[R] XML package installation -- an old question

[Shi, Tao]

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 <dtemplelang at ucdavis.edu>
To: r-help at 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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