Problem installing XML in Ubuntu 10.10

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Problem installing XML in Ubuntu 10.10

Abraham Mathew
Hello folks,


Here's is info on what system I'm working on.
> sessionInfo()
R version 2.13.0 (2011-04-13)
Platform: i686-pc-linux-gnu (32-bit)


I'm trying to install the XML package. However, I end up with the following
error message.

> install.packages("XML")
....
checking for xml2-config... no
Cannot find xml2-config
ERROR: configuration failed for package ‘XML’
* removing ‘/home/abraham/R/i686-pc-linux-gnu-library/2.13/XML’

The downloaded packages are in
‘/tmp/RtmpUsckPl/downloaded_packages’
Warning message:
In install.packages() :
installation of package 'XML' had non-zero exit status


When I run library(XML), I get that there is no package named XML.

Can anyone help diagnose the problem.


Thank You,
Abraham

        [[alternative HTML version deleted]]


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Re: Problem installing XML in Ubuntu 10.10

Phil Spector
Abraham -

      sudo apt-get install libxml2-dev

is what you need to get the development libraries and
xml2-config installed on your Ubuntu machine.

                                        - Phil



On Mon, 25 Apr 2011, Abraham Mathew wrote:

> Hello folks,
>
>
> Here's is info on what system I'm working on.
>> sessionInfo()
> R version 2.13.0 (2011-04-13)
> Platform: i686-pc-linux-gnu (32-bit)
>
>
> I'm trying to install the XML package. However, I end up with the following
> error message.
>
>> install.packages("XML")
> ....
> checking for xml2-config... no
> Cannot find xml2-config
> ERROR: configuration failed for package ?XML?
> * removing ?/home/abraham/R/i686-pc-linux-gnu-library/2.13/XML?
>
> The downloaded packages are in
> ?/tmp/RtmpUsckPl/downloaded_packages?
> Warning message:
> In install.packages() :
> installation of package 'XML' had non-zero exit status
>
>
> When I run library(XML), I get that there is no package named XML.
>
> Can anyone help diagnose the problem.
>
>
> Thank You,
> Abraham
>
> [[alternative HTML version deleted]]
>
>

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Re: Problem installing XML in Ubuntu 10.10

Abraham Mathew
This is kind of a second question (yeah, I know), but I also get a similar
error when I try to install the RCurl package

* installing *source* package ‘RCurl’ ...
checking for curl-config... no
Cannot find curl-config
ERROR: configuration failed for package ‘RCurl’
* removing ‘/home/abraham/R/i686-pc-linux-gnu-library/2.13/RCurl’

The downloaded packages are in
‘/tmp/RtmpNmbI03/downloaded_packages’
Warning message:
In install.packages() :
installation of package 'RCurl' had non-zero exit status



I never had any problems with installing packages. However, I recently
removed my windows
partition and things all weird now.


Thanks again.



On Mon, Apr 25, 2011 at 6:19 PM, Phil Spector <[hidden email]>wrote:

> Abraham -
>
>     sudo apt-get install libxml2-dev
>
> is what you need to get the development libraries and xml2-config installed
> on your Ubuntu machine.
>
>                                       - Phil
>
>
>
>
> On Mon, 25 Apr 2011, Abraham Mathew wrote:
>
>  Hello folks,
>>
>>
>> Here's is info on what system I'm working on.
>>
>>> sessionInfo()
>>>
>> R version 2.13.0 (2011-04-13)
>> Platform: i686-pc-linux-gnu (32-bit)
>>
>>
>> I'm trying to install the XML package. However, I end up with the
>> following
>> error message.
>>
>>  install.packages("XML")
>>>
>> ....
>> checking for xml2-config... no
>> Cannot find xml2-config
>> ERROR: configuration failed for package ?XML?
>> * removing ?/home/abraham/R/i686-pc-linux-gnu-library/2.13/XML?
>>
>> The downloaded packages are in
>> ?/tmp/RtmpUsckPl/downloaded_packages?
>> Warning message:
>> In install.packages() :
>> installation of package 'XML' had non-zero exit status
>>
>>
>> When I run library(XML), I get that there is no package named XML.
>>
>> Can anyone help diagnose the problem.
>>
>>
>> Thank You,
>> Abraham
>>
>>        [[alternative HTML version deleted]]
>>
>>
>>
        [[alternative HTML version deleted]]


