package installation error in unix

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package installation error in unix

uday
Hi,

Recently I have installed R in my Linux operating system , after installation I was trying to install some packages and I was getting error
installed.packages("hdf5")
  { Package LibPath Version Priority Depends
     Imports LinkingTo Suggests Enhances OS_type
     License Archs Built}
this is first time that I am using R in Linux, could somebody please tell me how to fix this error .
I am using  "R version 2.14.1 (2011-12-22)"

Thank you
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Re: package installation error in unix

Pascal Oettli-2
Hello,

There is a mistake. Type

 > install.packages("hdf5")

instead of

 > installed.packages("hdf5")

in order to install a package.

Best Regards,
Passcal


Le 19/07/2012 17:02, uday a écrit :

> Hi,
>
> Recently I have installed R in my Linux operating system , after
> installation I was trying to install some packages and I was getting error
> installed.packages("hdf5")
>    { Package LibPath Version Priority Depends
>       Imports LinkingTo Suggests Enhances OS_type
>       License Archs Built}
> this is first time that I am using R in Linux, could somebody please tell me
> how to fix this error .
> I am using  "R version 2.14.1 (2011-12-22)"
>
> Thank you
>
> --
> View this message in context: http://r.789695.n4.nabble.com/package-installation-error-in-unix-tp4636995.html
> Sent from the R help mailing list archive at Nabble.com.
>
> ______________________________________________
> [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.
>

______________________________________________
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Re: package installation error in unix

uday
Hi
Thanks for reply
after usinginstall.packages("hdf5")
I get error
{Installing package(s) into ‘/home/uday/R/x86_64-pc-linux-gnu-library/2.14’
(as ‘lib’ is unspecified)
trying URL 'http://cran.revolutionanalytics.com/src/contrib/hdf5_1.6.9.tar.gz'
Content type 'application/x-gzip' length 50870 bytes (49 Kb)
opened URL
==================================================
downloaded 49 Kb

* installing *source* package ‘hdf5’ ...
** package ‘hdf5’ successfully unpacked and MD5 sums checked
checking for gcc... gcc
checking for C compiler default output file name... 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 ANSI C... none needed
checking for library containing inflate... -lz
checking for library containing H5open... no
configure: error: Can't find HDF5
ERROR: configuration failed for package ‘hdf5’
* removing ‘/home/uday/R/x86_64-pc-linux-gnu-library/2.14/hdf5’
Warning in install.packages :
  installation of package ‘hdf5’ had non-zero exit status

The downloaded packages are in
        ‘/tmp/Rtmp7Ot3Yl/downloaded_packages’ }

So what is this non-zero exit status ?
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Re: package installation error in unix

Sarah Goslee
The error message is here: configure: error: Can't find HDF5

The hdf5 package is an interface to the HDF5 library, so you need to
install hdf5 and hdf5-devel through your package manager (yum or
apt-get or whatever you use to install things on your linux distro).

Or you can get it straight from the source:
http://www.hdfgroup.org/HDF5/release/obtain5.html

Sarah

On Thu, Jul 19, 2012 at 8:14 AM, uday <[hidden email]> wrote:

> Hi
> Thanks for reply
> after usinginstall.packages("hdf5")
> I get error
> {Installing package(s) into ‘/home/uday/R/x86_64-pc-linux-gnu-library/2.14’
> (as ‘lib’ is unspecified)
> trying URL
> 'http://cran.revolutionanalytics.com/src/contrib/hdf5_1.6.9.tar.gz'
> Content type 'application/x-gzip' length 50870 bytes (49 Kb)
> opened URL
> ==================================================
> downloaded 49 Kb
>
> * installing *source* package ‘hdf5’ ...
> ** package ‘hdf5’ successfully unpacked and MD5 sums checked
> checking for gcc... gcc
> checking for C compiler default output file name... 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 ANSI C... none needed
> checking for library containing inflate... -lz
> checking for library containing H5open... no
> configure: error: Can't find HDF5
> ERROR: configuration failed for package ‘hdf5’
> * removing ‘/home/uday/R/x86_64-pc-linux-gnu-library/2.14/hdf5’
> Warning in install.packages :
>   installation of package ‘hdf5’ had non-zero exit status
>
> The downloaded packages are in
>         ‘/tmp/Rtmp7Ot3Yl/downloaded_packages’ }
>
> So what is this non-zero exit status ?
>
>
> --
> View this message in context: http://r.789695.n4.nabble.com/package-installation-error-in-unix-tp4636995p4637026.html
> Sent from the R help mailing list archive at Nabble.com.
>
> ______________________________________________
> [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.



--
Sarah Goslee
http://www.stringpage.com
http://www.sarahgoslee.com
http://www.functionaldiversity.org

______________________________________________
[hidden email] mailing list
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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.