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

[Kasper Daniel Hansen]

Ali, I don't know how CentOS 6 relates to RHEL 6, but I have installed R
3.3 from source (by hand) on RHEL 6.  It required installing a number of
packages by hand, including bzip2 (1.0.6), xz (5.2.1), pcre (8.36), curl
(7.43.0) and possibly other packages I have forgotten.  But not glibc.  My
sysadmins only install stuff from the official Red hat sources.  We have

gcc --version
gcc (GCC) 4.4.7 20120313 (Red Hat 4.4.7-4)
Copyright (C) 2010 Free Software Foundation, Inc.
This is free software; see the source for copying conditions.  There is NO
warranty; not even for MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.

Best,
Kasper

On Mon, May 9, 2016 at 9:44 AM, Ali Siavosh-Haghighi <siavoa01 at nyumc.org>
wrote:

> Hi Bjorn,
> Installing the bzip2 itself is not the problem. R>3.2.5 requires one of
> the headers in bzip2-devel. There is no source for bzip2-devel-1.0.6 (could
> not find it and I contacted the developer and no response yet). The RPM
> installation complains about lack of newer version of glibc (a version that
> is the default for CentOS 7). So, unless R be wrapped with the necessary
> headers of bzip2-devel I dont see an easy installation for new  versions of
> R on CentOS 6. And we have very heavy R users.
> I appreciate any helpful comment
> ==============================================================
> 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
> http://www.med.nyu.edu/chibi/services/hpcf
> ==============================================================
>
>
> > On May 9, 2016, at 4:42 AM, Bjørn-Helge Mevik <b.h.mevik at usit.uio.no>
> wrote:
> >
> > Ali Siavosh-Haghighi <siavoa01 at nyumc.org> writes:
> >
> >> I did install zlib as a module and bypassed that error but
> bzip2-devel-1.0.6
> >> asks for some new version of glibc that is a bit more fundamental. That
> glibc
> >> and that bzip2 It is default for CentOS 7. So I was thinking if there
> is a way
> >> to install bzip2-devel as module as well but could not find the
> >> source.
> >
> > I guess there should be no problem in downloading the latest bzip2
> > source code, build it and install it and create a module file for it.
> > We recently had to do this for libcurl because the OS provided version
> > was too old (didn't support https).
> >
> > If you google "bzip source" you will find that the source code can be
> > found here:
> https://urldefense.proofpoint.com/v2/url?u=http-3A__www.bzip.org_&d=CwIGaQ&c=j5oPpO0eBH1iio48DtsedbOBGmuw5jHLjgvtN2r4ehE&r=XaOCmLUnAz9o9ru8VyC-GVRS6cJNKKW6WtTDkj1afBA&m=Im1-S_Gpzb4vbMNNYwsYReogsNXaH_YHZYF1e0OB0Gc&s=bWQk-f2kOA-fgOmk0fluNBVwcjM2j7pU7EUz2gk4mTk&e=
> >
> > --
> > Regards,
> > Bjørn-Helge Mevik, dr. scient,
> > Department for Research Computing, University of Oslo
> >
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