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Re: Problem installing XML in Ubuntu 10.10

Phil Spector
sudo apt-get install libcurl4-openssl-dev

  - Phil Spector
  Statistical Computing Facility
  Department of Statistics
  UC Berkeley
  [hidden email]


On Mon, 25 Apr 2011, Abraham Mathew wrote:

>
> This is kind of a second question (yeah, I know), but I also get a similar error when I try to install
> the RCurl package
>
> * installing *source* package ‘RCurl’ ...
> checking for curl-config... no
> Cannot find curl-config
> ERROR: configuration failed for package ‘RCurl’
> * removing ‘/home/abraham/R/i686-pc-linux-gnu-library/2.13/RCurl’
>
> The downloaded packages are in
> ‘/tmp/RtmpNmbI03/downloaded_packages’
> Warning message:
> In install.packages() :
> installation of package 'RCurl' had non-zero exit status
>
>
>
> I never had any problems with installing packages. However, I recently removed my windows
> partition and things all weird now.
>
>
> Thanks again.
>
>
>
> On Mon, Apr 25, 2011 at 6:19 PM, Phil Spector <[hidden email]> wrote:
>       Abraham -
>
>           sudo apt-get install libxml2-dev
>
>       is what you need to get the development libraries and xml2-config installed on your Ubuntu
>       machine.
>
>                                             - Phil
>
>
>
>       On Mon, 25 Apr 2011, Abraham Mathew wrote:
>
>       Hello folks,
>
>
>       Here's is info on what system I'm working on.
>             sessionInfo()
>
>       R version 2.13.0 (2011-04-13)
>       Platform: i686-pc-linux-gnu (32-bit)
>
>
>       I'm trying to install the XML package. However, I end up with the following
>       error message.
>
>             install.packages("XML")
>
>       ....
>       checking for xml2-config... no
>       Cannot find xml2-config
>       ERROR: configuration failed for package ?XML?
>       * removing ?/home/abraham/R/i686-pc-linux-gnu-library/2.13/XML?
>
>       The downloaded packages are in
>       ?/tmp/RtmpUsckPl/downloaded_packages?
>       Warning message:
>       In install.packages() :
>       installation of package 'XML' had non-zero exit status
>
>
>       When I run library(XML), I get that there is no package named XML.
>
>       Can anyone help diagnose the problem.
>
>
>       Thank You,
>       Abraham
>
>        [[alternative HTML version deleted]]
>
>
>
>
>
______________________________________________
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Re: Problem installing XML in Ubuntu 10.10

Dirk Eddelbuettel
In reply to this post by Abraham Mathew

On 25 April 2011 at 17:39, Abraham Mathew wrote:
| Hello folks,
|
|
| Here's is info on what system I'm working on.
| > sessionInfo()
| R version 2.13.0 (2011-04-13)
| Platform: i686-pc-linux-gnu (32-bit)
|
|
| I'm trying to install the XML package. However, I end up with the following
| error message.

You can install the prebuilt package

    r-cran-xml

directly from the Ubuntu repositories.  

Dirk

 
| > install.packages("XML")
| ....
| checking for xml2-config... no
| Cannot find xml2-config
| ERROR: configuration failed for package �XML�
| * removing �/home/abraham/R/i686-pc-linux-gnu-library/2.13/XML�
|
| The downloaded packages are in
| �/tmp/RtmpUsckPl/downloaded_packages�
| Warning message:
| In install.packages() :
| installation of package 'XML' had non-zero exit status
|
|
| When I run library(XML), I get that there is no package named XML.
|
| Can anyone help diagnose the problem.
|
|
| Thank You,
| Abraham
|
| [[alternative HTML version deleted]]
|
|
| ----------------------------------------------------------------------
| ______________________________________________
| [hidden email] mailing list
| https://stat.ethz.ch/mailman/listinfo/r-help
| PLEASE do read the posting guide http://www.R-project.org/posting-guide.html
| and provide commented, minimal, self-contained, reproducible code.

