[Bioperl-l] Fwd: [Gmod-ajax] Jbrowse on mac os 10.5

iphan isabelle.phan at sbri.org
Thu Mar 19 00:40:59 UTC 2009 

Hello Chris and Hilmar

Thanks very much for the explanations, now the fog is lifting :-)

> The four modules absolutely required
> are: DB_File, Data::Stag, IO::String, Scalar::Util.

Could this perhaps be explicitly stated in the INSTALL?

> My question is where do HTML::Tagset and Digest::MD5 sneak in during
> the installation.  They are not listed as prereqs for BioPerl

(See below)

I copied the Bio directory to $HOME/perl , which is included in my PERL5LIB.
Despite the fact that I don't have Data::Stag installed, I can get jbrowse
to work on my Mac :-)


Isabelle


--
Here goes:

In the unpacked BioPerl-1.6.0 directory, I issued the command:

sudo perl Build.PL --install_base=/Users/iphan/Documents/bioperl

This goes through cpan installs, until I get prompted:


*** (back in Bioperl Build.PL) ***
Install [a]ll optional external modules, [n]one, or choose [i]nteractively?
[n] 
 - ERROR: You chose to install Test::Harness but it failed to install
 - ERROR: You chose to install CPAN but it failed to install
 - ERROR: You chose to install Data::Stag but it failed to install
 * Optional prerequisite Ace is not installed
   (wanted for access of ACeDB database, used by Bio::DB::Ace and
Bio::DB::GFF::Adaptor::ace)
 * Optional prerequisite Spreadsheet::ParseExcel is not installed
   (wanted for parsing Excel files, used by Bio::SeqIO::excel)
 * XML::SAX (0.14) is installed, but we prefer to have 0.15
   (wanted for parsing xml, used by Bio::SearchIO::blastxml,
Bio::SeqIO::tigrxml and Bio::SeqIO::bsml_sax)
 * Optional prerequisite Math::Random is not installed
   (wanted for Random Phylogenetic Networks, used by
Bio::PhyloNetwork::RandomFactory)
 * Optional prerequisite Graph is not installed
   (wanted for ontology engine implementation for the GO parser, used by
Bio::PhyloNetwork)
 * Optional prerequisite SVG::Graph is not installed
   (wanted for creating SVG images, used by Bio::TreeIO::svggraph)
 * Optional prerequisite SOAP::Lite is not installed
   (wanted for Bibliographic queries, used by Bio::DB::Biblio::soap)
 * Optional prerequisite Bio::ASN1::EntrezGene is not installed
   (wanted for parsing entrezgene, used by Bio::SeqIO::entrezgene [circular
dependency!])
 * Optional prerequisite GraphViz is not installed
   (wanted for Phylogenetic Network Visulization, used by
Bio::PhyloNetwork::GraphViz)
 * Optional prerequisite Array::Compare is not installed
   (wanted for Phylogenetic Networks, used by Bio::PhyloNetwork)
 * Optional prerequisite Convert::Binary::C is not installed
   (wanted for strider functionality, used by Bio::SeqIO::strider)
 * Optional prerequisite Algorithm::Munkres is not installed
   (wanted for Phylogenetic Networks, used by Bio::PhyloNetwork)
 * Optional prerequisite XML::Twig is not installed
   (wanted for parsing xml, used by Bio::Variation::IO::xml,
Bio::DB::Taxonomy::entrez and Bio::DB::Biblio::eutils)
 * HTML::HeadParser (2.22) is installed, but we prefer to have 3
   (wanted for parsing <HEAD> section of HTML docs, used by
Bio::Tools::Analysis::DNA::ESEfinder)
 * Optional prerequisite HTTP::Request::Common is not installed
   (wanted for GenBank+GenPept sequence retrieval, remote http Blast jobs,
used by Bio::DB::*, Bio::Tools::Run::RemoteBlast,
Bio::Tools::Analysis::Protein* and Bio::Tools::Analysis::DNA*)
 * Optional prerequisite Set::Scalar is not installed
   (wanted for proper operation, used by Bio::Tree::Compatible)
 * Optional prerequisite LWP::UserAgent is not installed
   (wanted for remote access, used by Bio::DB::*,
Bio::Tools::Run::RemoteBlast and Bio::WebAgent)
 * Optional prerequisite XML::Parser::PerlSAX is not installed
   (wanted for parsing xml, used by Bio::SeqIO::tinyseq,
Bio::SeqIO::game::gameSubs, Bio::OntologyIO::InterProParser and
Bio::ClusterIO::dbsnp)
 * Optional prerequisite XML::SAX::Writer is not installed
   (wanted for writing xml, used by Bio::SeqIO::tigrxml)
 * Optional prerequisite Clone is not installed
   (wanted for cloning objects, used by Bio::Tools::Primer3)
 * Optional prerequisite XML::DOM::XPath is not installed
   (wanted for parsing interpro features, used by Bio::FeatureIO::interpro)
 * Optional prerequisite PostScript::TextBlock is not installed
   (wanted for EPS output, used by Bio::Tree::Draw::Cladogram)

