From Bent.Terp at biosci.ki.se  Tue Oct  5 11:27:02 2004
From: Bent.Terp at biosci.ki.se (Bent Terp)
Date: Mon Mar  7 02:30:08 2005
Subject: SRS8 installation problem: Unable to compile class for JSP
Message-ID: <200409241215.52245.Bent.Terp@biosci.ki.se>
  charset="iso-8859-1"

I'm having some problems with the installation.
I get through the installation procedure without errors , but opening /srs/ 
gives a long list of errors, which boils down to:

org.apache.jasper.JasperException: Unable to compile class for JSP
org.apache.jsp.tag.web.gentopcorners_tag cannot be resolved or is not a type
org.apache.jsp.tag.web.submitbutton_tag cannot be resolved or is not a type

/srs/docs/ work just fine.

Any ideas?

-- 
MVH / With kind regards,
        Bent Terp <Bent.Terp@biosci.ki.se>
        System Administrator
        Bioinformatics and Expression Analysis Core Facility
        Karolinska Institute, Department of Biosciences
        Hälsovagen 7-9, 141 57 Huddinge, Sweden
---


From benedict.arnold at bbsrc.ac.uk  Tue Oct  5 11:26:57 2004
From: benedict.arnold at bbsrc.ac.uk ("benedict arnold JIC)
Date: Mon Mar  7 02:30:08 2005
Subject: Problem indexing EMBL
Message-ID: <286D8A554155B54CBFB18EF26EE2F1692780FF@jie2ksrv1.jic.bbsrc.ac.uk>

Hi Carlos,

if I had to have a wild guess it looks like you've updated the SRS binaries from 7.1.3 to 7.1.3.1. If you're using EMBL as a virtual library then what is likely to have happened is that emblnew has been indexed using the 7.1.3.1 binaries and emblrelease has been indexed using the 7.1.3 binaries. Unfortunately, because of a efw bugs that were fixed between the two versions this creates incompatible indices and the creation of the EMBL virtual library fails due to the differing index types. There are 2 solutions, roll back to 7.1.3 binaries, re-index emblnew and then recreate the embl virtual library sortsets and links, or, solution 2, is to re-index emblrelease using the 7.1.3.1 binaries and do it that way. As embl release 80 has been recently released, you might want to do what I did and migrate to that now and index both emblrelease and emblnew using the srs7.1.3.1 binaries.

hope that helps

Ben Arnold
Computational Biology Group - User Support
John Innes Centre
Colney Lane
Norwich
NR4 7UH
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From j.abbott at imperial.ac.uk  Tue Oct  5 11:27:13 2004
From: j.abbott at imperial.ac.uk (James Abbott)
Date: Mon Mar  7 02:30:08 2005
Subject: Problem indexing EMBL
References: <6fae5589.0409091149.7e0241b9@posting.google.com>
Message-ID: <cj8tsu$92q$1@jura.cc.ic.ac.uk>

Hi Carlos,

Carlos Javier wrote:

>>Creating sort set for the div field of embl
>>Creating sort set for the acc field of embl
>>/gfs/srs/srs7.1.3/srs_tmp/srs/icarus/util/makeSortSets.i:100: error: 
>>Fatal internal error
>>  Reason: "NULL lib pointer", file: "library.c", line:4838
>>gmake: *** [EMBL/EMBL_sort.acc.pacc] Error 255
>>/gfs/srs/srs7.1.3/srs_tmp/srs/icarus/util/makeSortSets.i -libName EMBL 
>>-fldName 'pac' -odir /gfs/srs/srs7.1.3/srs_tmp/srs/index/
>>/gfs/srs/srs7.1.3/srs_tmp/srs/icarus/util/makeSortSets.i:100: error: 
>>Fatal internal error
>>  Reason: "NULL lib pointer", file: "library.c", line:4838

 From memory, you get this error when building a virtual library if you 
do not have all the 'member libraries' of the virtual libary enabled on 
your system. The Library definition for EMBL (look for the $EMBL_DB 
section at the top of $SRSDB/embl.i) contains a list of the databases 
which make up the EMBL virtual library:

  memberLibs:{
       $EMBLREL_DB
       $EMBLNEW_DB
       $EMBLCONT_DB
       $EMBLWGS_DB
     }

If you do not use the EMBL WGS, new or Contig databases, try commenting 
  these out of the list of memberLibs, then run srssection. Then try 
rerunning srscheck/srsdo, and see if that solves the problem.

Hope that helps,
James