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chrovis / cljam

A DNA Sequence Alignment/Map (SAM) library for Clojure

Home Page:https://chrovis.github.io/cljam

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The use of ByteBuffer & CharBuffer breaks cljam's binary compatibility

athos opened this issue · comments

commented

Once you build cljam on a Java 9+ environmont:

$ java -version
openjdk version "11" 2018-09-25
OpenJDK Runtime Environment 18.9 (build 11+28)
OpenJDK 64-Bit Server VM 18.9 (build 11+28, mixed mode)
$ lein uberjar
Compiling cljam.tools.main                                     
Compiling cljam.tools.cli                                                 
Compiling cljam.util.region                                                                                                                                                                                                                                                                       
Compiling cljam.util.chromosome                                                                                                                                                                                                                                                                   
Compiling cljam.util.whole-genome  
...
Created /Users/sohta/work/cljam/target/cljam-0.7.1-SNAPSHOT.jar
Created /Users/sohta/work/cljam/target/cljam-0.7.1-SNAPSHOT-standalone.jar
$

And use the generated JAR on Java 8, you'll run into a NoSuchMethodError:

$ java -version
java version "1.8.0_181"
Java(TM) SE Runtime Environment (build 1.8.0_181-b13)
Java HotSpot(TM) 64-Bit Server VM (build 25.181-b13, mixed mode)
$ lein repl
user=> (require '[cljam.io.sam.util.quality :as sam-qual])
nil
user=> (sam-qual/phred-bytes->fastq (.getBytes "A"))
NoSuchMethodError java.nio.CharBuffer.flip()Ljava/nio/CharBuffer;  cljam.io.sam.util.quality/phred-bytes->fastq (quality.clj:30)
user=>

The root cause of this issue is that Java 9 introduced some overriden methods for ByteBuffer and other Buffer impl classes, and that may sometimes break binary-level compatibility. See the links below for more details on the issue itself: