Thanks everyone for the replies to my question. The issue turns out to be
that I'm on a Rocks cluster head node, and the Rocks distribution disables
alternate repos by defaut so it's using the Rocks-6.1 repo which has the
old R.

In the meantime I've built R 3.0.2 from source, which seems a better idea
anyway, as I'll need multiple versions of R installed over time.

-M


On Fri, Oct 25, 2013 at 7:43 AM, Marc Schwartz <marc_schwartz@me.com> wrote:

>
> On Oct 25, 2013, at 1:29 AM, Prof Brian Ripley <ripley@stats.ox.ac.uk>
> wrote:
>
> > On 25/10/2013 02:33, Michael Stauffer wrote:
> >> Hi,
> >>
> >> I'm trying to install R on CentOS 6.4.
> >
> > This is not the right list.  But
> >
> > - As the posting guide says, we only support current R here.  R 2.10.0
> is ancient, and other people seem to have found 3.0.1 RPMs for Centos 6.3.
> >
> > - It seems your RPM is linked against Tcl/Tk 8.4, also ancient.  Tcl/Tk
> 8.6 is current.
> >
> > I suggest you install R 3.0.2 from the sources, in which case R-devel
> would be the right list.  For binary installations on CentOS, R-sig-Fedora
> is.
> >
>
> There are several inconsistencies in the output, as 3.0.1 is available as
> an RPM from the EPEL repos:
>
>   http://dl.fedoraproject.org/pub/epel/6/x86_64/repoview/R.html
>
> In addition, the output below shows that the R rpm being installed is from
> 'el5', rather than 'el6'. If this was CentOS 5, rather than 6, R 2.15.2 is
> available:
>
>   http://dl.fedoraproject.org/pub/epel/5/x86_64/repoview/R.html
>
> Something seems to be amiss with the configuration not getting the right
> yum repo paths.
>
> A Google search came up with this link:
>
>   http://lancegatlin.org/tech/centos-6-clear-the-yum-cache
>
> which might be helpful, as it suggests a similar issue of yum picking up
> incorrect versions. You may need to reinstall the EPEL repo RPM after these
> steps.
>
> Regards,
>
> Marc Schwartz
>
>
> >>
> >> Following some instructions online, I've done this:
> >>
> >> rpm -Uvh
> >>
> http://download.fedoraproject.org/pub/epel/6/i386/epel-release-6-8.noarch.rpm
> >>
> >> yum install R
> >>
> >> But yum fails, with this (full output below):
> >>
> >> Error: Package: R-core-2.10.0-2.el5.x86_64 (Rocks-6.1)
> >>            Requires: libtcl8.4.so()(64bit)
> >> Error: Package: R-core-2.10.0-2.el5.x86_64 (Rocks-6.1)
> >>            Requires: libtk8.4.so()(64bit)
> >>
> >> I have tcl/tk 8.5 already installed. Does anyone have any suggestion?
> >> Thanks!
> >>
> >> Full output:
> >>
> >> [root@picsl-cluster ~]# yum install R
> >> Repository base is listed more than once in the configuration
> >> Rocks-6.1
> >>                           | 1.9 kB     00:00
> >> base
> >>                            | 3.7 kB     00:00
> >> Setting up Install Process
> >> Resolving Dependencies
> >> --> Running transaction check
> >> ---> Package R.x86_64 0:2.10.0-2.el5 will be installed
> >> --> Processing Dependency: libRmath-devel = 2.10.0-2.el5 for package:
> >> R-2.10.0-2.el5.x86_64
> >> --> Processing Dependency: R-devel = 2.10.0-2.el5 for package:
> >> R-2.10.0-2.el5.x86_64
> >> --> Running transaction check
> >> ---> Package R-devel.x86_64 0:2.10.0-2.el5 will be installed
> >> --> Processing Dependency: R-core = 2.10.0-2.el5 for package:
> >> R-devel-2.10.0-2.el5.x86_64
> >> ---> Package libRmath-devel.x86_64 0:2.10.0-2.el5 will be installed
> >> --> Processing Dependency: libRmath = 2.10.0-2.el5 for package:
