[CORE-70] I2b2 compilation of CRC Cell fails Created: 02/Oct/12 Updated: 05/Jun/14 Resolved: 22/May/14 |
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| Status: | Closed |
| Project: | i2b2 Core Software |
| Component/s: | CRC Cell, Install |
| Affects Version/s: | 1.6.06 |
| Fix Version/s: | 1.7.00 |
| Type: | Bug | Priority: | Critical |
| Reporter: | George Kowalski | Assignee: | Mike Mendis |
| Resolution: | Fixed | Votes: | 0 |
| Labels: | None | ||
| Remaining Estimate: | Not Specified | ||
| Time Spent: | Not Specified | ||
| Original Estimate: | Not Specified | ||
| Environment: |
[jboss@mathews edu.harvard.i2b2.crc]$ uname -a Linux mathews.hmgc.mcw.edu 2.6.18-308.11.1.el5 #1 SMP Fri Jun 15 15:41:53 EDT 2012 x86_64 x86_64 x86_64 GNU/Linux [jboss@mathews edu.harvard.i2b2.crc]$ [jboss@mathews edu.harvard.i2b2.crc]$ java -version java version "1.6.0_26" Java(TM) SE Runtime Environment (build 1.6.0_26-b03) Java HotSpot(TM) 64-Bit Server VM (build 20.1-b02, mixed mode) [jboss@mathews edu.harvard.i2b2.crc]$ [jboss@mathews edu.harvard.i2b2.crc]$ ant -v Apache Ant(TM) version 1.8.2 compiled on December 20 2010 |
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| Participant/s: |
| Description |
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Installing version 1.6.06 on LInux machine. Get to step 2.1.6 of the CRC_Installation_Guide.pdf and run: ant -f master_build.xml clean build-all deploy Get the following error : compile: [javac] /home/jboss/src/Server/edu.harvard.i2b2.crc.loader/build.xml:78: warning: 'includeantruntime' was not set, defaulting to build.sysclasspath=last; set to false for repeatable builds [javac] Compiling 239 source files to /home/jboss/src/Server/edu.harvard.i2b2.crc.loader/classes [javac] /home/jboss/src/Server/edu.harvard.i2b2.crc.loader/src/server/edu/harvard/i2b2/crc/loader/util/CRCLoaderUtil.java:33: cannot find symbol [javac] symbol : class FRLocalHome [javac] location: package edu.harvard.i2b2.crc.loader.ejb.fr [javac] import edu.harvard.i2b2.crc.loader.ejb.fr.FRLocalHome; [javac] ^ [javac] /home/jboss/src/Server/edu.harvard.i2b2.crc.loader/src/server/edu/harvard/i2b2/crc/loader/util/CRCLoaderUtil.java:142: cannot find symbol [javac] symbol : class FRLocalHome [javac] location: class edu.harvard.i2b2.crc.loader.util.CRCLoaderUtil [javac] public FRLocalHome getFRBeanLocalHome() throws I2B2Exception, [javac] ^ [javac] /home/jboss/src/Server/edu.harvard.i2b2.crc.loader/src/server/edu/harvard/i2b2/crc/loader/util/security/HighEncryption.java:17: warning: sun.misc.BASE64Decoder is Sun proprietary API and may be removed in a future release [javac] import sun.misc.BASE64Decoder; [javac] ^ [javac] /home/jboss/src/Server/edu.harvard.i2b2.crc.loader/src/server/edu/harvard/i2b2/crc/loader/ejb/DataMartLoaderBeanMDB.java:46: cannot find symbol [javac] symbol : class FRLocal [javac] location: package edu.harvard.i2b2.crc.loader.ejb.fr [javac] import edu.harvard.i2b2.crc.loader.ejb.fr.FRLocal; [javac] ^ [javac] /home/jboss/src/Server/edu.harvard.i2b2.crc.loader/src/server/edu/harvard/i2b2/crc/loader/util/CRCLoaderUtil.java:144: cannot find symbol [javac] symbol : class FRLocalHome [javac] location: class edu.harvard.i2b2.crc.loader.util.CRCLoaderUtil [javac] return (FRLocalHome) serviceLocator [javac] ^ [javac] /home/jboss/src/Server/edu.harvard.i2b2.crc.loader/src/server/edu/harvard/i2b2/crc/loader/util/security/RijndaelAlgorithm.java:102: warning: sun.misc.BASE64Encoder is Sun proprietary API and may be removed in a future release [javac] return new String(new sun.misc.BASE64Encoder().encodeBuffer(encrypt(source.getBytes("UTF-8")))); [javac] ^ [javac] /home/jboss/src/Server/edu.harvard.i2b2.crc.loader/src/server/edu/harvard/i2b2/crc/loader/util/security/RijndaelAlgorithm.java:130: warning: sun.misc.BASE64Decoder is Sun proprietary API and may be removed in a future release [javac] new sun.misc.BASE64Decoder().decodeBuffer(source)), "UTF-8"); [javac] ^ [javac] /home/jboss/src/Server/edu.harvard.i2b2.crc.loader/src/server/edu/harvard/i2b2/crc/loader/ejb/DataMartLoaderBeanMDB.java:275: cannot find symbol [javac] symbol : class FRLocal [javac] location: class edu.harvard.i2b2.crc.loader.ejb.DataMartLoaderBeanMDB [javac] FRLocal testLocal = CRCLoaderUtil.getInstance() [javac] ^ [javac] Note: /home/jboss/src/Server/edu.harvard.i2b2.crc.loader/src/test/edu/harvard/i2b2/crc/loader/ws/CRCAxisAbstract.java uses or overrides 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. [javac] 5 errors [javac] 3 warnings BUILD FAILED /home/jboss/src/Server/edu.harvard.i2b2.crc/master_build.xml:12: The following error occurred while executing this line: /home/jboss/src/Server/edu.harvard.i2b2.crc.loader/build.xml:78: Compile failed; see the compiler error output for details. |
| Comments |
| Comment by George Kowalski [ 02/Oct/12 ] |
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Files I used to install , is this the current release I should be using ? Jira reports that 1.6.02 is the latest release version : [jboss@mathews src]$ ls -l total 92084 -rw-r--r-- 1 jboss jboss 66901637 Sep 27 15:34 i2b2core-src-1606.zip -rw-r--r-- 1 jboss jboss 21388723 Sep 27 15:34 i2b2createdb-1605.zip -rw-r--r-- 1 jboss jboss 5880894 Sep 27 15:34 i2b2webclient-1606.zip drwxr-xr-x 13 jboss jboss 4096 Sep 28 15:28 Server drwxr-xr-x 6 jboss jboss 4096 Aug 31 10:05 webclient [jboss@mathews src]$ |
| Comment by George Kowalski [ 02/Oct/12 ] |
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Found it in the gensrc directory , not getting included ?: ./gensrc/edu/harvard/i2b2/crc/loader/ejb/fr/FRLocal.java |
| Comment by George Kowalski [ 02/Oct/12 ] |
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Fixed. Just run a dos2unix build.xml in the /home/jboss/src/Server/edu.harvard.i2b2.crc.loader/ directory . The ^M chars in this file are screwing up the build process. G |
| Comment by George Kowalski [ 03/Oct/12 ] |
| The priority on this issue is no longer a blocker as I found a workaround. |
| Comment by Mike Mendis [ 22/May/14 ] |
| fixed in 1.7 |