[R] package installation error in unix

Sarah Goslee sarah.goslee at gmail.com
Thu Jul 19 18:05:16 CEST 2012

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:


On Thu, Jul 19, 2012 at 8:14 AM, uday <uday_143_4u at hotmail.com> 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.
> ______________________________________________
> R-help at r-project.org 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

More information about the R-help mailing list