--
Gauss once played himself in a zero-sum game and won $50.
                      -- #11 at http://www.gaussfacts.com


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Re: Problem installing XML in Ubuntu 10.10

Rolf Turner-3
On 26/04/11 10:46, Dirk Eddelbuettel wrote:

> On 25 April 2011 at 17:39, Abraham Mathew wrote:
> | Hello folks,
> |
> |
> | Here's is info on what system I'm working on.
> |>  sessionInfo()
> | R version 2.13.0 (2011-04-13)
> | Platform: i686-pc-linux-gnu (32-bit)
> |
> |
> | I'm trying to install the XML package. However, I end up with the following
> | error message.
>
> You can install the prebuilt package
>
>      r-cran-xml
>
> directly from the Ubuntu repositories.

Just out of idle curiosity I tried this.  (Don't want/need XML, but since
I've fairly recently started using Ubuntu, I like to see whether I can drive
these sudo apt-get tools .....)

So I did

     sudo apt-get install r-cran-xml

and it seemed to run without error.  Then I started R and tried

     library(XML)

and got the error

     Error in library(XML) : there is no package called 'XML'

So I then said ``Hmmmm.  Maybe I've misunderstood, and the sudo apt-get
bizzo
has just provided the underlying xml2-config stuff, and I still need to
do the install
of the R package XML.  So I tried that, and got the message:

     checking for xml2-config... no
     Cannot find xml2-config
     ERROR: configuration failed for package ‘XML’
     * removing ‘/home/rolf/Rlib/XML’

So either something's not working properly or I'm still not
understanding what
I should be doing.  Enlightenment?

     cheers,

         Rolf Turner

P. S. I *believe* that I have the Ubuntu repositories referenced
correctly in
my /etc/apt/sources.list file:

deb http://cran.stat.auckland.ac.nz/bin/linux/ubuntu lucid/

         R. T.

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Re: Problem installing XML in Ubuntu 10.10

Jim Lemon
On 04/26/2011 09:19 AM, Rolf Turner wrote:
> ...
> So either something's not working properly or I'm still not
> understanding what
> I should be doing. Enlightenment?
>
When the sender and the receiver understand what is being said,
that is communication.
When the sender understands, but the receiver does not,
that is jargon.
When neither understands,
that is voodoo.

Jim

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Re: Problem installing XML in Ubuntu 10.10

Ben Tupper-2
In reply to this post by Abraham Mathew
Hi,

On Apr 25, 2011, at 6:38 PM, Abraham Mathew wrote:

> This is kind of a second question (yeah, I know), but I also get a  
> similar
> error when I try to install the RCurl package
>
> * installing *source* package ‘RCurl’ ...
> checking for curl-config... no
> Cannot find curl-config
> ERROR: configuration failed for package ‘RCurl’
> * removing ‘/home/abraham/R/i686-pc-linux-gnu-library/2.13/RCurl’
>
> The downloaded packages are in
> ‘/tmp/RtmpNmbI03/downloaded_packages’
> Warning message:
> In install.packages() :
> installation of package 'RCurl' had non-zero exit status
>
>

I just went through a similar experience on CentOS.  My Linux skills  
are a bit wobbly, but I learned watching my local IT whiz get me  
straightened out.  Have you tried testing the curl companion command,  
curl-config, to see what you have installed?  For example...

$ curl-config --version
libcurl 7.19.7

If that doesn't work then it seems to me that you either don't have  
curl installed or if you do it isn't on your search path.

