[Biojava-dev] biojava / Security

[pjm]

I've just checked out the 1.3 branch and found it doesn't compile;

compile:
    [javac] Compiling 950 source files to
/nfs/pathdb/prod/external/build/biojava-1.3-2003-08-19/ant-build/classes/main
    [javac]
/nfs/pathdb/prod/external/build/biojava-1.3-2003-08-19/ant-build/src/main/org/biojava/bio/seq/io/agave/AgaveWriter.java:94:
cannot resolve symbol
    [javac] symbol  : class PCDATAFilterWriter  
    [javac] location: class org.biojava.bio.seq.io.agave.AgaveWriter
    [javac]     protected PCDATAFilterWriter mFilter;
    [javac]               ^
    [javac]
/nfs/pathdb/prod/external/build/biojava-1.3-2003-08-19/ant-build/src/main/org/biojava/bio/seq/io/agave/AgaveWriter.java:151:
cannot resolve symbol
    [javac] symbol  : class PCDATAFilterWriter  
    [javac] location: class org.biojava.bio.seq.io.agave.AgaveWriter
    [javac]         mFilter = new PCDATAFilterWriter(mOut);
    [javac]                       ^
    [javac]
/nfs/pathdb/prod/external/build/biojava-1.3-2003-08-19/ant-build/src/main/org/biojava/bio/seq/io/SeqIOTools.java:342:
cannot resolve symbol
    [javac] symbol  : class GenpeptFormat  
    [javac] location: class org.biojava.bio.seq.io.SeqIOTools
    [javac]         SequenceFormat former = new GenpeptFormat();
    [javac]                                     ^
    [javac] Note: Some input files use or override a deprecated API.
    [javac] Note: Recompile with -deprecation for details.
    [javac] 3 errors


The first 2 problems come down to the inner class PCDATAFilterWriter
being removed from the file AgaveWriter.java.

The last problem is a one line change;

          SequenceFormat former = new GenbankFormat();
---
>         SequenceFormat former = new GenpeptFormat();




"Schreiber, Mark" wrote:
> 
> I just made a bit of an effort to synchronize the bj-live and bj1.3 to catch most of the recent bug fixes which was pretty tricky and I'm not certain that I ported everything so something like this kind of daily email would be even more useful than I thought.
> 
> - Mark
> 
>         -----Original Message-----
>         From: Thomas Down [mailto:td2 at sanger.ac.uk]
>         Sent: Fri 15/08/2003 8:58 p.m.
>         To: Matthew Pocock
>         Cc: Schreiber, Mark; Warth,Rainer,LAUSANNE,NRC/BAS; Brian Repko; biojava-dev at biojava.org
>         Subject: Re: [Biojava-dev] biojava / Security
> 
> 
> 
>         On Fri, Aug 15, 2003 at 09:33:31AM +0100, Matthew Pocock wrote:
>         > Last time I checked, CVS notification sent messages
>         > /per file/ rather than per commit. That's painfull.
>         > Perhaps a daily single cvs mail would be better?
> 
>         I like that idea -- I'd certainly be more likely to take
>         a look that individual checkin e-mails.
> 
>         CVS can do most of the work already with something like:
> 
>            cvs -d $CVSROOT rdiff -u -D "24 hours ago" -D "now" biojava-live
> 
>         [Right now, that's a bit dull because nothing has changed
>         in the last day -- try a longer time interval if you want to test it].
> 
>         So long as it really is just one patch per day, I'd be happy
>         to see it posted to the existing biojava-dev list.
> 
>             Thomas
> 
> 
> =======================================================================
> Attention: The information contained in this message and/or attachments
> from AgResearch Limited is intended only for the persons or entities
> to which it is addressed and may contain confidential and/or privileged
> material. Any review, retransmission, dissemination or other use of, or
> taking of any action in reliance upon, this information by persons or
> entities other than the intended recipients is prohibited by AgResearch
> Limited. If you have received this message in error, please notify the
> sender immediately.
> =======================================================================
> 
> _______________________________________________
> biojava-dev mailing list
> biojava-dev at biojava.org
> http://biojava.org/mailman/listinfo/biojava-dev