[BioBrew Users] Possible error with 4.1.2 roll

[Jeremy Mann]

For some reason the genhdlist was failing with not finding
librpm-4.3.so.3. That library is avaialbe but in /usr/lib64. I fixed
it be installing the i386 version of rpm-libs. I'm redoing rocks-dist
now and will try another compute node installation.


On 5/23/06, Anoop Rajendra <anoop.rajendra at gmail.com> wrote:
> Programs like flex and byacc are build dependencies for a few
> bioinformatics applications. You'll need to have them installed
> before you actually start compilation. it wont matter if they are
> removed from the xml files. The build is going to fail.
>
> If I'm not mistaken these utilities are available on the OS-3 and
> OS-4 roll CDs from Rocks. You can install them and recompile the
> biobrew roll. If the roll is already compiled with these utilities,
> and you're trying to only install and not build the roll, then I'd
> suggest doing a copyroll on the OS-3 and OS-4 roll cds, before
> running the "kroll" command below.
>
> -Anoop
>
> On May 23, 2006, at 12:31 PM, Jeremy Mann wrote:
>
> > Now it errors that it can't find flex so something is wrong with this
> > roll, it keeps wanting to use the 4.1.1 non-existant roll.
> >
> > On 5/23/06, Jeremy Mann <jeremymann at gmail.com> wrote:
> >> Me too. All I can do for now is comment out byacc in the three XML
> >> files, biobrew.xml, biobrew-compute.xml and biobrew-frontend.xml. I
> >> hope nothing important needs it.
> >>
> >> On 5/23/06, Glen Otero <glen at callident.com> wrote:
> >> > Oh crap. More rocks issues. I'm at a loss here. I'm sure there's a
> >> > way to make this work, but I don't know it off the top of my head.
> >> > You might try reinstalling the new roll now that you've removed
> >> > remains of the old one.
> >> >
> >> > Glen
> >> >
> >> > On May 23, 2006, at 9:42 AM, Jeremy Mann wrote:
> >> >
> >> > > I upgraded the roll from 4.1.1 to 4.1.2 as you said yesterday:
> >> > >
> >> > > 1) insert the biobrew CD in the frontend node
> >> > > 2) cd /home/install
> >> > > 3) rocks-dist --install copyroll
> >> > > 4) rocks-dist dist
> >> > > 5) kroll biobrew > /tmp/install-biobrew.sh
> >> > > 6) chmod +x /tmp/install-biobrew.sh
> >> > > 7) /tmp/install-biobrew.sh
> >> > >
> >> > > After doing this, I went to rebuild a node and the installer
> >> says it
> >> > > can't find byacc-1.9-28. I issued a find command in /home/
> >> install and
> >> > > that version of byacc is in the old 4.1.1 roll. I then went into
> >> > > /home/install/rocks-dist/lan/i386/RedHat/RPMS and the symlink and
> >> > > torrent is for byacc-1.9-29.
> >> > >
> >> > > I was curious if I had to manually remove the 4.1.1 directory and
> >> > > issue another rocks-dist dist to update the changes. Now that
> >> I've
> >> > > already done that, the installer still wants to install the older
> >> > > BioBrew roll.
> >> > >
> >> > > On 5/23/06, Glen Otero <glen at callident.com> wrote:
> >> > >> Jeremy-
> >> > >>
> >> > >> I'm not sure what's going on here. Can you explain what
> >> you're doing
> >> > >> in more detail? What do you mean by deleting the directory and
> >> > >> rebuilding with rocks-dist?
> >> > >>
> >> > >> Glen
> >> > >>
> >> > >>
> >> > >> On May 23, 2006, at 7:07 AM, Jeremy Mann wrote:
> >> > >>
> >> > >> > I've upgraded our BioBrew roll from 4.1.1 to 4.1.2
> >> following the
> >> > >> > instructions from Glen Otero. When rebuilding an i386 node the
> >> > >> > installer errors on byacc. It says it cannot find
> >> byacc-1.9.28. The
> >> > >> > 4.1.2 roll has byacc-1.9.29. I still have the 4.1.1 roll,
> >> should I
> >> > >> > delete that directory and rebuild with rocks-dist to fix this?
> >> > >> >
> >> > >> > --
> >> > >> > Jeremy
> >> > >> > _______________________________________________
> >> > >> > BioBrew-Users mailing list
> >> > >> > BioBrew-Users at bioinformatics.org
> >> > >> > https://bioinformatics.org/mailman/listinfo/BioBrew-Users
> >> > >> >
> >> > >> >
> >> > >>
> >> > >> _______________________________________________
> >> > >> BioBrew-Users mailing list
> >> > >> BioBrew-Users at bioinformatics.org
> >> > >> https://bioinformatics.org/mailman/listinfo/BioBrew-Users
> >> > >>
> >> > >
> >> > >
> >> > > --
> >> > > Jeremy
> >> > > _______________________________________________
> >> > > BioBrew-Users mailing list
> >> > > BioBrew-Users at bioinformatics.org
> >> > > https://bioinformatics.org/mailman/listinfo/BioBrew-Users
> >> > >
> >> > >
> >> >
> >> > _______________________________________________
> >> > BioBrew-Users mailing list
> >> > BioBrew-Users at bioinformatics.org
> >> > https://bioinformatics.org/mailman/listinfo/BioBrew-Users
> >> >
> >>
> >>
> >> --
> >> Jeremy
> >>
> >
> >
> > --
> > Jeremy
> > _______________________________________________
> > BioBrew-Users mailing list
> > BioBrew-Users at bioinformatics.org
> > https://bioinformatics.org/mailman/listinfo/BioBrew-Users
>
> _______________________________________________
> BioBrew-Users mailing list
> BioBrew-Users at bioinformatics.org
> https://bioinformatics.org/mailman/listinfo/BioBrew-Users
>


-- 
Jeremy