[R] 'yum install R' failing with tcl/tk issue

Pascal Oettli kridox at ymail.com
Fri Oct 25 07:35:30 CEST 2013 

Hello,

Do you have headers installed (generally tcl-devel and tk-devel)?

Regards,
Pascal


On 25 October 2013 10:33, Michael Stauffer <mgstauff at gmail.com> wrote:
> Hi,
>
> I'm trying to install R on CentOS 6.4.
>
> 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)
>
>         [[alternative HTML version deleted]]
>
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-- 
Pascal Oettli
Project Scientist
JAMSTEC
Yokohama, Japan

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