ERRORS/WARNINGS FOUND IN PREREQUISITES.  You may wish to install the
versions
of the modules indicated above before proceeding with this installation

Checking features:
  Network.................. - ERROR: LWP::UserAgent is not installed
Running install for module LWP::UserAgent
Running make for G/GA/GAAS/libwww-perl-5.825.tar.gz

  CPAN: MD5 security checks disabled because Digest::MD5 not installed.
  Please consider installing the Digest::MD5 module.

libwww-perl-5.825/
libwww-perl-5.825/AUTHORS
libwww-perl-5.825/bin/
libwww-perl-5.825/bin/lwp-download
libwww-perl-5.825/bin/lwp-mirror
libwww-perl-5.825/bin/lwp-request
libwww-perl-5.825/bin/lwp-rget
libwww-perl-5.825/Changes
libwww-perl-5.825/lib/
libwww-perl-5.825/lib/Bundle/
libwww-perl-5.825/lib/Bundle/LWP.pm
libwww-perl-5.825/lib/File/
libwww-perl-5.825/lib/File/Listing.pm
libwww-perl-5.825/lib/HTML/
libwww-perl-5.825/lib/HTML/Form.pm
libwww-perl-5.825/lib/HTTP/
libwww-perl-5.825/lib/HTTP/Config.pm
libwww-perl-5.825/lib/HTTP/Cookies/
libwww-perl-5.825/lib/HTTP/Cookies/Microsoft.pm
libwww-perl-5.825/lib/HTTP/Cookies/Netscape.pm
libwww-perl-5.825/lib/HTTP/Cookies.pm
libwww-perl-5.825/lib/HTTP/Daemon.pm
libwww-perl-5.825/lib/HTTP/Date.pm
libwww-perl-5.825/lib/HTTP/Headers/
libwww-perl-5.825/lib/HTTP/Headers/Auth.pm
libwww-perl-5.825/lib/HTTP/Headers/ETag.pm
libwww-perl-5.825/lib/HTTP/Headers/Util.pm
libwww-perl-5.825/lib/HTTP/Headers.pm
libwww-perl-5.825/lib/HTTP/Message.pm
libwww-perl-5.825/lib/HTTP/Negotiate.pm
libwww-perl-5.825/lib/HTTP/Request/
libwww-perl-5.825/lib/HTTP/Request/Common.pm
libwww-perl-5.825/lib/HTTP/Request.pm
libwww-perl-5.825/lib/HTTP/Response.pm
libwww-perl-5.825/lib/HTTP/Status.pm
libwww-perl-5.825/lib/LWP/
libwww-perl-5.825/lib/LWP/Authen/
libwww-perl-5.825/lib/LWP/Authen/Basic.pm
libwww-perl-5.825/lib/LWP/Authen/Digest.pm
libwww-perl-5.825/lib/LWP/Authen/Ntlm.pm
libwww-perl-5.825/lib/LWP/ConnCache.pm
libwww-perl-5.825/lib/LWP/Debug.pm
libwww-perl-5.825/lib/LWP/DebugFile.pm
libwww-perl-5.825/lib/LWP/media.types
libwww-perl-5.825/lib/LWP/MediaTypes.pm
libwww-perl-5.825/lib/LWP/MemberMixin.pm
libwww-perl-5.825/lib/LWP/Protocol/
libwww-perl-5.825/lib/LWP/Protocol/cpan.pm
libwww-perl-5.825/lib/LWP/Protocol/data.pm
libwww-perl-5.825/lib/LWP/Protocol/file.pm
libwww-perl-5.825/lib/LWP/Protocol/ftp.pm
libwww-perl-5.825/lib/LWP/Protocol/GHTTP.pm
libwww-perl-5.825/lib/LWP/Protocol/gopher.pm
libwww-perl-5.825/lib/LWP/Protocol/http.pm
libwww-perl-5.825/lib/LWP/Protocol/http10.pm
libwww-perl-5.825/lib/LWP/Protocol/https.pm
libwww-perl-5.825/lib/LWP/Protocol/https10.pm
libwww-perl-5.825/lib/LWP/Protocol/loopback.pm
libwww-perl-5.825/lib/LWP/Protocol/mailto.pm
libwww-perl-5.825/lib/LWP/Protocol/nntp.pm
libwww-perl-5.825/lib/LWP/Protocol/nogo.pm
libwww-perl-5.825/lib/LWP/Protocol.pm
libwww-perl-5.825/lib/LWP/RobotUA.pm
libwww-perl-5.825/lib/LWP/Simple.pm
libwww-perl-5.825/lib/LWP/UserAgent.pm
libwww-perl-5.825/lib/LWP.pm
libwww-perl-5.825/lib/Net/
libwww-perl-5.825/lib/Net/HTTP/
libwww-perl-5.825/lib/Net/HTTP/Methods.pm
libwww-perl-5.825/lib/Net/HTTP/NB.pm
libwww-perl-5.825/lib/Net/HTTP.pm
libwww-perl-5.825/lib/Net/HTTPS.pm
libwww-perl-5.825/lib/WWW/
libwww-perl-5.825/lib/WWW/RobotRules/
libwww-perl-5.825/lib/WWW/RobotRules/AnyDBM_File.pm
libwww-perl-5.825/lib/WWW/RobotRules.pm
libwww-perl-5.825/lwpcook.pod
libwww-perl-5.825/lwptut.pod
libwww-perl-5.825/Makefile.PL
libwww-perl-5.825/MANIFEST