Cheers,
Ben





>
> I never had any problems with installing packages. However, I recently
> removed my windows
> partition and things all weird now.
>
>
> Thanks again.
>
>
>
> On Mon, Apr 25, 2011 at 6:19 PM, Phil Spector <[hidden email]
> >wrote:
>
>> Abraham -
>>
>>    sudo apt-get install libxml2-dev
>>
>> is what you need to get the development libraries and xml2-config  
>> installed
>> on your Ubuntu machine.
>>
>>                                      - Phil
>>
>>
>>
>>
>> On Mon, 25 Apr 2011, Abraham Mathew wrote:
>>
>> Hello folks,
>>>
>>>
>>> Here's is info on what system I'm working on.
>>>
>>>> sessionInfo()
>>>>
>>> R version 2.13.0 (2011-04-13)
>>> Platform: i686-pc-linux-gnu (32-bit)
>>>
>>>
>>> I'm trying to install the XML package. However, I end up with the
>>> following
>>> error message.
>>>
>>> install.packages("XML")
>>>>
>>> ....
>>> checking for xml2-config... no
>>> Cannot find xml2-config
>>> ERROR: configuration failed for package ?XML?
>>> * removing ?/home/abraham/R/i686-pc-linux-gnu-library/2.13/XML?
>>>
>>> The downloaded packages are in
>>> ?/tmp/RtmpUsckPl/downloaded_packages?
>>> Warning message:
>>> In install.packages() :
>>> installation of package 'XML' had non-zero exit status
>>>
>>>
>>> When I run library(XML), I get that there is no package named XML.
>>>
>>> Can anyone help diagnose the problem.
>>>
>>>
>>> Thank You,
>>> Abraham
>>>
>>>       [[alternative HTML version deleted]]
>>>
>>>
>>>
>
> [[alternative HTML version deleted]]
>
> ______________________________________________
> [hidden email] mailing list
> https://stat.ethz.ch/mailman/listinfo/r-help
> PLEASE do read the posting guide http://www.R-project.org/posting-guide.html
> and provide commented, minimal, self-contained, reproducible code.

Ben Tupper
Bigelow Laboratory for Ocean Sciences
180 McKown Point Rd. P.O. Box 475
West Boothbay Harbor, Maine   04575-0475
http://www.bigelow.org/

______________________________________________
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Re: Problem installing XML in Ubuntu 10.10

Phil Spector
Many of the libraries that are packaged by the various Linux
distributions come in two forms:

   1)  The basic library, which can be used by any program that
has been built to access the library, and

   2)  development versions (ending in -dev on Debian based systems,
and -devel on Red Hat based systems) which are required for compiling
any programs that need to access the library.

Often, all that's missing from an installation is one or two header (.h)
files, which is one of the things that the development packages provide.
Some of the more popular libraries, also include a "-config" command,
that allows other programs to know the appropriate flags to use when
creating programs that will access the libraries.  These commands are
also part of the development package.

So, for example, on a system with curl installed, but libcurl-openssl-dev
or libcurl4-openssl-dev not installed, curl itself will work fine, and even
some other programs that use curl will work, but you won't be able to compile
any program that needs to use the curl library.

It seems to me that many Linux users encounter this for the first time when
they build a library from source.  Using apt-get search with the appropriate
terms will usually point you to the right package that's missing, for
example  "apt-cache search curl dev" or "apt-cache search xml dev".  There will
usually be lots of packages listed, but  piping the results into a search
for Development will often narrow things down.  For example, the curl and
xml development packages can be found like this:

$ apt-cache search curl dev | grep Development
libcurl4-gnutls-dev - Development files and documentation for libcurl (GnuTLS)
libcurl4-openssl-dev - Development files and documentation for libcurl (OpenSSL)
libcurl-ocaml-dev - OCaml libcurl bindings (Development package)

$ apt-cache search xml dev | grep Development
libapiextractor-dev - Development files for the library headers parser
libgdome2-dev - Development files for libgdome2
libmagics++-dev - Development files for ECMWF  plotting software MAGICS++
libpoco-dev - Development files for POCO - The C++ Portable Components
libxmlrpc-epi-dev - Development files for libxmlrpc-epi0, a XML-RPC request library
libxmlsec1-dev - Development files for the XML security library
monodevelop - Development Environment for GNOME
libaprutil1-dev - The Apache Portable Runtime Utility Library - Development Headers
libsoup2.4-dev - an HTTP library implementation in C -- Development files
libwebkit-dev - Web content engine library for Gtk+ - Development files
libxml2-dev - Development files for the GNOME XML library

Interestingly, for xml, it's last one listed.

