[R-sig-hpc] Installing R-3.3 on a HPC cluster

Ali Siavosh-Haghighi siavoa01 at nyumc.org
Wed May 11 15:52:46 CEST 2016

Hi All,
For cluster running on CentOS-6 compiled and installed the following using gcc-5.2.0:

1. bzip2-1.0.6 (compiling with shared library option, then make a link in lib from libbz2.so.1.0.6 to libbz2.so.1)
2. zlib-1.2.8
3. XZ-5.2.2 (needed to make a link from liblzma.so.5.2.2 to liblzma.so.5.2, this particular link was not there)
4. pcre-8.38
5. curl-7.48.0

All the LD_LIBRARY_PATH, CPATH, LIBRARY_PATH and PATH of course needed to be edited to prepend paths to the library and the headers of the packages above.
Then ./configure went through (I disabled openMP option).
In previous releases (3.2) there has been a directory /src/extra containing at least some of these packages. For 3.3 the necessary packages are not there (possibly for license issue?) and thus gone smooth installation. 
Ali  Siavosh-Haghighi, Ph.D.
HPC System Administrator
High Performance Computing Facility
Center for Health Informatics and Bioinformatics
NYU Langone Medical Center
Phone: (646) 501-2907

> On May 11, 2016, at 5:18 AM, Sebastian Luna Valero <sebastian.luna.valero at gmail.com> wrote:
> Hi All,
> Adapting the installation instructions on the following blog post worked on
> our RHEL6 environment:
> https://urldefense.proofpoint.com/v2/url?u=http-3A__pj.freefaculty.org_blog_-3Fp-3D315&d=CwIGaQ&c=j5oPpO0eBH1iio48DtsedbOBGmuw5jHLjgvtN2r4ehE&r=XaOCmLUnAz9o9ru8VyC-GVRS6cJNKKW6WtTDkj1afBA&m=WHdhsE7rCGbWj0FHhGkyjj4KZkJ9joPRcGklAmigMbs&s=QlSqIZ9VLFuqCZpJnlWYNpMRgYSOn9uLcpHXsQTNVv4&e= 
> I hope it helps!
> Best regards,
> Sebastian
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