[R-sig-hpc] Installing R-3.3 on a HPC cluster
Kasper Daniel Hansen
kasperdanielhansen at gmail.com
Tue May 10 00:58:06 CEST 2016
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 (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.
On Mon, May 9, 2016 at 9:44 AM, Ali Siavosh-Haghighi <siavoa01 at nyumc.org>
> 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
> > On May 9, 2016, at 4:42 AM, Bjørn-Helge Mevik <b.h.mevik at usit.uio.no>
> > Ali Siavosh-Haghighi <siavoa01 at nyumc.org> writes:
> >> I did install zlib as a module and bypassed that error but
> >> asks for some new version of glibc that is a bit more fundamental. That
> >> 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:
> > --
> > Regards,
> > Bjørn-Helge Mevik, dr. scient,
> > Department for Research Computing, University of Oslo
> > _______________________________________________
> > R-sig-hpc mailing list
> > R-sig-hpc at r-project.org
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