> >> libRmath-devel-2.10.0-2.el5.x86_64
> >> --> Running transaction check
> >> ---> Package R-core.x86_64 0:2.10.0-2.el5 will be installed
> >> --> Processing Dependency: libtk8.4.so()(64bit) for package:
> >> R-core-2.10.0-2.el5.x86_64
> >> --> Processing Dependency: libtcl8.4.so()(64bit) for package:
> >> R-core-2.10.0-2.el5.x86_64
> >> --> Processing Dependency: libgfortran.so.1()(64bit) for package:
> >> R-core-2.10.0-2.el5.x86_64
> >> ---> Package libRmath.x86_64 0:2.10.0-2.el5 will be installed
> >> --> Running transaction check
> >> ---> Package R-core.x86_64 0:2.10.0-2.el5 will be installed
> >> --> Processing Dependency: libtk8.4.so()(64bit) for package:
> >> R-core-2.10.0-2.el5.x86_64
> >> --> Processing Dependency: libtcl8.4.so()(64bit) for package:
> >> R-core-2.10.0-2.el5.x86_64
> >> ---> Package compat-libgfortran-41.x86_64 0:4.1.2-39.el6 will be
> installed
> >> --> Finished Dependency Resolution
> >> Error: Package: R-core-2.10.0-2.el5.x86_64 (Rocks-6.1)
> >>            Requires: libtcl8.4.so()(64bit)
> >> Error: Package: R-core-2.10.0-2.el5.x86_64 (Rocks-6.1)
> >>            Requires: libtk8.4.so()(64bit)
> >>  You could try using --skip-broken to work around the problem
> >> ** Found 57 pre-existing rpmdb problem(s), 'yum check' output follows:
> >> foundation-git-1.7.11.4-0.x86_64 has missing requires of
> perl(SVN::Client)
> >> foundation-git-1.7.11.4-0.x86_64 has missing requires of perl(SVN::Core)
> >> foundation-git-1.7.11.4-0.x86_64 has missing requires of
> perl(SVN::Delta)
> >> foundation-git-1.7.11.4-0.x86_64 has missing requires of perl(SVN::Ra)
> >> 1:guestfish-1.7.17-26.el6.x86_64 has missing requires of libguestfs =
> ('1',
> >> '1.7.17', '26.el6')
> >> opt-perl-AcePerl-1.92-0.el6.x86_64 has missing requires of
> >> perl(Ace::Browser::LocalSiteDefs)
> >> opt-perl-BioPerl-1.6.901-0.el6.noarch has missing requires of
> >> perl(Apache::DBI)
> >> opt-perl-BioPerl-1.6.901-0.el6.noarch has missing requires of
> >> perl(Bio::ASN1::EntrezGene)
> >> opt-perl-BioPerl-1.6.901-0.el6.noarch has missing requires of
> >> perl(Bio::Expression::Contact)
> >> opt-perl-BioPerl-1.6.901-0.el6.noarch has missing requires of
> >> perl(Bio::Expression::DataSet)
> >> opt-perl-BioPerl-1.6.901-0.el6.noarch has missing requires of
> >> perl(Bio::Expression::Platform)
> >> opt-perl-BioPerl-1.6.901-0.el6.noarch has missing requires of
> >> perl(Bio::Expression::Sample)
> >> opt-perl-BioPerl-1.6.901-0.el6.noarch has missing requires of
> >> perl(Bio::Phylo::Factory)
> >> opt-perl-BioPerl-1.6.901-0.el6.noarch has missing requires of
> >> perl(Bio::Phylo::Forest::Tree)
> >> opt-perl-BioPerl-1.6.901-0.el6.noarch has missing requires of
> >> perl(Bio::Phylo::IO)
> >> opt-perl-BioPerl-1.6.901-0.el6.noarch has missing requires of
> >> perl(Bio::Phylo::Matrices)
> >> opt-perl-BioPerl-1.6.901-0.el6.noarch has missing requires of
> >> perl(Bio::Phylo::Matrices::Datum)
> >> opt-perl-BioPerl-1.6.901-0.el6.noarch has missing requires of
> >> perl(Bio::Phylo::Matrices::Matrix)
> >> opt-perl-BioPerl-1.6.901-0.el6.noarch has missing requires of
> >> perl(Convert::Binary::C)
> >> opt-perl-BioPerl-1.6.901-0.el6.noarch has missing requires of
> perl(DBD::Pg)
> >> opt-perl-BioPerl-1.6.901-0.el6.noarch has missing requires of
> >> perl(PostScript::TextBlock)
> >> opt-perl-BioPerl-1.6.901-0.el6.noarch has missing requires of
> >> perl(Test::Exception)
