Dear Shivali!

Can you please specify the command that you used to download and install
rhdf5 in your next post?

1.) I think, I solved a this issue already in current developmental version.
Try to install the latest version of rhdf5 from the devel branch (currently 2.7.3):
http://www.bioconductor.org/packages/2.14/bioc/html/rhdf5.html

2.) You added an include path to your local HDF5 installation:
>  -I/gpfs1/home/shivali/hdf5-1.8.12/include
Remove this include path. There can be a clash between your the local
HDF5 installation and the HDF5 version that is used by rhdf5. You don't need
to install HDF5 beforehand on your computer. rhdf5 brings its own HDF5
library.

Best,

Bernd




On 11.12.2013, at 10:23, shivali@embl-heidelberg.de wrote:

> 
> AIX- 5.3
> 
>        xlC_r -q64 -I/gpfs1/home/shivali/R-Updated/R-3.0.2/lib/R/include -DNDEBUG  -I/gpfs1/home/shivali/shivali/libiconv-1.14/include -I/usr/lpp/X11/include/X11 -I/gpfs1/home/shivali/software/gettext-0.18/include -I/gpfs1/home/shivali/software/libpng-1.6.2/include -I/gpfs1/home/shivali/hdf5-1.8.12/include   -Ihdf5/src   -O -qstrict  -c HandleList.cpp -o HandleList.o
> "HandleList.cpp", line 175.1: 1540-1101 (W) A return value of type "int" is expected.
> xlC_r: 1501-230 (S) Internal compiler error; please contact your Service Representative. For more information visit:
> http://www.ibm.com/support/docview.wss?uid=swg21110810
> make: 1254-004 The error code from the last command is 41.
> 
> 
> Stop.
> ERROR: compilation failed for package 'rhdf5'
> * removing '/gpfs1/home/shivali/R-Updated/R-3.0.2/lib/R/library/rhdf5'
> [ncmr0102][/gpfs1/home/shivali/R-Updated/R-3.0.2/bin]>
> 
> -- output of sessionInfo(): 
> 
> [ncmr0102][/gpfs1/home/shivali/R-Updated/R-3.0.2/bin]> R
> 
> R version 3.0.2 (2013-09-25) -- "Frisbee Sailing"
> Copyright (C) 2013 The R Foundation for Statistical Computing
> Platform: powerpc-ibm-aix5.3.0.0 (64-bit)
> 
> R is free software and comes with ABSOLUTELY NO WARRANTY.
> You are welcome to redistribute it under certain conditions.
> Type 'license()' or 'licence()' for distribution details.
> 
>  Natural language support but running in an English locale
> 
> R is a collaborative project with many contributors.
> Type 'contributors()' for more information and
> 'citation()' on how to cite R or R packages in publications.
> 
> Type 'demo()' for some demos, 'help()' for on-line help, or
> 'help.start()' for an HTML browser interface to help.
> Type 'q()' to quit R.
> 
> s> essionInfo()
> R version 3.0.2 (2013-09-25)
> Platform: powerpc-ibm-aix5.3.0.0 (64-bit)
> 
> locale:
> [1] en_US en_US en_US C en_US en_US
> 
> attached base packages:
> [1] stats     graphics  grDevices utils     datasets  methods   base
>> 
> 
> 
> --
> Sent via the guest posting facility at bioconductor.org.


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