically, the error message from the configuration script for the
XML package is complaining that it cannot find the executable xml2-config
in your PATH.
(You can also send _me_ the config.log file from the attempted installation.)
D.
On 8/15/13 10:13 AM, Shi, Tao wrote:
> 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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> PLEASE do read the posting guide http://www.R-project.org/posting-guide.html
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>
>
______________________________________________
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and provide commented, minimal, self-contained, reproducible code.
______________________________________________
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PLEASE do read the posting guide http://www.R-project.org/posting-guide.html
and provide commented, minimal, self-contained, reproducible code.
