[Biojava-l] uneeded aggrevation ;)

[Keith James]

>>>>> "Ewan" == Ewan Birney <birney@ebi.ac.uk> writes:

    Ewan> Ok. I'm attempting to exercise my young and green java
    Ewan> fingers again.


    Ewan> The README is not synchronised I think with reality
    Ewan> (still?). As far as I can figure out you need to have ant
    Ewan> installed. I've attached a cvs diff -u for the modifications
    Ewan> for the README to indicate that you have to have ant and not
    Ewan> mislead people with this build thang (or did I miss
    Ewan> something?)

Right. It was synchronised until the build tool was removed... I've
added your patch.

    Ewan> Now - ant doesn't want to build because apparently I don't
    Ewan> have a modern compiler - it tries to revert to a classic
    Ewan> compiler and then complains:


    Ewan> birney@delani biojava-live]$ ant Buildfile: build.xml

    Ewan> init:

    Ewan> prepare:

    Ewan> prepare-src:

    Ewan> compile: [javac] Modern compiler is not available - using
    Ewan> classic compiler [javac] Compiling 566 source files to
    Ewan> /home/birney/src/biojava-live/ant-build/classes/main

    Ewan> BUILD FAILED

    Ewan> /home/birney/src/biojava-live/build.xml:140: Cannot use
    Ewan> classic compiler, as it is not available A common solution
    Ewan> is to set the environment variable JAVA_HOME to your jdk
    Ewan> directory.


    Ewan> Now - as far as I can figure out - I've got a pretty up to
    Ewan> date jdk here:

    Ewan> [birney@delani biojava-live]$ java -version java version
    Ewan> "1.3.0_02" Java(TM) 2 Runtime Environment, Standard Edition
    Ewan> (build 1.3.0_02) Java HotSpot(TM) Client VM (build 1.3.0_02,
    Ewan> mixed mode) [birney@delani biojava-live]$ whihc java whihc:
    Ewan> Command not found.  [birney@delani biojava-live]$ which java
    Ewan> /usr/java/jdk1.3.0_02/bin//java [birney@delani
    Ewan> biojava-live]$ which javac /usr/java/jdk1.3.0_02/bin//javac


    Ewan> The hint about setting JAVA_HOME did work out though - it
    Ewan> would be nice for this to figure it out by where java/javac
    Ewan> is set.


    Ewan> And now I have got...

    Ewan> compile: [javac] Compiling 566 source files to
    Ewan> /home/birney/src/biojava-live/ant-build/classes/main [javac]
    Ewan> /home/birney/src/biojava-live/ant-build/src/main/org/biojava/bio/seq/db/emblcd/EmblCDROMIndexReader.java:63:
    Ewan> cannot resolve symbol [javac] symbol : class RecordParser
    Ewan> [javac] location: class
    Ewan> org.biojava.bio.seq.db.emblcd.EmblCDROMIndexReader [javac]
    Ewan> protected RecordParser recParser; [javac] ^ [javac]
    Ewan> /home/birney/src/biojava-live/ant-build/src/main/org/biojava/bio/seq/db/emblcd/EmblCDROMIndexReader.java:97:
    Ewan> cannot resolve symbol [javac] symbol : class RecordParser
    Ewan> [javac] location: class
    Ewan> org.biojava.bio.seq.db.emblcd.EmblCDROMIndexReader [javac]
    Ewan> recParser = new RecordParser(); [javac] ^ [javac] Note: Some
    Ewan> input files use or override a deprecated API.  [javac] Note:
    Ewan> Recompile with -deprecation for details.  [javac] 2 errors



    Ewan> Which of course is my fault probably for checking out the
    Ewan> main trunk (but someone left the main trunk
    Ewan> uncompilable.... beer oweing moment if I have ever seen it).


    Ewan> Now - do I just download the prebuild 1.1... or check it out
    Ewan> on the branch? Hmmmmmm







    Ewan> Diff:







    Ewan> diff -u -r1.8 README --- README 2001/05/16 20:43:24 1.8 +++
    Ewan> README 2001/07/31 08:31:03 @@ -29,22 +29,10 @@
 
    Ewan>    http://xml.apache.org/xerces-j/index.html
 
    Ewan> -In addition, the scripts will generate the non-cvs
    Ewan> directories docs and -class, which will contain the javadoc
    Ewan> documentation and the class files.
 
    Ewan> -To build the project, change to biojava-live and type: -
    -> javac build/Builder.java java build.Builder all java
    -> build.Builder docs
    Ewan> - -to build a list of packages type: -
    -> java build.Builder package package1 package2 ... packageN
    Ewan> - -If you use the Java based build tool Ant, supplied by the
    Ewan> Apache -Jakarta Project (see http://jakarta.apache.org) you
    Ewan> can use it to build -BioJava. To build the project, change
    Ewan> to biojava-live and type: +BioJava now uses the Java based
    Ewan> build tool Ant, supplied by the Apache +Jakarta Project (see
    Ewan> http://jakarta.apache.org) you can use it to +build
    Ewan> BioJava. To build the project, change to biojava-live and
    Ewan> type:
 
    Ewan>  ant package ant javadocs



    Ewan> -----------------------------------------------------------------
    Ewan> Ewan Birney. Mobile: +44 (0)7970 151230, Work: +44 1223
    Ewan> 494420 <birney@ebi.ac.uk>.
    Ewan> -----------------------------------------------------------------

    Ewan> _______________________________________________ Biojava-l
    Ewan> mailing list - Biojava-l@biojava.org
    Ewan> http://biojava.org/mailman/listinfo/biojava-l


-- 

-= Keith James - kdj@sanger.ac.uk - http://www.sanger.ac.uk/Users/kdj =-
The Sanger Centre, Wellcome Trust Genome Campus, Hinxton, Cambs CB10 1SA