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_schwa...@me.com> wrote: > > On Oct 25, 2013, at 1:29 AM, Prof Brian Ripley <rip...@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) > > [[alternative HTML version deleted]] ______________________________________________ R-help@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide http://www.R-project.org/posting-guide.html and provide commented, 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