  - Phil Spector
  Statistical Computing Facility
  Department of Statistics
  UC Berkeley
  [hidden email]






On Mon, 25 Apr 2011, Ben Tupper wrote:

> Hi,
>
> On Apr 25, 2011, at 6:38 PM, Abraham Mathew wrote:
>
>> This is kind of a second question (yeah, I know), but I also get a similar
>> error when I try to install the RCurl package
>>
>> * installing *source* package ?RCurl? ...
>> checking for curl-config... no
>> Cannot find curl-config
>> ERROR: configuration failed for package ?RCurl?
>> * removing ?/home/abraham/R/i686-pc-linux-gnu-library/2.13/RCurl?
>>
>> The downloaded packages are in
>> ?/tmp/RtmpNmbI03/downloaded_packages?
>> Warning message:
>> In install.packages() :
>> installation of package 'RCurl' had non-zero exit status
>>
>>
>
> I just went through a similar experience on CentOS.  My Linux skills are a
> bit wobbly, but I learned watching my local IT whiz get me straightened out.
> Have you tried testing the curl companion command, curl-config, to see what
> you have installed?  For example...
>
> $ curl-config --version
> libcurl 7.19.7
>
> If that doesn't work then it seems to me that you either don't have curl
> installed or if you do it isn't on your search path.
>
> Cheers,
> Ben
>
>
>
>
>
>>
>> I never had any problems with installing packages. However, I recently
>> removed my windows
>> partition and things all weird now.
>>
>>
>> Thanks again.
>>
>>
>>
>> On Mon, Apr 25, 2011 at 6:19 PM, Phil Spector
>> <[hidden email]>wrote:
>>
>>> Abraham -
>>>
>>>   sudo apt-get install libxml2-dev
>>>
>>> is what you need to get the development libraries and xml2-config
>>> installed
>>> on your Ubuntu machine.
>>>
>>>                                     - Phil
>>>
>>>
>>>
>>>
>>> On Mon, 25 Apr 2011, Abraham Mathew wrote:
>>>
>>> Hello folks,
>>>>
>>>>
>>>> Here's is info on what system I'm working on.
>>>>
>>>>> sessionInfo()
>>>>>
>>>> R version 2.13.0 (2011-04-13)
>>>> Platform: i686-pc-linux-gnu (32-bit)
>>>>
>>>>
>>>> I'm trying to install the XML package. However, I end up with the
>>>> following
>>>> error message.
>>>>
>>>> install.packages("XML")
>>>>>
>>>> ....
>>>> checking for xml2-config... no
>>>> Cannot find xml2-config
>>>> ERROR: configuration failed for package ?XML?
>>>> * removing ?/home/abraham/R/i686-pc-linux-gnu-library/2.13/XML?
>>>>
>>>> The downloaded packages are in
>>>> ?/tmp/RtmpUsckPl/downloaded_packages?
>>>> Warning message:
>>>> In install.packages() :
>>>> installation of package 'XML' had non-zero exit status
>>>>
>>>>
>>>> When I run library(XML), I get that there is no package named XML.
>>>>
>>>> Can anyone help diagnose the problem.
>>>>
>>>>
>>>> Thank You,
>>>> Abraham
>>>>
>>>>      [[alternative HTML version deleted]]
>>>>
>>>>
>>>>
>>
>> [[alternative HTML version deleted]]
>>
>> ______________________________________________
>> [hidden email] mailing list
>> https://stat.ethz.ch/mailman/listinfo/r-help
>> PLEASE do read the posting guide
>> http://www.R-project.org/posting-guide.html
>> and provide commented, minimal, self-contained, reproducible code.
>
> Ben Tupper
> Bigelow Laboratory for Ocean Sciences
> 180 McKown Point Rd. P.O. Box 475
> West Boothbay Harbor, Maine   04575-0475
> http://www.bigelow.org/
>
> ______________________________________________
> [hidden email] mailing list
> https://stat.ethz.ch/mailman/listinfo/r-help
> PLEASE do read the posting guide http://www.R-project.org/posting-guide.html
> and provide commented, minimal, self-contained, reproducible code.

______________________________________________
[hidden email] mailing list
https://stat.ethz.ch/mailman/listinfo/r-help
PLEASE do read the posting guide http://www.R-project.org/posting-guide.html
and provide commented, minimal, self-contained, reproducible code.