[R] 'yum install R' failing with tcl/tk issue
Marc Schwartz
marc_schwartz at me.com
Fri Oct 25 13:43:08 CEST 2013
On Oct 25, 2013, at 1:29 AM, Prof Brian Ripley <ripley at 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 at 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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