> >> opt-perl-BioPerl-1.6.901-0.el6.noarch has missing requires of
> >> perl(Test::Warn)
> >> opt-perl-BioPerl-DB-1.006900-0.el6.noarch has missing requires of
> >> perl(DBD::Oracle)
> >> opt-perl-BioPerl-Run-1.006900-0.el6.noarch has missing requires of
> >> perl(Bio::Tools::Run::StandAloneBlastPlus::BlastMethods)
> >> opt-perl-BioPerl-Run-1.006900-0.el6.noarch has missing requires of
> >> perl(Bio::Tools::Run::WrapperBase::CommandExts)
> >> opt-perl-Cache-Cache-1.06-0.el6.noarch has missing requires of
> >> perl(IPC::ShareLite)
> >> opt-perl-DBI-1.622-0.el6.x86_64 has missing requires of perl(Coro)
> >> opt-perl-DBI-1.622-0.el6.x86_64 has missing requires of
> perl(Coro::Handle)
> >> opt-perl-DBI-1.622-0.el6.x86_64 has missing requires of
> perl(Coro::Select)
> >> opt-perl-DBI-1.622-0.el6.x86_64 has missing requires of
> perl(RPC::PlClient)
> >>> = ('0', '0.2000', None)
> >> opt-perl-DBI-1.622-0.el6.x86_64 has missing requires of
> perl(RPC::PlServer)
> >>> = ('0', '0.2001', None)
> >> opt-perl-DBI-1.622-0.el6.x86_64 has missing requires of
> perl(Win32::ODBC)
> >> opt-perl-Data-Stag-0.11-0.el6.x86_64 has missing requires of perl(Tk)
> >> opt-perl-Data-Stag-0.11-0.el6.x86_64 has missing requires of
> perl(Tk::Label)
> >> opt-perl-Data-Stag-0.11-0.el6.x86_64 has missing requires of
> perl(Tk::Tree)
> >> opt-perl-Digest-Perl-MD5-1.8-0.el6.noarch has missing requires of
> >> /usr/bin/false
> >> opt-perl-HTTP-Cookies-6.01-0.el6.noarch has missing requires of
> perl(Win32)
> >> opt-perl-IPC-Run-0.92-0.el6.noarch has missing requires of
> >> perl(Win32::Process)
> >> opt-perl-IPC-Run-0.92-0.el6.noarch has missing requires of
> >> perl(Win32API::File)
> >> opt-perl-MLDBM-2.04-0.el6.noarch has missing requires of
> perl(FreezeThaw)
> >> opt-perl-Moose-2.0604-0.el6.x86_64 has missing requires of
> >> perl(Moose::Conflicts)
> >> opt-perl-Moose-2.0604-0.el6.x86_64 has missing requires of
> >> perl(Moose::Error::Util)
> >> opt-perl-Package-Stash-0.33-0.el6.noarch has missing requires of
> >> perl(Package::Stash::Conflicts)
> >> opt-perl-SOAP-Lite-0.715-0.el6.noarch has missing requires of
> >> perl(MIME::Lite)
> >> opt-perl-SOAP-Lite-0.715-0.el6.noarch has missing requires of
> >> perl(SOAP::Transport::TCP)
> >> opt-perl-Spreadsheet-ParseExcel-0.59-0.el6.noarch has missing requires
> of
> >> perl(Jcode)
> >> opt-perl-Spreadsheet-ParseExcel-0.59-0.el6.noarch has missing requires
> of
> >> perl(Spreadsheet::WriteExcel)
> >> opt-perl-Spreadsheet-ParseExcel-0.59-0.el6.noarch has missing requires
> of
> >> perl(Unicode::Map)
> >> opt-perl-XML-SAX-0.99-0.el6.noarch has missing requires of
> >> perl(XML::SAX::PurePerl::DTDDecls)
> >> opt-perl-XML-SAX-0.99-0.el6.noarch has missing requires of
> >> perl(XML::SAX::PurePerl::DocType)
> >> opt-perl-XML-SAX-0.99-0.el6.noarch has missing requires of
> >> perl(XML::SAX::PurePerl::EncodingDetect)
> >> opt-perl-XML-SAX-0.99-0.el6.noarch has missing requires of
> >> perl(XML::SAX::PurePerl::XMLDecl)
> >> opt-perl-YAML-0.84-0.el6.noarch has missing requires of
> perl(Test::Base) >=
> >> ('0', '0.47', None)
> >> opt-perl-YAML-0.84-0.el6.noarch has missing requires of
> >> perl(Test::Base::Filter)
> >> opt-perl-libwww-perl-6.04-0.el6.noarch has missing requires of
> >> perl(Authen::NTLM)
> >> opt-perl-libwww-perl-6.04-0.el6.noarch has missing requires of
> >> perl(HTTP::GHTTP)
>
>

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