[Biojava-l] uneeded aggrevation ;)

[Ewan Birney]

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


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


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


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

init:

prepare:

prepare-src:

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

BUILD FAILED

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


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

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


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


And now I have got...

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



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


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







Diff:







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



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