libwww-perl-5.825/META.yml
libwww-perl-5.825/README
libwww-perl-5.825/README.SSL
libwww-perl-5.825/t/
libwww-perl-5.825/t/base/
libwww-perl-5.825/t/base/common-req.t
libwww-perl-5.825/t/base/cookies.t
libwww-perl-5.825/t/base/date.t
libwww-perl-5.825/t/base/headers-auth.t
libwww-perl-5.825/t/base/headers-etag.t
libwww-perl-5.825/t/base/headers-util.t
libwww-perl-5.825/t/base/headers.t
libwww-perl-5.825/t/base/http-config.t
libwww-perl-5.825/t/base/http.t
libwww-perl-5.825/t/base/listing.t
libwww-perl-5.825/t/base/mediatypes.t
libwww-perl-5.825/t/base/message-old.t
libwww-perl-5.825/t/base/message-parts.t
libwww-perl-5.825/t/base/message.t
libwww-perl-5.825/t/base/negotiate.t
libwww-perl-5.825/t/base/protocols.t
libwww-perl-5.825/t/base/request.t
libwww-perl-5.825/t/base/response.t
libwww-perl-5.825/t/base/status-old.t
libwww-perl-5.825/t/base/status.t
libwww-perl-5.825/t/base/ua.t
libwww-perl-5.825/t/html/
libwww-perl-5.825/t/html/form-maxlength.t
libwww-perl-5.825/t/html/form-multi-select.t
libwww-perl-5.825/t/html/form-param.t
libwww-perl-5.825/t/html/form.t
libwww-perl-5.825/t/live/
libwww-perl-5.825/t/live/apache-listing.t
libwww-perl-5.825/t/live/apache.t
libwww-perl-5.825/t/live/https.t
libwww-perl-5.825/t/live/jigsaw-auth-b.t
libwww-perl-5.825/t/live/jigsaw-auth-d.t
libwww-perl-5.825/t/live/jigsaw-chunk.t
libwww-perl-5.825/t/live/jigsaw-md5-get.t
libwww-perl-5.825/t/live/jigsaw-md5.t
libwww-perl-5.825/t/live/jigsaw-neg-get.t
libwww-perl-5.825/t/live/jigsaw-neg.t
libwww-perl-5.825/t/live/jigsaw-te.t
libwww-perl-5.825/t/local/
libwww-perl-5.825/t/local/autoload-get.t
libwww-perl-5.825/t/local/autoload.t
libwww-perl-5.825/t/local/chunked.t
libwww-perl-5.825/t/local/get.t
libwww-perl-5.825/t/local/http.t
libwww-perl-5.825/t/local/protosub.t
libwww-perl-5.825/t/net/
libwww-perl-5.825/t/net/cgi-bin/
libwww-perl-5.825/t/net/cgi-bin/moved
libwww-perl-5.825/t/net/cgi-bin/nph-slowdata
libwww-perl-5.825/t/net/cgi-bin/slowread
libwww-perl-5.825/t/net/cgi-bin/test
libwww-perl-5.825/t/net/cgi-bin/timeout
libwww-perl-5.825/t/net/config.pl.dist
libwww-perl-5.825/t/net/http-get.t
libwww-perl-5.825/t/net/http-post.t
libwww-perl-5.825/t/net/http-timeout.t
libwww-perl-5.825/t/net/mirror.t
libwww-perl-5.825/t/net/moved.t
libwww-perl-5.825/t/net/proxy.t
libwww-perl-5.825/t/README
libwww-perl-5.825/t/robot/
libwww-perl-5.825/t/robot/rules-dbm.t
libwww-perl-5.825/t/robot/rules.t
libwww-perl-5.825/t/robot/ua-get.t
libwww-perl-5.825/t/robot/ua.t
libwww-perl-5.825/t/TEST
libwww-perl-5.825/talk-to-ourself
Removing previously used /Users/iphan/.cpan/build/libwww-perl-5.825

  CPAN.pm: Going to build G/GA/GAAS/libwww-perl-5.825.tar.gz

WARNING: LICENSE is not a known parameter.
Checking if your kit is complete...
Looks good
Warning: prerequisite Digest::MD5 0 not found.
Warning: prerequisite HTML::Tagset 0 not found.
'LICENSE' is not a known MakeMaker parameter name.
Writing Makefile for LWP
---- Unsatisfied dependencies detected during
[G/GA/GAAS/libwww-perl-5.825.tar.gz] -----
    HTML::Tagset
    Digest::MD5
Shall I follow them and prepend them to the queue
of modules we are processing right now? [yes]

If I hit return, I end up in an endless loop, where it keeps asking whether
I want to install HTML::Tagset and Digest::MD5.


I then updated CPAN with 'install Bundle::CPAN', and tried to build bioperl
again, but that made no difference.

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