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) ______________________________________________ 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, minimal, self-contained, reproducible code.