My hadoop is CDH4, but i don't install with Cloudera Manager.
i set $HADOOP_HOME=/usr/lib/hadoop-0.20-mapreduce
i can success to compile and build jar.
but when i want to run "ant build-test", it appears the following errors:
build-tests: [mkdir] Created dir: /home/genome/hadoop-bam/test-classes [javac] Compiling 7 source files to /home/genome/hadoop-bam/test-classes [javac] warning: [path] bad path element "/usr/lib/hadoop-0.20-mapreduce/lib/jaxb-api.jar": no such file or directory [javac] warning: [path] bad path element "/usr/lib/hadoop-0.20-mapreduce/lib/activation.jar": no such file or directory [javac] warning: [path] bad path element "/usr/lib/hadoop-0.20-mapreduce/lib/jsr173_1.0_api.jar": no such file or directory [javac] warning: [path] bad path element "/usr/lib/hadoop-0.20-mapreduce/lib/jaxb1-impl.jar": no such file or directory [javac] /home/genome/hadoop-bam/tests/fi/tkk/ics/hadoop/TestConfHelper.java:30: error: cannot find symbol [javac] import org.apache.hadoop.conf.Configuration; [javac] ^ [javac] symbol: class Configuration [javac] location: package org.apache.hadoop.conf [javac] /home/genome/hadoop-bam/tests/fi/tkk/ics/hadoop/TestFastqInputFormat.java:40: error: cannot find symbol [javac] import org.apache.hadoop.fs.Path; [javac] ^ [javac] symbol: class Path [javac] location: package org.apache.hadoop.fs [javac] /home/genome/hadoop-bam/tests/fi/tkk/ics/hadoop/TestFastqInputFormat.java:41: error: package org.apache.hadoop.io.compress does not exist [javac] import org.apache.hadoop.io.compress.GzipCodec; [javac] ^ [javac] /home/genome/hadoop-bam/tests/fi/tkk/ics/hadoop/TestFastqInputFormat.java:42: error: cannot find symbol [javac] import org.apache.hadoop.io.Text; [javac] ^ [javac] symbol: class Text [javac] location: package org.apache.hadoop.io [javac] /home/genome/hadoop-bam/tests/fi/tkk/ics/hadoop/TestFastqInputFormat.java:135: error: cannot find symbol [javac] private Text key; [javac] ^ [javac] symbol: class Text [javac] location: class TestFastqInputFormat [javac] /home/genome/hadoop-bam/tests/fi/tkk/ics/hadoop/TestLineReader.java:41: error: cannot find symbol [javac] private Text dest = new Text(); [javac] ^ [javac] symbol: class Text [javac] location: class TestLineReader [javac] /home/genome/hadoop-bam/tests/fi/tkk/ics/hadoop/TestQseqInputFormat.java:41: error: cannot find symbol [javac] import org.apache.hadoop.fs.FileSystem; [javac] ^ [javac] symbol: class FileSystem [javac] location: package org.apache.hadoop.fs [javac] /home/genome/hadoop-bam/tests/fi/tkk/ics/hadoop/TestQseqInputFormat.java:42: error: cannot find symbol [javac] import org.apache.hadoop.fs.FSDataInputStream; [javac] ^ [javac] symbol: class FSDataInputStream [javac] location: package org.apache.hadoop.fs [javac] /home/genome/hadoop-bam/tests/fi/tkk/ics/hadoop/TestQseqInputFormat.java:44: error: package org.apache.hadoop.io.compress does not exist
how could i solve it??
Last edit: ElsLiu 2013-11-18
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My hadoop is CDH4, but i don't install with Cloudera Manager.
i set $HADOOP_HOME=/usr/lib/hadoop-0.20-mapreduce
i can success to compile and build jar.
but when i want to run "ant build-test", it appears the following errors:
build-tests:
[mkdir] Created dir: /home/genome/hadoop-bam/test-classes
[javac] Compiling 7 source files to /home/genome/hadoop-bam/test-classes
[javac] warning: [path] bad path element "/usr/lib/hadoop-0.20-mapreduce/lib/jaxb-api.jar": no such file or directory
[javac] warning: [path] bad path element "/usr/lib/hadoop-0.20-mapreduce/lib/activation.jar": no such file or directory
[javac] warning: [path] bad path element "/usr/lib/hadoop-0.20-mapreduce/lib/jsr173_1.0_api.jar": no such file or directory
[javac] warning: [path] bad path element "/usr/lib/hadoop-0.20-mapreduce/lib/jaxb1-impl.jar": no such file or directory
[javac] /home/genome/hadoop-bam/tests/fi/tkk/ics/hadoop/TestConfHelper.java:30: error: cannot find symbol
[javac] import org.apache.hadoop.conf.Configuration;
[javac] ^
[javac] symbol: class Configuration
[javac] location: package org.apache.hadoop.conf
[javac] /home/genome/hadoop-bam/tests/fi/tkk/ics/hadoop/TestFastqInputFormat.java:40: error: cannot find symbol
[javac] import org.apache.hadoop.fs.Path;
[javac] ^
[javac] symbol: class Path
[javac] location: package org.apache.hadoop.fs
[javac] /home/genome/hadoop-bam/tests/fi/tkk/ics/hadoop/TestFastqInputFormat.java:41: error: package org.apache.hadoop.io.compress does not exist
[javac] import org.apache.hadoop.io.compress.GzipCodec;
[javac] ^
[javac] /home/genome/hadoop-bam/tests/fi/tkk/ics/hadoop/TestFastqInputFormat.java:42: error: cannot find symbol
[javac] import org.apache.hadoop.io.Text;
[javac] ^
[javac] symbol: class Text
[javac] location: package org.apache.hadoop.io
[javac] /home/genome/hadoop-bam/tests/fi/tkk/ics/hadoop/TestFastqInputFormat.java:135: error: cannot find symbol
[javac] private Text key;
[javac] ^
[javac] symbol: class Text
[javac] location: class TestFastqInputFormat
[javac] /home/genome/hadoop-bam/tests/fi/tkk/ics/hadoop/TestLineReader.java:41: error: cannot find symbol
[javac] private Text dest = new Text();
[javac] ^
[javac] symbol: class Text
[javac] location: class TestLineReader
[javac] /home/genome/hadoop-bam/tests/fi/tkk/ics/hadoop/TestQseqInputFormat.java:41: error: cannot find symbol
[javac] import org.apache.hadoop.fs.FileSystem;
[javac] ^
[javac] symbol: class FileSystem
[javac] location: package org.apache.hadoop.fs
[javac] /home/genome/hadoop-bam/tests/fi/tkk/ics/hadoop/TestQseqInputFormat.java:42: error: cannot find symbol
[javac] import org.apache.hadoop.fs.FSDataInputStream;
[javac] ^
[javac] symbol: class FSDataInputStream
[javac] location: package org.apache.hadoop.fs
[javac] /home/genome/hadoop-bam/tests/fi/tkk/ics/hadoop/TestQseqInputFormat.java:44: error: package org.apache.hadoop.io.compress does not exist
how could i solve it??
Last edit: ElsLiu 2013-11-18
This should be solved when using the latest code version. Please file a bug report at
https://github.com/HadoopGenomics/Hadoop-BAM/issues
otherwise.