[Bioperl-l] How to install 1.6.2

[Minh Bui]

HI Scott,

I installed it anyway but the terminal (i am using Ubuntu 10.10) and it says
that bp_seqfeature_load.pl (unchanged) --> I still can't use --summary
feature.

Is there other way to use this feature?




On Fri, Feb 4, 2011 at 11:09 AM, Scott Cain <scott at scottcain.net> wrote:

> Hi Minh,
>
> I don't know why that test failed, but if you don't need to parse or
> produce EMBL files, it doesn't matter (and even if you do, it still
> may not matter, depending on what the test was).  I suggest
> installing.
>
> Scott
>
>
> On Fri, Feb 4, 2011 at 11:05 AM, Minh Bui <buiduyminh at gmail.com> wrote:
> > Oh
> > One more thing, I just downloaded Bioperl 1.6.2 and
> >
> > When I tried to run perl Build.PL, i got this message.
> > *
> > Checking whether your kit is complete...
> > WARNING: the following files are missing in your kit:
> >    .shipit
> > Please inform the author.
> >
> > Checking prerequisites...
> > Install [a]ll optional external modules, [n]one, or choose
> [i]nteractively?
> > [n]
> > *
> >
> > Then I ran ./Build test but it failed.
> >
> > Test Summary Report
> > -------------------
> > t/SeqIO/embl.t                             (Wstat: 512 Tests: 85 Failed:
> 0)
> >  Non-zero exit status: 2
> >  Parse errors: Bad plan.  You planned 95 tests but ran 85.
> > Files=350, Tests=22459, 96 wallclock secs ( 2.78 usr  0.66 sys + 79.46
> cusr
> > 4.21 csys = 87.11 CPU)
> > Result: FAIL
> > Failed 1/350 test programs. 0/22459 subtests failed.
> >
> > Is there anyway to install 1.6.2 because I really need it. Thank you for
> > your help.
> >
> > On Fri, Feb 4, 2011 at 10:44 AM, Minh Bui <buiduyminh at gmail.com> wrote:
> >
> >> Hi,
> >>
> >> I am trying to use the "summary" feature in  bp_seqfeature_load.pl (for
> >> Gbrowse) but it requires Bioperl 1.6.2. I have been trying to install
> >> 1.6.2 but no luck.
> >>
> >> First, I used GIT :
> >>
> >> git clone git://github.com/bioperl/bioperl-live.git
> >>
> >> and I got this error:
> >> *
> >> "github.com[0: 207.97.227.239]: errno=Connection timed out
> >> fatal: unable to connect a socket (Connection timed out)"
> >>
> >> *
> >> Then, I downloaded snapshot Core Modules on this page
> http://www.bioperl.org/wiki/Getting_BioPerl but it doesn't work either.
> >>
> >>
> >> could someone please show me how to install 1.6.2 or if there is anyway
> to use summary feature, please let me know.
> >>
> >> Thank you very much,
> >>
> >>
> >> --
> >> Minh Bui.
> >>
> >
> >
> >
> > --
> > Minh Bui.
> > _______________________________________________
> > Bioperl-l mailing list
> > Bioperl-l at lists.open-bio.org
> > http://lists.open-bio.org/mailman/listinfo/bioperl-l
> >
>
>
>
> --
> ------------------------------------------------------------------------
> Scott Cain, Ph. D.                                   scott at scottcain dot
> net
> GMOD Coordinator (http://gmod.org/)                     216-392-3087
> Ontario Institute for Cancer Research
>



-- 
Minh Bui.