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

Chris Fields cjfields at illinois.edu
Wed Mar 18 21:20:26 EDT 2009

On Mar 18, 2009, at 7:40 PM, iphan wrote:

> 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?

Yes, along with the use of 'sudo' where needed.

>> 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  
> Despite the fact that I don't have Data::Stag installed, I can get  
> jbrowse
> to work on my Mac :-)
> Isabelle

Glad to hear you got Jbrowse running!  As for Data::Stag, it is used  
for one of the Bio::Annotation objects.  I think it's mainly used in  
UniProt sequence and (possibly) Stockholm alignment parsing.  You  
could possibly get by w/o it; if you face problems you can attempt  
installing it separately (it is pure perl, so there shouldn't be a  
significant issue).

As for the rest...

> --
> 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

The above is may play a part in the looping (it is attempting to  
forcibly install the modules).

> <SNIP>
> 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

Now that's not good, it shouldn't attempt to install this (it's not  

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

If you try installing libwww-perl does it give you similar errors?

Regardless, we'll probably need to shut down the automatic CPAN module  
installation via 'perl Build.PL' or make it optional.  I'll file a bug  
to track this.


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