samtools/htsjdk — pull request #11 by heuermh (2014-05-19 23:35:42+00:00)
Title: Remove unnecessary JAVA6_HOME property

The current ant build depends on a non-standard environmental variable property JAVA6_HOME

```bash
$ ant
Buildfile: /Users/xxx/working/htsjdk/build.xml

write-version-property:
[propertyfile] Creating new property file: /Users/xxx/working/htsjdk/htsjdk.version.property.xml

init:

compile-samtools:
[mkdir] Created dir: /Users/xxx/working/htsjdk/classes

BUILD FAILED
/Users/xxx/working/htsjdk/build.xml:119: The following error occurred while executing this line:
/Users/xxx/working/htsjdk/build.xml:264: /Users/xxx/working/htsjdk/${env.JAVA6_HOME}/lib does not exist.

Total time: 0 seconds
```

It is actually not necessary for the build.

```bash
$ ant
Buildfile: /Users/xxx/working/htsjdk/build.xml

write-version-property:
[propertyfile] Creating new property file: /Users/xxx/working/htsjdk/htsjdk.version.property.xml

init:

compile-samtools:
[mkdir] Created dir: /Users/xxx/working/htsjdk/classes
[javac] /Users/xxx/working/htsjdk/build.xml:259: warning: 'includeantruntime' was not set, defaulting to build.sysclasspath=last; set to false for repeatable builds
[javac] Compiling 222 source files to /Users/xxx/working/htsjdk/classes
[javac] Note: Some input files use or override a deprecated API.
[javac] Note: Recompile with -Xlint:deprecation for details.
[javac] Note: Some input files use unchecked or unsafe operations.
[javac] Note: Recompile with -Xlint:unchecked for details.

compile-tribble:
[javac] /Users/xxx/working/htsjdk/build.xml:259: warning: 'includeantruntime' was not set, defaulting to build.sysclasspath=last; set to false for repeatable builds
[javac] Compiling 72 source files to /Users/xxx/working/htsjdk/classes
[javac] Note: Some input files use or override a deprecated API.
[javac] Note: Recompile with -Xlint:deprecation for details.
[javac] Note: Some input files use unchecked or unsafe operations.
[javac] Note: Recompile with -Xlint:unchecked for details.

compile-variant:
[javac] /Users/xxx/working/htsjdk/build.xml:259: warning: 'includeantruntime' was not set, defaulting to build.sysclasspath=last; set to false for repeatable builds
[javac] Compiling 60 source files to /Users/xxx/working/htsjdk/classes
[javac] Note: Some input files use or override a deprecated API.
[javac] Note: Recompile with -Xlint:deprecation for details.
[javac] Note: Some input files use unchecked or unsafe operations.
[javac] Note: Recompile with -Xlint:unchecked for details.

compile-src:

compile-samtools-tests:
[mkdir] Created dir: /Users/xxx/working/htsjdk/testclasses
[javac] /Users/xxx/working/htsjdk/build.xml:282: warning: 'includeantruntime' was not set, defaulting to build.sysclasspath=last; set to false for repeatable builds
[javac] Compiling 62 source files to /Users/xxx/working/htsjdk/testclasses
[javac] Note: Some input files use or override a deprecated API.
[javac] Note: Recompile with -Xlint:deprecation for details.
[javac] Note: Some input files use unchecked or unsafe operations.
[javac] Note: Recompile with -Xlint:unchecked for details.

compile-tribble-tests:
[javac] /Users/xxx/working/htsjdk/build.xml:282: warning: 'includeantruntime' was not set, defaulting to build.sysclasspath=last; set to false for repeatable builds
[javac] Compiling 22 source files to /Users/xxx/working/htsjdk/testclasses
[javac] warning: Implicitly compiled files were not subject to annotation processing.
[javac] Use -proc:none to disable annotation processing or -implicit to specify a policy for implicit compilation.
[javac] Note: Some input files use unchecked or unsafe operations.
[javac] Note: Recompile with -Xlint:unchecked for details.
[javac] 1 warning

compile-variant-tests:
[javac] /Users/xxx/working/htsjdk/build.xml:282: warning: 'includeantruntime' was not set, defaulting to build.sysclasspath=last; set to false for repeatable builds
[javac] Compiling 18 source files to /Users/xxx/working/htsjdk/testclasses
[javac] Note: Some input files use or override a deprecated API.
[javac] Note: Recompile with -Xlint:deprecation for details.
[javac] Note: Some input files use unchecked or unsafe operations.
[javac] Note: Recompile with -Xlint:unchecked for details.

compile-tests:

compile:

htsjdk-jar:
[mkdir] Created dir: /Users/xxx/working/htsjdk/dist
[jar] Building jar: /Users/xxx/working/htsjdk/dist/htsjdk-1.112.jar
[copy] Copying 4 files to /Users/xxx/working/htsjdk/dist

all:

BUILD SUCCESSFUL
Total time: 8 seconds
```