[CORE-70] I2b2 compilation of CRC Cell fails - i2b2 JIRA

Details

Type: Bug
Status: Closed
Priority: Critical
Resolution: Fixed
Affects Version/s: 1.6.06
Fix Version/s: 1.7.00
Component/s: CRC Cell, Install
Labels:
None
Environment:

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[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

Show
[ 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

Description

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.

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George Kowalski added a comment - 02/Oct/12 2:25 PM

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]$

George Kowalski added a comment - 02/Oct/12 2:25 PM 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]$

George Kowalski added a comment - 02/Oct/12 3:39 PM

Found it in the gensrc directory , not getting included ?:

./gensrc/edu/harvard/i2b2/crc/loader/ejb/fr/FRLocal.java

George Kowalski added a comment - 02/Oct/12 3:39 PM Found it in the gensrc directory , not getting included ?: ./gensrc/edu/harvard/i2b2/crc/loader/ejb/fr/FRLocal.java

George Kowalski added a comment - 02/Oct/12 4:24 PM

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

George Kowalski added a comment - 02/Oct/12 4:24 PM 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

George Kowalski added a comment - 03/Oct/12 9:56 AM

The priority on this issue is no longer a blocker as I found a workaround.

George Kowalski added a comment - 03/Oct/12 9:56 AM The priority on this issue is no longer a blocker as I found a workaround.

Mike Mendis added a comment - 22/May/14 12:35 PM

fixed in 1.7

Mike Mendis added a comment - 22/May/14 12:35 PM fixed in 1.7

People

Assignee:: Mike Mendis

Reporter:: George Kowalski

Participant/s:: George Kowalski, Mike Mendis

Votes:: 0 Vote for this issue

Watchers:: 2 Start watching this issue

Dates

Created:: 02/Oct/12 2:23 PM

Updated:: 05/Jun/14 6:02 PM

Resolved:: 22/May/14 12:35 PM

i2b2 Core Software