R packages installation error in Ubuntu

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R packages installation error in Ubuntu

uday
Hi,

Recently I have installed R version 2.14.1, after installation I am trying to install some packages and I get error message. even I tried install.packages("Rcmdr") but still I am unable to fix this problem.
I would be very grateful if somebody can help me to fix this problem.

 install.packages("hdf5")
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’
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Re: R packages installation error in Ubuntu

Michael Weylandt
On Thu, Jul 19, 2012 at 2:41 PM, uday <[hidden email]> wrote:
> Hi,
>
> Recently I have installed R version 2.14.1, after installation I am trying
> to install some packages and I get error message. even I tried
> install.packages("Rcmdr")

Why would that help?

Also: don't double post. Sarah already told you how to fix this four
hours ago here:
https://stat.ethz.ch/pipermail/r-help/2012-July/318876.html

Michael

>  but still I am unable to fix this problem.
> I would be very grateful if somebody can help me to fix this problem.
>
>  install.packages("hdf5")
> 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’
>
> --
> View this message in context: http://r.789695.n4.nabble.com/R-packages-installation-error-in-Ubuntu-tp4637105.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.

______________________________________________
[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: R packages installation error in Ubuntu

uday
hi ,

last time I did not mention the specific version of linux and it was problem with only syntax but with correction I got new error.
I found that some people has  faced this problem before and some of them have mentioned that it may be because of dependencies issue and   install.packages("Rcmdr")  could fix this problem.
But Still I have not fixed the problem.

could you please tell me how to resolve this issue, this is the first time I am using R in ubuntu.
Thank you

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Re: R packages installation error in Ubuntu

Michael Weylandt
On Fri, Jul 20, 2012 at 12:38 PM, uday <[hidden email]> wrote:
> hi ,
>
> last time I did not mention the specific version of linux and it was problem
> with only syntax but with correction I got new error.

Nope -- you still have the same error Sarah responded to. It is
apt-get for Ubuntu (I believe) to get the needed HDF5 files.

For more info, check the first hit on "get HDF5 Ubuntu":

http://micro.stanford.edu/wiki/Install_HDF5#Ubuntu

Michael

> I found that some people has  faced this problem before and some of them
> have mentioned that it may be because of dependencies issue and
> install.packages("Rcmdr")  could fix this problem.
> But Still I have not fixed the problem.
>
> could you please tell me how to resolve this issue, this is the first time I
> am using R in ubuntu.
> Thank you
>
>
>
>
>
> --
> View this message in context: http://r.789695.n4.nabble.com/R-packages-installation-error-in-Ubuntu-tp4637105p4637250.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.

______________________________________________
[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.